|
| Status |
Public on Oct 04, 2023 |
| Title |
311E, DMSO 96hr bio rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
311E cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: 311E cell line
cell line: GEMM, esophagus mNC tumor
cell type: BRD4-NUTM1
genotype: DMSO
treatment: 96hr
|
| Growth protocol |
HBSS + 10% FBS + 1% pen/strep + 1x glutamax
|
| 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 |
| |
|
| 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: GRCm39/mm39 and GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 22, 2023 |
| Last update date |
Oct 04, 2023 |
| Contact name |
Chris French |
| E-mail(s) |
[email protected]
|
| Phone |
617-525-4415
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Pathology
|
| Lab |
French
|
| Street address |
77 avenue louis Pasteur, NRB 652
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE241474 |
A genetically engineered mouse model (GEMM) of NUT carcinoma (RNA-Seq) |
| GSE241477 |
A genetically engineered mouse model of NUT carcinoma |
|
| Relations |
| BioSample |
SAMN37115028 |
| SRA |
SRX21455955 |
