|
| Status |
Public on Apr 06, 2020 |
| Title |
CWC22-1 |
| Sample type |
SRA |
| |
|
| Source name |
retinal pigment epithelium cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: h-TERT RPE-1
treatment: CWC22 DsiRNA
|
| Treatment protocol |
For mRNA-seq, h-TERT RPE-1 cells were transfected at 60-70% confluency with 9 μl of Lipofectamine and 1.5 μl of 20 μM DsiRNAs (Integrated DNA Technologies) CWC27, CWC22 or control. A mix of 2 different DsiRNA targeting different regions of the CWC27 and CWC22 genes was used. Transfections for replicates were performed independently.
|
| Growth protocol |
hTERT-RPE-1 cells were propagated at 37°C in a humidified 5% CO 2 atmosphere in DMEM/F-12 GlutaMAX medium (31331-028, Life Technologies) supplemented with 10% FBS and 100 U/mL Penicillin-Streptomycin 1X (Life Technologies). HeLa and hTERT-RPE-1 cells were genotyped by Eurofins Forensik and routinely tested for mycoplasma by PCR.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
48 hours after transfection, RNAs were extracted using Monarch Total RNA Miniprep Kit (New England Biolabs)
RNA-seq was performed by Fasteris on paired-end libraries (stranded mRNA) run on Illumina HiSeq using 2x150 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
CWC22-deseq2.tabular
|
| Data processing |
After trimming of the adapters using cutadapt, the reads were mapped on hg38 (Gencode GRCh38.p12.genome.fa) using STAR (version 20201) with default parameters and adding the -quantMode GeneCounts option to generate gene count files. Gencode hg38 V29 gtf annotations were used.
For differential expression, DESeq2 was run on gene counts (from STAR) of controls vs CWC22 or CWC27 siRNA triplicates with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression DESeq2 outputs : CWC22-deseq2.tabular and CWC27-deseq2.tabular
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Herve Le Hir |
| E-mail(s) |
[email protected]
|
| Organization name |
IBENS
|
| Lab |
ENS, CNRS, INSERM, PSL Research University
|
| Street address |
46, Rue d’Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE145872 |
The CWC27/CWC22 heterodimer: a spliceosome building block linked to the inflammation response in retinal pigment epithelium |
|
| Relations |
| BioSample |
SAMN14178213 |
| SRA |
SRX7797597 |
