|
| Status |
Public on Aug 31, 2021 |
| Title |
Daxx +/+ LT.HSC 2 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic Stem 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_LTHSCwt_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 |
SAMN09940165 |
| SRA |
SRX4628147 |
