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| Status |
Public on May 03, 2013 |
| Title |
584-A2 DMSO 3 |
| Sample type |
SRA |
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| Source name |
584-A2_DMSO
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 584-A2
cell type: Head and Neck Squamous Cell Carcinoma cells
agent: DMSO
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| Treatment protocol |
Cells were treated with DMSO for a period of 72 hrs and allowed to recover in media for 72 hrs. RNA was isolated at 144 hrs.
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| Growth protocol |
Cells were maintained in Dulbecco's modified Eagle medium (UMSCC25 and CCL30) or RPMI-1640 (584-A2) supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin at 37°C in a 5% CO2 humidified incubator.
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| Extracted molecule |
total RNA |
| Extraction protocol |
4x10^6 cells from each of the cells lines UMSCC25, 584-A2, and CCL30 were plated and transduced 24 hrs later with the SBI shRNA library (Mountain View, CA) and 8 μg/mL polybrene (Sigma-Aldrich) at a multiplicity of infection of ~0.2. After 72 hrs, transfected cells were selected with puromycin (1 μg/mL) for 5 days. Library expressing cells were divided into six groups of 5x106 cells per T-75 flask where three were treated with vehicle (DMSO) and the remaining three groups were treated with AZD12908010 (1.0 μM for UMSCC25, 0.125 μM for 584-A2 and 0.5 μM for CCL30). After 72 hrs, the cells were placed in fresh media without drug for an additional 72 hrs. Total RNA was collected from each replicate using a RNeasy Mini Kit (Qiagen, Germantown, MD) and reverse transcribed using vector specific primers and MMLV reverse transcriptase (Invitrogen, Carlsbad, CA). The cDNA was amplified using nested PCR to isolate the shRNA sequences and to add Illumina adapter sequences. The samples were then sequenced on an Illumina Genome Analyzer IIx (Illumina, San Diego, CA), and shRNA sequences were identified and quantified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Sample 11
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| Data processing |
Basecalls performed using CASAVA
shRNA read were mapped to the SBI shRNA library using Bowtie version 0.12.5
Supplementary_files_format_and_content: read count table (text file) - each shRNA has its mapped read counts
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| Submission date |
Jul 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jihye Kim |
| E-mail(s) |
kim.jihey@gmail.com
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| Phone |
7209755448
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| Organization name |
Cleveland Clinic
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| Department |
Quantitative Health Sciences
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| Street address |
9500 Euclid Ave.
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| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44195 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE39305 |
A receptor tyrosine kinase network comprised of FGFRs, EGFR, ERBB2, and MET drives growth and survival of HNSCC cell lines. |
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| Relations |
| SRA |
SRX159617 |
| BioSample |
SAMN01087496 |
| 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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