{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA seq Blood rep1", "GSM4662085", null, "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 \u201c region  size 1000\u201d  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", null, "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\u00ae 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\u2019s protocol. Briefly  polyA RNA was purified from 1000\u00a0ng 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 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 \u00b5L 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 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 \u00b0C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 \u00b5g of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 \u00b0C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit\u2019s protocol  added A using Klenow  fragment 3\u2019 >5\u2019 exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 \u00b0C for 10 min on an overhead shaker. post that  lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. 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 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last  300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company\u2019s user guide.", "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", null, "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\u00ae 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 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl  pH 8.0  1% SDS  50 mM EDTA  1X proteinase inhibitor cocktail. Next  900 \u00b5L 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 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl  pH 8.0  1% SDS  1 mM EDTA at 65 \u00b0C overnight  treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex  3 \u00b5g of histone H3K27ac antibody Active Motif  39133 or H3K4me3 antibody EMD Millipore  07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher  11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer  with rotation at 4 \u00b0C for 3 h. post incubation  antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE  2% Triton X 100  0.2% sodium deoxycholate  2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning  the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl  pH 8.0  1% NP 40  0.7% sodium deoxycholate  500 mM LiCl  1 mM EDTA  1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library  eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre  ER81050 according to kit's protocol  added A using Klenow  fragment three prime >five prime exo  NEB  M0212S  ligated with Illumina TruSeq adaptor Illumina  FC 121 3001 and subsequently amplified by PCR Roche  kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS  0.2% NP 40  5% BSA  1 mM DTT  protease inhibitors  followed by incubation at  4 \u00b0C for 10 min on an overhead shaker. post that  lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al.  2013 Hi C: For brain tissue  two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl  pH 8.0  10 mM NaCl  20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue  60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS  muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al.  2014. 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 100 bp high throughput sequencing using HiSeq 2500  or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected  and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen  69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain  respectively  on the 10X Genomics platform. To isolate nuclei  freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits  NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA 0.01% Tween 20  0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl  pH 7.5  10 mM NaCl  3 mM MgCl2  1% BSA  0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last  300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics  PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction  and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.", "GEO Accession:GSM4662085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP213938", null, null, "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, null, null, 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", null, "United States", "2020-07-08", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["53002"], "units": {}, "query_ms": 12.56372599164024}