|
| Status |
Public on Jul 08, 2024 |
| Title |
WT3_KSL_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell type: Hematopoietic stem and progenitor cells (HSPCs, KSL)
genotype: WT
treatment: No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GMP (CD34+CD16/32+ LK) and LSK cells were FACS-sorted from the bone marrow
DNA was extracted according to a previously published protocol (Wu, J. et al. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Reports 33, 108395 (2020).)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ATAC data were first processed using the AIAP (v1.1) pipeline. As a part of the pipeline: locations of Tn5 insertion events were inferred from properly paired, non-PCR duplicate reads with MAPQ >= 10; each Tn5 insertion event was extended from insertion site up and down 75 bp to generate a 150 bp “pseudo read”; pseudo reads were piled up to generate an ATAC signal profile.
ATAC signal profiles were normalized against both sequencing depth and the percentage of reads in promoter regions, similar to the normalization in ArchR (Granja et al, Nature Genetics. 2021).
Assembly: mm10
Supplementary files format and content: bw: normalized signal profiles
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Changxu Fan |
| E-mail(s) |
fanc@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue, Room 5213
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE240584 |
Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [bulk ATAC] |
| GSE240585 |
Baf155 controls hematopoietic differentiation and regeneration through chromatin priming |
|
| Relations |
| BioSample |
SAMN36935263 |
| SRA |
SRX21329350 |
