|
| Status |
Public on Dec 03, 2021 |
| Title |
SS_MNUC1 |
| Sample type |
SRA |
| |
|
| Source name |
rat mammary tumor
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: rat mammary tumor tissue
treatment: vehicle administration
|
| Treatment protocol |
Control group was given 100 µL of corn oil by oral gavage as a vehicle, while treatment group was received orally 50 mg/kg of DATS-contained corn oil.
|
| Growth protocol |
21-day old female Sprague-Dawley rats were injected intraperitoneally 50 mg/kg body weight of MNU. One week after MNU injection, the rats were randomly divided into two groups and treatment was started 5 times a week for 10 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ttotal RNA was extracted using the Zymo Quick RNA Miniprep Plus kit (zymoresearch, Irvine, CA ).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data filtering: (1 )Remove reads with adaptor contamination. (2) Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3) Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Genome_build: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary_files_format_and_content: FPKM represents summary of gene expression level analysis by FPKM
|
| |
|
| Submission date |
Nov 26, 2021 |
| Last update date |
Dec 03, 2021 |
| Contact name |
Shivendra V Singh |
| E-mail(s) |
singhs@upmc.edu
|
| Phone |
412-623-3263
|
| Organization name |
University of Pittsburgh
|
| Department |
Pharmacology and Chemical Biology
|
| Lab |
Singh
|
| Street address |
5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE189640 |
Alteration of gene expression by diallyl trisulfide (DATS) administration in chemically-induced rat mammary tumors |
|
| Relations |
| BioSample |
SAMN23458118 |
| SRA |
SRX13238464 |
