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| Status |
Public on Jul 24, 2020 |
| Title |
H1299_siTAZ replicate3 |
| Sample type |
SRA |
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| Source name |
H1299 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: non-small cell lung cancer
cell line: H1299
knockdown: siTAZ
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| Treatment protocol |
Either H1299 or A549 cells were transfected with 30nM siControl, siYAP or siTAZ SMARTpool oligonucleotides for 48 hours and serum-starved for the last 18 hours.
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| Growth protocol |
H1299 were cultured in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Biological Industries, Israel) and 1% penicillin-streptomycin antibiotics solution. A549 cells were grown in DMEM (Biological Industries) supplemented with 10% heat-inactivated fetal bovine serum (Hyclone, USA) and 1% penicillin-streptomycin antibiotics solution (Biological Industries). Cells were maintained at 37˚C with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a NucleoSpin RNA kit (Macherey Nagel, Germany).
The polyA fraction was purified from 500ng of total RNA, followed by fragmentation and generation of double-stranded cDNA, Agencourt Ampure XP beads cleanup (Beckman Coulter, USA), end repair, A base addition, adapter ligation and PCR amplification. Libraries were quantified by Qubit (Thermo fisher scientific, USA) and TapeStation (Agilent, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
C-13
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| Data processing |
RNA-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). In short, reads were trimmed using cutadapt and mapped to genome GRCh38 (Gencode) using STAR v2.4.2a with default parameters. Genes having minimum five reads in at least one sample were considered. For A549 RNA-seq, batch correction was done using the sva (3.26.0) R package.Normalization of the counts and detection of differential expression was performed using DESeq2 with the betaPrior, cooksCutoff and independent filtering parameters set to False. Raw P values were adjusted for multiple testing, using the procedure of Benjamini and Hochberg. For A549 RNA-seq, batch correction was done using the sva (3.26.0) R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: text files include read counts and differential gene expression analysis
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| Submission date |
May 26, 2020 |
| Last update date |
Jul 24, 2020 |
| Contact name |
Moshe Oren |
| E-mail(s) |
moshe.oren@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Street address |
234 Herzl
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE151200 |
Division of labor between YAP and TAZ in non-small cell lung cancer [RNA] |
| GSE151201 |
Division of labor between YAP and TAZ in non-small cell lung cancer |
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| Relations |
| BioSample |
SAMN15018030 |
| SRA |
SRX8401287 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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