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Sample GSM5598220 Query DataSets for GSM5598220
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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