|
| Status |
Public on Jan 05, 2024 |
| Title |
G1E-ER4 24h - chiapet-SMC1A_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
G1E-ER4
|
| Organism |
Mus musculus |
| Characteristics |
cell type: G1E-ER4
treatment: 10 nM beta-estradiol for 24h
chip antibody: anti-SMC1 (Bethyl, cat: A300-055A)
|
| Treatment protocol |
Differentiation was induced by adding beta-estradiol (Sigma, cat: E8875) at a final concentration of 10 nM for 24 hrs or as otherwise indicated
|
| Growth protocol |
G1ER4 cells were cultured in Isocove’s modified Dulbecco’s medium (IMDM) supplemented with 15% fetal calf serum (FCS), 100 units (U) /mL penicillin and 100 g/mL streptomycin (PS), 2 U/mL recombinant human erythropoietin (EPO), and 50 ng/ml mouse recombinant SCF or 1% conditioned medium from murine SCF producer cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIA-PET was performed as previously described (Hnisz et al., Science, 2016) using G1-ER4 cells (150 million per replicate)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The data were analyzed using Origami software (https://github.com/younglab/origami) under release tag alpha20160828
Each ChIA-PET data set was processed as follows: the reads were first trimmed and aligned using origami-alignment, which trims the ChIA-PET linker if present and aligns trimmed PETs. PETs not having a linker were discarded from further analysis. Each end of a PET with a linker sequence was separately mapped to the hg19 genome assembly using bowtie with the following options: -v 1 –k 1 –m 1. After alignment, the separated PETs were re-paired in the final BAM output. After repairing, all duplicated PETs within the data were removed, since these were believed to be PCR duplicates. Peaks were called on the re-paired ChIA-PET reads using MACS1 v1.4.2 with the following parameters: --nolambda –nomodel –p 1e-9.
mm9
chiapet interactions; each row indicates a pair of regions, total counts for the interaction, a p-value, and a score given by a Bayes mixutre model
|
| |
|
| Submission date |
Jul 24, 2020 |
| Last update date |
Jan 05, 2024 |
| Contact name |
Jonathan Li |
| E-mail(s) |
iamjli@mit.edu
|
| Organization name |
Massachusetts Institute of Technology
|
| Lab |
Ernest Fraenkel
|
| Street address |
77 Massachusetts Ave
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE155103 |
GATA Switch Enhancers Mark Dynamically Regulated Chromatin Interaction Nodes during Erythroid Maturation |
|
| Relations |
| BioSample |
SAMN15641184 |
| SRA |
SRX8820359 |
