|
Status |
Public on Apr 18, 2020 |
Title |
Erythroid differentiation Extra Loci S1 replicate 2 |
Sample type |
SRA |
|
|
Source name |
Primary haematopoietic/erythroid progenitor cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57Bl6 tissue: Primary erythroid progenitor cells isolated from fetal liver immunophenotype: Lin- CD71:high Ter119- regions analysed: slc25a37, tal1, cd47, btg2
|
Treatment protocol |
Cells were grown, treated and processed as described in the Methods section of the paper.
|
Growth protocol |
Cells were grown, treated and processed as described in the Methods section of the paper.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Tiled-C combines 3C library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Enriched 3C library S1_Btg2_5000_iced.matrix S1_CD47_5000_iced.matrix S1_Slc25a37_2000_iced.matrix S1_Tal1_5000_iced.matrix Slc25a37_2000_coordinates.bed Tal1_5000_coordinates.bed Btg2_5000_coordinates.bed CD47_5000_coordinates.bed
|
Data processing |
CCseqBasic pipeline (https://github.com/Hughes-Genome-Group/CCseqBasicF/releases) Custom scripts (https://github.com/oudelaar/TiledC) ICE normalization (Imakaev et al. Nature Methods 2012) Genome_build: mm9 Supplementary_files_format_and_content: Sparse matrix format (bin1 \t bin2 \t ICE normalized interaction count \n) and bed file for bin number annotation. Processed data files have been down-sampled to be comparable between conditions as decribed in the Methods section of the paper.
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|
|
Submission date |
Apr 17, 2020 |
Last update date |
Apr 20, 2020 |
Contact name |
A Marieke Oudelaar |
E-mail(s) |
marieke.oudelaar@imm.ox.ac.uk
|
Organization name |
University of Oxford
|
Department |
MRC Weatherall Institute of Molecular Medicine
|
Street address |
John Radcliffe Hospital
|
City |
Oxford |
ZIP/Postal code |
OX3 9DS |
Country |
United Kingdom |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE137199 |
Dissection of the 4D chromatin structure of the alpha-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution [Tiled-C] |
GSE137477 |
Dynamics of the 4D genome during in vivo lineage specification and differentiation |
|
Relations |
BioSample |
SAMN14614716 |
SRA |
SRX8133355 |