NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4123853 Query DataSets for GSM4123853
Status Public on Apr 03, 2020
Title Th17_WT2 (RNA-seq)
Sample type SRA
 
Source name spleen, lymph nodes
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: in vitro-generated Th17 cells
culture time: 3 days
genotype: wild-type
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from 3x10^6 viable WT and NCOR1f/f,Cd4Cre in vitro-generated Th17 cells with QIAshredder, RNaeasy Mini Kit and RNase-Free DNase Set (Qiagen) according to manufacturer's protocol.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing was performed with custom programs based on Picard tools (v2.18.11, http://broadinstitute.github.io/picard/).
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. Tophat2 spliced alignments were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, preventing de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
The Bioconductor cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) pckage was used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (UCSC mm10)
Supplementary_files_format_and_content: tab-separated value files of FPKM estimates obtained from Cufflinks, enriched with Ensembl transcrit annotation.
 
Submission date Oct 16, 2019
Last update date Apr 04, 2020
Contact name Wilfried Ellmeier
E-mail(s) wilfried.ellmeier@meduniwien.ac.at
Organization name Medical University of Vienna
Department Institute of Immunology
Street address Lazarettgase 19
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL21103
Series (2)
GSE138933 RNA-seq analysis of WT and NCOR1f/f,Cd4Cre in vitro-generated Th17 cells
GSE138934 Role of NCOR1 in CD4+ T cells
Relations
BioSample SAMN13038867
SRA SRX7004456

Supplementary file Size Download File type/resource
GSM4123853_Th17_WT2_S43988_genes_fpkm.tsv.gz 1.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap