 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 16, 2019 |
| Title |
Chipseq_H3K27Ac_P14_Arm_D7_ShortLivedEffector_2 |
| Sample type |
SRA |
| |
|
| Source name |
CD8 P14
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
surface marker: B220-Ly6G-CD8+CD45.1+Klrg1+
infection status: acute
culture condition: ex vivo
chip antibody: abcam ab4729
|
| 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 6
|
| 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 17, 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 |
SAMN10057218 |
| SRA |
SRX4677974 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3388380_Chipseq_H3K27Ac_P14_Arm_D7_ShortLivedEffector_2.bw |
47.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
