|
| Status |
Public on Sep 18, 2019 |
| Title |
E13319 |
| Sample type |
SRA |
| |
|
| Source name |
FFPE duodenum
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: B6C3F1
genotype/variation: wildtype
gender: male
tissue: duodenum
treatment: control
|
| Treatment protocol |
B6C3F1 mice exposed to either Cr(VI) (180ppm in drinking water), captan (≤12000ppm in diet), or folpet (≤16000ppm in diet) for 28 days.
|
| Growth protocol |
Male B6C3F1 mice were bred, reared, and administered test compounds at Charles River Laboratories.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Formalin-fixed, paraffin-embedded duodenum tissue was scraped from sections mounted to glass slides directly into lysis buffer.
The TempO-Seq (BioSpyder Industries) targeted expression assay protocol was followed for library construction: RNA for approximately 3000 genes was amplified using targeted oligomers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA extracted from FFPE tissue.
processed data file: SP0071_gene_counts_GEO.csv
|
| Data processing |
No adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters.
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing.
Fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: SP0071_gene_counts_GEO.csv: Comma-separated text file includes raw count values for each gene_probe.
|
| |
|
| Submission date |
Sep 18, 2018 |
| Last update date |
Sep 18, 2019 |
| Contact name |
Grace Chappell |
| E-mail(s) |
gchappell@toxstrategies.com
|
| Organization name |
ToxStrategies, Inc.
|
| Department |
Health Sciences
|
| Street address |
9390 Research Blvd, Bldg 2, Ste. #100
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78723 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE120146 |
Transcriptomic signatures indicative of a non-genotoxic adverse outcome pathway for small intestine cancer in the duodenum of mice exposed to hexavalent chromium, captan, or folpet |
|
| Relations |
| BioSample |
SAMN10086514 |
| SRA |
SRX4712526 |
