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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", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep1", "GSM2386191", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386191", "GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq", "GSM2386191", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos m6A IP rep2", "GSM2386182", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "mettl3 morphant zebrafish embryos m6A IP rep1", "GSM2386181", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "control zebrafish embryos input rep2", "GSM2386180", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386180", "GSM2386180: control zebrafish embryos input rep2; Danio rerio; OTHER", "GSM2386180", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "control zebrafish embryos input rep1", "GSM2386179", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386179", "GSM2386179: control zebrafish embryos input rep1; Danio rerio; OTHER", "GSM2386179", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "control zebrafish embryos m6A IP rep2", "GSM2386178", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "control zebrafish embryos m6A IP rep1", "GSM2386177", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 151 bp.", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "control zebrafish embryos m6A miCLIP rep2", "GSM2572320", null, "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\u2019 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", null, "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.", null, "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", null, "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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2017-04-10", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "control zebrafish embryos m6A miCLIP rep1", "GSM2572319", null, "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\u2019 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", null, "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.", null, "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", null, "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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2017-04-10", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva F1 2 scar", "GSM3032175", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032175", "GSM3032175: Larva F1 2 scar; Danio rerio; OTHER", "GSM3032175", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032175", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2682085389, 3008788535, 2093169318, 1516220703, 1664627, "SRX3768872", "SRS3023386", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva F1 1 scar", "GSM3032174", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032174", "GSM3032174: Larva F1 1 scar; Danio rerio; OTHER", "GSM3032174", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032174", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2222016153, 2555237987, 1722216404, 1271855931, 1387101, "SRX3768871", "SRS3023388", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 5 scar", "GSM3032167", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032167", "GSM3032167: Larva 5 scar; Danio rerio; OTHER", "GSM3032167", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032167", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2173948352, 2439410929, 1714624642, 1343296377, 1365400, "SRX3768864", "SRS3023381", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 4 scar", "GSM3032166", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032166", "GSM3032166: Larva 4 scar; Danio rerio; OTHER", "GSM3032166", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032166", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 2080254513, 2296727471, 1625115068, 1232786300, 1300452, "SRX3768863", "SRS3023380", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "Germany", "2018-03-06", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 1 scar", "GSM2830049", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830049", "GSM2830049: Larva 1 scar; Danio rerio; OTHER", "GSM2830049", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830049", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 286107087, 390283378, 268551180, 159171790, 5555, "SRX3320753", "SRS2626327", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.00515, null, 8e-05, null, 0.99959, null, 0.24561, null, 130, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Larva 1 scar", "GSM2830049", null, "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 times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.", "Full organism", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830049", "GSM2830049: Larva 1 scar; Danio rerio; OTHER", "GSM2830049", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830049", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 232542409, 315925727, 218437491, 129610895, 4168, "SRX3320753", "SRS2626327", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.00786, null, 0.0, null, 0.99922, null, 0.31764, null, 130, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Time course 10h24h mRNA", "GSM2830047", null, "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\u2019s 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", null, "Trizol extraction of RNA. CEL seq", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Embryo|time point:10h  24h", "GSM2830047", "GSM2830047: Time course 10h24h mRNA; Danio rerio; OTHER", "GSM2830047", null, "1", "Trizol extraction of RNA. CEL seq", "GEO Accession:GSM2830047", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 216943159, 398650961, 516656316, 323899428, 26436, "SRX3320751", "SRS2626325", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 3e-05, 0.00111, 0.0, 0.0011, 0.99995, 1.0, 0.75, null, 100, 50, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2017-10-24", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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.", null, "pubmed:29644996", null, "Time course 3h6h8h mRNA", "GSM2830046", null, "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\u2019s 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", null, "Trizol extraction of RNA. CEL seq", null, "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", null, "1", "Trizol extraction of RNA. CEL seq", "GEO Accession:GSM2830046", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 219040774, 378529638, 475287684, 309516830, 25074, "SRX3320750", "SRS2626324", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 5e-05, 0.00116, 0.0, 0.00115, 0.99987, 1.0, 0.5, null, 100, 50, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "celseq", null, "Germany", "2017-10-24", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, null, null, null, "SCI IP", null, "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", null, null, null, null, null, null, null, null, "IP library sequencing data of treated sample", "SCIIP BKDL192540807 1a", "SCIIP BKDL192540807 1a", "IP library sequencing data of treated sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "China", "2020-06-28", "Undetermined", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, null, "SCI Input", null, "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", null, null, null, null, null, null, null, null, "Input library sequencing data of treated sample", "SCIIN BKDL192540809 1a", "SCIIN BKDL192540809 1a", "Input library sequencing data of treated sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "China", "2020-06-28", "Undetermined", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, null, "Control IP", null, "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", null, null, null, null, null, null, null, null, "IP library sequencing data of control sample", "controlIP BKDL192540808 1a", "controlIP BKDL192540808 1a", "IP library sequencing data of control sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "China", "2020-06-28", "Undetermined", "Larval", "Trunk", "Surface Structure"], [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", null, null, null, null, "Control Input", null, "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", null, null, null, null, null, null, null, null, "Input library sequencing data of control sample", "controlIN BKDL192540810 1a", "controlIN BKDL192540810 1a", "Input library sequencing data of control sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "China", "2020-06-28", "Undetermined", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, null, "PA H2O2 HA", null, "strain:AB|dev stage:9 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish", "PA H2O2 HA", "PA H2O2 HA", "mRNA of zebrafish tissue", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP285861", null, null, "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, null, null, 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", null, "China", "2020-09-30", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, null, "PA", null, "strain:AB|dev stage:8 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish", "PA", "PA", "mRNA of zebrafish tissue", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP285861", null, null, "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, null, null, 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", null, "China", "2020-09-30", "Larval", "Larval", "Trunk", "Surface Structure"], [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.", null, null, null, null, "CK", null, "strain:AB|dev stage:7 dpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic analysis of the developmental toxicity of microplastics inzebrafish", "CK", "CK", "mRNA of zebrafish tissue", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP285861", null, null, "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, null, null, 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", null, "China", "2020-09-30", "Larval", "Larval", "Trunk", "Surface Structure"], [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", null, "DP1 36hpf", "GSM7083138", null, "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\uff0craw 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\u00a0\u2265 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", null, "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\u2019 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\u2019 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 Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "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 prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342737", null, null, "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, null, null, 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", null, "China", "2023-03-06", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "DP2 36hpf", "GSM7083139", null, "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\uff0craw 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\u00a0\u2265 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", null, "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\u2019 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\u2019 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 Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "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 prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342737", null, null, "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, null, null, 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", null, "China", "2023-03-06", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "SP 36hpf", "GSM7083140", null, "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\uff0craw 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\u00a0\u2265 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", null, "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\u2019 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\u2019 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 Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "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 prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342737", null, null, "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, null, null, 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", null, "China", "2023-03-06", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [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", null, "mt input rep2", "GSM7039976", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "mt IP  rep2", "GSM7039975", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "mt input rep1", "GSM7039974", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "mt IP  rep1", "GSM7039973", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "sibling input rep2", "GSM7039972", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "sibling IP  rep2", "GSM7039971", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "sibling input rep1", "GSM7039970", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [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", null, "sibling IP  rep1", "GSM7039969", null, "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 \u00d7 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", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "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 \u03bcg 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\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "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, null, null, 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", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 48, 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"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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_selection\" = :p0 and \"tissue_curation\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "other", "p1": "Trunk", "p2": "Surface Structure"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "OTHER", "label": "OTHER", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=OTHER", "selected": false}, {"value": "RNA-Seq", "label": "RNA-Seq", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "RIP-Seq", "label": "RIP-Seq", "count": 14, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=RIP-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "other", "label": "other", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Larval", "label": "Larval", "count": 25, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Larval", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Larval", "label": "Larval", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&devstage_curation=Larval", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 14, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&devstage_curation=Undetermined", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&devstage_curation=Pharyngula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "Trunk", "label": "Trunk", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Surface+Structure", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "results": [{"value": "unknown", "label": "unknown", "count": 27, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&technology=unknown", "selected": false}, {"value": "10x", "label": "10x", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&technology=10x", "selected": false}, {"value": "bulk", "label": "bulk", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&technology=bulk", "selected": false}, {"value": "celseq", "label": "celseq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&technology=celseq", "selected": false}, {"value": "iclip", "label": "iclip", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure&technology=iclip", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 84.20237700920552}