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31 rows where experiment.library_selection = "other", technology = "unknown" and tissue_curation_coarse = "Surface Structure"

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devstage_curation_coarse 3

devstage_curation 3

tissue_curation 2

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Surface Structure · 31 ✖

technology 1

  • unknown · 31 ✖

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • other · 31 ✖
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
34115 34115 SRR31230228 SRX26610547 SRS23109428 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         TF L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:TF|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data TF L1 TF L1 TF     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     TF_L1_1.fq.gz TF_L1_2.fq.gz fastq fastq 6687564300.0 22291881.0 TF L1 1.fq.gz 0:150 1:150 A:1864117630;C:1488483222;G:1497677628;T:1837006551;N:279269 150 150     1864117630 1488483222 1497677628 1837006551 279269 SRX26610547 SRS23109428 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34116 34116 SRR31230229 SRX26610546 SRS23109427 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         HP L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:HP|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data HP L3 HP L3 HP     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     HP_L3_1.fq.gz HP_L3_2.fq.gz fastq fastq 6481773600.0 21605912.0 HP L3 1.fq.gz 0:150 1:150 A:1822457830;C:1426224217;G:1433346356;T:1799447632;N:297565 150 150     1822457830 1426224217 1433346356 1799447632 297565 SRX26610546 SRS23109427 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34117 34117 SRR31230230 SRX26610545 SRS23109426 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         HP L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:HP|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data HP L2 HP L2 HP     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     HP_L2_1.fq.gz HP_L2_2.fq.gz fastq fastq 6483969900.0 21613233.0 HP L2 1.fq.gz 0:150 1:150 A:1858850647;C:1400634811;G:1393756557;T:1830424227;N:303658 150 150     1858850647 1400634811 1393756557 1830424227 303658 SRX26610545 SRS23109426 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34118 34118 SRR31230231 SRX26610544 SRS23109422 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         HP L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:HP|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data HP L1 HP L1 HP     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     HP_L1_1.fq.gz HP_L1_2.fq.gz fastq fastq 6270987900.0 20903293.0 HP L1 1.fq.gz 0:150 1:150 A:1761336291;C:1386332040;G:1384745780;T:1738282105;N:291684 150 150     1761336291 1386332040 1384745780 1738282105 291684 SRX26610544 SRS23109422 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34119 34119 SRR31230232 SRX26610543 SRS23109425 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         MT L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:MT|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data MT L3 MT L3 MT     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     MT_L3_1.fq.gz MT_L3_2.fq.gz fastq fastq 6641395500.0 22137985.0 MT L3 1.fq.gz 0:150 1:150 A:1870037050;C:1459746735;G:1464312013;T:1846983464;N:316238 150 150     1870037050 1459746735 1464312013 1846983464 316238 SRX26610543 SRS23109425 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34120 34120 SRR31230233 SRX26610542 SRS23109421 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         MT L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:MT|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data MT L2 MT L2 MT     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     MT_L2_1.fq.gz MT_L2_2.fq.gz fastq fastq 6735230400.0 22450768.0 MT L2 1.fq.gz 0:150 1:150 A:1884876161;C:1494102137;G:1499635722;T:1856320830;N:295550 150 150     1884876161 1494102137 1499635722 1856320830 295550 SRX26610542 SRS23109421 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34121 34121 SRR31230234 SRX26610541 SRS23109424 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         MT L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:MT|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data MT L1 MT L1 MT     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     MT_L1_1.fq.gz MT_L1_2.fq.gz fastq fastq 6382458300.0 21274861.0 MT L1 1.fq.gz 0:150 1:150 A:1811407290;C:1396361259;G:1388659914;T:1785732773;N:297064 150 150     1811407290 1396361259 1388659914 1785732773 297064 SRX26610541 SRS23109424 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34122 34122 SRR31230235 SRX26610540 SRS23109423 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         NC L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:Control|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data NC L3 NC L3 control     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     NC_L3_1.fq.gz NC_L3_2.fq.gz fastq fastq 6815267400.0 22717558.0 NC L3 1.fq.gz 0:150 1:150 A:1909187573;C:1516756161;G:1522759558;T:1866449373;N:114735 150 150     1909187573 1516756161 1522759558 1866449373 114735 SRX26610540 SRS23109423 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34123 34123 SRR31230236 SRX26610539 SRS23109419 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         TF L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:TF|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data TF L3 TF L3 TF     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     TF_L3_1.fq.gz TF_L3_2.fq.gz fastq fastq 6547426200.0 21824754.0 TF L3 1.fq.gz 0:150 1:150 A:1829107582;C:1450999468;G:1461503884;T:1805507445;N:307821 150 150     1829107582 1450999468 1461503884 1805507445 307821 SRX26610539 SRS23109419 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34124 34124 SRR31230237 SRX26610538 SRS23109420 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         TF L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:TF|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data TF L2 TF L2 TF     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     TF_L2_1.fq.gz TF_L2_2.fq.gz fastq fastq 6327866400.0 21092888.0 TF L2 1.fq.gz 0:150 1:150 A:1792246492;C:1386064311;G:1383369731;T:1765884262;N:301604 150 150     1792246492 1386064311 1383369731 1765884262 301604 SRX26610538 SRS23109420 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34125 34125 SRR31230238 SRX26610537 SRS23109418 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         NC L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:Control|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data NC L2 NC L2 control     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     NC_L2_1.fq.gz NC_L2_2.fq.gz fastq fastq 6779235000.0 22597450.0 NC L2 1.fq.gz 0:150 1:150 A:1908783350;C:1490731242;G:1502686284;T:1876708170;N:325954 150 150     1908783350 1490731242 1502686284 1876708170 325954 SRX26610537 SRS23109418 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34126 34126 SRR31230239 SRX26610536 SRS23109417 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         NC L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:Control|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data NC L1 NC L1 control     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     NC_L1_1.fq.gz NC_L1_2.fq.gz fastq fastq 6318379500.0 21061265.0 NC L1 1.fq.gz 0:150 1:150 A:1785873867;C:1385813719;G:1388477232;T:1757923663;N:291019 150 150     1785873867 1385813719 1388477232 1757923663 291019 SRX26610536 SRS23109417 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
36617 36617 SRR941753 SRX326770 SRS463196 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 2 Pos2   strain:EK|isolate:4|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 2 Pectoral Posterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Pos_R2.fastq fastq 2119489050.0 42389781.0 Pos R2 0:50 A:551122430;C:507870866;G:499494183;T:555469321;N:5532250 50       551122430 507870866 499494183 555469321 5532250 SRX326770 SRS463196 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.90238   0.08924   0.71303   0.43405   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36618 36618 SRR941754 SRX326769 SRS463195 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising posterior most 2 fin rays Posterior pectoral fin replicate 1 Pos1   strain:EK|isolate:3|age:6 Month|sex:female                 RNA seq posterior pectoral fin replicate 1 Pectoral Fin Posterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598         1839141950.0 36782839.0 Pos R1 0:50 A:461313296;C:455413049;G:451484067;T:466101993;N:4829545 50       461313296 455413049 451484067 466101993 4829545 SRX326769 SRS463195 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.91205   0.06923   0.71656   0.42651   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36619 36619 SRR941751 SRX326756 SRS463187 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 2 Ant2   strain:EK|isolate:2|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 2 Pectoral Fin Anterior 2 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Ant_R2.fastq fastq 2146396250.0 42927925.0 Ant R2 0:50 A:562140204;C:509390346;G:501995610;T:567232459;N:5637631 50       562140204 509390346 501995610 567232459 5637631 SRX326756 SRS463187 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89956   0.09279   0.70997   0.44847   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
36620 36620 SRR941749 SRX326754 SRS463185 SRP027598 PRJNA187413 Danio rerio strain:EK Transcriptome or Gene expression PRJNA187413 Transcriptome Analysis Gene expression across the anteroposterior axis of the zebrafish pectoral fin.     tissue comprising anterior most 2 fin rays Anterior pectoral fin replicate 1 Ant1   strain:EK|isolate:1|age:6 Month|sex:female                 RNA seq anterior pectoral fin replicate 1 Pectoral Fin Anterior 1 1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP027598     Ant_R1.fastq fastq 2178096950.0 43561939.0 Ant R1 0:50 A:568580441;C:517705965;G:509551928;T:576519788;N:5738828 50       568580441 517705965 509551928 576519788 5738828 SRX326754 SRS463185 SRA065677 Duke Cell Biology|Poss Poss Lab, Duke Cell Biology 1 0.89833   0.08959   0.71494   0.44088   50   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2013-07-19 Adult Adult Fin Surface Structure
60021 60021 SRR12103084 SRX8627422 SRS6915731 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         SCI IP   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI IP|BioSampleModel:Model organism or animal                 IP library sequencing data of treated sample SCIIP BKDL192540807 1a SCIIP BKDL192540807 1a IP library sequencing data of treated sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz fastq fastq 7110503700.0 23701679.0 SCIIP BKDL192540807 1a 1.fq.gz 0:150 1:150 A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903 150 150     1520693228 1953670419 2215620460 1420407690 111903 SRX8627422 SRS6915731 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.9115 0.9147 0.19936 0.2033 0.81864 0.81919 0.66838 0.6677 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
60022 60022 SRR12103085 SRX8627421 SRS6915730 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         SCI Input   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI Input|BioSampleModel:Model organism or animal                 Input library sequencing data of treated sample SCIIN BKDL192540809 1a SCIIN BKDL192540809 1a Input library sequencing data of treated sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz fastq fastq 7774587300.0 25915291.0 SCIIN BKDL192540809 1a 1.fq.gz 0:150 1:150 A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571 150 150     1595151855 2243828590 2397611978 1537918306 76571 SRX8627421 SRS6915730 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.96018 0.96291 0.23754 0.23744 0.84904 0.85245 0.74661 0.74738 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
60023 60023 SRR12103086 SRX8627420 SRS6915729 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         Control IP   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control IP|BioSampleModel:Model organism or animal                 IP library sequencing data of control sample controlIP BKDL192540808 1a controlIP BKDL192540808 1a IP library sequencing data of control sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz fastq fastq 7359972600.0 24533242.0 controlIP BKDL192540808 1a 1.fq.gz 0:150 1:150 A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639 150 150     1569051886 2002692591 2333418000 1454676484 133639 SRX8627420 SRS6915729 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.92004 0.92293 0.20272 0.20739 0.83254 0.83291 0.68471 0.65224 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
60024 60024 SRR12103087 SRX8627419 SRS6915728 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         Control Input   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control Input|BioSampleModel:Model organism or animal                 Input library sequencing data of control sample controlIN BKDL192540810 1a controlIN BKDL192540810 1a Input library sequencing data of control sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz fastq fastq 7830123600.0 26100412.0 controlIN BKDL192540810 1a 1.fq.gz 0:150 1:150 A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635 150 150     1589371287 2296547915 2409439612 1534684151 80635 SRX8627419 SRS6915728 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.97501 0.97626 0.23177 0.23578 0.89497 0.8971 0.78501 0.77674 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
61422 61422 SRR12744939 SRX9217396 SRS7451218 SRP285861 PRJNA666534 Transcriptomic analysis of the developmental toxicity of microplastics in zebrafish PRJNA666534 Other This project was conduceted to explore the molecular mechanisms underlying the bioaccumulation depuration and developmental toxicity and immune dysfunction of microplastics in zebrafish larvae which provides novel insights into the ecological risks of MPs fragments.         PA H2O2 HA   strain:AB|dev stage:9 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish PA H2O2 HA PA H2O2 HA mRNA of zebrafish tissue     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP285861     PA_H2O2_HA.R1.fastq.gz PA_H2O2_HA.R2.fastq.gz fastq fastq 7307814724.0 24198062.0 PA H2O2 HA.R1.fastq.gz 0:151 1:151 A:1916647803;C:1726826237;G:1763771127;T:1900498448;N:71109 151 151     1916647803 1726826237 1763771127 1900498448 71109 SRX9217396 SRS7451218 SRA1135893 Henan Normal University|College of Environment Henan Normal University 2 0.94168 0.91408 0.0715 0.06936 0.6872 0.69163 0.46735 0.47262 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-09-30 Larval Larval Trunk Surface Structure
61423 61423 SRR12744940 SRX9217395 SRS7451217 SRP285861 PRJNA666534 Transcriptomic analysis of the developmental toxicity of microplastics in zebrafish PRJNA666534 Other This project was conduceted to explore the molecular mechanisms underlying the bioaccumulation depuration and developmental toxicity and immune dysfunction of microplastics in zebrafish larvae which provides novel insights into the ecological risks of MPs fragments.         PA   strain:AB|dev stage:8 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish PA PA mRNA of zebrafish tissue     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP285861     PA.R1.fastq.gz PA.R2.fastq.gz fastq fastq 7677365782.0 25421741.0 PA.R1.fastq.gz 0:151 1:151 A:2003403761;C:1825346100;G:1859847851;T:1988694897;N:73173 151 151     2003403761 1825346100 1859847851 1988694897 73173 SRX9217395 SRS7451217 SRA1135893 Henan Normal University|College of Environment Henan Normal University 2 0.94287 0.91685 0.06205 0.06006 0.6882 0.69234 0.45133 0.46041 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-09-30 Larval Larval Trunk Surface Structure
61424 61424 SRR12744941 SRX9217394 SRS7451216 SRP285861 PRJNA666534 Transcriptomic analysis of the developmental toxicity of microplastics in zebrafish PRJNA666534 Other This project was conduceted to explore the molecular mechanisms underlying the bioaccumulation depuration and developmental toxicity and immune dysfunction of microplastics in zebrafish larvae which provides novel insights into the ecological risks of MPs fragments.         CK   strain:AB|dev stage:7 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish CK CK mRNA of zebrafish tissue     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP285861     CK.R1.fastq.gz CK.R2.fastq.gz fastq fastq 7117128904.0 23566652.0 CK.R1.fastq.gz 0:151 1:151 A:1891245951;C:1659968846;G:1695470010;T:1870375334;N:68763 151 151     1891245951 1659968846 1695470010 1870375334 68763 SRX9217394 SRS7451216 SRA1135893 Henan Normal University|College of Environment Henan Normal University 2 0.93863 0.9111 0.08559 0.08339 0.68909 0.69461 0.46599 0.46482 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-09-30 Larval Larval Trunk Surface Structure
74097 74097 SRR23433707 SRX19347585 SRS16745103 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt input rep2 GSM7039976   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing mt input rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1 GSM7039976 GSM7039976: mt input rep2; Danio rerio; RIP Seq GSM7039976 r1 GSM7039976 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz fastq fastq 11987520719.0 46102921.0 GSM7039976 r1 0:129.98 1:130.04 A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407 129 130     2818961833 3185310727 3125514774 2857679978 53407 SRX19347585 SRS16745103 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92498 0.92723 0.26901 0.26318 0.72691 0.72646 0.55297 0.56674 103 103 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74098 74098 SRR23433708 SRX19347584 SRS16745102 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt IP rep2 GSM7039975   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing mt IP rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A GSM7039975 GSM7039975: mt IP rep2; Danio rerio; RIP Seq GSM7039975 r1 GSM7039975 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz fastq fastq 10153956215.0 38248544.0 GSM7039975 r1 0:132.74 1:132.73 A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740 132 132     2745473943 2337991849 2337827470 2732618213 44740 SRX19347584 SRS16745102 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.91716 0.92124 0.17169 0.17213 0.69057 0.69092 0.45478 0.4582 133 133 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74099 74099 SRR23433709 SRX19347583 SRS16745101 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt input rep1 GSM7039974   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing mt input rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1 GSM7039974 GSM7039974: mt input rep1; Danio rerio; RIP Seq GSM7039974 r1 GSM7039974 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz fastq fastq 11979139891.0 42665152.0 GSM7039974 r1 0:140.37 1:140.40 A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416 140 140     3143624979 2854874515 2775482425 3204809556 348416 SRX19347583 SRS16745101 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.89189 0.90001 0.35263 0.34917 0.71058 0.70907 0.54777 0.55293 125 125 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74100 74100 SRR23433710 SRX19347582 SRS16745100 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt IP rep1 GSM7039973   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing mt IP rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A GSM7039973 GSM7039973: mt IP rep1; Danio rerio; RIP Seq GSM7039973 r1 GSM7039973 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz fastq fastq 12145897814.0 43352862.0 GSM7039973 r1 0:140.09 1:140.07 A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089 140 140     3459248498 2615706052 2628261332 3442334843 347089 SRX19347582 SRS16745100 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.86681 0.87664 0.304 0.305 0.68012 0.67831 0.44055 0.4418 142 142 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74101 74101 SRR23433711 SRX19347581 SRS16745099 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling input rep2 GSM7039972   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing sibling input rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1 GSM7039972 GSM7039972: sibling input rep2; Danio rerio; RIP Seq GSM7039972 r1 GSM7039972 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz fastq fastq 12272791017.0 47579480.0 GSM7039972 r1 0:128.94 1:129.00 A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414 128 129     2905993856 3237323144 3186607999 2942811604 54414 SRX19347581 SRS16745099 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92733 0.92947 0.27234 0.26711 0.72391 0.72409 0.52625 0.55052 126 126 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74102 74102 SRR23433712 SRX19347580 SRS16745098 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling IP rep2 GSM7039971   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing sibling IP rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A GSM7039971 GSM7039971: sibling IP rep2; Danio rerio; RIP Seq GSM7039971 r1 GSM7039971 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz fastq fastq 10402768351.0 39113148.0 GSM7039971 r1 0:132.99 1:132.98 A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607 132 132     2806053427 2400476074 2403977422 2792214821 46607 SRX19347580 SRS16745098 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.90198 0.9063 0.18008 0.18091 0.69428 0.69396 0.44811 0.42925 147 147 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74103 74103 SRR23433713 SRX19347579 SRS16745097 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling input rep1 GSM7039970   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing sibling input rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1 GSM7039970 GSM7039970: sibling input rep1; Danio rerio; RIP Seq GSM7039970 r1 GSM7039970 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz fastq fastq 13094981449.0 46647417.0 GSM7039970 r1 0:140.35 1:140.37 A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966 140 140     3434495131 3120669719 3036482303 3502963330 370966 SRX19347579 SRS16745097 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.89276 0.90193 0.352 0.3489 0.70905 0.70719 0.52165 0.52427 142 142 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74104 74104 SRR23433714 SRX19347578 SRS16745096 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling IP rep1 GSM7039969   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing sibling IP rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A GSM7039969 GSM7039969: sibling IP rep1; Danio rerio; RIP Seq GSM7039969 r1 GSM7039969 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling1_IP_R1.fastq.gz sibling1_IP_R2.fastq.gz fastq fastq 12317957591.0 43954374.0 GSM7039969 r1 0:140.17 1:140.08 A:3509912915;C:2650796924;G:2663699373;T:3493137659;N:410720 140 140     3509912915 2650796924 2663699373 3493137659 410720 SRX19347578 SRS16745096 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.87054 0.88058 0.30375 0.30421 0.67783 0.67584 0.44329 0.44327 142 142 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure

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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");;