|
| Status |
Public on Aug 17, 2018 |
| Title |
Mouse ES cells replicate 3; Capture-C, local promoters viewpoints |
| Sample type |
SRA |
| |
|
| Source name |
E14 embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
cell type: E14 embryonic stem cell line
viewpoint analyzed: Prom_local_il9r, Prom_local_mpg, Prom_local_nprl3, Prom_local_snrnp25, Prom_local_rhbd
|
| Treatment protocol |
Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, as described in Davies et al, Nature Methods, 2016.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
*viewpoint_analysed*_corr_PF_BF_h.gfc
Processed data file: See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Prom_local_ES3
|
| Data processing |
Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
|
| |
|
| Submission date |
Dec 06, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL16417 |
| Series (2) |
| GSE107753 |
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Capture-C] |
| GSE107940 |
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains |
|
| Relations |
| BioSample |
SAMN08136892 |
| SRA |
SRX3447437 |
| SRA |
SRX4108331 |
