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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2020 |
| Title |
ATAC-seq Control 3 |
| Sample type |
SRA |
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| Source name |
Naïve CD8 T cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Naive CD8 T cells
surface marker: CD8+CD25-CD62LhiCD44low
treatment: Control
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| Growth protocol |
Naive OT-I (CD45+, CD8+, CD62L+, CD44-) CD8 T cells were sorted from spleen and/or LNs. T cells were enriched before FACS by utilizing Pan T cell MACS kit (Miltenyi Biotec) and sorted with BD FACS Aria (BD Bioscience).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs were extracted by DNA Clean & Concentrator (Zymo).
ATAC-seq libraries were constructed with 50K cells from each condition following Omni-ATAC protocol (Illumina FC-121-1031(Corces et al., 2017))
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ATAC-seq
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| Data processing |
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
Sequenced reads were trimmed with adaptor sequences (cutadapt v1.9.1, (Martin, 2011)) and mapped to the mouse genome (GRCm38, emsembl release 93) by Bowtie2 (v2.3.4.1, (Langmead and Salzberg, 2012)). Mitochondrial and duplicated reads were removed by SAMtools (v1.9, (Li et al., 2009)) and Picard (v2.9.0, https://broadinstitute.github.io/picard/), respectively.
Peaks were found by MACS2 (v.2.1.1, (Zhang et al., 2008)) and visualized by deepTools (v3.1.1, Ramirez et al., 2014, NAR).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a narrowPeak file including Chrom, ChromStart, ChromEnd, Name, Score, Strand, SignalValue, pValue, qValue, and Peak.
Supplementary_files_format_and_content: a bigWig file
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| Submission date |
Sep 05, 2019 |
| Last update date |
Jan 02, 2020 |
| Contact name |
Jaechul Lim |
| E-mail(s) |
jaechul.lim@snu.ac.kr
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| Organization name |
Seoul National University
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| Street address |
1 Gwanak-ro, 1 Gwanak-gu
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| City |
Seoul |
| State/province |
CT |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE136972 |
Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone [ATAC-seq] |
| GSE136980 |
Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone |
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| Relations |
| BioSample |
SAMN12703123 |
| SRA |
SRX6809270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4064140_Ctrl3.bw |
130.9 Mb |
(ftp)(http) |
BW |
| GSM4064140_Ctrl3.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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