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| Status |
Public on Oct 01, 2016 |
| Title |
Effector_H3K27Ac |
| Sample type |
SRA |
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| Source name |
CD8 T cell
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| Organism |
Mus musculus |
| Characteristics |
cell stage: Effector
strain: C57BL/6
antibody: Abcam, ab4729
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| Treatment protocol |
Naive CD45.2+ P14 TCR-Tg CD8+ T cells were isolated from the lymph nodes and adoptively transferred into CD45.1+ naïve recipient mice at 10,000 cells per mouse. One day later, the recipient mice were i.p. infected with 2×105 PFU of LCMV-Armstrong.
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| Growth protocol |
C57BL/6 and B6.SJL mice were from the Jackson Laboratory. All mouse experiments were performed under protocols approved by the Institutional Animal Use and Care Committee of the University of Iowa.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
On day 8 post-infection (p.i.), CD45.2+CD8+KLRG1+ IL-7Ra– cells were sort-purified as terminally differentiated effector CD8+ T cells. On ≥ day 60 p.i., CD45.2+CD8+CD62L+ cells were purified as central memory CD8+ T cells. From the lymph nodes of uninfected P14 TCR-Tg mice, CD62L+CD44lo-med CD8+ cells were isolated as naïve CD8+ T cells. The cell sorting was performed on on FACSAria (BD Biosciences).
Sorted CD8+ T cells were cross-linked with 1% formaldehyde in medium for 10 minutes, processed using truChIP Chromatin Shearing Reagent Kit (Covaris), and sonicated for 5 minutes on Covaris S2 ultrasonicator. The sheared chromatin was immunoprecipitated with anti-H3K4me1 (Abcam, ab8895), H3K4me3 (Millipore, 17-614), H3K27me3 (Millipore, 17-622), or H3K27Ac (Abcam, ab4729) and washed as previously described73. The immunoprecipitated DNA and input DNA segments were used for PCR quantification or library construction.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using Illumina Casava version 1.8
ChIP-Seq reads were mapped to mouse genome (mm9) using Bowtie v.0.12.5. Bowtie parameters allowed up to two mismatches per read.
Peak calling by MACS v.1.4.2. Peaks were called using bandwidth 300 bp; P-value of 1.00e-5.
Genome_build: mm9
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| Submission date |
Dec 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing He |
| Organization name |
Children's Hospital of Philadelphia
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| Lab |
Kai Tan
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| Street address |
3501 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19074 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE76029 |
Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses (ChIP-Seq) |
| GSE76031 |
Dynamic organization and activation of enhancers and super-enhancers dictate effector and memory CD8+ T cell responses |
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| Relations |
| BioSample |
SAMN04338378 |
| SRA |
SRX1482907 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1973001_Effector_H3K27Ac_Rep1.wig.gz |
31.9 Mb |
(ftp)(http) |
WIG |
| GSM1973001_Effector_H3K27Ac_Rep2.wig.gz |
29.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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