{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Emily Brockmann"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17287"],"description":["Biomechanical alterations of the extracellular matrix (ECM) and injury-induced or disease-induced cell loss are major contributors to pathological astrocyte activation (astrogliosis) in the CNS and the formation of glial scars. This in vitro experiment is intended to identify transcriptional alterations in mixed glial cultures grown on surfaces of different stiffness (rigid, 650 Pa hydrogel, 250 Pa hydrogel) and also in a confluent mixed glial monolayer on a stiff surface after injury by scratching with a plastic pipette tip.100,000 mixed glial cells were plated on different growth surfaces. After adhesion, confluent monolayers on different hyaluoronic acid/gelatin rigid or hydrogel surfaces were grown in low serum (0.5 % FBS) media for 48 h before RNA extraction. Adherent confluent monolayers on rigid PDL-coated surfaces were left uninjured or scratch-injured and were grown in low serum (0.5 % FBS) media for 48 h before RNA extraction."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA from the cells was isolated from snap-frozen cell pellets using the RNeasy mini kit (Qiagen) with the application of an on-column DNase digestion step. Total RNA was eluted using 35 µL sterile, RNase-free water and the eluate was frozen until further processing for RNA sequencing.","Library Construction - cDNA Libraries were constructed using the Illumina stranded mRNA kit.","Sample Collection - Cells were trypsinized with 0.5 % trypsin for 10 minutes at 37°C and collected by centrifugation at 300 g. Cell pellets were snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.","Sequencing - Libraries were sequenced on an Illumina NovaSeq X Plus platform, generating paired end reads with a length of 159 bp.","Sample Treatment - 100,000 mixed glial cells were plated on different growth surfaces in each well of a 6-well plate. PDL – rigid cell culture plastic surface coated with 0.00075 % w/v poly-D-lysine; PDL scratched – rigid cell culture plastic surface coated with 0.00075 % w/v poly-D-lysine, and the next morning, multiple scratches were applied to injure the confluent cell layer; Rigid OHA/GEL – rigid cell culture plastic surface pre-coated with 0.00075 % w/v poly-D-lysine, followed by coating with a mix of 1.25 % oxidized hyaluronic acid (OHA) and 2.5 % gelatin (GEL); 650 Pa OHA/GEL hydrogel – rigid cell culture plastic surface pre-coated with 0.00075 % w/v poly-D-lysine, followed by a mix of 5.0 % w/v oxidized hyaluronic acid and 2.5 % w/v gelatin and 0.75 % w/v microbial transglutaminase (mTG) for gelation by crosslinking; 250 Pa OHA/GEL hydrogel – rigid cell culture plastic surface pre-coated with 0.00075 % w/v poly-D-lysine, followed by a mix of 1.25 % w/v oxidized hyaluronic acid and 2.5 % w/v gelatin and 0.75 % w/v mTG for gelation by crosslinking. After plating, cells were allowed to attach overnight. On the next morning, medium was changed from DMEM + 10 % FBS (growth medium) to DMEM + 0.5 % FBS (assay medium). For the PDL scratched condition, the confluent cell layer was injured by multiple scratches applied with a 200 µL Eppendorf pipette plastic tip. Cells were allowed to grow in assay medium for 48 hours before cell harvest by trypsination.","Growth Protocol - Cells were propagated for 2 passages in Dulbecco’s modified Eagle’s medium (DMEM) containing 10 % heat-inactivated fetal bovine serum at 37 °C and 5 % CO2."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - Gene expression was then quantifies using featureCounts (version 2.0.1) and Ensembl gene annotations.","Sequence Alignment - Reads were filtered for unwanted RNA species using bwa mem (version 0.7.17). They were then aligned to the mm39 reference genome using STAR (version 2.7.10a)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Maik Hintze","Emily Brockmann"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of mixed glial cultures grown on different growth surfaces","description":"Biomechanical alterations of the extracellular matrix (ECM) and injury-induced or disease-induced cell loss are major contributors to pathological astrocyte activation (astrogliosis) in the CNS and the formation of glial scars. This in vitro experiment is intended to identify transcriptional alterations in mixed glial cultures grown on surfaces of different stiffness (rigid, 650 Pa hydrogel, 250 Pa hydrogel) and also in a confluent mixed glial monolayer on a stiff surface after injury by scratching with a plastic pipette tip.100,000 mixed glial cells were plated on different growth surfaces. After adhesion, confluent monolayers on different hyaluoronic acid/gelatin rigid or hydrogel surfaces were grown in low serum (0.5 % FBS) media for 48 h before RNA extraction. Adherent confluent monolayers on rigid PDL-coated surfaces were left uninjured or scratch-injured and were grown in low serum (0.5 % FBS) media for 48 h before RNA extraction.","dates":{"release":"2026-06-29T00:00:00Z","modification":"2026-07-01T12:40:42.377Z","creation":"2026-06-29T12:38:06.656Z"},"accession":"E-MTAB-17287","cross_references":{"ENA":["ERP195879"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}