RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

8 rows where experiment.library_selection = "other", technology = "bulk" and tissue_curation = "Trunk"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_strategy 2

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 8 ✖

technology 1

  • bulk · 8 ✖

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • other · 8 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
41511 41511 SRR5004963 SRX2336797 SRS1790193 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   zebrafish embryos ythdf2 RIP rep2 GSM2386192   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk zebrafish embryos ythdf2 RIP rep2 Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software zebrafish embryos   For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386192 GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq GSM2386192   1 For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386192 RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz fastq fastq 4007024510.0 19836755.0 GSM2386192 r1 0:101 1:101 A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309 101 101     769487104 1245093129 1251328145 740377823 738309 SRX2336797 SRS1790193 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.97768 0.97802 0.22786 0.21743 0.89885 0.89968 0.77584 0.83808 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41512 41512 SRR5004962 SRX2336796 SRS1790194 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   zebrafish embryos ythdf2 RIP rep1 GSM2386191   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk zebrafish embryos ythdf2 RIP rep1 Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software zebrafish embryos   For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386191 GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq GSM2386191   1 For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386191 RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP092907     ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz fastq fastq 6144583662.0 30418731.0 GSM2386191 r1 0:101 1:101 A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305 101 101     1227614258 1869131844 1825793436 1220118819 1925305 SRX2336796 SRS1790194 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.96857 0.96917 0.23397 0.22377 0.89832 0.90147 0.78619 0.8258 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41521 41521 SRR5004953 SRX2336787 SRS1790184 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   mettl3 morphant zebrafish embryos m6A IP rep2 GSM2386182   source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems mettl3 morphant zebrafish embryos m6A IP rep2 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386182 GSM2386182: mettl3 morphant zebrafish embryos m6A IP rep2; Danio rerio; OTHER GSM2386182   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386182 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     mettl3-mo_IP_rep2_1.fastq.gz mettl3-mo_IP_rep2_2.fastq.gz fastq fastq 12246129204.0 60624402.0 GSM2386182 r1 0:101 1:101 A:3253814653;C:2887966071;G:2921051332;T:3179545005;N:3752143 101 101     3253814653 2887966071 2921051332 3179545005 3752143 SRX2336787 SRS1790184 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.93906 0.94462 0.08073 0.07972 0.69148 0.69394 0.43224 0.48778 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41522 41522 SRR5004952 SRX2336785 SRS1790183 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   mettl3 morphant zebrafish embryos m6A IP rep1 GSM2386181   source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems mettl3 morphant zebrafish embryos m6A IP rep1 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.   genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386181 GSM2386181: mettl3 morphant zebrafish embryos m6A IP rep1; Danio rerio; OTHER GSM2386181   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp. GEO Accession:GSM2386181 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     mettl3-mo_IP_rep1_1.fastq.gz mettl3-mo_IP_rep1_2.fastq.gz fastq fastq 22767872412.0 75390306.0 GSM2386181 r1 0:151 1:151 A:6356270201;C:5175380564;G:5545741592;T:5686194578;N:4285477 151 151     6356270201 5175380564 5545741592 5686194578 4285477 SRX2336785 SRS1790183 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.94647 0.95162 0.07314 0.07248 0.70796 0.71021 0.54859 0.54624 151 151 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41523 41523 SRR5004951 SRX2336784 SRS1790182 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos input rep2 GSM2386180   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk control zebrafish embryos input rep2 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386180 GSM2386180: control zebrafish embryos input rep2; Danio rerio; OTHER GSM2386180   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386180 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_input_rep2_1.fastq.gz control_input_rep2_2.fastq.gz fastq fastq 20629042748.0 102123974.0 GSM2386180 r1 0:101 1:101 A:5541548211;C:4810650367;G:4699999124;T:5571342766;N:5502280 101 101     5541548211 4810650367 4699999124 5571342766 5502280 SRX2336784 SRS1790182 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.94898 0.9511 0.10842 0.10266 0.70465 0.70481 0.4986 0.48915 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41524 41524 SRR5004950 SRX2336783 SRS1790181 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos input rep1 GSM2386179   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk control zebrafish embryos input rep1 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386179 GSM2386179: control zebrafish embryos input rep1; Danio rerio; OTHER GSM2386179   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp. GEO Accession:GSM2386179 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_input_rep1_1.fastq.gz control_input_rep1_2.fastq.gz fastq fastq 27776308060.0 91974530.0 GSM2386179 r1 0:151 1:151 A:7467418896;C:6517753701;G:6333567394;T:7452805069;N:4763000 151 151     7467418896 6517753701 6333567394 7452805069 4763000 SRX2336783 SRS1790181 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.95616 0.95939 0.10401 0.09776 0.72263 0.73637 0.57906 0.58185 151 151 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41525 41525 SRR5004949 SRX2336782 SRS1790180 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos m6A IP rep2 GSM2386178   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems control zebrafish embryos m6A IP rep2 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386178 GSM2386178: control zebrafish embryos m6A IP rep2; Danio rerio; OTHER GSM2386178   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386178 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_IP_rep2_1.fastq.gz control_IP_rep2_2.fastq.gz fastq fastq 11899573964.0 58908782.0 GSM2386178 r1 0:101 1:101 A:3146907590;C:2817914269;G:2838718195;T:3092392965;N:3640945 101 101     3146907590 2817914269 2838718195 3092392965 3640945 SRX2336782 SRS1790180 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.93821 0.94281 0.08361 0.08174 0.69676 0.69816 0.4628 0.46386 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41526 41526 SRR5004948 SRX2336781 SRS1790179 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos m6A IP rep1 GSM2386177   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems control zebrafish embryos m6A IP rep1 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386177 GSM2386177: control zebrafish embryos m6A IP rep1; Danio rerio; OTHER GSM2386177   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp. GEO Accession:GSM2386177 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_IP_rep1_1.fastq.gz control_IP_rep1_2.fastq.gz fastq fastq 16582066208.0 54907504.0 GSM2386177 r1 0:151 1:151 A:4529890968;C:3812739433;G:4031512714;T:4204817283;N:3105810 151 151     4529890968 3812739433 4031512714 4204817283 3105810 SRX2336781 SRS1790179 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.93701 0.95377 0.07009 0.07008 0.70972 0.71173 0.54711 0.54995 151 151 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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