|
| Status |
Public on Jun 01, 2023 |
| Title |
5-day mVenus induction rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Breast epithelial cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10-A
passages: 12-15
dox-inducible protein: mVenus
|
| Treatment protocol |
Doxycycline (50 ng/ml) was added 20 hours after seeding to induce transgene expression. After 24 hours, fresh media containing doxycycline and DMSO or Torin2 (100 nM, only for mVenus-p16 cells) was added. Media was refreshed every 48 hours and cells were harvested after 5 days
|
| Growth protocol |
MCF10-A cells expressing either mVenus-p16, mVenus-p21, or mVenus alone under a doxycycline-inducible promoter (see Constructs section for additional details) were seeded at 150,000 cells/well in a 6-well plate and cultured in cultured in phenol red-free DMEM/F12 supplemented with 5% horse serum, 20 ng/mL EGF, 10 μg/mL insulin, 500 μg/mL hydrocortisone, and 100 ng/mL cholera toxin at 37˚C and 5% CO2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy mini kit according to manufacturer’s instructions
Library construction was performed using KAPA Stranded mRNA-Seq kit (Roche). mRNA was purified using oligo-dT beads. A-tailing was then performed, followed by dual-index 8mer adapter ligation and library amplification
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quality was checked using FastQC 0.11.3
RNA sequencing read alignment was performed using hisat2 and tabulated with featureCounts (subread package) against GENCODE v29 gene models
DESeq2 was used for differential analysis using 3 biological replicates
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Normalized abundance measurements were determined for each annotated gene using DESeq2
Supplementary_files_format_and_content: Raw counts
|
| |
|
| Submission date |
Jul 02, 2020 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Leighton Harrison Daigh |
| E-mail(s) |
ldaigh@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Chemical and Systems Biology
|
| Lab |
Lab of Tobias Meyer
|
| Street address |
318 Campus Dr, Clark W200
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE153683 |
Accumulating DNA damage and insufficient DNA repair in senescent cells underlie persistent DNA damage signaling |
|
| Relations |
| BioSample |
SAMN15423688 |
| SRA |
SRX8655730 |
