|
| Status |
Public on Apr 02, 2024 |
| Title |
YA014_CD274_OE_1_R1 |
| Sample type |
SRA |
| |
|
| Source name |
HaCaT cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human immortalized keratinocytes
genotype/variation: shRNA-mediated PD-L1 overexpressed HaCaT cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted from HaCaT cells using standard TRIzol protocols
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 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
|
| |
|
| Submission date |
Apr 02, 2021 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Long Qi Chen |
| E-mail(s) |
luoying@shyueyanghospital.com
|
| Organization name |
Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine
|
| Street address |
1200 Cailun Road, Pudong New Area
|
| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE171372 |
PDL1 triggered from binding eIF3I contributes to ameliorate diabetes associated wound healing defects by regulating IRS4 |
|
| Relations |
| BioSample |
SAMN18603634 |
| SRA |
SRX10504589 |
