run_metadata: 53002

This data as json

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
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 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 µg of histone H3K27ac antibody Active Motif 39133 or H3K4me3 antibody EMD Millipore 07 473 was mix with 12 µL M 280 sheep anti rabbit IgG Dynabeads ThermoFisher 11203D in 150 µL of 5 mg/mL BSA/1X PBS buffer with rotation at 4 °C for 3 h. post incubation antibody beads complex was washed once with BSA/1X PBS buffer. About 200 µg 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 µg 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 µL of elution buffer at 65 °C 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 3’ >5’ 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 °C for 10 min on an overhead shaker. post that lysate was filtered through 40 m 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: Tübingen adult tissues were dissected and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen 69504. Then 1 µg 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® 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 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL 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 °C. At last 300 µL chilled Diluted Nuclei Buffer 10x Genomics PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm 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.	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 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 µg of histone H3K27ac antibody Active Motif 39133 or H3K4me3 antibody EMD Millipore 07 473 was mix with 12 µL M 280 sheep anti rabbit IgG Dynabeads ThermoFisher 11203D in 150 µL of 5 mg/mL BSA/1X PBS buffer with rotation at 4 °C for 3 h. post incubation antibody beads complex was washed once with BSA/1X PBS buffer. About 200 µg 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 µg 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 µL of elution buffer at 65 °C 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 °C for 10 min on an overhead shaker. post that lysate was filtered through 40 m 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: Tübingen adult tissues were dissected and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen 69504. Then 1 µg 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® 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 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL 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 °C. At last 300 µL chilled Diluted Nuclei Buffer 10x Genomics PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm 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		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