|
| Status |
Public on Aug 28, 2021 |
| Title |
DMRT1-KI-F-3-1d-gonad |
| Sample type |
SRA |
| |
|
| Source name |
Gonad
|
| Organism |
Gallus gallus |
| Characteristics |
dmrt1-distruption: Case
tissue: Ovary
time: 1W
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the gonadal tissues of DMRT1 gene-disrupted male and female chickens along with control male and female chickens using Maxwell (Promega) based method. Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer and RiboGreen dye (Invitrogen), and quantified using a Trinean DropSense96 spectrophotometer. 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The double stranded library was quantified using QauntiFluor ONE dsDNA System and equals 330 ng in a total volume of 60 ml or less. The library was cyclized at 37 °C for 60 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball, the library was incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system with 100 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The raw reads were trimmed by filtering out adaptor-only nucleotides with 75 bp minimum length, using Trimmomatic.
Trimmed reads were aligned to the reference genome (Gallus gallus 6.0a) using HISAT2.
Mapped reads were quantified in gene units using FeatureCounts.
Genome_build: galGal6.0a
Supplementary_files_format_and_content: Tab-delimited text files include mapped counts for each sample.
|
| |
|
| Submission date |
May 11, 2020 |
| Last update date |
Aug 28, 2021 |
| Contact name |
JAE YONG HAN |
| E-mail(s) |
jaehan@snu.ac.kr
|
| Phone |
82-2-880-4810
|
| Organization name |
Seoul National University
|
| Department |
Department of Agricultural Biotechnology
|
| Lab |
Animal Genetic Engineering
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24996 |
| Series (1) |
| GSE150339 |
Distruption of DMRT1 induces feminization in Chicken |
|
| Relations |
| BioSample |
SAMN14891915 |
| SRA |
SRX8326419 |
