{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"unknown\" and tissue_curation = \"Tail\"", "rows": [[24854, "SRR25519420", "SRX21249697", "SRS18503946", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 4  3dpf", "GSM7681266", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681266", "GSM7681266: zebrafish  AR42 TFA 4  3dpf; Danio rerio; RNA Seq", "GSM7681266 r1", "GSM7681266", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_4.R1.fq.gz AR42_TFA_4.R2.fq.gz", "fastq fastq", 9896772900.0, 32989243.0, "GSM7681266 r1", "0:150 1:150", "A:2382403653;C:2457377213;G:2470646159;T:2586345875;N:0", 150, 150, null, null, 2382403653, 2457377213, 2470646159, 2586345875, 0, "SRX21249697", "SRS18503946", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70537, 0.88934, 0.03159, 0.04209, 0.78013, 0.75416, 0.50713, 0.45138, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24855, "SRR25519421", "SRX21249696", "SRS18503945", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 3  3dpf", "GSM7681265", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681265", "GSM7681265: zebrafish  AR42 TFA 3  3dpf; Danio rerio; RNA Seq", "GSM7681265 r1", "GSM7681265", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_3.R1.fq.gz AR42_TFA_3.R2.fq.gz", "fastq fastq", 10265927100.0, 34219757.0, "GSM7681265 r1", "0:150 1:150", "A:2473552302;C:2548535087;G:2562873160;T:2680966551;N:0", 150, 150, null, null, 2473552302, 2548535087, 2562873160, 2680966551, 0, "SRX21249696", "SRS18503945", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70516, 0.88765, 0.03163, 0.04168, 0.7782, 0.75083, 0.50851, 0.45305, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24856, "SRR25519422", "SRX21249695", "SRS18503944", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 2  3dpf", "GSM7681264", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681264", "GSM7681264: zebrafish  AR42 TFA 2  3dpf; Danio rerio; RNA Seq", "GSM7681264 r1", "GSM7681264", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_2.R2.fq.gz AR42_TFA_2.R1.fq.gz", "fastq fastq", 10003398900.0, 33344663.0, "GSM7681264 r1", "0:150 1:150", "A:2409580340;C:2483650756;G:2497057051;T:2613110753;N:0", 150, 150, null, null, 2409580340, 2483650756, 2497057051, 2613110753, 0, "SRX21249695", "SRS18503944", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70787, 0.89158, 0.03203, 0.04194, 0.77851, 0.75108, 0.5072, 0.45508, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24857, "SRR25519423", "SRX21249694", "SRS18503943", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 TFA 1  3dpf", "GSM7681263", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 TFA 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae with TFA modeling", "GSM7681263", "GSM7681263: zebrafish  AR42 TFA 1  3dpf; Danio rerio; RNA Seq", "GSM7681263 r1", "GSM7681263", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_TFA_1.R1.fq.gz AR42_TFA_1.R2.fq.gz", "fastq fastq", 7420308900.0, 24734363.0, "GSM7681263 r1", "0:150 1:150", "A:1791092728;C:1841012408;G:1852583633;T:1935620131;N:0", 150, 150, null, null, 1791092728, 1841012408, 1852583633, 1935620131, 0, "SRX21249694", "SRS18503943", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.69668, 0.87862, 0.03153, 0.04215, 0.77463, 0.74949, 0.50657, 0.45971, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24858, "SRR25519424", "SRX21249693", "SRS18503942", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 4  3dpf", "GSM7681262", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681262", "GSM7681262: zebrafish  DMSO TFA 4  3dpf; Danio rerio; RNA Seq", "GSM7681262 r1", "GSM7681262", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_4.R1.fq.gz DMSO_TFA_4.R2.fq.gz", "fastq fastq", 10178474100.0, 33928247.0, "GSM7681262 r1", "0:150 1:150", "A:2452172460;C:2526571372;G:2532799116;T:2666931152;N:0", 150, 150, null, null, 2452172460, 2526571372, 2532799116, 2666931152, 0, "SRX21249693", "SRS18503942", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.72132, 0.91072, 0.03161, 0.04366, 0.77709, 0.75016, 0.516, 0.45312, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24859, "SRR25519425", "SRX21249692", "SRS18503941", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 3  3dpf", "GSM7681261", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681261", "GSM7681261: zebrafish  DMSO TFA 3  3dpf; Danio rerio; RNA Seq", "GSM7681261 r1", "GSM7681261", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_3.R1.fq.gz DMSO_TFA_3.R2.fq.gz", "fastq fastq", 9483201300.0, 31610671.0, "GSM7681261 r1", "0:150 1:150", "A:2282797855;C:2354211318;G:2361918927;T:2484273200;N:0", 150, 150, null, null, 2282797855, 2354211318, 2361918927, 2484273200, 0, "SRX21249692", "SRS18503941", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71779, 0.90757, 0.03224, 0.04329, 0.77853, 0.74862, 0.51128, 0.44891, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24860, "SRR25519426", "SRX21249691", "SRS18503940", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 2  3dpf", "GSM7681260", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681260", "GSM7681260: zebrafish  DMSO TFA 2  3dpf; Danio rerio; RNA Seq", "GSM7681260 r1", "GSM7681260", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_2.R1.fq.gz DMSO_TFA_2.R2.fq.gz", "fastq fastq", 9372641700.0, 31242139.0, "GSM7681260 r1", "0:150 1:150", "A:2255045813;C:2327185536;G:2333956274;T:2456454077;N:0", 150, 150, null, null, 2255045813, 2327185536, 2333956274, 2456454077, 0, "SRX21249691", "SRS18503940", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71913, 0.91061, 0.0318, 0.04251, 0.7778, 0.74907, 0.51295, 0.45006, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24861, "SRR25519427", "SRX21249690", "SRS18503939", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO TFA 1  3dpf", "GSM7681259", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae with TFA modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO TFA 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae with TFA modeling", "GSM7681259", "GSM7681259: zebrafish  DMSO TFA 1  3dpf; Danio rerio; RNA Seq", "GSM7681259 r1", "GSM7681259", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_TFA_1.R1.fq.gz DMSO_TFA_1.R2.fq.gz", "fastq fastq", 8665981200.0, 28886604.0, "GSM7681259 r1", "0:150 1:150", "A:2086560929;C:2153111953;G:2157203992;T:2269104326;N:0", 150, 150, null, null, 2086560929, 2153111953, 2157203992, 2269104326, 0, "SRX21249690", "SRS18503939", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71996, 0.90816, 0.03211, 0.04297, 0.77739, 0.75097, 0.5122, 0.452, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24862, "SRR25519428", "SRX21249689", "SRS18503938", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 4  3dpf", "GSM7681258", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681258", "GSM7681258: zebrafish  AR42 4  3dpf; Danio rerio; RNA Seq", "GSM7681258 r1", "GSM7681258", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_4.R1.fq.gz AR42_4.R2.fq.gz", "fastq fastq", 10199154900.0, 33997183.0, "GSM7681258 r1", "0:150 1:150", "A:2461755295;C:2524481077;G:2536143078;T:2676775450;N:0", 150, 150, null, null, 2461755295, 2524481077, 2536143078, 2676775450, 0, "SRX21249689", "SRS18503938", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70676, 0.89456, 0.031, 0.04108, 0.77508, 0.747, 0.44642, 0.47521, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24863, "SRR25519429", "SRX21249688", "SRS18503937", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 3  3dpf", "GSM7681257", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681257", "GSM7681257: zebrafish  AR42 3  3dpf; Danio rerio; RNA Seq", "GSM7681257 r1", "GSM7681257", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_3.R1.fq.gz AR42_3.R2.fq.gz", "fastq fastq", 9953498100.0, 33178327.0, "GSM7681257 r1", "0:150 1:150", "A:2400858967;C:2463285586;G:2477369817;T:2611983730;N:0", 150, 150, null, null, 2400858967, 2463285586, 2477369817, 2611983730, 0, "SRX21249688", "SRS18503937", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70865, 0.89517, 0.03101, 0.04127, 0.77325, 0.74679, 0.50253, 0.50409, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24864, "SRR25519430", "SRX21249687", "SRS18503936", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 2  3dpf", "GSM7681256", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681256", "GSM7681256: zebrafish  AR42 2  3dpf; Danio rerio; RNA Seq", "GSM7681256 r1", "GSM7681256", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_2.R1.fq.gz AR42_2.R2.fq.gz", "fastq fastq", 10005489000.0, 33351630.0, "GSM7681256 r1", "0:150 1:150", "A:2413672248;C:2477611702;G:2491304598;T:2622900452;N:0", 150, 150, null, null, 2413672248, 2477611702, 2491304598, 2622900452, 0, "SRX21249687", "SRS18503936", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70639, 0.89204, 0.03035, 0.04087, 0.77502, 0.74955, 0.50558, 0.50545, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24865, "SRR25519431", "SRX21249686", "SRS18503935", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  AR42 1  3dpf", "GSM7681255", null, "source name:tail|tissue:tail|treatment:AR 42 treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  AR42 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:AR 42 treated larvae without xxx modeling", "GSM7681255", "GSM7681255: zebrafish  AR42 1  3dpf; Danio rerio; RNA Seq", "GSM7681255 r1", "GSM7681255", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "AR42_1.R1.fq.gz AR42_1.R2.fq.gz", "fastq fastq", 9698587800.0, 32328626.0, "GSM7681255 r1", "0:150 1:150", "A:2337968859;C:2400315331;G:2416067610;T:2544236000;N:0", 150, 150, null, null, 2337968859, 2400315331, 2416067610, 2544236000, 0, "SRX21249686", "SRS18503935", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70903, 0.89448, 0.02976, 0.04032, 0.77583, 0.74935, 0.50747, 0.5081, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24866, "SRR25519432", "SRX21249685", "SRS18503934", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 4  3dpf", "GSM7681254", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 4  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681254", "GSM7681254: zebrafish  DMSO 4  3dpf; Danio rerio; RNA Seq", "GSM7681254 r1", "GSM7681254", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_4.R1.fq.gz DMSO_4.R2.fq.gz", "fastq fastq", 9083670000.0, 30278900.0, "GSM7681254 r1", "0:150 1:150", "A:2191941100;C:2247936730;G:2258913579;T:2384878591;N:0", 150, 150, null, null, 2191941100, 2247936730, 2258913579, 2384878591, 0, "SRX21249685", "SRS18503934", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71071, 0.90457, 0.03362, 0.04688, 0.77106, 0.74357, 0.50842, 0.50975, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24867, "SRR25519433", "SRX21249684", "SRS18503933", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 3  3dpf", "GSM7681253", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 3  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681253", "GSM7681253: zebrafish  DMSO 3  3dpf; Danio rerio; RNA Seq", "GSM7681253 r1", "GSM7681253", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_3.R2.fq.gz DMSO_3.R1.fq.gz", "fastq fastq", 9394455000.0, 31314850.0, "GSM7681253 r1", "0:150 1:150", "A:2266296733;C:2324081714;G:2335347043;T:2468729510;N:0", 150, 150, null, null, 2266296733, 2324081714, 2335347043, 2468729510, 0, "SRX21249684", "SRS18503933", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70975, 0.90445, 0.03329, 0.04594, 0.77005, 0.7417, 0.51188, 0.5163, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24868, "SRR25519434", "SRX21249683", "SRS18503932", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 2  3dpf", "GSM7681252", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 2  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681252", "GSM7681252: zebrafish  DMSO 2  3dpf; Danio rerio; RNA Seq", "GSM7681252 r1", "GSM7681252", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_2.R1.fq.gz DMSO_2.R2.fq.gz", "fastq fastq", 9157453500.0, 30524845.0, "GSM7681252 r1", "0:150 1:150", "A:2209331568;C:2266614182;G:2273923578;T:2407584172;N:0", 150, 150, null, null, 2209331568, 2266614182, 2273923578, 2407584172, 0, "SRX21249683", "SRS18503932", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.70922, 0.90538, 0.03379, 0.04616, 0.7723, 0.74213, 0.50839, 0.50803, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [24869, "SRR25519435", "SRX21249682", "SRS18503931", "SRP453374", "PRJNA1002260", "Effects of AR 42 Treatment on Gene Expression in the Zebrafish Tail Fin Amputation TFA Model", "GSE240080", "Transcriptome Analysis", "We investigated the inflammatory environmental effects of AR 42 on neutrophil recruitment by performing an RNA seq analysis with tail tissue in the zebrafish TFA model. The RNA seq results showed that AR 42 modulates cytokine/chemokine signaling in the local inflammatory environment. Overall design: For RNA sequencing RNA seq analysis  the 3 dpf WT zebrafish larvae receiving DMSO or 10 \u00b5M AR 42 treatments were categorized into 4 groups: ? DMSO treated larvae without xxx modeling referred to as DMSO  ? AR 42 treated larvae without xxx modeling AR 42  ? DMSO treated larvae with TFA modeling DMSO TFA and ? AR 42 treated larvae with TFA modeling AR 42 TFA. And there are four biological replicates in each group. post tail fin amputation  larvae were immediately treated with DMSO or 10 \u00b5M AR 42 for 1 hr before sampling. Tail tissues posterior to the cloaca in each larva were collected n = 150 and immediately froze in liquid nitrogen before RNA isolation.", null, "pubmed:37728477", null, "zebrafish  DMSO 1  3dpf", "GSM7681251", null, "source name:tail|tissue:tail|treatment:DMSO treated larvae without xxx modeling|geo loc name:missing|collection date:missing", "zebrafish  DMSO 1  3dpf", "Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimmomatic version 0.36 Clean Reads were further treated with UMI soft in house to eliminate duplication bias introduced in library preparation and sequencing on using UMI. \uff08Default Parameter developed by Wuhan Seqhealth Co.  Ltd.\uff09 The de duplicated consensus sequences were mapped to GRCh38 using STAR software version 2.5.3a parameters    outSAMtype BAM SortedByCoordinate Read count extraction and normalization were performed using featureCounts\uff08Version 1.5.1\uff09\uff08parameter  T 10  d 30  D 1000  C  s 1  t {exon}  g {geneid}   primary  O  a {gff annotation file}\uff09 Assembly: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "tail", null, "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s instruction.", null, "tissue:tail|treatment:DMSO treated larvae without xxx modeling", "GSM7681251", "GSM7681251: zebrafish  DMSO 1  3dpf; Danio rerio; RNA Seq", "GSM7681251 r1", "GSM7681251", "1", "RNA was harvested using TRIzol Reagent Invitrogen  cat. NO 15596026\uff09. 2 ug of total RNA was used for the construction of sequencing libraries. total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit Catalog NO. DR08402  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP453374", null, null, "DMSO_1.R2.fq.gz DMSO_1.R1.fq.gz", "fastq fastq", 8769040200.0, 29230134.0, "GSM7681251 r1", "0:150 1:150", "A:2114427483;C:2170929931;G:2179906163;T:2303776623;N:0", 150, 150, null, null, 2114427483, 2170929931, 2179906163, 2303776623, 0, "SRX21249682", "SRS18503931", "SRA1687041", "Chongqing medical university", "Chongqing medical university", 2, 0.71002, 0.9037, 0.0335, 0.04604, 0.77155, 0.74308, 0.51339, 0.50801, 150, 150, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-08-04", "Larval", "Larval", "Tail", "Multi-system"], [69019, "SRR18305957", "SRX14443373", "SRS12250386", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X12", "GSM5949315", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "17656X12", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "GSM5949315", "GSM5949315: 17656X12; Danio rerio; RNA Seq", "GSM5949315 r1", "GSM5949315", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "12R1.fastq.gz 12R2.fastq.gz", "fastq fastq", 8760074136.0, 29006868.0, "GSM5949315 r1", "0:151 1:151", "A:2225927481;C:2151918912;G:2283765954;T:2098037222;N:424567", 151, 151, null, null, 2225927481, 2151918912, 2283765954, 2098037222, 424567, "SRX14443373", "SRS12250386", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.85829, 0.85613, 0.15473, 0.15346, 0.71192, 0.7161, 0.50878, 0.50915, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69020, "SRR18305958", "SRX14443372", "SRS12250385", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X11", "GSM5949314", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "17656X11", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "GSM5949314", "GSM5949314: 17656X11; Danio rerio; RNA Seq", "GSM5949314 r1", "GSM5949314", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "11R1.fastq.gz 11R2.fastq.gz", "fastq fastq", 7843778654.0, 25972777.0, "GSM5949314 r1", "0:151 1:151", "A:2038808042;C:1887346702;G:1979694397;T:1937559070;N:370443", 151, 151, null, null, 2038808042, 1887346702, 1979694397, 1937559070, 370443, "SRX14443372", "SRS12250385", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89301, 0.89144, 0.21031, 0.20901, 0.71088, 0.71455, 0.53793, 0.5369, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69021, "SRR18305959", "SRX14443371", "SRS12250384", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X10", "GSM5949313", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "17656X10", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "GSM5949313", "GSM5949313: 17656X10; Danio rerio; RNA Seq", "GSM5949313 r1", "GSM5949313", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "10R1.fastq.gz 10R2.fastq.gz", "fastq fastq", 7954023150.0, 26337825.0, "GSM5949313 r1", "0:151 1:151", "A:2028488675;C:1961022851;G:2035405718;T:1928722520;N:383386", 151, 151, null, null, 2028488675, 1961022851, 2035405718, 1928722520, 383386, "SRX14443371", "SRS12250384", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.86982, 0.86875, 0.15427, 0.15236, 0.71129, 0.71457, 0.52444, 0.51763, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69022, "SRR18305960", "SRX14443370", "SRS12250383", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X9", "GSM5949312", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "17656X9", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "GSM5949312", "GSM5949312: 17656X9; Danio rerio; RNA Seq", "GSM5949312 r1", "GSM5949312", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "9R1.fastq.gz 9R2.fastq.gz", "fastq fastq", 7859666572.0, 26025386.0, "GSM5949312 r1", "0:151 1:151", "A:2036985243;C:1891242195;G:1962197484;T:1968861339;N:380311", 151, 151, null, null, 2036985243, 1891242195, 1962197484, 1968861339, 380311, "SRX14443370", "SRS12250383", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89448, 0.89387, 0.17167, 0.16937, 0.70323, 0.70644, 0.49638, 0.49421, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69023, "SRR18305961", "SRX14443369", "SRS12250382", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X8", "GSM5949311", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "17656X8", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 wildtype|tissue:tail/posterior to yolk sac", "GSM5949311", "GSM5949311: 17656X8; Danio rerio; RNA Seq", "GSM5949311 r1", "GSM5949311", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "8R1.fastq.gz 8R2.fastq.gz", "fastq fastq", 7557954076.0, 25026338.0, "GSM5949311 r1", "0:151 1:151", "A:2056085755;C:1714978138;G:1811687097;T:1974839053;N:364033", 151, 151, null, null, 2056085755, 1714978138, 1811687097, 1974839053, 364033, "SRX14443369", "SRS12250382", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.90646, 0.90592, 0.22261, 0.22061, 0.69775, 0.70179, 0.47205, 0.47079, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69024, "SRR18305962", "SRX14443368", "SRS12250381", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X7", "GSM5949310", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "17656X7", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:36433 mutant|tissue:tail/posterior to yolk sac", "GSM5949310", "GSM5949310: 17656X7; Danio rerio; RNA Seq", "GSM5949310 r1", "GSM5949310", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "7R1.fastq.gz 7R2.fastq.gz", "fastq fastq", 6353509824.0, 21038112.0, "GSM5949310 r1", "0:151 1:151", "A:1703561525;C:1482787327;G:1549794410;T:1617059845;N:306717", 151, 151, null, null, 1703561525, 1482787327, 1549794410, 1617059845, 306717, "SRX14443368", "SRS12250381", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89285, 0.89264, 0.20804, 0.20747, 0.70098, 0.7038, 0.48387, 0.48103, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69025, "SRR18305963", "SRX14443367", "SRS12250380", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X5", "GSM5949309", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "17656X5", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "GSM5949309", "GSM5949309: 17656X5; Danio rerio; RNA Seq", "GSM5949309 r1", "GSM5949309", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "5R1.fastq.gz 5R2.fastq.gz", "fastq fastq", 8578103130.0, 28404315.0, "GSM5949309 r1", "0:151 1:151", "A:2316277649;C:1971907307;G:2061501994;T:2228007020;N:409160", 151, 151, null, null, 2316277649, 1971907307, 2061501994, 2228007020, 409160, "SRX14443367", "SRS12250380", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.89577, 0.89453, 0.22893, 0.22788, 0.70303, 0.70508, 0.48135, 0.48392, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69026, "SRR18305964", "SRX14443366", "SRS12250379", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X4", "GSM5949308", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "17656X4", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "GSM5949308", "GSM5949308: 17656X4; Danio rerio; RNA Seq", "GSM5949308 r1", "GSM5949308", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "4R1.fastq.gz 4R2.fastq.gz", "fastq fastq", 8433863098.0, 27926699.0, "GSM5949308 r1", "0:151 1:151", "A:2210033640;C:2006122016;G:2101172766;T:2116137389;N:397287", 151, 151, null, null, 2210033640, 2006122016, 2101172766, 2116137389, 397287, "SRX14443366", "SRS12250379", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.87323, 0.87203, 0.21174, 0.20953, 0.70668, 0.70989, 0.4827, 0.48242, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69027, "SRR18305965", "SRX14443365", "SRS12250378", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X3", "GSM5949307", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "17656X3", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "GSM5949307", "GSM5949307: 17656X3; Danio rerio; RNA Seq", "GSM5949307 r1", "GSM5949307", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "3R1.fastq.gz 3R2.fastq.gz", "fastq fastq", 9227012644.0, 30553022.0, "GSM5949307 r1", "0:151 1:151", "A:1700627427;C:2904365136;G:3075918116;T:1545659372;N:442593", 151, 151, null, null, 1700627427, 2904365136, 3075918116, 1545659372, 442593, "SRX14443365", "SRS12250378", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.71833, 0.7183, 0.09555, 0.09613, 0.7848, 0.78756, 0.69573, 0.69937, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69028, "SRR18305966", "SRX14443364", "SRS12250377", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X2", "GSM5949306", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "17656X2", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 wildtype|tissue:tail/posterior to yolk sac", "GSM5949306", "GSM5949306: 17656X2; Danio rerio; RNA Seq", "GSM5949306 r1", "GSM5949306", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "2R1.fastq.gz 2R2.fastq.gz", "fastq fastq", 9829302418.0, 32547359.0, "GSM5949306 r1", "0:151 1:151", "A:2452313634;C:2455608968;G:2590620889;T:2330290142;N:468785", 151, 151, null, null, 2452313634, 2455608968, 2590620889, 2330290142, 468785, "SRX14443364", "SRS12250377", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.87037, 0.86912, 0.17566, 0.17497, 0.71731, 0.72084, 0.51503, 0.5232, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [69029, "SRR18305967", "SRX14443363", "SRS12250376", "SRP363665", "PRJNA815356", "Gene expression data from lsd1 mutant zebrafish embryos", "GSE198476", "Transcriptome Analysis", "Gene expression of zebrafish lsd1 mutants and wildtype sibling tails were analyzed by RNA seq. Overall design: RNA Seq performed on 6 zebrafish lsd1 mutant and 5 wildtype sibling tails pooled in groups of 5 tails each  in triplicate at 24hpf. The Illumina NovaSeq 150 x 150 bp Sequencing 100 M read pairs sequencing protocol was used.", null, "pubmed:36594016", null, "17656X1", "GSM5949305", null, "source name:tail/posterior to yolk sac|age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "17656X1", "The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.2c. Differentially expressed genes were found using DESeq2 version 1.22.2 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts", "tail/posterior to yolk sac", "Tails frozen at  80C in RNA stabilization solution QIAGEN. Tails rinsed in 1X PBS prior to homogenization and lysis.", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", "Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.", "age:24 hpf|genotype:23095 mutant|tissue:tail/posterior to yolk sac", "GSM5949305", "GSM5949305: 17656X1; Danio rerio; RNA Seq", "GSM5949305 r1", "GSM5949305", "1", "Homogenization and total RNA isolation preformed according to PureLink RNA Micro kit Invitrogen 12183016. Homogenization was performed with a 18.5 gauge needle 10 times before proceeding directly to RNA isolation. Carrier RNA not utilized. Samples were DNase treated. Illumina TruSeq Stranded Total RNA kit with Ribo Zero Gold Illumina 20020598", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP363665", null, "loader:fastq load.py", "1R1.fastq.gz 1R2.fastq.gz", "fastq fastq", 8271481926.0, 27389013.0, "GSM5949305 r1", "0:151 1:151", "A:2197036792;C:1943518303;G:2039610176;T:2090922643;N:394012", 151, 151, null, null, 2197036792, 1943518303, 2039610176, 2090922643, 394012, "SRX14443363", "SRS12250376", "SRA1385506", "Huntsman Cancer Institute", "Oncological Sciences, University of Utah", 2, 0.87234, 0.87159, 0.21173, 0.21053, 0.70118, 0.70327, 0.46129, 0.45987, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2022-03-11", "Pharyngula", "Embryo", "Tail", "Multi-system"], [72464, "SRR22574253", "SRX18537350", "SRS16001767", "SRP411954", "PRJNA909445", "Danio rerio Raw sequence 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"SRS16001767", "SRA1555446", "Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers", "Fisheries College of Huazhong Agricultural University", 2, 0.95472, 0.95941, 0.14789, 0.14566, 0.81746, 0.81509, 0.46875, 0.39789, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-08", "Juvenile", "Juvenile", "Tail", "Multi-system"], [72467, "SRR22574256", "SRX18537347", "SRS16001767", "SRP411954", "PRJNA909445", "Danio rerio Raw sequence reads", "PRJNA909445", "Other", "Whole transcriptome analysis", null, null, null, "Model organism or animal sample from zebrafish", "zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish", null, "strain:zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish|age:60dpf|sex:pooled male and female|tissue:tail|BioSampleModel:Model organism 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Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  WT 3", "GSM7104974", null, "source name:tail|tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  WT 3", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . 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Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  WT 2", "GSM7104973", null, "source name:tail|tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  WT 2", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . 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The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP428084", null, "loader:fastq load.py", "WT_2_1.fq.gz WT_2_2.fq.gz", "fastq fastq", 7180810500.0, 23936035.0, "GSM7104973 r1", "0:150 1:150", "A:2019809904;C:1595398376;G:1580734574;T:1982292180;N:2575466", 150, 150, null, null, 2019809904, 1595398376, 1580734574, 1982292180, 2575466, "SRX19719609", "SRS17086726", "SRA1606833", "South China University of Technology", "South China University of Technology", 2, 0.93371, 0.93489, 0.11394, 0.11341, 0.66529, 0.66509, 0.466, 0.45682, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-19", "Larval", "Larval", "Tail", "Multi-system"], [74637, "SRR23908130", "SRX19719608", "SRS17086725", "SRP428084", "PRJNA946304", "Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf", "GSE227668", "Transcriptome Analysis", "To investigate the underlying  mechanisms of sirt6  in the regulation of HSCs and neutrophils lineage  expansion in zebrafish. Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  WT 1", "GSM7104972", null, "source name:tail|tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  WT 1", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt", "tail", null, "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf", "GSM7104972", "GSM7104972: tail  WT 1; Danio rerio; RNA Seq", "GSM7104972 r1", "GSM7104972", "1", "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP428084", null, "loader:fastq load.py", "WT_1_1.fq.gz WT_1_2.fq.gz", "fastq fastq", 7050094200.0, 23500314.0, "GSM7104972 r1", "0:150 1:150", "A:1871562366;C:1661769366;G:1671570884;T:1845060013;N:131571", 150, 150, null, null, 1871562366, 1661769366, 1671570884, 1845060013, 131571, "SRX19719608", "SRS17086725", "SRA1606833", "South China University of Technology", "South China University of Technology", 2, 0.95202, 0.95098, 0.07092, 0.06991, 0.67233, 0.67142, 0.46966, 0.46194, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-19", "Larval", "Larval", "Tail", "Multi-system"], [74638, "SRR23908131", "SRX19719607", "SRS17086724", "SRP428084", "PRJNA946304", "Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf", "GSE227668", "Transcriptome Analysis", "To investigate the underlying  mechanisms of sirt6  in the regulation of HSCs and neutrophils lineage  expansion in zebrafish. Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  S6M 3", "GSM7104971", null, "source name:tail|tissue:tail|genotype:sirt6 mutant|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  S6M 3", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt", "tail", null, "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "tissue:tail|genotype:sirt6 mutant|developmental stage:larvae at 3 dpf", "GSM7104971", "GSM7104971: tail  S6M 3; Danio rerio; RNA Seq", "GSM7104971 r1", "GSM7104971", "1", "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP428084", null, "loader:fastq load.py", "S6M_3_1.fq.gz S6M_3_2.fq.gz", "fastq fastq", 6956092800.0, 23186976.0, "GSM7104971 r1", "0:150 1:150", "A:1884077092;C:1614068450;G:1606370402;T:1849148133;N:2428723", 150, 150, null, null, 1884077092, 1614068450, 1606370402, 1849148133, 2428723, "SRX19719607", "SRS17086724", "SRA1606833", "South China University of Technology", "South China University of Technology", 2, 0.94414, 0.94532, 0.09282, 0.09424, 0.6618, 0.66074, 0.46511, 0.46037, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-19", "Larval", "Larval", "Tail", "Multi-system"], [74639, "SRR23908132", "SRX19719606", "SRS17086723", "SRP428084", "PRJNA946304", "Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf", "GSE227668", "Transcriptome Analysis", "To investigate the underlying  mechanisms of sirt6  in the regulation of HSCs and neutrophils lineage  expansion in zebrafish. Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  S6M 2", "GSM7104970", null, "source name:tail|tissue:tail|genotype:sirt6 mutant|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  S6M 2", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . 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The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP428084", null, "loader:fastq load.py", "S6M_2_1.fq.gz S6M_2_2.fq.gz", "fastq fastq", 6997999800.0, 23326666.0, "GSM7104970 r1", "0:150 1:150", "A:1906557458;C:1616508685;G:1606294212;T:1865774561;N:2864884", 150, 150, null, null, 1906557458, 1616508685, 1606294212, 1865774561, 2864884, "SRX19719606", "SRS17086723", "SRA1606833", "South China University of Technology", "South China University of Technology", 2, 0.94563, 0.94743, 0.08277, 0.08292, 0.67198, 0.67006, 0.47115, 0.46233, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-19", "Larval", "Larval", "Tail", "Multi-system"], [74640, "SRR23908133", "SRX19719605", "SRS17086722", "SRP428084", "PRJNA946304", "Effect of sirt6 deficiency on gene expression in zebrafish at 3 dpf", "GSE227668", "Transcriptome Analysis", "To investigate the underlying  mechanisms of sirt6  in the regulation of HSCs and neutrophils lineage  expansion in zebrafish. Overall design: We generated a sirt6 mutant zebrafish line using CRISPR/Cas9 methods", null, null, null, "tail  S6M 1", "GSM7104969", null, "source name:tail|tissue:tail|genotype:sirt6 mutant|developmental stage:larvae at 3 dpf|geo loc name:missing|collection date:missing", "tail  S6M 1", "The generated fastq files were subjected to FastQC  to check sequencing quality. The clean reads were mapped onto the GRCz11 zebrafish reference genome using HISAT2 v2.0.5. The mapped reads were then counted using FeatureCounts. The counts matrix was applied to DESeq2 for normalization  differentially expressed genes identification. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt", "tail", null, "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "tissue:tail|genotype:sirt6 mutant|developmental stage:larvae at 3 dpf", "GSM7104969", "GSM7104969: tail  S6M 1; Danio rerio; RNA Seq", "GSM7104969 r1", "GSM7104969", "1", "Larvae were collected at 3 dpf  then grouped into sirt6 mutant and WT groups through genotyping  total RNA was extracted with TRIzol Invitrogen from the tails including hematopoietic tissue. The poly A selected RNA was applied to the NGS RNA Library Prep kits Novogene to construct Sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP428084", null, "loader:fastq load.py", "S6M_1_1.fq.gz S6M_1_2.fq.gz", "fastq fastq", 6497003700.0, 21656679.0, "GSM7104969 r1", "0:150 1:150", "A:1747432287;C:1519036468;G:1518708333;T:1709176798;N:2649814", 150, 150, null, null, 1747432287, 1519036468, 1518708333, 1709176798, 2649814, "SRX19719605", "SRS17086722", "SRA1606833", "South China University of Technology", "South China University of Technology", 2, 0.94733, 0.94609, 0.08694, 0.08654, 0.66393, 0.66626, 0.46759, 0.45876, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-19", "Larval", "Larval", "Tail", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 37, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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