NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4695473 Query DataSets for GSM4695473
Status Public on Jan 05, 2024
Title G1E-ER4 0h - chiapet-SMC1A_rep2
Sample type SRA
 
Source name G1E-ER4
Organism Mus musculus
Characteristics cell type: G1E-ER4
treatment: 10 nM beta-estradiol for 0h
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 SAMN15641187
SRA SRX8820357

Supplementary file Size Download File type/resource
GSM4695473_chiapet-SMC1A_0h_rep2_interactions.csv.gz 18.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap