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| Status |
Public on Apr 25, 2012 |
| Title |
DKI-IL2-IgG ChIPSeq |
| Sample type |
SRA |
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| Source name |
Total T Cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
source tissue: Spleen
cell type: total T cells
chip antibody: Rabbit IgG
chip antibody manufacturer: R&D
chip antibody catalog #: AB-105-C
chip antibody lot #: ER11
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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 |
genomic DNA |
| 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against IgG
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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generated using CASAVA pipeline 1.4 and 1.7, rpkm files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts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 |
GPL9185 |
| 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 |
SRX132020 |
| BioSample |
SAMN00847472 |
| Named Annotation |
GSM904765_mm8-Tcell-DKI-IL2-IgG_ChIPSeq.bed.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM904765_mm8-Tcell-DKI-IL2-IgG_ChIPSeq.bed.gz |
26.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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