|
| Status |
Public on May 31, 2022 |
| Title |
AB183_72H_R1 |
| Sample type |
SRA |
| |
|
| Source name |
LS174T cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adenocarcinoma of the colon
cx-5361 treatment: treatment for 72 hours with 500 nM CX5461 (=72H)
|
| Treatment protocol |
LS174T cells were incubated with 500 nM CX5461 (Selleckchem) for 6 hours, 24 hours or 72 hours.
|
| Growth protocol |
LS174T cells were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum and 1% penicillin/ streptomycin. The cells were maintained in a humidified atmosphere with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested according to the protocol of the Quiagen RNAeasy Mini Kit. Total RNA was isolated by using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
cDNA libraries were generated with purified mRNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Libraries were size selected using Agentcourt AMPure XP beads, followed by amplification with 12 PCR cycles. The quality of the library was determined with the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq500 platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the human genome (hg19 assembly) using Bowtie2 (v2.2.7) with default parameters but allowing 1 mismatch in the seed alignment (-N 1 option).
Mapped reads per gene were counted using the summarizeOverlaps function in the GenomicAlignments R package.
Non-expressed genes were removed (mean read count per gene over all samples >1) and trimmed mean of M-values normalization was performed using edgeR
Assembly: hg19
Supplementary files format and content: Provided is a rawcount-matrix containing counts per gene for all conditions (removed were not expressed features) and a differential expression analysis file containing the changes in gene expression between 0 hour treatment and 6 hour, 24 hour and 72 hour treamtent with CX5461. Both tables are in text-format (*.txt).
|
| |
|
| Submission date |
May 24, 2022 |
| Last update date |
May 31, 2022 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE204749 |
RNA Polymerase I activity prevents terminal differentiation and growth arrest in colorectal cancer and induce vulnerability for senolytics |
|
| Relations |
| BioSample |
SAMN28646235 |
| SRA |
SRX15444224 |
