biostudies-arrayexpressLluis HernandezHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17232RNAseq was performed on 3 primary CLL paired samples with LINC00152 silencing vs Scrambled controls either growing in presence of a mix of micorenvironment- related agonist factor mix and Ibrutinib drug, as in a control (DMSO) medium without such factors/drug.biostudies-arrayexpressGrowth Protocol - Cells were seeded in a growth medium (RPMI1640, 10%FBS, with IL-2 (1.54 ng/mL) and CpG-ODN (0.38 mg/mL) to avoid spontaneous apoptosis.Sample Collection - Cryopreserved samples were thawed and purified with EasySep™ Human B Cell Enrichment Kit II (StemCell Technologies) to obtain ≥85–90% tumor puritySample Treatment - Paired treatments included DMSO vs agonist mix (as in Jayappa et al:PMID29034364), with CpG-ODN20006 (InvivoGen), Mega-CD40L (Enzo Biosciences), and IL-10 (Peprotech), and also including Ibrutinib (1μM). On both treatments silencing of LINC00152 was performed using two Locked Nucleic Acid (LNA) Gapmers (Exiqon) vs Scrambled control gapmer treatment, 1 μM Gapmer each for 3 days.Sequencing - Libraries were sequenced using a NextSeq2000 (Illumina, Inc.) in paired-end mode with a read length of 2×50 bp. More than 50 milions of paired-end reads were obtained for each sample/conditionLibrary Construction - Stranded mRNA libraries have been generated from 100 ng of total RNA using the Illumina® Stranded mRNA Prep Ligation kit (following the manufacturer’s instructions).Nucleic Acid Extraction - Total RNA extraction protocol was performed with RNeasy Plus mini kit (Qiagen)OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - The high throughput sequence alignment protocol was performed using the tool Kallisto.Data Transformation - The normalization data transformation protocol used was performed with the DESeq2 workflowMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2000RNA-seq of coding RNAHomo sapiensLINC00152 is a lncRNA modulated by microenvironmental stimuli that has pathogenetic and clinical relevance in CLLLluis HernandezTamara Bittolo, Riccardo Bomben, Cristina Martínez-Muñoz, Ruslana Shadrina, Robel Papotti, Filippo Vit, Federico Pozzo, Darío Romero, Amani Dhiflaoui, Patricia Fernández-Guzmán, Blanca De Moner, Núria Vilardell-Timoneda, Ian Márquez-López, Ariadna Giró, Ares Martínez-Farran, Ruth Orellana, Virginia Amador, Ferran Nadeu, Juan A. Piñeyroa, Dolors Colomer, Julio Delgado, Sílvia Beà, Elias Campo, Valter Gattei, Lluís HernándezfalseMicroenvironment-related long non-coding RNAs (LINC00152) in CLLRNAseq was performed on 3 primary CLL paired samples with LINC00152 silencing vs Scrambled controls either growing in presence of a mix of micorenvironment- related agonist factor mix and Ibrutinib drug, as in a control (DMSO) medium without such factors/drug.2026-08-15T00:00:00Z2026-08-15T15:10:53.193Z2026-06-24T13:42:13.369ZE-MTAB-17232ERP195677EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969