|
| Status |
Public on May 04, 2022 |
| Title |
Pituitary_Vancomycin P15 |
| Sample type |
SRA |
| |
|
| Source name |
Pituitary
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Crl:CD(SD)
Stage: Adult
genotype: wild type
sample well: F3
plate: plate_1
barcode: CCGCAG
|
| Treatment protocol |
8 mg/kg bw/day Vancomycin
Treatments were administered daily by oral gavage for 7 days from PD56 until PD62. Rats were exposed to 8 mg/kg bw/day Vancomycin, 3 mg/kg bw/day PFOS, 8 mg/kg bw/day Vancomycin + 3 mg/kg bw/day PFOS or corn oil (vehicle control).
|
| Growth protocol |
The animals were kept in cages placed in ScanTainers with controlled environmental conditions, with reversed light/dark cycles of 12 hours. Feed was given ad libitum with Lucerne free feed based on Altromin 1314. Acidified tap water was given ad libitum in BPA free bottles.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using Kit from Qiagen and stored at -80 ℃.
The initial reverse transcription and template switching were done using 4 µL total RNA with 2.5 ng/µL. 50 ng of ds cDNA was used to build the sequencing libraries by tagmentation with the Illumina Nextera XT Kit. Library was sequenced using an Illumina NovaSeq 6000 sequencing system.
3'Bulk RNA Barcoding sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Pituitary_Vancomycin
P15
|
| Data processing |
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Rat reference transcriptome from the UCSC website (release rn6, downloaded in August 2020) using BWA version 0.7.4.4 was used to align the second reads
Genome_build: rn6
Supplementary_files_format_and_content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,483 genes detected.
|
| |
|
| Submission date |
Feb 04, 2022 |
| Last update date |
May 04, 2022 |
| Contact name |
Frédéric Chalmel |
| E-mail(s) |
frederic.chalmel@inserm.fr
|
| Organization name |
Inserm U1085-Irset
|
| Department |
Physiology and physiopathology of the urogenital tract
|
| Street address |
9 avenue du Pr. Léon Bernard
|
| City |
Rennes |
| State/province |
France |
| ZIP/Postal code |
35000 |
| Country |
France |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE196133 |
BRB-seq analysis of PFOS-induced thyroid hormone system disrupted rats reveal organ-specific effects |
|
| Relations |
| BioSample |
SAMN25652184 |
| SRA |
SRX14044044 |
