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Status |
Public on Jan 12, 2023 |
Title |
H2810_replicate_2_GSK126 |
Sample type |
SRA |
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Source name |
pleura
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Organism |
Homo sapiens |
Characteristics |
tissue: pleura cell line: H2810 genotype: Bap1 wildtype treatment: GSK126 treatment
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Extracted molecule |
total RNA |
Extraction protocol |
for RNA seq: RNA was isolated from tumor cell lines and mouse tumors with the Qiagen All Prep DNA/RNA kit. Quantification and quality assessment for RNA were performed with a Bioanalyzer (RIN >6.5) (Agilent, Santa Clara, CA, USA). for RNAseq: Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
readcounts_human RNAseq_CRM.txt
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Data processing |
Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. The sequence reads were mapped to the mouse genome (mm10) or hg 38, using TopHat (2.0.12). TopHat was run with default. Reads with mapping quality less than 10 and non-primary alignments were discarded. Remaining reads were counted using HTSeq-count. Statistical analysis of the differential expression of genes was performed using DESeq2 Assembly: mm10, Grcm38 Supplementary files format and content: read counts table Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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Submission date |
Jan 08, 2023 |
Last update date |
Jan 12, 2023 |
Contact name |
Jitendra Badhai |
E-mail(s) |
j.badhai@nki.nl
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Organization name |
Netherlands Cancer Institute
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Department |
Division Molecular Genetics
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Lab |
Maarten van Lohuizen
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Street address |
Plesmanlaan 121
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City |
Amsterdam |
ZIP/Postal code |
1066CX |
Country |
Netherlands |
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Platform ID |
GPL16791 |
Series (1) |
GSE222376 |
Genetic screens reveal new targetable vulnerabilities in BAP1-deficient Mesothelioma |
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Relations |
BioSample |
SAMN32634654 |
SRA |
SRX18968848 |
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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