|
| Status |
Public on Feb 27, 2022 |
| Title |
cell line 1B1 repl1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line 1B1 repl1
|
| Organism |
Mus musculus |
| Characteristics |
clone: cell line 1B1 repl1
cell line: Embyonic stem cell (E14)
|
| Treatment protocol |
for -cohesin sample: 2h with 500nM dTag-13 (Sigma Aldrich, SML2601-1MG)
|
| Growth protocol |
Cells were cultured on gelatin-coated culture plates in Glasgow Minimum Essential Medium (Sigma) supplemented with 15% foetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher Scientific -25030024), 1% Sodium Pyruvate MEM (Thermo Fisher Scientific -11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher Scientific-11140035) 100 µM β-mercaptoethanol, 20 U/ml leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor PDO35901 (Axon, 1408) and 3 µM GSK3 inhibitor CHIR 99021 (Axon, 1386) in 8% CO2 at 37°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linking with 1% formaldehyde. Cells lysed with 1M Tris-HCL pH8.0; 5M NaCl; 10% NP40
SureSelect XT Library Prep kit Agilent
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cell line with Teto laco integration with flanking ectopic CTCF sites
|
| Data processing |
Library strategy: capture c
cHi-C paired end datasets were processed using HiC-Pro (version 2.11.4). HiC-Pro covers the whole analysis from fastq files to the interaction matrix
Genome_build: mm9
Supplementary_files_format_and_content: iced and binned matrix (6.4kb). The format of the matrix is the standard from HiC-Pro, namely, 3 columns: start end interactions. It's a sparce matrix annotation, no zero values are reported. The conversion bead to genomic coordinate file is also provided.
|
| |
|
| Submission date |
Feb 22, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Luca Giorgetti |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Street address |
Fabrikstrasse 24
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE197234 |
Cohesin and CTCF control chromosomal contact dynamics in living cells [capture C] |
| GSE197238 |
Cohesin and CTCF control chromosomal contact dynamics in living cells |
|
| Relations |
| BioSample |
SAMN26246146 |
| SRA |
SRX14287043 |
