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| Status |
Public on Aug 24, 2023 |
| Title |
ATAC_HPC5-2 |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell line: HPC5
cell type: BM-derived HPC
genotype: Etv6+/+
treatment: ATAC-seq
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed following the Fast-ATAC protocol5. Briefly, 10,000 of HPC5 cells were treated with transposition mix: 1) 22 uL nuclease-free water; 2) 25 uL 2 × TD Buffer; 3) 2.5 uL TDE1 transposase; 4) 0.5 uL 1% Digitonin (added right before removing supernatant from cell pellets), followed by incubation at 37°C on thermomixter at 300 rpm for 30 minutes. DNA was purified by using the MinElute Reaction Cleanup kit (Qiagen, 28204), and amplified for 5 cycles with the following mix: 10 uL transposed DNA, 2.2 uL nuclease-free water; 6.25 uL 10 uM barcoded Nextera primer-F; 6.25 uL 10 uM barcoded Nextera primer-R; 0.3 uL 100 × SYBR Green I (Invitrogen, S-7563); 25 uL NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541). PCR products were subsequently re-amplified for 6 additional PCR cycles and subjected to purification using SPRIselect beads (Beckman Coulter, B23317).
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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 |
FASTQ files were mapped to mm10 by using BWA-MEM (version 0.7.16a). Reads that could not be uniquely mapped to the mouse genome were removed by SAMtools (version 0.17). Peaks were called using MACS2 (version 2.1.1). bigWig files were generated using DeepTools (version 3.2.0). Footprint analysis was performed by using CUT&RUNTools. Downstream analysis for binding site distribution and peak annotation were performed using R Bioconductor packages DiffBind7, ChIPseeker8, and clusterProflier9,10.
Assembly: mm10
Supplementary files format and content: bigwig tracks to be loaded in a genome browser
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| Submission date |
Sep 18, 2022 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Kim Nichols |
| E-mail(s) |
kim.nichols@stjude.org
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Oncology
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| Lab |
Nichols Lab
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE213593 |
ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice [ATAC-seq] |
| GSE213597 |
ETV6 Represses Inflammatory Response Genes and Regulates HSPC Function During Stress Hematopoiesis in Mice |
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| Relations |
| BioSample |
SAMN30874536 |
| SRA |
SRX17595642 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6589558_ATAC_HPC5-2.rmdup.uq.bw |
263.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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