|
| Status |
Public on Aug 30, 2022 |
| Title |
FL1 5 Estrous |
| Sample type |
SRA |
| |
|
| Source name |
Dummerstorf high-fertility mouse line FL1
|
| Organism |
Mus musculus |
| Characteristics |
Stage: Estrous
gender: female
tissue: Ovar
age: 77 days
genotype: FL1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) recommended by manufacturer.
Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.
RNA: total RNA was extracted using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) recommended by manufacturer. Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were trimmed with bbduk.sh following manufacturer's protocol. ref=/data/resources/polyA.fa.gz,/data/resources/truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20
Reads were aligned with STAR aligner following the manufacturer's protocol. STAR --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
Amount of sequences aligned to transcripts was counted with cuffdiff
Genome_build: GRCm38.101
Supplementary_files_format_and_content: table with 2 columns in .txt format, column1: Ensemble Gene Accession Number, column2: corresponding counts
|
| |
|
| Submission date |
May 07, 2021 |
| Last update date |
Nov 30, 2024 |
| Contact name |
Ulrich Schweizer |
| E-mail(s) |
uschweiz@uni-bonn.de
|
| Organization name |
Universitätsklinikum Bonn
|
| Department |
Institut für Biochemie und Molekularbiologie
|
| Lab |
AG Schweizer
|
| Street address |
Nussallee 11
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE174082 |
Endocrine and molecular factors of increased female reproductive performance in mice |
|
| Relations |
| BioSample |
SAMN19069209 |
| SRA |
SRX10816621 |
