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| Status |
Public on Dec 21, 2023 |
| Title |
E82K_2 |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Peripheral blood
cell type: T-cell blasts
genotype: AIOLOS E82K heterozygous
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-Seq was performed using the Active Motif ATAC-Seq Kit following the manufacturer’s protocol and sequenced using the Illumina NextSeq 2000
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Alignment and mapping, QC, and peak calling with MACS2 were performed by the Basepair's ATAC-Seq piplines (https://www.basepairtech.com/)
Differential testing, annotation, and visualization were performed using R (v.4.3.1) and the following Bioconductor R packages (https://bioconductor.org/): DESeq2 (v.1.40.2), DiffBind (v.3.10.1), ChIPQC (v.1.36.1), ChIPseeker (v.1.36.0), clusterProfiler (v.4.8.2), and goseq (v.1.52.0) .
Assembly: hg38
Supplementary files format and content: tab-delimited gene matrix of raw (non-normalized) peak counts for each sample, with chromatin regions in the rows and samples in the columns
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| Submission date |
Sep 26, 2023 |
| Last update date |
Dec 21, 2023 |
| Contact name |
Julie E Niemela |
| E-mail(s) |
[email protected]
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| Phone |
301-827-2760
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| Organization name |
NIH Clinical center
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| Department |
Dept. of Lab. Medicine
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| Lab |
Immunology Service
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| Street address |
10 Center Dr.
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE244038 |
ATAC-seq to profile the chromatin accessibility in T-cell blasts from individuals with an AIOLOS E82K and Q402X mutation and healthy controls |
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| Relations |
| BioSample |
SAMN37544172 |
| SRA |
SRX21888071 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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