Tag: lncRNA

Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

Continue Reading Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

Index of /~ckern/FAANG_Project/Cattle_NCBI

Name Last modified Size Description Parent Directory   –   Aligned_Reads/ 2016-07-30 04:38 –   Cufflinks_Output/ 2017-11-11 11:53 –   FEELnc/ 2018-08-14 16:03 –   Gene_Expression/ 2016-09-01 14:14 –   Genome/ 2018-04-04 15:54 –   Intermediate_LncRNA.feelncclassifier.log 2016-08-05 15:59 18K   LncRNA/ 2018-08-08 11:07 –   Raw_Reads/ 2016-07-28 15:11 –  …

Continue Reading Index of /~ckern/FAANG_Project/Cattle_NCBI

ncRNA | Free Full-Text | LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells

As shown in Figure 2A, LINC00892 is strongly induced in Jurkat cells following treatment with a combination of PMA and ionomycin. The reason for the concomitant use of PMA and ionomycin to induce T cell activation is based on the need to activate multiple signal transduction pathways. PMA is a…

Continue Reading ncRNA | Free Full-Text | LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells

Roles of circRNAs | CMAR

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

Continue Reading Roles of circRNAs | CMAR

LncRNA Sequencing Helps to Find Deep Links to Disease

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not code for proteins and are typically greater than 200 nucleotides in length. Studies have shown that lncRNAs are quite complex in function and play an important role in various biological processes such as development, differentiation, proliferation, metastasis, apoptosis,…

Continue Reading LncRNA Sequencing Helps to Find Deep Links to Disease

MicrobioSeq Releases Nanopore-Based Microbial Epigenomics Solutions to Accelerate Your Research

MicrobioSeq is the microbial genomics division of CD Genomics, committed to delivering comprehensive microbial solutions to human health, agriculture, the environment, and industry by characterizing microbiomes and leveraging microorganisms. The company recently announced the launch of Nanopore-Based Microbial Epigenomics Solutions to detect more types of DNA modifications.   Epigenetic modifications…

Continue Reading MicrobioSeq Releases Nanopore-Based Microbial Epigenomics Solutions to Accelerate Your Research

GENCODE – Human Release 32 Statistics

Statistics about the GENCODE Release 32 The statistics derive from the gtf file that contains only the annotation of the main chromosomes. For details about the calculation of these statistics please see the README_stats.txt file. General stats Total No of Genes 60609 Protein-coding genes 19965 Long non-coding RNA genes 17910…

Continue Reading GENCODE – Human Release 32 Statistics

Special Issue : Methods and Tools in RNA Biology

A special issue of Non-Coding RNA (ISSN 2311-553X). Deadline for manuscript submissions: 30 November 2022 | Viewed by 9 Special Issue Editors Dr. Mirolyuba Ilieva E-Mail Website Guest Editor Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, DenmarkInterests: non-coding RNAs; stem cell biology; neuroscience Special…

Continue Reading Special Issue : Methods and Tools in RNA Biology

Biogenesis, biology and characterization of circular RNAs

Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…

Continue Reading Biogenesis, biology and characterization of circular RNAs

Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

Continue Reading Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

LncRNA PCAT1 activates SOX2 and suppresses radioimmune responses via regulating cGAS/STING signalling in non-small cell lung cancer

This article was originally published here Clin Transl Med. 2022 Apr;12(4):e792. doi: 10.1002/ctm2.792. ABSTRACT BACKGROUND: The expression of long non-coding RNA (lncRNA) prostate cancer-associated ncRNA transcripts 1 (PCAT1) is increased in non-small cell lung cancer (NSCLC). It stimulates tumour growth and metastasis, but its role in the radioimmune responses remain…

Continue Reading LncRNA PCAT1 activates SOX2 and suppresses radioimmune responses via regulating cGAS/STING signalling in non-small cell lung cancer

SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information

doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations Expand Affiliations 1 School of Information Engineering, Xijing University, Xi’an, China. 2 School of Computer Science, Northwestern Polytechnical University, Xi’an, China. Item in Clipboard Zhong-Hao Ren et al. Front Genet. 2022. Show details Display options Display options Format AbstractPubMedPMID doi: 10.3389/fgene.2022.839540. eCollection 2022. Affiliations 1 School…

Continue Reading SAWRPI: A Stacking Ensemble Framework With Adaptive Weight for Predicting ncRNA-Protein Interactions Using Sequence Information

ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Non-Coding RNA 2022, 8(2), 23; doi.org/10.3390/ncrna8020023 (registering DOI) Received: 1 March 2022 / Revised: 21 March 2022 / Accepted: 25 March 2022 / Published: 28 March 2022 Round 1 Reviewer 1 Report In recent years, a great process has been made in the research…

Continue Reading ncRNA | Free Full-Text | Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS  Google Scholar  Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…

Continue Reading Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis

The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes | Virology Journal

Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLOS ONE. 2014;9:91918. Article  Google Scholar  Bateman A, Birney E, Cerruti L, Durbin R, Etwiller…

Continue Reading The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes | Virology Journal

Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

Continue Reading Transcriptional kinetics and molecular functions of long noncoding RNAs

Spatial components of molecular tissue biology

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

Continue Reading Spatial components of molecular tissue biology

Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

There are four types of methods to extract longest transcript or longest CDS regeion with longest transcript from transcripts fasta file or GTF file. 1.Extract longest transcript from gencode transcripts fasta file. 2.Extract longest transcript from gtf format annotation file based on gencode/ensembl/ucsc database. 3.Extract longest CDS regeion with longest…

Continue Reading Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.

Postdoctoral Fellow job with EMBL

We are offering a 2-year postdoc position in the group of Dr. Marco Marcia (www.embl.org/groups/marcia/) at the European Molecular Biology Laboratory (EMBL), one of the highest-ranked scientific research organisations worldwide. The group is based in Grenoble, France. We are carrying out an exciting pioneering project that will decipher the molecular…

Continue Reading Postdoctoral Fellow job with EMBL

In Rett Models, Regulatory RNAs Appear To Be Altered

Regulatory RNAs involved in nerve cell signaling and structure were altered in cell and mouse models of Rett syndrome, with these changes also evident in tissue from deceased patients, a study reported. These findings aid in understanding the biological processes impaired in Rett and may reveal potential biomarkers to help…

Continue Reading In Rett Models, Regulatory RNAs Appear To Be Altered

Identification of Novel Diagnostic Biomarkers in Prostate Adenocarcinoma Based on the Stromal-Immune Score and Analysis of the WGCNA and ceRNA Network

This article was originally published here Dis Markers. 2022 Jan 15;2022:1909196. doi: 10.1155/2022/1909196. eCollection 2022. ABSTRACT Prostate cancer is still a significant global health burden in the coming decade. Novel biomarkers for detection and prognosis are needed to improve the survival of distant and advanced stage prostate cancer patients. The…

Continue Reading Identification of Novel Diagnostic Biomarkers in Prostate Adenocarcinoma Based on the Stromal-Immune Score and Analysis of the WGCNA and ceRNA Network

Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

Continue Reading Novel diagnostic biomarkers for keloid based on GEO database

Long non-coding RNA MSTRG.81401 short hairpin RNA relieves diabetic neuropathic pain and behaviors of depression by inhibiting P2X4 receptor expression in type 2 diabetic rats

1. Nicodemus JM, Enriquez C, Marquez A, Anaya CJ, Jolivalt CG (2017) Murine model and mechanisms of treatment-induced painful diabetic neuropathy. Neuroscience 354:136–145. doi.org/10.1016/j.neuroscience.2017.04.036 CAS  Article  PubMed  Google Scholar  2. Morimoto SS, Kanellopoulos D, Manning KJ, Alexopoulos GS (2015) Diagnosis and treatment of depression and cognitive impairment in late life….

Continue Reading Long non-coding RNA MSTRG.81401 short hairpin RNA relieves diabetic neuropathic pain and behaviors of depression by inhibiting P2X4 receptor expression in type 2 diabetic rats

Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

doi: 10.3389/fgene.2021.772557. eCollection 2021. Chun Huang  1 , Fei Ge  1 , Xiaoming Ma  1 , Rongfeng Dai  1 , Renqing Dingkao  2 , Zhuoma Zhaxi  3 , Getu Burenchao  3 , Pengjia Bao  1 , Xiaoyun Wu  1 , Xian Guo  1 , Min Chu  1 , Ping Yan  1 , Chunnian Liang  1 Affiliations Expand Affiliations 1 Key Laboratory of…

Continue Reading Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin . Catalog Introduction to transcriptome sequencing mRNA|miRNA|lncRNA|circRNA Introduction to analysis mRNA Group miRNA Group lncRNA Group circRNA Group mRNA|miRNA|lncRNA|circRNA Correlation analysis Reference Introduction to transcriptome sequencing Transcriptome (Transcriptome) Is a single or group of cells…

Continue Reading Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

Continue Reading ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

Science Papers Describe NanoProCas9 System, Inflammatory Protein Biomarkers, LncRNA Affects Muscle Tissue Formation in Aging

A conditionally activatable CRISPR-Cas9 prodrug system that can be leveraged for precision medicine is described in this week’s Science Advances. While CRISRP-Cas9 genome editing holds great therapeutic potential, the nonspecific distribution of Cas9 raises safety concerns relating to off-target activity at the tissue level. Aiming to overcome this limitation, Zhejiang…

Continue Reading Science Papers Describe NanoProCas9 System, Inflammatory Protein Biomarkers, LncRNA Affects Muscle Tissue Formation in Aging

Poly A vs total RNA

Poly A vs total RNA – Which is better for extracting noncoding RNA information 0 Hi everyone, In scRNAseq ,I want to extract lncRNA,miRNA etc Extracted molecule -polyA RNA or total RNA Since polyA RNA will not give much information about noncoding counterpart,will it be fruitful to go on with…

Continue Reading Poly A vs total RNA

miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

Continue Reading miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Omics data collection and merging of datasets from different studies

Omics data collection and merging of datasets from different studies 0 Hi! I’m going to do omics analysis on skin basal cell carcinoma. I’m currently trying to find publicly available data to use to make a data collection. I have looked after RNA-seq(high throughput) in GEO and found some studies…

Continue Reading Omics data collection and merging of datasets from different studies

Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

Continue Reading Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

Continue Reading Classifiers for predicting coronary artery disease

Running htseq-count to “grab” long non coding gene_id names

Running htseq-count to “grab” long non coding gene_id names 0 hi all, new to bioinformatics. so bare with me.. I am trying find long non coding RNA from RNA-seq data. As i checked the human gtf file there are 2 different types of long non coding RNA, “lnc_RNA” and “lncRNA”,…

Continue Reading Running htseq-count to “grab” long non coding gene_id names

Looking up Gene IDs in R

Looking up Gene IDs in R 1 Hello, Given a list of gene names, I need to create a table containing the Ensemble ID, chromosome, start, end of that gene. Example: ## ens_id gene view chr start end ## 1: ENSG00000243485 MIR1302-2HG Gene Expression chr1 29553 30267 ## 2: ENSG00000237613…

Continue Reading Looking up Gene IDs in R

Finding differentially expressed lncRNA

Finding differentially expressed lncRNA 0 Hi all, I’m trying to diff. expressed lncRNAs between two groups (of humans). I wanted to use the following pipeline: trimmomatic –> stringtie/cufflinks –> Cuffmerge/stringtie merge –> FEELnc to find lncRNAs. To find diff. expressed transcripts I want to use the following pipeline: trimmomatic –>…

Continue Reading Finding differentially expressed lncRNA

How do I check the expression level of a unannotated lncRNA in RNAseq dataset?

How do I check the expression level of a unannotated lncRNA in RNAseq dataset? 2 I plan to check a lncRNA expression level in RNAseq dataset, but the lncRNA was just identified and not annotated yet.Only I know is its position in chromatin and the sequence of it. so how…

Continue Reading How do I check the expression level of a unannotated lncRNA in RNAseq dataset?

normalization two different datasets tcga vs gtex

normalization two different datasets tcga vs gtex 0 using tcga and gtex to look for lncrna DE (using raw files) – what are the best ways to normalize? deseq2 and edger? also if i want to look at lncrnas of specific chromosomes, how should i approach normalization? tcga gtex normalization…

Continue Reading normalization two different datasets tcga vs gtex