|
| Status |
Public on Apr 18, 2020 |
| Title |
Erythroid differentiation Extra Loci S3 replicate 1 |
| 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:high
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.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Enriched 3C library
S3_Btg2_5000_iced.matrix
S3_CD47_5000_iced.matrix
S3_Slc25a37_2000_iced.matrix
S3_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.
|
| |
|
| 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 |
SAMN14614713 |
| SRA |
SRX8133358 |
