|
| Status |
Public on Feb 09, 2018 |
| Title |
RPE1_hTERT_5.3_12.3_3 |
| Sample type |
SRA |
| |
|
| Source name |
Retina pigmented epithelium cell line immortalized with hTERT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RPE1_hTERT
cell line origin: Human retina, pigmented epithelium
aneuploidy: trisomy of chromosome 5, trisomy of chromosome 12
|
| Growth protocol |
Cells were maintained in 10 cm dishes in Dulbecco’s Modified Eagle Medium (DMEM) at 37°C and 5% CO2. Culture medium was supplemented with growth factors from 5% Fetal Calf Serum (FCS) and 1% Penicillin/ Streptavidin to avoid bacterial growth and contamination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
TruSeq RNA library preparation and Illumina HiSeq2500 sequencing with 25 million 100bp single reads per library were performed by the Max Planck-Genome-Center Cologne, Germany.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
normalized to RPE1_hTERT_1/ RPE1_hTERT_2/ RPE1_hTERT_3
processed data file:
RPE1_5.3_12.3.txt
|
| Data processing |
Sequencing adapters were removed from the raw sequences with cutadapt.
Sequencing reads were mapped to the human genome using TopHat (v2.0.10) with the following parameters: “tophat2 -g1 -G”.
RefSeq information in the GTF file was downloaded from the UCSC genome browser. featureCounts (v1.4.3) was used to generate the count matrix with the same GTF file as for the alignment with the following parameters: “-t exon -g gene_id”.
Normalization and differential expression analysis was performed using the R/Bioconductor package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab- delimited text file containing the DeSeq2 normalized, log2 texpression fold changes of the aneuploid cell line to thecontrol cell line (log2FoldChange). baseMean=mean of normalized counts for all samples; lfcSE=standard error: condition treated vs untreated stat=Wald statistic: aneuploidy vs control; pvalue=Wald test p-value: aneuploidy vs control; padj="Benjamini-Hochberg adjusted p-values
|
| |
|
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Milena Dürrbaum |
| Organization name |
Max Planck Institute of Biochemistry
|
| Department |
Maintenance of Genome Stability
|
| Street address |
Am Klopferspitz 18
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE102852 |
The deregulated microRNAome contributes to the cellular response to aneuploidy [mRNA] |
| GSE102855 |
The deregulated microRNAome contributes to the cellular response to aneuploidy |
|
| Relations |
| BioSample |
SAMN07522731 |
| SRA |
SRX3110435 |
