|
| Status |
Public on Jan 20, 2020 |
| Title |
mRNA_control_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hTERT-RPE-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hTERT-immortalized retinal pigment epithelial cell line
treatment: control-siRNA (100 nM)
passages: 12-14
|
| Treatment protocol |
hTERT-RPE-1 cells were reversely transfected with siRNA via Lipofectamine RNAiMAX reagent and cultured for 24 h (PDCD4-siRNA: GCUUCUUUCUGACCUUUGU; control-siRNA (targeting renilla luciferase): AAACAUGCAGAAAAUGCUG)
|
| Growth protocol |
hTERT-RPE-1 adherent cells were cultured at coated plastic (T75 flask, Greiner Bio-One or cell culture plates, 10 cm, Corning (Falcon)) in DMEM/Ham's F12 medium (Biochrom).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Total RNA samples were extracted with TRIzol
RNA libraries for RNA-seq were prepared for sequencing using the TruSeq Standard mRNA LT Kit from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
siRNA_RPE_mRNA_res.txt
siRNA_RPE_mRNA_resLA.txt
siRNA_RPE_mRNA_normalized.txt
siRNA_RPE_RPF_mRNA_res.txt
|
| Data processing |
Reads were demultiplexed with Illumina's bcl2fastq
for ribosome profiling: adapter sequences were clipped with the FASTX-Toolkit (Hannon Lab, version 0.0.13.)
for ribosome profiling: 4 randomized nucleotides were trimmer using the FASTX-Toolkit (Hannon Lab, version 0.0.13.)
for ribosome profiling: rRNA was depleted by mapping against human rRNA using bowtie version 1.0.0
mapping to UCSC cannonical ORFs was performed with bowtie version 1.0.0
count tables were created using a custom script and differential expression determined with DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited txt files including standard DESeq2 output (baseMean, log2FoldChange (lfc), lfcSE, statx, pvalue, padj)
*normalized.txt: normalized reads
*resLA.txt: fully analyzed data; tested for significantly unchanged genes
*res.txt: fully analyzed data; tested for significantly changed genes
siRNA_RPE_RPF_mRNA_res.txt: combined file for RNA-seq and ribosome profiling fully analyzed data; tested for significantly changed genes
|
| |
|
| Submission date |
Oct 07, 2019 |
| Last update date |
Jan 20, 2020 |
| Contact name |
Astrid Haas |
| Organization name |
WWU Münster
|
| Department |
Biochemistry
|
| Street address |
Wilhelm-Klemm-Str.2
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE138533 |
Analysis of PDCD4 knockdown effects by high throughput sequencing of a human epithelial cell line |
|
| Relations |
| BioSample |
SAMN12985518 |
| SRA |
SRX6959640 |
