run_metadata: 61443

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
61443	SRR12774413	SRX9244924	SRS7477617	SRP286401	PRJNA667451	Cellular drivers of injury response and regeneration in the adult zebrafish heart	GSE159032	Transcriptome Analysis	We dissected cell type diversity in the regenerating zebrafish heart by single cell transcriptomics and discovered a high complexity of cell types specifically among the non muscle cells. Based on spatiotemporal information we systematically identified potential cellular regulators of cardiomyocyte regeneration including several fibroblast like cell types that express pro regenerative factors. We used high throughput lineage tracing12 to determine the origin of cell types in the regenerative niche. We showed that the endocardium like the epicardium gives rise to several distinct fibroblast cell types and found that this process is regulated by Wnt signalling. Our results reveal an unexpected functional specialization of fibroblast cell types during the regenerative process. Overall design: Single cell RNA seq of uninjured and injured / wnt inhibited and non inhibited zebrafish hearts. CRISPR based lineage tracing in a subset of these hearts. RNA velocity analysis in a subset of these hearts.		pubmed:35864193		Injured heart Hr20 scar	GSM4817981		source name:Heart tissue\|tissue:heart\|condition:Injured\|treatment:non treated\|strain:Zebrabow M\|10x chemistry version:v2	Injured heart Hr20 scar	Demultiplexing of the illumina sequencing results using cellranger 3.0.2 Mapping using cellranger 3.0.2 Filtering Normalizing and Clustering using seurat 3.0 Scar processing steps see Spanjaard et al. 2018 Nature Biotechnology Briefly scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single cell transcriptome data see previous paragraph. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing we selected only the most prevalent scar for each combination of barcode and UMI only the most prevalent UMI for each barcode and scar and only the most prevalent barcode for each UMI and scar. We then assessed similar Hamming distance of 2 or less scar sequences in each cell only keeping both if they obey criteria designed to test whether both sequences are verifiably correct see Spanjaard et al. for details. Finally we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type. scvelo velocyto.py for RNA velocity analysis Genome build: GRCz11 Supplementary files format and content: h5: HDF5 Feature Barcode Matrix Format Single cell transcript count table with list of cell barcodes and gene names Supplementary files format and content: csv format: List of scar transcripts with CIGAR cell name cell barcode and UMI sequence Supplementary files format and content: csv: list of scars used for tree building with scar sequence cell barcode library cell name number of reads CIGAR UMI sequence number of libraries where the scar is present in at least two cells creation probability number of embryo libraries from LINNAEUS in which this scar is observed and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building only the columns “Cell” “p” and “Scar” are necessary. Supplementary files format and content: loom: output from velocyto.py http://velocyto.org	Heart tissue	Cryoinjury: First fish were pre sedated in water containing 0.03 mg/ml Tricaine PHARMAQ pH 7. Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart a small incision was made through the body wall and the pericardium using microdissection forceps and scissors. Once the pericardial sac was opened the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper not allowing fish skin to dry. Then a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes. Wnt inhibition: IWR 1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild type fish were injected intraperitoneally with 25μl of 10μM IWR 1 in PBS or DMSO 0.1% in PBS10. The injection was performed at xxxdpi 2dpi for the 3dpi analysis and for later time points once every two days from 2dpi until the day of sacrifice.	The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 °C for 30 min in 500µl HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500µl cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4°C and washed two times with 500µl cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35µm diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics	Zebrafish were bred raised and maintained in accordance with the guidelines of the Max Delbrück Center for Molecular Medicine and the local authority for animal protection Landesamt für Gesundheit und Soziales Berlin Germany for the use of laboratory animals and followed the ‘Principles of Laboratory Animal Care’ NIH publication no. 86 23 revised 1985 as well as the current version of German Law on the Protection of Animals. Zebrafish strains AB were used for cryoinjury procedure and behavioral analysis.	tissue:heart\|condition:Injured\|xxx post injury dpi:30\|treatment:non treated\|strain:Zebrabow M\|10x chemistry version:v2	GSM4817981	GSM4817981: Injured heart Hr20 scar; Danio rerio; RNA Seq	GSM4817981		1	The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium ventricle and bulbus arteriosus except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. postwards the tissue was opened carefully with forceps and the heart tissue was incubated at 37 °C for 30 min in 500µl HBSS containing Liberase enzyme mix Sigma Aldrich 0.26 U/mL final concentration and Pluronic F 68 Thermo Fisher Scientific 0.1% while shaking at 750 r.p.m. with intermittent pipette mixing. post most of the tissue was dissociated the reaction was stopped by adding 500µl cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4°C and washed two times with 500µl cold HBSS containing 0.05% BSA then filtered through a cell strainer of 35µm diameter. The quality of the single cell suspension was then confirmed under the microscope and cells were counted prior to scRNA seq library preparation. Library were constructed following the manufacturer's protocols 10X Genomics	GEO Accession:GSM4817981	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP286401			Hr20_30dpi_scar_R1.fastq.gz Hr20_30dpi_scar_R2.fastq.gz	fastq fastq	1734128220.0	13984905.0	GSM4817981 r1	0:26 1:98	A:504149488;C:546423208;G:375429746;T:307316098;N:809680	26	98			504149488	546423208	375429746	307316098	809680	SRX9244924	SRS7477617	SRA1138631	GEO	Junker lab, Berlin Institute for Medical Systems Biology, Max-Delbueck-Center Berlin	2	0.00023	0.00304	0.00021	0.00021	0.99997	0.99671	0.0	0.69251	26	98	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Germany	2020-10-05	Undetermined	Embryo	Heart	Cardiovascular System