Tag: GRCm38
Assembly Table.
Assembly Table. A. mellifera (Apr 2011 Amel_4.5/amel5) A. carolinensis (May 2010 AnoCar2.0/anoCar2) A. thaliana (Feb 2011 TAIR10/araTha1) B. taurus (Aug 2006 Btau_3.1/bosTau3) B. taurus (Nov 2014 Bos_taurus_UMD_3.1.1/bosTau8) C. familiaris (May 2005 CanFam2.0/canFam2) C. familiaris (Sep 2011 CanFam3.1/canFam3) C. porcellus (Feb 2008 Cavpor3.0/cavPor3) C. elegans (Oct 2010 WBcel215/ce10) C. elegans (Feb…
Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-‘omics analysis of the liver metabolic response to viral infection
Introduction The metabolome is an incredibly diverse collection of small molecules (<1,500 Da) in biological systems involved in virtually every cellular process, including cellular energy production, macromolecule synthesis, epigenetic modifications, cell signalling and more (for recent reviews see [Citation1–6]). It responds rapidly (in seconds) to both internal (signalling, allostery) and external…
Errors after running jobscript for cellranger vdj pipeline
Errors after running jobscript for cellranger vdj pipeline 0 Hello, Below is pasted my jobscript to be submitted to run cellranger vdj pipeline on my fasta sample files. 1 #!/bin/bash 2 #PBS -N RED_aregvdj 3 #PBS -q serial 4 #PBS -l nodes=1:ppn=24 5 #PBS -l walltime=03:00:00 6 #PBS -l pmem=3300mb…
RHOJ controls EMT-associated resistance to chemotherapy
Mice Rosa26-YFP48, Rosa-tDTomato49, K14creER, Lgr5creER (ref. 50), KrasLSLG12D (ref. 51) and Trp53fl/fl (ref. 52) mice were obtained from the NCI mouse repository and Jackson Laboratories. Rhojfl/fl mice53 were a gift from A. Uemura. All mice used in this study were composed of males and females with mixed genetic background. Mouse…
Bipotent transitional liver progenitor cells contribute to liver regeneration
Mice All mice experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC) at the Center for Excellence in Molecular Cell Science, Shanghai Institutes of Biological Sciences, Chinese Academy of Science. The approved animal protocol number is SIBCB-S374-1702-001-C1. The CK19-CreER, HNF4α-DreER, R26-tdTomato (R26-tdT),…
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
I am working on analysis for an RNASeq experiment with the end goal of using DESeq2 to generate a list of differentially expressed genes. We have 4 biological replicates for 4 conditions (differing genotypes in mice). We have 50 bp single ended Illumina read sets, on total RNA (they had…
Fumarate induces vesicular release of mtDNA to drive innate immunity
Mice Mice were of mixed genetic background C57BL/6 and 129/SvJ. Mice were bred and maintained under specific-pathogen-free conditions at the Breeding Unit (BRU) at the CRUK Cambridge Institute. Fh1fl/fl (ref. 4) and R26-Cre-ERT2 (ref. 5) mice were gifts from E. Gottlieb and D. Winton, respectively. Experimental mice were homozygous for…
Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut
Animal studies Animal care and study protocols were approved by the AAALAC-accredited Institutional Animal Care and Use Committee of the College of Agricultural Life Sciences at the University of Wisconsin-Madison (UW-Madison). All experiments with mice were performed under protocols approved by the UW-Madison Animal Care and Use Committee (Protocol number…
Nociceptor neurons affect cancer immunosurveillance
Secondary use of biopsies as research specimens The ten melanoma samples used in this study were collected by Sanford Health and classified by a board-certified pathologist. Their secondary use as research specimens (fully de-identified formalin-fixed, paraffin-embedded (FFPE) blocks) was approved under Sanford Health IRB protocol 640 (titled ‘Understanding and improving…
In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states
Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…
Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq
Software official website ： Hisat2： Manual | HISAT2 StringTie：StringTie article ：Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial ： 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…
how to build index for cdna?
Hello, I can build index for Mus_musculus.GRCm38.dna_sm.toplevel.fa, but when build for Mus_musculus.GRCm38.cdna.all.fa, there is a bug: “rsem-extract-reference-transcripts Mus_musculus.GRCm38.cdna.all.fa 0 Mus_musculus.GRCm38.cdna.all.fa.gtf None 0 Mus_musculus.GRCm38.cdna.all” failed! Plase check if you provide correct parameters/options for the pipeline! Traceback (most recent call last): File “../indrops.py”, line 1770, in project.build_transcriptome(args.genome_fasta_gz, args.ensembl_gtf_gz, mode=args.mode) File “../indrops.py”, line…
deeptools plotHeatMap – Convert bed files to gene list?
I might suggest limiting your search to genes: gtf2bed < Mus_musculus.GRCm38.102.gtf | grep -w “gene” > sorted-mm10.genes.bed But that’s up to you. Otherwise, I think you may also get transcripts/exons, which may be more than you want. Again, up to you. If hnf4a-ko-downreg-clusters.bed is the file containing peaks, as described…
Htseq is giving me 0 counts using the GFF3 of miRBase
Hello! I am trying to annotate a miRNA-seq so that it gives me mature miRNAs where I already have 5p and 3p. For this, I have used the index mm10.fa and the miRBase mmu.gff3. I have aligned with HISAT2 and am trying to count with HTSeq, however I get 0…
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…
Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition
INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…
python – How can I fix the dash bio error: devtools cannot load source map dashbio@1.0.1 bundle.js.map?
I am implementing a website in Python with Django framework and using django-plotly-dash to display data. I am trying to use dash_bio’s IGV feature to display some chromosome data, but when I attempt to call the functionality, I receive the following errors and the callback that returns ‘dashbio.igv’ is unable…
Why are there more lincRNA genes than transcripts in Mus_musculus.GRCm38.100.gtf?
Why are there more lincRNA genes than transcripts in Mus_musculus.GRCm38.100.gtf? 1 Hi All, There are 52446 annotated genes (ENSMUSG IDs) and 142,699 transcripts (ENSMUST IDs) in Mus_musculus.GRCm38.100.gtf. It makes sense that there are WAY more transcripts than genes. My question, however, is – why are there more genes than transcripts…
Characterization and expression of DNA sequences encoding the growth hormone gene in African Pygmy Mouse (Mus minutoides)
Abstract We determined the nucleotide sequence of the growth hormone (Gh) gene in Mus minutoides, one of the smallest mammals, where was predicted to be distinct in the functional regions between M. minutoides and Mus musculus. To investigate the evolutionary characteristics of Gh in M. minutoides, we constructed a phylogenetic…
Good or bad idea to annotate with newer genome build?
Good or bad idea to annotate with newer genome build? 0 Hello Biostars Community, If the probe sequences on a mouse methylation beadchip array is based on the (mm10) GRCm38 genome build, would it be a bad idea to annotate the probes with the latest genome build (mm39) GRCm39? I…
STAR align multiple files
STAR align multiple files 1 Hi everybody, I am doing alignment to 36 PE samples using star. to make it little bit easy task I wrote a bash loop to align them all with the same command. here is my loop: for i in $(ls raw_data); do STAR –genomeDir index.150…
IOError [errno 2] No such file or directory: ‘-o’
TopHat error: IOError [errno 2] No such file or directory: ‘-o’ 2 Hello everyone. I’m now running tophat in our server. First, I just simply tried “tophat -p 8 -G <gtf_file> <ref_genome> <fa1><fa2>” and it worked. Then I wrote a for loop scripts but It reported error: [2019-04-03 10:49:16] Beginning…
