RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

9 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.library_strategy = "RIP-Seq" and tissue_curation_coarse = "Undetermined"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 2

experiment.library_layout 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Undetermined · 9 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RIP-Seq · 9 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 9 ✖
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
33123 33123 SRR29672615 SRX25176099 SRS21866000 SRP517393 PRJNA1130538 ac4C transcriptomes of Zebrafish and Worm GSE271258 Other ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.       Zebrafish ac4C GSM8372406   tissue:Animal organ cells|cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215|geo loc name:missing|collection date:missing Zebrafish ac4C The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene. Animal organ cells   Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched   cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215 GSM8372406 GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq GSM8372406 r1 GSM8372406 1 Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP517393     Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz fastq fastq 816231517.0 3830403.0 GSM8372406 r1 0:102.34 1:110.76 A:199381841;C:207571478;G:205740791;T:203535549;N:1858 102 110     199381841 207571478 205740791 203535549 1858 SRX25176099 SRS21866000 SRA1914369 Fujian Medical University Fujian Medical University 2 0.60415 0.60545 0.08824 0.08794 0.78796 0.78733 0.43432 0.43842 126 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-07-01 Undetermined Undetermined Undetermined Undetermined
66086 66086 SRR15900240 SRX12190888 SRS10168725 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM+CH 2   strain:AB|isolate:CH2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab CH2 tchenlab CH2 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_CH_5.8.IP_R1.fastq.gz EOM_CH_5.8.IP_R2.fastq.gz EOM_CH_5.8.Input_R1.fastq.gz EOM_CH_5.8.Input_R2.fastq.gz fastq fastq fastq fastq 13391108400.0 44637028.0 EOM CH 5.8.IP R1.fastq.gz 0:150 1:150 A:2721241817;C:3886076819;G:4096587749;T:2611313908;N:75888107 150 150     2721241817 3886076819 4096587749 2611313908 75888107 SRX12190888 SRS10168725 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.8442 0.59467 0.17491 0.14724 0.86147 0.89112 0.7593 0.63363 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66087 66087 SRR15900241 SRX12190887 SRS10168724 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM+CH 1   strain:AB|isolate:CH1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab CH1 tchenlab CH1 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_CH_4.16.IP_R1.fastq.gz EOM_CH_4.16.IP_R2.fastq.gz EOM_CH_4.16.Input_R1.fastq.gz EOM_CH_4.16.Input_R2.fastq.gz fastq fastq fastq fastq 12428976000.0 41429920.0 EOM CH 4.16.IP R1.fastq.gz 0:150 1:150 A:2486344612;C:3648199763;G:3865825828;T:2365039093;N:63566704 150 150     2486344612 3648199763 3865825828 2365039093 63566704 SRX12190887 SRS10168724 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.91763 0.6223 0.18817 0.15102 0.84891 0.87957 0.74757 0.64429 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66088 66088 SRR15900242 SRX12190886 SRS10168723 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM 3   strain:AB|isolate:T3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab T3 tchenlab T3 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_5.9.IP_R1.fastq.gz EOM_5.9.IP_R2.fastq.gz EOM_5.9.Input_R1.fastq.gz EOM_5.9.Input_R2.fastq.gz fastq fastq fastq fastq 12301780200.0 41005934.0 EOM 5.9.IP R1.fastq.gz 0:150 1:150 A:2415542475;C:3651603114;G:3847935468;T:2318868176;N:67830967 150 150     2415542475 3651603114 3847935468 2318868176 67830967 SRX12190886 SRS10168723 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.87516 0.65874 0.18282 0.16547 0.85561 0.87657 0.72193 0.61862 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66089 66089 SRR15900243 SRX12190885 SRS10168722 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM 2   strain:AB|isolate:T2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab T2 tchenlab T2 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_5.8.IP_R1.fastq.gz EOM_5.8.IP_R2.fastq.gz EOM_5.8.Input_R1.fastq.gz EOM_5.8.Input_R2.fastq.gz fastq fastq fastq fastq 12373139700.0 41243799.0 EOM 5.8.IP R1.fastq.gz 0:150 1:150 A:2429212483;C:3679585650;G:3865741937;T:2330164654;N:68434976 150 150     2429212483 3679585650 3865741937 2330164654 68434976 SRX12190885 SRS10168722 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.88644 0.67829 0.18408 0.16867 0.84652 0.8704 0.76376 0.64158 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66090 66090 SRR15900244 SRX12190884 SRS10168721 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM 1   strain:AB|isolate:T1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab T1 tchenlab T1 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_4.16.IP_R1.fastq.gz EOM_4.16.IP_R2.fastq.gz EOM_4.16.Input_R1.fastq.gz EOM_4.16.Input_R2.fastq.gz fastq fastq fastq fastq 13638730800.0 45462436.0 EOM 4.16.IP R1.fastq.gz 0:150 1:150 A:2673949221;C:4057121296;G:4266457677;T:2562131972;N:79070634 150 150     2673949221 4057121296 4266457677 2562131972 79070634 SRX12190884 SRS10168721 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.87634 0.65649 0.18403 0.16375 0.85486 0.87913 0.69253 0.6405 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66091 66091 SRR15900245 SRX12190883 SRS10168720 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         DMSO 3   strain:AB|isolate:C3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab C3 tchenlab C3 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py DMSO_5.9.IP_R1.fastq.gz DMSO_5.9.IP_R2.fastq.gz DMSO_5.9.Input_R1.fastq.gz DMSO_5.9.Input_R2.fastq.gz fastq fastq fastq fastq 12477964200.0 41593214.0 DMSO 5.9.IP R1.fastq.gz 0:150 1:150 A:2462053397;C:3697418372;G:3878832850;T:2368512335;N:71147246 150 150     2462053397 3697418372 3878832850 2368512335 71147246 SRX12190883 SRS10168720 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.94535 0.75289 0.20051 0.18779 0.84139 0.8646 0.74818 0.65269 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66092 66092 SRR15900246 SRX12190882 SRS10168719 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         DMSO 2   strain:AB|isolate:C2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab C2 tchenlab C2 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py DMSO_5.8.IP_R1.fastq.gz DMSO_5.8.IP_R2.fastq.gz DMSO_5.8.Input_R1.fastq.gz DMSO_5.8.Input_R2.fastq.gz fastq fastq fastq fastq 12272849400.0 40909498.0 DMSO 5.8.IP R1.fastq.gz 0:150 1:150 A:2381041881;C:3673513092;G:3850518138;T:2295835815;N:71940474 150 150     2381041881 3673513092 3850518138 2295835815 71940474 SRX12190882 SRS10168719 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.88711 0.71046 0.18073 0.17436 0.84654 0.8674 0.76218 0.63257 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66093 66093 SRR15900247 SRX12190881 SRS10168718 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         DMSO 1   strain:AB|isolate:C1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab C1 tchenlab C1 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py DMSO_4.16.IP_R1.fastq.gz DMSO_4.16.IP_R2.fastq.gz DMSO_4.16.Input_R1.fastq.gz DMSO_4.16.Input_R2.fastq.gz fastq fastq fastq fastq 12900597000.0 43001990.0 DMSO 4.16.IP R1.fastq.gz 0:150 1:150 A:2517062962;C:3854768074;G:4032734290;T:2426295392;N:69736282 150 150     2517062962 3854768074 4032734290 2426295392 69736282 SRX12190881 SRS10168718 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.75605 0.5734 0.16268 0.14503 0.8714 0.89422 0.72976 0.64046 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined

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");;