|
| Status |
Public on Jun 14, 2017 |
| Title |
Mouse D39 mutant erythroid cells ATAC-seq biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Ter119+ Erythroid cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6
tissue: Phenylhydrazine treated spleen
|
| Treatment protocol |
Ter119+ cells were isolated from mouse spleens
|
| Growth protocol |
C57BL/6 mice were treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using an auto-MACS (Miltenyi Biotec).
Illumina Nextera DNA library kit, subjected to ATAC-seq (Assay for Transposase-Accessible Chromatin)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible, options: -m 9 –x 0.125)
Alignment of ChIP-seq data with bowtie 1.1.2 to mm9 (options: -m 2, -k 1, --best)
Samtools rmdup (to remove PCR duplicates)
Deeptools bamcoverage was used (options: --normalizeUsingRPKM) to normalise the reads for RPKM, and generate the bigWig file for visualisation
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of RPKM
|
| |
|
| Submission date |
Apr 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jelena M Telenius |
| E-mail(s) |
jelena.telenius@ndcls.ox.ac.uk
|
| Organization name |
Oxford University
|
| Department |
Weatherall Institute of Molecular Medicine (WIMM)
|
| Lab |
Genome Biology Research Group
|
| Street address |
MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE97866 |
Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (ATAC-Seq) |
| GSE97871 |
Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo |
|
| Relations |
| BioSample |
SAMN06759648 |
| SRA |
SRX2741743 |
