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| Status |
Public on Sep 08, 2020 |
| Title |
CD4+ splenic T cells_MAW-Lane2-2 |
| Sample type |
SRA |
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| Source name |
CD4+ splenic T cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD4+ splenic T cells
genotype: WT
Sex: M
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATACseq libraries were prepared for primary cells using the FAST-ATACseq protocol described previously (PMID: 27526324)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
CD4_WT.bed.gz
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| Data processing |
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
Raw reads were subjected to adapter and quality trimming on left side using bbduk.sh from BBTools.
For the determination of fragment sizes and nucleosome repeat length profiles, ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with the parameters -reorder --mm --no-mixed --no-discordant --very-sensitive -X 1000.
Only uniquely aligned, correctly paired reads were retained and bed files containing the identified fragments were generated using custom python scripts, and shifted by +4 bp or -5bp, respectively, for reads mapped to the + or - strand.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: The BED files contain the ATAC-seq fragments of properly paired reads only, and shifted by +4 bp or -5bp, respectively, for reads mapped to the + or - strand , and this data can be directly used to extract fragment sizes and nucleosome repeat lengths in selected genomic regions.
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| Submission date |
Nov 29, 2019 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Boris Bartholdy |
| Organization name |
Albert Einstein College of Medicine
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| Department |
Cell Biology
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| Street address |
1300 Morris Park Ave
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE141184 |
H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [ATAC-seq] |
| GSE141187 |
H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction |
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| Relations |
| BioSample |
SAMN13429305 |
| SRA |
SRX7241848 |
| 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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