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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 21, 2023 |
| Title |
ATACseq.human.CD8.Positive.Tcells.Day6.Donor2 |
| Sample type |
SRA |
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| Source name |
CD8 Positive T-Cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: CD8 Positive T-Cells
cell type: Primary T cells
sample type: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 2
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| Treatment protocol |
Human cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.Mouse cells were activated with Mouse T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat#11453D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.
Cells were treated with inhibitors (Compound 14 and FHT1015) on Day 3 and Day 6 and taken down for one timepoint at Day9. Cells were treated with degraders (ACBI1 and AU-15330, 100nM) on Day 3 and Day 6 and taken down for one timepoint at Day9.
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| Growth protocol |
Human and mouse T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Regions of tagmented genomic DNA were purified Qiagen's MinElute DNA purification Kit.
Custom PCR primers were used to amplify tagmented DNA for a total of 7 cycles to prevent over amplification.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
Output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
Assembly: hg19, mm10
Supplementary files format and content: bigWig, broadPeak
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| Submission date |
Aug 30, 2022 |
| Last update date |
Mar 21, 2023 |
| Contact name |
Cigall Kadoch |
| E-mail(s) |
cigall_kadoch@dfci.harvard.edu
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| Organization name |
Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute
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| Street address |
450 Brookline Avenue
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE212339 |
Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion [ATAC-seq] |
| GSE212357 |
Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion |
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| Relations |
| BioSample |
SAMN30596115 |
| SRA |
SRX17356132 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6528082_ATACseq.human.CD8.Positive.Tcells.Day6.Donor2.broadPeak.gz |
1.4 Mb |
(ftp)(http) |
BROADPEAK |
| GSM6528082_ATACseq.human.CD8.Positive.Tcells.Day6.Donor2.bw |
257.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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