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Sample GSM3068138 Query DataSets for GSM3068138
Status Public on Apr 06, 2018
Title INS-KD rep2
Sample type SRA
 
Source name EndoC βH1
Organism Homo sapiens
Characteristics cell type: Pancreatic Beta cells
treatment: shRNA induced
cell line: EndoC BetaH1
Treatment protocol A lenti-viral system were used to deliver shRNA construct into EndoC-βH1 cells. To performing knockdown experiments, the viral transduced cells were treated with 1 mg/mL doxycycline for 7 days. ). The media was changed every 48 h. No doxycycline was added in the negative control samples.
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 × 10^5/cm2 on ECM-gel (1%) (Sigma-Aldrich, cat. # E1270) /fibronectin (2 µg/ml; Sigma–Aldrich, cat #. F1141) coated plates and cultured at 37 °C and 5% CO2.
Extracted molecule total RNA
Extraction protocol The total RNA from 5 × 10^5 EndoC-βH1 cells that were induced with shRNA was isolated with a NucleoSpin RNA XS kit (Clontech).
The c-DNA library was prepared with a SMART-Seq® v4 Ultra® Low Input RNA Kit (Clontech, Cat. #634888) with 10 ng input RNA. The full-length cDNA output of the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing was processed with the Nextera XT DNA Library Preparation Kit (Illumina, Cat. # FC-131-1024).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description replicate 1 in *read_group_tracking file
Data processing The reads for each library were mapped to the hg19 human genome assembly using TopHat2
Quantification and differential analysis of the reads were performed using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: zip archive of cufflinks output. Merged transcriptome annotation merged.gtf
 
Submission date Mar 26, 2018
Last update date Apr 06, 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)
GSE112345 Viral shRNA Knockdown of INS Promotor Activity in EndoC-βH1 Cells 
GSE112346 4C-seq of insulin promoter, knockdown of INS promoter activity and Genome-wide maps of chromatin state in EndoC-βH1 Cells
Relations
BioSample SAMN08796422
SRA SRX3848682

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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