{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation = \"Liver\"", "rows": [[38003, "SRR1265754", "SRX529148", "SRS598845", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Liver Replicate 3 sRNAseq", "GSM1376637", null, "source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type Singapore strain", "Female Liver Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Liver", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Liver|genetic background:Wild type Singapore strain", "GSM1376637", "GSM1376637: Female Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376637", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376637", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZL012_GCCAAT_L008_R1.fastq.gz", "fastq", 105717543.0, 2072893.0, "GSM1376637 r1", "0:51", "A:22408978;C:25732405;G:31681641;T:25880225;N:14294", 51, null, null, null, 22408978, 25732405, 31681641, 25880225, 14294, "SRX529148", "SRS598845", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.05572, null, 0.0017, null, 0.99691, null, 0.56539, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Liver", "Liver and Biliary System"], [38004, "SRR1265753", "SRX529147", "SRS598844", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Liver Replicate 2 sRNAseq", "GSM1376636", null, "source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type Singapore strain", "Female Liver Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Liver", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Liver|genetic background:Wild type Singapore strain", "GSM1376636", "GSM1376636: Female Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376636", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376636", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZL011_ACAGTG_L008_R1.fastq.gz", "fastq", 484614546.0, 9502246.0, "GSM1376636 r1", "0:51", "A:98373224;C:113894197;G:148444486;T:123841427;N:61212", 51, null, null, null, 98373224, 113894197, 148444486, 123841427, 61212, "SRX529147", "SRS598844", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01517, null, 0.00112, null, 0.9964, null, 0.61558, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Liver", "Liver and Biliary System"], [38005, "SRR1265752", "SRX529146", "SRS598843", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Female Liver Replicate 1 sRNAseq", "GSM1376635", null, "source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type Singapore strain", "Female Liver Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Female Liver", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Liver|genetic background:Wild type Singapore strain", "GSM1376635", "GSM1376635: Female Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376635", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376635", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZL010_TGACCA_L008_R1.fastq.gz", "fastq", 304949706.0, 5979406.0, "GSM1376635 r1", "0:51", "A:62732698;C:71083849;G:92267430;T:78825237;N:40492", 51, null, null, null, 62732698, 71083849, 92267430, 78825237, 40492, "SRX529146", "SRS598843", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01218, null, 0.001, null, 0.99709, null, 0.55264, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Liver", "Liver and Biliary System"], [38006, "SRR1265751", "SRX529145", "SRS598842", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Liver Replicate 3 sRNAseq", "GSM1376634", null, "source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type Singapore strain", "Male Liver Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Liver", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Liver|genetic background:Wild type Singapore strain", "GSM1376634", "GSM1376634: Male Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376634", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376634", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZL009_GATCAG_L007_R1.fastq.gz", "fastq", 287383266.0, 5634966.0, "GSM1376634 r1", "0:51", "A:54829818;C:73200212;G:89994996;T:69332773;N:25467", 51, null, null, null, 54829818, 73200212, 89994996, 69332773, 25467, "SRX529145", "SRS598842", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00273, null, 0.00026, null, 0.99791, null, 0.69537, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Liver", "Liver and Biliary System"], [38007, "SRR1265750", "SRX529144", "SRS598841", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Liver Replicate 2 sRNAseq", "GSM1376633", null, "source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type Singapore strain", "Male Liver Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Liver", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Liver|genetic background:Wild type Singapore strain", "GSM1376633", "GSM1376633: Male Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376633", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376633", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZL008_ACTTGA_L007_R1.fastq.gz", "fastq", 595761753.0, 11681603.0, "GSM1376633 r1", "0:51", "A:111507488;C:155297338;G:186229891;T:142672923;N:54113", 51, null, null, null, 111507488, 155297338, 186229891, 142672923, 54113, "SRX529144", "SRS598841", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00597, null, 0.00067, null, 0.99679, null, 0.72807, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Liver", "Liver and Biliary System"], [38008, "SRR1265749", "SRX529143", "SRS598840", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Male Liver Replicate 1 sRNAseq", "GSM1376632", null, "source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type Singapore strain", "Male Liver Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Male Liver", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Liver|genetic background:Wild type Singapore strain", "GSM1376632", "GSM1376632: Male Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376632", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376632", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZL007_CAGATC_L007_R1.fastq.gz", "fastq", 976402599.0, 19145149.0, "GSM1376632 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX529143", "SRS598840", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00348, null, 0.00035, null, 0.99742, null, 0.69292, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Liver", "Liver and Biliary System"], [53015, "SRR9662024", "SRX6422900", "SRS5079690", "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 Liver rep2", "GSM3934892", null, "source name:Tissue|strain:Tuebingen|tissue:Liver", "YueLab RNA Seq Liver rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks 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 HiC matrix was generated using HiC Pro Genome build: zv10 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", "Tissue", null, "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. 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.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Liver", "GSM3934892", "GSM3934892: YueLab RNA Seq Liver rep2; Danio rerio; RNA Seq", "GSM3934892", null, "1", "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. 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\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.", "GEO Accession:GSM3934892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Liver-rep2_1.fastq.gz YueLab-RNA-Seq-Liver-rep2_2.fastq.gz", "fastq fastq", 2453892473.0, 18494458.0, "GSM3934892 r1", "0:66.33 1:66.36", "A:639899749;C:572026186;G:561420643;T:680465509;N:80386", 66, 66, null, null, 639899749, 572026186, 561420643, 680465509, 80386, "SRX6422900", "SRS5079690", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.95181, 0.96045, 0.10335, 0.09874, 0.7665, 0.76238, 0.5468, 0.55172, 67, 65, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Liver", "Liver and Biliary System"], [53016, "SRR9662023", "SRX6422899", "SRS5079689", "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 Liver rep1", "GSM3934891", null, "source name:Tissue|strain:Tuebingen|tissue:Liver", "YueLab RNA Seq Liver rep1", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks 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 HiC matrix was generated using HiC Pro Genome build: zv10 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", "Tissue", null, "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. 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.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Liver", "GSM3934891", "GSM3934891: YueLab RNA Seq Liver rep1; Danio rerio; RNA Seq", "GSM3934891", null, "1", "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. 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\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.", "GEO Accession:GSM3934891", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Liver-rep1_1.fastq.gz YueLab-RNA-Seq-Liver-rep1_2.fastq.gz", "fastq fastq", 3947397329.0, 32675197.0, "GSM3934891 r1", "0:60.48 1:60.33", "A:1018232733;C:908244909;G:926976675;T:1093882633;N:60379", 60, 60, null, null, 1018232733, 908244909, 926976675, 1093882633, 60379, "SRX6422899", "SRS5079689", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.97167, 0.9794, 0.0735, 0.06958, 0.79279, 0.79454, 0.54083, 0.54983, 60, 60, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Liver", "Liver and Biliary System"], [70306, "SRR19661766", "SRX15711496", "SRS13405891", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h2 S8 L001 R1", null, "strain:not collected|isolate:9|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "9", "60h2 S8 L001 R1", "60h2 S8 L001 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h2_S8_L001_R1_001.fastq.gz 60h2_S8_L001_R2_001.fastq.gz", "fastq fastq", 988020461.0, 4273934.0, "60h2 S8 L001 R1 001.fastq.gz", "0:115.36 1:115.82", "A:264286562;C:230326008;G:231614619;T:260866155;N:927117", 115, 115, null, null, 264286562, 230326008, 231614619, 260866155, 927117, "SRX15711496", "SRS13405891", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94418, 0.94354, 0.04632, 0.04674, 0.82063, 0.82199, 0.49098, 0.49175, 79, 79, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70313, "SRR19661773", "SRX15711489", "SRS13405884", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h1 S7 L004 R1", null, "strain:not collected|isolate:7|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7", "60h1 S7 L004 R1", "60h1 S7 L004 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h1_S7_L004_R1_001.fastq.gz 60h1_S7_L004_R2_001.fastq.gz", "fastq fastq", 859059787.0, 3783762.0, "60h1 S7 L004 R1 001.fastq.gz", "0:113.26 1:113.78", "A:228878542;C:201258003;G:202624816;T:225356012;N:942414", 113, 113, null, null, 228878542, 201258003, 202624816, 225356012, 942414, "SRX15711489", "SRS13405884", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.93549, 0.93547, 0.04114, 0.04156, 0.83976, 0.84258, 0.51763, 0.50606, 151, 151, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70324, "SRR19661784", "SRX15711478", "SRS13405873", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h1 S7 L003 R1", null, "strain:not collected|isolate:5|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "5", "60h1 S7 L003 R1", "60h1 S7 L003 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h1_S7_L003_R1_001.fastq.gz 60h1_S7_L003_R2_001.fastq.gz", "fastq fastq", 861950674.0, 3784961.0, "60h1 S7 L003 R1 001.fastq.gz", "0:113.44 1:114.29", "A:229059608;C:201979412;G:204483606;T:225306157;N:1121891", 113, 114, null, null, 229059608, 201979412, 204483606, 225306157, 1121891, "SRX15711478", "SRS13405873", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.93591, 0.93506, 0.04081, 0.04127, 0.83966, 0.84287, 0.5149, 0.51471, 84, 84, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70333, "SRR19661793", "SRX15711469", "SRS13405864", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h3 S9 L004 R1", null, "strain:not collected|isolate:23|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "23", "60h3 S9 L004 R1", "60h3 S9 L004 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h3_S9_L004_R1_001.fastq.gz 60h3_S9_L004_R2_001.fastq.gz", "fastq fastq", 1069762288.0, 4677877.0, "60h3 S9 L004 R1 001.fastq.gz", "0:114.07 1:114.61", "A:286765598;C:249053001;G:250729965;T:282118693;N:1095031", 114, 114, null, null, 286765598, 249053001, 250729965, 282118693, 1095031, "SRX15711469", "SRS13405864", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94728, 0.94711, 0.05297, 0.05422, 0.8241, 0.82789, 0.48666, 0.46516, 103, 103, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70334, "SRR19661794", "SRX15711468", "SRS13405863", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h3 S9 L003 R1", null, "strain:not collected|isolate:21|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "21", "60h3 S9 L003 R1", "60h3 S9 L003 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h3_S9_L003_R1_001.fastq.gz 60h3_S9_L003_R2_001.fastq.gz", "fastq fastq", 1075584819.0, 4688707.0, "60h3 S9 L003 R1 001.fastq.gz", "0:114.26 1:115.14", "A:287532279;C:250477581;G:253661779;T:282618621;N:1294559", 114, 115, null, null, 287532279, 250477581, 253661779, 282618621, 1294559, "SRX15711468", "SRS13405863", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94671, 0.94632, 0.05164, 0.05273, 0.82428, 0.82915, 0.48857, 0.49523, 140, 140, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70335, "SRR19661795", "SRX15711467", "SRS13405862", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h1 S7 L002 R1", null, "strain:not collected|isolate:3|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3", "60h1 S7 L002 R1", "60h1 S7 L002 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h1_S7_L002_R1_001.fastq.gz 60h1_S7_L002_R2_001.fastq.gz", "fastq fastq", 861878746.0, 3787766.0, "60h1 S7 L002 R1 001.fastq.gz", "0:113.54 1:114.01", "A:228906675;C:202479789;G:203764253;T:225956042;N:771987", 113, 114, null, null, 228906675, 202479789, 203764253, 225956042, 771987, "SRX15711467", "SRS13405862", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.93509, 0.93555, 0.0402, 0.04089, 0.83899, 0.8411, 0.51834, 0.51745, 101, 101, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70336, "SRR19661796", "SRX15711466", "SRS13405861", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h3 S9 L002 R1", null, "strain:not collected|isolate:19|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "19", "60h3 S9 L002 R1", "60h3 S9 L002 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h3_S9_L002_R1_001.fastq.gz 60h3_S9_L002_R2_001.fastq.gz", "fastq fastq", 1074021192.0, 4687833.0, "60h3 S9 L002 R1 001.fastq.gz", "0:114.32 1:114.79", "A:286968360;C:250769179;G:252395676;T:283023861;N:864116", 114, 114, null, null, 286968360, 250769179, 252395676, 283023861, 864116, "SRX15711466", "SRS13405861", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94808, 0.94832, 0.05209, 0.05256, 0.82438, 0.82651, 0.49332, 0.49331, 141, 141, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70337, "SRR19661797", "SRX15711465", "SRS13405860", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h3 S9 L001 R1", null, "strain:not collected|isolate:17|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "17", "60h3 S9 L001 R1", "60h3 S9 L001 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h3_S9_L001_R1_001.fastq.gz 60h3_S9_L001_R2_001.fastq.gz", "fastq fastq", 1119531285.0, 4890160.0, "60h3 S9 L001 R1 001.fastq.gz", "0:114.22 1:114.71", "A:299225983;C:261253222;G:262858023;T:295162128;N:1031929", 114, 114, null, null, 299225983, 261253222, 262858023, 295162128, 1031929, "SRX15711465", "SRS13405860", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94835, 0.94781, 0.05256, 0.0531, 0.82412, 0.82706, 0.49397, 0.49498, 151, 151, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70338, "SRR19661798", "SRX15711464", "SRS13405859", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h2 S8 L004 R1", null, "strain:not collected|isolate:15|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "15", "60h2 S8 L004 R1", "60h2 S8 L004 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h2_S8_L004_R1_001.fastq.gz 60h2_S8_L004_R2_001.fastq.gz", "fastq fastq", 948410773.0, 4105044.0, "60h2 S8 L004 R1 001.fastq.gz", "0:115.26 1:115.77", "A:254458117;C:220561299;G:221934286;T:250478553;N:978518", 115, 115, null, null, 254458117, 220561299, 221934286, 250478553, 978518, "SRX15711464", "SRS13405859", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94293, 0.9431, 0.04627, 0.0468, 0.82256, 0.82582, 0.48311, 0.48501, 150, 151, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70339, "SRR19661799", "SRX15711463", "SRS13405858", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.", null, null, null, null, "60h2 S8 L003 R1", null, "strain:not collected|isolate:13|age:not collected|dev stage:hatching|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "13", "60h2 S8 L003 R1", "60h2 S8 L003 R1", "sorting", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP381845", null, null, "60h2_S8_L003_R1_001.fastq.gz 60h2_S8_L003_R2_001.fastq.gz", "fastq fastq", 950927809.0, 4105298.0, "60h2 S8 L003 R1 001.fastq.gz", "0:115.41 1:116.23", "A:254408486;C:221307652;G:223835820;T:250222170;N:1153681", 115, 116, null, null, 254408486, 221307652, 223835820, 250222170, 1153681, "SRX15711463", "SRS13405858", "SRA1437609", "Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.94289, 0.94218, 0.04567, 0.04626, 0.82045, 0.82467, 0.48517, 0.45898, 151, 150, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-06-15", "Hatching", "Embryo", "Liver", "Liver and Biliary System"], [70340, "SRR19661800", "SRX15711462", "SRS13405857", "SRP381845", "PRJNA849172", "Danio rerio Raw sequence reads", "PRJNA849172", "Other", "Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. 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Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. 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"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": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Embryo", "p1": "Liver"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": 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"/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver", "results": [{"value": "Oligo-dT", "label": "Oligo-dT", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver&experiment.library_selection=size+fractionation", "selected": false}, {"value": "cDNA", "label": "cDNA", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation=Liver&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": 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