biostudies-arrayexpressMonika Drobna-ŚledzińskaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14919The 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.biostudies-arrayexpressNucleic 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%.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensRoman JaksikMonika Drobna-ŚledzińskaMałgorzata DawidowskafalseTranscriptomic analysis of pediatric T-cell acute lymphoblastic leukemiaThe 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.2025-12-31T00:00:00Z2025-12-31T02:02:55.116Z2025-03-07T16:47:18.463ZE-MTAB-14919ERP170079EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184