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| Status |
Public on Mar 11, 2015 |
| Title |
Mel202 DD-wt-SF3B1 plus Shld (2 days) |
| Sample type |
SRA |
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| Source name |
MEL202 cell line
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| Organism |
Homo sapiens |
| Characteristics |
clone: DD-wt-SF3B1 (2 days)
treatment: plus Shld
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| Extracted molecule |
total RNA |
| Extraction protocol |
The gel-free protocol was employed for the TruSeq RNA Sample Prep Kit per manufacturer’s specifications, and performed on the Beckman Coulter Biomek FXp robotics platform. The standard RNA fragmentation profile was used as recommended by Illumina (94 degrees Celsius for 8 minutes). The PCR-amplified RNA-seq library products were then quantified using the Advanced Analytical Fragment Analyzer Standard Sensitivity NGS Fragment Analysis Kit (catalog number DNF-479). The samples were diluted to 10 nanomolar in Qiagen Elution Buffer (Qiagen material number 1014609), denatured, and loaded at 2.75 picomolar on an Illumina HiSeq2500 in Rapid Run mode using TruSeq Rapid PE Cluster Kit – HS (catalog number PE-402-4001) and TruSeq Rapid SBS Kit – HS (200 cycle) reagents (catalog number FC-402-4001).
The RNA-seq libraries were sequenced at 100 base-pair paired-end with a 7-base-pair index using the standard Illumina primers. The sequence intensity files were generated on the instrument using the Illumina Real Time Analysis software. The intensity files were demultiplexed and fastq files created using the CASAVA 1.8.2 software suite.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
wildtype-SF3B1-specific Degron knockdown
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| Data processing |
Methods are described in detail in "A chemical genetics approach for the functional assessment of novel cancer genes", Zhou et al. (submitted). Briefly, reads were aligned to the reference human genome (hg19) with a modified version of Tophat using UCSC KnownGene as a reference.
For each sample, transcripts were assembled using CLASS with KnownGenes as the reference. All assemblies were then merged with Cuffmerge.
Gene expression was quantified using Cufflinks with the merged CLASS transcripts as the reference.
Expression levels were rescaled so that the upper quantile gene expression value in each sample was 10.
Genome_build: hg19
Supplementary_files_format_and_content: matrix listing rescaled gene expression values, with CLASS/Cuffmerge identifier and HUGO or KnownGene gene if applicable.
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| Submission date |
Mar 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Adnan Derti |
| E-mail(s) |
adnan.derti@gmail.com
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| Organization name |
personal
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| Department |
Bioinformatics
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| Street address |
100 Alden Street
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| City |
Dedham |
| State/province |
MA |
| ZIP/Postal code |
02026 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
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| Relations |
| BioSample |
SAMN03396770 |
| SRA |
SRX950587 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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