NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3388392 Query DataSets for GSM3388392
Status Public on Apr 16, 2019
Title Chipseq_Input_P14_Cl13_D7_TerminallyExhaused_2
Sample type SRA
 
Source name CD8 P14
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
surface marker: B220-Ly6G-CD8+CD45.1+Tim3+Blimp1YFP+
infection status: chronic
culture condition: ex vivo
chip antibody: N/A
Extracted molecule genomic DNA
Extraction protocol cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Isolated cells were further sorted based on their surface markers.
Lymphocytic choriomeningitis virus infection protocol: For acute viral infections, mice were intravenously (i.v.) injected with 2×10^5 plaque-forming unit (PFU) LCMV Armstrong. For chronic viral infections, mice were intravenously (i.v.) injected with 2×10^6 PFU LCMV clone 13.
One million FACS sorted cells were used for ChIP. DNA-protein crosslinking, nuclei isolation, and chromatin sonication were performed using truChIP Chromatin Shearing Kit (Covaris) according to manufacturer’s instructions. ChIPmentation was performed according to the published protocol (Schmidl, C., Rendeiro, A. F., Sheffield, N. C., & Bock, C. (2015). ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nature Methods, 12(10), 963–965. http://doi.org/10.1038/nmeth.3542).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 3000 according to the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Description sample 18
Data processing alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. ChIP-seq reads were mapped to the mouse genome (build mm10) with Bowtie 1.1.1.
peaks: Peaks were identified using MACS (v 1.4.3; default p-value threshold of 1E-5) .
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for histone modification ChIP-seq
 
Submission date Sep 13, 2018
Last update date Apr 16, 2019
Contact name Tuoqi Wu
E-mail(s) tuoqiwu@gmail.com
Organization name National Institute of Allergy and Infectious Diseases
Street address 49 Convent Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21493
Series (2)
GSE119941 Single-Cell Transcriptomics Identifies TOX as a Key Transcriptional Regulator of Progenitor-Like CD8 T Cells in Chronic Infection [ChIP-seq]
GSE119943 Single-Cell Transcriptomics Identifies TOX as a Key Transcriptional Regulator of Progenitor-Like CD8 T Cells in Chronic Infection
Relations
BioSample SAMN10057203
SRA SRX4677986

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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