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run_metadata

19 rows where experiment.library_selection = "PCR" and tissue_curation = "Blood"

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experiment.library_strategy 2

devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Blood · 19 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • PCR · 19 ✖

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
30066 30066 SRR27676305 SRX23343658 SRS20205511 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b mt 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:9</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b mt 2 smart seq of setdb1b mt 2 smart seq of setdb1b mt 2 smart seq of setdb1b mt of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b mt_2_R2.fastq.gz.gz smart-seq of setdb1b mt_2_R1.fastq.gz.gz fastq fastq 11957458200.0 39858194.0 smart seq of setdb1b mt 2 R1.fastq.gz.gz 0:150 1:150 A:3692371435;C:1893324720;G:2810967928;T:3560751613;N:42504 150 150     3692371435 1893324720 2810967928 3560751613 42504 SRX23343658 SRS20205511 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.76332 0.82639 0.22191 0.23939 0.87093 0.87117 0.59757 0.60008 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30067 30067 SRR27676306 SRX23343657 SRS20205510 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b mt 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:8</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b mt 1 smart seq of setdb1b mt 1 smart seq of setdb1b mt 1 smart seq of setdb1b mt of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b mt_1_R1.fastq.gz.gz smart-seq of setdb1b mt_1_R2.fastq.gz.gz fastq fastq 9537788700.0 31792629.0 smart seq of setdb1b mt 1 R1.fastq.gz.gz 0:150 1:150 A:3044433376;C:1450924984;G:2142347814;T:2900047705;N:34821 150 150     3044433376 1450924984 2142347814 2900047705 34821 SRX23343657 SRS20205510 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.74808 0.79354 0.21148 0.22263 0.87405 0.87545 0.58431 0.58836 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30068 30068 SRR27676307 SRX23343656 SRS20205509 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b control 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:7</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b control 2 smart seq of setdb1b control 2 smart seq of setdb1b control 2 smart seq of setdb1b control of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b control_2_R1.fastq.gz.gz smart-seq of setdb1b control_2_R2.fastq.gz.gz fastq fastq 7963596600.0 26545322.0 smart seq of setdb1b control 2 R1.fastq.gz.gz 0:150 1:150 A:2522387513;C:1217203824;G:1776725064;T:2447251088;N:29111 150 150     2522387513 1217203824 1776725064 2447251088 29111 SRX23343656 SRS20205509 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.77121 0.80578 0.22631 0.23757 0.85953 0.86298 0.58219 0.58387 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30069 30069 SRR27676308 SRX23343655 SRS20205508 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b control 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:6</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b control 1 smart seq of setdb1b control 1 smart seq of setdb1b control 1 smart seq of setdb1b control of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b control_1_R2.fastq.gz.gz smart-seq of setdb1b control_1_R1.fastq.gz.gz fastq fastq 11867370900.0 39557903.0 smart seq of setdb1b control 1 R1.fastq.gz.gz 0:150 1:150 A:3969636478;C:1678555005;G:2520767064;T:3698368678;N:43675 150 150     3969636478 1678555005 2520767064 3698368678 43675 SRX23343655 SRS20205508 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.73517 0.73836 0.23036 0.23129 0.86407 0.86675 0.59652 0.59533 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30070 30070 SRR27676309 SRX23343654 SRS20205505 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip mt 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:5</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip mt RNA seq of atf7ip mt 2 RNA seq of atf7ip mt 2 mRNAseq of atf7ip mt of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip mt_2_R2.fastq.gz.gz RNA-seq of atf7ip mt_2_R1.fastq.gz.gz fastq fastq 2881485000.0 9604950.0 RNA seq of atf7ip mt 2 R1.fastq.gz.gz 0:150 1:150 A:714870764;C:672086586;G:819085358;T:675370688;N:71604 150 150     714870764 672086586 819085358 675370688 71604 SRX23343654 SRS20205505 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.95105 0.94782 0.0877 0.08683 0.67838 0.68085 0.4943 0.49308 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30071 30071 SRR27676310 SRX23343653 SRS20205506 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip mt 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:4</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip mt RNA seq of atf7ip mt 1 RNA seq of atf7ip mt 1 mRNAseq of atf7ip mt of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip mt_1_R2.fastq.gz.gz RNA-seq of atf7ip mt_1_R1.fastq.gz.gz fastq fastq 5215476900.0 17384923.0 RNA seq of atf7ip mt 1 R1.fastq.gz.gz 0:150 1:150 A:1305694077;C:1250588317;G:1437727006;T:1221425310;N:42190 150 150     1305694077 1250588317 1437727006 1221425310 42190 SRX23343653 SRS20205506 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.95459 0.9546 0.09418 0.0933 0.67353 0.67643 0.49356 0.49989 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30072 30072 SRR27676311 SRX23343652 SRS20205507 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip control 3   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 3|id</u><u>:3</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip control RNA seq of atf7ip control 3 RNA seq of atf7ip control 3 mRNAseq of atf7ip control of replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip control_3_R2.fastq.gz.gz RNA-seq of atf7ip control_3_R1.fastq.gz.gz fastq fastq 6742549200.0 22475164.0 RNA seq of atf7ip control 3 R1.fastq.gz.gz 0:150 1:150 A:1698977237;C:1657996046;G:1800441072;T:1584967439;N:167406 150 150     1698977237 1657996046 1800441072 1584967439 167406 SRX23343652 SRS20205507 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.96114 0.9601 0.05191 0.05152 0.69219 0.69398 0.48597 0.48633 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30073 30073 SRR27676312 SRX23343651 SRS20205504 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip control 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip control RNA seq of atf7ip control 2 RNA seq of atf7ip control 2 mRNAseq of atf7ip control of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip control_2_R2.fastq.gz.gz RNA-seq of atf7ip control_2_R1.fastq.gz.gz fastq fastq 6962540400.0 23208468.0 RNA seq of atf7ip control 2 R1.fastq.gz.gz 0:150 1:150 A:1794934846;C:1640272261;G:1855642638;T:1671491013;N:199642 150 150     1794934846 1640272261 1855642638 1671491013 199642 SRX23343651 SRS20205504 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.95531 0.95468 0.05949 0.05926 0.71019 0.71129 0.50401 0.50622 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30074 30074 SRR27676313 SRX23343650 SRS20205503 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip control 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip control RNA seq of atf7ip control 1 RNA seq of atf7ip control 1 mRNAseq of atf7ip control of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip control_1_R1.fastq.gz.gz RNA-seq of atf7ip control_1_R2.fastq.gz.gz fastq fastq 8543359800.0 28477866.0 RNA seq of atf7ip control 1 R1.fastq.gz.gz 0:150 1:150 A:2200058170;C:2049588985;G:2219737118;T:2073765388;N:210139 150 150     2200058170 2049588985 2219737118 2073765388 210139 SRX23343650 SRS20205503 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.96026 0.95618 0.05646 0.05613 0.68424 0.6856 0.48963 0.49334 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
63788 63788 SRR14055354 SRX10431257 SRS8565312 SRP311888 PRJNA716463 Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype PRJNA716463 Other Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.       Model organism or animal sample from Danio rerio RNA RBC mutant rep3   strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal                 RNA RBC mutant rep3 RNA RBC mutant rep3 RNA RBC mutant rep3 PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP311888     1049RBC-mu-3_FRAS190320004-1a_1.fq.gz 1049RBC-mu-3_FRAS190320004-1a_2.fq.gz fastq fastq 13709534700.0 45698449.0 1049RBC mu 3 FRAS190320004 1a 1.fq.gz 0:150 1:150 A:3530756610;C:3372588726;G:3372560453;T:3433404064;N:224847 150 150     3530756610 3372588726 3372560453 3433404064 224847 SRX10431257 SRS8565312 SRA1209808 Tsinghua university|School of Life Sciences Tsinghua university 2 0.92707 0.92658 0.05411 0.05405 0.75607 0.75568 0.45262 0.45118 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-03-24 Hatching Embryo Blood Hematopoietic System
63789 63789 SRR14055355 SRX10431256 SRS8565311 SRP311888 PRJNA716463 Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype PRJNA716463 Other Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.       Model organism or animal sample from Danio rerio RNA RBC mutant rep2   strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal                 RNA RBC mutant rep2 RNA RBC mutant rep2 RNA RBC mutant rep2 PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP311888     1049RBC-mu-2_FRAS190320003-1a_1.fq.gz 1049RBC-mu-2_FRAS190320003-1a_2.fq.gz fastq fastq 11921348400.0 39737828.0 1049RBC mu 2 FRAS190320003 1a 1.fq.gz 0:150 1:150 A:3056981846;C:2949479942;G:2955534362;T:2959157195;N:195055 150 150     3056981846 2949479942 2955534362 2959157195 195055 SRX10431256 SRS8565311 SRA1209808 Tsinghua university|School of Life Sciences Tsinghua university 2 0.92527 0.92379 0.04988 0.05004 0.76629 0.76723 0.45068 0.44998 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-03-24 Hatching Embryo Blood Hematopoietic System
63790 63790 SRR14055358 SRX10431253 SRS8565308 SRP311888 PRJNA716463 Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype PRJNA716463 Other Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.       Model organism or animal sample from Danio rerio RNA RBC mutant rep1   strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal                 RNA RBC mutant rep1 RNA RBC mutant rep1 RNA RBC mutant rep1 PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP311888     1049RBC-mu-1_FRAS190320002-1a_1.fq.gz 1049RBC-mu-1_FRAS190320002-1a_2.fq.gz fastq fastq 12136778100.0 40455927.0 1049RBC mu 1 FRAS190320002 1a 1.fq.gz 0:150 1:150 A:3129750481;C:2985406228;G:2964648069;T:3056774126;N:199196 150 150     3129750481 2985406228 2964648069 3056774126 199196 SRX10431253 SRS8565308 SRA1209808 Tsinghua university|School of Life Sciences Tsinghua university 2 0.83132 0.8312 0.04768 0.04763 0.77455 0.77508 0.47219 0.46709 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-03-24 Hatching Embryo Blood Hematopoietic System
63791 63791 SRR14055359 SRX10431252 SRS8565307 SRP311888 PRJNA716463 Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype PRJNA716463 Other Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.       Model organism or animal sample from Danio rerio RNA RBC sibling rep3   strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal                 RNA RBC sibling rep3 RNA RBC sibling rep3 RNA RBC sibling rep3 PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP311888     1049RBC-sib-3_FRAS190320001-1a_1.fq.gz 1049RBC-sib-3_FRAS190320001-1a_2.fq.gz fastq fastq 13833315900.0 46111053.0 1049RBC sib 3 FRAS190320001 1a 1.fq.gz 0:150 1:150 A:3515133007;C:3462086735;G:3467124241;T:3388720799;N:251118 150 150     3515133007 3462086735 3467124241 3388720799 251118 SRX10431252 SRS8565307 SRA1209808 Tsinghua university|School of Life Sciences Tsinghua university 2 0.93805 0.93649 0.04283 0.04244 0.80752 0.80817 0.44958 0.44864 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-03-24 Hatching Embryo Blood Hematopoietic System
63792 63792 SRR14055360 SRX10431251 SRS8565306 SRP311888 PRJNA716463 Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype PRJNA716463 Other Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.       Model organism or animal sample from Danio rerio RNA RBC sibling rep2   strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal                 RNA RBC sibling rep2 RNA RBC sibling rep2 RNA RBC sibling rep2 PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP311888     1049RBC-sib-2_FRAS190320000-1a_1.fq.gz 1049RBC-sib-2_FRAS190320000-1a_2.fq.gz fastq fastq 10846357200.0 36154524.0 1049RBC sib 2 FRAS190320000 1a 1.fq.gz 0:150 1:150 A:2755761785;C:2720527184;G:2723864022;T:2645998029;N:206180 150 150     2755761785 2720527184 2723864022 2645998029 206180 SRX10431251 SRS8565306 SRA1209808 Tsinghua university|School of Life Sciences Tsinghua university 2 0.94927 0.94734 0.04134 0.04034 0.80505 0.80586 0.43562 0.43266 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-03-24 Hatching Embryo Blood Hematopoietic System
63793 63793 SRR14055361 SRX10431250 SRS8565305 SRP311888 PRJNA716463 Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype PRJNA716463 Other Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.       Model organism or animal sample from Danio rerio RNA RBC sibling rep1   strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal                 RNA RBC sibling rep1 RNA RBC sibling rep1 RNA RBC sibling rep1 PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP311888     1049RBC-sib-1_FRAS190319999-1a_1.fq.gz 1049RBC-sib-1_FRAS190319999-1a_2.fq.gz fastq fastq 10945070100.0 36483567.0 1049RBC sib 1 FRAS190319999 1a 1.fq.gz 0:150 1:150 A:2787518303;C:2738688307;G:2737440984;T:2681219061;N:203445 150 150     2787518303 2738688307 2737440984 2681219061 203445 SRX10431250 SRS8565305 SRA1209808 Tsinghua university|School of Life Sciences Tsinghua university 2 0.94824 0.94818 0.04162 0.04125 0.80247 0.80284 0.44015 0.43533 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-03-24 Hatching Embryo Blood Hematopoietic System
71666 71666 SRR21912675 SRX17898597 SRS15415408 SRP402754 PRJNA890767 Input of Setdb1 ChIP seq PRJNA890767 Other           Input of Setdb1 ChIP seq 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal                 Input of Setdb1 ChIP seq Input of Setdb1 ChIP seq 2 Input of Setdb1 ChIP seq 2 Input of Setdb1 ChIP seq of replicate 2     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402754     Input of Setdb1 ChIP seq_2_R1.fastq.gz Input of Setdb1 ChIP seq_2_R2.fastq.gz fastq fastq 10384123200.0 34613744.0 Input of Setdb1 ChIP seq 2 R1.fastq.gz 0:150 1:150 A:2881450025;C:2101684440;G:2781250994;T:2619703377;N:34364 150 150     2881450025 2101684440 2781250994 2619703377 34364 SRX17898597 SRS15415408 SRA1520925 East China Normal University|School of Life Sciences East China Normal University 2 0.85089 0.8531 0.74147 0.74359 0.72295 0.72243 0.49118 0.48923 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic System
71667 71667 SRR21912676 SRX17898596 SRS15415407 SRP402754 PRJNA890767 Input of Setdb1 ChIP seq PRJNA890767 Other           Input of Setdb1 ChIP seq 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal                 Input of Setdb1 ChIP seq Input of Setdb1 ChIP seq 1 Input of Setdb1 ChIP seq 1 Input of Setdb1 ChIP seq of replicate 1     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402754     Input of Setdb1 ChIP seq_1_R1.fastq.gz Input of Setdb1 ChIP seq_1_R2.fastq.gz fastq fastq 12920086500.0 43066955.0 Input of Setdb1 ChIP seq 1 R1.fastq.gz 0:150 1:150 A:3743886319;C:2621020407;G:3091990806;T:3463122519;N:66449 150 150     3743886319 2621020407 3091990806 3463122519 66449 SRX17898596 SRS15415407 SRA1520925 East China Normal University|School of Life Sciences East China Normal University 2 0.84709 0.84605 0.73727 0.73696 0.71622 0.71825 0.49278 0.49029 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic System
71668 71668 SRR21913250 SRX17899172 SRS15415910 SRP402767 PRJNA890871 Setdb1 ChIP seq PRJNA890871 Other           Setdb1 ChIP seq 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal                 Setdb1 ChIP seq Setdb1 ChIP seq 2 Setdb1 ChIP seq 2 Setdb1 ChIP seq of replicate 2     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402767     Setdb1 ChIP seq_2_R1.fastq.gz Setdb1 ChIP seq_2_R2.fastq.gz fastq fastq 12909692700.0 43032309.0 Setdb1 ChIP seq 2 R1.fastq.gz 0:150 1:150 A:3496408461;C:2593261434;G:3585073580;T:3234906241;N:42984 150 150     3496408461 2593261434 3585073580 3234906241 42984 SRX17899172 SRS15415910 SRA1520950 East China Normal University|School of Life Sciences East China Normal University 2 0.80561 0.80471 0.69212 0.69176 0.71924 0.71999 0.49445 0.4953 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic System
71669 71669 SRR21913251 SRX17899171 SRS15415909 SRP402767 PRJNA890871 Setdb1 ChIP seq PRJNA890871 Other           Setdb1 ChIP seq 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|sex:pooled male and female|tissue:hematopoietic stem cell|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal                 Setdb1 ChIP seq Setdb1 ChIP seq 1 Setdb1 ChIP seq 1 Setdb1 ChIP seq of replicate 1     ChIP-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP402767     Setdb1 ChIP seq_1_R1.fastq.gz Setdb1 ChIP seq_1_R2.fastq.gz fastq fastq 9908302200.0 33027674.0 Setdb1 ChIP seq 1 R1.fastq.gz 0:150 1:150 A:2799788817;C:2060083633;G:2416457009;T:2631940230;N:32511 150 150     2799788817 2060083633 2416457009 2631940230 32511 SRX17899171 SRS15415909 SRA1520950 East China Normal University|School of Life Sciences East China Normal University 2 0.7718 0.77187 0.66177 0.66128 0.72088 0.71963 0.49562 0.49458 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2022-10-15 Larval Larval Blood Hematopoietic 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");;