{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jack Barrington"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15344"],"description":["Intracerebral haemorrhage (ICH) is a major area of unmet clinical need. Inflammation is part of a secondary injury phase linked to both brain damage and repair. Here, we looked to identify the major molecular pathways promoting innate immune activation and recruitment in the first day of injury. To do this, we induced ICH in six month old C57BL/6 male mice (n=4) and isolated RNA from the right (ipsilateral) hemisphere 24 hours later. We used RNA isolated from right hemispheres of six month old naive male C57BL/6 mice (n=3) as controls."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The loaded flow cell was then pair-end sequenced (101 + 101 cycles, plus indices) on an Illumina HiSeq4000 instrument.","Nucleic Acid Extraction - RNA was isolated using the RNeasy lipid tissue mini kit (Qiagen) as per manufacturer’s protocol.","Sample Treatment - Naive mice were perfused with PBS and right hemispheres were processed for RNA.","Library Construction - RNA-Seq libraries were generated using the TruSeq Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s instructions.","Sample Treatment - A model of intraparenchymal brain haemorrhage was used that created an active bleed within the brain by using collagenase VII-S (Sigma, C2399) to break down the basal lamina of cerebrovascular beds. To do this, mice were initially induced under anaesthesia using 4 % isoflurane in 70 % N2O and 30 % O2 and fur was shaven from the head. Mice were then transferred to a feedback-controlled heating pad set to 37 ˚C, securely fixed to a stereotactic frame (Stoetling), anaesthesia maintained at 1.5-2.0 % isoflurane in 30 % N2O and 70 % O2 using a nose cone, and Videne (EcoLab) applied to the scalp. A longitudinal midline incision above the skull was performed and periosteum stripped away from the midline on both sides. A burr-hole was created using a micro-drill and a glass micropipette (BLAUBRAND, pulled at 70 ˚C) inserted at the following co-ordinates from bregma: anterior-posterior 0.0 mm, lateral -2.0 mm, deep -2.7 mm. 0.5 µL of 0.09 units µL-1 of collagenase dissolved in saline was then injected at a rate of 1 µL min-1. The needle was left in situ for 10 min before removal and wounds sutured. The scalp was cleaned once more with Videne and a topical analgesia was applied (EMLA cream, AstraZeneca) before animals were given a subcutaneous bolus of saline (10 mL kg-1) and buprenorphine (50 µg kg-1, Vetergesic, UK) before being recovered in 28 ˚C housing. Animals were then transferred to ventilated cages suspended over a heating pad with free access to mashed food and water in normal housing conditions.","Sample Collection - Mice were PBS perfused and right (ipsilateral) hemispheres were extracted and homogenised using lysing matrix D tubes (MPBio) in a Qiagen Tissue Lyser II."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Demultiplexing of the output data (allowing one mismatch) and BCL-to-Fastq conversion was performed with CASAVA 1.8.3. Sequencing quality for each sample was determined using the FastQC program. Low-quality sequence data were removed utilizing the trimmomatic program. STAR v2.4.0 was utilized to map the trimmed sequence into the murine genome (mm10 genome with gencode M16 annotation). Raw counts for each sample were generated by the htseq-count program and subsequently normalized relative to respective library sizes using DESeq2 package for the R statistical program. The DESeq2 program was additionally used to plot the PCA with all sample data to visualize different clusters at multiple levels that describes the maximum variance within the data set. Log2FC values were shrunken using the apeglm estimator. Genes of interest were identified by pairwise comparisons. False discovery rate (FDR) adjusted p values were used to evaluate significance."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Leo Zeef","Jack Barrington"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of ipsilateral mouse brain homogenates 1 day following collagenase-induced ICH vs naive controls","description":"Intracerebral haemorrhage (ICH) is a major area of unmet clinical need. Inflammation is part of a secondary injury phase linked to both brain damage and repair. Here, we looked to identify the major molecular pathways promoting innate immune activation and recruitment in the first day of injury. To do this, we induced ICH in six month old C57BL/6 male mice (n=4) and isolated RNA from the right (ipsilateral) hemisphere 24 hours later. We used RNA isolated from right hemispheres of six month old naive male C57BL/6 mice (n=3) as controls.","dates":{"release":"2025-08-13T00:00:00Z","modification":"2025-08-13T15:37:48.227Z","creation":"2025-07-09T15:03:33.699Z"},"accession":"E-MTAB-15344","cross_references":{"ENA":["ERP175149"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}