run_metadata: 33017

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
33017	SRR29633215	SRX25139204	SRS21831217	SRP516661	PRJNA1129181	A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing	GSE271002	Transcriptome Analysis	To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.		pubmed:40252728		Control ablation 4dpf	GSM8366960		source name:Dissected larval intestines\|tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Control\|geo loc name:missing\|collection date:missing	Control ablation 4dpf	Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files	Dissected larval intestines		Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		tissue:Dissected larval intestines\|cell type:Mix of intestinal cells\|genotype:AB\|treatment:Control	GSM8366960	GSM8366960: Control ablation 4dpf; Danio rerio; RNA Seq	GSM8366960 r1	GSM8366960	1	Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP516661		loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz	Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz	fastq fastq fastq fastq	115286504000.0	360270325.0	GSM8366960 r1	0:150 1:150 2:10 3:10	A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542	150	150	10	10	32679027944	17748865933	17885040590	39764959491	3203542	SRX25139204	SRS21831217	SRA1911905	Karolinska Institutet	Karolinska Institutet	2	0.39015	0.90036	0.10989	0.19421	0.97845	0.79401	0.69547	0.6103	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Sweden	2024-06-27	Larval	Larval	Gut	Digestive System