RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

102 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Endothelium"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation 7

experiment.library_selection 4

devstage_curation_coarse 4

technology 3

experiment.library_strategy 3

tissue_curation_coarse 1

tissue_curation 1

  • Endothelium · 102 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 102 ✖

experiment.library_layout 1

  • SINGLE · 102 ✖
Link 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
30006 30006 SRR27663958 SRX23331822 SRS20194274 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB biol rep 3 GSM8027552   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted|geo loc name:missing|collection date:missing NFKB biol rep 3 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted GSM8027552 GSM8027552: NFKB biol rep 3; Danio rerio; RNA Seq GSM8027552 r1 GSM8027552 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 6-RNA-1001_S6_L001_R1_001.fastq.gz fastq 7566894200.0 75668942.0 GSM8027552 r1 0:100 A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405 100       2055514007 1776454819 1779667416 1955100553 157405 SRX23331822 SRS20194274 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30007 30007 SRR27663959 SRX23331821 SRS20194275 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB biol rep 2 GSM8027551   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted|geo loc name:missing|collection date:missing NFKB biol rep 2 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted GSM8027551 GSM8027551: NFKB biol rep 2; Danio rerio; RNA Seq GSM8027551 r1 GSM8027551 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 5-RNA-0901_S5_L001_R1_001.fastq.gz fastq 8077393600.0 80773936.0 GSM8027551 r1 0:100 A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097 100       2195547260 1863472493 1887149224 2131055526 169097 SRX23331821 SRS20194275 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30008 30008 SRR27663960 SRX23331820 SRS20194273 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB biol rep 1 GSM8027550   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted|geo loc name:missing|collection date:missing NFKB biol rep 1 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB sorted GSM8027550 GSM8027550: NFKB biol rep 1; Danio rerio; RNA Seq GSM8027550 r1 GSM8027550 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 4-RNA-1001_S4_L001_R1_001.fastq.gz fastq 6536957300.0 65369573.0 GSM8027550 r1 0:100 A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037 100       1764502914 1531091007 1533764634 1707464708 134037 SRX23331820 SRS20194273 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30009 30009 SRR27663961 SRX23331819 SRS20194272 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB+ biol rep 3 GSM8027549   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing NFKB+ biol rep 3 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted GSM8027549 GSM8027549: NFKB+ biol rep 3; Danio rerio; RNA Seq GSM8027549 r1 GSM8027549 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 3-RNA-1001_S3_L001_R1_001.fastq.gz fastq 10375249700.0 103752497.0 GSM8027549 r1 0:100 A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287 100       2873369145 2335823279 2356855554 2808985435 216287 SRX23331819 SRS20194272 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30010 30010 SRR27663962 SRX23331818 SRS20194271 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB+ biol rep 2 GSM8027548   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing NFKB+ biol rep 2 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted GSM8027548 GSM8027548: NFKB+ biol rep 2; Danio rerio; RNA Seq GSM8027548 r1 GSM8027548 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 2-RNA-1001_S2_L001_R1_001.fastq.gz fastq 5743794100.0 57437941.0 GSM8027548 r1 0:100 A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042 100       1588561398 1297479370 1310669617 1546965673 118042 SRX23331818 SRS20194271 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
30011 30011 SRR27663963 SRX23331817 SRS20194270 SRP484810 PRJNA1066877 p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation GSE253758 Transcriptome Analysis While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia lymphoma anemia and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics. Particularly our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65 the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary our results uncover the functional role of pro inflammatory signaling during HSPC specification revealed their oscillatory dynamics and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification NFKB+ or NFKB endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.   pubmed:39242546   NFKB+ biol rep 1 GSM8027547   tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing NFKB+ biol rep 1 Data was analyzed by ROSALIND® https://rosalind.bio/ with a HyperScale architecture developed by ROSALIND Inc. San Diego CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change p values adjusted p values and normalized abundance values per sample for each gene endothelial cells 22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope dechorionated with pronase Millipore Sigma; 11459643001 anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer. RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440. Zebrafish Danio rerio embryos and adults were mated staged raised and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle. cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted GSM8027547 GSM8027547: NFKB+ biol rep 1; Danio rerio; RNA Seq GSM8027547 r1 GSM8027547 1 RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484810   loader:fastq load.py 1-RNA-0917_S1_L001_R1_001.fastq.gz fastq 6201542500.0 62015425.0 GSM8027547 r1 0:100 A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300 100       1696049302 1431941155 1441395671 1632027072 129300 SRX23331817 SRS20194270 SRA1788753 Iowa State University Iowa State University                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2024-01-19 Multi-stage Multi-stage Endothelium Cardiovascular System
38364 38364 SRR1793802 SRX869237 SRS840014 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0012 GSM1604058   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0012 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604058 GSM1604058: d red ZF sample 0012; Danio rerio; RNA Seq GSM1604058   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604058 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0012.fastq.gz fastq 136949295.0 3912837.0 GSM1604058 r1 0:35 A:38967686;C:29235653;G:29781723;T:38764742;N:199491 35       38967686 29235653 29781723 38764742 199491 SRX869237 SRS840014 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.50546   0.22201   0.91524   0.49457   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38365 38365 SRR1793801 SRX869236 SRS840015 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   d red ZF sample 0008 GSM1604057   tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf d red ZF sample 0008 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Dorsal endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604057 GSM1604057: d red ZF sample 0008; Danio rerio; RNA Seq GSM1604057   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604057 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     d_red_ZF_sample_0008.fastq.gz fastq 230204380.0 6577268.0 GSM1604057 r1 0:35 A:63286154;C:49924891;G:50948035;T:65703538;N:341762 35       63286154 49924891 50948035 65703538 341762 SRX869236 SRS840015 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.59898   0.14092   0.89073   0.49292   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38366 38366 SRR1793800 SRX869235 SRS840013 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0011 GSM1604056   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0011 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604056 GSM1604056: V red ZF sample 0011; Danio rerio; RNA Seq GSM1604056   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604056 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0011.fastq.gz fastq 146319705.0 4180563.0 GSM1604056 r1 0:35 A:40991954;C:30892087;G:32112709;T:42103782;N:219173 35       40991954 30892087 32112709 42103782 219173 SRX869235 SRS840013 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57038   0.16086   0.89014   0.53016   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
38367 38367 SRR1793799 SRX869234 SRS840016 SRP053359 PRJNA274951 Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein GSE65751 Transcriptome Analysis How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6 embryos per group were used for FACS isolation of Kaede photconverted red ECs.   pubmed:25992545   V red ZF sample 0007 GSM1604055   tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf V red ZF sample 0007 Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules. Ventral endothelial cells   RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 The vPCV vs dPCV endothelial cells were analyzed at 24hpf strain:Tgfli1:gal4;uasKaede|developmental stage:24hpf GSM1604055 GSM1604055: V red ZF sample 0007; Danio rerio; RNA Seq GSM1604055   1 RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. Each CEL Seq primer cointained a barcode and a unique moleculare identifier Teemu et al. 2011 GEO Accession:GSM1604055 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP053359     V_red_ZF_sample_0007.fastq.gz fastq 219537045.0 6272487.0 GSM1604055 r1 0:35 A:61562432;C:46586451;G:48274564;T:62792331;N:321267 35       61562432 46586451 48274564 62792331 321267 SRX869234 SRS840016 SRA236924 GEO Itai Yanai, Biology, Technion - Israel Institute of Technology 1 0.57949   0.1659   0.88187   0.51446   35   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate celseq   Israel 2015-02-09 Pharyngula Embryo Endothelium Cardiovascular System
40968 40968 SRR3498282 SRX1756828 SRS1433359 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   6dpf E1 GSM2150746   source name:Endothelial cell|developmental stage:6 dpf|tissue:Endothelial|stain:GFP 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6 dpf|tissue:Endothelial|stain:GFP GSM2150746 GSM2150746: 6dpf E1; Danio rerio; RNA Seq GSM2150746   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150746 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_036_004_TGACCA_L002_R1.fastq.gz fastq 446212036.0 5871211.0 GSM2150746 r1 0:76 A:121356950;C:99664887;G:97289960;T:122019647;N:5880592 76       121356950 99664887 97289960 122019647 5880592 SRX1756828 SRS1433359 SRA424807 GEO Internal Medicine, Yale University 1 0.76652   0.13082   0.73985   0.47925   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40969 40969 SRR3498281 SRX1756827 SRS1433358 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   72hpf E1 GSM2150745   source name:Endothelial cell|developmental stage:72 hpf|tissue:Endothelial|stain:GFP 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72 hpf|tissue:Endothelial|stain:GFP GSM2150745 GSM2150745: 72hpf E1; Danio rerio; RNA Seq GSM2150745   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150745 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_035_003_TTAGGC_L002_R1.fastq.gz fastq 533039908.0 7013683.0 GSM2150745 r1 0:76 A:141643030;C:119112106;G:118099940;T:147160011;N:7024821 76       141643030 119112106 118099940 147160011 7024821 SRX1756827 SRS1433358 SRA424807 GEO Internal Medicine, Yale University 1 0.86605   0.1329   0.72253   0.49856   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40970 40970 SRR3498280 SRX1756826 SRS1433357 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   48hpf E1 GSM2150744   source name:Endothelial cell|developmental stage:48 hpf|tissue:Endothelial|stain:GFP 48hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48 hpf|tissue:Endothelial|stain:GFP GSM2150744 GSM2150744: 48hpf E1; Danio rerio; RNA Seq GSM2150744   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150744 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_034_002_CGATGT_L002_R1.fastq.gz fastq 485202316.0 6384241.0 GSM2150744 r1 0:76 A:128473144;C:107489507;G:107138177;T:135707012;N:6394476 76       128473144 107489507 107138177 135707012 6394476 SRX1756826 SRS1433357 SRA424807 GEO Internal Medicine, Yale University 1 0.89084   0.1385   0.71985   0.4908   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40971 40971 SRR3498279 SRX1756825 SRS1433356 SRP074847 PRJNA321312 mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81335 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   24hpf E1 GSM2150743   source name:Endothelial cell|developmental stage:24 hpf|tissue:Endothelial|stain:GFP 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample . Endothelial cell   Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24 hpf|tissue:Endothelial|stain:GFP GSM2150743 GSM2150743: 24hpf E1; Danio rerio; RNA Seq GSM2150743   1 Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150743 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer   SRP074847     EF_033_001_ATCACG_L002_R1.fastq.gz fastq 426238476.0 5608401.0 GSM2150743 r1 0:76 A:113332066;C:95045840;G:93307502;T:118935708;N:5617360 76       113332066 95045840 93307502 118935708 5617360 SRX1756825 SRS1433356 SRA424807 GEO Internal Medicine, Yale University 1 0.88651   0.15752   0.72805   0.48414   76   B   usable mapping rate illumina early_illumina unknown small_rna trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
40972 40972 SRR3498294 SRX1756840 SRS1433371 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 72hpf E2 GSM2150819   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP NoEndo 72hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150819 GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq GSM2150819   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150819 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_72hpf_E2.fastq.gz fastq 797509876.0 10493551.0 GSM2150819 r1 0:76 A:182564842;C:199547592;G:199064466;T:216287390;N:45586 76       182564842 199547592 199064466 216287390 45586 SRX1756840 SRS1433371 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40973 40973 SRR3498293 SRX1756839 SRS1433370 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 72hpf E1 GSM2150818   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP NoEndo 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150818 GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq GSM2150818   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150818 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_72hpf_E1.fastq.gz fastq 1864172232.0 24528582.0 GSM2150818 r1 0:76 A:426671762;C:469538477;G:458132395;T:509711525;N:118073 76       426671762 469538477 458132395 509711525 118073 SRX1756839 SRS1433370 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40974 40974 SRR3498292 SRX1756838 SRS1433369 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 6dpf E1 GSM2150817   source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP NoEndo 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6dpf|tissue:Endothelial|stain:GFP GSM2150817 GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq GSM2150817   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150817 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_6dpf_E1.fastq.gz fastq 1414849364.0 18616439.0 GSM2150817 r1 0:76 A:315250036;C:366906308;G:364673112;T:367938758;N:81150 76       315250036 366906308 364673112 367938758 81150 SRX1756838 SRS1433369 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40975 40975 SRR3498291 SRX1756837 SRS1433368 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 48hpf E2 GSM2150816   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP NoEndo 48hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150816 GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq GSM2150816   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150816 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_48hpf_E2.fastq.gz fastq 553364740.0 7281115.0 GSM2150816 r1 0:76 A:129173344;C:134804122;G:141026546;T:148331467;N:29261 76       129173344 134804122 141026546 148331467 29261 SRX1756837 SRS1433368 SRA424808 GEO Internal Medicine, Yale University 1 1e-05   0.0   0.99997   0.0   76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40976 40976 SRR3498290 SRX1756836 SRS1433367 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 48hpf E1 GSM2150815   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP NoEndo 48hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150815 GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq GSM2150815   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150815 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_48hpf_E1.fastq.gz fastq 1204752152.0 15852002.0 GSM2150815 r1 0:76 A:297517299;C:293969730;G:317491224;T:295696492;N:77407 76       297517299 293969730 317491224 295696492 77407 SRX1756836 SRS1433367 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40977 40977 SRR3498289 SRX1756835 SRS1433366 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   NoEndo 24hpf E1 GSM2150814   source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP NoEndo 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24hpf|tissue:Endothelial|stain:GFP GSM2150814 GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq GSM2150814   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150814 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     NoEndo_24hpf_E1.fastq.gz fastq 1422085704.0 18711654.0 GSM2150814 r1 0:76 A:347700492;C:356065333;G:376424133;T:341806001;N:89745 76       347700492 356065333 376424133 341806001 89745 SRX1756835 SRS1433366 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
40978 40978 SRR3498288 SRX1756834 SRS1433365 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 72hpf E2 GSM2150813   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP Endo 72hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150813 GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq GSM2150813   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150813 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_72hpf_E2.fastq.gz fastq 438128980.0 5764855.0 GSM2150813 r1 0:76 A:101851745;C:114159902;G:115733669;T:106360221;N:23443 76       101851745 114159902 115733669 106360221 23443 SRX1756834 SRS1433365 SRA424808 GEO Internal Medicine, Yale University 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40979 40979 SRR3498287 SRX1756833 SRS1433364 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 72hpf E1 GSM2150812   source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP Endo 72hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:72hpf|tissue:Endothelial|stain:GFP GSM2150812 GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq GSM2150812   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150812 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_72hpf_E1.fastq.gz fastq 1267915068.0 16683093.0 GSM2150812 r1 0:76 A:321606522;C:310505837;G:323829249;T:311892892;N:80568 76       321606522 310505837 323829249 311892892 80568 SRX1756833 SRS1433364 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40980 40980 SRR3498286 SRX1756832 SRS1433363 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 6dpf E1 GSM2150811   source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP Endo 6dpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:6dpf|tissue:Endothelial|stain:GFP GSM2150811 GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq GSM2150811   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150811 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_6dpf_E1.fastq.gz fastq 890474824.0 11716774.0 GSM2150811 r1 0:76 A:230419087;C:212029155;G:232306960;T:215672618;N:47004 76       230419087 212029155 232306960 215672618 47004 SRX1756832 SRS1433363 SRA424808 GEO Internal Medicine, Yale University 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Larval Larval Endothelium Cardiovascular System
40981 40981 SRR3498285 SRX1756831 SRS1433362 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 48hpf E2 GSM2150810   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP Endo 48hpf E2 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150810 GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq GSM2150810   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150810 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_48hpf_E2.fastq.gz fastq 1254556624.0 16507324.0 GSM2150810 r1 0:76 A:316229540;C:323340793;G:307552357;T:307354555;N:79379 76       316229540 323340793 307552357 307354555 79379 SRX1756831 SRS1433362 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40982 40982 SRR3498284 SRX1756830 SRS1433361 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 48hpf E1 GSM2150809   source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP Endo 48hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:48hpf|tissue:Endothelial|stain:GFP GSM2150809 GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq GSM2150809   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150809 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_48hpf_E1.fastq.gz fastq 1449497080.0 19072330.0 GSM2150809 r1 0:76 A:362564557;C:370330864;G:364749441;T:351760774;N:91444 76       362564557 370330864 364749441 351760774 91444 SRX1756830 SRS1433361 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Hatching Embryo Endothelium Cardiovascular System
40983 40983 SRR3498283 SRX1756829 SRS1433360 SRP074848 PRJNA321321 microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues GSE81340 Transcriptome Analysis Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate parent bioproject:PRJNA321317 pubmed:28350988;pubmed:33273096   Endo 24hpf E1 GSM2150808   source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP Endo 24hpf E1 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... Endothelial cell   Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. developmental stage:24hpf|tissue:Endothelial|stain:GFP GSM2150808 GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq GSM2150808   1 Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2150808 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer   SRP074848     Endo_24hpf_E1.fastq.gz fastq 1527500440.0 20098690.0 GSM2150808 r1 0:76 A:356712587;C:354608109;G:432977038;T:383106520;N:96186 76       356712587 354608109 432977038 383106520 96186 SRX1756829 SRS1433360 SRA424808 GEO Internal Medicine, Yale University 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina early_illumina unknown size_fractionation trueseq bulk unknown unknown   United States 2016-05-11 Pharyngula Embryo Endothelium Cardiovascular System
41146 41146 SRR3742564 SRX1896783 SRS1539775 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Mt GSM2224910   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells Mt HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells GSM2224910 GSM2224910: Mt; Danio rerio; RNA Seq GSM2224910   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224910 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160123_I114_FCH52M2BBXX_L2_WHFISoiqRAABRAAPEI-144_1.fq.gz fastq 262444686.0 5356014.0 GSM2224910 r1 0:49 A:66548564;C:63544339;G:66582385;T:65755749;N:13649 49       66548564 63544339 66582385 65755749 13649 SRX1896783 SRS1539775 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.92714   0.05568   0.73423   0.48371   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41147 41147 SRR3742565 SRX1896783 SRS1539775 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Mt GSM2224910   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells Mt HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells GSM2224910 GSM2224910: Mt; Danio rerio; RNA Seq GSM2224910   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224910 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160204_I136_FCH55MNBBXX_L6_WHFISoiqRAABRAAPEI-144_1.fq.gz fastq 448147973.0 9145877.0 GSM2224910 r2 0:49 A:113623842;C:108767789;G:113689061;T:112055179;N:12102 49       113623842 108767789 113689061 112055179 12102 SRX1896783 SRS1539775 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.91636   0.05377   0.73545   0.48441   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41148 41148 SRR3742562 SRX1896782 SRS1539774 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Sib GSM2224909   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells Sib HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells GSM2224909 GSM2224909: Sib; Danio rerio; RNA Seq GSM2224909   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224909 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160123_I114_FCH52M2BBXX_L2_WHFISoiqRAAARAAPEI-100_1.fq.gz fastq 180708423.0 3687927.0 GSM2224909 r1 0:49 A:45675389;C:44261209;G:46002295;T:44768361;N:1169 49       45675389 44261209 46002295 44768361 1169 SRX1896782 SRS1539774 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.93956   0.0479   0.75276   0.47889   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41149 41149 SRR3742563 SRX1896782 SRS1539774 SRP077871 PRJNA327749 Gene expression profiles of endothelial cells from mutants and siblings of tsu3994 GSE83987 Transcriptome Analysis Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994   pubmed:28003365   Sib GSM2224909   tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells Sib HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample kdrl:GFP+ Endothelial cells   Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.   genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells GSM2224909 GSM2224909: Sib; Danio rerio; RNA Seq GSM2224909   1 Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’ end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary. GEO Accession:GSM2224909 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   SRP077871     160204_I136_FCH55MNBBXX_L6_WHFISoiqRAAARAAPEI-100_1.fq.gz fastq 454459418.0 9274682.0 GSM2224909 r2 0:49 A:114982478;C:111450118;G:115561207;T:112452344;N:13271 49       114982478 111450118 115561207 112452344 13271 SRX1896782 SRS1539774 SRA437681 GEO Anming Meng, School of Lifesciences, Tsinghua University 1 0.92536   0.04644   0.75103   0.47559   49   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2016-07-04 Pharyngula Embryo Endothelium Cardiovascular System
41827 41827 SRR5251446 SRX2557171 SRS1974564 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR139 B1 nicoli mutmir AG01645   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR139 B1 AG01645.1 AG01645.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01645.1_R1.fastq.gz fastq 1574284140.0 20714265.0 AG01645.1 R1.fastq.gz 0:76 A:485471345;C:270854124;G:374164721;T:443766613;N:27337 76       485471345 270854124 374164721 443766613 27337 SRX2557171 SRS1974564 SRA537606 Yale University|Genetics Yale University 1 0.82142   0.14068   0.8002   0.5444   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-27 Undetermined Embryo Endothelium Cardiovascular System
41828 41828 SRR5251445 SRX2557170 SRS1974563 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR139 B2 nicoli mutmir AG01646   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR139 B2 AG01646.1 AG01646.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01646.1_R1.fastq.gz fastq 1484740104.0 19536054.0 AG01646.1 R1.fastq.gz 0:76 A:453388316;C:246477203;G:365031959;T:419816346;N:26280 76       453388316 246477203 365031959 419816346 26280 SRX2557170 SRS1974563 SRA537606 Yale University|Genetics Yale University 1 0.82649   0.1897   0.79862   0.52759   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41829 41829 SRR5251444 SRX2557169 SRS1974562 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR139 B3 nicoli mutmir AG01647   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR139 B3 AG01647.1 AG01647.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01647.1_R1.fastq.gz fastq 881298660.0 11596035.0 AG01647.1 R1.fastq.gz 0:76 A:270675838;C:160127586;G:228157662;T:222301246;N:36328 76       270675838 160127586 228157662 222301246 36328 SRX2557169 SRS1974562 SRA537606 Yale University|Genetics Yale University 1 0.76133   0.15034   0.83341   0.56596   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41830 41830 SRR5251443 SRX2557168 SRS1974561 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR139 B1 nicoli mutmir AG01648   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR139 B1 AG01648.1 AG01648.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01648.1_R1.fastq.gz fastq 637896880.0 8393380.0 AG01648.1 R1.fastq.gz 0:76 A:192829278;C:112701153;G:153321271;T:179019095;N:26083 76       192829278 112701153 153321271 179019095 26083 SRX2557168 SRS1974561 SRA537606 Yale University|Genetics Yale University 1 0.75971   0.1181   0.82171   0.56797   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41831 41831 SRR5251442 SRX2557167 SRS1974560 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR139 B2 nicoli mutmir AG01649   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR139 B2 AG01649.1 AG01649.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01649.1_R1.fastq.gz fastq 849868328.0 11182478.0 AG01649.1 R1.fastq.gz 0:76 A:258225905;C:148467172;G:205165181;T:237974100;N:35970 76       258225905 148467172 205165181 237974100 35970 SRX2557167 SRS1974560 SRA537606 Yale University|Genetics Yale University 1 0.75096   0.14506   0.81507   0.5545   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41832 41832 SRR5251441 SRX2557166 SRS1974559 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR139 B3 nicoli mutmir AG01650   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR139 B3 AG01650.1 AG01650.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01650.1_R1.fastq.gz fastq 998464668.0 13137693.0 AG01650.1 R1.fastq.gz 0:76 A:311526420;C:176545041;G:251852786;T:258497630;N:42791 76       311526420 176545041 251852786 258497630 42791 SRX2557166 SRS1974559 SRA537606 Yale University|Genetics Yale University 1 0.76479   0.11192   0.82674   0.54621   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41833 41833 SRR5251440 SRX2557165 SRS1974558 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR24 B1 nicoli mutmir AG01651   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR24 B1 AG01651.1 AG01651.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01651.1_R1.fastq.gz fastq 570492252.0 7506477.0 AG01651.1 R1.fastq.gz 0:76 A:162512811;C:104071716;G:135730697;T:168149427;N:27601 76       162512811 104071716 135730697 168149427 27601 SRX2557165 SRS1974558 SRA537606 Yale University|Genetics Yale University 1 0.73988   0.10157   0.86647   0.54252   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41834 41834 SRR5251439 SRX2557164 SRS1974557 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR24 B2 nicoli mutmir AG01652   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR24 B2 AG01652.1 AG01652.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01652.1_R1.fastq.gz fastq 1072886148.0 14116923.0 AG01652.1 R1.fastq.gz 0:76 A:338399596;C:192703439;G:242960887;T:298769761;N:52465 76       338399596 192703439 242960887 298769761 52465 SRX2557164 SRS1974557 SRA537606 Yale University|Genetics Yale University 1 0.76456   0.11024   0.89197   0.59214   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41835 41835 SRR5251438 SRX2557163 SRS1974556 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR24 B3 nicoli mutmir AG01653   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR24 B3 AG01653.1 AG01653.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01653.1_R1.fastq.gz fastq 1016374144.0 13373344.0 AG01653.1 R1.fastq.gz 0:76 A:310958343;C:168702106;G:223420046;T:313241363;N:52286 76       310958343 168702106 223420046 313241363 52286 SRX2557163 SRS1974556 SRA537606 Yale University|Genetics Yale University 1 0.75735   0.12224   0.79756   0.55136   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41836 41836 SRR5251437 SRX2557162 SRS1974555 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR24 B1 nicoli mutmir AG01654   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR24 B1 AG01654.1 AG01654.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01654.1_R1.fastq.gz fastq 782170112.0 10291712.0 AG01654.1 R1.fastq.gz 0:76 A:238316720;C:132163709;G:179301544;T:232350598;N:37541 76       238316720 132163709 179301544 232350598 37541 SRX2557162 SRS1974555 SRA537606 Yale University|Genetics Yale University 1 0.7683   0.10712   0.80034   0.55804   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41837 41837 SRR5251436 SRX2557161 SRS1974554 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR24 B2 nicoli mutmir AG01655   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR24 B2 AG01655.1 AG01655.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01655.1_R1.fastq.gz fastq 1053946340.0 13867715.0 AG01655.1 R1.fastq.gz 0:76 A:318351311;C:191163031;G:240348413;T:304030367;N:53218 76       318351311 191163031 240348413 304030367 53218 SRX2557161 SRS1974554 SRA537606 Yale University|Genetics Yale University 1 0.77588   0.07983   0.83934   0.56228   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41838 41838 SRR5251435 SRX2557160 SRS1974553 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR24 B3 nicoli mutmir AG01656   strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR24 B3 AG01656.1 AG01656.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01656.1_R1.fastq.gz fastq 1182467736.0 15558786.0 AG01656.1 R1.fastq.gz 0:76 A:344465226;C:204677242;G:269228338;T:364036735;N:60195 76       344465226 204677242 269228338 364036735 60195 SRX2557160 SRS1974553 SRA537606 Yale University|Genetics Yale University 1 0.78956   0.13495   0.81517   0.56342   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41839 41839 SRR5251434 SRX2557159 SRS1974552 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR223 B1 nicoli mutmir AG01657   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR223 B1 AG01657.1 AG01657.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01657.1_R1.fastq.gz fastq 536336712.0 7057062.0 AG01657.1 R1.fastq.gz 0:76 A:158301607;C:93070120;G:121382262;T:163555487;N:27236 76       158301607 93070120 121382262 163555487 27236 SRX2557159 SRS1974552 SRA537606 Yale University|Genetics Yale University 1 0.76425   0.1278   0.84222   0.55305   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41840 41840 SRR5251433 SRX2557158 SRS1974551 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR223 B2 nicoli mutmir AG01658   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR223 B2 AG01658.1 AG01658.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01658.1_R1.fastq.gz fastq 798581856.0 10507656.0 AG01658.1 R1.fastq.gz 0:76 A:241352089;C:134327379;G:183394123;T:239469845;N:38420 76       241352089 134327379 183394123 239469845 38420 SRX2557158 SRS1974551 SRA537606 Yale University|Genetics Yale University 1 0.76221   0.13398   0.82459   0.55228   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41841 41841 SRR5251432 SRX2557157 SRS1974550 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs WT miR223 B3 nicoli mutmir AG01659   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs WT miR223 B3 AG01659.1 AG01659.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01659.1_R1.fastq.gz fastq 1093998948.0 14394723.0 AG01659.1 R1.fastq.gz 0:76 A:330741822;C:186325335;G:249557623;T:327320449;N:53719 76       330741822 186325335 249557623 327320449 53719 SRX2557157 SRS1974550 SRA537606 Yale University|Genetics Yale University 1 0.77108   0.14674   0.80955   0.55819   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
41842 41842 SRR5251431 SRX2557156 SRS1974549 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR223 B1 nicoli mutmir AG01660   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR223 B1 AG01660.1 AG01660.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01660.1_R1.fastq.gz fastq 849905492.0 11182967.0 AG01660.1 R1.fastq.gz 0:76 A:250953875;C:146191904;G:190040699;T:262674911;N:44103 76       250953875 146191904 190040699 262674911 44103 SRX2557156 SRS1974549 SRA537606 Yale University|Genetics Yale University 1 0.7687   0.14192   0.82842   0.5344   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-02-13 Undetermined Embryo Endothelium Cardiovascular System
41843 41843 SRR5251430 SRX2557155 SRS1974548 SRP099466 PRJNA374579 microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos PRJNA374579 Other Proper functioning of an organism requires cells and tissues to behave in uniform well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.       QuantSeq mutant miRNAs Mut miR223 B2 nicoli mutmir AG01661   strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal                 QuantSeq mutant miRNAs Mut miR223 B2 AG01661.1 AG01661.1 1     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP099466     AG01661.1_R1.fastq.gz fastq 840115400.0 11054150.0 AG01661.1 R1.fastq.gz 0:76 A:257057495;C:141775085;G:188281166;T:252960590;N:41064 76       257057495 141775085 188281166 252960590 41064 SRX2557155 SRS1974548 SRA537606 Yale University|Genetics Yale University 1 0.74292   0.10759   0.83615   0.55136   76   B   usable mapping rate illumina hiseq_era unknown small_rna lexogen bulk unknown unknown   United States 2017-03-28 Undetermined Embryo Endothelium Cardiovascular System
42141 42141 SRR5443688 SRX2733020 SRS2120917 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 3 GSM2574373   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574373 GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq GSM2574373   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574373 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M3_S6_L001_R1_001.fastq.gz fastq 1290470348.0 17096427.0 GSM2574373 r1 0:75.48 1:0 A:320847705;C:319435806;G:300073193;T:350044923;N:68721 75 0     320847705 319435806 300073193 350044923 68721 SRX2733020 SRS2120917 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.94339   0.05762   0.72232   0.50799   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42142 42142 SRR5443689 SRX2733020 SRS2120917 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 3 GSM2574373   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574373 GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq GSM2574373   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574373 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M3_S6_L002_R1_001.fastq.gz fastq 1274417413.0 16883601.0 GSM2574373 r2 0:75.48 1:0 A:316659737;C:315517172;G:296527344;T:345645123;N:68037 75 0     316659737 315517172 296527344 345645123 68037 SRX2733020 SRS2120917 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.94193   0.05753   0.7236   0.50991   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42143 42143 SRR5443690 SRX2733020 SRS2120917 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 3 GSM2574373   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574373 GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq GSM2574373   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574373 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M3_S6_L003_R1_001.fastq.gz fastq 1267650302.0 16794051.0 GSM2574373 r3 0:75.48 1:0 A:316851687;C:313922763;G:294562163;T:342271337;N:42352 75 0     316851687 313922763 294562163 342271337 42352 SRX2733020 SRS2120917 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93935   0.05711   0.72421   0.51344   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42144 42144 SRR5443691 SRX2733020 SRS2120917 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 3 GSM2574373   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574373 GSM2574373: 48hpf zebrafish FAC sorted endothelial cell mutant 3; Danio rerio; RNA Seq GSM2574373   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574373 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M3_S6_L004_R1_001.fastq.gz fastq 1272371755.0 16856553.0 GSM2574373 r4 0:75.48 1:0 A:317627046;C:315030569;G:295859300;T:343808592;N:46248 75 0     317627046 315030569 295859300 343808592 46248 SRX2733020 SRS2120917 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.94038   0.05657   0.72391   0.5115   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42145 42145 SRR5443684 SRX2733019 SRS2120916 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 2 GSM2574372   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574372 GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq GSM2574372   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574372 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M2_S4_L001_R1_001.fastq.gz fastq 1110761224.0 14715439.0 GSM2574372 r1 0:75.48 1:0 A:275638341;C:274879264;G:260426963;T:299738013;N:78643 75 0     275638341 274879264 260426963 299738013 78643 SRX2733019 SRS2120916 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93377   0.0583   0.73697   0.503   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42146 42146 SRR5443685 SRX2733019 SRS2120916 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 2 GSM2574372   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574372 GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq GSM2574372   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574372 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M2_S4_L002_R1_001.fastq.gz fastq 1096460187.0 14525794.0 GSM2574372 r2 0:75.48 1:0 A:271912949;C:271463678;G:257186071;T:295823949;N:73540 75 0     271912949 271463678 257186071 295823949 73540 SRX2733019 SRS2120916 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.9322   0.05825   0.74054   0.50344   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42147 42147 SRR5443686 SRX2733019 SRS2120916 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 2 GSM2574372   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574372 GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq GSM2574372   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574372 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M2_S4_L003_R1_001.fastq.gz fastq 1091010366.0 14453885.0 GSM2574372 r3 0:75.48 1:0 A:272182496;C:270174883;G:255585422;T:293013773;N:53792 75 0     272182496 270174883 255585422 293013773 53792 SRX2733019 SRS2120916 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93152   0.05837   0.74168   0.50083   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42148 42148 SRR5443687 SRX2733019 SRS2120916 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 2 GSM2574372   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574372 GSM2574372: 48hpf zebrafish FAC sorted endothelial cell mutant 2; Danio rerio; RNA Seq GSM2574372   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574372 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M2_S4_L004_R1_001.fastq.gz fastq 1094982987.0 14506489.0 GSM2574372 r4 0:75.48 1:0 A:272880331;C:271041484;G:256630523;T:294374054;N:56595 75 0     272880331 271041484 256630523 294374054 56595 SRX2733019 SRS2120916 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93087   0.05679   0.73791   0.51669   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42149 42149 SRR5443680 SRX2733018 SRS2120918 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 1 GSM2574371   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574371 GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq GSM2574371   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574371 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M1_S2_L001_R1_001.fastq.gz fastq 1191104867.0 15788220.0 GSM2574371 r1 0:75.44 1:0 A:291253611;C:297887900;G:280714676;T:321180057;N:68623 75 0     291253611 297887900 280714676 321180057 68623 SRX2733018 SRS2120918 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93937   0.05486   0.73841   0.50505   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42150 42150 SRR5443681 SRX2733018 SRS2120918 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 1 GSM2574371   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574371 GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq GSM2574371   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574371 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M1_S2_L002_R1_001.fastq.gz fastq 1175231750.0 15577911.0 GSM2574371 r2 0:75.44 1:0 A:287141469;C:293942288;G:277159611;T:316919071;N:69311 75 0     287141469 293942288 277159611 316919071 69311 SRX2733018 SRS2120918 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93883   0.05461   0.73841   0.50615   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42151 42151 SRR5443682 SRX2733018 SRS2120918 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 1 GSM2574371   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574371 GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq GSM2574371   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574371 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M1_S2_L003_R1_001.fastq.gz fastq 1170671016.0 15517791.0 GSM2574371 r3 0:75.44 1:0 A:287726896;C:292922993;G:275775803;T:314197498;N:47826 75 0     287726896 292922993 275775803 314197498 47826 SRX2733018 SRS2120918 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93571   0.05459   0.74168   0.50894   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42152 42152 SRR5443683 SRX2733018 SRS2120918 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell mutant 1 GSM2574371   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:mafba uq4bh mutant 48hpf zebrafish FAC sorted endothelial cell mutant 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:mafba uq4bh mutant GSM2574371 GSM2574371: 48hpf zebrafish FAC sorted endothelial cell mutant 1; Danio rerio; RNA Seq GSM2574371   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574371 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     M1_S2_L004_R1_001.fastq.gz fastq 1174626578.0 15569716.0 GSM2574371 r4 0:75.44 1:0 A:288367287;C:293885435;G:276774483;T:315550752;N:48621 75 0     288367287 293885435 276774483 315550752 48621 SRX2733018 SRS2120918 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93712   0.05466   0.73969   0.50987   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42153 42153 SRR5443676 SRX2733017 SRS2120915 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 3 GSM2574370   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574370 GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq GSM2574370   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574370 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S3_S5_L001_R1_001.fastq.gz fastq 1200317760.0 15909907.0 GSM2574370 r1 0:75.44 1:0 A:296365402;C:297373974;G:283266985;T:323244649;N:66750 75 0     296365402 297373974 283266985 323244649 66750 SRX2733017 SRS2120915 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92986   0.05547   0.72805   0.50801   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42154 42154 SRR5443677 SRX2733017 SRS2120915 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 3 GSM2574370   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574370 GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq GSM2574370   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574370 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S3_S5_L002_R1_001.fastq.gz fastq 1186590046.0 15727830.0 GSM2574370 r2 0:75.45 1:0 A:292748835;C:294033369;G:280237781;T:319506249;N:63812 75 0     292748835 294033369 280237781 319506249 63812 SRX2733017 SRS2120915 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92874   0.05356   0.72839   0.51335   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42155 42155 SRR5443678 SRX2733017 SRS2120915 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 3 GSM2574370   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574370 GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq GSM2574370   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574370 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S3_S5_L003_R1_001.fastq.gz fastq 1179030774.0 15627890.0 GSM2574370 r3 0:75.44 1:0 A:292569213;C:292307681;G:278072717;T:316039886;N:41277 75 0     292569213 292307681 278072717 316039886 41277 SRX2733017 SRS2120915 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92502   0.0542   0.73129   0.50553   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42156 42156 SRR5443679 SRX2733017 SRS2120915 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 3 GSM2574370   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 3 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574370 GSM2574370: 48hpf zebrafish FAC sorted endothelial cell wt 3; Danio rerio; RNA Seq GSM2574370   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574370 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S3_S5_L004_R1_001.fastq.gz fastq 1186517148.0 15727062.0 GSM2574370 r4 0:75.44 1:0 A:294065343;C:294086528;G:279977232;T:318344594;N:43451 75 0     294065343 294086528 279977232 318344594 43451 SRX2733017 SRS2120915 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92801   0.05486   0.7263   0.51617   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42157 42157 SRR5443672 SRX2733016 SRS2120914 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 2 GSM2574369   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574369 GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq GSM2574369   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574369 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S2_S3_L001_R1_001.fastq.gz fastq 1118226721.0 14818796.0 GSM2574369 r1 0:75.46 1:0 A:277321886;C:276240373;G:264607012;T:299984813;N:72637 75 0     277321886 276240373 264607012 299984813 72637 SRX2733016 SRS2120914 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92813   0.0608   0.73511   0.49445   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42158 42158 SRR5443673 SRX2733016 SRS2120914 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 2 GSM2574369   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574369 GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq GSM2574369   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574369 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S2_S3_L002_R1_001.fastq.gz fastq 1097382503.0 14542648.0 GSM2574369 r2 0:75.46 1:0 A:271913618;C:271165534;G:259952446;T:294280610;N:70295 75 0     271913618 271165534 259952446 294280610 70295 SRX2733016 SRS2120914 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92628   0.05901   0.73434   0.50436   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42159 42159 SRR5443674 SRX2733016 SRS2120914 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 2 GSM2574369   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574369 GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq GSM2574369   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574369 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S2_S3_L003_R1_001.fastq.gz fastq 1100385244.0 14582533.0 GSM2574369 r3 0:75.46 1:0 A:274241238;C:272082346;G:260277831;T:293731839;N:51990 75 0     274241238 272082346 260277831 293731839 51990 SRX2733016 SRS2120914 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92524   0.06015   0.73805   0.50957   71   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42160 42160 SRR5443675 SRX2733016 SRS2120914 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 2 GSM2574369   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 2 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574369 GSM2574369: 48hpf zebrafish FAC sorted endothelial cell wt 2; Danio rerio; RNA Seq GSM2574369   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574369 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S2_S3_L004_R1_001.fastq.gz fastq 1100058192.0 14577978.0 GSM2574369 r4 0:75.46 1:0 A:273957130;C:271919703;G:260365193;T:293764097;N:52069 75 0     273957130 271919703 260365193 293764097 52069 SRX2733016 SRS2120914 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.92546   0.06173   0.73985   0.52271   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42161 42161 SRR5443668 SRX2733015 SRS2120913 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 1 GSM2574368   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574368 GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq GSM2574368   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574368 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S1_S1_L001_R1_001.fastq.gz fastq 1086391308.0 14398072.0 GSM2574368 r1 0:75.45 1:0 A:265407098;C:273473167;G:256935933;T:290517430;N:57680 75 0     265407098 273473167 256935933 290517430 57680 SRX2733015 SRS2120913 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93916   0.05822   0.73785   0.51199   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42162 42162 SRR5443669 SRX2733015 SRS2120913 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 1 GSM2574368   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574368 GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq GSM2574368   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574368 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S1_S1_L002_R1_001.fastq.gz fastq 1073108602.0 14221959.0 GSM2574368 r2 0:75.45 1:0 A:261964537;C:270187564;G:253958473;T:286941827;N:56201 75 0     261964537 270187564 253958473 286941827 56201 SRX2733015 SRS2120913 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93746   0.05835   0.73734   0.50609   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42163 42163 SRR5443670 SRX2733015 SRS2120913 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 1 GSM2574368   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574368 GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq GSM2574368   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574368 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S1_S1_L003_R1_001.fastq.gz fastq 1064653834.0 14110138.0 GSM2574368 r3 0:75.45 1:0 A:261657368;C:268193214;G:251551872;T:283215565;N:35815 75 0     261657368 268193214 251551872 283215565 35815 SRX2733015 SRS2120913 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93651   0.05738   0.74042   0.51489   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
42164 42164 SRR5443671 SRX2733015 SRS2120913 SRP103805 PRJNA382558 mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. GSE97649 Transcriptome Analysis 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant   pubmed:26253536   48hpf zebrafish FAC sorted endothelial cell wt 1 GSM2574368   tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype 48hpf zebrafish FAC sorted endothelial cell wt 1 adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample purified endothelial cell   48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols   transgene:kdrl eGFP|genotype:wildtype GSM2574368 GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq GSM2574368   1 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM2574368 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP103805     S1_S1_L004_R1_001.fastq.gz fastq 1072543375.0 14214599.0 GSM2574368 r4 0:75.45 1:0 A:263268340;C:270054371;G:253632532;T:285551360;N:36772 75 0     263268340 270054371 253632532 285551360 36772 SRX2733015 SRS2120913 SRA553927 GEO Australian Institute for Bioengineering and Nanotechnology 1 0.93658   0.05706   0.73935   0.5115   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Australia 2017-04-11 Hatching Embryo Endothelium Cardiovascular System
47740 47740 SRR6848349 SRX3803619 SRS3055252 SRP135898 PRJNA438687 Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos GSE111963 Transcriptome Analysis We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf   pubmed:30006544   hhex overexpression rep2 GSM3045716   tissue:FACS sorted endothelial cells|genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells hhex overexpression rep2 The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak FACS sorted endothelial cells   For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.   genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells GSM3045716 GSM3045716: hhex overexpression rep2; Danio rerio; RNA Seq GSM3045716   1 For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. GEO Accession:GSM3045716 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP135898     Sebastien_OE_2_R1.fastq.gz fastq 2514724985.0 34768823.0 GSM3045716 r1 0:72.33 1:0 A:565805246;C:704077993;G:741187599;T:503446013;N:208134 72 0     565805246 704077993 741187599 503446013 208134 SRX3803619 SRS3055252 SRA667127 GEO MPI for heart and lung research 1 0.94763   0.26354   0.80702   0.62768   74   B   usable mapping rate illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   Germany 2018-03-16 Hatching Embryo Endothelium Cardiovascular System
47741 47741 SRR6848348 SRX3803618 SRS3055251 SRP135898 PRJNA438687 Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos GSE111963 Transcriptome Analysis We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf   pubmed:30006544   hhex overexpression rep1 GSM3045715   tissue:FACS sorted endothelial cells|genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells hhex overexpression rep1 The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak FACS sorted endothelial cells   For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.   genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells GSM3045715 GSM3045715: hhex overexpression rep1; Danio rerio; RNA Seq GSM3045715   1 For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. GEO Accession:GSM3045715 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP135898     Sebastien_OE_1_R1.fastq.gz fastq 2201523348.0 30479961.0 GSM3045715 r1 0:72.23 1:0 A:510844407;C:602803512;G:634953285;T:452682176;N:239968 72 0     510844407 602803512 634953285 452682176 239968 SRX3803618 SRS3055251 SRA667127 GEO MPI for heart and lung research 1 0.94219   0.27653   0.80466   0.66516   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   Germany 2018-03-16 Hatching Embryo Endothelium Cardiovascular System
47742 47742 SRR6848347 SRX3803617 SRS3055250 SRP135898 PRJNA438687 Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos GSE111963 Transcriptome Analysis We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf   pubmed:30006544   hhex mutant rep2 GSM3045714   tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells hhex mutant rep2 The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak FACS sorted endothelial cells   For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.   genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells GSM3045714 GSM3045714: hhex mutant rep2; Danio rerio; RNA Seq GSM3045714   1 For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. GEO Accession:GSM3045714 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP135898     Sebastien_Mut_2_R1.fastq.gz fastq 2377033794.0 32865413.0 GSM3045714 r1 0:72.33 1:0 A:531221225;C:668093793;G:704926379;T:472544720;N:247677 72 0     531221225 668093793 704926379 472544720 247677 SRX3803617 SRS3055250 SRA667127 GEO MPI for heart and lung research 1 0.93202   0.25789   0.81617   0.66408   74   B   usable mapping rate illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   Germany 2018-03-16 Hatching Embryo Endothelium Cardiovascular System
47743 47743 SRR6848346 SRX3803616 SRS3055249 SRP135898 PRJNA438687 Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos GSE111963 Transcriptome Analysis We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf   pubmed:30006544   hhex mutant rep1 GSM3045713   tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells hhex mutant rep1 The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak FACS sorted endothelial cells   For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.   genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells GSM3045713 GSM3045713: hhex mutant rep1; Danio rerio; RNA Seq GSM3045713   1 For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. GEO Accession:GSM3045713 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP135898     Sebastien_Mut_1_R1.fastq.gz fastq 2492708175.0 34527636.0 GSM3045713 r1 0:72.19 1:0 A:555859455;C:702003394;G:740775583;T:493818885;N:250858 72 0     555859455 702003394 740775583 493818885 250858 SRX3803616 SRS3055249 SRA667127 GEO MPI for heart and lung research 1 0.93924   0.25343   0.81889   0.6311   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   Germany 2018-03-16 Hatching Embryo Endothelium Cardiovascular System
47744 47744 SRR6848345 SRX3803615 SRS3055248 SRP135898 PRJNA438687 Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos GSE111963 Transcriptome Analysis We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf   pubmed:30006544   Sibling rep2 GSM3045712   tissue:FACS sorted endothelial cells|genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells Sibling rep2 The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak FACS sorted endothelial cells   For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.   genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells GSM3045712 GSM3045712: Sibling rep2; Danio rerio; RNA Seq GSM3045712   1 For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. GEO Accession:GSM3045712 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP135898     Sebastien_WT_2_R1.fastq.gz fastq 2451974351.0 33830383.0 GSM3045712 r1 0:72.48 1:0 A:557370317;C:679644672;G:720300776;T:494468929;N:189657 72 0     557370317 679644672 720300776 494468929 189657 SRX3803615 SRS3055248 SRA667127 GEO MPI for heart and lung research 1 0.91674   0.25327   0.80868   0.70337   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   Germany 2018-03-16 Hatching Embryo Endothelium Cardiovascular System
47745 47745 SRR6848344 SRX3803614 SRS3055247 SRP135898 PRJNA438687 Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos GSE111963 Transcriptome Analysis We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf   pubmed:30006544   Sibling rep1 GSM3045711   tissue:FACS sorted endothelial cells|genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells Sibling rep1 The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak FACS sorted endothelial cells   For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.   genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells GSM3045711 GSM3045711: Sibling rep1; Danio rerio; RNA Seq GSM3045711   1 For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. GEO Accession:GSM3045711 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP135898     Sebastien_WT_1_R1.fastq.gz fastq 2685019288.0 37185023.0 GSM3045711 r1 0:72.21 1:0 A:629322492;C:731250924;G:769793846;T:554311522;N:340504 72 0     629322492 731250924 769793846 554311522 340504 SRX3803614 SRS3055247 SRA667127 GEO MPI for heart and lung research 1 0.90551   0.24697   0.80695   0.65765   75   B   usable mapping rate illumina nextseq full_length cdna_unspecified smarter bulk unknown unknown   Germany 2018-03-16 Hatching Embryo Endothelium Cardiovascular System
49040 49040 SRR7633494 SRX4497225 SRS3618225 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 endo 03 GSM3317066   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA G2 endo 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G2 mRNA GSM3317066 GSM3317066: G2 endo 03; Danio rerio; RNA Seq GSM3317066   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317066 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S18_trimmed.fastq.gz fastq 950344310.0 18847513.0 GSM3317066 r1 0:50.42 1:0 A:270135652;C:209210468;G:202674675;T:268256430;N:67085 50 0     270135652 209210468 202674675 268256430 67085 SRX4497225 SRS3618225 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89759   0.1428   0.69132   0.4729   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49041 49041 SRR7633493 SRX4497224 SRS3618224 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 endo 02 GSM3317065   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA G2 endo 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G2 mRNA GSM3317065 GSM3317065: G2 endo 02; Danio rerio; RNA Seq GSM3317065   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317065 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S17_trimmed.fastq.gz fastq 1635110054.0 32380584.0 GSM3317065 r1 0:50.50 1:0 A:462134552;C:361057634;G:349465446;T:462337205;N:115217 50 0     462134552 361057634 349465446 462337205 115217 SRX4497224 SRS3618224 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.80201   0.12711   0.70471   0.44427   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49042 49042 SRR7633492 SRX4497223 SRS3618223 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 endo 01 GSM3317064   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA G2 endo 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G2 mRNA GSM3317064 GSM3317064: G2 endo 01; Danio rerio; RNA Seq GSM3317064   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317064 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S16_trimmed.fastq.gz fastq 1302352614.0 25794210.0 GSM3317064 r1 0:50.49 1:0 A:370194702;C:286011167;G:276758200;T:369297736;N:90809 50 0     370194702 286011167 276758200 369297736 90809 SRX4497223 SRS3618223 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89468   0.15745   0.69447   0.47938   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49043 49043 SRR7633491 SRX4497222 SRS3618222 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 endo 03 GSM3317063   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA G0 endo 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G0 mRNA GSM3317063 GSM3317063: G0 endo 03; Danio rerio; RNA Seq GSM3317063   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317063 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S15_trimmed.fastq.gz fastq 1248556473.0 24725241.0 GSM3317063 r1 0:50.50 1:0 A:350256976;C:280431139;G:270771772;T:347009294;N:87292 50 0     350256976 280431139 270771772 347009294 87292 SRX4497222 SRS3618222 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.90514   0.13266   0.69236   0.47977   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49044 49044 SRR7633490 SRX4497221 SRS3618221 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 endo 02 GSM3317062   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA G0 endo 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G0 mRNA GSM3317062 GSM3317062: G0 endo 02; Danio rerio; RNA Seq GSM3317062   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317062 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S14_trimmed.fastq.gz fastq 372093672.0 7456111.0 GSM3317062 r1 0:49.90 1:0 A:113486766;C:74400549;G:71245468;T:112935661;N:25228 49 0     113486766 74400549 71245468 112935661 25228 SRX4497221 SRS3618221 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89644   0.12968   0.70658   0.47231   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49045 49045 SRR7633489 SRX4497220 SRS3618220 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 endo 01 GSM3317061   tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA G0 endo 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:human APOL1 G0 mRNA GSM3317061 GSM3317061: G0 endo 01; Danio rerio; RNA Seq GSM3317061   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317061 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S13_trimmed.fastq.gz fastq 1450133780.0 28705598.0 GSM3317061 r1 0:50.52 1:0 A:407543677;C:323333189;G:313321100;T:405835253;N:100561 50 0     407543677 323333189 313321100 405835253 100561 SRX4497220 SRS3618220 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.8994   0.13347   0.6942   0.47759   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49046 49046 SRR7633488 SRX4497219 SRS3618219 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control endo 03 GSM3317060   tissue:zebrafish endothelium|line:fli:EGFP|treatment:control control endo 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:control GSM3317060 GSM3317060: control endo 03; Danio rerio; RNA Seq GSM3317060   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317060 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S12_trimmed.fastq.gz fastq 1720199608.0 34019943.0 GSM3317060 r1 0:50.56 1:0 A:474252335;C:393152371;G:382256277;T:470417173;N:121452 50 0     474252335 393152371 382256277 470417173 121452 SRX4497219 SRS3618219 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.90252   0.11709   0.69668   0.47424   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49047 49047 SRR7633487 SRX4497218 SRS3618218 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control endo 02 GSM3317059   tissue:zebrafish endothelium|line:fli:EGFP|treatment:control control endo 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:control GSM3317059 GSM3317059: control endo 02; Danio rerio; RNA Seq GSM3317059   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317059 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S11_trimmed.fastq.gz fastq 322327295.0 6605687.0 GSM3317059 r1 0:48.80 1:0 A:109722776;C:53179948;G:51091267;T:108312123;N:21181 48 0     109722776 53179948 51091267 108312123 21181 SRX4497218 SRS3618218 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.8922   0.1261   0.72811   0.46128   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
49048 49048 SRR7633486 SRX4497217 SRS3618217 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control endo 01 GSM3317058   tissue:zebrafish endothelium|line:fli:EGFP|treatment:control control endo 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish endothelium Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:fli:EGFP|treatment:control GSM3317058 GSM3317058: control endo 01; Danio rerio; RNA Seq GSM3317058   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317058 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S10_trimmed.fastq.gz fastq 1484074935.0 29385409.0 GSM3317058 r1 0:50.50 1:0 A:411414710;C:336260838;G:326730208;T:409563857;N:105322 50 0     411414710 336260838 326730208 409563857 105322 SRX4497217 SRS3618217 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.88777   0.11462   0.70102   0.47353   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Endothelium Cardiovascular System
52238 52238 SRR9044114 SRX5820656 SRS4749302 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         CT1   strain:AB|isolate:ctrl MO fluorescence activated cell sorting 1|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells1 ct1 20191 ct1 20191 ctrl MO 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     CT1.gz fastq 3222866250.0 21485775.0 CT1.gz 0:150 1:0 A:845914701;C:771891741;G:774348916;T:830705072;N:5820 150 0     845914701 771891741 774348916 830705072 5820 SRX5820656 SRS4749302 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.95232   0.09195   0.7837   0.45885   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
52239 52239 SRR9044115 SRX5820655 SRS4749299 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         CT2   strain:AB|isolate:ctrl MO fluorescence activated cell sorting 2|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells2 ct1 20192 ct1 20192 ctrl MO 2     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     CT2.gz fastq 3992117700.0 26614118.0 CT2.gz 0:150 1:0 A:1040923084;C:961956867;G:964333886;T:1024896832;N:7031 150 0     1040923084 961956867 964333886 1024896832 7031 SRX5820655 SRS4749299 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.95545   0.087   0.78488   0.46466   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2019-05-11 Adult Adult Endothelium Cardiovascular System
52240 52240 SRR9044116 SRX5820654 SRS4749301 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         SCMO1   strain:AB|isolate:5c MO fluorescence activated cell sorting 3|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells3 5c 20191 5c 20191 5c MO 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     SCMO1.gz fastq 2137379550.0 14249197.0 SCMO1.gz 0:150 1:0 A:558129907;C:517045618;G:515434728;T:546767387;N:1910 150 0     558129907 517045618 515434728 546767387 1910 SRX5820654 SRS4749301 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.94546   0.08686   0.78709   0.56163   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
52241 52241 SRR9044117 SRX5820653 SRS4749300 SRP197695 PRJNA542436 Regulation of hematopoiesis and endothelium function by endocytic trafficking PRJNA542436 Other Endocytic trafficking in endothelium         SCMO2   strain:AB|isolate:5c MO fluorescence activated cell sorting 4|cultivar:not applicable|ecotype:not applicable|age:1 year|sex:male and female|tissue:fli1a+ endothelium|BioSampleModel:Model organism or animal                 RNA seq of endothelial cells4 5c 20192 5c 20192 5c MO 2     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP197695     SCMO2.gz fastq 3909804300.0 26065362.0 SCMO2.gz 0:150 1:0 A:1033271905;C:928576644;G:928527559;T:1019420939;N:7253 150 0     1033271905 928576644 928527559 1019420939 7253 SRX5820653 SRS4749300 SRA885405 Chinese academy of sciences|institute of zoology Chinese academy of sciences 1 0.94475   0.096   0.7867   0.55845   150   B   usable mapping rate illumina novaseq_era unknown other unknown bulk unknown unknown   China 2020-01-17 Adult Adult Endothelium Cardiovascular System
69580 69580 SRR18927184 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L001_R1_001.fastq.gz fastq 744134237.0 10221322.0 GSM6068604 r1 0:72.80 1:0 A:200415459;C:170890467;G:175699158;T:196451943;N:677210 72 0     200415459 170890467 175699158 196451943 677210 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93677   0.0458   0.76144   0.51338   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69581 69581 SRR18927185 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L002_R1_001.fastq.gz fastq 713336563.0 9806369.0 GSM6068604 r2 0:72.74 1:0 A:192232089;C:164110978;G:167926911;T:188411430;N:655155 72 0     192232089 164110978 167926911 188411430 655155 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93575   0.0459   0.7628   0.52271   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69582 69582 SRR18927186 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L003_R1_001.fastq.gz fastq 718617566.0 9871758.0 GSM6068604 r3 0:72.80 1:0 A:193895503;C:165112470;G:169254039;T:189730714;N:624840 72 0     193895503 165112470 169254039 189730714 624840 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.9355   0.04598   0.76459   0.5158   73   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69583 69583 SRR18927187 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L004_R1_001.fastq.gz fastq 727564590.0 9976511.0 GSM6068604 r4 0:72.93 1:0 A:196363760;C:167163486;G:171092104;T:192383180;N:562060 72 0     196363760 167163486 171092104 192383180 562060 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93595   0.04601   0.76353   0.51732   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69584 69584 SRR18927188 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L001_R1_001.fastq.gz fastq 697802741.0 9548738.0 GSM6068603 r1 0:73.08 1:0 A:187922068;C:160061203;G:164649390;T:184626878;N:543202 73 0     187922068 160061203 164649390 184626878 543202 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93586   0.05129   0.76424   0.52169   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69585 69585 SRR18927189 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L002_R1_001.fastq.gz fastq 662903444.0 9078930.0 GSM6068603 r2 0:73.02 1:0 A:178605669;C:152357709;G:156008633;T:175409889;N:521544 73 0     178605669 152357709 156008633 175409889 521544 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93653   0.05146   0.7628   0.51778   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69586 69586 SRR18927190 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L003_R1_001.fastq.gz fastq 668311097.0 9143688.0 GSM6068603 r3 0:73.09 1:0 A:180289485;C:153373494;G:157331239;T:176839110;N:477769 73 0     180289485 153373494 157331239 176839110 477769 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93696   0.05225   0.7637   0.51732   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69587 69587 SRR18927191 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L004_R1_001.fastq.gz fastq 680968806.0 9296775.0 GSM6068603 r4 0:73.25 1:0 A:183838465;C:156195225;G:160056448;T:180449193;N:429475 73 0     183838465 156195225 160056448 180449193 429475 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93695   0.05036   0.76394   0.52148   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69588 69588 SRR18927192 SRX15004842 SRS12753554 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 GSM6068602   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068602 GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq GSM6068602 r1 GSM6068602 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_01_S7_L001_R1_001.fastq.gz fastq 860623909.0 11793192.0 GSM6068602 r1 0:72.98 1:0 A:231785480;C:197544026;G:202920509;T:227621795;N:752099 72 0     231785480 197544026 202920509 227621795 752099 SRX15004842 SRS12753554 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93103   0.0562   0.76179   0.51243   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69589 69589 SRR18927193 SRX15004842 SRS12753554 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 GSM6068602   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068602 GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq GSM6068602 r1 GSM6068602 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_01_S7_L002_R1_001.fastq.gz fastq 829335984.0 11372967.0 GSM6068602 r2 0:72.92 1:0 A:223480519;C:190755977;G:194990382;T:219387236;N:721870 72 0     223480519 190755977 194990382 219387236 721870 SRX15004842 SRS12753554 SRA1410588 Department of Anatomy &amp; Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93059   0.05558   0.76106   0.51174   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;