|
| Status |
Public on Nov 01, 2022 |
| Title |
4-NQO + isotype control rep3 |
| Sample type |
SRA |
| |
|
| Source name |
esophagus enriched for invading cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: esophagus enriched for invading cells
treatment: isotype
|
| Treatment protocol |
Beginning 2.5 weeks prior to sacrifice, mice were injected intraperitoneally with 10 µg of DTA-1 or isotype control antibodies twice weekly and harvested the day following the final injection.
|
| Growth protocol |
To establish ESCC tumors, 8-week-old mice were treated with 100 μg/ml 4-NQO in the drinking water ad lib for 16 weeks, followed by 12 weeks of normal water.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Esophagi were removed and tissue was enriched for invading tumor cells. Tissue was minced and flash frozen on dry ice. RNA was isolated using Qiagen RNeasy Mini Kit (#74104).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw counts
|
| |
|
| Submission date |
May 09, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Marie-Pier Tetreault |
| E-mail(s) |
marie-pier.tetreault@northwestern.edu
|
| Phone |
312-503-1915
|
| Organization name |
Northwestern University
|
| Department |
Medicine/GI&Hep division
|
| Lab |
Tarry 15-762
|
| Street address |
300 East Superior Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60605 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE202545 |
RNA-seq analysis of mouse esophageal tissue following GITR agonism in a model of esophageal squamous cell cancer |
|
| Relations |
| BioSample |
SAMN28161013 |
| SRA |
SRX15210871 |
