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Status |
Public on Jan 20, 2020 |
Title |
mRNA_PDCD4-KD_rep2 |
Sample type |
SRA |
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Source name |
hTERT-RPE-1
|
Organism |
Homo sapiens |
Characteristics |
cell type: hTERT-immortalized retinal pigment epithelial cell line treatment: PDCD4-siRNA2 (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)
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiScanSQ |
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Description |
siRNA_RPE_mRNA_res.txt siRNA_RPE_mRNA_resLA.txt siRNA_RPE_mRNA_normalized.txt siRNA_RPE_RPF_mRNA_res.txt didnt work well (too few reads); was not possible to consider
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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
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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 |
SAMN12985536 |
SRA |
SRX6959638 |