 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 28, 2020 |
| Title |
a100ul-2input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
Pig iPS
|
| Organism |
Sus scrofa |
| Characteristics |
breed: domestic pig
developmental stage: adult
cell type: Induced pluripotent stem cells (iPSCs)
genotype/variation: overexpressing IRF1-flag
|
| Treatment protocol |
Before RNA extraction, feeder cells were removed in order to avoid sequencing artifacts. Dissociated pig PC-iPS cells were plated onto six-well plates and cultured for 1 hour.
|
| Growth protocol |
LCDMV culture system maitain pig iPS selfrenew and growth.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The suspended cells were collected for RNA extraction according to the RNA extrac kit, leaving behind the attached cells (primarily consisting of feeders). Total RNA samples (2 µg each) were suspended in 15 µL RNAase-free ddH2O, packed in dry ice, and submitted to Anoroad Gene Technology Corporation (Beijing, China) for RNA sequencing.
Approximately 2 µg total RNA (each sample) and the Oligo(dT) magnetic head were used for generating RNA-Seq cDNA libraries, and then, RNA -seq was conducted following the manufacturer's standard procedures.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
bcl2fastq2 v.2.17.1.14 software was used for generating fastq files.
We removed low-quality reads including those with ≥ 5% unidentified nucleotides, > 5 nt aligned to the adapter, and with > 50% of bases with phred quality < 19. Then,for RNA-seq data, high-quality reads of four non-strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4); for ChIPSeq data,high-quality reads of four non-strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Bowtie2.
For RNASeq, mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3);for ChIPSeq, we remove PCR duplicate used samtools.
For RNASeq,, reads counts of sequence files were obtained using featureCounts(v.1.6.4); For ChIPSeq, we used MACS2 to call peaks.
For RNASeq, Differentially expressed genes of samples were obtained using DESeq2; for ChipSeq, ChipSeeker was used for annotating peaks.
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: For RNASeq, Comma-delimited text files include FPKM values for each sample. For ChIPSeq, we provided bigWig file for every sample.
|
| |
|
| Submission date |
Jan 12, 2020 |
| Last update date |
Nov 29, 2020 |
| Contact name |
Jianyong Han |
| E-mail(s) |
[email protected]
|
| 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 |
GPL19176 |
| Series (1) |
| GSE143484 |
IRF-1 expressed in the early blastocyst inner cell mass of pigs enhances the pluripotency of induced pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN13830686 |
| SRA |
SRX7544046 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4260283_input.bw |
214.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
