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run_metadata

102 rows where experiment.library_strategy = "RNA-Seq", technology = "unknown" and tissue_curation = "Tail"

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devstage_curation_coarse 5

devstage_curation 5

experiment.platform 3

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Tail · 102 ✖

technology 1

  • unknown · 102 ✖

experiment.library_strategy 1

  • RNA-Seq · 102 ✖

experiment.library_source 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
24854 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 TFA 4 3dpf GSM7681266   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24855 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 TFA 3 3dpf GSM7681265   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24856 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 TFA 2 3dpf GSM7681264   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24857 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 TFA 1 3dpf GSM7681263   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24858 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO TFA 4 3dpf GSM7681262   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24859 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO TFA 3 3dpf GSM7681261   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24860 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO TFA 2 3dpf GSM7681260   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24861 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO TFA 1 3dpf GSM7681259   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24862 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 4 3dpf GSM7681258   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24863 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 3 3dpf GSM7681257   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24864 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 2 3dpf GSM7681256   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24865 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 µM 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 µM 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.   pubmed:37728477   zebrafish AR42 1 3dpf GSM7681255   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24866 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO 4 3dpf GSM7681254   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24867 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO 3 3dpf GSM7681253   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24868 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO 2 3dpf GSM7681252   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
24869 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 µM 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 µM 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.   pubmed:37728477   zebrafish DMSO 1 3dpf GSM7681251   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. （Default Parameter developed by Wuhan Seqhealth Co. Ltd.） 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（Version 1.5.1）（parameter T 10 d 30 D 1000 C s 1 t {exon} g {geneid} primary O a {gff annotation file}） 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   RNA was harvested using TRIzol Reagent Invitrogen cat. NO 15596026）. 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.   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）. 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP453374     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     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   China 2023-08-04 Larval Larval Tail Multi-system
36147 36147 SRR33446914 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L001_R1_001.fastq.gz fastq 392062720.0 5158720.0 GSM8970925 r1 0:76 A:111393933;C:84178440;G:86759120;T:109728583;N:2644 76       111393933 84178440 86759120 109728583 2644 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36148 36148 SRR33446915 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L002_R1_001.fastq.gz fastq 382539160.0 5033410.0 GSM8970925 r2 0:76 A:108549273;C:82135694;G:84877971;T:106974218;N:2004 76       108549273 82135694 84877971 106974218 2004 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36149 36149 SRR33446916 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L003_R1_001.fastq.gz fastq 390689020.0 5140645.0 GSM8970925 r3 0:76 A:110921885;C:83926202;G:86538209;T:109300187;N:2537 76       110921885 83926202 86538209 109300187 2537 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36150 36150 SRR33446917 SRX28687233 SRS24954089 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 4 GSM8970925   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970925 GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970925 r1 GSM8970925 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-4_S18_L004_R1_001.fastq.gz fastq 385026032.0 5066132.0 GSM8970925 r4 0:76 A:109282089;C:82666299;G:85291625;T:107783812;N:2207 76       109282089 82666299 85291625 107783812 2207 SRX28687233 SRS24954089 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36151 36151 SRR33446918 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L001_R1_001.fastq.gz fastq 242078544.0 3185244.0 GSM8970924 r1 0:76 A:70805011;C:50935537;G:52720022;T:67616569;N:1405 76       70805011 50935537 52720022 67616569 1405 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36152 36152 SRR33446919 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L002_R1_001.fastq.gz fastq 236879840.0 3116840.0 GSM8970924 r2 0:76 A:69118193;C:49900432;G:51722708;T:66137243;N:1264 76       69118193 49900432 51722708 66137243 1264 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36153 36153 SRR33446920 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L003_R1_001.fastq.gz fastq 241246952.0 3174302.0 GSM8970924 r3 0:76 A:70493049;C:50814403;G:52594412;T:67343618;N:1470 76       70493049 50814403 52594412 67343618 1470 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36154 36154 SRR33446921 SRX28687232 SRS24954088 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 3 GSM8970924   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970924 GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq GSM8970924 r1 GSM8970924 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-3_S17_L004_R1_001.fastq.gz fastq 238296936.0 3135486.0 GSM8970924 r4 0:76 A:69600911;C:50177666;G:51934697;T:66582348;N:1314 76       69600911 50177666 51934697 66582348 1314 SRX28687232 SRS24954088 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36155 36155 SRR33446922 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L001_R1_001.fastq.gz fastq 293546884.0 3862459.0 GSM8970923 r1 0:76 A:86721485;C:61000183;G:63592308;T:82231012;N:1896 76       86721485 61000183 63592308 82231012 1896 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36156 36156 SRR33446923 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L002_R1_001.fastq.gz fastq 287313668.0 3780443.0 GSM8970923 r2 0:76 A:84719789;C:59732524;G:62422596;T:80437282;N:1477 76       84719789 59732524 62422596 80437282 1477 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36157 36157 SRR33446924 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L003_R1_001.fastq.gz fastq 293081612.0 3856337.0 GSM8970923 r3 0:76 A:86491724;C:60944765;G:63551581;T:82091805;N:1737 76       86491724 60944765 63551581 82091805 1737 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36158 36158 SRR33446925 SRX28687231 SRS24954087 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / uncut tail replicate 2 GSM8970923   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured SB431542 treated GSM8970923 GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970923 r1 GSM8970923 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     White-2_S16_L004_R1_001.fastq.gz fastq 289340284.0 3807109.0 GSM8970923 r4 0:76 A:85390241;C:60135471;G:62741618;T:81071340;N:1614 76       85390241 60135471 62741618 81071340 1614 SRX28687231 SRS24954087 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36159 36159 SRR33446926 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L001_R1_001.fastq.gz fastq 293676616.0 3864166.0 GSM8970922 r1 0:76 A:85055525;C:61514402;G:62951777;T:84153135;N:1777 76       85055525 61514402 62951777 84153135 1777 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36160 36160 SRR33446927 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L002_R1_001.fastq.gz fastq 287550712.0 3783562.0 GSM8970922 r2 0:76 A:83130155;C:60249305;G:61817163;T:82352632;N:1457 76       83130155 60249305 61817163 82352632 1457 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36161 36161 SRR33446928 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L003_R1_001.fastq.gz fastq 293005460.0 3855335.0 GSM8970922 r3 0:76 A:84798214;C:61435286;G:62865004;T:83905146;N:1810 76       84798214 61435286 62865004 83905146 1810 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36162 36162 SRR33446929 SRX28687230 SRS24954086 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 4 GSM8970922   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970922 GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970922 r1 GSM8970922 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-4_S15_L004_R1_001.fastq.gz fastq 289004668.0 3802693.0 GSM8970922 r4 0:76 A:83595831;C:60570265;G:62006632;T:82830364;N:1576 76       83595831 60570265 62006632 82830364 1576 SRX28687230 SRS24954086 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36163 36163 SRR33446930 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L001_R1_001.fastq.gz fastq 300231768.0 3950418.0 GSM8970921 r1 0:76 A:88106516;C:61818857;G:65466450;T:84838096;N:1849 76       88106516 61818857 65466450 84838096 1849 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36164 36164 SRR33446931 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L002_R1_001.fastq.gz fastq 293677452.0 3864177.0 GSM8970921 r2 0:76 A:86015379;C:60508410;G:64229226;T:82922956;N:1481 76       86015379 60508410 64229226 82922956 1481 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36165 36165 SRR33446932 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L003_R1_001.fastq.gz fastq 299518280.0 3941030.0 GSM8970921 r3 0:76 A:87800455;C:61713738;G:65389216;T:84612972;N:1899 76       87800455 61713738 65389216 84612972 1899 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36166 36166 SRR33446933 SRX28687229 SRS24954085 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 3 GSM8970921   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970921 GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970921 r1 GSM8970921 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-3_S14_L004_R1_001.fastq.gz fastq 295680204.0 3890529.0 GSM8970921 r4 0:76 A:86636984;C:60930934;G:64539123;T:83571354;N:1809 76       86636984 60930934 64539123 83571354 1809 SRX28687229 SRS24954085 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36167 36167 SRR33446934 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L001_R1_001.fastq.gz fastq 266233396.0 3503071.0 GSM8970920 r1 0:76 A:78387833;C:55246603;G:58347116;T:74250158;N:1686 76       78387833 55246603 58347116 74250158 1686 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36168 36168 SRR33446935 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L002_R1_001.fastq.gz fastq 260317404.0 3425229.0 GSM8970920 r2 0:76 A:76487964;C:54052872;G:57202492;T:72572684;N:1392 76       76487964 54052872 57202492 72572684 1392 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36169 36169 SRR33446936 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L003_R1_001.fastq.gz fastq 265513676.0 3493601.0 GSM8970920 r3 0:76 A:78116084;C:55123773;G:58227738;T:74044386;N:1695 76       78116084 55123773 58227738 74044386 1695 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36170 36170 SRR33446937 SRX28687228 SRS24954084 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       SB 431542 treated / cut tail replicate 2 GSM8970920   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated|geo loc name:missing|collection date:missing SB 431542 treated / cut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision SB431542 treated GSM8970920 GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq GSM8970920 r1 GSM8970920 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Red-2_S13_L004_R1_001.fastq.gz fastq 262010532.0 3447507.0 GSM8970920 r4 0:76 A:77058783;C:54402656;G:57452833;T:73094822;N:1438 76       77058783 54402656 57452833 73094822 1438 SRX28687228 SRS24954084 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36171 36171 SRR33446938 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L001_R1_001.fastq.gz fastq 334535736.0 4401786.0 GSM8970919 r1 0:76 A:104303278;C:67025244;G:65441286;T:97763807;N:2121 76       104303278 67025244 65441286 97763807 2121 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36172 36172 SRR33446939 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L002_R1_001.fastq.gz fastq 325405780.0 4281655.0 GSM8970919 r2 0:76 A:101185453;C:65289632;G:63869692;T:95059316;N:1687 76       101185453 65289632 63869692 95059316 1687 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36173 36173 SRR33446940 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L003_R1_001.fastq.gz fastq 333272540.0 4385165.0 GSM8970919 r3 0:76 A:103781471;C:66831319;G:65274288;T:97383334;N:2128 76       103781471 66831319 65274288 97383334 2128 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36174 36174 SRR33446941 SRX28687227 SRS24954083 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 4 GSM8970919   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970919 GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq GSM8970919 r1 GSM8970919 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-4_S24_L004_R1_001.fastq.gz fastq 328778432.0 4326032.0 GSM8970919 r4 0:76 A:102340372;C:65917125;G:64384673;T:96134375;N:1887 76       102340372 65917125 64384673 96134375 1887 SRX28687227 SRS24954083 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36175 36175 SRR33446942 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L001_R1_001.fastq.gz fastq 254273428.0 3345703.0 GSM8970918 r1 0:76 A:73868437;C:53712396;G:55649268;T:71041836;N:1491 76       73868437 53712396 55649268 71041836 1491 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36176 36176 SRR33446943 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L002_R1_001.fastq.gz fastq 247479256.0 3256306.0 GSM8970918 r2 0:76 A:71749772;C:52269437;G:54304263;T:69154447;N:1337 76       71749772 52269437 54304263 69154447 1337 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36177 36177 SRR33446944 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L003_R1_001.fastq.gz fastq 252975424.0 3328624.0 GSM8970918 r3 0:76 A:73431938;C:53451559;G:55422676;T:70667726;N:1525 76       73431938 53451559 55422676 70667726 1525 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36178 36178 SRR33446945 SRX28687226 SRS24954082 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 2 GSM8970918   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 2 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970918 GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq GSM8970918 r1 GSM8970918 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-2_S23_L004_R1_001.fastq.gz fastq 249310400.0 3280400.0 GSM8970918 r4 0:76 A:72326303;C:52679056;G:54605938;T:69697722;N:1381 76       72326303 52679056 54605938 69697722 1381 SRX28687226 SRS24954082 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36179 36179 SRR33446946 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L001_R1_001.fastq.gz fastq 270570108.0 3560133.0 GSM8970917 r1 0:76 A:78499185;C:56484520;G:59318322;T:76266342;N:1739 76       78499185 56484520 59318322 76266342 1739 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36180 36180 SRR33446947 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L002_R1_001.fastq.gz fastq 263995348.0 3473623.0 GSM8970917 r2 0:76 A:76492301;C:55131794;G:58036716;T:74333178;N:1359 76       76492301 55131794 58036716 74333178 1359 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36181 36181 SRR33446948 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L003_R1_001.fastq.gz fastq 269322036.0 3543711.0 GSM8970917 r3 0:76 A:78091756;C:56257589;G:59094882;T:75876132;N:1677 76       78091756 56257589 59094882 75876132 1677 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36182 36182 SRR33446949 SRX28687225 SRS24954081 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / uncut tail replicate 1 GSM8970917   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Uninjured|geo loc name:missing|collection date:missing DMSO treated / uncut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Uninjured GSM8970917 GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq GSM8970917 r1 GSM8970917 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Pink-1_S22_L004_R1_001.fastq.gz fastq 265691820.0 3495945.0 GSM8970917 r4 0:76 A:77002713;C:55467944;G:58293660;T:74926013;N:1490 76       77002713 55467944 58293660 74926013 1490 SRX28687225 SRS24954081 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36183 36183 SRR33446950 SRX28687224 SRS24954080 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 4 GSM8970916   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970916 GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970916 r1 GSM8970916 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-4_S21_L001_R1_001.fastq.gz fastq 349029392.0 4592492.0 GSM8970916 r1 0:76 A:99839652;C:73943935;G:76249851;T:98993782;N:2172 76       99839652 73943935 76249851 98993782 2172 SRX28687224 SRS24954080 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36184 36184 SRR33446951 SRX28687224 SRS24954080 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 4 GSM8970916   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970916 GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970916 r1 GSM8970916 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-4_S21_L002_R1_001.fastq.gz fastq 340876568.0 4485218.0 GSM8970916 r2 0:76 A:97335332;C:72249777;G:74668638;T:96621097;N:1724 76       97335332 72249777 74668638 96621097 1724 SRX28687224 SRS24954080 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36185 36185 SRR33446952 SRX28687224 SRS24954080 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 4 GSM8970916   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970916 GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970916 r1 GSM8970916 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-4_S21_L003_R1_001.fastq.gz fastq 347633196.0 4574121.0 GSM8970916 r3 0:76 A:99370315;C:73701054;G:75983700;T:98575995;N:2132 76       99370315 73701054 75983700 98575995 2132 SRX28687224 SRS24954080 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36186 36186 SRR33446953 SRX28687224 SRS24954080 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 4 GSM8970916   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 4 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970916 GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq GSM8970916 r1 GSM8970916 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-4_S21_L004_R1_001.fastq.gz fastq 343592352.0 4520952.0 GSM8970916 r4 0:76 A:98157486;C:72839122;G:75134528;T:97459296;N:1920 76       98157486 72839122 75134528 97459296 1920 SRX28687224 SRS24954080 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36187 36187 SRR33446954 SRX28687223 SRS24954079 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 3 GSM8970915   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970915 GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970915 r1 GSM8970915 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-3_S20_L001_R1_001.fastq.gz fastq 304693500.0 4009125.0 GSM8970915 r1 0:76 A:89126862;C:63666599;G:66255160;T:85642963;N:1916 76       89126862 63666599 66255160 85642963 1916 SRX28687223 SRS24954079 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36188 36188 SRR33446955 SRX28687223 SRS24954079 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 3 GSM8970915   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970915 GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970915 r1 GSM8970915 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-3_S20_L002_R1_001.fastq.gz fastq 297396892.0 3913117.0 GSM8970915 r2 0:76 A:86844888;C:62174886;G:64844462;T:83531083;N:1573 76       86844888 62174886 64844462 83531083 1573 SRX28687223 SRS24954079 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36189 36189 SRR33446956 SRX28687223 SRS24954079 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 3 GSM8970915   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970915 GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970915 r1 GSM8970915 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-3_S20_L003_R1_001.fastq.gz fastq 303170840.0 3989090.0 GSM8970915 r3 0:76 A:88574880;C:63384769;G:65999210;T:85210123;N:1858 76       88574880 63384769 65999210 85210123 1858 SRX28687223 SRS24954079 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36190 36190 SRR33446957 SRX28687223 SRS24954079 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 3 GSM8970915   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 3 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970915 GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq GSM8970915 r1 GSM8970915 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-3_S20_L004_R1_001.fastq.gz fastq 299538876.0 3941301.0 GSM8970915 r4 0:76 A:87486058;C:62643433;G:65200414;T:84207227;N:1744 76       87486058 62643433 65200414 84207227 1744 SRX28687223 SRS24954079 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36191 36191 SRR33446958 SRX28687222 SRS24954078 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 1 GSM8970914   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970914 GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq GSM8970914 r1 GSM8970914 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-1_S19_L001_R1_001.fastq.gz fastq 356071020.0 4685145.0 GSM8970914 r1 0:76 A:101990320;C:75361307;G:78194540;T:100522661;N:2192 76       101990320 75361307 78194540 100522661 2192 SRX28687222 SRS24954078 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36192 36192 SRR33446959 SRX28687222 SRS24954078 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 1 GSM8970914   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970914 GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq GSM8970914 r1 GSM8970914 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-1_S19_L002_R1_001.fastq.gz fastq 349258684.0 4595509.0 GSM8970914 r2 0:76 A:99883376;C:73952042;G:76902800;T:98518682;N:1784 76       99883376 73952042 76902800 98518682 1784 SRX28687222 SRS24954078 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36193 36193 SRR33446960 SRX28687222 SRS24954078 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 1 GSM8970914   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970914 GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq GSM8970914 r1 GSM8970914 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-1_S19_L003_R1_001.fastq.gz fastq 355553156.0 4678331.0 GSM8970914 r3 0:76 A:101770613;C:75287760;G:78157774;T:100334741;N:2268 76       101770613 75287760 78157774 100334741 2268 SRX28687222 SRS24954078 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36194 36194 SRR33446961 SRX28687222 SRS24954078 SRP583344 PRJNA1259437 Inhibition of TGF beta signalling during zebrafish larval tail regeneration. GSE296469 Transcriptome Analysis This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.       DMSO treated / cut tail replicate 1 GSM8970914   source name:Larval tail|tissue:Larval tail|genotype:Wild type|treatment:Tail excision|geo loc name:missing|collection date:missing DMSO treated / cut tail replicate 1 demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file Larval tail SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%. 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference tissue:Larval tail|genotype:Wild type|treatment:Tail excision GSM8970914 GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq GSM8970914 r1 GSM8970914 1 100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP583344     Orange-1_S19_L004_R1_001.fastq.gz fastq 351537316.0 4625491.0 GSM8970914 r4 0:76 A:100573823;C:74441165;G:77263744;T:99256707;N:1877 76       100573823 74441165 77263744 99256707 1877 SRX28687222 SRS24954078 SRA2124571 University of Sheffield University of Sheffield                       B   usable mapping rate illumina nextseq 3prime cdna_unspecified lexogen bulk unknown unknown   United Kingdom 2025-05-06 Larval Larval Tail Multi-system
36478 36478 SRR527835 SRX171222 SRS352108 SRP014596 PRJNA171539 Transcriptomic analysis of zebrafish during development and homeostasis GSE39703 Transcriptome Analysis Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail   pubmed:23684812   tail GSM977960   tissue:entire adult tail|genotype:Wild type|strain:AB|Stage:adult tail tail Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification entire adult tail   Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions   genotype:Wild type|strain:AB|Stage:adult tail GSM977960 GSM977960: tail; Danio rerio; RNA Seq GSM977960 1 GSM977960: tail 1   GEO Accession:GSM977960 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP014596         534897504.0 14858264.0 GSM977960 r1 0:36 A:144900139;C:122639505;G:130189210;T:136990883;N:177767 36       144900139 122639505 130189210 136990883 177767 SRX171222 SRS352108 SRA056408 GEO ITG 1 0.89933   0.04578   0.71254   0.41668   36   B   usable mapping rate illumina early_illumina unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2012-07-27 Adult Adult Tail Multi-system
38049 38049 SRR1519899 SRX657112 SRS662299 SRP044634 PRJNA255636 mRNA sequencing of embryonic tails of sih mutants at 28 hpf GSE59563 Transcriptome Analysis We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf       sih3 GSM1439473   tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf sih3 Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts tail derived cells sih embryos lack heart contraction RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. Embryos were grown in normal conditions genotype/variation:sih|embryonic stage:28 hpf GSM1439473 GSM1439473: sih3; Danio rerio; RNA Seq GSM1439473   1 RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. GEO Accession:GSM1439473 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP044634     JGZ-06.fastq.gz fastq 1416036978.0 26222907.0 GSM1439473 r1 0:54 A:342287675;C:370618836;G:361870457;T:341179934;N:80076 54       342287675 370618836 361870457 341179934 80076 SRX657112 SRS662299 SRA175990 GEO IGBMC 1 0.96217   0.03055   0.76869   0.44925   54   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   France 2014-07-18 Pharyngula Embryo Tail Multi-system
38050 38050 SRR1519898 SRX657111 SRS662291 SRP044634 PRJNA255636 mRNA sequencing of embryonic tails of sih mutants at 28 hpf GSE59563 Transcriptome Analysis We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf       WT3 GSM1439472   tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf WT3 Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts tail derived cells sih embryos lack heart contraction RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. Embryos were grown in normal conditions genotype/variation:WT|embryonic stage:28 hpf GSM1439472 GSM1439472: WT3; Danio rerio; RNA Seq GSM1439472   1 RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. GEO Accession:GSM1439472 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP044634     JGZ-05.fastq.gz fastq 1787680692.0 33105198.0 GSM1439472 r1 0:54 A:442553431;C:457003567;G:446438405;T:441598672;N:86617 54       442553431 457003567 446438405 441598672 86617 SRX657111 SRS662291 SRA175990 GEO IGBMC 1 0.96318   0.03918   0.75371   0.4423   54   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   France 2014-07-18 Pharyngula Embryo Tail Multi-system
38051 38051 SRR1519897 SRX657110 SRS662290 SRP044634 PRJNA255636 mRNA sequencing of embryonic tails of sih mutants at 28 hpf GSE59563 Transcriptome Analysis We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf       sih2 GSM1439471   tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf sih2 Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts tail derived cells sih embryos lack heart contraction RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. Embryos were grown in normal conditions genotype/variation:sih|embryonic stage:28 hpf GSM1439471 GSM1439471: sih2; Danio rerio; RNA Seq GSM1439471   1 RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. GEO Accession:GSM1439471 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP044634     JGZ-04.fastq.gz fastq 1813069386.0 33575359.0 GSM1439471 r1 0:54 A:462594376;C:449896725;G:440482879;T:460019095;N:76311 54       462594376 449896725 440482879 460019095 76311 SRX657110 SRS662290 SRA175990 GEO IGBMC 1 0.95859   0.05282   0.74199   0.47244   54   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   France 2014-07-18 Pharyngula Embryo Tail Multi-system
38052 38052 SRR1519896 SRX657109 SRS662289 SRP044634 PRJNA255636 mRNA sequencing of embryonic tails of sih mutants at 28 hpf GSE59563 Transcriptome Analysis We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf       WT2 GSM1439470   tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf WT2 Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts tail derived cells sih embryos lack heart contraction RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. Embryos were grown in normal conditions genotype/variation:WT|embryonic stage:28 hpf GSM1439470 GSM1439470: WT2; Danio rerio; RNA Seq GSM1439470   1 RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. GEO Accession:GSM1439470 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP044634     JGZ-03.fastq.gz fastq 1866194316.0 34559154.0 GSM1439470 r1 0:54 A:483946414;C:453986455;G:443561481;T:484623941;N:76025 54       483946414 453986455 443561481 484623941 76025 SRX657109 SRS662289 SRA175990 GEO IGBMC 1 0.95615   0.06195   0.73594   0.47144   54   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   France 2014-07-18 Pharyngula Embryo Tail Multi-system
38053 38053 SRR1519895 SRX657108 SRS662288 SRP044634 PRJNA255636 mRNA sequencing of embryonic tails of sih mutants at 28 hpf GSE59563 Transcriptome Analysis We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf       sih1 GSM1439469   tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf sih1 Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts tail derived cells sih embryos lack heart contraction RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. Embryos were grown in normal conditions genotype/variation:sih|embryonic stage:28 hpf GSM1439469 GSM1439469: sih1; Danio rerio; RNA Seq GSM1439469   1 RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. GEO Accession:GSM1439469 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP044634     JGZ-02.fastq.gz fastq 1451212470.0 26874305.0 GSM1439469 r1 0:54 A:368354355;C:360129390;G:353350795;T:369317437;N:60493 54       368354355 360129390 353350795 369317437 60493 SRX657108 SRS662288 SRA175990 GEO IGBMC 1 0.94911   0.04509   0.74604   0.46107   54   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   France 2014-07-18 Pharyngula Embryo Tail Multi-system
38054 38054 SRR1519894 SRX657107 SRS662287 SRP044634 PRJNA255636 mRNA sequencing of embryonic tails of sih mutants at 28 hpf GSE59563 Transcriptome Analysis We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf       WT1 GSM1439468   tissue:tail derived cells|genotype/variation:WT|embryonic stage:28 hpf WT1 Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts tail derived cells sih embryos lack heart contraction RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. Embryos were grown in normal conditions genotype/variation:WT|embryonic stage:28 hpf GSM1439468 GSM1439468: WT1; Danio rerio; RNA Seq GSM1439468   1 RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent. GEO Accession:GSM1439468 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP044634     JGZ-01.fastq.gz fastq 1583485146.0 29323799.0 GSM1439468 r1 0:54 A:405051413;C:391145102;G:382645289;T:404569188;N:74154 54       405051413 391145102 382645289 404569188 74154 SRX657107 SRS662287 SRA175990 GEO IGBMC 1 0.94743   0.05464   0.73156   0.46572   54   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   France 2014-07-18 Pharyngula Embryo Tail Multi-system
41312 41312 SRR4199307 SRX2148087 SRS1679265 SRP087617 PRJNA342262 Proliferation independent regulation of organ size by Notch signaling GSE86571 Transcriptome Analysis Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.   pubmed:28085667   NICD rep3 GSM2306087   source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf NICD rep3 Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample. dissociated embryo tails Zebrafish embryos positive for GFP were selected. Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Zebrafish embryos were raised for 36 hpf in the 28.5C incubator. strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf GSM2306087 GSM2306087: NICD rep3; Danio rerio; RNA Seq GSM2306087   1 Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2306087 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP087617     mutant3.fastq.gz fastq 1706861931.0 33467881.0 GSM2306087 r1 0:51 1:0 A:400027681;C:444926525;G:399939257;T:461913972;N:54496 51 0     400027681 444926525 399939257 461913972 54496 SRX2148087 SRS1679265 SRA464955 GEO Stowers Institute for Medical Research 1 0.75848   0.06958   0.73616   0.47901   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2016-09-08 Pharyngula Embryo Tail Multi-system
41313 41313 SRR4199306 SRX2148086 SRS1679264 SRP087617 PRJNA342262 Proliferation independent regulation of organ size by Notch signaling GSE86571 Transcriptome Analysis Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.   pubmed:28085667   NICD rep2 GSM2306086   source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf NICD rep2 Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample. dissociated embryo tails Zebrafish embryos positive for GFP were selected. Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Zebrafish embryos were raised for 36 hpf in the 28.5C incubator. strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf GSM2306086 GSM2306086: NICD rep2; Danio rerio; RNA Seq GSM2306086   1 Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2306086 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP087617     mutant2.fastq.gz fastq 1745551857.0 34226507.0 GSM2306086 r1 0:51 1:0 A:414724753;C:449494336;G:403529006;T:477747391;N:56371 51 0     414724753 449494336 403529006 477747391 56371 SRX2148086 SRS1679264 SRA464955 GEO Stowers Institute for Medical Research 1 0.77355   0.08842   0.71674   0.48589   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2016-09-08 Pharyngula Embryo Tail Multi-system
41314 41314 SRR4199305 SRX2148085 SRS1679263 SRP087617 PRJNA342262 Proliferation independent regulation of organ size by Notch signaling GSE86571 Transcriptome Analysis Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.   pubmed:28085667   NICD rep1 GSM2306085   source name:dissociated embryo tails|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf NICD rep1 Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample. dissociated embryo tails Zebrafish embryos positive for GFP were selected. Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Zebrafish embryos were raised for 36 hpf in the 28.5C incubator. strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd|tissue:dissociated embryo tails|age:36 hpf GSM2306085 GSM2306085: NICD rep1; Danio rerio; RNA Seq GSM2306085   1 Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2306085 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP087617     mutant1.fastq.gz fastq 1606289064.0 31495864.0 GSM2306085 r1 0:51 1:0 A:383363329;C:409816147;G:373853062;T:439205035;N:51491 51 0     383363329 409816147 373853062 439205035 51491 SRX2148085 SRS1679263 SRA464955 GEO Stowers Institute for Medical Research 1 0.80199   0.09405   0.71382   0.48651   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2016-09-08 Pharyngula Embryo Tail Multi-system
41315 41315 SRR4199304 SRX2148084 SRS1679262 SRP087617 PRJNA342262 Proliferation independent regulation of organ size by Notch signaling GSE86571 Transcriptome Analysis Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.   pubmed:28085667   WT rep3 GSM2306084   source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type WT rep3 Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample. dissociated embryo tails Zebrafish embryos positive for GFP were selected. Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Zebrafish embryos were raised for 36 hpf in the 28.5C incubator. strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type GSM2306084 GSM2306084: WT rep3; Danio rerio; RNA Seq GSM2306084   1 Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2306084 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP087617     WT3.fastq.gz fastq 1621399650.0 31792150.0 GSM2306084 r1 0:51 1:0 A:394689371;C:400826196;G:384059217;T:441773624;N:51242 51 0     394689371 400826196 384059217 441773624 51242 SRX2148084 SRS1679262 SRA464955 GEO Stowers Institute for Medical Research 1 0.87053   0.08236   0.7218   0.4831   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2016-09-08 Pharyngula Embryo Tail Multi-system
41316 41316 SRR4199303 SRX2148083 SRS1679261 SRP087617 PRJNA342262 Proliferation independent regulation of organ size by Notch signaling GSE86571 Transcriptome Analysis Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.   pubmed:28085667   WT rep2 GSM2306083   source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type WT rep2 Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample. dissociated embryo tails Zebrafish embryos positive for GFP were selected. Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Zebrafish embryos were raised for 36 hpf in the 28.5C incubator. strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type GSM2306083 GSM2306083: WT rep2; Danio rerio; RNA Seq GSM2306083   1 Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2306083 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP087617     WT2.fastq.gz fastq 1626903774.0 31900074.0 GSM2306083 r1 0:51 1:0 A:394214874;C:407655291;G:379120984;T:445859413;N:53212 51 0     394214874 407655291 379120984 445859413 53212 SRX2148083 SRS1679261 SRA464955 GEO Stowers Institute for Medical Research 1 0.81975   0.09539   0.70869   0.4872   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2016-09-08 Pharyngula Embryo Tail Multi-system
41317 41317 SRR4199302 SRX2148082 SRS1679260 SRP087617 PRJNA342262 Proliferation independent regulation of organ size by Notch signaling GSE86571 Transcriptome Analysis Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.   pubmed:28085667   WT rep1 GSM2306082   source name:dissociated embryo tails|strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type WT rep1 Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample. dissociated embryo tails Zebrafish embryos positive for GFP were selected. Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. Zebrafish embryos were raised for 36 hpf in the 28.5C incubator. strain:Tgcldnb:lynGFPzf106|tissue:dissociated embryo tails|age:36 hpf type GSM2306082 GSM2306082: WT rep1; Danio rerio; RNA Seq GSM2306082   1 Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols. GEO Accession:GSM2306082 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP087617     WT1.fastq.gz fastq 1646867622.0 32291522.0 GSM2306082 r1 0:51 1:0 A:400030238;C:412959654;G:377713613;T:456111038;N:53079 51 0     400030238 412959654 377713613 456111038 53079 SRX2148082 SRS1679260 SRA464955 GEO Stowers Institute for Medical Research 1 0.81411   0.10419   0.70621   0.48075   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2016-09-08 Pharyngula Embryo Tail Multi-system
41419 41419 SRR4423117 SRX2245301 SRS1745860 SRP091534 PRJNA347637 Danio rerio and Xenopus laevis Raw sequence reads PRJNA347637 Other To study the transcriptome during development         Adult FT Dr   strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish: Adult female tail 172 3 172 3 Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   SRP091534     femaletailRID0172BC03largeZF.fastq fastq 1414932187.0 9757587.0 femaletailRID0172BC03largeZF.fastq 0:145.01 A:343007105;C:362895564;G:422320111;T:286709407;N:0 145       343007105 362895564 422320111 286709407 0 SRX2245301 SRS1745860 SRA485147 Universiteit van Amsterdam|SILS Universiteit van Amsterdam 1 0.96057   0.21796   0.95177   0.76663   141   B   usable mapping rate ion_torrent ion_torrent unknown cdna_unspecified unknown bulk unknown unknown   Netherlands 2016-10-19 Adult Adult Tail Multi-system
63892 63892 SRR14213374 SRX10579919 SRS8684387 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Tail3 GSM5237143   source name:zebrafish tail|genotype:wild type|tissue:tail|strain:TLAB Tail3 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish tail   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:tail|strain:TLAB GSM5237143 GSM5237143: Tail3; Danio rerio; RNA Seq GSM5237143   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237143 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Tail3.fastq fastq 1351349800.0 13513498.0 GSM5237143 r1 0:100 A:344334043;C:321881505;G:312915864;T:372166616;N:51772 100       344334043 321881505 312915864 372166616 51772 SRX10579919 SRS8684387 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.93634   0.09976   0.75521   0.48801   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Tail Multi-system
63893 63893 SRR14213373 SRX10579918 SRS8684386 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Tail2 GSM5237142   source name:zebrafish tail|genotype:wild type|tissue:tail|strain:TLAB Tail2 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish tail   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:tail|strain:TLAB GSM5237142 GSM5237142: Tail2; Danio rerio; RNA Seq GSM5237142   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237142 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Tail2.fastq fastq 1669271300.0 16692713.0 GSM5237142 r1 0:100 A:422977972;C:402400334;G:387344093;T:456484890;N:64011 100       422977972 402400334 387344093 456484890 64011 SRX10579918 SRS8684386 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.93177   0.10145   0.75532   0.47775   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Tail Multi-system
63894 63894 SRR14213372 SRX10579917 SRS8684385 SRP314470 PRJNA721381 RNA Seq from zebrafish adult tissues GSE171906 Transcriptome Analysis The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.   pubmed:34556579   Tail1 GSM5237141   source name:zebrafish tail|genotype:wild type|tissue:tail|strain:TLAB Tail1 Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM zebrafish tail   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|tissue:tail|strain:TLAB GSM5237141 GSM5237141: Tail1; Danio rerio; RNA Seq GSM5237141   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM5237141 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP314470     Tail1.fastq fastq 2117983600.0 21179836.0 GSM5237141 r1 0:100 A:534692684;C:517420692;G:497313091;T:568475177;N:81956 100       534692684 517420692 497313091 568475177 81956 SRX10579917 SRS8684385 SRA1217576 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.93316   0.11572   0.74951   0.48824   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2021-04-12 Undetermined Undetermined Tail Multi-system
69019 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.   pubmed:36594016   17656X12 GSM5949315   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69020 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.   pubmed:36594016   17656X11 GSM5949314   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69021 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.   pubmed:36594016   17656X10 GSM5949313   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69022 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.   pubmed:36594016   17656X9 GSM5949312   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69023 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.   pubmed:36594016   17656X8 GSM5949311   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69024 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.   pubmed:36594016   17656X7 GSM5949310   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69025 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.   pubmed:36594016   17656X5 GSM5949309   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69026 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.   pubmed:36594016   17656X4 GSM5949308   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69027 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.   pubmed:36594016   17656X3 GSM5949307   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69028 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.   pubmed:36594016   17656X2 GSM5949306   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
69029 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.   pubmed:36594016   17656X1 GSM5949305   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP363665   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     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   United States 2022-03-11 Pharyngula Embryo Tail Multi-system
72464 72464 SRR22574253 SRX18537350 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   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 or animal                 wt 2 R1.fastq wt 2 R1.fastq wt 2 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     wt_2_R1.fastq.gz wt_2_R2.fastq.gz fastq fastq 20138999100.0 67129997.0 wt 2 R1.fastq.gz 0:150 1:150 A:5269495885;C:4709732469;G:4941455861;T:5217751419;N:563466 150 150     5269495885 4709732469 4941455861 5217751419 563466 SRX18537350 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95899 0.96368 0.14222 0.14005 0.82102 0.81862 0.43313 0.43965 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72465 72465 SRR22574254 SRX18537349 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   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 or animal                 wt 1 R1.fastq wt 1 R1.fastq wt 1 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     wt_1_R1.fastq.gz wt_1_R2.fastq.gz fastq fastq 23358126000.0 77860420.0 wt 1 R1.fastq.gz 0:150 1:150 A:6038817592;C:5541964880;G:5789495907;T:5987202665;N:644956 150 150     6038817592 5541964880 5789495907 5987202665 644956 SRX18537349 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.95378 0.95798 0.14042 0.13872 0.82065 0.81809 0.45238 0.37872 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72466 72466 SRR22574255 SRX18537348 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   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 or animal                 mut 2 R1.fastq mut 2 R1.fastq mut 2 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     mut_2_R1.fastq.gz mut_2_R2.fastq.gz fastq fastq 19326017700.0 64420059.0 mut 2 R1.fastq.gz 0:150 1:150 A:5060790268;C:4512966975;G:4744771851;T:5006953597;N:535009 150 150     5060790268 4512966975 4744771851 5006953597 535009 SRX18537348 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   China 2022-12-08 Juvenile Juvenile Tail Multi-system
72467 72467 SRR22574256 SRX18537347 SRS16001767 SRP411954 PRJNA909445 Danio rerio Raw sequence reads PRJNA909445 Other Whole transcriptome analysis       Model organism or animal sample from zebrafish zebrafish strains with IBs wild type fish and without xxx runx2b gene editing fish   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 or animal                 mut 1 R1.fastq mut 1 R1.fastq mut 1 R1.fastq tail muscule     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP411954     mut_1_R1.fastq.gz mut_1_R2.fastq.gz fastq fastq 22794782400.0 75982608.0 mut 1 R1.fastq.gz 0:150 1:150 A:5961354939;C:5333450654;G:5606279874;T:5893060023;N:636910 150 150     5961354939 5333450654 5606279874 5893060023 636910 SRX18537347 SRS16001767 SRA1555446 Fisheries College of Huazhong Agricultural University|Fisheries College of Huazhong Agricultural Univers Fisheries College of Huazhong Agricultural University 2 0.9557 0.95853 0.14259 0.13878 0.81771 0.81533 0.45125 0.3948 150 150 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2022-12-08 Juvenile Juvenile Tail Multi-system
74635 74635 SRR23908128 SRX19719610 SRS17086727 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       tail WT 3 GSM7104974   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’s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt tail   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.   tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf GSM7104974 GSM7104974: tail WT 3; Danio rerio; RNA Seq GSM7104974 r1 GSM7104974 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP428084   loader:fastq load.py WT_3_1.fq.gz WT_3_2.fq.gz fastq fastq 6599139300.0 21997131.0 GSM7104974 r1 0:150 1:150 A:1862099481;C:1460254817;G:1446030038;T:1828044493;N:2710471 150 150     1862099481 1460254817 1446030038 1828044493 2710471 SRX19719610 SRS17086727 SRA1606833 South China University of Technology South China University of Technology 2 0.93499 0.93641 0.11822 0.11847 0.66561 0.66636 0.47204 0.47094 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-03-19 Larval Larval Tail Multi-system
74636 74636 SRR23908129 SRX19719609 SRS17086726 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       tail WT 2 GSM7104973   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’s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt tail   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.   tissue:tail|genotype:WT|developmental stage:larvae at 3 dpf GSM7104973 GSM7104973: tail WT 2; Danio rerio; RNA Seq GSM7104973 r1 GSM7104973 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP428084   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     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   China 2023-03-19 Larval Larval Tail Multi-system
74637 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       tail WT 1 GSM7104972   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’s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt tail   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP428084   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     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   China 2023-03-19 Larval Larval Tail Multi-system
74638 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       tail S6M 3 GSM7104971   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’s approach for controlling the false discovery rate . Assembly: GRCz11 Supplementary files format and content: gene fpkm.txt tail   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP428084   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     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   China 2023-03-19 Larval Larval Tail Multi-system

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