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Sample GSM6124228 Query DataSets for GSM6124228
Status Public on Nov 01, 2022
Title 4-NQO + DTA-1 rep1
Sample type SRA
 
Source name esophagus enriched for invading cells
Organism Mus musculus
Characteristics tissue: esophagus enriched for invading cells
treatment: DTA-1
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 SAMN28161012
SRA SRX15210872

Supplementary file Size Download File type/resource
GSM6124228_6343_ES.txt.gz 189.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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