|
| Status |
Public on Dec 08, 2020 |
| Title |
Knock Down YAP Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
ESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
developmental stage: pluripotent
treatment: Transient transfection with siRNAs targeting mYAP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from three independent experiments were extracted by TriSure (Bioline) and subjected to high-throughput sequencing with Illumina Genome Analyzer platform (Illumina).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
KD YAP-1
KD_analysys.xlsx
|
| Data processing |
Reads mapping and transcripts expression quantification with Rsem/STAR (default parameters) on the RefSeq transcripts annotation (mm10 retrieved from the UCSC genome browser).
edgeR was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files contain the output of genes abundance quantification obtained using RSEM. The two .xls files contain the results of the differential expression analysis carried out using edgeR. Each xlsx file contains a CPM tab with the Counts Per Million expression levels for all expressed genes and a Deregulated tab with the genes deregulated at FDR <= 0.05 and their associated logFC.
|
| |
|
| Submission date |
Sep 09, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Federico Zambelli |
| Organization name |
University of Milan
|
| Department |
Department of Biosciences
|
| Street address |
Via Giovanni Celoria 26
|
| City |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE157706 |
Expression profile of mouse embryonic stem cells upon knockdown or overexpression of YAP |
| GSE157707 |
YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation |
|
| Relations |
| BioSample |
SAMN16086861 |
| SRA |
SRX9099551 |
