|
| Status |
Public on Jun 08, 2023 |
| Title |
eRBC_Hic_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary embryonic red blood cells (Embryonic day 10)
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Primary embryonic red blood cells (Embryonic day 10)
genotype: WT
|
| Growth protocol |
Primary fibroblasts and HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10 x 106 cells were fixed with formaldehyde 2% for 10 minutes at room temperature. Chromatin was digested with MboI overnight and 5′ overhangs were filled with Biotin-14-dATP and religated in nuclei. DNA fragments were purified and shared to an average size of 500 bp using a Covaris machine.
Hi-C libraries were generated using the TruSeq Illumina system.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Hi-C experiments were processed following the HiC-Pro (v2.11.1) pipeline using the merge data from both replicates to generate .validPairs files with interacting regions.
.validPairs files were normalized to contain the same number of interacting pairs.
Assembly: GRCg6a
Supplementary files format and content: .validPairs files containing the interacting pairs for each sample. validPairs files can be used to generate Hi-C matrices with HiC-Pro.
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Mayra Furlan-Magaril |
| E-mail(s) |
mfurlan@ifc.unam.mx
|
| Phone |
525512291890
|
| Organization name |
IFC-UNAM
|
| Department |
Molecular Genetics
|
| Lab |
Genome Topology
|
| Street address |
Circuito exterior s/n
|
| City |
Mexico City |
| State/province |
Mexico City |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL19005 |
| Series (2) |
| GSE206192 |
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [Hi-C] |
| GSE206194 |
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes |
|
| Relations |
| BioSample |
SAMN29126840 |
| SRA |
SRX15715852 |
