{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nicolas Germain"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15359"],"description":["Recapitulate the myeloid sarcoma gene expression using Gelma hydrogels in leukemic cell lines RNA-seq was performed onleukemic cell lines K562, Molm-13, PL-21, OCI-AML under two conditions (GelMA and control) to assess differential gene expression related to phenotype."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Cell lines were analyzed after 15 days of culture in suspension. Cells within GelMA 5% hydrogels were collected after dissociation with collagenase type I. All samples were stored at −80 °C until RNA extraction.","Library Construction - RNA libraries were prepared using the AccuraCode RNA-Seq Kit (Cat. no. 10710174, Singleron Biotechnologies GmbH) following the manufacturer’s instructions. Polyadenylated mRNA was isolated using AccuraCode beads (Cat. no. 1200030080). cDNA was synthesized with sample-specific barcodes and unique molecular identifiers (UMIs), pooled, and amplified to construct sequencing libraries.","Sequencing - Sequencing was performed on an Illumina NovaSeq X platform using paired-end 150 bp reads, following the manufacturer’s protocol.","Nucleic Acid Extraction - Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. RNA quantity and purity were assessed with a NanoDrop spectrophotometer (260/280 and 260/230 ratios), and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Kit. Only samples with RNA Integrity Number (RIN) greater than 7 were retained for library preparation"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw reads were demultiplexed, trimmed, and aligned to the human GRCh38 reference genome using STAR. Read counts were generated using featureCounts and normalized using the DESeq2 median-of-ratios method."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Microprep kit","Illumina NovaSeq X","accuracode RNA-seq Kit"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Nicolas Germain"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome profiling of myeloid cell lines in Gelatin Methacrylate Hydrogels","description":"Recapitulate the myeloid sarcoma gene expression using Gelma hydrogels in leukemic cell lines RNA-seq was performed onleukemic cell lines K562, Molm-13, PL-21, OCI-AML under two conditions (GelMA and control) to assess differential gene expression related to phenotype.","dates":{"release":"2025-09-01T00:00:00Z","modification":"2025-09-01T01:02:27.514Z","creation":"2025-07-14T13:37:21.264Z"},"accession":"E-MTAB-15359","cross_references":{"ENA":["ERP176757"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}