|
| Status |
Public on May 21, 2020 |
| Title |
5uM cadmium treated #1 [Cd1_S64] |
| Sample type |
SRA |
| |
|
| Source name |
rat insulinoma cells_5uM cadmium
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: INS-1 832/13
tissue: liver
cell type: rat insulinoma cells
treatment: 5uM cadmium
molecule subtype: small RNA
|
| Treatment protocol |
Cells were treated for 24 hours prior to RNA isolation.
|
| Growth protocol |
Cells were seeded 1 million/well in a 12-well plate 24 hours prior to exposure
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
RNA was isolated using Norgen Total RNA Purification kit.
See description column in Samples section
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cd1_S64_L006
processed data file: miRquant_RPMMM.csv
|
| Data processing |
Small RNA-seq samples were processed using miRquant2.0 and normalized counts were determined using DESeq2
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: rn6
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the reads per million mapped to miRs (RPMMM) for small RNA-seq or DESeq2 normalized counts for RNA-seq for each of the samples.
|
| |
|
| Submission date |
May 21, 2019 |
| Last update date |
May 21, 2020 |
| Contact name |
Praveen Sethupathy |
| Organization name |
Cornell University
|
| Lab |
Dr. Sethupathy Lab
|
| Street address |
Cornell University College of Veterinary Medicine, Box 17
|
| City |
Ithica |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE131544 |
Arsenic is more potent than cadmium or manganese in disrupting the INS-1 beta cell microRNA landscape |
|
| Relations |
| BioSample |
SAMN11793562 |
| SRA |
SRX5874080 |
