Categories
Tag: DEG
Unravelling cell type-specific responses to Parkinson’s Disease at single cell resolution | Molecular Neurodegeneration
Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…
Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir
Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…
pytorch – Batched tensor creation inside torch.vmap
I want to create a tensor with torch.zeros based on the shape of an input to the function. Then I want to vectorize the function with torch.vmap. Something like this: poly_batched = torch.tensor([[1, 2, 3, 4], [1, 2, 3, 4]]) def polycompanion(polynomial): deg = polynomial.shape[-1] – 2 companion = torch.zeros((deg+1,…
Gadolinium Oxide Nanoparticles reinforce immune response
Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…
Highly dynamic inflammatory and excitability transcriptional profiles in hippocampal CA1 following status epilepticus
Dynamic mRNA signatures in the early phase of epileptogenesis after Pilocarpine-induced SE To decipher transcriptional changes early after pilocarpine-induced SE in the hippocampal CA1 subfield, we compared mRNA expression profiles of pilocarpine-induced SE animals and non-SE controls in hippocampal CA1 at five different time points, i.e. 6, 12, 24, 36…
Help me confirm if my reads are properly normalized and transformed or do I need to re-do
Help me confirm if my reads are properly normalized and transformed or do I need to re-do 0 Hello, can you help me confirm whether or not my reads dataset were normalized properly prior to my work on them? The data source is 40 florets from Arabidopsis for 3 replicates…
Opinion on miRNA pipeline
Opinion on miRNA pipeline 0 Dear colleagues, I am currently in the process of evaluating miRNA Seq data and would like to present my pipeline for your review. Given the absence of a dedicated bioinformatician in my department, particularly for this specific use case, I am eager to gather feedback…
Filter genes by expression for voomLmFit
Filter genes by expression for voomLmFit 1 @78889942 Last seen 1 day ago Switzerland Following up on limma::voom vs edgeR::voomLmFit – when to use? I’m wondering: With limma::voom, we always filtered out lowly-expressed genes (typically using edgeR::filterByExpr) beforehand, because voom did not work well for low-count genes (and also because…
Key Genes for Pyroptosis-induced Salivary Gland Inflammation
Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…
SELLAS Life Sciences Announces Positive Recommendation from REGAL Independent Data Monitoring … | News
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Genomic Data Analysis Service Market Size, Market Share and Global Market Analysis Report, 2023 – 2030
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Music compensates for altered gene expression in age-related cognitive disorders
Global impact of music on the human transcriptome We first aimed at quantifying the global effect of music on the transcriptomes of the two groups of donors separately. ACD patients exposed to music showed 2.3 times more DEGs (n = 2605) than controls (n = 1148); Table 2. Moreover, while the proportion up-regulated/down-regulated DEGs…
Solved A monoclonal antibody is produced using a genetically
A monoclonal antibody is produced using a genetically modified CHO cell culture in a bioreactor of 5m3 volume that is operated at 37\deg C. The CHO cells have an oxygen requirement of 3 x 10–10 mmol per hour and per number of cells. The critical oxygen requirement is 0.015 mM….
Complex design with a mixture of male and female mice
DEseq2 : Complex design with a mixture of male and female mice 0 @2bfe541c Last seen 4 hours ago France Hello everyone, I’m working on a scientific project that poses a particular problem. The experimental design includes 3 times and 2 conditions (WT and KO). Each time*condition has 3 mice….
Military scientists identify remains of Indiana soldier who died in German WWII battle | Us
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Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
Hello all, Background: I’ve inherited a new RNAseq data set and am thinking about updating my approaches (last time I did this I was using HISAT and Cuffdiff). I’d like some opinions on best strategies to disentangle/filter out parasite microbe reads from infected host reads before preforming a differential gene…
Single-cell RNAseq analysis of spinal locomotor circuitry in larval zebrafish
. 2023 Nov 17:12:RP89338. doi: 10.7554/eLife.89338. Affiliations Expand Affiliation 1 Vollum Institute, Oregon Health & Science University, Portland, United States. Item in Clipboard Jimmy J Kelly et al. Elife. 2023. Show details Display options Display options Format AbstractPubMedPMID . 2023 Nov 17:12:RP89338. doi: 10.7554/eLife.89338. Affiliation 1 Vollum Institute, Oregon Health &…
Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters
Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters 1 Hello, I need to compare some samples from different bulk RNA-Seq with some clusters of a scRNA-Seq (not whole sample) to find DEGs. We have undifferentiated samples performed by bulk RNA-Seq and fully differentiated samples (mature ones) are 2-3 clusters…
GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21
Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…
Bioinformatics analysis of immune cell infiltration patterns and potential diagnostic markers in atherosclerosis
A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…
The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment
Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…
The CRTC-1 transcriptional domain is required for COMPASS complex-mediated longevity in C. elegans
CRTC-1-binding proteins To identify CRTC-1 protein interactions, we tagged endogenous CRTC-1 via clustered regularly interspaced short palindromic repeats–associated protein 9 (CRISPR–Cas9) editing to generate a crtc-1::3xFLAG strain and performed immunoprecipitation (IP) followed by liquid chromatography coupled to mass spectrometry (LC–MS). We found 137 potential CRTC-1 interacting proteins (Fig. 1a and…
Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens
Developing an epigenetic screening platform in human T cells Staphylococcus aureus Cas9 (SaCas9) has been extensively used for genome editing in vivo as its compact size (3,159 bp) relative to the conventional Streptococcus pyogenes Cas9 (SpCas9) enables packaging into adeno-associated virus26,27,28. However, SaCas9 has not been widely used for targeted gene…
Problem With Volcano Plot
Problem With Volcano Plot 0 Hi, I’m working with CMScaller and I’m performing the Volcano plot with the function: subVolcano. Usage subVolcano( deg, geneID = “rownames”, lfc = log2(2), padj = 0.05, ave = 0, topN = 10, cexText = 1, classCol = getOption(“subClassCol”), … ) But I have a…
Spark-Based Label Diffusion and Label Selection Community Detection Algorithm for Metagenome Sequence Clustering
PLDLS, a parallel community detection algorithm in the spark framework, is designed to address the randomness of label selection during clustering and improve the completeness of metagenome sequence clustering. The algorithm combines four steps of node scoring and core node selection, core node diffusion and fast label selection, improved label…
DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle
Overview of this study In this study, we measured the DNA methylome from mouse liver and skeletal muscle, integrated the data with the transcriptome and proteome of these mouse tissues22,23, and examined how tissue-dominant protein and gene expression were associated with DNA hypomethylation (Fig. 1). In this study, we measured DNA…
Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple
Phenotypic response of two pineapple varieties to cold stress Notable differences in flowering time were observed for the two genotypes used in this study. The first signs of flowering were observed up to two weeks later in Dole-17 (precocious flowering tolerant) than in MD2 (precocious flowering susceptible) (Supplementary Figure S1)….
Epigenetic regulation during cancer transitions across 11 tumour types
Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…
Testing the interaction term in single-cell RNAseq DEG analysis
Testing the interaction term in single-cell RNAseq DEG analysis 0 I wonder if there is a way to test for the “interaction term” in Seurat. I have two categorical variables and would like to know if the interaction between these two variables is significantly different in a scRNAseq (2 x…
Recombinant Human Retinoblastoma-Like 2 (RBL2), transfected HEK293 cell lysate
Recombinant Human Retinoblastoma-Like 2 (RBL2), transfected HEK293 cell lysate | RayBiotech The store will not work correctly in the case when cookies are disabled. JavaScript seems to be disabled in your browser. For the best experience on our site, be sure to turn on…
deal with PCA and my samples
deal with PCA and my samples 0 Hello everyone, I am writing to inquire about my PCA plot following the meta-analysis of three PCOS studies. I am concerned about the proximity of some normal samples to the PCOS samples in my PCA plot. I would like to understand whether this…
Transcriptome de novo from different library types
Transcriptome de novo from different library types 0 Hello guys, I sequenced RNA from whole individuals from 4 different experimental conditions (non-model isopod species). The thing is that I used different library prep protocols: Condition 1 and condition 2: samples were made with library prep kit X (stranded, reverse–forward) Condition…
Cross validate RNA-seq and ATAC-seq
Cross validate RNA-seq and ATAC-seq 1 Hi, I have RNA-seq and ATAC-seq for the same samples. I wish to cross-validate two datasets. I got DEGs from RNA-seq and DARs from ATAC-seq. I annotated DARs (differentially accessible regions) using Homer, so I got their nearest gene information. Would it be reasonable…
Identification of hub genes associated with gastric cancer
Introduction GC is a common malignant tumor of digestive system. According to the International Agency for Research on Cancer (IARC) of the World Health Organization, there were 19.29 million new cancer cases and 9.96 million deaths worldwide in 2020, of which the number of new cases of GC was 1089,103…
NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection
NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…
Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep
Global changes of the transcriptome during postnatal muscle growth The number of myofibers is thought to remain fixed following birth, muscle fiber hypertrophy growth is the primaryway of muscle growth. The average CSA is generally used to measure the hypertrophy of skeletal muscle fibers. To systematically identify the growth of postnatal…
NUS scientist wins top science award
NUS scientist who found way to cool buildings with less energy wins top science award SINGAPORE – As temperatures around the world surge due to global warming, Associate Professor Qiu Cheng-Wei’s scientific discoveries in thermal conduction could pave the way for cooling down buildings with less energy. For his contributions,…
To draw a heatmap displaying DEGs associated with a specific KEGG pathway.
To draw a heatmap displaying DEGs associated with a specific KEGG pathway. 0 Hello, I hope all of you having a great day. I have difficulties drawing a heatmap displaying DEGs associated with a given KEGG pathway in R studio. I used to conduct enrichment analysis for KEGG pathways, using…
Analyzing contributions to DEG signature
I am trying to perform an analysis that I’ve not seen others done and would like some guidance. I ran a DEG analysis comparing populations A and B. I account for batch effects by incorporating the batch as a covariate in the design formula, eg: ~batch + group I have…
How to interpret the negative Log2FC from DESeq2 output?
How to interpret the negative Log2FC from DESeq2 output? 1 Hi, I have a gene with log2fc = -1.67 when comparing KD and control conditions (bulk condition) using DESeq2. Now, I have another experiment condition where I want to set sample comparisons in a way that I get the same…
Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice
Mouse strains All mouse procedures were approved by the Institutional Animal Care and Use Committees at Binghamton or Stanford University; and were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals, Eighth Edition. All mice were originally obtained from Jackson Laboratories, and…
DESeq2 lfcshrink, shrinkage apeglm vs normal
DESeq2 lfcshrink, shrinkage apeglm vs normal 0 Hi all, I have some question about the lfcshrink() function of DESeq2. When analyzed using the unshrinkage method in DESeq2, the fold change was overcalculated (Log2FC= ~30), so we are trying to apply the shrinkage methods in DESeq2. There are three methods (apeglm,…
Mitigating a TDP-43 proteinopathy by concentrating on ataxin-2 utilizing
Concentrating on ataxin-2 with RfxCas13d Due to its potential to affect TDP-43-associated toxicity20,25,26, ataxin-2 has emerged as a doubtlessly broadly relevant goal for ALS-FTD, as TDP-43 pathology is noticed in ~97% of ALS instances1,4,5 and ~45% FTD occurrences1,2,4. Given this, we sought to find out if RNA-targeting CRISPR effector proteins…
DESeq2 gene length normalisation
Dear Prof. Love, I was wondering if you could help me with a query about the DESeq2 package in R please. I have sequenced RNA transcripts from six separate species and am comparing gene expression between pairs of species. The issue I am facing is that I cannot work out…
The mutational signature of hypertrophic cardiomyopathy
Introduction Hypertrophic cardiomyopathy (HCM), characterized by asymmetric hypertrophy of the ventricular wall, is a condition where the heart becomes thickened without a distinct inducement.1,2 Epidemiological investigation shows that the estimated prevalence rate of HCM in the general population is 1:500.3,4 The clinical manifestations vary greatly, with no symptoms and mild…
GSEApy plot TypeError
GSEApy plot TypeError 0 I’m using GSEApy to do my enrichment analysis. I sorted my pre_res based on nes. I was trying to get GSEA plot for the first term, which is the most enriched. The most enriched was ‘Mitotic G2/M Transition Checkpoint (GO:0044818)’. Here is the code I attempted…
Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma
Study approval and patient consent The study protocol was approved by the Ethics Committee of Qinghai Provincial People’s Hospital (approval number: 2023-141) and conducted in accordance with the ethical principles for medical research involving human subjects described in the Declaration of Helsinki in addition to relevant Chinese laws and institutional…
pyDESeq2 Index Error?
I was trying to do a DEG analysis using DESeq2 but keeps giving me InvalidIndexError when my index object shouldn’t be a problem running the pyDESeq2 package. Here is my code: counts = pd.read_csv(‘filename.csv’) counts = counts.set_index(‘GeneID’) counts = counts.T metadata = pd.DataFrame(zip(counts.index, [‘Ctr’,’Ctr’,’Ctr’,Ctr’, ‘KO’,’KO’,’KO’,’KO’, ‘C2′,’C2′,’C2′,’C2’], columns = [‘Sample’, ‘Condition’])…
small RNAseq analysis of non human samples
small RNAseq analysis of non human samples 0 Hello all, Please share a workflow/pipeline for RNAseq analysis focused on small RNA of insects such as roaches. Since annotation is available for protein coding only, in this scenario how do i deal with question of regulation of small RNA Any help…
Exporting DEGs obtained from DESeq2
Hi, I am not sure if my “action” is against the rules of biostar, and if so, please cancel my post. My question has been discussed on bioconductor but I have realized that I may not get an an answer so I decided to open a new question and ask…
RNA sequencing and gene expression analysis in a Mouse model
Introduction Chronic obstructive pulmonary disease (COPD) is a condition that is characterized by persistent respiratory symptoms and airflow limitations that are not fully reversible. The severe complications of the disease may adversely affect its morbidity and mortality.1 According to World Health Organization (WHO) statistics, over 3 million people per year…
Transcriptomic landscape of the interaction between the entomopathogenic fungus Beauveria bassiana and its tolerant host Tribolium castaneum revealed by dual RNA-seq
Fungal infection To test a natural way of interaction between adult T. castaneum with B. bassiana conidia, insects were maintained feeding on conidia-covered corn kernels during different short time periods (i.e., 3, 6, 12, and 24h), and then separated and maintained in rearing conditions. At all time periods assayed, T….
Large fold change when analyzing expression profiling from microarray
Large fold change when analyzing expression profiling from microarray 0 Hi, dear all. I am trying to analyze a expression profiling dataset from GEO, which was detected by Affymetrix microarray. Its data processing method was described as “The data were analyzed with Microarray Suite GCOS using Affymetrix default analysis settings…
DEG gene list and find common TF from public ChlP-Seq data
DEG gene list and find common TF from public ChlP-Seq data 0 RNA-seq of treated sample gave me a list of DEG genes. am trying to find what transcriptional factor do these DEG have in common. have a bed file that contains all the publicly available TF ChiP-seq of a…
Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency
RNA-sequencing and Amplicon-sequencing alignment statistics On average, the total number of reads mapped for all samples in low and high-RFI animals were 303,428,164 and 318,958,134, for Angus (AN); 317,776,686 and 299,963,316 for Charolais (CH); and 328,016,010 and 332,007,994 for Kinsella (KN). The majority of reads were successfully uniquely mapped to…
Gene enrichment analysis of prokaryotes gene
Gene enrichment analysis of prokaryotes gene 0 I am wondering what are the good tools (web tools or R-packages) to conduct enrichment analysis using DEG data of prokaryotes (like E. coli, C. perfringens, S. aureus, and so on). Many web tools and R-packages are only available to eukaryotes, especially humans…
High pvalues when using clusterProfiler for seurat
High pvalues when using clusterProfiler for seurat 0 Hi, I am trying to run clusterProfiler::GSEA version 4.8.3 for each cluster of my SeuratObj When ranking the DEG based on logFC I get decent ES/NES scores however my q/p values are usually > 0.05 sometimes even >0.5. However, when I re-run…
r – DEseq2 results, enrichGO and ENSEMBL ID not matching
I am trying to do DEG and then use enrichGO on the results. I used code initially in DESEQ2 dds=DESeqDataSet(se,design=~TRAIT) dds=DESeq(dds) res=results(dds) I currently have results from DESEq2 which looks like this: log2 fold change (MLE): TRAIT S vs N Wald test p-value: TRAIT S vs N DataFrame with 42800…
Transcriptional linkage analysis with in vivo AAV-Perturb-seq
Experimental procedures Plasmid design and cloning AAV genome plasmids (Fig. 1a and Extended Data Figs. 1a,g,h and 5a) were based on Addgene plasmid 60231 (ref. 12). To achieve widespread transgene expression, the hSyn promoter was replaced by the ubiquitous CBh promoter (pAS088). For the triple-colour experiments (Extended Data Fig. 1a),…
Can I infer the fraction of replicating cells from bulk RNA-seq data?
Can I infer the fraction of replicating cells from bulk RNA-seq data? 0 Hi, This is a bit of a shot in the dark, but here goes nothing: I have RNAseq from a cancer cell line. Control vs 2 treatments. Two timepoints at 12 and 48h. I have already run…
High-quality single-cell transcriptomics from ovarian histological sections during folliculogenesis
Introduction Single-cell RNA sequencing (RNA-seq) was first achieved by using a quantitative cDNA amplification method and applied to mouse oocytes (Kurimoto et al, 2006; Tang et al, 2009). It has since provided unprecedented opportunities for the study of cellular differentiations, states, and diseases in various biological fields, including developmental biology,…
how to adjust other conditions when calling DEGs by DESeq2
how to adjust other conditions when calling DEGs by DESeq2 1 @98162ba4 Last seen 6 hours ago United States I’d like to call DEG by DESeq2. The following is the sample meta-data: I want to call DEGs in wk2 vs wk0, however, condition “Diet” and “Treatment” have two values too….
Find potential important genes from bulk-RNA seq experiment
Find potential important genes from bulk-RNA seq experiment 0 Hi Biostars, After finding DEG genes, I try to find important genes that may cause for a disease so I do pathway analysis with GSEA and find pathway with highest enrichment score using gseKEGG() and gseGO(). Is that genes in the…
Why we are using filtering >0 for up and
Why we are using filtering >0 for up and <0 for down after TopTags() to extract de genes ids? 0 How to extract list of DE genes after EdgeR? With summary() I get number of Up and Down expressed genes. And I would like to extract the gene IDs for…
Ferroptosis-related factors in the substantia nigra are associated with Parkinson’s disease
Cell types and their proportion in the SN of PD patients Based on the cell annotation results on the Single Cell Portal uploaded by Prof. Macosko’s group, cells were extracted and classified into different types from human SN samples (Fig. 1A). After 135,344 cells were extracted from 34 PD samples and…
Dcd file and VMD
Dear Cp2k developers, I use FIST on Cp2k version 2.0.0, with a system in a monoclinic cell that I specify by giving the three vectors A,B and C. Indeed, in the output I get INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.1199999E+03 The corresponding .dcd file contains in the array cell(6) only the diagonal part of…
Filtering mitochondrial genes in DESEq results
Filtering mitochondrial genes in DESEq results 1 Hi all! I took bulk RNAseq data done on leukaemia cells into R and I carried out deseq. I have three questions: I am confused about the limits people place on differentially expressed genes (DEGs). So far, I have only filtered for the…
Weighted analysis
Weighted analysis 0 I am a newer bioinformatician so my knowledge is still growing. We have bulk rna seq data from two datasets and are hoping to compare them. Is there an analysis method that weights each DEG in regards to LFC and pvalue? When we previously compared the two…
Asymmetric/biased log2FC values for low-expressed genes in DESeq2
Asymmetric/biased log2FC values for low-expressed genes in DESeq2 0 Hello everyone, I apologize if this question seems a bit naive. When we ran DESeq2 for our scRNAseq data (where we first pseudobulked the data by samples), we observed that genes with low expression (those with low baseMean values) exhibited an…
Permutation test in DESeq2?
Permutation test in DESeq2? 1 @320194bc Last seen 6 hours ago United States Hello Michael Love , I used DESeq2 to find DE genes between 2 groups in our dataset. Now, I’m trying to see if the number of DE genes is significant. So I repeated the following steps many…
DESeq2 design comparing changes through 2 timepoints of 2 different treatments.
Hi, I have RNAseq data of a experiment on cell lines as follows: 3 conditions: Control, TreatmentA, TreatmentB. 2 timepoints: 12h, 48h. Initial assessment using pairwise comparisons between groups showed that both treatments up/down-regulate similar genes and pathways. However, the temporal dynamics between the 2 treatments are different. I did…
regression – How to fit polynomial as a PDF to kaggle housing data in Python?
Questions: How to fit a polynomial (or composite function that consists of some standard pdf and polynomial) to target data? How to implement this sort of solution in Python? Situation: Hello! I’m new to data science, currently building a portfolio. One of the projects (Kaggle House Prices) has a target…
Compositional analysis in the Human snRNA-seq data
Paired vs Unpaired t-test: Compositional analysis in the Human snRNA-seq data 0 Hi all, I have a 6 case and 6 age-, gender-matched control human brain snRNA-seq data (one-to-one matched). All samples were integrated and analyzed together, and I would like to compare the difference in cell proportion between control…
Single-cell brain organoid screening identifies developmental defects in autism
Stem cell and cerebral organoid culture conditions Feeder-free hES cells or iPS cells were cultured on hES cell-qualified Matrigel (Corning, catalogue no. 354277)-coated plates with Essential8 stem cell medium supplemented with bovine serum albumin (BSA). H9 embryonic stem cells were obtained from WiCell. Cells were maintained in a 5% CO2 incubator at 37 °C….
Producing Bulk samples from 10X data
Producing Bulk samples from 10X data 0 Hi Everyone I am aware about an approach that’s called pseudobulking in single cell where bulk-like samples are generated from scRNAseq data (in absence of bulk data) to find which genes might be important at population level. But there is something my boss…
Cluster annotation in single cell
Cluster annotation in single cell 0 Dear Fellows, In Single cell, once we perform a clustering, for example, “umap”, which generate X number of clusters. Next is to perform annotation for cluster, which can be done by looking at differentially expressed genes within each cluster. if we get DEG within…
Single-cell transcriptomes reveal a molecular link between diabetic kidney and retinal lesions
Animals The animal experiments were approved by the Institutional Animal Care and Use Committee of Jinling Hospital (Nanjing, China), in accordance with the approved guidelines of the Institutional Animal Care and Use Committee of Jinling Hospital. 7 weeks old male wild-type (wt) and leptin receptor-deficient (db/db) mice on the C57BLKS/J…
How to extract gene lists following DEG analysis?
How to extract gene lists following DEG analysis? 0 Hello, After gene read counts, I performed DEseq2 using R software. Then, I filtered my DEG file based on pvalue <0.01 & log2FC > |1|. Then, I conducted functional annotation based on arabidopsis database. The result was as below: Actually, there…
Generation of inactivated IL2RG and RAG1 monkeys with severe combined immunodeficiency using base editing
Animals The gene targeting experiment was conducted on cynomolgus monkeys, which served as the experimental subjects. These monkeys were housed at Guangdong LANDAU Biotechnology Co. Ltd and TOPGENE Biotechnology Co. Ltd, where they received unrestricted access to water and were provided with a standard diet in accordance with standard care…
TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development
Curation of early-embryo development single-cell RNA-seq data sets for studying cell-cell communication To identify and study eLRs, we collected public early embryo development scRNA-seq datasets from the mouse MII-oocyte stage to the late blastocyst stage to ensure that scRNA-seq datasets represented every stage of early embryo development. In addition, to…
Multiomic interpretation of fungus-infected ant metabolomes during manipulated summit disease
Infection mortality, observations of manipulation, and LC–MS/MS Similar to previous laboratory infections with O. camponoti-floridani24, we collected C. floridanus displaying manipulated summiting between four hours before (zeitgeber time, ZT 20) to half an hour after dawn (ZT 0.5), beginning three weeks after infection (Fig. 1). Sham-treated healthy ants showed no mortality…
Avoiding false discoveries: Revisiting an Alzheimer’s disease snRNA-Seq dataset
Reviewer #1 (Public Review): Murphy, Fancy and Skene performed a reanalysis of snRNA-seq data from Alzheimer Disease (AD) patients and healthy controls published previously by Mathys et al. (2019), arriving at the conclusion that many of the transcriptional differences described in the original publication were false positives. This was achieved…
KRTA6A and FA2H Are Hub Genes Associated With Cgas-STING-related Immunogenic Cell Death in Lung Adenocarcinoma
Abstract Background/Aim: The immunogenic cell death (ICD) pathway plays a crucial prognostic role in lung adenocarcinoma (LUAD) therapy. The cyclic GMP–AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is an upstream mechanism that drives ICD activation, but the interaction of hub genes remains unclear. The present study aimed to investigate…
microarray DEG analysis
microarray DEG analysis 1 Hi, I was following this microarray bioinformatic differential gene expression analyses tutorial R code: github.com/Lindseynicer/How-to-analyze-GEO-microarray-data/blob/main/GSE_analysis_microarray.Rmd I analysed GSE30929 instead. However, when I run this line of code fit2 <- contrasts.fit(fit, contrasts) fit2 <- eBayes(fit2) topTable(fit2) topTable1 <- topTable(fit2, coef=1) topTable2 <- topTable(fit2, coef=2) topTable3 <- topTable(fit2,…
DEG by deseq2 by Race
DEG by deseq2 by Race 1 @0f70ccd9 Last seen 23 hours ago United States Hi Mike and community, I am recently doing DEG analysis by using Deseq2. I am trying to get differentially expressed genes in African American (AAM) and European American (EAM) prostate cancer populations by using the TCGA…
Bioconductor ORA
Answer: Comparing the effect of single drug and two-drug combination with control in RNA by Michael Love 40k For questions about statistical analysis, I recommend to work with a local statistician or someone familiar with linear models in R. Answer: DESeq2 batch design by Michael Love 40k Sorry, I only…
Screenshot of Phase 3 of Morganton Park South |
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Converting gene id to entrez id with clusterprofiler
Converting gene id to entrez id with clusterprofiler 0 Hi, Im new to R and i’ve been trying to use clusterprofiler to convert my gene_ids to entrez_id for further analysis. I work on the msu7 rice genome and my gene ids looks like this (LOC_Os08g09610, LOC_Os06g05660). Since, it was a…
What are the reasons to find so few Differentially expressed genes (DEGs)?
What are the reasons to find so few Differentially expressed genes (DEGs)? 1 HI, After the differential gene expression analysis, I had got only 15 genes with logFC < 1.5. Is it because of the Transcriptome reference annotation, expression quantification method, and DEG detection methods which are affecting the optimal…
Measure quantity of mitochondrial DNA in aged bones or calculate it from nuclear DNA quantitative PCR results?
Sample selection Samples from two mass gravesites located near one another and dating back to the Second World War were selected because of their challenging yet relevant characteristics in forensic genetic examinations (skeletonized human remains, long postmortem interval, and DNA degradation). The samples were the diaphyses of femurs, cut below…
Make heatmap for RNA-seq with non replicate
Make heatmap for RNA-seq with non replicate 0 Hi all, degs = rownames(subset(DEG, PValue < 0.05 & abs(logFC > 9))) rownames(counts) = DEG[rownames(counts), ‘symbol’] counts_degs = counts[degs,] pheatmap(counts_degs, clustering_method = ‘ward.D’, scale=”row”) Could I use TPM matrix instead of raw count matrix to make heat map using the code above?…
Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage | Parasites & Vectors
Morphological observation of continuous in vitro cultured B. gibsoni (Wuhan isolate) Babesia gibsoni was successfully cultured in vitro in 20% serum. After splitting, parasitemia reached 10% ± 1.5% on day 3 (Fig. 1A). Fig. 1 Changes in parasitemia and morphology of in vitro cultured B. gibsoni (Wuhan isolate). A Changes in parasitemia of…
Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing
Ndrg2 expression is reduced in tolerogenic DCs To identify potential targets for gene editing in DCs, we compared transcriptomic profiles of treatment induced tolerogenic DCs, which confer a variety of clinical benefits11,12,13,14,15,16,17 with untreated DCs. Bone marrow-derived DCs were cultivated from wild-type (WT) mice (C57/BL6) according to standard protocols25. Vitamin…
GO enrichment of DEGs – DeNovo RNAseq
GO enrichment of DEGs – DeNovo RNAseq 0 Hi, I did DeNovo assembly of a few RNAseq samples sing Trinity. After that, I mapped the raw data to the DeNovo assembly and did quantification and DEG analysis. The annotation of the assembly was done using Trinotate. The GO ids, gene…
SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response
SF3B1 MUT cells show selective sensitivity to PARP inhibitors To identify candidate therapeutic targets for cancers with SF3B1 hotspot mutations, we utilized the leukemia K562K700E (SF3B1K700E) and parental (SF3B1WT) isogenic cells1, to model one of the most prevalent SF3B1 hotspot mutations seen in patients8,19,20 (Fig. 1a,b and Supplementary Fig. 1a)….
Differential Gene Expression analysis in Bulk RNA Seq
Differential Gene Expression analysis in Bulk RNA Seq – using Count Matrix as input 1 Hello everyone, I am going to do the differential gene expression (DEG) analysis in the bulk RNA seq data. The sample used are the NAFLD samples downloaded from the NCBI Gene Expression Omnibus (GEO) (link…
Transcriptomic analysis of neutrophil apoptosis induced by large B-cell lymphoma
introduce Difuse large B-cell lymphoma is the most common subtype of non-Hodgkin lymphoma, accounting for 30 percent of new cases in NHL each year. Although approximately 50-60% of human patients are cured by R-CHOP immunochemotherapy, more than 30% of patients are refractory to these regimens or relapse after remission, and…
Integrate transcriptomics and CNV
Integrate transcriptomics and CNV 1 Dear Community, I have two omics datasets (WGS and transcriptomics) on tumor/normal cells. I have performed CNV calling on genomics data and DEG on transcriptomics data. Is there any methods/ approach to compare among these two dataset? Best, CNV omics • 181 views • link…
Read length for single -ended RNA seq data analysis
Read length for single -ended RNA seq data analysis 0 Hi! all, I am fairly new to the RNA seq data analysis, In order to perform DEG between two conditions, I have 3 samples per each condition(single ended) all of them have common problems as per FAST QC viz, failure…