RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

26 rows where devstage_curation = "Pharyngula" and tissue_curation = "Blood"

✎ View and edit SQL

This data as json, CSV (advanced)

technology 3

tissue_curation_coarse 1

tissue_curation 1

  • Blood · 26 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 26 ✖
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
30018 30018 SRR27988043 SRX23641260 SRS20476222 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 3   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal                 RNA seq hamp / 36 hpf blood replicate 3 B 6 B 6 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz fastq fastq 8752665900.0 29175553.0 KO 3 R1 001.fastq.gz 0:150 1:150 A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682 150 150     2204170575 2174083961 2224694970 2149603712 112682 SRX23641260 SRS20476222 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.91553 0.91645 0.01276 0.01288 0.85884 0.85839 0.35101 0.40996 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30019 30019 SRR27988044 SRX23641259 SRS20476221 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 2   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal                 RNA seq hamp / 36 hpf blood replicate 2 B 5 B 5 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz fastq fastq 8060498700.0 26868329.0 KO 2 R1 001.fastq.gz 0:150 1:150 A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983 150 150     2045797336 1985847523 2035528018 1993222840 102983 SRX23641259 SRS20476221 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.9213 0.92027 0.0167 0.01676 0.8242 0.82475 0.41081 0.41111 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30020 30020 SRR27988045 SRX23641258 SRS20476220 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 1   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal                 RNA seq hamp / 36 hpf blood replicate 1 B 4 B 4 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz fastq fastq 8707637700.0 29025459.0 KO 1 R1 001.fastq.gz 0:150 1:150 A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563 150 150     2222026435 2133480283 2182087972 2169932447 110563 SRX23641258 SRS20476220 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.91531 0.91359 0.02185 0.0221 0.81213 0.8128 0.37868 0.42351 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30021 30021 SRR27988046 SRX23641257 SRS20476219 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 3   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal                 RNA seq wild type 36 hpf blood replicate 3 B 3 B 3 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz fastq fastq 8829371400.0 29431238.0 WT 3 R1 001.fastq.gz 0:150 1:150 A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894 150 150     2278837675 2141723937 2193442375 2215253519 113894 SRX23641257 SRS20476219 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.90531 0.9043 0.03015 0.03017 0.8101 0.8112 0.43085 0.43002 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30022 30022 SRR27988047 SRX23641256 SRS20476218 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 2   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal                 RNA seq wild type 36 hpf blood replicate 2 B 2 B 2 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz fastq fastq 7365643800.0 24552146.0 WT 2 R1 001.fastq.gz 0:150 1:150 A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827 150 150     1867985067 1819016430 1870006707 1808540769 94827 SRX23641256 SRS20476218 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.90612 0.90536 0.01714 0.01746 0.88109 0.88156 0.32469 0.39232 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30023 30023 SRR27988048 SRX23641255 SRS20476217 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 1   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal                 RNA seq wild type 36 hpf blood replicate 1 B 1 B 1 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz fastq fastq 8631863400.0 28772878.0 WT 1 R1 001.fastq.gz 0:150 1:150 A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557 150 150     2186212554 2135990723 2179142081 2130408485 109557 SRX23641255 SRS20476217 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.90461 0.90281 0.01388 0.01365 0.83871 0.83895 0.36511 0.41074 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
51876 51876 SRR8922974 SRX5704273 SRS4643334 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: WT6 GSM3728533   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type erythroid cells: WT6 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type GSM3728533 GSM3728533: erythroid cells: WT6; Danio rerio; RNA Seq GSM3728533   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728533 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_TAGCTT_LWT6.1_val_1.fq.gz J633_AHFHNLBGX2_TAGCTT_LWT6.2_val_2.fq.gz fastq fastq 8611605345.0 32335443.0 GSM3728533 r1 0:133.59 1:132.74 A:1724489451;C:2542199793;G:2626828499;T:1716562999;N:1524603 133 132     1724489451 2542199793 2626828499 1716562999 1524603 SRX5704273 SRS4643334 SRA875634 GEO Albert Einstein College of Medicine 2 0.91241 0.96131 0.10384 0.10826 0.77761 0.7767 0.69985 0.69519 128 128 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51877 51877 SRR8922973 SRX5704272 SRS4643333 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: WT5 GSM3728532   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type erythroid cells: WT5 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type GSM3728532 GSM3728532: erythroid cells: WT5; Danio rerio; RNA Seq GSM3728532   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728532 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_TGACCA_LWT5.1_val_1.fq.gz J633_AHFHNLBGX2_TGACCA_LWT5.2_val_2.fq.gz fastq fastq 8110446942.0 28906836.0 GSM3728532 r1 0:140.70 1:139.87 A:1479901358;C:2533764326;G:2613647627;T:1481710129;N:1423502 140 139     1479901358 2533764326 2613647627 1481710129 1423502 SRX5704272 SRS4643333 SRA875634 GEO Albert Einstein College of Medicine 2 0.92578 0.97511 0.09182 0.09201 0.80503 0.80324 0.76985 0.7675 150 150 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51878 51878 SRR8922972 SRX5704271 SRS4643332 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: WT4 GSM3728531   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type erythroid cells: WT4 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type GSM3728531 GSM3728531: erythroid cells: WT4; Danio rerio; RNA Seq GSM3728531   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728531 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_TTAGGC_LWT4.2_val_2.fq.gz J633_AHFHNLBGX2_TTAGGC_LWT4.1_val_1.fq.gz fastq fastq 8627466135.0 32957109.0 GSM3728531 r1 0:131.12 1:130.66 A:1686521982;C:2592728511;G:2670950174;T:1675745501;N:1519967 131 130     1686521982 2592728511 2670950174 1675745501 1519967 SRX5704271 SRS4643332 SRA875634 GEO Albert Einstein College of Medicine 2 0.91773 0.96731 0.11151 0.1134 0.78792 0.78597 0.73657 0.73692 104 104 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51879 51879 SRR8922971 SRX5704270 SRS4643331 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: WT3 GSM3728530   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type erythroid cells: WT3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type GSM3728530 GSM3728530: erythroid cells: WT3; Danio rerio; RNA Seq GSM3728530   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728530 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_CGATGT_LWT3.2_val_2.fq.gz J633_AHFHNLBGX2_CGATGT_LWT3.1_val_1.fq.gz fastq fastq 7675701402.0 28099783.0 GSM3728530 r1 0:136.90 1:136.26 A:1496106079;C:2307580110;G:2386093773;T:1484556287;N:1365153 136 136     1496106079 2307580110 2386093773 1484556287 1365153 SRX5704270 SRS4643331 SRA875634 GEO Albert Einstein College of Medicine 2 0.91833 0.96754 0.10771 0.10822 0.80135 0.80158 0.76757 0.7524 150 150 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51880 51880 SRR8922970 SRX5704269 SRS4643330 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: WT2 GSM3728529   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant erythroid cells: WT2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant GSM3728529 GSM3728529: erythroid cells: WT2; Danio rerio; RNA Seq GSM3728529   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728529 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_ATCACG_LWT2.2_val_2.fq.gz J633_AHFHNLBGX2_ATCACG_LWT2.1_val_1.fq.gz fastq fastq 8749226933.0 32236600.0 GSM3728529 r1 0:135.97 1:135.43 A:1818348438;C:2523018672;G:2595068272;T:1811215171;N:1576380 135 135     1818348438 2523018672 2595068272 1811215171 1576380 SRX5704269 SRS4643330 SRA875634 GEO Albert Einstein College of Medicine 2 0.91533 0.96543 0.12825 0.13005 0.77394 0.77344 0.70772 0.67993 143 143 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51881 51881 SRR8922969 SRX5704268 SRS4643329 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: Mut6 GSM3728528   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant erythroid cells: Mut6 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant GSM3728528 GSM3728528: erythroid cells: Mut6; Danio rerio; RNA Seq GSM3728528   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728528 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_GGCTAC_LMut6.2_val_2.fq.gz J633_AHFHNLBGX2_GGCTAC_LMut6.1_val_1.fq.gz fastq fastq 7989745578.0 29813232.0 GSM3728528 r1 0:134.59 1:133.41 A:1487912329;C:2465671654;G:2552013900;T:1482837472;N:1310223 134 133     1487912329 2465671654 2552013900 1482837472 1310223 SRX5704268 SRS4643329 SRA875634 GEO Albert Einstein College of Medicine 2 0.91636 0.96506 0.12513 0.13214 0.80255 0.80277 0.77309 0.77779 106 106 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51882 51882 SRR8922968 SRX5704267 SRS4643327 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: Mut5 GSM3728527   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant erythroid cells: Mut5 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant GSM3728527 GSM3728527: erythroid cells: Mut5; Danio rerio; RNA Seq GSM3728527   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728527 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_GATCAG_LMut5.2_val_2.fq.gz J633_AHFHNLBGX2_GATCAG_LMut5.1_val_1.fq.gz fastq fastq 8500296799.0 30812271.0 GSM3728527 r1 0:138.28 1:137.59 A:1566669253;C:2640866820;G:2726747970;T:1564531299;N:1481457 138 137     1566669253 2640866820 2726747970 1564531299 1481457 SRX5704267 SRS4643327 SRA875634 GEO Albert Einstein College of Medicine 2 0.91987 0.9688 0.10388 0.10646 0.80338 0.80176 0.75914 0.71799 52 52 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51883 51883 SRR8922967 SRX5704266 SRS4643328 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: Mut4 GSM3728526   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant erythroid cells: Mut4 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant GSM3728526 GSM3728526: erythroid cells: Mut4; Danio rerio; RNA Seq GSM3728526   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728526 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_ACTTGA_LMut4.2_val_2.fq.gz J633_AHFHNLBGX2_ACTTGA_LMut4.1_val_1.fq.gz fastq fastq 8415322795.0 32199684.0 GSM3728526 r1 0:130.80 1:130.55 A:1593557159;C:2583771193;G:2657553064;T:1578891748;N:1549631 130 130     1593557159 2583771193 2657553064 1578891748 1549631 SRX5704266 SRS4643328 SRA875634 GEO Albert Einstein College of Medicine 2 0.92078 0.97122 0.12063 0.12061 0.81994 0.81822 0.76635 0.7826 149 148 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51884 51884 SRR8922966 SRX5704265 SRS4643326 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: Mut3 GSM3728525   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant erythroid cells: Mut3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant GSM3728525 GSM3728525: erythroid cells: Mut3; Danio rerio; RNA Seq GSM3728525   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728525 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_CAGATC_LMut3.2_val_2.fq.gz J633_AHFHNLBGX2_CAGATC_LMut3.1_val_1.fq.gz fastq fastq 5373096143.0 19350806.0 GSM3728525 r1 0:139.04 1:138.63 A:990313321;C:1667762750;G:1723819167;T:990236765;N:964140 139 138     990313321 1667762750 1723819167 990236765 964140 SRX5704265 SRS4643326 SRA875634 GEO Albert Einstein College of Medicine 2 0.92305 0.97223 0.10386 0.10158 0.8062 0.80415 0.79641 0.78792 150 149 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
51885 51885 SRR8922965 SRX5704264 SRS4643325 SRP192854 PRJNA533283 RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish GSE129952 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.       erythroid cells: Mut1 GSM3728524   tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant erythroid cells: Mut1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample erythroid cells   Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.   age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant GSM3728524 GSM3728524: erythroid cells: Mut1; Danio rerio; RNA Seq GSM3728524   1 Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. GEO Accession:GSM3728524 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP192854     J633_AHFHNLBGX2_GCCAAT_LMut1.1_val_1.fq.gz J633_AHFHNLBGX2_GCCAAT_LMut1.2_val_2.fq.gz fastq fastq 7256147960.0 27513744.0 GSM3728524 r1 0:132.21 1:131.52 A:1506751800;C:2097058291;G:2163719918;T:1487337753;N:1280198 132 131     1506751800 2097058291 2163719918 1487337753 1280198 SRX5704264 SRS4643325 SRA875634 GEO Albert Einstein College of Medicine 2 0.90512 0.95369 0.12564 0.13165 0.77153 0.77098 0.74915 0.74717 122 122 B B biological fallback assumption illumina nextseq full_length rrna_depletion smarter bulk unknown unknown   United States 2019-04-17 Pharyngula Embryo Blood Hematopoietic System
53001 53001 SRR12173589 SRX8688333 SRS6966994 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA seq Blood rep2 GSM4662086   source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood YueLab RNA seq Blood rep2 RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter “ region size 1000” and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged YueLab RNA seq Blood   RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Blood GSM4662086 GSM4662086: YueLab RNA seq Blood rep2; Danio rerio; RNA Seq GSM4662086   1 RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… GEO Accession:GSM4662086 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP213938     YueLab-RNA-seq-Blood-rep2_2.fastq.gz YueLab-RNA-seq-Blood-rep2_1.fastq.gz fastq fastq 9750305560.0 32285780.0 GSM4662086 r1 0:151 1:151 A:2564237490;C:2313022617;G:2328740350;T:2544206938;N:98165 151 151     2564237490 2313022617 2328740350 2544206938 98165 SRX8688333 SRS6966994 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.90976 0.90587 0.07014 0.06953 0.85415 0.85624 0.51898 0.51696 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   United States 2020-07-08 Pharyngula Embryo Blood Hematopoietic System
53002 53002 SRR12173588 SRX8688332 SRS6966993 SRP213938 PRJNA553572 A map of cis regulatory elements and 3D genome structures in zebrafish GSE134055 Other The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.   pubmed:33239788;pubmed:35649578   YueLab RNA seq Blood rep1 GSM4662085   source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood YueLab RNA seq Blood rep1 RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter “ region size 1000” and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged YueLab RNA seq Blood   RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions strain:Tuebingen|tissue:Blood GSM4662085 GSM4662085: YueLab RNA seq Blood rep1; Danio rerio; RNA Seq GSM4662085   1 RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… GEO Accession:GSM4662085 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP213938     YueLab-RNA-seq-Blood-rep1_1.fastq.gz YueLab-RNA-seq-Blood-rep1_2.fastq.gz fastq fastq 10181340496.0 33713048.0 GSM4662085 r1 0:151 1:151 A:2735674306;C:2352790027;G:2376786768;T:2715986044;N:103351 151 151     2735674306 2352790027 2376786768 2715986044 103351 SRX8688332 SRS6966993 SRA919194 GEO Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine 2 0.91563 0.91373 0.11339 0.11315 0.82235 0.82266 0.48854 0.48669 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   United States 2020-07-08 Pharyngula Embryo Blood Hematopoietic System
58407 58407 SRR11309042 SRX7913591 SRS6320433 SRP252869 PRJNA612697 RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish GSE146995 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.   pubmed:33651979   cd41gfp WT3 GSM4411870   tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf cd41gfp WT3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample hematopoietic stem and progenitor cells   cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.   develpmental stage:40 hpf GSM4411870 GSM4411870: cd41gfp WT3; Danio rerio; RNA Seq GSM4411870   1 cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol. GEO Accession:GSM4411870 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP252869     cd41gfp_WT3_2.fq.gz cd41gfp_WT3_1.fq.gz fastq fastq 11085766500.0 36952555.0 GSM4411870 r1 0:150 1:150 A:2992020230;C:2573519486;G:2581891304;T:2938153427;N:182053 150 150     2992020230 2573519486 2581891304 2938153427 182053 SRX7913591 SRS6320433 SRA1055135 GEO Albert Einstein College of Medicine 2 0.77434 0.77183 0.20553 0.20573 0.77171 0.77922 0.5109 0.495 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-15 Pharyngula Embryo Blood Hematopoietic System
58408 58408 SRR11309041 SRX7913590 SRS6320432 SRP252869 PRJNA612697 RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish GSE146995 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.   pubmed:33651979   cd41gfp WT2 GSM4411869   tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf cd41gfp WT2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample hematopoietic stem and progenitor cells   cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.   develpmental stage:40 hpf GSM4411869 GSM4411869: cd41gfp WT2; Danio rerio; RNA Seq GSM4411869   1 cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol. GEO Accession:GSM4411869 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP252869     cd41gfp_WT2_1.fq.gz cd41gfp_WT2_2.fq.gz fastq fastq 11221423200.0 37404744.0 GSM4411869 r1 0:150 1:150 A:2921284710;C:2714470786;G:2708278380;T:2877145192;N:244132 150 150     2921284710 2714470786 2708278380 2877145192 244132 SRX7913590 SRS6320432 SRA1055135 GEO Albert Einstein College of Medicine 2 0.75116 0.75065 0.18086 0.18146 0.79586 0.80016 0.52492 0.52828 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-15 Pharyngula Embryo Blood Hematopoietic System
58409 58409 SRR11309040 SRX7913589 SRS6320431 SRP252869 PRJNA612697 RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish GSE146995 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.   pubmed:33651979   cd41gfp WT1 GSM4411868   tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf cd41gfp WT1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample hematopoietic stem and progenitor cells   cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.   develpmental stage:40 hpf GSM4411868 GSM4411868: cd41gfp WT1; Danio rerio; RNA Seq GSM4411868   1 cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol. GEO Accession:GSM4411868 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP252869     cd41gfp_WT1_1.fq.gz cd41gfp_WT1_2.fq.gz fastq fastq 11115852900.0 37052843.0 GSM4411868 r1 0:150 1:150 A:3004371197;C:2577587578;G:2575472481;T:2958199318;N:222326 150 150     3004371197 2577587578 2575472481 2958199318 222326 SRX7913589 SRS6320431 SRA1055135 GEO Albert Einstein College of Medicine 2 0.76528 0.76415 0.19581 0.19637 0.77039 0.77579 0.65251 0.64941 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-15 Pharyngula Embryo Blood Hematopoietic System
58410 58410 SRR11309039 SRX7913588 SRS6320430 SRP252869 PRJNA612697 RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish GSE146995 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.   pubmed:33651979   cd41gfp mut3 GSM4411867   tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant cd41gfp mut3 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample hematopoietic stem and progenitor cells   cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.   develpmental stage:40 hpf mutant GSM4411867 GSM4411867: cd41gfp mut3; Danio rerio; RNA Seq GSM4411867   1 cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol. GEO Accession:GSM4411867 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP252869     cd41gfp_mut3_2.fq.gz cd41gfp_mut3_1.fq.gz fastq fastq 11157315900.0 37191053.0 GSM4411867 r1 0:150 1:150 A:2980738665;C:2622591667;G:2625477229;T:2928292016;N:216323 150 150     2980738665 2622591667 2625477229 2928292016 216323 SRX7913588 SRS6320430 SRA1055135 GEO Albert Einstein College of Medicine 2 0.77032 0.76857 0.22483 0.22518 0.78685 0.79226 0.64484 0.52439 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-15 Pharyngula Embryo Blood Hematopoietic System
58411 58411 SRR11309038 SRX7913587 SRS6320429 SRP252869 PRJNA612697 RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish GSE146995 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.   pubmed:33651979   cd41gfp mut2 GSM4411866   tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant cd41gfp mut2 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample hematopoietic stem and progenitor cells   cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.   develpmental stage:40 hpf mutant GSM4411866 GSM4411866: cd41gfp mut2; Danio rerio; RNA Seq GSM4411866   1 cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol. GEO Accession:GSM4411866 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP252869     cd41gfp_mut2_1.fq.gz cd41gfp_mut2_2.fq.gz fastq fastq 10547871900.0 35159573.0 GSM4411866 r1 0:150 1:150 A:2823130170;C:2469329724;G:2474038085;T:2781202013;N:171908 150 150     2823130170 2469329724 2474038085 2781202013 171908 SRX7913587 SRS6320429 SRA1055135 GEO Albert Einstein College of Medicine 2 0.77081 0.76762 0.19951 0.20063 0.78518 0.7905 0.62792 0.62645 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-15 Pharyngula Embryo Blood Hematopoietic System
58412 58412 SRR11309037 SRX7913586 SRS6320428 SRP252869 PRJNA612697 RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish GSE146995 Transcriptome Analysis The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.   pubmed:33651979   cd41gfp mut1 GSM4411865   tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant cd41gfp mut1 basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample hematopoietic stem and progenitor cells   cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.   develpmental stage:40 hpf mutant GSM4411865 GSM4411865: cd41gfp mut1; Danio rerio; RNA Seq GSM4411865   1 cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol. GEO Accession:GSM4411865 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP252869     cd41gfp_mut1_2.fq.gz cd41gfp_mut1_1.fq.gz fastq fastq 11189402700.0 37298009.0 GSM4411865 r1 0:150 1:150 A:2871209944;C:2750231891;G:2743649245;T:2824098453;N:213167 150 150     2871209944 2750231891 2743649245 2824098453 213167 SRX7913586 SRS6320428 SRA1055135 GEO Albert Einstein College of Medicine 2 0.74106 0.73935 0.17858 0.18025 0.80574 0.81231 0.60677 0.65263 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-15 Pharyngula Embryo Blood Hematopoietic System
65667 65667 SRR15483581 SRX11783409 SRS9786607 SRP332734 PRJNA755310 Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae GSE182213 Transcriptome Analysis The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.   pubmed:34525360   draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate GSM5525114   tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities hematopoietic cells   draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.   developmental stage:30 hpf line:draculin:mCherry;gata1:GFP GSM5525114 GSM5525114: draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate; Danio rerio; RNA Seq GSM5525114   1 draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. GEO Accession:GSM5525114 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP332734   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG1 3 S1 L001 R1 001.fastq.gz read2PairFiles=DG1 3 S1 L001 R2 001.fastq.gz read3PairFiles=DG1 3 S1 L001 I1 001.fastq.gz DG1-3_S1_L001_I1_001.fastq.gz DG1-3_S1_L001_R1_001.fastq.gz DG1-3_S1_L001_R2_001.fastq.gz fastq fastq fastq 53654080172.0 174201559.0 GSM5525114 r1 0:150 1:150 2:8 A:6842604916;C:6327854414;G:6203934909;T:6755061460;N:778151 150 150 8   6842604916 6327854414 6203934909 6755061460 778151 SRX11783409 SRS9786607 SRA1278863 GEO Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine 1 0.92988   0.06632   0.84691   0.45741   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-16 Pharyngula Embryo Blood Hematopoietic System
65668 65668 SRR15483580 SRX11783408 SRS9786605 SRP332734 PRJNA755310 Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae GSE182213 Transcriptome Analysis The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.   pubmed:34525360   draculin:mCherry+;gata1:GFP at 30 hpf #1 GSM5525113   tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP draculin:mCherry+;gata1:GFP at 30 hpf #1 Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities hematopoietic cells   draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.   developmental stage:30 hpf line:draculin:mCherry;gata1:GFP GSM5525113 GSM5525113: draculin:mCherry+;gata1:GFP at 30 hpf #1; Danio rerio; RNA Seq GSM5525113   1 draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. GEO Accession:GSM5525113 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP332734   loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG1 2 S1 L001 R1 001.fastq.gz read2PairFiles=DG1 2 S1 L001 R2 001.fastq.gz read3PairFiles=DG1 2 S1 L001 I1 001.fastq.gz DG1-2_S1_L001_I1_001.fastq.gz DG1-2_S1_L001_R1_001.fastq.gz DG1-2_S1_L001_R2_001.fastq.gz fastq fastq fastq 65514487192.0 212709374.0 GSM5525113 r1 0:150 1:150 2:8 A:8050271487;C:8057897221;G:7684156435;T:8113136954;N:944003 150 150 8   8050271487 8057897221 7684156435 8113136954 944003 SRX11783408 SRS9786605 SRA1278863 GEO Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine 1 0.94401   0.03521   0.88339   0.35428   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-08-16 Pharyngula Embryo Blood Hematopoietic System

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");;