{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Anthony Boureux"],"organism":["Homo sapiens"],"software":["MinKNOW software versions 20.06.15"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13763"],"description":["Two sets of 10 samples from patients with CMML were used for this study. The first set (CMML11 to CMML20) includes 10 blood samples supplied by Eric Jourdan (Biological Resource Center CHU-Nimes, France). Peripheral blood mononuclear cells were separated by Ficoll-Hypaque density gradient and preserved in RNA Later. The second set (CMML1 to CMML10), delivered by Eric Solary (Gustave Roussy Institut) consisted of 10 samples from Bone marrow or peripheral blood separated on Fycoll-Hypaque. CD14+ monocytes were then sorted from PBMCs with magnetic beads and the AutoMacs system as previously described by Merlevede et al. (2016).  RNA-seq experiments were performed on the twenty samples described above and libraries have been prepared using the “TruSeq Stranded Total RNA Gold” Kit from Illumina. Whole genome sequencing was performed on 1 CMML (sample 10)  using the Illumina TruSeq DNA PCR-Free Library Preparation Kit.  RNA-Seq full length sequencing were performed on 2 CMMLs (samples 7 and 13) : converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech) and sequenced with the SQK-PBK004 kit (PCR Barcoding kit) on MinION sequencer from Oxford Nanopore Technologies."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - 10 samples from Bone marrow or peripheral blood separated on Fycoll-Hypaque. CD14+ monocytes were then sorted from PBMCs with magnetic beads and the AutoMacs system as previously described by Merlevede et al. (2016)","Nucleic Acid Extraction - Total RNA was isolated using mini RNeasy kit (Qiagen) according to the manufacturer instructions. The quantity and quality of extracted RNA was evaluated using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 BioAnalyzer.","Sequencing - Sequencing was performed with the SQK-PBK004 72-hour sequencing protocol run on the MinION MkIC for each sample, using the FLO-MIN106 flowcell and the MinKNOW software from Oxford Nanopore Technologies.","Library Construction - Libraries have been prepared using the “TruSeq Stranded Total RNA Gold” Kit from Illumina.","Nucleic Acid Extraction - Total DNA was isolated using mini DNAeasy kit (Qiagen) according to the manufacturer instructions. The quantity and quality of extracted DNA was evaluated using the NanoDrop ND-1000 spectrophotometer and the Agilent 2100 BioAnalyzer.","Library Construction - Genomic DNA (1µg) has been used to prepare a library for whole genome sequencing, using the Illumina TruSeq DNA PCR-Free Library Preparation Kit, according to the manufacturer's instructions.","Sequencing - Libraries have been sequenced on a HiSeq2000 platform from Illumina (Illumina Inc., CA, USA), as paired-end 100 bp reads.","Library Construction - 10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards an average of 9 fmol of amplified cDNA was used to prepare library following SQK-PBK004 kit (PCR Barcoding kit; ONT).","Sample Collection - Peripheral blood mononuclear cells were separated by Ficoll-Hypaque density gradient and preserved in RNA Later"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were aligned to the reference genome (human GRCh38) using CRAC software (VN:2.5.0) with the following command line {crac -- no-ambiguity -- stranded -- detailed-sam -i /data/indexes/crac/GRCh38 -k 22 --bam --nb-tags-infos-stored 10000 --nb-threads 15 r fastq/*.fastq.gz}.","Data Transformation - Annotations, classification and metrics used for the filtering process were returned by CracTools-chimCT (https://github.com/Bio2M/cractools-chimct). Some filters based on information provided by the CracTools-chimCT are used to select Chimeric RNA. Among them, the ChimValue, which depends on methodological parameters including the mapping score quality and the number of reads from the predicted chRNA. We consider the support of Spanning Reads (SR), which is the read containing the chimeric junction, the warning flags given by the annotation (pseudogenes, anchored reads, superfamily genes..) and the spanning paired-end information (PE). The file lists all of the predicted chRNAs and pinned in four classes."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["MinION","Illumina HiSeq 2000"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq."],"pubmed_authors":["Anthony Boureux","Florence Rufflé, Jérôme Reboul, Anthony Boureux, Benoit Guibert, Chloé Bessière, Raissa Silva, Eric Jourdan, Jean-Baptiste Gaillard, Anne Boland, Jean-François Deleuze, Catherine Sénamaud-Beaufor, Dorothée Selimoglu-Buet, Eric Solary, Nicolas Gilbert, Thérèse Commes"],"additional_accession":[]},"is_claimable":false,"name":"Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq","description":"Two sets of 10 samples from patients with CMML were used for this study. The first set (CMML11 to CMML20) includes 10 blood samples supplied by Eric Jourdan (Biological Resource Center CHU-Nimes, France). Peripheral blood mononuclear cells were separated by Ficoll-Hypaque density gradient and preserved in RNA Later. The second set (CMML1 to CMML10), delivered by Eric Solary (Gustave Roussy Institut) consisted of 10 samples from Bone marrow or peripheral blood separated on Fycoll-Hypaque. CD14+ monocytes were then sorted from PBMCs with magnetic beads and the AutoMacs system as previously described by Merlevede et al. (2016).  RNA-seq experiments were performed on the twenty samples described above and libraries have been prepared using the “TruSeq Stranded Total RNA Gold” Kit from Illumina. Whole genome sequencing was performed on 1 CMML (sample 10)  using the Illumina TruSeq DNA PCR-Free Library Preparation Kit.  RNA-Seq full length sequencing were performed on 2 CMMLs (samples 7 and 13) : converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech) and sequenced with the SQK-PBK004 kit (PCR Barcoding kit) on MinION sequencer from Oxford Nanopore Technologies.","dates":{"release":"2025-07-22T00:00:00Z","modification":"2025-07-23T00:01:07.766Z","creation":"2024-02-05T12:31:46.419Z"},"accession":"E-MTAB-13763","cross_references":{"pubmed":["39318504"],"ENA":["ERP157153"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1093/nargab/lqae117"]}}