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
60041,SRR12125406,SRX8646725,SRS6930268,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 5.25hpf,GSM4648254,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648254,GSM4648254: TL emb6 5.25hpf; Danio rerio; RNA Seq,GSM4648254,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648254,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_5_25hpf.fastq,fastq,629273169.0,9988463.0,GSM4648254 r1,0:63,A:187901113;C:108762017;G:141486490;T:190996993;N:126556,63,,,,187901113,108762017,141486490,190996993,126556,SRX8646725,SRS6930268,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83255,,0.08071,,0.78056,,0.60842,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60042,SRR12125405,SRX8646724,SRS6930266,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 5.25hpf,GSM4648253,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648253,GSM4648253: TL emb5 5.25hpf; Danio rerio; RNA Seq,GSM4648253,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648253,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_5_25hpf.fastq,fastq,628500159.0,9976193.0,GSM4648253 r1,0:63,A:185452655;C:102493031;G:141851568;T:198575851;N:127054,63,,,,185452655,102493031,141851568,198575851,127054,SRX8646724,SRS6930266,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.81984,,0.07983,,0.77232,,0.54808,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60043,SRR12125404,SRX8646723,SRS6930265,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 5.25hpf,GSM4648252,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648252,GSM4648252: TL emb4 5.25hpf; Danio rerio; RNA Seq,GSM4648252,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648252,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_5_25hpf.fastq,fastq,418163886.0,6637522.0,GSM4648252 r1,0:63,A:126255886;C:72281485;G:95392900;T:124146654;N:86961,63,,,,126255886,72281485,95392900,124146654,86961,SRX8646723,SRS6930265,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82908,,0.07514,,0.78025,,0.63356,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60044,SRR12125403,SRX8646722,SRS6930267,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 5.25hpf,GSM4648251,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648251,GSM4648251: AB emb6 5.25hpf; Danio rerio; RNA Seq,GSM4648251,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648251,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_5_25hpf.fastq,fastq,853663797.0,13550219.0,GSM4648251 r1,0:63,A:255371849;C:147150704;G:193587744;T:257383442;N:170058,63,,,,255371849,147150704,193587744,257383442,170058,SRX8646722,SRS6930267,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83677,,0.09016,,0.77445,,0.60529,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60045,SRR12125402,SRX8646721,SRS6930264,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 5.25hpf,GSM4648250,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648250,GSM4648250: AB emb5 5.25hpf; Danio rerio; RNA Seq,GSM4648250,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648250,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_5_25hpf.fastq,fastq,1197811755.0,19012885.0,GSM4648250 r1,0:63,A:366408232;C:210221584;G:280850075;T:340089873;N:241991,63,,,,366408232,210221584,280850075,340089873,241991,SRX8646721,SRS6930264,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86965,,0.06886,,0.79364,,0.73599,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60046,SRR12125401,SRX8646720,SRS6930263,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 5.25hpf,GSM4648249,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648249,GSM4648249: AB emb4 5.25hpf; Danio rerio; RNA Seq,GSM4648249,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648249,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_5_25hpf.fastq,fastq,629932527.0,9998929.0,GSM4648249 r1,0:63,A:193361276;C:107009709;G:146668961;T:182764345;N:128236,63,,,,193361276,107009709,146668961,182764345,128236,SRX8646720,SRS6930263,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85596,,0.07156,,0.78731,,0.71237,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60047,SRR12125400,SRX8646719,SRS6930262,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 5.25hpf,GSM4648248,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648248,GSM4648248: TL emb3 5.25hpf; Danio rerio; RNA Seq,GSM4648248,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648248,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_5_25hpf.fastq,fastq,1069366364.0,15960692.0,GSM4648248 r1,0:67,A:323825047;C:184028766;G:241899926;T:319408897;N:203728,67,,,,323825047,184028766,241899926,319408897,203728,SRX8646719,SRS6930262,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83558,,0.07461,,0.78476,,0.63113,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60048,SRR12125399,SRX8646718,SRS6930261,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 5.25hpf,GSM4648247,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648247,GSM4648247: TL emb2 5.25hpf; Danio rerio; RNA Seq,GSM4648247,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648247,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_5_25hpf.fastq,fastq,899735898.0,13428894.0,GSM4648247 r1,0:67,A:271859449;C:157711028;G:206650787;T:263341201;N:173433,67,,,,271859449,157711028,206650787,263341201,173433,SRX8646718,SRS6930261,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84037,,0.07528,,0.78498,,0.66749,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60049,SRR12125398,SRX8646717,SRS6930260,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 5.25hpf,GSM4648246,,source name:Whole embryo|strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648246,GSM4648246: TL emb1 5.25hpf; Danio rerio; RNA Seq,GSM4648246,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648246,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_5_25hpf.fastq,fastq,539868982.0,8057746.0,GSM4648246 r1,0:67,A:164876385;C:95791327;G:123943212;T:155156126;N:101932,67,,,,164876385,95791327,123943212,155156126,101932,SRX8646717,SRS6930260,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83865,,0.06636,,0.78953,,0.69934,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60050,SRR12125397,SRX8646716,SRS6930259,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 5.25hpf,GSM4648245,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648245,GSM4648245: AB emb3 5.25hpf; Danio rerio; RNA Seq,GSM4648245,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648245,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_5_25hpf.fastq,fastq,493512486.0,7365858.0,GSM4648245 r1,0:67,A:151344823;C:86707549;G:113245311;T:142120578;N:94225,67,,,,151344823,86707549,113245311,142120578,94225,SRX8646716,SRS6930259,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84007,,0.0974,,0.77979,,0.68149,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60051,SRR12125396,SRX8646715,SRS6930258,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 5.25hpf,GSM4648244,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648244,GSM4648244: AB emb2 5.25hpf; Danio rerio; RNA Seq,GSM4648244,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648244,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_5_25hpf.fastq,fastq,1157452269.0,17275407.0,GSM4648244 r1,0:67,A:355287094;C:204659659;G:273293682;T:323995566;N:216268,67,,,,355287094,204659659,273293682,323995566,216268,SRX8646715,SRS6930258,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87638,,0.06853,,0.80426,,0.77626,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60052,SRR12125395,SRX8646714,SRS6930257,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 5.25hpf,GSM4648243,,source name:Whole embryo|strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 5.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:5.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648243,GSM4648243: AB emb1 5.25hpf; Danio rerio; RNA Seq,GSM4648243,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648243,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_5_25hpf.fastq,fastq,1327040056.0,19806568.0,GSM4648243 r1,0:67,A:409987389;C:235374040;G:312942941;T:368491782;N:243904,67,,,,409987389,235374040,312942941,368491782,243904,SRX8646714,SRS6930257,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.8667,,0.06371,,0.80588,,0.77484,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Gastrula,Embryo,Whole Organism,All anatomical structures
60053,SRR12125394,SRX8646713,SRS6930256,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 4.25hpf,GSM4648242,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648242,GSM4648242: TL emb6 4.25hpf; Danio rerio; RNA Seq,GSM4648242,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648242,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_4_25hpf.fastq,fastq,648226908.0,10289316.0,GSM4648242 r1,0:63,A:186626188;C:108596134;G:148654113;T:204221173;N:129300,63,,,,186626188,108596134,148654113,204221173,129300,SRX8646713,SRS6930256,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84314,,0.06862,,0.77398,,0.56825,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60054,SRR12125393,SRX8646712,SRS6930255,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 4.25hpf,GSM4648241,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648241,GSM4648241: TL emb5 4.25hpf; Danio rerio; RNA Seq,GSM4648241,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648241,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_4_25hpf.fastq,fastq,734406057.0,11657239.0,GSM4648241 r1,0:63,A:210803716;C:130159870;G:171759422;T:221537069;N:145980,63,,,,210803716,130159870,171759422,221537069,145980,SRX8646712,SRS6930255,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85492,,0.06162,,0.78212,,0.38833,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60055,SRR12125392,SRX8646711,SRS6930254,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 4.25hpf,GSM4648240,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648240,GSM4648240: TL emb4 4.25hpf; Danio rerio; RNA Seq,GSM4648240,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648240,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_4_25hpf.fastq,fastq,848080548.0,13461596.0,GSM4648240 r1,0:63,A:244171248;C:146950905;G:197166889;T:259622371;N:169135,63,,,,244171248,146950905,197166889,259622371,169135,SRX8646711,SRS6930254,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85266,,0.06536,,0.78356,,0.61672,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60056,SRR12125391,SRX8646710,SRS6930253,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 4.25hpf,GSM4648239,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648239,GSM4648239: AB emb6 4.25hpf; Danio rerio; RNA Seq,GSM4648239,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648239,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_4_25hpf.fastq,fastq,801023769.0,12714663.0,GSM4648239 r1,0:63,A:229516390;C:133164924;G:183459290;T:254724395;N:158770,63,,,,229516390,133164924,183459290,254724395,158770,SRX8646710,SRS6930253,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84498,,0.08229,,0.76516,,0.54649,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60057,SRR12125390,SRX8646709,SRS6930252,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 4.25hpf,GSM4648238,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648238,GSM4648238: AB emb5 4.25hpf; Danio rerio; RNA Seq,GSM4648238,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648238,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_4_25hpf.fastq,fastq,916020630.0,14540010.0,GSM4648238 r1,0:63,A:265921679;C:156404174;G:214021996;T:279489346;N:183435,63,,,,265921679,156404174,214021996,279489346,183435,SRX8646709,SRS6930252,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86891,,0.06574,,0.78332,,0.64733,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60058,SRR12125389,SRX8646708,SRS6930251,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 4.25hpf,GSM4648237,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648237,GSM4648237: AB emb4 4.25hpf; Danio rerio; RNA Seq,GSM4648237,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648237,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_4_25hpf.fastq,fastq,648949077.0,10300779.0,GSM4648237 r1,0:63,A:189284026;C:107954215;G:152710596;T:198865842;N:134398,63,,,,189284026,107954215,152710596,198865842,134398,SRX8646708,SRS6930251,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86363,,0.07026,,0.77701,,0.64544,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60059,SRR12125388,SRX8646707,SRS6930250,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 4.25hpf,GSM4648236,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648236,GSM4648236: TL emb3 4.25hpf; Danio rerio; RNA Seq,GSM4648236,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648236,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_4_25hpf.fastq,fastq,516466016.0,7708448.0,GSM4648236 r1,0:67,A:159159432;C:88645898;G:115271897;T:153289294;N:99495,67,,,,159159432,88645898,115271897,153289294,99495,SRX8646707,SRS6930250,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83753,,0.06603,,0.78255,,0.63318,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60060,SRR12125387,SRX8646706,SRS6930249,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 4.25hpf,GSM4648235,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648235,GSM4648235: TL emb2 4.25hpf; Danio rerio; RNA Seq,GSM4648235,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648235,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_4_25hpf.fastq,fastq,733560086.0,10948658.0,GSM4648235 r1,0:67,A:223892555;C:125768367;G:165649772;T:218113018;N:136374,67,,,,223892555,125768367,165649772,218113018,136374,SRX8646706,SRS6930249,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83779,,0.067,,0.77987,,0.63741,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60061,SRR12125386,SRX8646705,SRS6930248,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 4.25hpf,GSM4648234,,source name:Whole embryo|strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648234,GSM4648234: TL emb1 4.25hpf; Danio rerio; RNA Seq,GSM4648234,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648234,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_4_25hpf.fastq,fastq,996559273.0,14874019.0,GSM4648234 r1,0:67,A:306056021;C:172219093;G:225165148;T:292935389;N:183622,67,,,,306056021,172219093,225165148,292935389,183622,SRX8646705,SRS6930248,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83661,,0.06598,,0.78042,,0.64801,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60062,SRR12125385,SRX8646704,SRS6930247,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 4.25hpf,GSM4648233,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648233,GSM4648233: AB emb3 4.25hpf; Danio rerio; RNA Seq,GSM4648233,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648233,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_4_25hpf.fastq,fastq,995183629.0,14853487.0,GSM4648233 r1,0:67,A:306982973;C:172407171;G:224381340;T:291223894;N:188251,67,,,,306982973,172407171,224381340,291223894,188251,SRX8646704,SRS6930247,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83741,,0.07596,,0.77484,,0.64838,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60063,SRR12125384,SRX8646703,SRS6930246,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 4.25hpf,GSM4648232,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648232,GSM4648232: AB emb2 4.25hpf; Danio rerio; RNA Seq,GSM4648232,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648232,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_4_25hpf.fastq,fastq,816027371.0,12179513.0,GSM4648232 r1,0:67,A:254674603;C:143689351;G:189951309;T:227560983;N:151125,67,,,,254674603,143689351,189951309,227560983,151125,SRX8646703,SRS6930246,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87586,,0.0588,,0.79683,,0.77034,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60064,SRR12125383,SRX8646702,SRS6930245,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 4.25hpf,GSM4648231,,source name:Whole embryo|strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 4.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:4.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648231,GSM4648231: AB emb1 4.25hpf; Danio rerio; RNA Seq,GSM4648231,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648231,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_4_25hpf.fastq,fastq,908152237.0,13554511.0,GSM4648231 r1,0:67,A:285792221;C:161035180;G:211856601;T:249299580;N:168655,67,,,,285792221,161035180,211856601,249299580,168655,SRX8646702,SRS6930245,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87466,,0.05237,,0.80671,,0.80003,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60065,SRR12125382,SRX8646701,SRS6930244,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 3.25hpf,GSM4648230,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648230,GSM4648230: TL emb6 3.25hpf; Danio rerio; RNA Seq,GSM4648230,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648230,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_3_25hpf.fastq,fastq,406690011.0,6455397.0,GSM4648230 r1,0:63,A:120677773;C:70454448;G:91897989;T:123574695;N:85106,63,,,,120677773,70454448,91897989,123574695,85106,SRX8646701,SRS6930244,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84562,,0.05274,,0.78709,,0.6243,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60066,SRR12125381,SRX8646700,SRS6930243,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 3.25hpf,GSM4648229,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648229,GSM4648229: TL emb5 3.25hpf; Danio rerio; RNA Seq,GSM4648229,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648229,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_3_25hpf.fastq,fastq,1342709172.0,21312844.0,GSM4648229 r1,0:63,A:393268889;C:230336007;G:306128117;T:412697568;N:278591,63,,,,393268889,230336007,306128117,412697568,278591,SRX8646700,SRS6930243,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84679,,0.05277,,0.78376,,0.61146,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60067,SRR12125380,SRX8646699,SRS6930241,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 3.25hpf,GSM4648228,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648228,GSM4648228: TL emb4 3.25hpf; Danio rerio; RNA Seq,GSM4648228,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648228,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_3_25hpf.fastq,fastq,679340970.0,10783190.0,GSM4648228 r1,0:63,A:202043678;C:117431893;G:154094046;T:205633514;N:137839,63,,,,202043678,117431893,154094046,205633514,137839,SRX8646699,SRS6930241,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84563,,0.05116,,0.78691,,0.63857,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60068,SRR12125379,SRX8646698,SRS6930240,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 3.25hpf,GSM4648227,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648227,GSM4648227: AB emb6 3.25hpf; Danio rerio; RNA Seq,GSM4648227,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648227,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_3_25hpf.fastq,fastq,1053160038.0,16716826.0,GSM4648227 r1,0:63,A:309310336;C:174248829;G:236443053;T:332944871;N:212949,63,,,,309310336,174248829,236443053,332944871,212949,SRX8646698,SRS6930240,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84084,,0.0644,,0.77297,,0.55261,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60069,SRR12125378,SRX8646697,SRS6930242,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 3.25hpf,GSM4648226,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648226,GSM4648226: AB emb5 3.25hpf; Danio rerio; RNA Seq,GSM4648226,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648226,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_3_25hpf.fastq,fastq,767622366.0,12184482.0,GSM4648226 r1,0:63,A:230696545;C:135055273;G:178818369;T:222896193;N:155986,63,,,,230696545,135055273,178818369,222896193,155986,SRX8646697,SRS6930242,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87843,,0.04331,,0.79555,,0.72222,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60070,SRR12125377,SRX8646696,SRS6930239,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 3.25hpf,GSM4648225,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648225,GSM4648225: AB emb4 3.25hpf; Danio rerio; RNA Seq,GSM4648225,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648225,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_3_25hpf.fastq,fastq,579009312.0,9190624.0,GSM4648225 r1,0:63,A:175049727;C:97082374;G:133102260;T:173656136;N:118815,63,,,,175049727,97082374,133102260,173656136,118815,SRX8646696,SRS6930239,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86011,,0.05008,,0.78492,,0.67432,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60071,SRR12125376,SRX8646695,SRS6930238,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 3.25hpf,GSM4648224,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648224,GSM4648224: TL emb3 3.25hpf; Danio rerio; RNA Seq,GSM4648224,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648224,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_3_25hpf.fastq,fastq,718330718.0,10721354.0,GSM4648224 r1,0:67,A:219495085;C:119739206;G:164136215;T:214827087;N:133125,67,,,,219495085,119739206,164136215,214827087,133125,SRX8646695,SRS6930238,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82675,,0.05622,,0.7864,,0.61084,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60072,SRR12125423,SRX8646694,SRS6930237,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 3.25hpf,GSM4648223,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648223,GSM4648223: TL emb2 3.25hpf; Danio rerio; RNA Seq,GSM4648223,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648223,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_3_25hpf.fastq,fastq,846806836.0,12638908.0,GSM4648223 r1,0:67,A:258192271;C:142127876;G:194759995;T:251567003;N:159691,67,,,,258192271,142127876,194759995,251567003,159691,SRX8646694,SRS6930237,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82715,,0.05329,,0.7891,,0.63308,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60073,SRR12125422,SRX8646693,SRS6930236,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 3.25hpf,GSM4648222,,source name:Whole embryo|strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648222,GSM4648222: TL emb1 3.25hpf; Danio rerio; RNA Seq,GSM4648222,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648222,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_3_25hpf.fastq,fastq,967198332.0,14435796.0,GSM4648222 r1,0:67,A:295354111;C:161347921;G:222828106;T:287484566;N:183628,67,,,,295354111,161347921,222828106,287484566,183628,SRX8646693,SRS6930236,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82551,,0.05319,,0.78474,,0.63465,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60074,SRR12125421,SRX8646692,SRS6930235,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 3.25hpf,GSM4648221,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648221,GSM4648221: AB emb3 3.25hpf; Danio rerio; RNA Seq,GSM4648221,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648221,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_3_25hpf.fastq,fastq,1097446667.0,16379801.0,GSM4648221 r1,0:67,A:335650326;C:184923523;G:253014446;T:323651876;N:206496,67,,,,335650326,184923523,253014446,323651876,206496,SRX8646692,SRS6930235,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83064,,0.05743,,0.78236,,0.62817,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60075,SRR12125420,SRX8646691,SRS6930234,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 3.25hpf,GSM4648220,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648220,GSM4648220: AB emb2 3.25hpf; Danio rerio; RNA Seq,GSM4648220,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648220,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_3_25hpf.fastq,fastq,1052234397.0,15704991.0,GSM4648220 r1,0:67,A:323684738;C:185585498;G:254328718;T:288441126;N:194317,67,,,,323684738,185585498,254328718,288441126,194317,SRX8646691,SRS6930234,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.87949,,0.03749,,0.80779,,0.79902,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60076,SRR12125419,SRX8646690,SRS6930233,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 3.25hpf,GSM4648219,,source name:Whole embryo|strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 3.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:3.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648219,GSM4648219: AB emb1 3.25hpf; Danio rerio; RNA Seq,GSM4648219,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648219,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_3_25hpf.fastq,fastq,1673968267.0,24984601.0,GSM4648219 r1,0:67,A:518959586;C:292464694;G:402352389;T:459881035;N:310563,67,,,,518959586,292464694,402352389,459881035,310563,SRX8646690,SRS6930233,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86486,,0.03996,,0.80647,,0.78106,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60077,SRR12125418,SRX8646689,SRS6930232,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb6 2.25hpf,GSM4648218,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb6 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648218,GSM4648218: TL emb6 2.25hpf; Danio rerio; RNA Seq,GSM4648218,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648218,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb6_2_25hpf.fastq,fastq,653742054.0,10376858.0,GSM4648218 r1,0:63,A:191909466;C:110924763;G:150375764;T:200399289;N:132772,63,,,,191909466,110924763,150375764,200399289,132772,SRX8646689,SRS6930232,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83788,,0.05116,,0.78354,,0.60585,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60078,SRR12125417,SRX8646688,SRS6930230,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb5 2.25hpf,GSM4648217,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb5 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648217,GSM4648217: TL emb5 2.25hpf; Danio rerio; RNA Seq,GSM4648217,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648217,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb5_2_25hpf.fastq,fastq,781357626.0,12402502.0,GSM4648217 r1,0:63,A:228115778;C:132378621;G:181704836;T:238999917;N:158474,63,,,,228115778,132378621,181704836,238999917,158474,SRX8646688,SRS6930230,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.84083,,0.05244,,0.78226,,0.60881,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60079,SRR12125416,SRX8646687,SRS6930229,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb4 2.25hpf,GSM4648216,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,TL emb4 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648216,GSM4648216: TL emb4 2.25hpf; Danio rerio; RNA Seq,GSM4648216,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648216,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb4_2_25hpf.fastq,fastq,421965369.0,6697863.0,GSM4648216 r1,0:63,A:124392499;C:67934245;G:96491307;T:133060705;N:86613,63,,,,124392499,67934245,96491307,133060705,86613,SRX8646687,SRS6930229,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83068,,0.05472,,0.78311,,0.5438,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60080,SRR12125415,SRX8646686,SRS6930228,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb6 2.25hpf,GSM4648215,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb6 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648215,GSM4648215: AB emb6 2.25hpf; Danio rerio; RNA Seq,GSM4648215,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648215,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb6_2_25hpf.fastq,fastq,628644744.0,9978488.0,GSM4648215 r1,0:63,A:184633079;C:102913810;G:143484876;T:197486280;N:126699,63,,,,184633079,102913810,143484876,197486280,126699,SRX8646686,SRS6930228,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83277,,0.06148,,0.77617,,0.55775,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60081,SRR12125414,SRX8646685,SRS6930231,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb5 2.25hpf,GSM4648214,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb5 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648214,GSM4648214: AB emb5 2.25hpf; Danio rerio; RNA Seq,GSM4648214,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648214,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb5_2_25hpf.fastq,fastq,814541301.0,12929227.0,GSM4648214 r1,0:63,A:242788318;C:140374211;G:193168440;T:238045602;N:164730,63,,,,242788318,140374211,193168440,238045602,164730,SRX8646685,SRS6930231,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.86463,,0.04609,,0.78914,,0.69402,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60082,SRR12125413,SRX8646684,SRS6930227,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb4 2.25hpf,GSM4648213,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,AB emb4 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:2,GSM4648213,GSM4648213: AB emb4 2.25hpf; Danio rerio; RNA Seq,GSM4648213,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648213,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb4_2_25hpf.fastq,fastq,616851396.0,9791292.0,GSM4648213 r1,0:63,A:184681235;C:102359437;G:145006560;T:184679393;N:124771,63,,,,184681235,102359437,145006560,184679393,124771,SRX8646684,SRS6930227,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85058,,0.04957,,0.79017,,0.66075,,63,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60083,SRR12125412,SRX8646683,SRS6930226,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb3 2.25hpf,GSM4648212,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb3 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648212,GSM4648212: TL emb3 2.25hpf; Danio rerio; RNA Seq,GSM4648212,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648212,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb3_2_25hpf.fastq,fastq,1186700114.0,17711942.0,GSM4648212 r1,0:67,A:370074693;C:200098953;G:261433673;T:354868674;N:224121,67,,,,370074693,200098953,261433673,354868674,224121,SRX8646683,SRS6930226,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82908,,0.0523,,0.7837,,0.61246,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60084,SRR12125411,SRX8646682,SRS6930225,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb2 2.25hpf,GSM4648211,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb2 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648211,GSM4648211: TL emb2 2.25hpf; Danio rerio; RNA Seq,GSM4648211,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648211,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb2_2_25hpf.fastq,fastq,952230197.0,14212391.0,GSM4648211 r1,0:67,A:293613397;C:158998327;G:211896479;T:287542246;N:179748,67,,,,293613397,158998327,211896479,287542246,179748,SRX8646682,SRS6930225,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.82682,,0.05463,,0.78581,,0.60992,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60085,SRR12125410,SRX8646681,SRS6930224,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,TL emb1 2.25hpf,GSM4648210,,source name:Whole embryo|strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,TL emb1 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:TL|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648210,GSM4648210: TL emb1 2.25hpf; Danio rerio; RNA Seq,GSM4648210,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648210,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,TL_emb1_2_25hpf.fastq,fastq,889434246.0,13275138.0,GSM4648210 r1,0:67,A:284892995;C:151063100;G:198507402;T:254807861;N:162888,67,,,,284892995,151063100,198507402,254807861,162888,SRX8646681,SRS6930224,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.81409,,0.04129,,0.79819,,0.67976,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60086,SRR12125409,SRX8646680,SRS6930223,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb3 2.25hpf,GSM4648209,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb3 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648209,GSM4648209: AB emb3 2.25hpf; Danio rerio; RNA Seq,GSM4648209,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648209,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb3_2_25hpf.fastq,fastq,1018630279.0,15203437.0,GSM4648209 r1,0:67,A:317428176;C:175810114;G:228314923;T:296891187;N:185879,67,,,,317428176,175810114,228314923,296891187,185879,SRX8646680,SRS6930223,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.83444,,0.04892,,0.78577,,0.65007,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60087,SRR12125408,SRX8646679,SRS6930222,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb2 2.25hpf,GSM4648208,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb2 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648208,GSM4648208: AB emb2 2.25hpf; Danio rerio; RNA Seq,GSM4648208,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648208,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb2_2_25hpf.fastq,fastq,1455828193.0,21728779.0,GSM4648208 r1,0:67,A:456676551;C:251609741;G:334731434;T:412538456;N:272011,67,,,,456676551,251609741,334731434,412538456,272011,SRX8646679,SRS6930222,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85982,,0.04242,,0.79399,,0.72904,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures
60088,SRR12125407,SRX8646678,SRS6930221,SRP269528,PRJNA643503,Variability of an early developmental cell population underlies stochastic laterality defects,GSE153621,Transcriptome Analysis,Embryonic development seemingly proceeds with almost perfect precision. However  it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here  we quantified embryo to embryo variability in vertebrate development  by studying cell number variation in the zebrafish endoderm. We noticed that the size of a sub population of the endoderm  the dorsal forerunner cells which later forms the left right organizer  is highly variable between individual embryos. We found that the frequency of left right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells  and we observed that these fluctuations are largely stochastic. Hence  a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary  we here dissect cause and consequence of embryo to embryo variability in a vertebrate model. Overall design: Transcriptomic comparison of Individual embryos from two zebrafish strains AB and TL at 2.25  3.25  4.25 and 5.25 hpf with two biological replicates.,,pubmed:33440143,,AB emb1 2.25hpf,GSM4648207,,source name:Whole embryo|strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,AB emb1 2.25hpf,R1 contains only barcode information  not used for mapping  not included. Basecall was done with bcl2fastq v2.19.0.316. Because of low complexity in the last two bases of the barcodes in the R1  the following options were used: mask short adapter reads = 12  and minimum trimmed read length = 12. The resulting reads were further demultiplexed with the R package scruff 1.2.5 using only the first 4 bases of the barcode in the run for the biological replicate ID 1 and mapped with STAR 2.7.1a using quantMode GeneCounts and the DanRer11v96 transcriptome as reference. Normalization and differential expression analysis was done with edgeR 3.26.8 Genome build: DanRer11v96 Supplementary files format and content: tab delimited table with raw gene counts for all the samples at each timepoint.,Whole embryo,,RNA extraction was carried according to the manufacturer’s recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,Naturally spawned embryos were collected in Trizol Thermo Fisher at the desired stage post an incubation at 28.5ºC.,strain:AB|developmental stage:2.25hpf|tissue:Whole embryo|biological replicate id:1,GSM4648207,GSM4648207: AB emb1 2.25hpf; Danio rerio; RNA Seq,GSM4648207,,1,RNA extraction was carried according to the manufacturer's recommendations Every sample was barcoded  pooled and the libraries were prepared according to the CEL seq2 protocol Hashimshony  et al.  Genome Biology  2016 with different RPI index for each timepoint. Two sequencing runs were done for each of the biological replicates.,GEO Accession:GSM4648207,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP269528,,,AB_emb1_2_25hpf.fastq,fastq,1156150325.0,17255975.0,GSM4648207 r1,0:67,A:367116449;C:201866700;G:266919704;T:320031593;N:215879,67,,,,367116449,201866700,266919704,320031593,215879,SRX8646678,SRS6930221,SRA1093450,GEO,"Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine",1,0.85881,,0.03651,,0.80346,,0.76662,,67,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2020-07-01,Blastula,Embryo,Whole Organism,All anatomical structures