|
| Status |
Public on Dec 13, 2023 |
| Title |
RNA-seq_pgEpiSC-3 |
| Sample type |
SRA |
| |
|
| Source name |
Pig pre-gastrulation epiblast stem cells (pig pgEpiSCs)
|
| Organism |
Sus scrofa |
| Characteristics |
developmental stage: E10 embryonic epiblast
tissue: Embryonic epiblast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat.N: 74106)
We used an rRNA depletion protocol (Globin-Zero Gold rRNA Removal Kit, Illumina, Cat.N: GZG1224) coupled with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Cat.N: E7420S) to construct the strand-specific RNA-seq library for each sample. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen, Life Technologies, Cat.N: Q32851) and sequenced on HiSeq 4000 platform (Illumina) to produce an average of ~127.83 million 150-bp paired-end raw reads and ~126.01 million high-quality reads for each library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
High quality reads were mapped to the pig reference genome (Sscrofa 11.1, GCA_000003025.6) using STAR alignment tool (version 2.6.0c) with parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 10
Expression level of protein coding genes (gene annotation file [GTF] from Ensembl Sscrofa 11.1 release 92) were quantified as transcripts per million (TPM) using Kallisto(version 0.44.0).
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.
|
| |
|
| Submission date |
Mar 02, 2021 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Jianyong Han |
| E-mail(s) |
hanjy@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
State Key Laboratory of Agrobiotechnology
|
| Lab |
Han lab
|
| Street address |
2rd, Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (2) |
| GSE168105 |
Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [RNA-seq] |
| GSE168107 |
Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines |
|
| Relations |
| BioSample |
SAMN18124999 |
| SRA |
SRX10224042 |
