|
Status |
Public on May 18, 2016 |
Title |
EndoC T-Ag 460 GFP |
Sample type |
SRA |
|
|
Source name |
Endo-ßH1C cell line (pancreas), T-Ag siRNA 460, GFP expression
|
Organism |
Homo sapiens |
Characteristics |
cell line: Endo-beta-H1C cell type: pancreatic beta-cell line gain of function: GFP sirna treatment: T-Antigen siRNA 460
|
Extracted molecule |
total RNA |
Extraction protocol |
ABI picopure RNA extraction kit. KAPA stranded RNA-Seq kit.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
RSq48 PolyA RNA Processed data file: normalizedCounts_endoC.txt
|
Data processing |
Raw reads were mapped to hg19 transcriptome using STAR version 2.3.0.1. A custom script was used to count transcripts. Genome_build: hg19 transcriptome, aggregated from UCSC, RefSeq and GENCODE v12 databases. Supplementary_files_format_and_content: normalizedCounts_endoC.txt: The processed data file contains 9 tab-delimited columns: the first column is gene symbol, and columns that come after are DESeq normalized counts of the respective samples. We used the DESeq (Huber et al. [PMID: 20979621]) normalization.
|
|
|
Submission date |
May 18, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Seung Kim |
E-mail(s) |
seungkim@stanford.edu
|
Organization name |
Stanford University
|
Department |
Developmental Biology
|
Lab |
Seung Kim Lab
|
Street address |
279 Campus Dr B303
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (2) |
GSE57973 |
Age-dependent gene expression changes in human islets |
GSE79469 |
Age-dependent pancreatic gene regulation reveals mechanisms governing human β-cell function |
|
Relations |
BioSample |
SAMN05011595 |
SRA |
SRX1775525 |