|
| Status |
Public on Sep 20, 2023 |
| Title |
PER-403,36h,1uM taz [PER-403 S1] |
| Sample type |
SRA |
| |
|
| Source name |
PER403
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PER403
cell type: NUT carcinoma cell line
genotype: BRD4-NUTM1
treatment: 1uM taz
time point: 36h
|
| Growth protocol |
DMEM supplemented with either 10% FBS (10-15) or 20% BGS (PER-403).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAeasy (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. ERCC92 spike-in RNA is added to normalize reads.
RNA libraries for RNA-seq were prepared using the Roche KAPA HyperPrep RNA RiboErase Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
1uM taz
|
| Data processing |
Quality-controlled reads are aligned to the human genome (GRCh38/hg38) and to ERCC92 spike-in sequences using a splice-aware aligner (STAR89) with Ensembl. transcriptome annotations.
Differential expression (DE) analysis is performed using RUVSeq to identify unwanted variation followed by edgeR91 and/or DESeq2
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 18, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Chris A French |
| E-mail(s) |
[email protected]
|
| Phone |
6175254415
|
| Organization name |
BWH
|
| Department |
Pathology
|
| Street address |
75 francis st.
|
| City |
boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE232838 |
Effect of EZH2 inhibition on NUT carcinoma gene expression over time |
|
| Relations |
| BioSample |
SAMN35167217 |
| SRA |
SRX20432912 |
