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17 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue_curation_coarse = "Liver and Biliary System"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Liver and Biliary System · 17 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 17 ✖

experiment.library_layout 1

  • SINGLE · 17 ✖
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
31986 31986 SRR28894021 SRX24452441 SRS21206092 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 4   strain:elovl2 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 4 8 8 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-4 fastq 4367010000.0 29113400.0 elovl2 4.gz 0:150 A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734 150       1161921878 1015107709 1012841192 1177020487 118734 SRX24452441 SRS21206092 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31987 31987 SRR28894022 SRX24452440 SRS21206091 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 3   strain:elovl2 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 3 7 7 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-3 fastq 5125533150.0 34170221.0 elovl2 3.gz 0:150 A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776 150       1365645170 1189846405 1184721703 1385180096 139776 SRX24452440 SRS21206091 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31988 31988 SRR28894023 SRX24452439 SRS21206090 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 2   strain:elovl2 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 2 6 6 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-2 fastq 3261375750.0 21742505.0 elovl2 2.gz 0:150 A:878478836;C:747963062;G:743760185;T:891083235;N:90432 150       878478836 747963062 743760185 891083235 90432 SRX24452439 SRS21206090 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31989 31989 SRR28894024 SRX24452438 SRS21206089 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 1   strain:elovl2 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 1 5 5 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-1 fastq 3629422950.0 24196153.0 elovl2 1.gz 0:150 A:974034477;C:836070594;G:831068189;T:988151010;N:98680 150       974034477 836070594 831068189 988151010 98680 SRX24452438 SRS21206089 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31990 31990 SRR28894025 SRX24452437 SRS21206088 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 4   strain:WT 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 4 4 4 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-4 fastq 4037472900.0 26916486.0 WT 4.gz 0:150 A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413 150       1083383010 932278459 925831402 1095868616 111413 SRX24452437 SRS21206088 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31991 31991 SRR28894026 SRX24452436 SRS21206087 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 3   strain:WT 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 3 3 3 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-3 fastq 3651994200.0 24346628.0 WT 3.gz 0:150 A:978819903;C:844506880;G:836704943;T:991863415;N:99059 150       978819903 844506880 836704943 991863415 99059 SRX24452436 SRS21206087 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31992 31992 SRR28894027 SRX24452435 SRS21206086 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 2   strain:WT 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 2 2 2 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-2 fastq 3845338950.0 25635593.0 WT 2.gz 0:150 A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950 150       1033991995 885977441 878907105 1046356459 105950 SRX24452435 SRS21206086 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31993 31993 SRR28894028 SRX24452434 SRS21206085 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 1   strain:WT 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 1 1 1 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-1 fastq 3756883050.0 25045887.0 WT 1.gz 0:150 A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839 150       1005244721 868304979 865360007 1017811504 161839 SRX24452434 SRS21206085 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
40709 40709 SRR3420429 SRX1660365 SRS1360335 SRP072296 PRJNA316313 Codon optimality and mRNA decay in zebrafish and Xenopus PRJNA316313 Other Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.         AG01295 liver   strain:TUAB|age:adult|sex:pooled male and female|tissue:Liver|BioSampleModel:Model organism or animal                 AG01295 liver AG01295 liver 1 1     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</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> SRP072296     AG01295_SEQ0273_R1.fastq.gz fastq 887443260.0 11676885.0 AG01295 run 1 0:76 A:230924609;C:202487813;G:205378868;T:248612177;N:39793 76       230924609 202487813 205378868 248612177 39793 SRX1660365 SRS1360335 SRA395141 Yale University|Giraldez Lab Yale University 1 0.95421   0.04352   0.84062   0.23556   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2016-06-17 Adult Adult Liver Liver and Biliary System
43824 43824 SRR6152619 SRX3264623 SRS2576849 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 1 rna ctl 1   strain:AB strain|isolate:Male fish tank 1|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 1 rna ctl 1 rna ctl 1 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1477820550.0 29556411.0 RZY 323.fastq 0:50 A:341022361;C:372071364;G:361979807;T:401982416;N:764602 50       341022361 372071364 361979807 401982416 764602 SRX3264623 SRS2576849 SRA617983 Nord University|FBA Nord University 1 0.88633   0.09624   0.85886   0.58198   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43825 43825 SRR6152620 SRX3264622 SRS2576848 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 2 rna ctl 2   strain:AB strain|isolate:Male fish tank 2|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 2 rna ctl 2 rna ctl 2 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1267834350.0 25356687.0 RZY 324.fastq 0:50 A:294105777;C:312048823;G:312619877;T:348380931;N:678942 50       294105777 312048823 312619877 348380931 678942 SRX3264622 SRS2576848 SRA617983 Nord University|FBA Nord University 1 0.90606   0.10033   0.83309   0.58402   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43826 43826 SRR6152623 SRX3264619 SRS2576845 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 1 rna low 1C 1   strain:AB strain|isolate:Male fish tank 7|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 1 rna low 1C 1 rna low 1C 1 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1477820550.0 29556411.0 RZY 319.fastq 0:50 A:341022361;C:372071364;G:361979807;T:401982416;N:764602 50       341022361 372071364 361979807 401982416 764602 SRX3264619 SRS2576845 SRA617983 Nord University|FBA Nord University 1 0.88641   0.09616   0.85882   0.58903   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43827 43827 SRR6152624 SRX3264618 SRS2576843 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 2 rna low 1C 2   strain:AB strain|isolate:Male fish tank 8|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 2 rna low 1C 2 rna low 1C 2 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1250104800.0 25002096.0 RZY 320.fastq 0:50 A:298225313;C:301950518;G:305099451;T:344161142;N:668376 50       298225313 301950518 305099451 344161142 668376 SRX3264618 SRS2576843 SRA617983 Nord University|FBA Nord University 1 0.88702   0.09849   0.82548   0.57466   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43828 43828 SRR6152625 SRX3264617 SRS2576844 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 3 rna ctl 3   strain:AB strain|isolate:Male fish tank 3|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 3 rna ctl 3 rna ctl 3 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1375388050.0 27507761.0 RZY 325.fastq 0:50 A:331719333;C:330944665;G:333352358;T:378627997;N:743697 50       331719333 330944665 333352358 378627997 743697 SRX3264617 SRS2576844 SRA617983 Nord University|FBA Nord University 1 0.89565   0.12552   0.83189   0.57988   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43829 43829 SRR6152626 SRX3264616 SRS2576842 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers control 4 rna ctl 4   strain:AB strain|isolate:Male fish tank 4|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers control 4 rna ctl 4 rna ctl 4 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1433558100.0 28671162.0 RZY 326.fastq 0:50 A:340242659;C:350821208;G:346146280;T:395614030;N:733923 50       340242659 350821208 346146280 395614030 733923 SRX3264616 SRS2576842 SRA617983 Nord University|FBA Nord University 1 0.90327   0.11496   0.82335   0.57528   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43830 43830 SRR6152627 SRX3264615 SRS2576841 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 3 rna low 1C 3   strain:AB strain|isolate:Male fish tank 9|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 3 rna low 1C 3 rna low 1C 3 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1453888750.0 29077775.0 RZY 321.fastq 0:50 A:335835385;C:357658223;G:359480232;T:400135740;N:779170 50       335835385 357658223 359480232 400135740 779170 SRX3264615 SRS2576841 SRA617983 Nord University|FBA Nord University 1 0.89454   0.08578   0.84009   0.584   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System
43831 43831 SRR6152628 SRX3264614 SRS2576840 SRP119651 PRJNA413770 Cross generational effects of a marginal 1 C metabolite deficiency PRJNA413770 Other The effect of a deficiency in one carbon 1 C metabolites in the adult generation on DNA methylation and gene expression in adult offspring livers was investigated through the use of high throughput RNA sequencing and reduced representation bisulfite sequencing.Individuals in the F0 generation were either fed a normal diet or one marginally deficient in 1 C metabolites folate vitamins B12 and B6 methionine and choline from larval stages and mated within each diet group. The resulting offspring were fed the control diet throughout their lives and Livers of adult offspring were harvested post 113 dpf and RNA and DNA extracted for RNA sequencing and RRBS.       F1 livers low 1C 4 rna low 1C 4   strain:AB strain|isolate:Male fish tank 10|age:113 dpf|dev stage:adult|sex:male|tissue:liver|biomaterial provider:NIFES Kaja Helvik Skjaerven|birth location:NIFES|breeding method:Ref: Skjaerven K. H. et al. Sci Rep 6 34535 doi:10.1038/srep34535 2016|collected by:Kaja Helvik Skjaerven and Anne Catrin Adam|collection date:2013 11 12|health state:Good|BioSampleModel:Model organism or animal                 F1 livers low 1C 4 rna low 1C 4 rna low 1C 4 Directional sequencing of mRNA fragments     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2000   SRP119651         1336779650.0 26735593.0 RZY 322.fastq 0:50 A:310390083;C:329159312;G:327197131;T:369319794;N:713330 50       310390083 329159312 327197131 369319794 713330 SRX3264614 SRS2576840 SRA617983 Nord University|FBA Nord University 1 0.91491   0.10744   0.81773   0.57357   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2017-10-10 Adult Adult Liver Liver and Biliary System

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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");;