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Sample GSM5260598 Query DataSets for GSM5260598
Status Public on Apr 30, 2023
Title BRSST+sgLuc 1% input
Sample type SRA
 
Source name Murine whole bone marrow
Organism Mus musculus
Characteristics tissue: Whole bone marrow
strain: C57BL/6
treatment: BRSST+sgLuc
chip antibody: None
Treatment protocol Murine bone marrow cells were crosslinked directly after isolation using 1% formaldehyde for 5 min.
Growth protocol 1-4x10^4 LSK cells from Cas9 knockin mice were transduced with the given sgRNA combinations and transplanted after 24 h into irradiated (7 Gy) C57Bl/6J mice. Complete BM was harvested after presenting with signs of leukemia or after 6 month and secondarily transplanted into irradiated Bl6 mice.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody and protein A magnetic beads. DNA was eluted from the beads using 0.75% SDS, protease treatment and the Qia MinElute PCR extraction Kit.
For library construction the TruSeq ChIP Library Preparation Kit from Illumina was used. Size selection was done via agarose gels.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description 17_15
Input data for BM transplanted mice transduced with BRSST sgRNA +sgLuc
Data processing Base calling was performed using standard Illumina software.
Sequencing reads were aligned to the murine mm9 genome using BWA software.
Peak calling was done utilizing MACS2 software.
Peak visualization was performed using the IGV genome browser tool.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig files
 
Submission date Apr 22, 2021
Last update date Apr 30, 2023
Contact name Dorit Borchert
E-mail(s) Borchert.Dorit@mh-hannover.de
Organization name Hannover Medical School
Department Pediatric Hematology and Oncology
Street address Carl-Neuberg-Str. 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL21103
Series (2)
GSE173133 Genome-wide maps of chromatin state from secondary murine BM Tx transduced with BRSST gRNA +/- sgEzh2 [ChIP-seq]
GSE173497 Oncofetal gene reactivation drives EZH2-mutant myeloid leukemia pathogenesis
Relations
BioSample SAMN18835744
SRA SRX10659896

Supplementary file Size Download File type/resource
GSM5260598_mouseBM_17_15_Input.ChIP.bwa.mm9.rpm.bw 267.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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