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Sample GSM3369655 Query DataSets for GSM3369655
Status Public on Aug 31, 2021
Title Daxx +/+ CMP 1
Sample type SRA
 
Source name Hematopoietic Progenitor Cell
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
genotype: Daxx +/+ 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 HiSeq 1500
 
Description 180806_CMPwt_EncodePeaks_m.bed
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.
Genome_build: mm10
Supplementary_files_format_and_content: Bed file with merged ATAC-seq peak positions
 
Submission date Aug 31, 2018
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 GPL18480
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 SAMN09940158
SRA SRX4628154

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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