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| Status |
Public on Dec 12, 2015 |
| Title |
LN2 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
Lymph node tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: lymph node metastasis
tumor site: lymph node
patient identifier: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
QIAGEN AllPrep DNA and RNA extraction kit.
Ovation RNA-Seq System V2 (Part No. 7102, Nugen Technologies, San Carlos, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Processed data file: P2_LN.txt
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| Data processing |
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 8
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.
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| Submission date |
Dec 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Najeeb Halabi |
| E-mail(s) |
nah2024@qatar-med.cornell.edu
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| Organization name |
Weill Cornell Medicine in Qatar
|
| Street address |
Education City
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| City |
Doha |
| ZIP/Postal code |
24144 |
| Country |
Qatar |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE75935 |
Combined Genome and Transcriptome Sequencing to Identify Allelic Selection in Epithelial Ovarian Cancer |
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| Relations |
| Reanalyzed by |
GSE81474 |
| BioSample |
SAMN04331989 |
| SRA |
SRX1478399 |
| 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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