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
10060,ERR4795364,ERX4665135,ERS5281176,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 4,E MTAB 9727:Sample 4,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 4 s,Sample 4 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 4,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz,fastq,5410723202.0,71707309.0,E MTAB 9727:Sample 4,0:75.46 1:0,A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666,75,0,,,1330416803,531269504,734031980,2814959249,45666,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.33614,,0.21532,,0.99019,,0.41002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10061,ERR4795365,ERX4665135,ERS5281176,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 4,E MTAB 9727:Sample 4,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 4 s,Sample 4 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 4,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz,fastq,5414184547.0,71707309.0,E MTAB 9727:Sample 4 1,0:0 1:75.50,A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967,0,75,,,1582938104,1052565419,1177180395,1600161662,1338967,ERX4665135,ERS5281176,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.84976,,0.28521,,0.85038,,0.5124,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10062,ERR4795362,ERX4665134,ERS5281175,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 3,E MTAB 9727:Sample 3,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 3 s,Sample 3 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 3,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz,fastq,4823193891.0,63965519.0,E MTAB 9727:Sample 3,0:75.40 1:0,A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086,75,0,,,1323978162,446831209,581746343,2470114091,524086,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.36549,,0.19722,,0.95552,,0.4702,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10063,ERR4795363,ERX4665134,ERS5281175,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 3,E MTAB 9727:Sample 3,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 3 s,Sample 3 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 3,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz,fastq,4828889391.0,63965519.0,E MTAB 9727:Sample 3 1,0:0 1:75.49,A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756,0,75,,,1434099697,964508763,893584575,1534727600,1968756,ERX4665134,ERS5281175,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.85811,,0.26231,,0.82731,,0.48618,,76,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10064,ERR4795360,ERX4665133,ERS5281174,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 2,E MTAB 9727:Sample 2,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 2 s,Sample 2 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 2,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz,fastq,5598371393.0,74235388.0,E MTAB 9727:Sample 2,0:75.41 1:0,A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655,75,0,,,1526486973,558020193,717587491,2795646081,630655,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.28059,,0.19252,,0.96404,,0.4874,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10065,ERR4795361,ERX4665133,ERS5281174,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 2,E MTAB 9727:Sample 2,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 2 s,Sample 2 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 2,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz,fastq,5600151371.0,74235388.0,E MTAB 9727:Sample 2 1,0:0 1:75.44,A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060,0,75,,,1850568176,1035622971,1071138281,1640475883,2346060,ERX4665133,ERS5281174,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.7679,,0.30371,,0.82651,,0.43401,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10066,ERR4795358,ERX4665132,ERS5281173,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 1,E MTAB 9727:Sample 1,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 1 s,Sample 1 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz,fastq,4996502316.0,66258508.0,E MTAB 9727:Sample 1,0:75.41 1:0,A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936,75,0,,,1330744174,451622042,591151500,2622422664,561936,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.29754,,0.17671,,0.9669,,0.45463,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
10067,ERR4795359,ERX4665132,ERS5281173,ERP124847,PRJEB41113,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E-MTAB-9727,Transcriptome Analysis,The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration  and their dysregulation can result in congenital anomalies of the viscera  ventral wall defects  and mesothelioma tumors. Nonetheless  the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here  we combine genetic lineage tracing  in toto live imaging  and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos  we chart the origin of mesothelial progenitors to the lateral most  hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation  documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally  hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium  we find de novo expression of LPM associated transcription factors  and in particular of Hand2  indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together  our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2  contributing to our understanding of mesothelial pathologies and mesothelioma.,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,,Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Sample 1,E MTAB 9727:Sample 1,,isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01,,,,,,,,,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,E MTAB 9727:Sample 1 s,Sample 1 s,Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche  followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3  without xxx glutamine and sodium pyruvate  Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently  they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon        round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing  the cells were resuspended in 1X PBS.  drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering  to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al.  2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch  a 4 bp random molecular barcode UMI  a cell specific barcode  the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter  provided by Single Cell Discoveries. post sorting  the plates were immediately placed on ice and stored at −80°C.  In brief  ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,Experimental Factor: replicate:lateral plate mesoderm plate 1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,SINGLE,ILLUMINA,NextSeq 500,,ERP124847,NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma,ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14,SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz,fastq,4999908389.0,66258508.0,E MTAB 9727:Sample 1 1,0:0 1:75.46,A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512,0,75,,,1591945117,933968124,986108614,1485824022,2062512,ERX4665132,ERS5281173,ERA3048543,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,1,0.81333,,0.2466,,0.83027,,0.51572,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Switzerland,2021-04-01,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30508,SRR27764648,SRX23429609,SRS20284060,SRP486518,PRJNA1070582,Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition,GSE254439,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells  or ßcatCA unexpressing GFP  cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:39546611,,Mosaic GFP control GFP min lot2,GSM8042248,,source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing,Mosaic GFP control GFP min lot2,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,early embryonic cell,,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|tissue:early embryonic cell|developmental stage:9 hpf,GSM8042248,GSM8042248: Mosaic GFP control GFP min lot2; Danio rerio; RNA Seq,GSM8042248 r1,GSM8042248,1,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP486518,,,Mosaic_GFP_control_GFP_min_lot2.fastq.gz,fastq,7474464.0,207624.0,GSM8042248 r1,0:36,A:1796571;C:1274347;G:1548876;T:2854637;N:33,36,,,,1796571,1274347,1548876,2854637,33,SRX23429609,SRS20284060,SRA1793856,"Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University","Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University",1,0.82922,,0.20207,,0.86143,,0.54661,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2024-01-29,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30509,SRR27764649,SRX23429608,SRS20284059,SRP486518,PRJNA1070582,Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition,GSE254439,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells  or ßcatCA unexpressing GFP  cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:39546611,,Mosaic GFP control GFP min lot1,GSM8042247,,source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing,Mosaic GFP control GFP min lot1,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,early embryonic cell,,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|tissue:early embryonic cell|developmental stage:9 hpf,GSM8042247,GSM8042247: Mosaic GFP control GFP min lot1; Danio rerio; RNA Seq,GSM8042247 r1,GSM8042247,1,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP486518,,,Mosaic_GFP_control_GFP_min_lot1.fastq.gz,fastq,8256240.0,229340.0,GSM8042247 r1,0:36,A:1947003;C:1345938;G:1692065;T:3271133;N:101,36,,,,1947003,1345938,1692065,3271133,101,SRX23429608,SRS20284059,SRA1793856,"Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University","Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University",1,0.83305,,0.17754,,0.8619,,0.61474,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2024-01-29,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30510,SRR27764650,SRX23429607,SRS20284058,SRP486518,PRJNA1070582,Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition,GSE254439,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells  or ßcatCA unexpressing GFP  cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:39546611,,Mosaic beta catCA GFP min lot2,GSM8042246,,source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing,Mosaic beta catCA GFP min lot2,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,early embryonic cell,,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|tissue:early embryonic cell|developmental stage:9 hpf,GSM8042246,GSM8042246: Mosaic beta catCA GFP min lot2; Danio rerio; RNA Seq,GSM8042246 r1,GSM8042246,1,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP486518,,,Mosaic_beta-catCA_GFP_min_lot2.fastq.gz,fastq,856836.0,23801.0,GSM8042246 r1,0:36,A:217589;C:147419;G:175612;T:316201;N:15,36,,,,217589,147419,175612,316201,15,SRX23429607,SRS20284058,SRA1793856,"Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University","Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University",1,0.82481,,0.28434,,0.95371,,0.61551,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2024-01-29,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
30511,SRR27764651,SRX23429606,SRS20284057,SRP486518,PRJNA1070582,Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition,GSE254439,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing GFP+ cells  or ßcatCA unexpressing GFP  cells from ß catCA mosaically introduced zebrafish early embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:39546611,,Mosaic beta catCA GFP min lot1,GSM8042245,,source name:early embryonic cell|strain:AB|tissue:early embryonic cell|developmental stage:9 hpf loc name:missing|collection date:missing,Mosaic beta catCA GFP min lot1,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Assembly: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,early embryonic cell,,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|tissue:early embryonic cell|developmental stage:9 hpf,GSM8042245,GSM8042245: Mosaic beta catCA GFP min lot1; Danio rerio; RNA Seq,GSM8042245 r1,GSM8042245,1,Cells were dissolved in TRIzol reagent Invitrogen and extracted. Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP486518,,,Mosaic_beta-catCA_GFP_min_lot1.fastq.gz,fastq,7181388.0,199483.0,GSM8042245 r1,0:36,A:1744919;C:1207643;G:1456829;T:2771919;N:78,36,,,,1744919,1207643,1456829,2771919,78,SRX23429606,SRS20284057,SRA1793856,"Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University","Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University",1,0.83629,,0.16823,,0.84774,,0.64548,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2024-01-29,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
38099,SRR1531457,SRX665245,SRS670059,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end  replicate,GSM1448802,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448802,GSM1448802: shield stage  secti1d from dorsal to ventral end  replicate; Danio rerio; RNA Seq,GSM1448802,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448802,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_DV2_R2.fastq.gz dr_shield_DV2_R1.fastq.gz,fastq fastq,2735350014.0,26817157.0,GSM1448802 r1,0:51 1:51,A:650077339;C:412458828;G:411687121;T:1237686190;N:23440536,51,51,,,650077339,412458828,411687121,1237686190,23440536,SRX665245,SRS670059,SRA177126,GEO,Hubrecht Institute,2,0.02556,0.75175,0.01912,0.10697,0.99076,0.79819,0.54093,0.55229,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38100,SRR1531455,SRX665244,SRS670058,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end,GSM1448801,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448801,GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448801,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_DV_R1.fastq.gz dr_shield_DV_R2.fastq.gz,fastq fastq,1605318738.0,15738419.0,GSM1448801 r1,0:51 1:51,A:361176217;C:248822696;G:253372108;T:726629351;N:15318366,51,51,,,361176217,248822696,253372108,726629351,15318366,SRX665244,SRS670058,SRA177126,GEO,Hubrecht Institute,2,0.02633,0.68496,0.02344,0.10104,0.99638,0.80006,0.46031,0.57655,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38101,SRR1531456,SRX665244,SRS670058,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from dorsal to ventral end,GSM1448801,,tissue:whole embryo|Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from dorsal to ventral end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:dorsal ventral|section thickness:18 µm|embedding strategy:intact embryo,GSM1448801,GSM1448801: shield stage  secti1d from dorsal to ventral end; Danio rerio; RNA Seq,GSM1448801,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_DV_R1.fastq.gz miseq_dr_shield_DV_R2.fastq.gz,fastq fastq,114907294.0,229320.0,GSM1448801 r2,0:251 1:250.08,A:37813553;C:24168661;G:19441624;T:33483456;N:0,251,250,,,37813553,24168661,19441624,33483456,0,SRX665244,SRS670058,SRA177126,GEO,Hubrecht Institute,2,0.26022,0.46204,0.03083,0.05933,0.94627,0.89301,0.56728,0.55478,251,250,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38102,SRR1531453,SRX665243,SRS670056,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from ventral to dorsal end,GSM1448800,,tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448800,GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448800,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VD_R1.fastq.gz dr_shield_VD_R2.fastq.gz,fastq fastq,1840839492.0,18047446.0,GSM1448800 r1,0:51 1:51,A:421253850;C:292045914;G:295175858;T:814744774;N:17619096,51,51,,,421253850,292045914,295175858,814744774,17619096,SRX665243,SRS670056,SRA177126,GEO,Hubrecht Institute,2,0.01815,0.6287,0.01468,0.09567,0.99452,0.80975,0.5259,0.58926,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38103,SRR1531454,SRX665243,SRS670056,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from ventral to dorsal end,GSM1448800,,tissue:whole embryo|Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from ventral to dorsal end,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:ventral dorsal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448800,GSM1448800: shield stage  secti1d from ventral to dorsal end; Danio rerio; RNA Seq,GSM1448800,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_VD_R2.fastq.gz miseq_dr_shield_VD_R1.fastq.gz,fastq fastq,158531701.0,316379.0,GSM1448800 r2,,,,,,,,,,,,SRX665243,SRS670056,SRA177126,GEO,Hubrecht Institute,2,0.06803,0.1733,0.00916,0.026,0.94085,0.88899,0.58254,0.5723,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38104,SRR1531451,SRX665242,SRS670055,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from right to left,GSM1448799,,tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448799,GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448799,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_RL_R1.fastq.gz dr_shield_RL_R2.fastq.gz,fastq fastq,2003076918.0,19638009.0,GSM1448799 r1,0:51 1:51,A:457537608;C:308292947;G:312973612;T:905317961;N:18954790,51,51,,,457537608,308292947,312973612,905317961,18954790,SRX665242,SRS670055,SRA177126,GEO,Hubrecht Institute,2,0.02111,0.7573,0.01656,0.11316,0.99364,0.8005,0.4501,0.59142,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38105,SRR1531452,SRX665242,SRS670055,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from right to left,GSM1448799,,tissue:whole embryo|Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from right to left,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:right left|section thickness:18 µm|embedding strategy:intact embryo,GSM1448799,GSM1448799: shield stage  secti1d from right to left; Danio rerio; RNA Seq,GSM1448799,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_RL_R1.fastq.gz miseq_dr_shield_RL_R2.fastq.gz,fastq fastq,154180181.0,307695.0,GSM1448799 r2,0:251 1:250.08,A:50801230;C:32293099;G:25917988;T:45167860;N:4,251,250,,,50801230,32293099,25917988,45167860,4,SRX665242,SRS670055,SRA177126,GEO,Hubrecht Institute,2,0.31553,0.64085,0.03613,0.06829,0.94101,0.8938,0.60272,0.58117,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38106,SRR1531449,SRX665241,SRS670053,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from left to right,GSM1448798,,tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448798,GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448798,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_LR_R1.fastq.gz dr_shield_LR_R2.fastq.gz,fastq fastq,1755442542.0,17210221.0,GSM1448798 r1,0:51 1:51,A:401133098;C:265688355;G:264899378;T:807011867;N:16709844,51,51,,,401133098,265688355,264899378,807011867,16709844,SRX665241,SRS670053,SRA177126,GEO,Hubrecht Institute,2,0.02829,0.71918,0.02455,0.14486,0.99484,0.79866,0.50383,0.57925,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38107,SRR1531450,SRX665241,SRS670053,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from left to right,GSM1448798,,tissue:whole embryo|Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from left to right,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:left right|section thickness:18 µm|embedding strategy:intact embryo,GSM1448798,GSM1448798: shield stage  secti1d from left to right; Danio rerio; RNA Seq,GSM1448798,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_LR_R1.fastq.gz miseq_dr_shield_LR_R2.fastq.gz,fastq fastq,139755993.0,278913.0,GSM1448798 r2,0:251 1:250.07,A:46536591;C:28346077;G:23036783;T:41836538;N:4,251,250,,,46536591,28346077,23036783,41836538,4,SRX665241,SRS670053,SRA177126,GEO,Hubrecht Institute,2,0.27443,0.57858,0.06346,0.09954,0.94194,0.89522,0.55896,0.56169,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38108,SRR1531448,SRX665240,SRS670054,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole  replicate,GSM1448797,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole  replicate,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448797,GSM1448797: shield stage  secti1d from vegetal to animal pole  replicate; Danio rerio; RNA Seq,GSM1448797,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448797,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VA2_R1.fastq.gz dr_shield_VA2_R2.fastq.gz,fastq fastq,1962884532.0,19243966.0,GSM1448797 r1,0:51 1:51,A:449529690;C:292065368;G:287973067;T:916330652;N:16985755,51,51,,,449529690,292065368,287973067,916330652,16985755,SRX665240,SRS670054,SRA177126,GEO,Hubrecht Institute,2,0.04512,0.77455,0.03997,0.11233,0.99293,0.78488,0.50931,0.5171,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38109,SRR1531446,SRX665239,SRS670057,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole,GSM1448796,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448796,GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq,GSM1448796,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_VA_R2.fastq.gz dr_shield_VA_R1.fastq.gz,fastq fastq,2367839934.0,23214117.0,GSM1448796 r1,0:51 1:51,A:544061124;C:369321045;G:383489434;T:1047897582;N:23070749,51,51,,,544061124,369321045,383489434,1047897582,23070749,SRX665239,SRS670057,SRA177126,GEO,Hubrecht Institute,2,0.02284,0.57831,0.0199,0.08251,0.99579,0.81653,0.4451,0.5792,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38110,SRR1531447,SRX665239,SRS670057,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from vegetal to animal pole,GSM1448796,,tissue:whole embryo|Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from vegetal to animal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:vegetal animal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448796,GSM1448796: shield stage  secti1d from vegetal to animal pole; Danio rerio; RNA Seq,GSM1448796,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_VA_R1.fastq.gz miseq_dr_shield_VA_R2.fastq.gz,fastq fastq,139677889.0,278764.0,GSM1448796 r2,0:251 1:250.06,A:45877333;C:29821713;G:24032460;T:39946380;N:3,251,250,,,45877333,29821713,24032460,39946380,3,SRX665239,SRS670057,SRA177126,GEO,Hubrecht Institute,2,0.21444,0.33364,0.02489,0.04529,0.95156,0.901,0.56549,0.55749,251,251,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38111,SRR1531444,SRX665238,SRS670052,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from animal to vegetal pole,GSM1448795,,tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from animal to vegetal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448795,GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq,GSM1448795,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,,dr_shield_AV_R1.fastq.gz dr_shield_AV_R2.fastq.gz,fastq fastq,2059615110.0,20192305.0,GSM1448795 r1,0:51 1:51,A:487942041;C:328047311;G:336282927;T:886836259;N:20506572,51,51,,,487942041,328047311,336282927,886836259,20506572,SRX665238,SRS670052,SRA177126,GEO,Hubrecht Institute,2,0.01633,0.50842,0.0136,0.07269,0.99541,0.82183,0.51242,0.59281,51,51,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
38112,SRR1531445,SRX665238,SRS670052,SRP045064,PRJNA256975,Genome wide RNA tomography in the zebrafish embryo,GSE59873,Other,Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes  they are unable to yield spatially resolved information in embryos or tissues. Microscopy based approaches  using for example in situ hybridization  can provide spatial information about gene expression  but are limited to analyzing one or a few genes at a time. Here  we present a method where we combine traditional histological techniques with low input RNA sequencing and mathematical image reconstruction to generate a high resolution genome wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly  our method enables searching for genes that are expressed in specific spatial patterns without xxx image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs. Overall design: To generate spatially resolved RNA seq data for zebrafish embryos shield stage  10 somites  15 somites  18 somites and mouse forelimbs E10.5  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired end to improve three prime annotations.,,pubmed:25417113,,shield stage  secti1d from animal to vegetal pole,GSM1448795,,tissue:whole embryo|Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,shield stage  secti1d from animal to vegetal pole,Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript Table S1. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: mm10 and zv9 with improved three prime annotation Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections,whole embryo,Unfixed samples zebrafish embryos or mouse forelimbs were embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice.,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,,Stage:shield stage|sectioning direction:animal vegetal|section thickness:18 µm|embedding strategy:intact embryo,GSM1448795,GSM1448795: shield stage  secti1d from animal to vegetal pole; Danio rerio; RNA Seq,GSM1448795,,1,RNA was isolated by TRIzol extraction mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012,GEO Accession:GSM1448795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP045064,,instrument model:Illumina MiSeq,miseq_dr_shield_AV_R1.fastq.gz miseq_dr_shield_AV_R2.fastq.gz,fastq fastq,176530873.0,352271.0,GSM1448795 r2,0:251 1:250.12,A:57029265;C:38838035;G:30065677;T:50597891;N:5,251,250,,,57029265,38838035,30065677,50597891,5,SRX665238,SRS670052,SRA177126,GEO,Hubrecht Institute,2,0.20318,0.26844,0.02342,0.03751,0.95499,0.9069,0.4325,0.57102,251,251,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_plate,celseq,,Netherlands,2014-07-29,Gastrula,Embryo,Whole Organism,All anatomical structures
39741,SRR2089842,SRX1085056,SRS981139,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 5,GSM1812032,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 5,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812032,GSM1812032: cFD + spt cMO replicate 5; Danio rerio; RNA Seq,GSM1812032,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812032,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_5_1.bz2 cMO_5_2.bz2,fastq fastq,2590806954.0,12825777.0,GSM1812032 r1,0:101 1:101,A:729527639;C:388090931;G:473627524;T:996733909;N:2826951,101,101,,,729527639,388090931,473627524,996733909,2826951,SRX1085056,SRS981139,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.34765,0.81821,0.09574,0.11092,0.96846,0.84273,0.56486,0.60514,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39742,SRR2089841,SRX1085055,SRS981140,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 4,GSM1812031,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 4,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812031,GSM1812031: cFD + spt cMO replicate 4; Danio rerio; RNA Seq,GSM1812031,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812031,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_4_2.bz2 cMO_4_1.bz2,fastq fastq,4576986902.0,22658351.0,GSM1812031 r1,0:101 1:101,A:1236262881;C:739179623;G:837030962;T:1759535468;N:4977968,101,101,,,1236262881,739179623,837030962,1759535468,4977968,SRX1085055,SRS981140,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.4938,0.83831,0.1798,0.13149,0.96593,0.84766,0.57231,0.63621,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39743,SRR2089840,SRX1085054,SRS981143,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 3,GSM1812030,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 3,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812030,GSM1812030: cFD + spt cMO replicate 3; Danio rerio; RNA Seq,GSM1812030,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812030,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_3_1.bz2 cMO_3_2.bz2,fastq fastq,2769659976.0,13711188.0,GSM1812030 r1,0:101 1:101,A:801844710;C:425581810;G:477170945;T:1062200254;N:2862257,101,101,,,801844710,425581810,477170945,1062200254,2862257,SRX1085054,SRS981143,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.36913,0.82247,0.20581,0.12151,0.97656,0.84589,0.57375,0.61151,101,101,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39744,SRR2089839,SRX1085053,SRS981142,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 2,GSM1812029,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 2,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812029,GSM1812029: cFD + spt cMO replicate 2; Danio rerio; RNA Seq,GSM1812029,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812029,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_2_1.bz2 cMO_2_2.bz2,fastq fastq,2482029348.0,12287274.0,GSM1812029 r1,0:101 1:101,A:675627490;C:417393063;G:437628865;T:948867297;N:2512633,101,101,,,675627490,417393063,437628865,948867297,2512633,SRX1085053,SRS981142,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.49124,0.82814,0.19593,0.12778,0.96694,0.84814,0.61289,0.65915,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39745,SRR2089838,SRX1085052,SRS981141,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD + spt cMO replicate 1,GSM1812028,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,cFD + spt cMO replicate 1,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD and the spt cMO,GSM1812028,GSM1812028: cFD + spt cMO replicate 1; Danio rerio; RNA Seq,GSM1812028,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812028,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cMO_1_1.bz2 cMO_1_2.bz2,fastq fastq,7585699334.0,37552967.0,GSM1812028 r1,0:101 1:101,A:1977695961;C:1274396713;G:1452711269;T:2871964961;N:8930430,101,101,,,1977695961,1274396713,1452711269,2871964961,8930430,SRX1085052,SRS981141,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.48942,0.85323,0.16329,0.18148,0.97236,0.8565,0.59311,0.63618,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39746,SRR2089837,SRX1085051,SRS981144,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 5,GSM1812027,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 5,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812027,GSM1812027: cFD only replicate 5; Danio rerio; RNA Seq,GSM1812027,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812027,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_5_1.bz2 cntrl_5_2.bz2,fastq fastq,4762488754.0,23576677.0,GSM1812027 r1,0:101 1:101,A:1380401515;C:716191196;G:808857049;T:1851642812;N:5396182,101,101,,,1380401515,716191196,808857049,1851642812,5396182,SRX1085051,SRS981144,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.4168,0.81605,0.16291,0.11435,0.97185,0.84354,0.6892,0.61855,101,101,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39747,SRR2089836,SRX1085050,SRS981145,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 4,GSM1812026,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 4,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812026,GSM1812026: cFD only replicate 4; Danio rerio; RNA Seq,GSM1812026,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812026,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_4_1.bz2 cntrl_4_2.bz2,fastq fastq,3719006042.0,18410921.0,GSM1812026 r1,0:101 1:101,A:1038933535;C:615185731;G:647242496;T:1413253009;N:4391271,101,101,,,1038933535,615185731,647242496,1413253009,4391271,SRX1085050,SRS981145,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.46956,0.82686,0.12167,0.11363,0.97025,0.85074,0.58699,0.63586,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39748,SRR2089835,SRX1085049,SRS981146,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 3,GSM1812025,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 3,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812025,GSM1812025: cFD only replicate 3; Danio rerio; RNA Seq,GSM1812025,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812025,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_3_2.bz2 cntrl_3_1.bz2,fastq fastq,2513713250.0,12444125.0,GSM1812025 r1,0:101 1:101,A:709549704;C:390305955;G:451783096;T:959236114;N:2838381,101,101,,,709549704,390305955,451783096,959236114,2838381,SRX1085049,SRS981146,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.41236,0.81226,0.11339,0.11567,0.97051,0.85305,0.60801,0.4295,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39749,SRR2089834,SRX1085048,SRS981148,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 2,GSM1812024,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 2,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812024,GSM1812024: cFD only replicate 2; Danio rerio; RNA Seq,GSM1812024,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812024,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_2_1.bz2 cntrl_2_2.bz2,fastq fastq,6157457728.0,30482464.0,GSM1812024 r1,0:101 1:101,A:1679764131;C:1000368713;G:1086099790;T:2384200862;N:7024232,101,101,,,1679764131,1000368713,1086099790,2384200862,7024232,SRX1085048,SRS981148,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.47785,0.82086,0.20529,0.14023,0.97226,0.85232,0.65332,0.66262,101,101,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
39750,SRR2089833,SRX1085047,SRS981147,SRP060505,PRJNA289199,Transcriptome wide profiling of Spadetail regulated genes in early somite progenitors,GSE70623,Transcriptome Analysis,We integrate zebrafish embryology with photoactivatable caged morpholinos cMO  the photoactivatable lineage tracer caged fluorescein dextran cFD  fluorescence activated cell sorting FACS and RNA sequencing RNA seq to identify Spadetail regulated genes in mesodermal cells enriched for early somite progenitors. Overall design: 1 to 4 cell stage zebrafish embryos were injected with either cFD alone or in combination with the spt cMO and allowed to develop until 6 hpf.  Early ventral somite progenitors were then optically targeted with ultraviolet 360 nm light using a 100 µm diameter circular diaphragm.  Embryos were permitted to develop until 9 hpf  dechorionated  and dissociated into single cells. Fluorescein positive cells were then isolated by FACS.  Five experimental replicates were performed.  Sequencing libraries were then prepared from purified cells according to the CEL Seq protocol Hashimshony  T et al.  Cell Reports. 2012. In short  total RNA from each sample were individually barcoded and combined prior to sequencing on a HiSeq 2000. Reads were processed and aligned to zebrafish assembly Zv8 using custom CEL seq scripts within the Galaxy bioinformatics platform. Count files were then analyzed using EdgeR statistical analysis to determine differentially expressed genes.,,pubmed:27376691,,cFD only replicate 1,GSM1812023,,tissue:embryo|strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,cFD only replicate 1,Basecalls performed using HiSeq control software v 1.5.15 Paired end reads passing initial QC from two sequencing lanes were concatenated head to tail Data was processed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012 using custom scripts http://yanailab.technion.ac.il: De multiplexing of read 1 file using a unique 8 bp barcode  filtering/truncation of read 2 quality  score >20; 35 bp  alignment of read 2 35 bp reads to Zv8 reference  and feature counting Count files analyzed using EdgeR to identify differentially expressed genes Genome build: Zv8 Supplementary files format and content: Tab delimited text files of raw counts and normalized abundance measurements from EdgeR analysis,embryo,1 cell stage embryos were injected with either caged fluorescein dextran cFD alone or in combination were the spt caged morpholino cMO and allowed to develop until 6 hpf.  Embryos were then irradiated with UV light using a 100 μm diameter diaphragm targeting ventral somites uncaging cFD alone or cFD and the spt cMO simultaneously.  Embryos were then allowed to develop until 9 hpf and then dissociated into single cells.  Fluorescein positive cells were isolated using fluorescence activated cell sorting FACS directly into lysis buffer RNAqueous Micro Total RNA Isolation Kit; Ambion and immediately lysed.  Lysed cells in lysis buffer were then stored in  80 °C until all samples for 5 biological replicates were obtained.,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,Zebrafish embryos were obtained from natural spawning,strain:WT AB|cell type:ventral somite progenitors|Stage:late gastrulation 9 hpf|treatment:cFD al1,GSM1812023,GSM1812023: cFD only replicate 1; Danio rerio; RNA Seq,GSM1812023,,1,post collection of 5 biological replicates  total RNA was obtained from each sample using the RNAqueous Micro Total RNA Isolation Kit Ambion and RNA integrity was assessed by bioanalyzer analysis RIN 8.1   9.9 Libraries were constructed according to the CEL seq protocol Hashimshony  T et al.  Cell Reports. 2012.  Barcode information on read 1 of paired end reads: cntrl 1  CATCACGC; cntrl 2  GTCGTTCC; cntrl 3  GTCGTGAA; cntrl 4  TCACACGC; cntrl 5  TCACAGAG; cMO 1  TGATGCGC; cMO 2  ACGACTCC; cMO 3  ACGACGAA; cMO 4  ATGTGCGC; cMO 5  CGTGTGAG.,GEO Accession:GSM1812023,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP060505,,,cntrl_1_1.bz2 cntrl_1_2.bz2,fastq fastq,4291177304.0,21243452.0,GSM1812023 r1,0:101 1:101,A:1182202535;C:708780301;G:753724632;T:1641921837;N:4547999,101,101,,,1182202535,708780301,753724632,1641921837,4547999,SRX1085047,SRS981147,SRA276152,GEO,"James Chen, Chemical and Systems Biology, Stanford University",2,0.45088,0.8425,0.11253,0.11641,0.97835,0.84778,0.46728,0.64503,101,101,B,B,mate1-mate2 similar by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,United States,2015-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
40599,SRR3231354,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.1_R1_001.fastq.gz 8hpf_wt_Plate4.1_R2_001.fastq.gz,fastq fastq,2340114249.0,31038332.0,GSM2090871 r1,0:75.50 1:75.29,A:719873895;C:416010081;G:472221417;T:731461092;N:547764,75,75,,,719873895,416010081,472221417,731461092,547764,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00529,,0.00355,,0.99655,,0.52173,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40600,SRR3231355,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.2_R1_001.fastq.gz 8hpf_wt_Plate4.2_R2_001.fastq.gz,fastq fastq,2340187687.0,31038332.0,GSM2090871 r2,0:75.50 1:75.29,A:718375391;C:414519064;G:478873036;T:728401149;N:19047,75,75,,,718375391,414519064,478873036,728401149,19047,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",1,0.00524,,0.00333,,0.99634,,0.47321,,76,,T,,under 1.2% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40601,SRR3231356,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4.3_R1_001.fastq.gz 8hpf_wt_Plate4.3_R2_001.fastq.gz,fastq fastq,2331948832.0,15464230.0,GSM2090871 r3,0:75.51 1:75.29,A:710801790;C:413559417;G:478178818;T:728790143;N:618664,75,75,,,710801790,413559417,478178818,728790143,618664,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00263,0.00843,0.0023,0.00555,0.99955,0.99437,0.37837,0.52459,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40602,SRR3231357,SRX1637105,SRS1342922,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate4.1,GSM2090871,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090871,GSM2090871: 8hpf wt Plate4.1; Danio rerio; RNA Seq,GSM2090871,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate4_R1_001.fastq.gz 8hpf_wt_Plate4_R2_001.fastq.gz,fastq fastq,2346532249.0,15562065.0,GSM2090871 r4,0:75.50 1:75.29,A:726362504;C:417435976;G:471522192;T:731180603;N:30974,75,75,,,726362504,417435976,471522192,731180603,30974,SRX1637105,SRS1342922,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0024,0.00837,0.00209,0.00548,0.99975,0.99409,0.2,0.53439,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40603,SRR3231350,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.1_R2_001.fastq.gz 8hpf_wt_Plate3.1_R1_001.fastq.gz,fastq fastq,1401297283.0,9290433.0,GSM2090870 r1,0:75.49 1:75.34,A:419635887;C:271951633;G:296507210;T:413191086;N:11467,75,75,,,419635887,271951633,296507210,413191086,11467,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00163,0.00616,0.00116,0.00341,0.99951,0.99425,0.125,0.59722,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40604,SRR3231351,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.2_R1_001.fastq.gz 8hpf_wt_Plate3.2_R2_001.fastq.gz,fastq fastq,1401701707.0,9293054.0,GSM2090870 r2,0:75.50 1:75.34,A:422173594;C:272799681;G:292195265;T:414209404;N:323763,75,75,,,422173594,272799681,292195265,414209404,323763,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00183,0.0057,0.00134,0.00307,0.99959,0.9948,0.18965,0.59402,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40605,SRR3231352,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3.3_R1_001.fastq.gz 8hpf_wt_Plate3.3_R2_001.fastq.gz,fastq fastq,1395747908.0,9253276.0,GSM2090870 r3,0:75.50 1:75.34,A:416176386;C:270989429;G:295563056;T:412655214;N:363823,75,75,,,416176386,270989429,295563056,412655214,363823,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00148,0.0058,0.00112,0.00312,0.99969,0.99476,0.16279,0.54093,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40606,SRR3231353,SRX1637104,SRS1342923,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate3.1,GSM2090870,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090870,GSM2090870: 8hpf wt Plate3.1; Danio rerio; RNA Seq,GSM2090870,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate3_R1_001.fastq.gz 8hpf_wt_Plate3_R2_001.fastq.gz,fastq fastq,1407551761.0,9332199.0,GSM2090870 r4,0:75.49 1:75.34,A:425795996;C:274090898;G:292401737;T:415244521;N:18609,75,75,,,425795996,274090898,292401737,415244521,18609,SRX1637104,SRS1342923,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00196,0.00615,0.00142,0.00325,0.99926,0.99403,0.39682,0.57712,74,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40607,SRR3231346,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.1_R1_001.fastq.gz 8hpf_wt_Plate2.1_R2_001.fastq.gz,fastq fastq,952595024.0,6315631.0,GSM2090869 r1,0:75.47 1:75.36,A:302137554;C:151875219;G:168962721;T:329611160;N:8370,75,75,,,302137554,151875219,168962721,329611160,8370,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00829,0.04086,0.00683,0.01381,0.99898,0.97133,0.21481,0.68244,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40608,SRR3231347,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.2_R1_001.fastq.gz 8hpf_wt_Plate2.2_R2_001.fastq.gz,fastq fastq,946451815.0,6274940.0,GSM2090869 r2,0:75.47 1:75.36,A:302374789;C:151074230;G:165028305;T:327758585;N:215906,75,75,,,302374789,151074230,165028305,327758585,215906,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00869,0.03997,0.00704,0.01272,0.99888,0.97183,0.24342,0.68028,75,74,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40609,SRR3231348,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2.3_R2_001.fastq.gz 8hpf_wt_Plate2.3_R1_001.fastq.gz,fastq fastq,947126047.0,6279272.0,GSM2090869 r3,0:75.48 1:75.36,A:299035197;C:150983123;G:168162807;T:328697140;N:247780,75,75,,,299035197,150983123,168162807,328697140,247780,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00868,0.03867,0.00717,0.01319,0.99864,0.97356,0.29285,0.66677,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40610,SRR3231349,SRX1637103,SRS1342924,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate2.1,GSM2090869,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090869,GSM2090869: 8hpf wt Plate2.1; Danio rerio; RNA Seq,GSM2090869,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate2_R1_001.fastq.gz 8hpf_wt_Plate2_R2_001.fastq.gz,fastq fastq,948028451.0,6285580.0,GSM2090869 r4,0:75.47 1:75.36,A:304286797;C:151414365;G:164490323;T:327824187;N:12779,75,75,,,304286797,151414365,164490323,327824187,12779,SRX1637103,SRS1342924,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0086,0.04012,0.00712,0.01343,0.99888,0.97177,0.29411,0.66575,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40611,SRR3231342,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.1_R1_001.fastq.gz 8hpf_wt_Plate1.1_R2_001.fastq.gz,fastq fastq,1189452130.0,7888435.0,GSM2090868 r1,0:75.47 1:75.32,A:375847699;C:199289576;G:245818831;T:368358068;N:137956,75,75,,,375847699,199289576,245818831,368358068,137956,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00377,0.02162,0.00304,0.01018,0.99931,0.9848,0.29032,0.61771,75,73,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40612,SRR3231343,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.2_R1_001.fastq.gz 8hpf_wt_Plate1.2_R2_001.fastq.gz,fastq fastq,1238856894.0,8215764.0,GSM2090868 r2,0:75.47 1:75.32,A:389215255;C:208182440;G:256176425;T:385173832;N:108942,75,75,,,389215255,208182440,256176425,385173832,108942,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00375,0.02269,0.00298,0.01135,0.99928,0.98423,0.40579,0.61686,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40613,SRR3231344,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1.3_R1_001.fastq.gz 8hpf_wt_Plate1.3_R2_001.fastq.gz,fastq fastq,1240573542.0,8227185.0,GSM2090868 r3,0:75.47 1:75.32,A:389703162;C:207657187;G:257329681;T:385780094;N:103418,75,75,,,389703162,207657187,257329681,385780094,103418,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00354,0.02325,0.00287,0.01111,0.99922,0.98309,0.47368,0.60449,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40614,SRR3231345,SRX1637102,SRS1342925,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf wt Plate1.1,GSM2090868,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf wt Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:wildtype|protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090868,GSM2090868: 8hpf wt Plate1.1; Danio rerio; RNA Seq,GSM2090868,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_wt_Plate1_R1_001.fastq.gz 8hpf_wt_Plate1_R2_001.fastq.gz,fastq fastq,1215460175.0,8061085.0,GSM2090868 r4,0:75.46 1:75.32,A:382475416;C:204057930;G:251490776;T:377293780;N:142273,75,75,,,382475416,204057930,251490776,377293780,142273,SRX1637102,SRS1342925,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00394,0.02131,0.00309,0.0101,0.99928,0.98472,0.34285,0.61368,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40615,SRR3231338,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.1_R2_001.fastq.gz,fastq fastq,660308475.0,4377096.0,GSM2090867 r1,0:75.49 1:75.36,A:203051507;C:115872485;G:122313924;T:219064434;N:6125,75,75,,,203051507,115872485,122313924,219064434,6125,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00239,0.00751,0.00191,0.00364,0.99941,0.99385,0.5625,0.71067,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40616,SRR3231339,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.2_R2_001.fastq.gz,fastq fastq,659386859.0,4370960.0,GSM2090867 r2,0:75.50 1:75.36,A:204037715;C:116060649;G:120151402;T:218981853;N:155240,75,75,,,204037715,116060649,120151402,218981853,155240,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00303,0.00736,0.00246,0.00371,0.99941,0.99429,0.45614,0.65738,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40617,SRR3231340,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4.3_R2_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4.3_R1_001.fastq.gz,fastq fastq,656929514.0,4354565.0,GSM2090867 r3,0:75.50 1:75.36,A:200970859;C:115371071;G:121921931;T:218498053;N:167600,75,75,,,200970859,115371071,121921931,218498053,167600,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00267,0.00746,0.00211,0.00354,0.99926,0.99371,0.58181,0.66467,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40618,SRR3231341,SRX1637101,SRS1342933,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate4.1,GSM2090867,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate4.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090867,GSM2090867: 8hpf Tdrd6a :  Plate4.1; Danio rerio; RNA Seq,GSM2090867,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate4_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate4_R2_001.fastq.gz,fastq fastq,659750831.0,4373567.0,GSM2090867 r4,0:75.49 1:75.36,A:205228191;C:116070031;G:119659384;T:218783801;N:9424,75,75,,,205228191,116070031,119659384,218783801,9424,SRX1637101,SRS1342933,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00286,0.00728,0.00232,0.00355,0.99945,0.99439,0.47169,0.69696,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40619,SRR3231334,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.1_R2_001.fastq.gz,fastq fastq,991807830.0,6574461.0,GSM2090866 r1,0:75.50 1:75.35,A:306057776;C:164673747;G:183621348;T:337443425;N:11534,75,75,,,306057776,164673747,183621348,337443425,11534,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00573,0.01848,0.00474,0.0066,0.99918,0.98362,0.36274,0.59804,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40620,SRR3231335,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.2_R2_001.fastq.gz,fastq fastq,985873592.0,6535185.0,GSM2090866 r2,0:75.50 1:75.35,A:306272693;C:164036011;G:179508984;T:335829272;N:226632,75,75,,,306272693,164036011,179508984,335829272,226632,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00561,0.0179,0.00465,0.00654,0.99918,0.98437,0.31,0.63328,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40621,SRR3231336,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3.3_R2_001.fastq.gz,fastq fastq,985261576.0,6530964.0,GSM2090866 r3,0:75.51 1:75.35,A:302874779;C:163594572;G:182423657;T:336116219;N:252349,75,75,,,302874779,163594572,182423657,336116219,252349,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0057,0.01777,0.00484,0.00661,0.99926,0.98482,0.3146,0.64967,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40622,SRR3231337,SRX1637100,SRS1342932,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate3.1,GSM2090866,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate3.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090866,GSM2090866: 8hpf Tdrd6a :  Plate3.1; Danio rerio; RNA Seq,GSM2090866,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate3_R2_001.fastq.gz,fastq fastq,988364061.0,6551921.0,GSM2090866 r4,0:75.50 1:75.35,A:308483971;C:164508093;G:179109944;T:336245723;N:16330,75,75,,,308483971,164508093,179109944,336245723,16330,SRX1637100,SRS1342932,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00558,0.0188,0.00462,0.00684,0.99912,0.98354,0.38775,0.62734,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40623,SRR3231330,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.1_R2_001.fastq.gz,fastq fastq,1347558297.0,8935001.0,GSM2090865 r1,0:75.49 1:75.32,A:428692990;C:233467157;G:260154804;T:425229674;N:13672,75,75,,,428692990,233467157,260154804,425229674,13672,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00717,0.02482,0.00583,0.01367,0.9977,0.98301,0.54347,0.62642,74,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40624,SRR3231331,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.2_R2_001.fastq.gz,fastq fastq,1347477358.0,8934352.0,GSM2090865 r2,0:75.50 1:75.32,A:431085993;C:234267083;G:255942417;T:425873702;N:308163,75,75,,,431085993,234267083,255942417,425873702,308163,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00723,0.02422,0.00571,0.01316,0.99748,0.9825,0.4935,0.61373,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40625,SRR3231332,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2.3_R2_001.fastq.gz,fastq fastq,1342511024.0,8901101.0,GSM2090865 r3,0:75.50 1:75.32,A:424536537;C:232976344;G:259737347;T:424897714;N:363082,75,75,,,424536537,232976344,259737347,424897714,363082,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00707,0.02424,0.00579,0.01341,0.99788,0.98277,0.3897,0.60237,75,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40626,SRR3231333,SRX1637099,SRS1342934,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate2.1,GSM2090865,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate2.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090865,GSM2090865: 8hpf Tdrd6a :  Plate2.1; Danio rerio; RNA Seq,GSM2090865,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate2_R2_001.fastq.gz,fastq fastq,1349985043.0,8951395.0,GSM2090865 r4,0:75.49 1:75.32,A:433870230;C:234813106;G:255398294;T:425882927;N:20486,75,75,,,433870230,234813106,255398294,425882927,20486,SRX1637099,SRS1342934,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.00663,0.02406,0.00536,0.01336,0.99772,0.98281,0.48872,0.63184,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40627,SRR3231326,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.1_R2_001.fastq.gz,fastq fastq,2529086421.0,16774294.0,GSM2090864 r1,0:75.43 1:75.34,A:796779684;C:413533280;G:487547543;T:830919763;N:306151,75,75,,,796779684,413533280,487547543,830919763,306151,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.05805,0.15018,0.04986,0.07872,0.98729,0.92443,0.5,0.46925,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40628,SRR3231327,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.2_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.2_R2_001.fastq.gz,fastq fastq,2629569381.0,17440212.0,GSM2090864 r2,0:75.43 1:75.34,A:823719446;C:431439564;G:506909577;T:867265650;N:235144,75,75,,,823719446,431439564,506909577,867265650,235144,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0575,0.1556,0.04944,0.08069,0.98648,0.92245,0.5,0.58664,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40629,SRR3231328,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1.3_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1.3_R2_001.fastq.gz,fastq fastq,2626839769.0,17422028.0,GSM2090864 r3,0:75.43 1:75.35,A:822264952;C:429448970;G:507899334;T:867005630;N:220883,75,75,,,822264952,429448970,507899334,867005630,220883,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.05904,0.1574,0.05085,0.08206,0.98685,0.92133,0.50407,0.58481,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
40630,SRR3231329,SRX1637098,SRS1342905,SRP071848,PRJNA315399,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [scRNA Seq],GSE79283,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Single cell were sorted directly in Trizolfrom embryos spawned by mz tdrd6a /  mother and wt mother carrying a kop::egfp f nos1 three primeUTR  transgene. Therepost single cell trizol extractio was performed followed by RT  IVT and RNA seq library prep.,parent bioproject:PRJNA315403,pubmed:30086300,,8hpf Tdrd6a :  Plate1.1,GSM2090864,,tissue:Germ cells|cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,8hpf Tdrd6a :  Plate1.1,post sequencing  read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser Meyer et al.  2013  Junker et al 2015 using bwa Li and Durbin  2010 with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL seq only sequences the most 3’ prime end of a transcript and generates one read per transcript. Genome build: zv9 Supplementary files format and content: The sc fdata file contains all cells at least 1100 transcripts en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.,Germ cells,,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,Zebrafish were maintained under standard conditions.,cell line:Primary cells|developmental stage:8hpf|genotype/variation:Tdrd6a : |protocol:CEL seq Hashimshony et al.  Cell reports 2012,GSM2090864,GSM2090864: 8hpf Tdrd6a :  Plate1.1; Danio rerio; RNA Seq,GSM2090864,,1,mRNA was extracted from single cells by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. The RNA pellet was then processed using the CEL seq protocol Hashimshony et al.  2012 and sequenced on an Illumina Nextseq using 75bp paired end sequencing.,GEO Accession:GSM2090864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP071848,,,8hpf_Tdrd6a-:-_Plate1_R1_001.fastq.gz 8hpf_Tdrd6a-:-_Plate1_R2_001.fastq.gz,fastq fastq,2592347629.0,17194377.0,GSM2090864 r4,0:75.43 1:75.34,A:813940505;C:424856630;G:499860954;T:853378694;N:310846,75,75,,,813940505,424856630,499860954,853378694,310846,SRX1637098,SRS1342905,SRA385812,GEO,"Rene Ketting, RNA silencing, IMB",2,0.0589,0.14612,0.05081,0.07706,0.98756,0.92829,0.52503,0.46498,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,3prime,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Germany,2016-03-16,Gastrula,Embryo,Gonad,Reproductive System
52970,SRR9621260,SRX6384174,SRS5043692,SRP212628,PRJNA551686,Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition,GSE133526,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing cells from ß catCA mosaically introduced or ß catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:31624259,,Uninjected lot2,GSM3911299,,tissue:Uninjected|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,Uninjected lot2,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,Uninjected,,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,GSM3911299,GSM3911299: Uninjected lot2; Danio rerio; RNA Seq,GSM3911299,,1,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,GEO Accession:GSM3911299,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP212628,,,Uninjected_lot2.fastq.gz,fastq,81923616.0,2275656.0,GSM3911299 r1,0:36,A:20021902;C:13634804;G:16949301;T:31316849;N:760,36,,,,20021902,13634804,16949301,31316849,760,SRX6384174,SRS5043692,SRA915905,GEO,"Division of Transcriptomics, Medical Institute of Bioregulation",1,0.83319,,0.14054,,0.83603,,0.62168,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2019-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
52971,SRR9621259,SRX6384173,SRS5043691,SRP212628,PRJNA551686,Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition,GSE133526,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing cells from ß catCA mosaically introduced or ß catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:31624259,,Uninjected lot1,GSM3911298,,tissue:Uninjected|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,Uninjected lot1,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,Uninjected,,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,GSM3911298,GSM3911298: Uninjected lot1; Danio rerio; RNA Seq,GSM3911298,,1,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,GEO Accession:GSM3911298,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP212628,,,Uninjected_lot1.fastq.gz,fastq,7869564.0,218599.0,GSM3911298 r1,0:36,A:1915747;C:1320159;G:1596920;T:3036688;N:50,36,,,,1915747,1320159,1596920,3036688,50,SRX6384173,SRS5043691,SRA915905,GEO,"Division of Transcriptomics, Medical Institute of Bioregulation",1,0.8098,,0.20175,,0.8547,,0.54458,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2019-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
52972,SRR9621258,SRX6384172,SRS5043690,SRP212628,PRJNA551686,Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition,GSE133526,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing cells from ß catCA mosaically introduced or ß catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:31624259,,Ubiquitous beta catCA GFP pls lot2,GSM3911297,,tissue:Ubiquitous beta catCA GFP pls|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,Ubiquitous beta catCA GFP pls lot2,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,Ubiquitous beta catCA GFP pls,,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,GSM3911297,GSM3911297: Ubiquitous beta catCA GFP pls lot2; Danio rerio; RNA Seq,GSM3911297,,1,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,GEO Accession:GSM3911297,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP212628,,,Ubiquitous_beta-catCA_GFP_pls_lot2.fastq.gz,fastq,4191336.0,116426.0,GSM3911297 r1,0:36,A:1023598;C:694666;G:854764;T:1618296;N:12,36,,,,1023598,694666,854764,1618296,12,SRX6384172,SRS5043690,SRA915905,GEO,"Division of Transcriptomics, Medical Institute of Bioregulation",1,0.83432,,0.2051,,0.88998,,0.58415,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2019-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
52973,SRR9621257,SRX6384171,SRS5043689,SRP212628,PRJNA551686,Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition,GSE133526,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing cells from ß catCA mosaically introduced or ß catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:31624259,,Ubiquitous beta catCA GFP pls lot1,GSM3911296,,tissue:Ubiquitous beta catCA GFP pls|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,Ubiquitous beta catCA GFP pls lot1,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,Ubiquitous beta catCA GFP pls,,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,GSM3911296,GSM3911296: Ubiquitous beta catCA GFP pls lot1; Danio rerio; RNA Seq,GSM3911296,,1,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,GEO Accession:GSM3911296,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP212628,,,Ubiquitous_beta-catCA_GFP_pls_lot1.fastq.gz,fastq,55588716.0,1544131.0,GSM3911296 r1,0:36,A:13286161;C:9047641;G:11261383;T:21993098;N:433,36,,,,13286161,9047641,11261383,21993098,433,SRX6384171,SRS5043689,SRA915905,GEO,"Division of Transcriptomics, Medical Institute of Bioregulation",1,0.81894,,0.17022,,0.84193,,0.59003,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2019-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
52974,SRR9621256,SRX6384170,SRS5043688,SRP212628,PRJNA551686,Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition,GSE133526,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing cells from ß catCA mosaically introduced or ß catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:31624259,,Mosaic beta catCA GFP pls lot2,GSM3911295,,tissue:Mosaic beta catCA GFP pls|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,Mosaic beta catCA GFP pls lot2,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,Mosaic beta catCA GFP pls,,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,GSM3911295,GSM3911295: Mosaic beta catCA GFP pls lot2; Danio rerio; RNA Seq,GSM3911295,,1,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,GEO Accession:GSM3911295,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP212628,,,Mosaic_beta-catCA_GFP_pls_lot2.fastq.gz,fastq,24255900.0,673775.0,GSM3911295 r1,0:36,A:5793155;C:4032308;G:4838956;T:9591331;N:150,36,,,,5793155,4032308,4838956,9591331,150,SRX6384170,SRS5043688,SRA915905,GEO,"Division of Transcriptomics, Medical Institute of Bioregulation",1,0.82302,,0.1753,,0.83593,,0.5557,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2019-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
52975,SRR9621255,SRX6384169,SRS5043687,SRP212628,PRJNA551686,Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition,GSE133526,Transcriptome Analysis,Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength dependent manner to pattern developing tissues. However  developing tissues also undergo dynamic morphogenesis  which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/ß catenin signalling gradient  which acts as a morphogen to establish embryonic anterior posterior patterning  revealed that unfit cells with abnormal Wnt/ß catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/ß catenin gradient formation and consequent anterior posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues  this system may support tissue robustness and disease prevention. Overall design: ß catCA constitutive active form of ß catenin expressing cells from ß catCA mosaically introduced or ß catCA ubiquitously expressing zebrafish early embryos  or cells from uninjected zebrafish embryos were sorted by FACS cell sorter. Total RNAs were extracted and analyzed by RNA seq.,,pubmed:31624259,,Mosaic beta catCA GFP pls lot1,GSM3911294,,tissue:Mosaic beta catCA GFP pls|strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,Mosaic beta catCA GFP pls lot1,Sequenced reads were mapped to the GRCz10 reference genome using Bowtie2 ver. 2.3.1. UMI counts were extracted per HTSeq ver. 0.6.1 from the CEL Seq2 pipeline. Genome build: GRCz10 Supplementary files format and content: Tab delimited text file for expression data normalized by regularized logarithm.,Mosaic beta catCA GFP pls,,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,,strain:AB|cell type:early embryonic cell|developmental stage:9 hpf,GSM3911294,GSM3911294: Mosaic beta catCA GFP pls lot1; Danio rerio; RNA Seq,GSM3911294,,1,Samples were prepared according to the CEL Seq2 protocol described in Hashimshony et al. Geneome Biology 2016. Libraries preparation was performed according to the published CEL Seq2 protocol.,GEO Accession:GSM3911294,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP212628,,,Mosaic_beta-catCA_GFP_pls_lot1.fastq.gz,fastq,25688556.0,713571.0,GSM3911294 r1,0:36,A:6408873;C:4398036;G:5206478;T:9674982;N:187,36,,,,6408873,4398036,5206478,9674982,187,SRX6384169,SRS5043687,SRA915905,GEO,"Division of Transcriptomics, Medical Institute of Bioregulation",1,0.82974,,0.19036,,0.83479,,0.6196,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Japan,2019-06-28,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
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