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Status |
Public on Apr 25, 2012 |
Title |
WT IL15 48hr RNASeq |
Sample type |
SRA |
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Source name |
CD8+ T Cells
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 source tissue: Spleen cell type: CD8+ T Cells treatment: IL-15 20ng/ml time: 48h
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Treatment protocol |
For ChIP-Seq, not treated or treated with 100 U/ml IL-2 for 1 hr. For RNA-Seq, not treated or treated by 500 U/ml IL-2 or 20 ng/ml IL-15 for indicated times
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Growth protocol |
For ChIP-Seq, Preactivated mouse splenic T cells were pre-activated with plate-bound anti-CD3 and soluble anti-CD28 for 3 days, washed, rested overnight. For RNA-Seq, 1.5 μg of total RNA isolated from WT and DKI CD8+ T cells
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Extracted molecule |
total RNA |
Extraction protocol |
For ChIP-Seq, cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication. For RNA-Seq, Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer II |
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Description |
treated IL-15 20ng/ml
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Data processing |
For ChIP-Seq, Basecalls performed using CASAVA version 1.4; For RNA-Seq, Basecalls performed using CASAVA version 1.7 ChIP-Seq reads were aligned to the mm8 genome assembly using CASAVA pipeline 1.4 and 1.7 Aligned reads are converted to BED format using CASAVA pipeline For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database Genome_build: mm8 Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.4 and 1.7, rpkm files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts
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Submission date |
Mar 28, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Peng Li |
E-mail(s) |
peng.li@nih.gov
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Organization name |
NIH
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Department |
NHLBI
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Lab |
LMI
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Street address |
9000 Rockville Pike
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City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
20892 |
Country |
USA |
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Platform ID |
GPL9250 |
Series (2) |
GSE36882 |
Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function (ChIP-Seq and RNA-Seq) |
GSE36890 |
Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function |
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Relations |
SRA |
SRX132026 |
BioSample |
SAMN00847478 |
Supplementary file |
Size |
Download |
File type/resource |
GSM904771_mm8_WT_CD8_IL15_48h.txt.gz |
443.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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