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Sample GSM2098929 Query DataSets for GSM2098929
Status Public on May 18, 2016
Title Acetate 4
Sample type SRA
 
Source name OT-I T cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Lymph node
Treatment protocol 5 mM acetate was added during the last 3 days of culture
Growth protocol OVA-specific OT-I memory T cells were activated with 10^–9 M OVA peptide in the presence of splenocytes for 3 d, followed by 3-4 d culture in IL-15 (10 ng/mL) in absence of OVA peptide.
Extracted molecule total RNA
Extraction protocol The total RNA input material was used to make barcoded and ready to sequence libraries using the Illumina TruSeq Stranded mRNA Sample Preparation Kits.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The prepared libraries were sequenced on the Illumina NextSeq 500 using a v2 kit with 75 cycles and high output.
The resulting reads were mapped to the mm10 reference genome using the STAR software version 2.4.0h (GitHub, Inc.).
Resulting mapping files in bam format were analyzed using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) from the HTSeq framework (version 0.6.0) for read count numbers to specific genomic features (whole genes).
Finally, the raw count files were inputted to the statistical analysis software DESeq2 (version 1.6.3) from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: mapped raw read counts
 
Submission date Mar 25, 2016
Last update date May 15, 2019
Contact name Christoph Hess
E-mail(s) chess@uhbs.ch
Organization name University Basel
Department Department of Biomedicine
Lab Immunobiology
Street address Hebelstrasse 20
City Basel
ZIP/Postal code 4031
Country Switzerland
 
Platform ID GPL19057
Series (1)
GSE79600 Memory CD8+ T cells require stress-levels of acetate for optimal function
Relations
BioSample SAMN04579672
SRA SRX1661566

Supplementary file Size Download File type/resource
GSM2098929_4-3dacetate1_R1.counts.txt.gz 100.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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