{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Shilpee Dutt"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14224"],"description":["Glioblastoma (GBM)is the most aggressive brain tumor with poor overall survival due to high recurrence rate. The recurrent GBM tumors are highly aggressive and resistant to therapy. In the current study, we explored the potential role of Y-box binding protein 3 (YBX3) in glioblastoma aggressiveness. We found significantly high expression of YBX3 in GBM compared to low-grade glioma, and the expression of YBX3 significantly correlated with poor overall and disease-free survival of GBM patients. Knockdown of YBX3 in established GBM primary cultures and cell line abrogated the invasion and migration of GBM cells in vitro, and tumorigenicity and metastasis in vivo. Further, we found high expression of YBX3 in the recurrent GBM patient biopsies. To decipher the genes and biological pathways by which YBX3 regulates the GBM aggressiveness, we performed RNA-Seq experiment on LN229-Relapse and patient-derived primary culture relapse cells (PS1) after stable knockdown of YBX3."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - The suspension was collected in a microcentrifuge tube, and RNA was extracted by adding chloroform and precipitating it with isopropanol. RNA samples were quantitated on a Qubit fluorometer, and appropriate dilutions were loaded onto a high-sensitivity RNA screen tape to determine the RNA integrity number (RIN). Samples with 28S/18S peak integrated area ratios of >2 were used for library preparation.","Sample Collection - Cells were grown to 60% confluence in 10-cm culture dishes, media was removed, and RNA-Isoplus Reagent (Takara Bio) was added to the culture dishes and kept for 2 min on ice for complete cell lysis.","Library Construction - 1.5 μg of QC-verified RNA samples was used for poly (A) mRNA isolation from total RNA using the NEB Next Poly (A) mRNA Kit (Cat. no. NEB# 7490), according to the manufacturer’s protocol. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat. no. E7760L) was used to construct double-stranded cDNA libraries from the polyA RNA fraction using RNA fragmentation, first-strand cDNA synthesis with random primers, second-strand cDNA synthesis, end repair of double-stranded cDNA, adapter ligation, removal of excess adapter using sample purification beads, PCR enrichment of adapter-ligated DNA, and clean-up of PCR products as instructed by the manufacturer. The cleaned libraries were quantitated on a Qubit fluorometer, and appropriate dilutions were loaded on a high-sensitivity D1000 screen tape to determine the size range of the fragments and average library size.","Sequencing - The prepared libraries were sequenced on an Illumina NovaSeq 6000 sequencer to generate 2 × 150 bp reads per sample using the NGS service providers miBiome Therapeutics LLP (Mumbai, India) and Nucleome Informatics Private Limited (Hyderabad, India)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Shilpee Dutt"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of in vitro radio-resistant human GBM cell line (LN229) and patient-derived culture (PS1) post YBX3 knockdown","description":"Glioblastoma (GBM)is the most aggressive brain tumor with poor overall survival due to high recurrence rate. The recurrent GBM tumors are highly aggressive and resistant to therapy. In the current study, we explored the potential role of Y-box binding protein 3 (YBX3) in glioblastoma aggressiveness. We found significantly high expression of YBX3 in GBM compared to low-grade glioma, and the expression of YBX3 significantly correlated with poor overall and disease-free survival of GBM patients. Knockdown of YBX3 in established GBM primary cultures and cell line abrogated the invasion and migration of GBM cells in vitro, and tumorigenicity and metastasis in vivo. Further, we found high expression of YBX3 in the recurrent GBM patient biopsies. To decipher the genes and biological pathways by which YBX3 regulates the GBM aggressiveness, we performed RNA-Seq experiment on LN229-Relapse and patient-derived primary culture relapse cells (PS1) after stable knockdown of YBX3.","dates":{"release":"2025-12-21T00:00:00Z","modification":"2025-12-21T02:02:23.41Z","creation":"2024-07-05T14:37:00.777Z"},"accession":"E-MTAB-14224","cross_references":{"ENA":["ERP161741"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}