 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 03, 2021 |
| Title |
WT_ATACseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HSPCs
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
cell type: HSPCs
|
| Growth protocol |
200,000 HSPCs were sorted from mouse bone marrow samples. Each independent biological replicate was generated from HSPCs isolated from two mice of the same genotyping group and age-matched. Sorted HSPCs were cryopreserved in BAMBAKER Serum-free cell freezing medium (Wako Chemicals).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were defrosted, washed twice in PBS and 50,000 viable HSPCs were then processed following the OMIM-ATAC-Seq protocol from Corces et al., Nature Methods 2017 with a dead cell pre-cleanup step with DNase I (Worthington cat#LS002007, 30 min at 37°C) followed by two cold PBS washes.
Libraries were prepared utilizing 2xTD buffer (15027866, Illumina) and Robust Tn5 Transposase (EMQZ1422, Creative Biogene) and cleaned up with a Zymo DNA Clean and Concentrator-5 kit (cat#D4014). OMIM-ATAC-Seq libraries were amplified with a total of 11 PCR cycles with ATAC-Seq primers (Buenrostro et al., 2015 (PMID: 25559105).
Paired-End, 100bp sequenced on an Illumina NOVASeq.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT.IDR.narrowpeak
|
| Data processing |
Base calling using Illumina RTA 2.4.11
ATAC-Seq chromatin accessible regions were determined using ENCODE pipeline standards (https://github.com/ENCODE-DCC/atac-seq-pipeline; git commit 2b693ab)
Sequencing indices were trimmed from merged fastq files using cutadapt (v1.9.1) and then aligned to mm10 using bowtie2 (v2.2.6).
After de-duplication, reads were tn5 shifted, replicate peaks were called, and fold enrichment signal files were generated using macs2 (v2.1.0).
Final peaks were determined using IDR (v2.0.4) of true replicates.
Genome_build: Encode: mm10_no_alt_analysis_set (ENCSR425FOI)
Supplementary_files_format_and_content: Bigwig files contain fold change signal over background generated from macs2.
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Stephen Nimer |
| Organization name |
University of Miami
|
| Department |
Sylvester Comprehensive Cancer Center
|
| Street address |
1120 NW 14th ST
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE145875 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia [ATAC-Seq] |
| GSE145878 |
p300 suppresses the transition of myelodysplastic syndrome to acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN14180037 |
| SRA |
SRX7798302 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4338307_ATAC-WT1.narrowPeak.gz |
2.0 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
