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run_metadata

26 rows where devstage_curation_coarse = "Undetermined" and tissue_curation_coarse = "Skeletal Element"

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experiment.platform 2

experiment.library_selection 2

tissue_curation_coarse 1

  • Skeletal Element · 26 ✖

tissue_curation 1

technology 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Undetermined · 26 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
30210 30210 SRR27722348 SRX23388314 SRS20249507 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         2 F5 NPs   isolate:b1 F5|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 2 F5 NPs 2 F5 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701134_L1EGI0701134--WT_M5.R1.raw.fastq.gz L1EGI0701134_L1EGI0701134--WT_M5.R2.raw.fastq.gz fastq fastq 6858985646.0 22711873.0 L1EGI0701134 L1EGI0701134 WT M5.R1.raw.fastq.gz 0:151 1:151 A:1775374486;C:1607590004;G:1736749854;T:1739241353;N:29949 151 151     1775374486 1607590004 1736749854 1739241353 29949 SRX23388314 SRS20249507 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30211 30211 SRR27722349 SRX23388313 SRS20249506 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         2 F4 NPs   isolate:b1 F4|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 2 F4 NPs 2 F4 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701133--WT_M4.R1.raw.fastq.gz L1EGI0701133--WT_M4.R2.raw.fastq.gz fastq fastq 8367706978.0 27707639.0 L1EGI0701133 WT M4.R1.raw.fastq.gz 0:151 1:151 A:2190978299;C:1972956945;G:2068607164;T:2135130434;N:34136 151 151     2190978299 1972956945 2068607164 2135130434 34136 SRX23388313 SRS20249506 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30212 30212 SRR27722350 SRX23388312 SRS20249505 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         2 F3 NPs   isolate:b1 F3|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 2 F3 NPs 2 F3 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701132--WT_M3.R1.raw.fastq.gz L1EGI0701132--WT_M3.R2.raw.fastq.gz fastq fastq 8356526334.0 27670617.0 L1EGI0701132 WT M3.R1.raw.fastq.gz 0:151 1:151 A:2162579680;C:1984443655;G:2083109306;T:2126359754;N:33939 151 151     2162579680 1984443655 2083109306 2126359754 33939 SRX23388312 SRS20249505 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30213 30213 SRR27722351 SRX23388311 SRS20249504 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         2 F2 NPs   isolate:b1 F2|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 2 F2 NPs 2 F2 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701131--WT_M2.R1.raw.fastq.gz L1EGI0701131--WT_M2.R2.raw.fastq.gz fastq fastq 8143546874.0 26965387.0 L1EGI0701131 WT M2.R1.raw.fastq.gz 0:151 1:151 A:2114633540;C:1938964033;G:2015877300;T:2074038855;N:33146 151 151     2114633540 1938964033 2015877300 2074038855 33146 SRX23388311 SRS20249504 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30214 30214 SRR27722352 SRX23388310 SRS20249503 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         2 F1 NPs   isolate:b1 F1|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 2 F1 NPs 2 F1 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701130--WT_M1.R1.raw.fastq.gz L1EGI0701130--WT_M1.R2.raw.fastq.gz fastq fastq 9004594174.0 29816537.0 L1EGI0701130 WT M1.R1.raw.fastq.gz 0:151 1:151 A:2356139884;C:2114457727;G:2228436842;T:2305522562;N:37159 151 151     2356139884 2114457727 2228436842 2305522562 37159 SRX23388310 SRS20249503 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30215 30215 SRR27722353 SRX23388309 SRS20249502 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         1 F5 WT   isolate:b1 F5|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 1 F5 WT 1 F5 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701128--WT_F5.R1.raw.fastq.gz L1EGI0701128--WT_F5.R2.raw.fastq.gz fastq fastq 9595399794.0 31772847.0 L1EGI0701128 WT F5.R1.raw.fastq.gz 0:151 1:151 A:2471647902;C:2293433569;G:2400056012;T:2430223486;N:38825 151 151     2471647902 2293433569 2400056012 2430223486 38825 SRX23388309 SRS20249502 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30216 30216 SRR27722354 SRX23388308 SRS20249501 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         1 F4 WT   isolate:b1 F4|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 1 F4 WT 1 F4 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701127--WT_F4.R1.raw.fastq.gz L1EGI0701127--WT_F4.R2.raw.fastq.gz fastq fastq 7628679456.0 25260528.0 L1EGI0701127 WT F4.R1.raw.fastq.gz 0:151 1:151 A:2006324404;C:1789150133;G:1873940582;T:1959232617;N:31720 151 151     2006324404 1789150133 1873940582 1959232617 31720 SRX23388308 SRS20249501 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30217 30217 SRR27722355 SRX23388307 SRS20249500 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         1 F3 WT   isolate:b1 F3|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 1 F3 WT 1 F3 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701126--WT_F3.R1.raw.fastq.gz L1EGI0701126--WT_F3.R2.raw.fastq.gz fastq fastq 8853107954.0 29314927.0 L1EGI0701126 WT F3.R1.raw.fastq.gz 0:151 1:151 A:2281668777;C:2122390553;G:2205818678;T:2243193679;N:36267 151 151     2281668777 2122390553 2205818678 2243193679 36267 SRX23388307 SRS20249500 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30218 30218 SRR27722356 SRX23388306 SRS20249499 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         4 M5 NPs   isolate:b1 M5|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 4 M5 NPs 4 M5 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701146--NPs_M5.R1.raw.fastq.gz L1EGI0701146--NPs_M5.R2.raw.fastq.gz fastq fastq 7440341686.0 24636893.0 L1EGI0701146 NPs M5.R1.raw.fastq.gz 0:151 1:151 A:1926837197;C:1774447312;G:1865805171;T:1873221668;N:30338 151 151     1926837197 1774447312 1865805171 1873221668 30338 SRX23388306 SRS20249499 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30219 30219 SRR27722357 SRX23388305 SRS20249498 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         4 M4 NPs   isolate:b1 M4|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 4 M4 NPs 4 M4 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701145_L1EGI0701145--NPs_M4.R1.raw.fastq.gz L1EGI0701145_L1EGI0701145--NPs_M4.R2.raw.fastq.gz fastq fastq 7482324518.0 24775909.0 L1EGI0701145 L1EGI0701145 NPs M4.R1.raw.fastq.gz 0:151 1:151 A:2074937139;C:1646093888;G:1749156387;T:2012102736;N:34368 151 151     2074937139 1646093888 1749156387 2012102736 34368 SRX23388305 SRS20249498 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30220 30220 SRR27722358 SRX23388304 SRS20249497 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         4 M3 NPs   isolate:b1 M3|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 4 M3 NPs 4 M3 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701144--NPs_M3.R1.raw.fastq.gz L1EGI0701144--NPs_M3.R2.raw.fastq.gz fastq fastq 8439432280.0 27945140.0 L1EGI0701144 NPs M3.R1.raw.fastq.gz 0:151 1:151 A:2168219326;C:2022693060;G:2132822366;T:2115662612;N:34916 151 151     2168219326 2022693060 2132822366 2115662612 34916 SRX23388304 SRS20249497 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30221 30221 SRR27722359 SRX23388303 SRS20249496 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         4 M2 NPs   isolate:b1 M2|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 4 M2 NPs 4 M2 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701143--NPs_M2.R1.raw.fastq.gz L1EGI0701143--NPs_M2.R2.raw.fastq.gz fastq fastq 7033808614.0 23290757.0 L1EGI0701143 NPs M2.R1.raw.fastq.gz 0:151 1:151 A:1828789906;C:1675914023;G:1760006026;T:1769068832;N:29827 151 151     1828789906 1675914023 1760006026 1769068832 29827 SRX23388303 SRS20249496 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30222 30222 SRR27722360 SRX23388302 SRS20249495 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         4 M1 NPs   isolate:b1 M1|host:male|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 4 M1 NPs 4 M1 NPs bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701142--NPs_M1.R1.raw.fastq.gz L1EGI0701142--NPs_M1.R2.raw.fastq.gz fastq fastq 8087463964.0 26779682.0 L1EGI0701142 NPs M1.R1.raw.fastq.gz 0:151 1:151 A:2097695704;C:1931279917;G:2029894750;T:2028560473;N:33120 151 151     2097695704 1931279917 2029894750 2028560473 33120 SRX23388302 SRS20249495 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30223 30223 SRR27722361 SRX23388301 SRS20249494 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         3 M5 WT   isolate:b1 M5|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 3 M5 WT 3 M5 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701140--NPs_F5.R1.raw.fastq.gz L1EGI0701140--NPs_F5.R2.raw.fastq.gz fastq fastq 8478344376.0 28073988.0 L1EGI0701140 NPs F5.R1.raw.fastq.gz 0:151 1:151 A:2202734913;C:2015133130;G:2106431143;T:2154009977;N:35213 151 151     2202734913 2015133130 2106431143 2154009977 35213 SRX23388301 SRS20249494 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30224 30224 SRR27722362 SRX23388300 SRS20249493 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         3 M4 WT   isolate:b1 M4|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 3 M4 WT 3 M4 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701139--NPs_F4.R1.raw.fastq.gz L1EGI0701139--NPs_F4.R2.raw.fastq.gz fastq fastq 8569883596.0 28377098.0 L1EGI0701139 NPs F4.R1.raw.fastq.gz 0:151 1:151 A:2215047248;C:2038336388;G:2145335785;T:2171128844;N:35331 151 151     2215047248 2038336388 2145335785 2171128844 35331 SRX23388300 SRS20249493 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30225 30225 SRR27722363 SRX23388299 SRS20249492 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         3 M3 WT   isolate:b1 M3|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 3 M3 WT 3 M3 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701138--NPs_F3.R1.raw.fastq.gz L1EGI0701138--NPs_F3.R2.raw.fastq.gz fastq fastq 7930364168.0 26259484.0 L1EGI0701138 NPs F3.R1.raw.fastq.gz 0:151 1:151 A:2046759305;C:1898600276;G:1959125241;T:2025847086;N:32260 151 151     2046759305 1898600276 1959125241 2025847086 32260 SRX23388299 SRS20249492 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30226 30226 SRR27722364 SRX23388298 SRS20249491 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         3 M2 WT   isolate:b1 M2|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 3 M2 WT 3 M2 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701137--NPs_F2.R1.raw.fastq.gz L1EGI0701137--NPs_F2.R2.raw.fastq.gz fastq fastq 6914965272.0 22897236.0 L1EGI0701137 NPs F2.R1.raw.fastq.gz 0:151 1:151 A:1789644342;C:1644676301;G:1738643678;T:1741972870;N:28081 151 151     1789644342 1644676301 1738643678 1741972870 28081 SRX23388298 SRS20249491 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30227 30227 SRR27722365 SRX23388297 SRS20249490 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         3 M1 WT   isolate:b1 M1|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 3 M1 WT 3 M1 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701136--NPs_F1.R1.raw.fastq.gz L1EGI0701136--NPs_F1.R2.raw.fastq.gz fastq fastq 7957071840.0 26347920.0 L1EGI0701136 NPs F1.R1.raw.fastq.gz 0:151 1:151 A:2056500264;C:1899503313;G:1979706436;T:2021329536;N:32291 151 151     2056500264 1899503313 1979706436 2021329536 32291 SRX23388297 SRS20249490 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30228 30228 SRR27722366 SRX23388296 SRS20249489 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         1 F2 WT   isolate:b1 F2|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 1 F2 WT 1 F2 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701125--WT_F2.R1.raw.fastq.gz L1EGI0701125--WT_F2.R2.raw.fastq.gz fastq fastq 7960683760.0 26359880.0 L1EGI0701125 WT F2.R1.raw.fastq.gz 0:151 1:151 A:2087534093;C:1862286963;G:1962292721;T:2048536454;N:33529 151 151     2087534093 1862286963 1962292721 2048536454 33529 SRX23388296 SRS20249489 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
30229 30229 SRR27722367 SRX23388295 SRS20249488 SRP485828 PRJNA1068830 skeletal toxicity studies of polystyrene nanoplastic in zebrafish PRJNA1068830 Other Employing standard polystyrene NPs as the representative the investigation of the bone loss in the caudal fin from environmentally realistic concentration of NPs was assessed in zebrafish.         1 F1 WT   isolate:b1 F1|host:female|collection date:2022 09 06|geo loc name:China:qingdao|tissue:b1|BioSampleModel:Invertebrate                 skeletal toxicity studies of polystyrene nanoplastic in zebrafish 1 F1 WT 1 F1 WT bone     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP485828     L1EGI0701124--WT_F1.R1.raw.fastq.gz L1EGI0701124--WT_F1.R2.raw.fastq.gz fastq fastq 8373285522.0 27726111.0 L1EGI0701124 WT F1.R1.raw.fastq.gz 0:151 1:151 A:2148645285;C:1996284185;G:2121066399;T:2107255525;N:34128 151 151     2148645285 1996284185 2121066399 2107255525 34128 SRX23388295 SRS20249488 SRA1791477 zhejiang university|the college of animal science zhejiang university                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-01-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
58579 58579 SRR11425295 SRX8003661 SRS6377641 SRP254053 PRJNA615232 Control of osteoblast regeneration by a train of Erk activity waves GSE147551 Transcriptome Analysis We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.   pubmed:33408418   high Erk activity; rep1 GSM4433141   tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales high Erk activity; rep1 Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq high Erk activity Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube. fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales GSM4433141 GSM4433141: high Erk activity; rep1; Danio rerio; RNA Seq GSM4433141   1 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 GEO Accession:GSM4433141 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP254053     3G_plus_1.fq.gz 3G_plus_2.fq.gz fastq fastq 4698595200.0 46985952.0 GSM4433141 r1 0:100 1:100 A:1261622105;C:1085007643;G:1066886112;T:1285079340;N:0 100 100     1261622105 1085007643 1066886112 1285079340 0 SRX8003661 SRS6377641 SRA1059429 GEO Poss, Cell Biology, Duke University 1 0.86576   0.11767   0.81262   0.52377   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
58580 58580 SRR11425294 SRX8003660 SRS6377640 SRP254053 PRJNA615232 Control of osteoblast regeneration by a train of Erk activity waves GSE147551 Transcriptome Analysis We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.   pubmed:33408418   low Erk activity; rep3 GSM4433140   tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales low Erk activity; rep3 Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq low Erk activity Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube. fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales GSM4433140 GSM4433140: low Erk activity; rep3; Danio rerio; RNA Seq GSM4433140   1 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 GEO Accession:GSM4433140 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP254053     6B_minus_1.fq.gz 6B_minus_2.fq.gz fastq fastq 4707217000.0 47072170.0 GSM4433140 r1 0:100 1:100 A:1268188059;C:1086056259;G:1067448053;T:1285524629;N:0 100 100     1268188059 1086056259 1067448053 1285524629 0 SRX8003660 SRS6377640 SRA1059429 GEO Poss, Cell Biology, Duke University 1 0.88883   0.05585   0.82071   0.47905   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
58581 58581 SRR11425293 SRX8003659 SRS6377639 SRP254053 PRJNA615232 Control of osteoblast regeneration by a train of Erk activity waves GSE147551 Transcriptome Analysis We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.   pubmed:33408418   low Erk activity; rep2 GSM4433139   tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales low Erk activity; rep2 Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq low Erk activity Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube. fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales GSM4433139 GSM4433139: low Erk activity; rep2; Danio rerio; RNA Seq GSM4433139   1 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 GEO Accession:GSM4433139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP254053     5G_minus_1.fq.gz 5G_minus_2.fq.gz fastq fastq 4705295600.0 47052956.0 GSM4433139 r1 0:100 1:100 A:1240779500;C:1112511484;G:1096653049;T:1255351567;N:0 100 100     1240779500 1112511484 1096653049 1255351567 0 SRX8003659 SRS6377639 SRA1059429 GEO Poss, Cell Biology, Duke University 1 0.89254   0.04065   0.81197   0.46307   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
58582 58582 SRR11425292 SRX8003658 SRS6377638 SRP254053 PRJNA615232 Control of osteoblast regeneration by a train of Erk activity waves GSE147551 Transcriptome Analysis We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.   pubmed:33408418   low Erk activity; rep1 GSM4433138   tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales low Erk activity; rep1 Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq low Erk activity Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube. fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales GSM4433138 GSM4433138: low Erk activity; rep1; Danio rerio; RNA Seq GSM4433138   1 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 GEO Accession:GSM4433138 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP254053     3G_minus_1.fq.gz 3G_minus_2.fq.gz fastq fastq 4707783400.0 47077834.0 GSM4433138 r1 0:100 1:100 A:1275040914;C:1077730597;G:1059242617;T:1295769272;N:0 100 100     1275040914 1077730597 1059242617 1295769272 0 SRX8003658 SRS6377638 SRA1059429 GEO Poss, Cell Biology, Duke University 1 0.8629   0.13994   0.7838   0.50568   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
58583 58583 SRR11425297 SRX8003657 SRS6377637 SRP254053 PRJNA615232 Control of osteoblast regeneration by a train of Erk activity waves GSE147551 Transcriptome Analysis We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.   pubmed:33408418   high Erk activity; rep3 GSM4433143   tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales high Erk activity; rep3 Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq high Erk activity Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube. fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales GSM4433143 GSM4433143: high Erk activity; rep3; Danio rerio; RNA Seq GSM4433143   1 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 GEO Accession:GSM4433143 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP254053     6B_plus_1.fq.gz 6B_plus_2.fq.gz fastq fastq 4703728000.0 47037280.0 GSM4433143 r1 0:100 1:100 A:1231849303;C:1116643672;G:1102072724;T:1253162301;N:0 100 100     1231849303 1116643672 1102072724 1253162301 0 SRX8003657 SRS6377637 SRA1059429 GEO Poss, Cell Biology, Duke University 1 0.89702   0.07131   0.82978   0.49499   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-25 Undetermined Undetermined Bone or Cartilage Skeletal Element
58584 58584 SRR11425296 SRX8003656 SRS6377636 SRP254053 PRJNA615232 Control of osteoblast regeneration by a train of Erk activity waves GSE147551 Transcriptome Analysis We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.   pubmed:33408418   high Erk activity; rep2 GSM4433142   tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales high Erk activity; rep2 Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq high Erk activity Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube. fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales GSM4433142 GSM4433142: high Erk activity; rep2; Danio rerio; RNA Seq GSM4433142   1 RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01 GEO Accession:GSM4433142 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP254053     5G_plus_1.fq.gz 5G_plus_2.fq.gz fastq fastq 4708623600.0 47086236.0 GSM4433142 r1 0:100 1:100 A:1200601624;C:1150903127;G:1136628277;T:1220490572;N:0 100 100     1200601624 1150903127 1136628277 1220490572 0 SRX8003656 SRS6377636 SRA1059429 GEO Poss, Cell Biology, Duke University 1 0.90729   0.03751   0.84433   0.50342   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-03-25 Undetermined Undetermined Bone or Cartilage Skeletal Element

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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");;