|
| Status |
Public on Mar 08, 2023 |
| Title |
KTZ_Low (PND22_Ktz3_m104) |
| Sample type |
SRA |
| |
|
| Source name |
Ovary
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Ovary
strain: Crl:CD(SD)
age: PND22
genotype: wild type
sample well: H10
barcode: TCGCGG
treatment: KTZ
dose: 3 mg/kg bw/day
|
| Treatment protocol |
Rat dams were exposed to DES or KTZ from GD7. The rats were weighed and gavaged each morning with either vehicle control or test substances until three distinct postnatal stages (postnatal days 6, 14, and 22) using three different doses 3, 6 and 12 µg/kg bw/day for DES and 3, 6 and 12 mg/kg bw/day for KTZ.
|
| Growth protocol |
Time-mated Sprague-Dawley rats were delivered at gestational day (GD) 3. Animals were kept under standard conditions with 12 h light/dark cycles and fed a standard soy- and alfalfa-free diet based on Altromin 1314 along with tap water in Bisphenol A-free bottles provided ad libitum. Animals were kept in pairs until GD17, thereafter individually.
|
| 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 |
FREIA_WP2_KTZ.unq.refseq.umi.dat
PND22_Ktz3_m104
|
| 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
Assembly: 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 |
Jul 19, 2022 |
| Last update date |
Mar 08, 2023 |
| 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) |
| GSE208545 |
Transcriptional profiling of developing rat ovary following intrauterine exposure to known endocrine disruptors |
|
| Relations |
| BioSample |
SAMN29827319 |
| SRA |
SRX16341901 |
