|
| Status |
Public on Oct 31, 2020 |
| Title |
6hNutlin_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary lung fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
passage: 28
agent: Nutlin-3a
time point: 6h
|
| Treatment protocol |
The day after splitting IMR90 cells seeding at 300k cells/mL, cells were treated with DMSO, or Nutlin-3a (3ug/mL) for 6, 9, or 12 hours
|
| Growth protocol |
IMR90 cells were grown under 3% oxygen, 5% carbon dioxide in DMEM with 10% FBS
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted in phenol-chroform, then purified with column purification. PolyA RNAs were selected using NEBNext Poly(A) mRNA Magnetic Isolation Module
RNA-seq libaries were prepared using NEB Next Ultra II Directional RNA library prep kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
fastq files were aligned using STAR
Htseq2 was used to count the number of reads for each gene
Deseq2 was used to generate normalized counts
Deseq2 was used to identify significant differences
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files of normalized counts for all samples, or for statistics for comparisons of each Nutlin sample with the DMSO control
|
| |
|
| Submission date |
Oct 17, 2019 |
| Last update date |
Oct 31, 2020 |
| Contact name |
Katherine A Alexander |
| E-mail(s) |
kaalexa@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
Smilow Center for Translational Research
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE139003 |
RNA-seq timecourse of p53 activation with Nutlin-3a in IMR90 cells |
|
| Relations |
| BioSample |
SAMN13046983 |
| SRA |
SRX7010834 |
