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| Status |
Public on Dec 26, 2018 |
| Title |
3002R |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD 20+ DLBCL
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cryopreserved tumour samples was extracted using the iPrep Trizol® Plus RNA kit (Life Technologies)
Library was prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology) with an input total RNA of 1µg
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Fusion transcripts were detected using three different approaches: tophat-fusion, defuse, and EASANA fusion (GenoSplice technology)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2014_2 were also provide
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| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pierre de la Grange |
| E-mail(s) |
pierre.delagrange@genosplice.com
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| Organization name |
GenoSplice technology
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| Department |
Paris Biotech Santé
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| Street address |
29, rue du Faubourg Saint-Jacques
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| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE81816 |
Identification of novel recurrent ETV6-IGH fusions in primary central nervous system lymphoma using high throughput RNA sequencing |
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| Relations |
| BioSample |
SAMN05171570 |
| SRA |
SRX1797721 |
| 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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