|
| Status |
Public on Mar 30, 2023 |
| Title |
ProB rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ProB
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: B cell Progenitor
tissue: bone marrow
|
| Treatment protocol |
Bone marrow or thymic cells were stained with flourescent antibodies and sorted by FACS according to established markers.
|
| Growth protocol |
Adult (8-12 weeks old) Wild-type C57/Bl6 mice were sacrificed and cells were harvested from bone marrow and/or thymus.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected after sorting into microcentrifuge tubes containing staining media (1xDPBS,1mM EDTA with 5% serum) and centrifuged at 500xg for 5 minutes at 4˚C . Cell pellet was washed with ice-cold 1xDPBS and centrifuged as above. Cells were lysed in (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifuged at 500xg for 10 minutes. Samples were suspended 25µL 2xTD Buffer, 2.5µL transposase (Illumina), and 22.5µL nuclease free water and incubated at 37˚C for 30 minutes at 600rpm. Samples were purified using the MinElute Reaction Clean up kit (Qiagen).
Library fragments were amplified using NEBnext PCR mastermix and custom Nextera primers, and size selected using Ampure XP Beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
data was processed using the ENCODE ATAC-seq Pipeline version 1.4.2
Parameters for pipeline were: atac.multimapping=0, atac.smooth_win=150, atac.enable_idr=true, atac.idr_thresh=0.1
Master peaklist was generated by chromVAR v1.02 and the filterPeaks function using default parameters
Peaks were annotated using annotatePeaks.pl function in HOMER v4.10.2
Genome_build: mm10
Supplementary_files_format_and_content: Annotated Master peak-list output from chromVAR and HOMER
|
| |
|
| Submission date |
Sep 27, 2021 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Camilla Forsberg |
| E-mail(s) |
cforsber@soe.ucsc.edu
|
| Phone |
8314592111
|
| Organization name |
Institute for the Biology of Stem Cells, University of California Santa Cruz
|
| Street address |
1156 High Street
|
| City |
Santa Cruz |
| State/province |
California |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE184851 |
Dynamics of Chromatin Accessibility during Hematopoietic Stem Cell Differentiation into Lineage-Committed Progeny |
|
| Relations |
| BioSample |
SAMN21856612 |
| SRA |
SRX12375672 |
