|
| Status |
Public on Aug 17, 2018 |
| Title |
Mouse erythroid cells biological replicate 3, technical replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
Primary erythroid cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6
cell type: Ter-119+ cells isolated from phenylhydrazine treated spleen
viewpoint analyzed: a_R2, a_CTCF, b_HS2, b_CTCF
|
| 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.
Tri-C combines 3C library preparation (NlaIII restriction enzyme) with oligonucleotide capture enrichment that is optimized to detect multiway interactions with viewpoints of interest, as described in detail in the Supplementary Methods of the paper.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments
a_R2_Tri-C_Samples_Combined.txt
a_CTCF_Tri-C_Samples_Combined.txt
b_HS2_Tri-C_Samples_Combined.txt
b_CTCF_Tri-C_Samples_Combined.txt
C57-3c_S4
|
| Data processing |
Library strategy: Tri-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)
Removal of PCR duplicates, mapping of reads to restriction enzyme fragments, proximity exclusion (if within ~1 kb of viewpoint) (custom scripts)
Calculation of normalized multi-way interaction frequencies with viewpoints (custom scripts)
Processing of interaction frequencies into a contact matrix (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (interacting restriction enzyme fragment1 \t interacting restriction enzyme fragment2 \t sample1_raw_count \t sample2_raw_count \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 |
GPL19057 |
| Series (2) |
| GSE107755 |
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Tri-C] |
| GSE107940 |
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains |
|
| Relations |
| BioSample |
SAMN08136942 |
| SRA |
SRX3447459 |
