|
| Status |
Public on Nov 04, 2019 |
| Title |
RNAseq_APCres_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SW480TetOnAPC cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human colorectal cancer cell line
cell line: SW480TetOnAPC
treatment: Dox
shRNA: none
|
| Treatment protocol |
SW480TetOnAPC cells were treated with 0.5 µg/ml doxycycline or ethanol for 48 hours to restore APC expression.
|
| Growth protocol |
SW480TetOnAPC cells were grown in RPMI 1640 (Sigma). All media were supplemented with 10% FBS (Sigma) and 1% penicillin/streptomycin (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For global gene expression analysis, total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) including on-column digestion of DNA. Poly-A+ RNA was purified from total RNA with the NEBNextPoly(A) mRNA Magnetic Isolation Module (NEB).
RNA sequencing libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
processed data file:
RNAseq_SW480_logFC.txt
|
| Data processing |
For RNA-seq analysis, reads were aligned to the human genome (hg19) with BOWTIE v0.12.8 (Langmead, 2010) using default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Reads per gene (Ensembl database GRCh37.p13) were counted with the "summarizeOverlaps" function in the R package {GenomicFeatures}.
Non- or weakly expressed genes were removed (threshold: mean read count per gene over all samples >1).
Differential gene expression was called using EdgeR and adjusting the calculated p-value with the Benjamini-Höchberg procedure.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file containing gene names, gene description, log2FC, log2CPM, p-value, Benjamini-Höchberg-adjusted p-value
|
| |
|
| Submission date |
Nov 14, 2017 |
| Last update date |
Nov 04, 2019 |
| 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 |
GPL10999 |
| Series (1) |
| GSE106858 |
A MYC/GCN2/eIF2alpha negative feedback loop limits protein synthesis to prevent MYC-dependent apoptosis in colorectal cancer |
|
| Relations |
| BioSample |
SAMN08023376 |
| SRA |
SRX3389386 |
