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
58876,SRR11519059,SRX8090404,SRS6457255,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 8h,GSM4467035,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 8h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467035,GSM4467035: zfishRibo0wt 8h; Danio rerio; RNA Seq,GSM4467035,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467035,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_8h.fastq.gz,fastq,2563906360.0,33735610.0,GSM4467035 r1,0:76 1:0,A:590255680;C:624101877;G:608571176;T:740906665;N:70962,76,0,,,590255680,624101877,608571176,740906665,70962,SRX8090404,SRS6457255,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.94866,,0.2361,,0.74771,,0.53846,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58877,SRR11519058,SRX8090403,SRS6457254,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 7h,GSM4467034,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 7h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467034,GSM4467034: zfishRibo0wt 7h; Danio rerio; RNA Seq,GSM4467034,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467034,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_7h.fastq.gz,fastq,2491297176.0,32780226.0,GSM4467034 r1,0:76 1:0,A:571076928;C:610953845;G:621275453;T:687921883;N:69067,76,0,,,571076928,610953845,621275453,687921883,69067,SRX8090403,SRS6457254,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.89902,,0.20302,,0.75806,,0.55195,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58878,SRR11519057,SRX8090402,SRS6457252,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 6h,GSM4467033,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 6h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467033,GSM4467033: zfishRibo0wt 6h; Danio rerio; RNA Seq,GSM4467033,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467033,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_6h.fastq.gz,fastq,2493888016.0,32814316.0,GSM4467033 r1,0:76 1:0,A:559295503;C:631458142;G:596937380;T:706126363;N:70628,76,0,,,559295503,631458142,596937380,706126363,70628,SRX8090402,SRS6457252,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95152,,0.21188,,0.74221,,0.53579,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58879,SRR11519056,SRX8090401,SRS6457253,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 5h,GSM4467032,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467032,GSM4467032: zfishRibo0wt 5h; Danio rerio; RNA Seq,GSM4467032,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467032,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_5h.fastq.gz,fastq,2863999124.0,37684199.0,GSM4467032 r1,0:76 1:0,A:639720186;C:714899862;G:693238952;T:816060855;N:79269,76,0,,,639720186,714899862,693238952,816060855,79269,SRX8090401,SRS6457253,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95365,,0.16575,,0.73448,,0.54672,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58880,SRR11519055,SRX8090400,SRS6457251,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 4h,GSM4467031,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 4h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467031,GSM4467031: zfishRibo0wt 4h; Danio rerio; RNA Seq,GSM4467031,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467031,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_4h.fastq.gz,fastq,2533223184.0,33331884.0,GSM4467031 r1,0:76 1:0,A:569364722;C:632186324;G:613168396;T:718432798;N:70944,76,0,,,569364722,632186324,613168396,718432798,70944,SRX8090400,SRS6457251,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95769,,0.13224,,0.74361,,0.52423,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58881,SRR11519054,SRX8090399,SRS6457250,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 3h,GSM4467030,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 3h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467030,GSM4467030: zfishRibo0wt 3h; Danio rerio; RNA Seq,GSM4467030,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467030,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_3h.fastq.gz,fastq,2541195888.0,33436788.0,GSM4467030 r1,0:76 1:0,A:558746776;C:641083540;G:621728982;T:719565542;N:71048,76,0,,,558746776,641083540,621728982,719565542,71048,SRX8090399,SRS6457250,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96383,,0.07472,,0.75911,,0.53085,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58882,SRR11519053,SRX8090398,SRS6457248,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 2h,GSM4467029,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 2h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467029,GSM4467029: zfishRibo0wt 2h; Danio rerio; RNA Seq,GSM4467029,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467029,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_2h.fastq.gz,fastq,2547048496.0,33513796.0,GSM4467029 r1,0:76 1:0,A:558670296;C:645907430;G:621049936;T:721349864;N:70970,76,0,,,558670296,645907430,621049936,721349864,70970,SRX8090398,SRS6457248,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96389,,0.07455,,0.76,,0.5204,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58883,SRR11519052,SRX8090397,SRS6457249,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 1h,GSM4467028,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 1h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467028,GSM4467028: zfishRibo0wt 1h; Danio rerio; RNA Seq,GSM4467028,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467028,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_1h.fastq.gz,fastq,2275344240.0,29938740.0,GSM4467028 r1,0:76 1:0,A:500070609;C:581032656;G:552335537;T:641843953;N:61485,76,0,,,500070609,581032656,552335537,641843953,61485,SRX8090397,SRS6457249,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96342,,0.07649,,0.75875,,0.52233,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58884,SRR11519051,SRX8090396,SRS6457247,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishRibo0wt 0h,GSM4467027,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:ribosomal depletion,zfishRibo0wt 0h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:ribosomal depletion,GSM4467027,GSM4467027: zfishRibo0wt 0h; Danio rerio; RNA Seq,GSM4467027,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishRibo0wt_0h.fastq.gz,fastq,2501315724.0,32912049.0,GSM4467027 r1,0:76 1:0,A:558030973;C:625466039;G:640038484;T:677712201;N:68027,76,0,,,558030973,625466039,640038484,677712201,68027,SRX8090396,SRS6457247,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.89966,,0.07039,,0.76067,,0.53601,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58885,SRR11519050,SRX8090395,SRS6457246,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 8h,GSM4467026,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 8h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:8|treatment:n1|rna extraction protocol:poly A capture,GSM4467026,GSM4467026: zfishPolyAwt 8h; Danio rerio; RNA Seq,GSM4467026,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_8h.fastq.gz,fastq,2429894268.0,31972293.0,GSM4467026 r1,0:76 1:0,A:584937045;C:568630282;G:592436865;T:683842155;N:47921,76,0,,,584937045,568630282,592436865,683842155,47921,SRX8090395,SRS6457246,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95736,,0.15618,,0.75418,,0.52643,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58886,SRR11519049,SRX8090394,SRS6457244,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 7h,GSM4467025,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 7h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7|treatment:n1|rna extraction protocol:poly A capture,GSM4467025,GSM4467025: zfishPolyAwt 7h; Danio rerio; RNA Seq,GSM4467025,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_7h.fastq.gz,fastq,2281973188.0,30025963.0,GSM4467025 r1,0:76 1:0,A:516000892;C:564004239;G:579333444;T:622588743;N:45870,76,0,,,516000892,564004239,579333444,622588743,45870,SRX8090394,SRS6457244,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95915,,0.16556,,0.76386,,0.55386,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58887,SRR11519048,SRX8090393,SRS6457245,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 6h,GSM4467024,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 6h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6|treatment:n1|rna extraction protocol:poly A capture,GSM4467024,GSM4467024: zfishPolyAwt 6h; Danio rerio; RNA Seq,GSM4467024,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_6h.fastq.gz,fastq,2454586516.0,32297191.0,GSM4467024 r1,0:76 1:0,A:567790148;C:604134902;G:616413817;T:666199328;N:48321,76,0,,,567790148,604134902,616413817,666199328,48321,SRX8090393,SRS6457245,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96147,,0.15865,,0.75818,,0.54565,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58888,SRR11519047,SRX8090392,SRS6457243,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 5h,GSM4467023,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5|treatment:n1|rna extraction protocol:poly A capture,GSM4467023,GSM4467023: zfishPolyAwt 5h; Danio rerio; RNA Seq,GSM4467023,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_5h.fastq.gz,fastq,2380658352.0,31324452.0,GSM4467023 r1,0:76 1:0,A:550918628;C:580438305;G:597695173;T:651558275;N:47971,76,0,,,550918628,580438305,597695173,651558275,47971,SRX8090392,SRS6457243,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95989,,0.13789,,0.74341,,0.53449,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58889,SRR11519046,SRX8090391,SRS6457242,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 4h,GSM4467022,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 4h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4|treatment:n1|rna extraction protocol:poly A capture,GSM4467022,GSM4467022: zfishPolyAwt 4h; Danio rerio; RNA Seq,GSM4467022,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_4h.fastq.gz,fastq,2502092216.0,32922266.0,GSM4467022 r1,0:76 1:0,A:548423476;C:643758588;G:642975850;T:666884976;N:49326,76,0,,,548423476,643758588,642975850,666884976,49326,SRX8090391,SRS6457242,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96016,,0.13161,,0.75891,,0.55871,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58890,SRR11519045,SRX8090390,SRS6457241,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 3h,GSM4467021,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 3h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3|treatment:n1|rna extraction protocol:poly A capture,GSM4467021,GSM4467021: zfishPolyAwt 3h; Danio rerio; RNA Seq,GSM4467021,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_3h.fastq.gz,fastq,2608496776.0,34322326.0,GSM4467021 r1,0:76 1:0,A:571388906;C:671364625;G:682368179;T:683322566;N:52500,76,0,,,571388906,671364625,682368179,683322566,52500,SRX8090390,SRS6457241,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96969,,0.15298,,0.78098,,0.56768,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58891,SRR11519044,SRX8090389,SRS6457240,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 2h,GSM4467020,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 2h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2|treatment:n1|rna extraction protocol:poly A capture,GSM4467020,GSM4467020: zfishPolyAwt 2h; Danio rerio; RNA Seq,GSM4467020,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_2h.fastq.gz,fastq,2260403400.0,29742150.0,GSM4467020 r1,0:76 1:0,A:522189473;C:552060968;G:566138267;T:619970621;N:44071,76,0,,,522189473,552060968,566138267,619970621,44071,SRX8090389,SRS6457240,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96297,,0.08765,,0.78399,,0.5331,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58892,SRR11519043,SRX8090388,SRS6457239,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 1h,GSM4467019,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 1h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:1|treatment:n1|rna extraction protocol:poly A capture,GSM4467019,GSM4467019: zfishPolyAwt 1h; Danio rerio; RNA Seq,GSM4467019,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_1h.fastq.gz,fastq,2028859368.0,26695518.0,GSM4467019 r1,0:76 1:0,A:459973220;C:509741356;G:517627384;T:541479126;N:38282,76,0,,,459973220,509741356,517627384,541479126,38282,SRX8090388,SRS6457239,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96767,,0.10368,,0.81858,,0.54455,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58893,SRR11519042,SRX8090387,SRS6457238,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,zfishPolyAwt 0h,GSM4467018,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:poly A capture,zfishPolyAwt 0h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:0|treatment:n1|rna extraction protocol:poly A capture,GSM4467018,GSM4467018: zfishPolyAwt 0h; Danio rerio; RNA Seq,GSM4467018,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,zfishPolyAwt_0h.fastq.gz,fastq,2169902904.0,28551354.0,GSM4467018 r1,0:76 1:0,A:474038869;C:559780620;G:574573413;T:561466815;N:43187,76,0,,,474038869,559780620,574573413,561466815,43187,SRX8090387,SRS6457238,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96674,,0.163,,0.82217,,0.613,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58894,SRR11519041,SRX8090386,SRS6457237,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 7h,GSM4467017,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 7h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467017,GSM4467017: TreatedAamanitin zfishPolyAalpha 7h; Danio rerio; RNA Seq,GSM4467017,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467017,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_7h.fastq.gz,fastq,2361788996.0,31076171.0,GSM4467017 r1,0:76 1:0,A:550131486;C:580761959;G:573878255;T:656632345;N:384951,76,0,,,550131486,580761959,573878255,656632345,384951,SRX8090386,SRS6457237,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96384,,0.06318,,0.79511,,0.51195,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58895,SRR11519040,SRX8090385,SRS6457236,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 7.5h,GSM4467016,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:7.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 7.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:7.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467016,GSM4467016: TreatedAamanitin zfishPolyAalpha 7.5h; Danio rerio; RNA Seq,GSM4467016,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467016,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_7.5h.fastq.gz,fastq,2405402204.0,31650029.0,GSM4467016 r1,0:76 1:0,A:529762191;C:612570337;G:631609968;T:631055682;N:404026,76,0,,,529762191,612570337,631609968,631055682,404026,SRX8090385,SRS6457236,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.9627,,0.13637,,0.80726,,0.55163,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58896,SRR11519039,SRX8090384,SRS6457234,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 6h,GSM4467015,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 6h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467015,GSM4467015: TreatedAamanitin zfishPolyAalpha 6h; Danio rerio; RNA Seq,GSM4467015,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467015,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_6h.fastq.gz,fastq,2482330696.0,32662246.0,GSM4467015 r1,0:76 1:0,A:568483604;C:615759760;G:619464491;T:678208852;N:413989,76,0,,,568483604,615759760,619464491,678208852,413989,SRX8090384,SRS6457234,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.9624,,0.08888,,0.79105,,0.52285,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58897,SRR11519038,SRX8090383,SRS6457235,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 6.5h,GSM4467014,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:6.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 6.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:6.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467014,GSM4467014: TreatedAamanitin zfishPolyAalpha 6.5h; Danio rerio; RNA Seq,GSM4467014,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467014,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_6.5h.fastq.gz,fastq,2637121340.0,34698965.0,GSM4467014 r1,0:76 1:0,A:607991115;C:648768142;G:648963472;T:730955221;N:443390,76,0,,,607991115,648768142,648963472,730955221,443390,SRX8090383,SRS6457235,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96223,,0.05876,,0.78693,,0.51118,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58898,SRR11519037,SRX8090382,SRS6457233,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 5h,GSM4467013,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467013,GSM4467013: TreatedAamanitin zfishPolyAalpha 5h; Danio rerio; RNA Seq,GSM4467013,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467013,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_5h.fastq.gz,fastq,2488582152.0,32744502.0,GSM4467013 r1,0:76 1:0,A:569517166;C:606998078;G:629019285;T:682632018;N:415605,76,0,,,569517166,606998078,629019285,682632018,415605,SRX8090382,SRS6457233,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96455,,0.0816,,0.77991,,0.53634,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58899,SRR11519036,SRX8090381,SRS6457232,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 5.5h,GSM4467012,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:5.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 5.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:5.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467012,GSM4467012: TreatedAamanitin zfishPolyAalpha 5.5h; Danio rerio; RNA Seq,GSM4467012,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_5.5h.fastq.gz,fastq,2425602320.0,31915820.0,GSM4467012 r1,0:76 1:0,A:536016829;C:611729182;G:629092064;T:648359281;N:404964,76,0,,,536016829,611729182,629092064,648359281,404964,SRX8090381,SRS6457232,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96886,,0.1261,,0.79448,,0.57531,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58900,SRR11519035,SRX8090380,SRS6457230,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 4h,GSM4467011,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 4h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467011,GSM4467011: TreatedAamanitin zfishPolyAalpha 4h; Danio rerio; RNA Seq,GSM4467011,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_4h.fastq.gz,fastq,2373912972.0,31235697.0,GSM4467011 r1,0:76 1:0,A:569897416;C:557100774;G:583613577;T:662902355;N:398850,76,0,,,569897416,557100774,583613577,662902355,398850,SRX8090380,SRS6457230,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95642,,0.0677,,0.76345,,0.52714,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58901,SRR11519034,SRX8090379,SRS6457231,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 4.5h,GSM4467010,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:4.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 4.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:4.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467010,GSM4467010: TreatedAamanitin zfishPolyAalpha 4.5h; Danio rerio; RNA Seq,GSM4467010,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_4.5h.fastq.gz,fastq,2546367536.0,33504836.0,GSM4467010 r1,0:76 1:0,A:590944153;C:611757423;G:635042837;T:708195614;N:427509,76,0,,,590944153,611757423,635042837,708195614,427509,SRX8090379,SRS6457231,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.96201,,0.06212,,0.76796,,0.51597,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58902,SRR11519033,SRX8090378,SRS6457229,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 3h,GSM4467009,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 3h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467009,GSM4467009: TreatedAamanitin zfishPolyAalpha 3h; Danio rerio; RNA Seq,GSM4467009,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467009,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_3h.fastq.gz,fastq,1948147824.0,25633524.0,GSM4467009 r1,0:76 1:0,A:457244322;C:470380368;G:477864112;T:542349043;N:309979,76,0,,,457244322,470380368,477864112,542349043,309979,SRX8090378,SRS6457229,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95922,,0.062,,0.7654,,0.51597,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58903,SRR11519032,SRX8090377,SRS6457227,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 3.5h,GSM4467008,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:3.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 3.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:3.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467008,GSM4467008: TreatedAamanitin zfishPolyAalpha 3.5h; Danio rerio; RNA Seq,GSM4467008,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467008,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_3.5h.fastq.gz,fastq,2227727048.0,29312198.0,GSM4467008 r1,0:76 1:0,A:527821645;C:534611304;G:542982010;T:621939292;N:372797,76,0,,,527821645,534611304,542982010,621939292,372797,SRX8090377,SRS6457227,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95504,,0.0734,,0.76195,,0.52369,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58904,SRR11519031,SRX8090376,SRS6457228,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 2h,GSM4467007,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 2h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467007,GSM4467007: TreatedAamanitin zfishPolyAalpha 2h; Danio rerio; RNA Seq,GSM4467007,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467007,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_2h.fastq.gz,fastq,2433943624.0,32025574.0,GSM4467007 r1,0:76 1:0,A:584104490;C:574542508;G:593162776;T:681731342;N:402508,76,0,,,584104490,574542508,593162776,681731342,402508,SRX8090376,SRS6457228,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95487,,0.07062,,0.7737,,0.52084,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
58905,SRR11519030,SRX8090375,SRS6457226,SRP255886,PRJNA624126,Early zebrafish development time course transcriptome,GSE148391,Transcriptome Analysis,Early zebrafish development time course transcriptome Overall design: Three RNA seq datasets of zebrafish embryos expanding the first 8 hours of development. Wild type embryos were sequenced using two different RNA extractions protocols: poly A capture and ribosomal depletion. Also  we sequenced embryos  using poly A capture  that were treated with alpha amanitin 200ng/ul to inhibit zygotic transcription.,,,,TreatedAamanitin zfishPolyAalpha 2.5h,GSM4467006,,tissue:zebrafish early embryo|developmental stage:early embryo|time post fertilization in hrs:2.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,TreatedAamanitin zfishPolyAalpha 2.5h,Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a   using Ensembl 98 gene models. TPM values were generated using RSEM version v1.3.0 . Genome build: danRer11 Supplementary files format and content: comma delimited csv files include TPM values for each Sample,zebrafish early embryo,For treated embryos: α amanitin was injected into single cell stage zebrafish embryos to inhibit zygotic transcription 200ng/ul.,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,Adults zebrafish females were crossed and fertilized embryos were collected and incubated at 28 degree Celsius. 25 embryos for each set with a biological replicate were collected from their respective plates at an interval of one hr. and up to 8hrs.,developmental stage:early embryo|time post fertilization in hrs:2.5|treatment:alpha amanitin injected|rna extraction protocol:poly A capture,GSM4467006,GSM4467006: TreatedAamanitin zfishPolyAalpha 2.5h; Danio rerio; RNA Seq,GSM4467006,,1,poly A capture and ribo depletion RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4467006,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP255886,,,TreatedAamanitin_zfishPolyAalpha_2.5h.fastq.gz,fastq,2366850900.0,31142775.0,GSM4467006 r1,0:76 1:0,A:568200471;C:563625483;G:574695892;T:659934763;N:394291,76,0,,,568200471,563625483,574695892,659934763,394291,SRX8090375,SRS6457226,SRA1064259,GEO,"Computational Biology, Stowers Institute for Medical Research",1,0.95458,,0.07207,,0.76824,,0.5319,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-09,Adult,Adult,Embryo Imprecise,All anatomical structures
67896,SRR17413277,SRX13584926,SRS11474974,SRP353328,PRJNA793867,A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish,GSE192947,Other,Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.,,pubmed:36212030,,Day7 DTR Utricle scRNAseq,GSM5769452,,tissue:Regenerating adult zebrafish utricle|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,Day7 DTR Utricle scRNAseq,Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.,Regenerating adult zebrafish utricle,,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,GSM5769452,GSM5769452: Day7 DTR Utricle scRNAseq; Danio rerio; RNA Seq,GSM5769452 r1,GSM5769452,1,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP353328,,assembly:danRer11|intentional duplicate,Day7_DTR_U.bam,10X Genomics bam file,2849239393.0,31310323.0,GSM5769452 r1,0:91,A:858626231;C:575307401;G:606715228;T:805233227;N:3357306,91,,,,858626231,575307401,606715228,805233227,3357306,SRX13584926,SRS11474974,SRA1351664,"Shawn Burgess, NHGRI, NIH","Shawn Burgess, NHGRI, NIH",1,0.91015,,0.2597,,0.79793,,0.63791,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2022-01-03,Adult,Adult,Embryo Imprecise,All anatomical structures
67898,SRR17413279,SRX13584924,SRS11474972,SRP353328,PRJNA793867,A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish,GSE192947,Other,Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.,,pubmed:36212030,,Day5 DTR Utricle scRNAseq,GSM5769450,,tissue:Regenerating adult zebrafish utricle|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,Day5 DTR Utricle scRNAseq,Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.,Regenerating adult zebrafish utricle,,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,GSM5769450,GSM5769450: Day5 DTR Utricle scRNAseq; Danio rerio; RNA Seq,GSM5769450 r1,GSM5769450,1,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP353328,,assembly:danRer11|intentional duplicate,Day5_DTR_U.bam,10X Genomics bam file,2108613143.0,23171573.0,GSM5769450 r1,0:91,A:630798536;C:410880567;G:472693816;T:591719855;N:2520369,91,,,,630798536,410880567,472693816,591719855,2520369,SRX13584924,SRS11474972,SRA1351664,"Shawn Burgess, NHGRI, NIH","Shawn Burgess, NHGRI, NIH",1,0.90102,,0.26787,,0.78169,,0.58941,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2022-01-03,Adult,Adult,Embryo Imprecise,All anatomical structures
67900,SRR17413281,SRX13584922,SRS11474970,SRP353328,PRJNA793867,A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish,GSE192947,Other,Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.,,pubmed:36212030,,Day4 DTR Utricle scRNAseq,GSM5769448,,tissue:Regenerating adult zebrafish utricle|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,Day4 DTR Utricle scRNAseq,Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.,Regenerating adult zebrafish utricle,,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,GSM5769448,GSM5769448: Day4 DTR Utricle scRNAseq; Danio rerio; RNA Seq,GSM5769448 r1,GSM5769448,1,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP353328,,assembly:danRer11|intentional duplicate,Day4_DTR_U.bam,10X Genomics bam file,2310069216.0,25385376.0,GSM5769448 r1,0:91,A:691773479;C:459225201;G:516620832;T:639722216;N:2727488,91,,,,691773479,459225201,516620832,639722216,2727488,SRX13584922,SRS11474970,SRA1351664,"Shawn Burgess, NHGRI, NIH","Shawn Burgess, NHGRI, NIH",1,0.88896,,0.27187,,0.79519,,0.64162,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2022-01-03,Adult,Adult,Embryo Imprecise,All anatomical structures
67902,SRR17413283,SRX13584920,SRS11474968,SRP353328,PRJNA793867,A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish,GSE192947,Other,Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.,,pubmed:36212030,,Untreated DTR Utricle scRNAseq,GSM5769446,,tissue:Untreated DTR utricle|strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1,Untreated DTR Utricle scRNAseq,Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.,Untreated DTR utricle,,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,strain:myo6b:hDTR|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1,GSM5769446,GSM5769446: Untreated DTR Utricle scRNAseq; Danio rerio; RNA Seq,GSM5769446 r1,GSM5769446,1,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP353328,,assembly:danRer11|intentional duplicate,DTR_U.bam,10X Genomics bam file,2486194893.0,27320823.0,GSM5769446 r1,0:91,A:754059770;C:498471983;G:530934655;T:699780715;N:2947770,91,,,,754059770,498471983,530934655,699780715,2947770,SRX13584920,SRS11474968,SRA1351664,"Shawn Burgess, NHGRI, NIH","Shawn Burgess, NHGRI, NIH",1,0.91702,,0.25265,,0.81193,,0.71391,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2022-01-03,Adult,Adult,Embryo Imprecise,All anatomical structures
67904,SRR17413285,SRX13584918,SRS11474966,SRP353328,PRJNA793867,A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish,GSE192947,Other,Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.,,pubmed:36212030,,Day4 WT Utricle scRNAseq,GSM5769444,,tissue:Day 4 post DT wild type utricle|strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,Day4 WT Utricle scRNAseq,Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.,Day 4 post DT wild type utricle,,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:0.05 ng/ul Diphtheria Toxin,GSM5769444,GSM5769444: Day4 WT Utricle scRNAseq; Danio rerio; RNA Seq,GSM5769444 r1,GSM5769444,1,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP353328,,assembly:danRer11|intentional duplicate,Day4_WT_U.bam,10X Genomics bam file,2435489420.0,26763620.0,GSM5769444 r1,0:91,A:730493532;C:496911409;G:514401329;T:690809405;N:2873745,91,,,,730493532,496911409,514401329,690809405,2873745,SRX13584918,SRS11474966,SRA1351664,"Shawn Burgess, NHGRI, NIH","Shawn Burgess, NHGRI, NIH",1,0.91842,,0.23511,,0.8187,,0.73072,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2022-01-03,Adult,Adult,Embryo Imprecise,All anatomical structures
67906,SRR17413287,SRX13584916,SRS11474964,SRP353328,PRJNA793867,A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish,GSE192947,Other,Using adult zebrafish inner ears as a model for sensorineural regeneration  we performed a targeted ablation of the mechanosensory receptors in the saccule and utricle and characterized the single cell epigenome and transcriptome at consecutive time points following hair cell death. Overall design: To elucidate the transcriptional regulatory network that controls tissue regeneration  we characterized the gene expression profiles scRNA seq and the map of accessible regions scATAC seq associated with the response to hair cell ablation in adult zebrafish sensory epithelia. We dissected out saccules and utricles at three time points: Days 4  5 and 7 post DT  and each were processed separately in both scRNA seq and scATAC seq experiments. Untreated Tgmyo6b:DTR transgenic zebrafish and wild type DT injected and untreated zebrafish lacking the Tgmyo6b:DTR transgene were used as non regenerating controls. Cell suspensions of isolated sensory epithelia were subjected to single cell sequencing for both their transcriptome and open chromatin regions using 10X Genomics Chromium Single Cell Gene Expression and Single Cell ATAC Sequencing. We also include biological triplicates of untreated wild type saccules and utricles for bulk ATAC seq.,,pubmed:36212030,,Untreated WT Utricle scRNAseq,GSM5769442,,tissue:Untreated wild type utricle|strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1,Untreated WT Utricle scRNAseq,Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics.  Cell Ranger Version 3.0.2 10x Genomics was used to demultiplex  for barcode processing  for single cell gene counts  for single cell accessibility counts  and aggregating files. For bulk ATAC seq  libraries were sequenced on an Illumina HiSeq 2500 platform and run as indexed 50 base single end reads. Bulk ATAC seq reads were aligned to reference zebrafish genome danRer11 using bowtie2. Peaks were called by MACS2 from individual replicate. Genome build: danRer11 Supplementary files format and content: scRNA seq and scATAC seq outputs were generated using the 10x Cell Ranger pipeline. scRNA seq H5 filtered feature bc matrix files contain the UMI counts for each cell. scATAC seq processed data files include three file formats per sample: CSV  TBI  and H5. CSV singlecell.csv files contain per barcode QC information associated with the fragments per barcode  ATAC signal per barcode  and cell calling information. TBI Fragments.tsv.gz.tbi files are tabix index of the fragment intervals. H5 filtered peak bc matrix.h5 files contain only detected cellular barcodes. For bulk ATAC seq  narrowPeak files contain MACS2 called peaks in BED format.,Untreated wild type utricle,,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,strain:TAB 5|embryo age:6 mpf 10 mpf adult zebrafish|treatment:N1,GSM5769442,GSM5769442: Untreated WT Utricle scRNAseq; Danio rerio; RNA Seq,GSM5769442 r1,GSM5769442,1,For single cell experiments  non regenerating untreated and regenerating inner ears saccule and utricle were dissected at consecutive time points and dissociated into single cells using trypsin and collagenase. For bulk ATAC seq experiments  untreated inner ears saccule and utricle were harvested and samples prepared in triplicate. Nuclei were extracted and chromatin digested by tn5 transposase. DNA fragments were extracted and then amplified by PCR. Libraries were amplified by PCR with indexed primers. For scRNA seq  cDNA libraries were generatated with Chromium Controller and Chromium Single Cell three prime GEM  Library and Gel Bead Kit V3 10x Genomics. For scATAC seq  libraries were generated with the Chromium Controller and Chromium Single Cell ATAC Library & Gel Bead Kit 1000111  10X Genomics. For bulk ATAC seq  libraries were generated using Nextera DNA Library Preparation Kit Catalog # FC 121 1030. Transposed DNA were amplified by PCR with indexed primers and libraries were purified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP353328,,assembly:danRer11|intentional duplicate,WT_U.bam,10X Genomics bam file,2925188357.0,32144927.0,GSM5769442 r1,0:91,A:884460893;C:605377533;G:601265913;T:830622848;N:3461170,91,,,,884460893,605377533,601265913,830622848,3461170,SRX13584916,SRS11474964,SRA1351664,"Shawn Burgess, NHGRI, NIH","Shawn Burgess, NHGRI, NIH",1,0.92311,,0.22358,,0.82394,,0.62304,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_droplet,10x,,United States,2022-01-03,Adult,Adult,Embryo Imprecise,All anatomical structures
72740,SRR23110572,SRX19061958,SRS16477633,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  DAPI neg,GSM6940305,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940305,GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq,GSM6940305 r1,GSM6940305,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP418118,,,22-25_mm_Adult_Calvaria_DAPI_neg-1_S17_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-1_S17_L001_R2_001.fastq.gz,fastq fastq,12188552084.0,82667752.0,GSM6940305 r1,0:27 1:120.44,A:3475006284;C:2574166578;G:2653428285;T:3480007630;N:5943307,27,120,,,3475006284,2574166578,2653428285,3480007630,5943307,SRX19061958,SRS16477633,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00168,0.91388,0.00076,0.19968,0.99697,0.85754,0.48044,0.49798,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72741,SRR23110573,SRX19061958,SRS16477633,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  DAPI neg,GSM6940305,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940305,GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq,GSM6940305 r1,GSM6940305,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP418118,,,22-25_mm_Adult_Calvaria_DAPI_neg-2_S18_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-2_S18_L001_R2_001.fastq.gz,fastq fastq,13976267234.0,94800658.0,GSM6940305 r2,0:27 1:120.43,A:3999552660;C:2970812323;G:3076032177;T:3923173900;N:6696174,27,120,,,3999552660,2970812323,3076032177,3923173900,6696174,SRX19061958,SRS16477633,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00195,0.91588,0.00083,0.19869,0.99659,0.85788,0.46543,0.49295,27,121,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72742,SRR23110574,SRX19061958,SRS16477633,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  DAPI neg,GSM6940305,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940305,GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq,GSM6940305 r1,GSM6940305,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP418118,,,22-25_mm_Adult_Calvaria_DAPI_neg-3_S19_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-3_S19_L001_R2_001.fastq.gz,fastq fastq,10663177356.0,72321436.0,GSM6940305 r3,0:27 1:120.44,A:3038724608;C:2260787836;G:2334365122;T:3024224853;N:5074937,27,120,,,3038724608,2260787836,2334365122,3024224853,5074937,SRX19061958,SRS16477633,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00183,0.91595,0.00078,0.19615,0.99667,0.85476,0.42574,0.51753,27,120,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72743,SRR23110575,SRX19061958,SRS16477633,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  DAPI neg,GSM6940305,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940305,GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq,GSM6940305 r1,GSM6940305,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP418118,,,22-25_mm_Adult_Calvaria_DAPI_neg-4_S20_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-4_S20_L001_R2_001.fastq.gz,fastq fastq,11848567942.0,80365988.0,GSM6940305 r4,0:27 1:120.43,A:3428903160;C:2496116909;G:2566987382;T:3350843744;N:5716747,27,120,,,3428903160,2496116909,2566987382,3350843744,5716747,SRX19061958,SRS16477633,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00179,0.91204,0.00085,0.20828,0.99715,0.8717,0.43575,0.50701,27,118,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72744,SRR23110576,SRX19061957,SRS16477632,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,GSM6940304,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940304,GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq,GSM6940304 r1,GSM6940304,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418118,,,22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz,fastq fastq,8988220186.0,60952087.0,GSM6940304 r1,0:27 1:120.46,A:2662713057;C:1786705322;G:2011325980;T:2520873526;N:6602301,27,120,,,2662713057,1786705322,2011325980,2520873526,6602301,SRX19061957,SRS16477632,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00497,0.89429,0.00168,0.18434,0.99125,0.8325,0.54009,0.54971,27,121,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72745,SRR23110577,SRX19061957,SRS16477632,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,GSM6940304,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940304,GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq,GSM6940304 r1,GSM6940304,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418118,,,22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R2_001.fastq.gz,fastq fastq,10409092984.0,70587244.0,GSM6940304 r2,0:27 1:120.46,A:3082040103;C:2069527173;G:2331562542;T:2918295355;N:7667811,27,120,,,3082040103,2069527173,2331562542,2918295355,7667811,SRX19061957,SRS16477632,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00486,0.89223,0.0016,0.18706,0.99095,0.83382,0.52631,0.56473,27,121,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72746,SRR23110578,SRX19061957,SRS16477632,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,GSM6940304,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940304,GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq,GSM6940304 r1,GSM6940304,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418118,,,22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R2_001.fastq.gz,fastq fastq,7852584028.0,53251179.0,GSM6940304 r3,0:27 1:120.46,A:2332795259;C:1555674536;G:1745851459;T:2212480038;N:5782736,27,120,,,2332795259,1555674536,1745851459,2212480038,5782736,SRX19061957,SRS16477632,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00478,0.89367,0.0014,0.1895,0.99062,0.83086,0.53588,0.55948,27,120,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures
72747,SRR23110579,SRX19061957,SRS16477632,SRP418118,PRJNA925134,BMP dependent cellular dynamics during cranial suture establishment in zebrafish,GSE223147,Transcriptome Analysis,Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics,,pubmed:39138165,,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,GSM6940304,,source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing,22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg,Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial “Integration and Label Transfer” from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files,calvaria,,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer’s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz’s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer’s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5°C. For adults  in the institute vivarium according to Protocol 20771.,cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen,GSM6940304,GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq,GSM6940304 r1,GSM6940304,1,We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1 mM EDTA  and 400 mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4 °C  rinsed in suspension media 1% FBS  0.8 mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418118,,,22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R2_001.fastq.gz,fastq fastq,11611263604.0,78739888.0,GSM6940304 r4,0:27 1:120.46,A:3440640044;C:2312536251;G:2595707458;T:3253782284;N:8597567,27,120,,,3440640044,2312536251,2595707458,3253782284,8597567,SRX19061957,SRS16477632,SRA1576283,"Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles","Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles",2,0.00481,0.89424,0.0015,0.18882,0.99115,0.8325,0.51954,0.5663,27,120,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-01-18,Adult,Adult,Embryo Imprecise,All anatomical structures