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run_metadata

48 rows where experiment.library_selection = "other" and tissue_curation = "Trunk"

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technology 5

experiment.library_strategy 3

devstage_curation 3

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 48 ✖

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • other · 48 ✖

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
34115 34115 SRR31230228 SRX26610547 SRS23109428 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         TF L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:TF|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data TF L1 TF L1 TF     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     TF_L1_1.fq.gz TF_L1_2.fq.gz fastq fastq 6687564300.0 22291881.0 TF L1 1.fq.gz 0:150 1:150 A:1864117630;C:1488483222;G:1497677628;T:1837006551;N:279269 150 150     1864117630 1488483222 1497677628 1837006551 279269 SRX26610547 SRS23109428 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34116 34116 SRR31230229 SRX26610546 SRS23109427 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         HP L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:HP|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data HP L3 HP L3 HP     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     HP_L3_1.fq.gz HP_L3_2.fq.gz fastq fastq 6481773600.0 21605912.0 HP L3 1.fq.gz 0:150 1:150 A:1822457830;C:1426224217;G:1433346356;T:1799447632;N:297565 150 150     1822457830 1426224217 1433346356 1799447632 297565 SRX26610546 SRS23109427 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34117 34117 SRR31230230 SRX26610545 SRS23109426 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         HP L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:HP|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data HP L2 HP L2 HP     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     HP_L2_1.fq.gz HP_L2_2.fq.gz fastq fastq 6483969900.0 21613233.0 HP L2 1.fq.gz 0:150 1:150 A:1858850647;C:1400634811;G:1393756557;T:1830424227;N:303658 150 150     1858850647 1400634811 1393756557 1830424227 303658 SRX26610545 SRS23109426 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34118 34118 SRR31230231 SRX26610544 SRS23109422 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         HP L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:HP|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data HP L1 HP L1 HP     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     HP_L1_1.fq.gz HP_L1_2.fq.gz fastq fastq 6270987900.0 20903293.0 HP L1 1.fq.gz 0:150 1:150 A:1761336291;C:1386332040;G:1384745780;T:1738282105;N:291684 150 150     1761336291 1386332040 1384745780 1738282105 291684 SRX26610544 SRS23109422 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34119 34119 SRR31230232 SRX26610543 SRS23109425 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         MT L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:MT|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data MT L3 MT L3 MT     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     MT_L3_1.fq.gz MT_L3_2.fq.gz fastq fastq 6641395500.0 22137985.0 MT L3 1.fq.gz 0:150 1:150 A:1870037050;C:1459746735;G:1464312013;T:1846983464;N:316238 150 150     1870037050 1459746735 1464312013 1846983464 316238 SRX26610543 SRS23109425 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34120 34120 SRR31230233 SRX26610542 SRS23109421 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         MT L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:MT|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data MT L2 MT L2 MT     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     MT_L2_1.fq.gz MT_L2_2.fq.gz fastq fastq 6735230400.0 22450768.0 MT L2 1.fq.gz 0:150 1:150 A:1884876161;C:1494102137;G:1499635722;T:1856320830;N:295550 150 150     1884876161 1494102137 1499635722 1856320830 295550 SRX26610542 SRS23109421 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34121 34121 SRR31230234 SRX26610541 SRS23109424 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         MT L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:MT|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data MT L1 MT L1 MT     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     MT_L1_1.fq.gz MT_L1_2.fq.gz fastq fastq 6382458300.0 21274861.0 MT L1 1.fq.gz 0:150 1:150 A:1811407290;C:1396361259;G:1388659914;T:1785732773;N:297064 150 150     1811407290 1396361259 1388659914 1785732773 297064 SRX26610541 SRS23109424 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34122 34122 SRR31230235 SRX26610540 SRS23109423 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         NC L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:Control|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data NC L3 NC L3 control     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     NC_L3_1.fq.gz NC_L3_2.fq.gz fastq fastq 6815267400.0 22717558.0 NC L3 1.fq.gz 0:150 1:150 A:1909187573;C:1516756161;G:1522759558;T:1866449373;N:114735 150 150     1909187573 1516756161 1522759558 1866449373 114735 SRX26610540 SRS23109423 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34123 34123 SRR31230236 SRX26610539 SRS23109419 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         TF L3   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:TF|Replicate:3|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data TF L3 TF L3 TF     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     TF_L3_1.fq.gz TF_L3_2.fq.gz fastq fastq 6547426200.0 21824754.0 TF L3 1.fq.gz 0:150 1:150 A:1829107582;C:1450999468;G:1461503884;T:1805507445;N:307821 150 150     1829107582 1450999468 1461503884 1805507445 307821 SRX26610539 SRS23109419 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34124 34124 SRR31230237 SRX26610538 SRS23109420 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         TF L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:TF|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data TF L2 TF L2 TF     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     TF_L2_1.fq.gz TF_L2_2.fq.gz fastq fastq 6327866400.0 21092888.0 TF L2 1.fq.gz 0:150 1:150 A:1792246492;C:1386064311;G:1383369731;T:1765884262;N:301604 150 150     1792246492 1386064311 1383369731 1765884262 301604 SRX26610538 SRS23109420 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34125 34125 SRR31230238 SRX26610537 SRS23109418 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         NC L2   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:Control|Replicate:2|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data NC L2 NC L2 control     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     NC_L2_1.fq.gz NC_L2_2.fq.gz fastq fastq 6779235000.0 22597450.0 NC L2 1.fq.gz 0:150 1:150 A:1908783350;C:1490731242;G:1502686284;T:1876708170;N:325954 150 150     1908783350 1490731242 1502686284 1876708170 325954 SRX26610537 SRS23109418 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
34126 34126 SRR31230239 SRX26610536 SRS23109417 SRP543263 PRJNA1182301 Zebrafish Transcriptome data PRJNA1182301 Other Improving symptoms of light induced anxiety like insomnia in a zebrafish model.         NC L1   breed:Danio rerio|age:3 days|collection date:2022 10|geo loc name:not collected|sex:mixed|tissue:whole body|treatment:Control|Replicate:1|BioSampleModel:Model organism or animal                 Zebrafish Transcriptome data NC L1 NC L1 control     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 1500   SRP543263     NC_L1_1.fq.gz NC_L1_2.fq.gz fastq fastq 6318379500.0 21061265.0 NC L1 1.fq.gz 0:150 1:150 A:1785873867;C:1385813719;G:1388477232;T:1757923663;N:291019 150 150     1785873867 1385813719 1388477232 1757923663 291019 SRX26610536 SRS23109417 SRA2005827 Shanghai Ocean University|College of Food Science & Technology Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-11-05 Larval Larval Trunk Surface Structure
41511 41511 SRR5004963 SRX2336797 SRS1790193 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   zebrafish embryos ythdf2 RIP rep2 GSM2386192   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk zebrafish embryos ythdf2 RIP rep2 Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software zebrafish embryos   For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386192 GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq GSM2386192   1 For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386192 RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz fastq fastq 4007024510.0 19836755.0 GSM2386192 r1 0:101 1:101 A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309 101 101     769487104 1245093129 1251328145 740377823 738309 SRX2336797 SRS1790193 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.97768 0.97802 0.22786 0.21743 0.89885 0.89968 0.77584 0.83808 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41512 41512 SRR5004962 SRX2336796 SRS1790194 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   zebrafish embryos ythdf2 RIP rep1 GSM2386191   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk zebrafish embryos ythdf2 RIP rep1 Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software zebrafish embryos   For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386191 GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq GSM2386191   1 For RIP seq RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386191 RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP092907     ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz fastq fastq 6144583662.0 30418731.0 GSM2386191 r1 0:101 1:101 A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305 101 101     1227614258 1869131844 1825793436 1220118819 1925305 SRX2336796 SRS1790194 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.96857 0.96917 0.23397 0.22377 0.89832 0.90147 0.78619 0.8258 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41521 41521 SRR5004953 SRX2336787 SRS1790184 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   mettl3 morphant zebrafish embryos m6A IP rep2 GSM2386182   source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems mettl3 morphant zebrafish embryos m6A IP rep2 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386182 GSM2386182: mettl3 morphant zebrafish embryos m6A IP rep2; Danio rerio; OTHER GSM2386182   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386182 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     mettl3-mo_IP_rep2_1.fastq.gz mettl3-mo_IP_rep2_2.fastq.gz fastq fastq 12246129204.0 60624402.0 GSM2386182 r1 0:101 1:101 A:3253814653;C:2887966071;G:2921051332;T:3179545005;N:3752143 101 101     3253814653 2887966071 2921051332 3179545005 3752143 SRX2336787 SRS1790184 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.93906 0.94462 0.08073 0.07972 0.69148 0.69394 0.43224 0.48778 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41522 41522 SRR5004952 SRX2336785 SRS1790183 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   mettl3 morphant zebrafish embryos m6A IP rep1 GSM2386181   source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems mettl3 morphant zebrafish embryos m6A IP rep1 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.   genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386181 GSM2386181: mettl3 morphant zebrafish embryos m6A IP rep1; Danio rerio; OTHER GSM2386181   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp. GEO Accession:GSM2386181 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     mettl3-mo_IP_rep1_1.fastq.gz mettl3-mo_IP_rep1_2.fastq.gz fastq fastq 22767872412.0 75390306.0 GSM2386181 r1 0:151 1:151 A:6356270201;C:5175380564;G:5545741592;T:5686194578;N:4285477 151 151     6356270201 5175380564 5545741592 5686194578 4285477 SRX2336785 SRS1790183 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.94647 0.95162 0.07314 0.07248 0.70796 0.71021 0.54859 0.54624 151 151 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41523 41523 SRR5004951 SRX2336784 SRS1790182 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos input rep2 GSM2386180   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk control zebrafish embryos input rep2 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386180 GSM2386180: control zebrafish embryos input rep2; Danio rerio; OTHER GSM2386180   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386180 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_input_rep2_1.fastq.gz control_input_rep2_2.fastq.gz fastq fastq 20629042748.0 102123974.0 GSM2386180 r1 0:101 1:101 A:5541548211;C:4810650367;G:4699999124;T:5571342766;N:5502280 101 101     5541548211 4810650367 4699999124 5571342766 5502280 SRX2336784 SRS1790182 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.94898 0.9511 0.10842 0.10266 0.70465 0.70481 0.4986 0.48915 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41524 41524 SRR5004950 SRX2336783 SRS1790181 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos input rep1 GSM2386179   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk control zebrafish embryos input rep1 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk GSM2386179 GSM2386179: control zebrafish embryos input rep1; Danio rerio; OTHER GSM2386179   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp. GEO Accession:GSM2386179 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_input_rep1_1.fastq.gz control_input_rep1_2.fastq.gz fastq fastq 27776308060.0 91974530.0 GSM2386179 r1 0:151 1:151 A:7467418896;C:6517753701;G:6333567394;T:7452805069;N:4763000 151 151     7467418896 6517753701 6333567394 7452805069 4763000 SRX2336783 SRS1790181 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.95616 0.95939 0.10401 0.09776 0.72263 0.73637 0.57906 0.58185 151 151 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41525 41525 SRR5004949 SRX2336782 SRS1790180 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos m6A IP rep2 GSM2386178   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems control zebrafish embryos m6A IP rep2 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386178 GSM2386178: control zebrafish embryos m6A IP rep2; Danio rerio; OTHER GSM2386178   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. GEO Accession:GSM2386178 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_IP_rep2_1.fastq.gz control_IP_rep2_2.fastq.gz fastq fastq 11899573964.0 58908782.0 GSM2386178 r1 0:101 1:101 A:3146907590;C:2817914269;G:2838718195;T:3092392965;N:3640945 101 101     3146907590 2817914269 2838718195 3092392965 3640945 SRX2336782 SRS1790180 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.93821 0.94281 0.08361 0.08174 0.69676 0.69816 0.4628 0.46386 101 101 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41526 41526 SRR5004948 SRX2336781 SRS1790179 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos m6A IP rep1 GSM2386177   source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems control zebrafish embryos m6A IP rep1 Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: m6A peak locus.xls: m6A peaks indentified by macs2 software Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples zebrafish embryos   For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp.   genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Synaptic Systems GSM2386177 GSM2386177: control zebrafish embryos m6A IP rep1; Danio rerio; OTHER GSM2386177   1 For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 151 bp. GEO Accession:GSM2386177 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     control_IP_rep1_1.fastq.gz control_IP_rep1_2.fastq.gz fastq fastq 16582066208.0 54907504.0 GSM2386177 r1 0:151 1:151 A:4529890968;C:3812739433;G:4031512714;T:4204817283;N:3105810 151 151     4529890968 3812739433 4031512714 4204817283 3105810 SRX2336781 SRS1790179 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.93701 0.95377 0.07009 0.07008 0.70972 0.71173 0.54711 0.54995 151 151 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk bulk bulk   China 2016-11-08 Pharyngula Embryo Trunk Surface Structure
41527 41527 SRR5441898 SRX2731753 SRS2119651 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos m6A miCLIP rep2 GSM2572320   source name:zebrafish embryos|cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam control zebrafish embryos m6A miCLIP rep2 library strategy: miCLIP seq Reads were trimmed for adaptor sequence using fastx clipper from FASTX Toolkit fastx clipper a AGATCGGAAGAGCACACG n Q 33. Low quality bases were filtered by fastq filter.pl a custom perl script from CLIP Tool Kit CTK and reads shorter than 24 nt would be discard. The forward reads were demultiplexed based on 5’ barcodes for individual replicates by fastq2collapse.pl to remove PCR amplified reads. The reverse reads were reversed complemented and processed like their forward mates. And then paired end reads were mixed for downstream analysis. Random barcodes of remained reads were stripped by stripBarcode.pl. Then the barcode sequence was moved to header line for each read. Remained reads were mapped to the zebrafish genomes version zv9 with BWA v0.7.10. The CIMS pipeline https://zhanglab.c2b2.columbia.edu/index.php/CTK Documentation was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage k and the number of mutation m for each nucleotide. The filter for the dataset was k >= 15 and m/k <= 50% and only mutation positions within RRACH motif were identified as m6A for downstream analysis to exclude the potential m6Am modification. Genome build: zv9 Supplementary files format and content: Single nucleotide resolution m6A sites identified by CIMS software. zebrafish embryos   For miCLIP seq mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam GSM2572320 GSM2572320: control zebrafish embryos m6A miCLIP rep2; Danio rerio; OTHER GSM2572320   1 For miCLIP seq mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq2000 or HiSeq3000 Illumina in single read or paired read mode creating reads with a length of 101 bp GEO Accession:GSM2572320 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     miCLIP_Abcam_rep2_1.fastq.gz miCLIP_Abcam_rep2_2.fastq.gz fastq fastq 5381144865.0 26771865.0 GSM2572320 r1 0:101 1:100 A:1590037266;C:1121098903;G:1187084038;T:1482144584;N:780074 101 100     1590037266 1121098903 1187084038 1482144584 780074 SRX2731753 SRS2119651 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.55442 0.60543 0.10037 0.11559 0.75432 0.747 0.55512 0.44818 101 100 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk clip iclip   China 2017-04-10 Pharyngula Embryo Trunk Surface Structure
41528 41528 SRR5441897 SRX2731752 SRS2119650 SRP092907 PRJNA352850 Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos GSE89655 Other RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells   pubmed:28869969   control zebrafish embryos m6A miCLIP rep1 GSM2572319   source name:zebrafish embryos|cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam control zebrafish embryos m6A miCLIP rep1 library strategy: miCLIP seq Reads were trimmed for adaptor sequence using fastx clipper from FASTX Toolkit fastx clipper a AGATCGGAAGAGCACACG n Q 33. Low quality bases were filtered by fastq filter.pl a custom perl script from CLIP Tool Kit CTK and reads shorter than 24 nt would be discard. The forward reads were demultiplexed based on 5’ barcodes for individual replicates by fastq2collapse.pl to remove PCR amplified reads. The reverse reads were reversed complemented and processed like their forward mates. And then paired end reads were mixed for downstream analysis. Random barcodes of remained reads were stripped by stripBarcode.pl. Then the barcode sequence was moved to header line for each read. Remained reads were mapped to the zebrafish genomes version zv9 with BWA v0.7.10. The CIMS pipeline https://zhanglab.c2b2.columbia.edu/index.php/CTK Documentation was used to collapse PCR duplicates based on their mapped coordinates and to determine the unique tag coverage k and the number of mutation m for each nucleotide. The filter for the dataset was k >= 15 and m/k <= 50% and only mutation positions within RRACH motif were identified as m6A for downstream analysis to exclude the potential m6Am modification. Genome build: zv9 Supplementary files format and content: Single nucleotide resolution m6A sites identified by CIMS software. zebrafish embryos   For miCLIP seq mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp.   cell type:normal zebrafish embryos cells|age:28hpf|tissue:trunk|enrichment antibody vendor:Abcam GSM2572319 GSM2572319: control zebrafish embryos m6A miCLIP rep1; Danio rerio; OTHER GSM2572319   1 For miCLIP seq mRNA was isolate from the trunck region of zebrafish embryos at 28hpf and the RNA integrity was checked using an Agilent Bioanalyzer 2100. 10 ug of mRNA was first fragmented and immunoprecipitated with m6A antibody and thus obtained m6A containing RNA was subjected to cDNA library construction according to previously reported method [Linder et al. 2015; PMID: 26121403]. The libraries were sequenced using HiSeq2000 or HiSeq3000 Illumina in single read or paired read mode creating reads with a length of 101 bp GEO Accession:GSM2572319 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   SRP092907     miCLIP_Abcam_rep1_1.fastq.gz miCLIP_Abcam_rep1_2.fastq.gz fastq fastq 6036174318.0 30030718.0 GSM2572319 r1 0:101 1:100 A:1726466495;C:1297674104;G:1364186585;T:1647084426;N:762708 101 100     1726466495 1297674104 1364186585 1647084426 762708 SRX2731752 SRS2119650 SRA491654 GEO Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) 2 0.5985 0.66835 0.09404 0.1086 0.74491 0.73596 0.54343 0.45047 101 100 B B biological fallback assumption illumina hiseq_era unknown other trueseq bulk clip iclip   China 2017-04-10 Pharyngula Embryo Trunk Surface Structure
43983 43983 SRR6811832 SRX3768872 SRS3023386 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva F1 2 scar GSM3032175   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva F1 2 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032175 GSM3032175: Larva F1 2 scar; Danio rerio; OTHER GSM3032175   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032175 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     F1_2_scar_R1.fastq.gz F1_2_scar_R2.fastq.gz fastq fastq 9301928572.0 75015553.0 GSM3032175 r1 0:26 1:98 A:2682085389;C:3008788535;G:2093169318;T:1516220703;N:1664627 26 98     2682085389 3008788535 2093169318 1516220703 1664627 SRX3768872 SRS3023386 SRA623333 GEO Max Delbrück Center 2 0.0001 0.00173 4e-05 8e-05 0.99983 0.99667 0.33333 0.531 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43984 43984 SRR6811831 SRX3768871 SRS3023388 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva F1 1 scar GSM3032174   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva F1 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032174 GSM3032174: Larva F1 1 scar; Danio rerio; OTHER GSM3032174   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032174 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     F1_1_scar_R1.fastq.gz F1_1_scar_R2.fastq.gz fastq fastq 7772713576.0 62683174.0 GSM3032174 r1 0:26 1:98 A:2222016153;C:2555237987;G:1722216404;T:1271855931;N:1387101 26 98     2222016153 2555237987 1722216404 1271855931 1387101 SRX3768871 SRS3023388 SRA623333 GEO Max Delbrück Center 2 0.00014 0.00171 8e-05 0.00012 0.99985 0.99642 0.44444 0.45454 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43991 43991 SRR6811824 SRX3768864 SRS3023381 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 5 scar GSM3032167   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 5 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032167 GSM3032167: Larva 5 scar; Danio rerio; OTHER GSM3032167   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032167 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z5_scar_R1.fastq.gz Z5_scar_R2.fastq.gz fastq fastq 7672645700.0 61876175.0 GSM3032167 r1 0:26 1:98 A:2173948352;C:2439410929;G:1714624642;T:1343296377;N:1365400 26 98     2173948352 2439410929 1714624642 1343296377 1365400 SRX3768864 SRS3023381 SRA623333 GEO Max Delbrück Center 2 0.00013 0.00164 9e-05 8e-05 0.99989 0.99669 0.83333 0.4918 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
43992 43992 SRR6811823 SRX3768863 SRS3023380 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 4 scar GSM3032166   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 4 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM3032166 GSM3032166: Larva 4 scar; Danio rerio; OTHER GSM3032166   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM3032166 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z4_scar_R1.fastq.gz Z4_scar_R2.fastq.gz fastq fastq 7236183804.0 58356321.0 GSM3032166 r1 0:26 1:98 A:2080254513;C:2296727471;G:1625115068;T:1232786300;N:1300452 26 98     2080254513 2296727471 1625115068 1232786300 1300452 SRX3768863 SRS3023380 SRA623333 GEO Max Delbrück Center 2 0.00014 0.0016 0.00011 7e-05 0.99993 0.99634 0.33333 0.46694 26 98 T T mates < 9% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2018-03-06 Larval Larval Trunk Surface Structure
44013 44013 SRR6211477 SRX3320753 SRS2626327 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 1 scar GSM2830049   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830049 GSM2830049: Larva 1 scar; Danio rerio; OTHER GSM2830049   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830049 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z2_1_scar_R1.fastq.gz Z2_1_scar_R2.fastq.gz Z2_1_scar_R3.fastq.gz fastq fastq fastq 1358915680.0 8493223.0 GSM2830049 r1 0:130 1:14 2:16 A:286107087;C:390283378;G:268551180;T:159171790;N:5555 130 14 16   286107087 390283378 268551180 159171790 5555 SRX3320753 SRS2626327 SRA623333 GEO Max Delbrück Center 1 0.00515   8e-05   0.99959   0.24561   130   T   under 1.2% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
44014 44014 SRR6211478 SRX3320753 SRS2626327 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Larva 1 scar GSM2830049   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva Larva 1 scar Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight tim… Full organism   Single cell dissociation. 10X Genomics Chromium   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva GSM2830049 GSM2830049: Larva 1 scar; Danio rerio; OTHER GSM2830049   1 Single cell dissociation. 10X Genomics Chromium GEO Accession:GSM2830049 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP121343     Z2_2_scar_R1.fastq.gz Z2_2_scar_R2.fastq.gz Z2_2_scar_R3.fastq.gz fastq fastq fastq 1103410080.0 6896313.0 GSM2830049 r2 0:130 1:14 2:16 A:232542409;C:315925727;G:218437491;T:129610895;N:4168 130 14 16   232542409 315925727 218437491 129610895 4168 SRX3320753 SRS2626327 SRA623333 GEO Max Delbrück Center 1 0.00786   0.0   0.99922   0.31764   130   T   under 1.2% mapping rate illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   Germany 2017-10-24 Larval Larval Trunk Surface Structure
44015 44015 SRR6211474 SRX3320751 SRS2626325 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Time course 10h24h mRNA GSM2830047   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h 24h Time course 10h24h mRNA Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1 2 3 4 6 8 10 and 24 hours 2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample we calculated the percentage of unscarred RFP. We fit a negative exponential to this data assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode. Full organism   Trizol extraction of RNA. CEL seq   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h 24h GSM2830047 GSM2830047: Time course 10h24h mRNA; Danio rerio; OTHER GSM2830047   1 Trizol extraction of RNA. CEL seq GEO Accession:GSM2830047 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     dyn_RNA_10h24h_S13_R2_001.fastq.gz dyn_RNA_10h24h_S13_R1_001.fastq.gz fastq fastq 1456176300.0 9707842.0 GSM2830047 r1 0:100 1:50 A:216943159;C:398650961;G:516656316;T:323899428;N:26436 100 50     216943159 398650961 516656316 323899428 26436 SRX3320751 SRS2626325 SRA623333 GEO Max Delbrück Center 2 3e-05 0.00111 0.0 0.0011 0.99995 1.0 0.75   100 50 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_plate celseq   Germany 2017-10-24 Undetermined Embryo Trunk Surface Structure
44016 44016 SRR6211473 SRX3320750 SRS2626324 SRP121343 PRJNA415636 Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars GSE106121 Other A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.   pubmed:29644996   Time course 3h6h8h mRNA GSM2830046   source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:3h 6h 8h Time course 3h6h8h mRNA Library strategy: Targeted amplification Embryos were injected with Cas9 and sgRNA at the 1 cell stage. post 1 2 3 4 6 8 10 and 24 hours 2 3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample we calculated the percentage of unscarred RFP. We fit a negative exponential to this data assuming that the fraction of unscarred RFP at t=0 was one. Genome build: N/A Supplementary files format and content: List of scar sequences with CIGAR and cell barcode. Full organism   Trizol extraction of RNA. CEL seq   strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:3h 6h 8h GSM2830046 GSM2830046: Time course 3h6h8h mRNA; Danio rerio; OTHER GSM2830046   1 Trizol extraction of RNA. CEL seq GEO Accession:GSM2830046 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP121343     dyn_RNA_3h6h8h_S12_R1_001.fastq.gz dyn_RNA_3h6h8h_S12_R2_001.fastq.gz fastq fastq 1382400000.0 9216000.0 GSM2830046 r1 0:100 1:50 A:219040774;C:378529638;G:475287684;T:309516830;N:25074 100 50     219040774 378529638 475287684 309516830 25074 SRX3320750 SRS2626324 SRA623333 GEO Max Delbrück Center 2 5e-05 0.00116 0.0 0.00115 0.99987 1.0 0.5   100 50 T T mates < 9% mapping rate illumina nextseq unknown other unknown sc single_cell_plate celseq   Germany 2017-10-24 Undetermined Embryo Trunk Surface Structure
60021 60021 SRR12103084 SRX8627422 SRS6915731 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         SCI IP   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI IP|BioSampleModel:Model organism or animal                 IP library sequencing data of treated sample SCIIP BKDL192540807 1a SCIIP BKDL192540807 1a IP library sequencing data of treated sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz fastq fastq 7110503700.0 23701679.0 SCIIP BKDL192540807 1a 1.fq.gz 0:150 1:150 A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903 150 150     1520693228 1953670419 2215620460 1420407690 111903 SRX8627422 SRS6915731 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.9115 0.9147 0.19936 0.2033 0.81864 0.81919 0.66838 0.6677 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
60022 60022 SRR12103085 SRX8627421 SRS6915730 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         SCI Input   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI Input|BioSampleModel:Model organism or animal                 Input library sequencing data of treated sample SCIIN BKDL192540809 1a SCIIN BKDL192540809 1a Input library sequencing data of treated sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz fastq fastq 7774587300.0 25915291.0 SCIIN BKDL192540809 1a 1.fq.gz 0:150 1:150 A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571 150 150     1595151855 2243828590 2397611978 1537918306 76571 SRX8627421 SRS6915730 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.96018 0.96291 0.23754 0.23744 0.84904 0.85245 0.74661 0.74738 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
60023 60023 SRR12103086 SRX8627420 SRS6915729 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         Control IP   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control IP|BioSampleModel:Model organism or animal                 IP library sequencing data of control sample controlIP BKDL192540808 1a controlIP BKDL192540808 1a IP library sequencing data of control sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz fastq fastq 7359972600.0 24533242.0 controlIP BKDL192540808 1a 1.fq.gz 0:150 1:150 A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639 150 150     1569051886 2002692591 2333418000 1454676484 133639 SRX8627420 SRS6915729 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.92004 0.92293 0.20272 0.20739 0.83254 0.83291 0.68471 0.65224 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
60024 60024 SRR12103087 SRX8627419 SRS6915728 SRP269070 PRJNA642405 Changes of m6A RNA methylation following spinal cord injury PRJNA642405 Other Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury         Control Input   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control Input|BioSampleModel:Model organism or animal                 Input library sequencing data of control sample controlIN BKDL192540810 1a controlIN BKDL192540810 1a Input library sequencing data of control sample     RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP269070     controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz fastq fastq 7830123600.0 26100412.0 controlIN BKDL192540810 1a 1.fq.gz 0:150 1:150 A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635 150 150     1589371287 2296547915 2409439612 1534684151 80635 SRX8627419 SRS6915728 SRA1091926 Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and Nantong University 2 0.97501 0.97626 0.23177 0.23578 0.89497 0.8971 0.78501 0.77674 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-06-28 Undetermined Larval Trunk Surface Structure
61422 61422 SRR12744939 SRX9217396 SRS7451218 SRP285861 PRJNA666534 Transcriptomic analysis of the developmental toxicity of microplastics in zebrafish PRJNA666534 Other This project was conduceted to explore the molecular mechanisms underlying the bioaccumulation depuration and developmental toxicity and immune dysfunction of microplastics in zebrafish larvae which provides novel insights into the ecological risks of MPs fragments.         PA H2O2 HA   strain:AB|dev stage:9 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish PA H2O2 HA PA H2O2 HA mRNA of zebrafish tissue     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP285861     PA_H2O2_HA.R1.fastq.gz PA_H2O2_HA.R2.fastq.gz fastq fastq 7307814724.0 24198062.0 PA H2O2 HA.R1.fastq.gz 0:151 1:151 A:1916647803;C:1726826237;G:1763771127;T:1900498448;N:71109 151 151     1916647803 1726826237 1763771127 1900498448 71109 SRX9217396 SRS7451218 SRA1135893 Henan Normal University|College of Environment Henan Normal University 2 0.94168 0.91408 0.0715 0.06936 0.6872 0.69163 0.46735 0.47262 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-09-30 Larval Larval Trunk Surface Structure
61423 61423 SRR12744940 SRX9217395 SRS7451217 SRP285861 PRJNA666534 Transcriptomic analysis of the developmental toxicity of microplastics in zebrafish PRJNA666534 Other This project was conduceted to explore the molecular mechanisms underlying the bioaccumulation depuration and developmental toxicity and immune dysfunction of microplastics in zebrafish larvae which provides novel insights into the ecological risks of MPs fragments.         PA   strain:AB|dev stage:8 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish PA PA mRNA of zebrafish tissue     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP285861     PA.R1.fastq.gz PA.R2.fastq.gz fastq fastq 7677365782.0 25421741.0 PA.R1.fastq.gz 0:151 1:151 A:2003403761;C:1825346100;G:1859847851;T:1988694897;N:73173 151 151     2003403761 1825346100 1859847851 1988694897 73173 SRX9217395 SRS7451217 SRA1135893 Henan Normal University|College of Environment Henan Normal University 2 0.94287 0.91685 0.06205 0.06006 0.6882 0.69234 0.45133 0.46041 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-09-30 Larval Larval Trunk Surface Structure
61424 61424 SRR12744941 SRX9217394 SRS7451216 SRP285861 PRJNA666534 Transcriptomic analysis of the developmental toxicity of microplastics in zebrafish PRJNA666534 Other This project was conduceted to explore the molecular mechanisms underlying the bioaccumulation depuration and developmental toxicity and immune dysfunction of microplastics in zebrafish larvae which provides novel insights into the ecological risks of MPs fragments.         CK   strain:AB|dev stage:7 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish CK CK mRNA of zebrafish tissue     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP285861     CK.R1.fastq.gz CK.R2.fastq.gz fastq fastq 7117128904.0 23566652.0 CK.R1.fastq.gz 0:151 1:151 A:1891245951;C:1659968846;G:1695470010;T:1870375334;N:68763 151 151     1891245951 1659968846 1695470010 1870375334 68763 SRX9217394 SRS7451216 SRA1135893 Henan Normal University|College of Environment Henan Normal University 2 0.93863 0.9111 0.08559 0.08339 0.68909 0.69461 0.46599 0.46482 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-09-30 Larval Larval Trunk Surface Structure
66757 66757 SRR23717090 SRX19578259 SRS16961241 SRP342737 PRJNA773778 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq] GSE186425 Other Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. parent bioproject:PRJNA773771 pubmed:37016019   DP1 36hpf GSM7083138   source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing DP1 36hpf For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq Zebrafish trunk region   For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…   tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf GSM7083138 GSM7083138: DP1 36hpf; Danio rerio; OTHER GSM7083138 r1 GSM7083138 1 For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342737     36hpf-DP1_FKDL202627688-1a_1.raw.fq.gz 36hpf-DP1_FKDL202627688-1a_2.raw.fq.gz fastq fastq 36641999100.0 122139997.0 GSM7083138 r1 0:150 1:150 A:11840633171;C:5285812067;G:6638992204;T:12876249105;N:312553 150 150     11840633171 5285812067 6638992204 12876249105 312553 SRX19578259 SRS16961241 SRA1600575 Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES 2 0.8912 0.01571 0.09673 0.00653 0.86145 0.99849 0.61834 0.72033 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-03-06 Pharyngula Embryo Trunk Surface Structure
66758 66758 SRR23717091 SRX19578258 SRS16961240 SRP342737 PRJNA773778 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq] GSE186425 Other Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. parent bioproject:PRJNA773771 pubmed:37016019   DP2 36hpf GSM7083139   source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing DP2 36hpf For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq Zebrafish trunk region   For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…   tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf GSM7083139 GSM7083139: DP2 36hpf; Danio rerio; OTHER GSM7083139 r1 GSM7083139 1 For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342737     36hpf-DP2_FKDL202627692-1a_1.raw.fq.gz 36hpf-DP2_FKDL202627692-1a_2.raw.fq.gz fastq fastq 45339599100.0 151131997.0 GSM7083139 r1 0:150 1:150 A:14092451998;C:7125629842;G:9985822921;T:14135305628;N:388711 150 150     14092451998 7125629842 9985822921 14135305628 388711 SRX19578258 SRS16961240 SRA1600575 Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES 2 0.79702 0.00323 0.08737 0.00105 0.88663 0.99882 0.62618 0.6 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-03-06 Pharyngula Embryo Trunk Surface Structure
66759 66759 SRR23717092 SRX19578257 SRS16961239 SRP342737 PRJNA773778 Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.STRT seq] GSE186425 Other Using a combination of single cell multi omics lineage tracing and functional assays we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population but where and how HSPC heterogeneity occurs remain unclear. Here we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1 kdrl+runx1+ and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency we performed scRNA seq with the sorted ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. parent bioproject:PRJNA773771 pubmed:37016019   SP 36hpf GSM7083140   source name:Zebrafish trunk region|tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf loc name:missing|collection date:missing SP 36hpf For scRNA seq and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters using the GRCz11 reference genome. For STRT seq raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates MACS2 was used for the peak calling. Assembly: GRCz11 Library strategy: STRT seq Zebrafish trunk region   For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepared according to Hyp…   tissue:Zebrafish trunk region 36hpf|cells:single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells|Stage:36 hpf GSM7083140 GSM7083140: SP 36hpf; Danio rerio; OTHER GSM7083140 r1 GSM7083140 1 For 10x Genomics based scRNA seq and scATAC seq in zebrafish 40 000 mCherry+ GFP cells 40 000 mCherry+ GFP+ cells and 30 000 mCherry GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish ECs kdrl+runx1 HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG libraries were prepare…   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP342737     36hpf-SP_FKDL202627693-1a_1.raw.fq.gz 36hpf-SP_FKDL202627693-1a_2.raw.fq.gz fastq fastq 44757872400.0 149192908.0 GSM7083140 r1 0:150 1:150 A:13194662551;C:6817138207;G:9879151250;T:14866177703;N:742689 150 150     13194662551 6817138207 9879151250 14866177703 742689 SRX19578257 SRS16961239 SRA1600575 Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES 2 0.7854 0.00221 0.062 0.00084 0.90995 0.99904 0.43661 0.67741 150 150 B T mate2 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-03-06 Pharyngula Embryo Trunk Surface Structure
74097 74097 SRR23433707 SRX19347585 SRS16745103 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt input rep2 GSM7039976   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing mt input rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1 GSM7039976 GSM7039976: mt input rep2; Danio rerio; RIP Seq GSM7039976 r1 GSM7039976 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz fastq fastq 11987520719.0 46102921.0 GSM7039976 r1 0:129.98 1:130.04 A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407 129 130     2818961833 3185310727 3125514774 2857679978 53407 SRX19347585 SRS16745103 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92498 0.92723 0.26901 0.26318 0.72691 0.72646 0.55297 0.56674 103 103 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74098 74098 SRR23433708 SRX19347584 SRS16745102 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt IP rep2 GSM7039975   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing mt IP rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A GSM7039975 GSM7039975: mt IP rep2; Danio rerio; RIP Seq GSM7039975 r1 GSM7039975 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz fastq fastq 10153956215.0 38248544.0 GSM7039975 r1 0:132.74 1:132.73 A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740 132 132     2745473943 2337991849 2337827470 2732618213 44740 SRX19347584 SRS16745102 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.91716 0.92124 0.17169 0.17213 0.69057 0.69092 0.45478 0.4582 133 133 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74099 74099 SRR23433709 SRX19347583 SRS16745101 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt input rep1 GSM7039974   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing mt input rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1 GSM7039974 GSM7039974: mt input rep1; Danio rerio; RIP Seq GSM7039974 r1 GSM7039974 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz fastq fastq 11979139891.0 42665152.0 GSM7039974 r1 0:140.37 1:140.40 A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416 140 140     3143624979 2854874515 2775482425 3204809556 348416 SRX19347583 SRS16745101 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.89189 0.90001 0.35263 0.34917 0.71058 0.70907 0.54777 0.55293 125 125 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74100 74100 SRR23433710 SRX19347582 SRS16745100 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   mt IP rep1 GSM7039973   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing mt IP rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A GSM7039973 GSM7039973: mt IP rep1; Danio rerio; RIP Seq GSM7039973 r1 GSM7039973 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz fastq fastq 12145897814.0 43352862.0 GSM7039973 r1 0:140.09 1:140.07 A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089 140 140     3459248498 2615706052 2628261332 3442334843 347089 SRX19347582 SRS16745100 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.86681 0.87664 0.304 0.305 0.68012 0.67831 0.44055 0.4418 142 142 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74101 74101 SRR23433711 SRX19347581 SRS16745099 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling input rep2 GSM7039972   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing sibling input rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1 GSM7039972 GSM7039972: sibling input rep2; Danio rerio; RIP Seq GSM7039972 r1 GSM7039972 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz fastq fastq 12272791017.0 47579480.0 GSM7039972 r1 0:128.94 1:129.00 A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414 128 129     2905993856 3237323144 3186607999 2942811604 54414 SRX19347581 SRS16745099 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.92733 0.92947 0.27234 0.26711 0.72391 0.72409 0.52625 0.55052 126 126 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74102 74102 SRR23433712 SRX19347580 SRS16745098 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling IP rep2 GSM7039971   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing sibling IP rep2 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A GSM7039971 GSM7039971: sibling IP rep2; Danio rerio; RIP Seq GSM7039971 r1 GSM7039971 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz fastq fastq 10402768351.0 39113148.0 GSM7039971 r1 0:132.99 1:132.98 A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607 132 132     2806053427 2400476074 2403977422 2792214821 46607 SRX19347580 SRS16745098 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.90198 0.9063 0.18008 0.18091 0.69428 0.69396 0.44811 0.42925 147 147 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74103 74103 SRR23433713 SRX19347579 SRS16745097 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling input rep1 GSM7039970   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing sibling input rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1 GSM7039970 GSM7039970: sibling input rep1; Danio rerio; RIP Seq GSM7039970 r1 GSM7039970 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz fastq fastq 13094981449.0 46647417.0 GSM7039970 r1 0:140.35 1:140.37 A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966 140 140     3434495131 3120669719 3036482303 3502963330 370966 SRX19347579 SRS16745097 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.89276 0.90193 0.352 0.3489 0.70905 0.70719 0.52165 0.52427 142 142 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure
74104 74104 SRR23433714 SRX19347578 SRS16745096 SRP422577 PRJNA934472 Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq] GSE225136 Other The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16 an RNA methyltransferase identified recently is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16 and Mettl16 deficiency destabilizes mybl2b mRNA which is mediated by m6A reader Igf2bp1. Moreover we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and mettl16 / zebrafish embryos at 3 dpf for triplicates parent bioproject:PRJNA934075 pubmed:38605226   sibling IP rep1 GSM7039969   source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing sibling IP rep1 Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample trunk region of zebrafish embryos   Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A GSM7039969 GSM7039969: sibling IP rep1; Danio rerio; RIP Seq GSM7039969 r1 GSM7039969 1 Total RNA was isolated from the trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003 Synaptic Systems was applied for m6A immunoprecipitation. Then the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP422577   loader:fastq load.py sibling1_IP_R1.fastq.gz sibling1_IP_R2.fastq.gz fastq fastq 12317957591.0 43954374.0 GSM7039969 r1 0:140.17 1:140.08 A:3509912915;C:2650796924;G:2663699373;T:3493137659;N:410720 140 140     3509912915 2650796924 2663699373 3493137659 410720 SRX19347578 SRS16745096 SRA1590470 Huazhong University of Science and Technology Huazhong University of Science and Technology 2 0.87054 0.88058 0.30375 0.30421 0.67783 0.67584 0.44329 0.44327 142 142 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-02-12 Undetermined Embryo Trunk Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;