|
| Status |
Public on Jul 09, 2018 |
| Title |
YAP/TAZ-dKO_1kPa_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293A cells, YAP/TAZ-dKO, 1kPa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293A
genotype/variation: YAP/TAZ-dKO
matrices: 1kPa
|
| Treatment protocol |
Cells were seeded onto high or low stiffness hydrogels coated with fibronectin. No other treatments.
|
| Growth protocol |
Cells were cultured in DMEM containing 10% FBS and antibotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by TRIzol (Thermo Fisher Scientific) from HEK293A cells seeded on high and low stiffness fibronectin-coated hydrogels.
The resulting RNA was then used to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101) or Set B (Illumina, RS-122-2102).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.8 software was used for basecalling.
Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters.
Only uniquely mapped reads were kept for further analysis.
FPKM values for each gene were computed using cufflinks v2.2.1 with default parameters according to Gencode human annotation release 24.
Genome_build: hg19
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values.
|
| |
|
| Submission date |
May 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Ren |
| Organization name |
University of California, San Diego School of Medicine
|
| Street address |
9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE98547 |
RAP2 Mediates Mechanotransduction to Hippo pathway |
|
| Relations |
| BioSample |
SAMN06891199 |
| SRA |
SRX2783828 |
