{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Jack Green"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16723"],"description":["This experiment explored the impact of cell volume increase and regulatory volume decrease (RVD) on the transcriptome of mouse macrophages.  Bone marrow-derived macrophages (BMDMs) were isolated from CX3CR1-cre LRRC8A-flox, or littermate wild-type (CX3CR1-cre negative, LRRC8A flox) mice (PMID: 33216713), or Cre control (CX3CR1-cre positive, no LRRC8A flox) and incubated in DMEM (D6429, Sigma)  (Isotonic, 310 mOsm/kg) or 50% H2O (Hypotonic, 170 mOsm/kg) for 4 hours.   Following hypotonic stimulation, wild-type BMDMs undergo cell swelling and RVD whereas LRRC8A knockout BMDMs fail to undergo RVD and remain swollen."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA samples were assessed for quality and integrity using a 2200 TapeStation (Agilent Technologies) and then libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer's protocol.","Sample Collection - Primary BMDMs from CX3CR1-Cre LRRC8A flox and wild-type littermates (CX3CR1-cre negative, LRRC8A flox) were incubated in DMEM + 50% PBS or 50% H2O for 4 hours.   BMDMs were lysed in RNA lysis buffer (Purelink RNA miniprep kit).","Nucleic Acid Extraction - RNA was isolated using a Purelink RNA miniprep kit following the manufacturer’s instructions.","Sequencing - Briefly, polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads, fragmented using divalent cations under elevated temperature and then reverse transcribed into first strand cDNA using random primers. Second strand cDNA was then synthesized using DNA Polymerase I and Rnase H. Following a single “A” base addition, adapters were ligated to the cDNA fragments, and the products then purified and enriched by PCR to create the final cDNA library. Adapter indices were used to multiplex libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed (allowing one mismatch) and BCL-to-Fastq conversion performed using Illumina's bcl2fastq software, version 2.20.0.422."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Jack Green"],"additional_accession":[]},"is_claimable":false,"name":"Disruption of macrophage cell volume drives inflammatory responses and type I interferon signalling","description":"This experiment explored the impact of cell volume increase and regulatory volume decrease (RVD) on the transcriptome of mouse macrophages.  Bone marrow-derived macrophages (BMDMs) were isolated from CX3CR1-cre LRRC8A-flox, or littermate wild-type (CX3CR1-cre negative, LRRC8A flox) mice (PMID: 33216713), or Cre control (CX3CR1-cre positive, no LRRC8A flox) and incubated in DMEM (D6429, Sigma)  (Isotonic, 310 mOsm/kg) or 50% H2O (Hypotonic, 170 mOsm/kg) for 4 hours.   Following hypotonic stimulation, wild-type BMDMs undergo cell swelling and RVD whereas LRRC8A knockout BMDMs fail to undergo RVD and remain swollen.","dates":{"release":"2026-03-15T00:00:00Z","modification":"2026-03-15T02:04:33.556Z","creation":"2026-03-05T11:18:31.528Z"},"accession":"E-MTAB-16723","cross_references":{"ENA":["ERP189935"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}