|
| Status |
Public on Nov 23, 2020 |
| Title |
Mia PaCa-2 cells, R1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreas - MIA PaCa-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Mia PaCa-2
cell type: epithelial cell
cell condition: adherent, single cells and loosely attached clusters
genotype: wild-type
treatment: Positive control
|
| Treatment protocol |
DMEM + 10 %FBS supplemented with ADH-6
|
| Growth protocol |
DMEM + 10 %FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriZol LS and Rneasy Mini Kit (Qiagen) according to manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| 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 the Homo sapian (GRCh38/hg38) genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Genome_build: Homo sapiens (GRCh38/hg38) genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Nov 22, 2020 |
| Last update date |
Nov 23, 2020 |
| Contact name |
Mohamed Al-Sayegh |
| E-mail(s) |
[email protected]
|
| Phone |
+97126284560
|
| Organization name |
New York University Abu Dhabi
|
| Department |
Biology
|
| Lab |
Al-Sayegh Lab
|
| Street address |
Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188
|
| City |
Abu Dhabi |
| ZIP/Postal code |
00000 |
| Country |
United Arab Emirates |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE161952 |
Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function |
|
| Relations |
| BioSample |
SAMN16869788 |
| SRA |
SRX9551723 |
