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
10176,ERR5858457,ERX5504346,ERS6343450,ERP128749,PRJEB44676,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10390,Transcriptome Analysis,To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Naive,SAMEA8658904,University Of Edinburgh,ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10390:Naive p,Naive p,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128749,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,Naive.bam,bam,44972162730.0,499690697.0,E MTAB 10390:Naive,0:90,A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100,90,,,,13658826375,8733304343,9348137569,13228064343,3830100,ERX5504346,ERS6343450,ERA4142789,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.89428,,0.32693,,0.75276,,0.5314,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-05-24,Larval,Larval,Spinal Cord,Nervous System
26536,SRR26130973,SRX21844394,SRS18942411,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X49 2,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 6|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo6,10X49 2,10X49 2,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X49_2_S5_L001_R1_001.fastq.gz 10X49_2_S5_L001_R2_001.fastq.gz 10X49_2_S5_L002_R1_001.fastq.gz 10X49_2_S5_L002_R2_001.fastq.gz 10X49_2_S5_L003_R1_001.fastq.gz 10X49_2_S5_L003_R2_001.fastq.gz 10X49_2_S5_L004_R1_001.fastq.gz 10X49_2_S5_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3126113844.0,37215641.0,10X49 2 S5 L001 R1 001.fastq.gz,0:28 1:56,A:898881980;C:657306128;G:664563758;T:905262774;N:99204,28,56,,,898881980,657306128,664563758,905262774,99204,SRX21844394,SRS18942411,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01241,0.88203,0.00542,0.35268,0.98129,0.7586,0.40274,0.5074,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26537,SRR26130974,SRX21844393,SRS18942407,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X49 1,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 5|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo5,10X49 1,10X49 1,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X49_1_S4_L001_R1_001.fastq.gz 10X49_1_S4_L001_R2_001.fastq.gz 10X49_1_S4_L002_R1_001.fastq.gz 10X49_1_S4_L002_R2_001.fastq.gz 10X49_1_S4_L003_R1_001.fastq.gz 10X49_1_S4_L003_R2_001.fastq.gz 10X49_1_S4_L004_R1_001.fastq.gz 10X49_1_S4_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3315364752.0,39468628.0,10X49 1 S4 L001 R1 001.fastq.gz,0:28 1:56,A:957164498;C:690985782;G:704099796;T:963009918;N:104758,28,56,,,957164498,690985782,704099796,963009918,104758,SRX21844393,SRS18942407,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.0143,0.88325,0.00601,0.35854,0.97816,0.75868,0.4158,0.50825,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26538,SRR26130975,SRX21844392,SRS18942399,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X47 2,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 4|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo4,10X47 2,10X47 2,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X47_2_S2_L001_R1_001.fastq.gz 10X47_2_S2_L001_R2_001.fastq.gz 10X47_2_S2_L002_R1_001.fastq.gz 10X47_2_S2_L002_R2_001.fastq.gz 10X47_2_S2_L003_R1_001.fastq.gz 10X47_2_S2_L003_R2_001.fastq.gz 10X47_2_S2_L004_R1_001.fastq.gz 10X47_2_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3525979800.0,41975950.0,10X47 2 S2 L001 R1 001.fastq.gz,0:28 1:56,A:1030048762;C:725438274;G:855378888;T:915005070;N:108806,28,56,,,1030048762,725438274,855378888,915005070,108806,SRX21844392,SRS18942399,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.0126,0.69252,0.00546,0.25721,0.98005,0.85295,0.39068,0.51992,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26539,SRR26130976,SRX21844391,SRS18942406,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X47 1,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 3|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo3,10X47 1,10X47 1,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X47_1_S1_L001_R1_001.fastq.gz 10X47_1_S1_L001_R2_001.fastq.gz 10X47_1_S1_L002_R1_001.fastq.gz 10X47_1_S1_L002_R2_001.fastq.gz 10X47_1_S1_L003_R1_001.fastq.gz 10X47_1_S1_L003_R2_001.fastq.gz 10X47_1_S1_L004_R1_001.fastq.gz 10X47_1_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,3288490212.0,39148693.0,10X47 1 S1 L001 R1 001.fastq.gz,0:28 1:56,A:950740376;C:692224998;G:723085676;T:922337432;N:101730,28,56,,,950740376,692224998,723085676,922337432,101730,SRX21844391,SRS18942406,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01086,0.86383,0.0052,0.31674,0.98244,0.78309,0.39399,0.52299,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26540,SRR26130977,SRX21844390,SRS18942410,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X39 2,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 2|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo2,10X39 2,10X39 2,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X39_2_S2_L001_R1_001.fastq.gz 10X39_2_S2_L001_R2_001.fastq.gz 10X39_2_S2_L002_R1_001.fastq.gz 10X39_2_S2_L002_R2_001.fastq.gz 10X39_2_S2_L003_R1_001.fastq.gz 10X39_2_S2_L003_R2_001.fastq.gz 10X39_2_S2_L004_R1_001.fastq.gz 10X39_2_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,20594785932.0,245176023.0,10X39 2 S2 L001 R1 001.fastq.gz,0:28 1:56,A:5909286071;C:4378110318;G:4489721587;T:5804002561;N:13665395,28,56,,,5909286071,4378110318,4489721587,5804002561,13665395,SRX21844390,SRS18942410,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01117,0.90005,0.00416,0.25843,0.98056,0.77926,0.45338,0.53366,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System
26541,SRR26130978,SRX21844389,SRS18942405,SRP462307,PRJNA1019490,Single Cell RNA seq of Zebrafish Hypothalamus,PRJNA1019490,Other,Brain nuclei are traditionally defined by their anatomy  activity  and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions  ranging from sleep and wakefulness to feeding  stress  and reward in all vertebrates.,,,,,10X39 1,,breed:NA|age:Adult|collection date:2021|geo loc name:Israel|sex:not applicable|tissue:Brain Hypothalamus|sample type:single cell 1|BioSampleModel:Model organism or animal,,,,,,,,,SC ZF Hypo1,10X39 1,10X39 1,we worked swiftly with cold  well oxygenated solutions  optimizing Papain incubation times for tissue age and brain region. We used caution with Ca2+ and Mg2+ in aCSF to avoid RNA extraction/RT interference  favoring Ca2+/Mg2+ free aCSF if not diluted downstream. Modified aCSF had specific component concentrations  and our materials included essential equipment and anesthesia. We prepared aCSF from an 8x stock with adjusted CaCl2 and MgSO4 concentrations  kept it fresh  and oxygenated it. The zebrafish procedure began with lethal anesthesia  brain dissection in ice cold aCSF  embedding in 1.5% gel  and vibratome sectioning. Tissue was dissociated in the Papain vial  triturated  filtered  and washed  followed by centrifugation. The pellet was resuspended in aCSF with DNase  assessed for cell viability  counted  and diluted for use.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP462307,,,10X39_1_S1_L004_R2_001.fastq.gz 10X39_1_S1_L004_R1_001.fastq.gz 10X39_1_S1_L003_R2_001.fastq.gz 10X39_1_S1_L003_R1_001.fastq.gz 10X39_1_S1_L002_R2_001.fastq.gz 10X39_1_S1_L002_R1_001.fastq.gz 10X39_1_S1_L001_R2_001.fastq.gz 10X39_1_S1_L001_R1_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,13293718116.0,158258549.0,10X39 1 S1 L001 R1 001.fastq.gz,0:28 1:56,A:3791388201;C:2833705086;G:2863082386;T:3796683434;N:8859009,28,56,,,3791388201,2833705086,2863082386,3796683434,8859009,SRX21844389,SRS18942405,SRA1717104,Technion - Israel Institute of Technology|Neuroscince,Technion - Israel Institute of Technology,2,0.01078,0.90504,0.00392,0.24179,0.98098,0.77741,0.42922,0.52858,28,56,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_generic,generic-scrnaseq-only,,Israel,2023-09-21,Adult,Adult,Brain,Nervous System