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
10212,ERR6511331,ERX6138167,ERS7264190,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
10213,ERR6511329,ERX6138165,ERS7264188,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep1,SAMEA9541418,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,cDNA786327,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep1.tar.gz,nanopore,1745399583.0,1644167.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,0:1061.57,A:449704009;C:421915878;G:378879857;T:494899839;N:0,1061,,,,449704009,421915878,378879857,494899839,0,ERX6138165,ERS7264188,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.01112,,0.0,,0.99997,,1.0,,546,,T,,long read,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
10215,ERR6511330,ERX6138166,ERS7264189,ERP131213,PRJEB46978,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159,Other,Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep2,SAMEA9541419,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,cDNA123791,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep2.tar.gz,nanopore,2038398139.0,1955617.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,0:1042.33,A:518369802;C:477535545;G:441294056;T:601198736;N:0,1042,,,,518369802,477535545,441294056,601198736,0,ERX6138166,ERS7264189,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,Embryo,Undetermined,Embryo Imprecise
36739,SRR867022,SRX286270,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish Bcat,Danio rerio boot,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,500Application ReadForward1,SRP022549,,,s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta,SOLiD_native SOLiD_native,9801985250.0,196039705.0,Zebrafish DV patterning Boot,0:50,0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939,50,,,,,,,,,SRX286270,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.59289,,0.09435,,0.92669,,0.7658,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
36740,SRR867023,SRX286271,SRS420566,SRP022549,PRJNA202401,Danio rerio Transcriptome or Gene expression,PRJNA202401,Other,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish,General Sample for Danio rerio,ICH,,strain:wild type,,,,,,,,,Full transcriptome analysis of early dorsoventral DV patterning in zebrafish ICH,Danio rerio ICH,1,RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,500Application ReadForward1,SRP022549,,,s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual,SOLiD_native SOLiD_native,10810535400.0,216210708.0,Zebrafish DV patterning ICH,0:50,0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417,50,,,,,,,,,SRX286271,SRS420566,SRA075737,BAYGEN|NGSP,BAYGEN,1,0.42474,,0.06136,,0.93434,,0.75757,,50,,B,,usable mapping rate,legacy,early,3prime,rrna_depletion,unknown,bulk,unknown,unknown,,Hungary,2013-05-23,Undetermined,Undetermined,Undetermined,Undetermined
66222,SRR16148348,SRX12433220,SRS10400589,SRP339629,PRJNA767802,RNA seq and ATAC seq of WT and Gli3 / zebrafish,PRJNA767802,Other,WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.,,,Replicate 3 RNAseq Gli3 / ,,RNAseq Gli3KO 3,,strain:Gli3 / ex5 3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Gli3 / EGFP cells,6,6,Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339629,,assembly:GRCz11,Gli3KO3_aligned.sorted.bam,bam,5067915101.0,25431299.0,Gli3KO3 aligned.sorted.bam,0:99.63 1:99.65,A:1368455893;C:1172445678;G:1173478123;T:1353535407;N:0,99,99,,,1368455893,1172445678,1173478123,1353535407,0,SRX12433220,SRS10400589,SRA1303956,Rutgers University|Genetics,Rutgers University,2,0.95469,0.95749,0.09504,0.09606,0.73951,0.73963,0.54439,0.54442,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2021-10-01,Hatching,Embryo,Undetermined,Embryo Imprecise
66223,SRR16148349,SRX12433219,SRS10400587,SRP339629,PRJNA767802,RNA seq and ATAC seq of WT and Gli3 / zebrafish,PRJNA767802,Other,WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.,,,Replicate 2 RNAseq Gli3 / ,,RNAseq Gli3KO 2,,strain:Gli3 / ex5 2|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Gli3 / EGFP cells,5,5,Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339629,,assembly:GRCz11,V300059050_Gli3KO2_aligned.cordinatesort.bam,bam,10961381631.0,54976705.0,V300059050 Gli3KO2 aligned.cordinatesort.bam,0:99.70 1:99.68,A:2988819475;C:2499700971;G:2467906402;T:3004531404;N:423379,99,99,,,2988819475,2499700971,2467906402,3004531404,423379,SRX12433219,SRS10400587,SRA1303956,Rutgers University|Genetics,Rutgers University,2,0.94015,0.9439,0.12356,0.12485,0.75315,0.75304,0.51072,0.50897,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2021-10-01,Hatching,Embryo,Undetermined,Embryo Imprecise
66224,SRR16148350,SRX12433218,SRS10400586,SRP339629,PRJNA767802,RNA seq and ATAC seq of WT and Gli3 / zebrafish,PRJNA767802,Other,WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.,,,Replicate 1 RNAseq Gli3 / ,,RNAseq Gli3KO 1,,strain:Gli3 / ex5 1|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Gli3 / EGFP cells,4,4,Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339629,,assembly:GRCz11,V300059050_Gli3KO1_aligned.cordinatesort.bam,bam,10204176056.0,51177828.0,V300059050 Gli3KO1 aligned.cordinatesort.bam,0:99.68 1:99.71,A:2761524632;C:2342024573;G:2322758345;T:2777476126;N:392380,99,99,,,2761524632,2342024573,2322758345,2777476126,392380,SRX12433218,SRS10400586,SRA1303956,Rutgers University|Genetics,Rutgers University,2,0.94248,0.9466,0.11206,0.11246,0.73634,0.73582,0.50038,0.49971,100,91,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2021-10-01,Hatching,Embryo,Undetermined,Embryo Imprecise
66225,SRR16148351,SRX12433217,SRS10400585,SRP339629,PRJNA767802,RNA seq and ATAC seq of WT and Gli3 / zebrafish,PRJNA767802,Other,WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.,,,Replicate 3 RNAseq WT,,RNAseq WT 3,,strain:WT3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: WT EGFP cells,3,3,Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339629,,assembly:GRCz11,Gli3WT3_aligned.sorted.bam,bam,6055778800.0,30391313.0,Gli3WT3 aligned.sorted.bam,0:99.60 1:99.66,A:1632778751;C:1402895889;G:1402788250;T:1617315910;N:0,99,99,,,1632778751,1402895889,1402788250,1617315910,0,SRX12433217,SRS10400585,SRA1303956,Rutgers University|Genetics,Rutgers University,2,0.95971,0.96273,0.09206,0.09219,0.72458,0.72391,0.55162,0.55278,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2021-10-01,Hatching,Embryo,Undetermined,Embryo Imprecise
66226,SRR16148353,SRX12433215,SRS10400584,SRP339629,PRJNA767802,RNA seq and ATAC seq of WT and Gli3 / zebrafish,PRJNA767802,Other,WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.,,,Replicate 2 RNAseq WT,,RNAseq WT 2,,strain:WT2|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: WT EGFP cells,2,2,Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339629,,assembly:GRCz11,Gli3WT2_aligned.sorted.bam,bam,6030526704.0,30274232.0,Gli3WT2 aligned.sorted.bam,0:99.58 1:99.62,A:1627670320;C:1395587022;G:1395639693;T:1611629669;N:0,99,99,,,1627670320,1395587022,1395639693,1611629669,0,SRX12433215,SRS10400584,SRA1303956,Rutgers University|Genetics,Rutgers University,2,0.95942,0.96186,0.08632,0.08652,0.72671,0.72732,0.53408,0.55623,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2021-10-01,Hatching,Embryo,Undetermined,Embryo Imprecise
66227,SRR16148354,SRX12433214,SRS10400582,SRP339629,PRJNA767802,RNA seq and ATAC seq of WT and Gli3 / zebrafish,PRJNA767802,Other,WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.,,,Replicate 1 RNAseq WT,,RNAseq WT 1,,strain:WT1|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: WT EGFP cells,1,1,Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339629,,assembly:GRCz11,V300059050_Gli3WT_aligned.cordinatesort.bam,bam,8907848854.0,44671741.0,V300059050 Gli3WT aligned.cordinatesort.bam,0:99.68 1:99.73,A:2444869517;C:2007841709;G:1991672704;T:2463143463;N:321461,99,99,,,2444869517,2007841709,1991672704,2463143463,321461,SRX12433214,SRS10400582,SRA1303956,Rutgers University|Genetics,Rutgers University,2,0.94004,0.94329,0.13907,0.13978,0.74943,0.74897,0.507,0.5105,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2021-10-01,Hatching,Embryo,Undetermined,Embryo Imprecise