|
| Status |
Public on Apr 15, 2020 |
| Title |
Erythroid differentiation S2 ATAC-seq replicate 3.1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary haematopoietic/erythroid progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: e13.5
tissue: fetal liver
cell type: Primary erythroid progenitor cells isolated from fetal liver
immunophenotype: Lin- CD71:high Ter119:med
|
| Growth protocol |
Cells were FACS-sorted from fetal liver or bone marrow of C57BL/6 mice as described in the Methods section of the paper
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were transposed with Tn5 transposase for ATAC-seq library preparation as described in the Methods section of the paper
ATAC-seq transposed DNA was amplified using custom barcoded oligonucleotides as described in the Methods section of the paper
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RBAT57
S2-expt35.mm9.bw
S2-expt35.mm10.bw
|
| Data processing |
NGseqBasic pipeline (https://doi.org/10.1101/393413)
Custom scripts (https://github.com/rbeagrie/alpha-tiledc)
Genome_build: mm9 & mm10
Supplementary_files_format_and_content: BigWig files of genome-wide read density
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Robert A Beagrie |
| E-mail(s) |
robert.beagrie@ndcls.ox.ac.uk
|
| Organization name |
MRC Weatherall Institute of Molecular Medicine
|
| Department |
Molecular Haematology Unit
|
| Street address |
Headley Way
|
| City |
Oxford |
| ZIP/Postal code |
OX39DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE137114 |
Dissection of the 4D chromatin structure of the alpha-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution [ATAC-seq] |
| GSE137477 |
Dynamics of the 4D genome during in vivo lineage specification and differentiation |
|
| Relations |
| BioSample |
SAMN12716062 |
| SRA |
SRX6820178 |
