|
| Status |
Public on May 18, 2016 |
| Title |
EndoC ctrl GFP 1 |
| Sample type |
SRA |
| |
|
| Source name |
Endo-ßH1C cell line (pancreas), scrambled control, GFP expression
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Endo-beta-H1C
cell type: pancreatic beta-cell line
gain of function: GFP
sirna treatment: scrambled control
|
| 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 |
RSq54
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 |
SAMN05011601 |
| SRA |
SRX1775531 |
