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Sample GSM3042017 Query DataSets for GSM3042017
Status Public on Apr 06, 2018
Title INS_A_beta_1
Sample type SRA
 
Source name EndoC βH1
Organism Homo sapiens
Characteristics cell type: Pancreatic beta cells
cell line: EndoC betaH1
Treatment protocol Cells were fixed by formaldehyde. The cross-linked chromatin was digested by BglII (New England Biolabs) and re-ligated by T4 DNA ligase (New England Biolabs). After reversal of crosslinks, DNA was digested by NlaIII (New England Biolabs) and re-ligated by T4 DNA ligase (New England Biolabs). The DNA product served as template for 4C-PCR.
Growth protocol EndoC βH1 cells were grown in were cultured in low-glucose Dulbecco's modified Eagle's medium (Life Technology, cat. # 11885) with 2% BSA (fatty acid free and heat shocked, Equitech, cat. #BAH66), 50 μM 2-mercaptoethanol, 10 mM nicotinamide, 5.5 mg/ml human transferrin (Sigma–Aldrich, cat. #T8158), 6.7 ng/ml sodium selenite, 100 U/ml penicillin, and 0.1 mg/ml streptomycin. Cells were seeded at a density of 6 × 105/cm2 on ECM-gel (1%) (Sigma-Aldrich, cat. # E1270) /fibronectin (2 g/ml; Sigma–Aldrich, cat #. F1141) coated plates and cultured at 37 °C and 5% CO2. Hela cells were grown in low-glucose Dulbecco's modified Eagle's medium with 10% Fetal Bovine Serum and cultured at 37 °C and 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Phenol-Chloroform and ethanol precipitate.
Direct PCR from 4C library
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description Pancreatic β cells
Data processing Library strategy: 4C-seq
Barcode sequences were removed from the reads.
The reads were mapped with Bowtie2 version2.2.
The reads mapped to the bait (self-ligation reads) were filtered out.
The remain reads were mapped with Bowtie2 again.
Genome_build: hg19
Supplementary_files_format_and_content: BED
 
Submission date Mar 15, 2018
Last update date Nov 29, 2018
Contact name Gary Felsenfeld
E-mail(s) garyf@intra.niddk.nih.gov
Phone 301-496-4173
Organization name National Institutes of Health
Department NIDDK
Lab LMB
Street address 5 Memorial Drive, Room 212
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL16791
Series (2)
GSE111863 4C-seq of insulin promoter
GSE112346 4C-seq of insulin promoter, knockdown of INS promoter activity and Genome-wide maps of chromatin state in EndoC-βH1 Cells
Relations
Reanalyzed by GSE123131
BioSample SAMN08715766
SRA SRX3795451

Supplementary file Size Download File type/resource
GSM3042017_INS_A_beta_1_clear.bed.gz 4.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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