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| Status |
Public on Feb 13, 2019 |
| Title |
invitro 10U rep2 (re-analyzed) (atac-seq) |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: CD8+ T cell
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Isolated cells were lysed in 10 mM Tris pH 7.5, 10 mM NaCl, 3mM MgCl2, 0.1% NP-40
Lysed cells were treated with Nextera transposase for 30 minutes at 37°C, followed by PCR amplification.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ATACdensity.tsv
invitro_CD8Resting
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| Data processing |
Basecalls and demultiplexing performed in illumina basespace
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie v 1.0
Unmapped reads were trimmed of adapters and to a length of 36nt with trim_galore and remapped and merged with first bam file
Merged duplicate
bam files were filtered to extract fragments less than 100 nt, and peak summits were called using MACS2 with parameters
Peak summits from individual replicates were expanded to region of 500bp and overlapping regions from all samples were merged
Tn5 insertions sites per peak were computed for all replicates using all reads and normalized with limma/voom
Genome_build: mm10
Supplementary_files_format_and_content: tsv containing ATAC-seq density
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| Submission date |
Dec 11, 2018 |
| Last update date |
Feb 13, 2019 |
| Contact name |
James Scott-Browne |
| E-mail(s) |
[email protected]
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| Organization name |
National Jewish Health
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| Street address |
1400 Jackson St, K806
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| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE123629 |
Nr4a transcription factors limit CAR-T cell function in solid tumors [ATAC-Seq] |
| GSE123739 |
Nr4a transcription factors limit CAR-T cell function in solid tumors |
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| Relations |
| Reanalysis of |
GSM2356809 |
| BioSample |
SAMN10580039 |
| SRA |
SRX5124820 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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