|
Status |
Public on Apr 15, 2020 |
Title |
Erythroid differentiation S1 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-
|
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 |
RBAT55 S1-expt35.mm10.bw S1-expt35.mm9.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 |
SAMN12716033 |
SRA |
SRX6820176 |