|
| Status |
Public on Jun 23, 2020 |
| Title |
SKO+Glis1 day 8 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic cell infection with retrovirus SKO+Glis1
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: SKO+Glis1
strain: ICR
tissue: mouse embryonic fibroblast cell
age: day 8 in reprogramming process
|
| Extracted molecule |
total RNA |
| Extraction protocol |
medium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rpkm.anno
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Millon Mapped Fragments (FPKM) were calculated using a protocol from Trapnell,C.et al, 2010(replicate 1);Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009(replicate 2). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM /rpkm values for each Sample ...
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
Jun 23, 2020 |
| Contact name |
LI LINPENG |
| E-mail(s) |
568638721@qq.com
|
| Organization name |
GIBH
|
| Street address |
KAIYUAN ROAD 190
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE131491 |
Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction [RNA-Seq] |
| GSE131692 |
Glis1 Activate Glycolytic Process and Increase H3K27Ac Level on Pluripotent and Second Wave Genes Promoter Facilitating Pluripotency Induction |
|
| Relations |
| BioSample |
SAMN11785252 |
| SRA |
SRX5866837 |
