|
| Status |
Public on Sep 17, 2018 |
| Title |
KYSE140-shp63-ma_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
KYSE140
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KYSE140
cell type: Esophageal squamous carcinoma cells
genotype/variation: ShRNA mediated TP63 knock down
|
| Growth protocol |
cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using RNeasy Kit (Qiagen).
Standard Illumina protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FCHCGHHBBXX-HKHUMwnxEAAJRAAPEI-212_L3
|
| Data processing |
Raw fastq files were pseudoaligned to Ensemble version 82 transcripts using Kallisto (vn: 0.43.0)
Kallisto output files were later summarized into gene level abundance and counts using tximport Bioconductor package followed by DESeq2 to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: abundance.tsv output from kallisto containing abundance in TPM and estimated fragment counts for all Ensemble 82 transcripts.
|
| |
|
| Submission date |
Nov 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Phillip H Koeffler |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Science Institute
|
| Lab |
H. Phillip Koeffler's lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE106564 |
Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [RNA-seq] |
| GSE106565 |
Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung |
|
| Relations |
| BioSample |
SAMN07981404 |
| SRA |
SRX3367079 |
