run_metadata: 55493

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
55493	SRR10510887	SRX7199558	SRS5705113	SRP231168	PRJNA591000	RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish	GSE140810	Transcriptome Analysis	Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines chemokines and neurotrophic factors. To identify additional secreted signalling molecules we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.		pubmed:32366533		Sham 2	GSM4186871		tissue:Macrophage lineage cells\|age:4 dpf	Sham 2	Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts filtering on counts per million CPM to avoid artefacts due to library depth. Specifically a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples corresponding to the smallest sample group as defined by Group once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3 Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3 Injury 5 and Injury 6 were removed and filtering and normalisation re performed prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.	Macrophage lineage cells	Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi sham and injured larvae were anaesthesised larval heads were transected the tissue was homogenised and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.	RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.		age:4 dpf	GSM4186871	GSM4186871: Sham 2; Danio rerio; RNA Seq	GSM4186871		1	RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.	GEO Accession:GSM4186871	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP231168			180809_A00291_0059_BH3FLKDRXX_2_11398HL0008L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0008L01_2.fastq.gz	fastq fastq	3597238000.0	35972380.0	GSM4186871 r1	0:50 1:50	A:971087314;C:774572159;G:820049074;T:1031281870;N:247583	50	50			971087314	774572159	820049074	1031281870	247583	SRX7199558	SRS5705113	SRA1000323	GEO	Centre for Discovery Brain Sciences, University of Edinburgh	2	0.85164	0.83175	0.26819	0.26552	0.75621	0.76378	0.52787	0.53623	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United Kingdom	2019-11-21	Larval	Larval	Blood	Hematopoietic System