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Status |
Public on Apr 13, 2020 |
Title |
Erythroid differentiation HSPC Tiled-C replicate 1 |
Sample type |
SRA |
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Source name |
Primary haematopoietic/erythroid progenitor cells
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Organism |
Mus musculus |
Characteristics |
strain: C57Bl6 tissue: Primary haematopoietic progenitor cells isolated from bone marrow cell type: Primary haematopoietic/erythroid progenitor cells immunophenotype: LSK Flt3- CD48- CD150+ regions analyzed: alpha-globin
|
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 |
Cells were grown, treated and processed as described in the Methods section of the paper. 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 |
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Description |
Tiled-C product (DNA) Enriched 3C library HSPC-1 HSC_comb_downsampled_2000_iced.matrix HSC_comb_downsampled_5000_iced.matrix alpha_2000_coordinates.bed alpha_5000_coordinates.bed
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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 |
Sep 10, 2019 |
Last update date |
Apr 13, 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 |
SAMN12722979 |
SRA |
SRX6827632 |