ABSTRACT: RNA-Seq data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 75bp paired-end protocol to a minimum mean reads of 50 million.
Project description:WGS cancer data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 50x.
Project description:WGS blood data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 67 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x.
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net ) | Human genome-wide CIT-aCGH-V6-4.4K : 67 glioblastomas | Submitter : Aurelien de Reynies <reyniesa@ligue-cancer.fr> | Project leader : Francois Berger <fberger@ujf-grenoble.fr>
Project description:The goal of this study was to investigate molecular pathways associated with PDE10A in ovarian cancer. We used CRISPR/Cas9 to knockout PDE10A in SKOV3 cells. We used the Illumina NextSeq500 to generate between 30-35 million paired end 75bp sequencing reads per sample for transcript level abundance.
Project description:We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation timeseries. We detected 13,689 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Analysis of transcript expression over the timeseries revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development.
Project description:We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation timeseries. We detected 13,689 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Analysis of transcript expression over the timeseries revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development. Timeseries of C2C12 myoblast RNA-Seq
Project description:Total RNA was isolated from mouse Asxl2-/- and WT LK cells following standard protocol with TRIZol reagent (Life Technologies) followed by RNA library preparation with the Illumina TruSeq strand-specific mRNA sample preparation system. All RNA-seq libraries were sequenced with a read length of single-end 75bp using the Illumina NextSeq 500, and final of over 45 million reads per sample.
Project description:A Cartes d'Identite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net: mRNA profiles were obtained using HumanGeneChip HG-U133 Plus 2.0 arrays (Affymetrix) for the 67 samples from the study (63 MPM tumors and 4 normal pleural samples). We used the RMA algorithm (Bioconductor affy package) to normalize the data. For each gene symbol, probe with the highest expression variance was kept.
Project description:To verify genes that are directly regulated by BysR, we used DNA affinity purification sequencing analysis (DAP-seq) for genome-wide recognition of BysR binding sites in vitro. The HALO-fusion BysR protein was successfully expressed and purified. After affinity purification and sequencing, at least 22 million double-end reads per sample were generated and with > 99 % of reads uniquely mapped to the JP2-270 genome. A total of 470 enriched common peaks of two replicates with –log10(P-value) ≥ 2 were called . The mean width of DAP-seq peaks was < 1,000. In total, 367 (78%) of these peaks were found to locate in the -1 kbp to 1 kbp regions by the analysis of peak summit positions relative to the start codons of JP2-270 open reading frames.
Project description:Comparison of Gene Expression in Uterine Smooth Muscle Tumors (including normal myometrium, benign uterine leiomyoma, malignant uterine and extra-uterine leiomyosarcoma). Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis.
