{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Monika Drobna-Śledzińska"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14919"],"description":["The aim of this study was to investigate the transcriptome of 35 primary samples of pediatric patients diagnosed with T-cell acute lymphoblastic leukemia and 6 samples of healthy T-cell precursor subsets from pediatric donors (3 samples of CD34+ and 3 samples of CD4+ CD8+ thymic subsets). Samples were collected before treatment. Sequencing libraries were obtained with Illumina TruSeq Stranded mRNA protocol, with modified conditions of RNA fragmentation (90°C for 2 minutes). All libraries were sequenced on Illumina NovaSeq6000 platform, in 2x150PE mode (paired end sequencing with 150 nt reads), with a coverage of 150M reads/sample."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated using miRNeasy Kit (Qiagen). RNA isolates were DNase treated and purified with use of RNA Clean and Concentrator Kit (Zymo Research).","Library Construction - Libraries were generated with Illumina TruSeq Stranded mRNA Prep Kit. Modified fragmentation conditions were used (90'C for 2 minutes)","Sequencing - Libraries were sequenced on Illumina NovaSeq6000 platform, using the following settings: 2x150 (paired end sequencing with 150nt reads), depth of coverage: 150M reads/sample (22.5 Gbp/sample).","Sample Collection - Leukemic T-cells were obtained from bone marrow samples by isolation of mononuclear cells, using density gradient centrifugation, followed by immunomagnetic separation, with use of Human T Lymphocyte Enrichment Set-DM (Becton Dickinson) in case of samples with blast percentage below 85%. Thymocyte CD4+ CD8+ and CD34+ samples, obtained from children undergoing cardiac surgery (UZ Gent), were used as controls. Immature CD34+ thymocytes were purified based on MACS purification using CD34 microbeads (Miltenyi Biotec) without lineage depletion, while CD4 and CD8 labeling was used to sort the CD4+ CD8+ double-positive subset by a FACSAriaIII (BDBiosciences). The purity of each subset was at least 98%."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Read counts for individual genes were obtained using featureCounts from the Subread package using the NCBI Reference Sequence transcript database (GCF_000001405.39_GRCh38.p13).","Sequence Alignment - Sequencing reads were aligned to the GRCh38 reference genome using STAR ver. 2.7.3a, with NCBI Reference Sequence transcript database (GCF_000001405.39_GRCh38.p13)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Roman Jaksik","Monika Drobna-Śledzińska","Małgorzata Dawidowska"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic analysis of pediatric T-cell acute lymphoblastic leukemia","description":"The aim of this study was to investigate the transcriptome of 35 primary samples of pediatric patients diagnosed with T-cell acute lymphoblastic leukemia and 6 samples of healthy T-cell precursor subsets from pediatric donors (3 samples of CD34+ and 3 samples of CD4+ CD8+ thymic subsets). Samples were collected before treatment. Sequencing libraries were obtained with Illumina TruSeq Stranded mRNA protocol, with modified conditions of RNA fragmentation (90°C for 2 minutes). All libraries were sequenced on Illumina NovaSeq6000 platform, in 2x150PE mode (paired end sequencing with 150 nt reads), with a coverage of 150M reads/sample.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:55.116Z","creation":"2025-03-07T16:47:18.463Z"},"accession":"E-MTAB-14919","cross_references":{"ENA":["ERP170079"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}