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Sample GSM5137303 Query DataSets for GSM5137303
Status Public on Aug 31, 2021
Title Daxx F/F LT.HSC 3dpi 2
Sample type SRA
 
Source name Hematopoietic Stem Cell
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
genotype: Daxx F/F Cre +/-
Extracted molecule genomic DNA
Extraction protocol Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry.
ATAC-seq libraries were created as described in Buenrostro et al. 2015. Briefly, cells were lysed and treated with Tn5 Transposase from the Nextera Library Prep kit from Illumina for 30 min at 37°C. DNA was purified with Qiagen MinElute PCR purification kit and libraries were generated by PCR amplification using Nextera Index Primers from Illumina.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description tagmented genomic DNA
LTHSC_ATACseq_3dpi_DaxxFFvsDaxxWtWt_diffsite.txt
DaxxFF.idr.conservative_peak.narrowPeak
Data processing Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with the following options: --alignIntronMax 1 --alignMatesGapMax 1800.
Reads mapping to the the mitochondrial genome and non-uniquely were removed. In addition, read duplicates were removed and start position of reads was offset by +4 bp if mapping to the positive strand and -5 bp if mapping to the negative strand.
For peak calling the ENCODE ATAC-seq analysis pipeline 0.3.4 was used.
Peak files were sorted by coordinate and overlapping peaks were merged with bedtools merge.
Identification of differentially accessible sites using diffreps with 600 bp window size.
Genome_build: mm10
Supplementary_files_format_and_content: Bed/NarrowPeak file with merged ATAC-seq peak positions and/or tab-delimited files with differentially accessible regions identified with diffreps
 
Submission date Mar 05, 2021
Last update date Aug 31, 2021
Contact name Paolo Salomoni
E-mail(s) paolo.salomoni@dzne.de
Organization name DZNE e.V.
Street address Sigmund-Freud-Str. 27
City Bonn
ZIP/Postal code 53127
Country Germany
 
Platform ID GPL24247
Series (2)
GSE119306 Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation [ATAC-Seq]
GSE119309 Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation
Relations
BioSample SAMN18167555
SRA SRX10246406

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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