|
| Status |
Public on Aug 11, 2021 |
| Title |
XBP1 knock-down cells under control condition, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
A1847 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A1847 cells
condition: shXBP1
carm1 status: WT
xbp1 status: KD
treatment: ctr
replicate: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy mini Kit (Qiagen, 74106) and digested with DNase I (Qiagen, 79254)
RNA-Seq libraries were constructed using 3’mRNA-seq Library Prep Kit (Lexogen) and sequenced with Illumina NextSeq 500 using 75 nt single read
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
shXBP1.ctr.3
|
| Data processing |
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene
|
| |
|
| Submission date |
Aug 29, 2020 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE157116 |
CARM1 determines endoplasmic reticulum stress response by controlling XBP1 in ovarian cancer [RNA-seq] |
| GSE157118 |
CARM1 determines endoplasmic reticulum stress response by controlling XBP1 in ovarian cancer |
|
| Relations |
| BioSample |
SAMN15940912 |
| SRA |
SRX9035224 |
