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run_metadata

719 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Tail"

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devstage_curation 7

technology 5

devstage_curation_coarse 4

experiment.platform 3

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Tail · 719 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 719 ✖

experiment.library_selection 1

  • cDNA · 719 ✖
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
28818 28818 SRR26711836 SRX22410952 SRS19443730 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 4 GSM7885889   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885889 GSM7885889: rad21 heterozugous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885889 r1 GSM7885889 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-8-HET_S32_L001_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L001_R1_001.fastq.gz fastq fastq 3261739218.0 21610373.0 GSM7885889 r1 0:75.52 1:75.42 A:816426262;C:810367718;G:804831968;T:829974289;N:138981 75 75     816426262 810367718 804831968 829974289 138981 SRX22410952 SRS19443730 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96738 0.97053 0.05473 0.05415 0.72283 0.72338 0.46691 0.46731 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28819 28819 SRR26711837 SRX22410952 SRS19443730 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 4 GSM7885889   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885889 GSM7885889: rad21 heterozugous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885889 r1 GSM7885889 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-8-HET_S32_L002_R2_001.fastq.gz Rad21-BIO-8-HET_S32_L002_R1_001.fastq.gz fastq fastq 3279254436.0 21726495.0 GSM7885889 r2 0:75.52 1:75.42 A:821154343;C:814711347;G:809025779;T:834224252;N:138715 75 75     821154343 814711347 809025779 834224252 138715 SRX22410952 SRS19443730 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96764 0.97012 0.05449 0.05364 0.72362 0.72478 0.46065 0.44816 75 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28820 28820 SRR26711838 SRX22410951 SRS19443729 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 4 GSM7885888   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885888 GSM7885888: rad21 homozygous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885888 r1 GSM7885888 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-4-MUT_S31_L001_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L001_R2_001.fastq.gz fastq fastq 3815700579.0 25275353.0 GSM7885888 r1 0:75.53 1:75.43 A:962537652;C:941667596;G:934433379;T:976947974;N:113978 75 75     962537652 941667596 934433379 976947974 113978 SRX22410951 SRS19443729 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96535 0.96731 0.06446 0.06372 0.71928 0.71956 0.47233 0.47166 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28821 28821 SRR26711839 SRX22410951 SRS19443729 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 4 GSM7885888   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885888 GSM7885888: rad21 homozygous tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885888 r1 GSM7885888 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-4-MUT_S31_L002_R1_001.fastq.gz Rad21-BIO-4-MUT_S31_L002_R2_001.fastq.gz fastq fastq 3837906036.0 25422663.0 GSM7885888 r2 0:75.53 1:75.43 A:968455256;C:947191550;G:939808490;T:982330983;N:119757 75 75     968455256 947191550 939808490 982330983 119757 SRX22410951 SRS19443729 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96615 0.96781 0.0624 0.06196 0.71725 0.71827 0.47042 0.46294 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28822 28822 SRR26711840 SRX22410950 SRS19443727 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 4 GSM7885887   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885887 GSM7885887: rad21 heterozugous tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885887 r1 GSM7885887 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-8-HET_S30_L001_R2_001.fastq.gz Rad21-8-HET_S30_L001_R1_001.fastq.gz fastq fastq 4150580457.0 27506773.0 GSM7885887 r1 0:75.51 1:75.39 A:1061191322;C:1016515755;G:1039117012;T:1033588629;N:167739 75 75     1061191322 1016515755 1039117012 1033588629 167739 SRX22410950 SRS19443727 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96699 0.96687 0.0501 0.04959 0.71642 0.72017 0.44914 0.44833 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28823 28823 SRR26711841 SRX22410950 SRS19443727 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 4 GSM7885887   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885887 GSM7885887: rad21 heterozugous tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885887 r1 GSM7885887 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-8-HET_S30_L002_R2_001.fastq.gz Rad21-8-HET_S30_L002_R1_001.fastq.gz fastq fastq 4170430033.0 27638560.0 GSM7885887 r2 0:75.50 1:75.39 A:1067297262;C:1021226653;G:1043544460;T:1038184807;N:176851 75 75     1067297262 1021226653 1043544460 1038184807 176851 SRX22410950 SRS19443727 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96619 0.96635 0.05062 0.05015 0.7139 0.71918 0.44965 0.45175 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28824 28824 SRR26711842 SRX22410949 SRS19443728 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 4 GSM7885886   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885886 GSM7885886: rad21 homozygous tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885886 r1 GSM7885886 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-4-MUT_S29_L001_R1_001.fastq.gz Rad21-4-MUT_S29_L001_R2_001.fastq.gz fastq fastq 3860758586.0 25585267.0 GSM7885886 r1 0:75.50 1:75.40 A:962978350;C:961963514;G:957530709;T:978120083;N:165930 75 75     962978350 961963514 957530709 978120083 165930 SRX22410949 SRS19443728 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96679 0.96899 0.05708 0.05592 0.71991 0.72021 0.44331 0.44736 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28825 28825 SRR26711843 SRX22410949 SRS19443728 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 4 GSM7885886   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885886 GSM7885886: rad21 homozygous tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885886 r1 GSM7885886 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-4-MUT_S29_L002_R1_001.fastq.gz Rad21-4-MUT_S29_L002_R2_001.fastq.gz fastq fastq 3886411017.0 25755387.0 GSM7885886 r2 0:75.50 1:75.40 A:969709828;C:968345638;G:963787543;T:984390915;N:177093 75 75     969709828 968345638 963787543 984390915 177093 SRX22410949 SRS19443728 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96682 0.96836 0.05697 0.05624 0.71812 0.71819 0.4505 0.44685 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28826 28826 SRR26711844 SRX22410948 SRS19443726 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 4 GSM7885885   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885885 GSM7885885: stag2b tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885885 r1 GSM7885885 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-4_S28_L001_R1_001.fastq.gz S2B-BIO-4_S28_L001_R2_001.fastq.gz fastq fastq 3727162917.0 24693169.0 GSM7885885 r1 0:75.53 1:75.41 A:922580573;C:935922329;G:933433047;T:935120514;N:106454 75 75     922580573 935922329 933433047 935120514 106454 SRX22410948 SRS19443726 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96731 0.96936 0.04393 0.04403 0.72234 0.72397 0.46015 0.45955 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28827 28827 SRR26711845 SRX22410948 SRS19443726 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 4 GSM7885885   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885885 GSM7885885: stag2b tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885885 r1 GSM7885885 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-4_S28_L002_R1_001.fastq.gz S2B-BIO-4_S28_L002_R2_001.fastq.gz fastq fastq 3749916462.0 24844024.0 GSM7885885 r2 0:75.53 1:75.41 A:928588967;C:941571510;G:939049263;T:940598432;N:108290 75 75     928588967 941571510 939049263 940598432 108290 SRX22410948 SRS19443726 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96668 0.96881 0.04401 0.04387 0.72387 0.72519 0.45814 0.457 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28828 28828 SRR26711846 SRX22410947 SRS19443724 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 4 GSM7885884   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885884 GSM7885884: stag2b tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885884 r1 GSM7885884 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-4_S27_L001_R1_001.fastq.gz S2B-4_S27_L001_R2_001.fastq.gz fastq fastq 4559287327.0 30217717.0 GSM7885884 r1 0:75.49 1:75.39 A:1129871064;C:1144626195;G:1141080047;T:1143531432;N:178589 75 75     1129871064 1144626195 1141080047 1143531432 178589 SRX22410947 SRS19443724 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96507 0.96728 0.04397 0.04385 0.72338 0.72456 0.44876 0.45623 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28829 28829 SRR26711847 SRX22410947 SRS19443724 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 4 GSM7885884   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885884 GSM7885884: stag2b tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885884 r1 GSM7885884 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-4_S27_L002_R1_001.fastq.gz S2B-4_S27_L002_R2_001.fastq.gz fastq fastq 4586674313.0 30399355.0 GSM7885884 r2 0:75.49 1:75.39 A:1137101056;C:1151500029;G:1147768493;T:1150129054;N:175681 75 75     1137101056 1151500029 1147768493 1150129054 175681 SRX22410947 SRS19443724 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96454 0.96735 0.04449 0.04408 0.72435 0.72583 0.45339 0.45434 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28830 28830 SRR26711848 SRX22410946 SRS19443725 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 4 GSM7885883   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885883 GSM7885883: Wild type tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885883 r1 GSM7885883 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-4_S26_L001_R2_001.fastq.gz WT-BIO-4_S26_L001_R1_001.fastq.gz fastq fastq 5251141754.0 34808166.0 GSM7885883 r1 0:75.48 1:75.38 A:1316653671;C:1303617399;G:1296205519;T:1334442750;N:222415 75 75     1316653671 1303617399 1296205519 1334442750 222415 SRX22410946 SRS19443725 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96497 0.96673 0.04868 0.04837 0.72332 0.72324 0.47006 0.45832 75 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28831 28831 SRR26711849 SRX22410946 SRS19443725 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 4 GSM7885883   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885883 GSM7885883: Wild type tailbud Wnt stimulation replicate 4; Danio rerio; RNA Seq GSM7885883 r1 GSM7885883 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-4_S26_L002_R2_001.fastq.gz WT-BIO-4_S26_L002_R1_001.fastq.gz fastq fastq 5280302307.0 35001391.0 GSM7885883 r2 0:75.48 1:75.38 A:1324401398;C:1310930748;G:1303177704;T:1341576726;N:215731 75 75     1324401398 1310930748 1303177704 1341576726 215731 SRX22410946 SRS19443725 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96424 0.96713 0.04917 0.04864 0.72241 0.72271 0.46443 0.45274 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28832 28832 SRR26711850 SRX22410945 SRS19443723 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 4 GSM7885882   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885882 GSM7885882: Wild type tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885882 r1 GSM7885882 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT4_S25_L001_R1_001.fastq.gz WT4_S25_L001_R2_001.fastq.gz fastq fastq 7405469360.0 49089434.0 GSM7885882 r1 0:75.49 1:75.37 A:1847973647;C:1841169648;G:1840295933;T:1875743550;N:286582 75 75     1847973647 1841169648 1840295933 1875743550 286582 SRX22410945 SRS19443723 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96338 0.96738 0.04317 0.04296 0.71737 0.71851 0.45679 0.45543 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28833 28833 SRR26711851 SRX22410945 SRS19443723 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 4 GSM7885882   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 4 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885882 GSM7885882: Wild type tailbud no treatment replicate 4; Danio rerio; RNA Seq GSM7885882 r1 GSM7885882 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT4_S25_L002_R1_001.fastq.gz WT4_S25_L002_R2_001.fastq.gz fastq fastq 7449020435.0 49378676.0 GSM7885882 r2 0:75.48 1:75.37 A:1859225781;C:1852173354;G:1850890621;T:1886441454;N:289225 75 75     1859225781 1852173354 1850890621 1886441454 289225 SRX22410945 SRS19443723 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96307 0.9662 0.04334 0.04269 0.7167 0.71679 0.45909 0.45956 75 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28834 28834 SRR26711852 SRX22410944 SRS19443721 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 3 GSM7885881   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885881 GSM7885881: rad21 heterozugous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885881 r1 GSM7885881 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-7-HET_S24_L001_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L001_R2_001.fastq.gz fastq fastq 3984218790.0 26397905.0 GSM7885881 r1 0:75.51 1:75.42 A:1024724878;C:960806363;G:958470013;T:1040115284;N:102252 75 75     1024724878 960806363 958470013 1040115284 102252 SRX22410944 SRS19443721 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95932 0.96163 0.06729 0.06702 0.71979 0.71981 0.4528 0.4607 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28835 28835 SRR26711853 SRX22410944 SRS19443721 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 3 GSM7885881   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885881 GSM7885881: rad21 heterozugous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885881 r1 GSM7885881 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-7-HET_S24_L002_R1_001.fastq.gz Rad21-BIO-7-HET_S24_L002_R2_001.fastq.gz fastq fastq 4008829445.0 26560912.0 GSM7885881 r2 0:75.51 1:75.42 A:1031275075;C:966838521;G:964312635;T:1046301501;N:101713 75 75     1031275075 966838521 964312635 1046301501 101713 SRX22410944 SRS19443721 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.9587 0.96152 0.06791 0.06665 0.71989 0.72157 0.45962 0.46712 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28836 28836 SRR26711854 SRX22410943 SRS19443722 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 3 GSM7885880   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885880 GSM7885880: rad21 homozygous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885880 r1 GSM7885880 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-3-MUT_S23_L001_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L001_R2_001.fastq.gz fastq fastq 5599192259.0 37097144.0 GSM7885880 r1 0:75.51 1:75.43 A:1432393511;C:1358888032;G:1349825352;T:1457936919;N:148445 75 75     1432393511 1358888032 1349825352 1457936919 148445 SRX22410943 SRS19443722 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96008 0.96296 0.0752 0.07458 0.71518 0.71595 0.45869 0.45262 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28837 28837 SRR26711855 SRX22410943 SRS19443722 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 3 GSM7885880   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885880 GSM7885880: rad21 homozygous tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885880 r1 GSM7885880 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-3-MUT_S23_L002_R1_001.fastq.gz Rad21-BIO-3-MUT_S23_L002_R2_001.fastq.gz fastq fastq 5635998309.0 37340801.0 GSM7885880 r2 0:75.51 1:75.43 A:1442157325;C:1367898781;G:1358570964;T:1467225614;N:145625 75 75     1442157325 1367898781 1358570964 1467225614 145625 SRX22410943 SRS19443722 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95976 0.96205 0.07516 0.07494 0.71415 0.71498 0.4588 0.45974 75 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28838 28838 SRR26711856 SRX22410942 SRS19443720 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 3 GSM7885879   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885879 GSM7885879: rad21 heterozugous tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885879 r1 GSM7885879 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-7-HET_S22_L001_R1_001.fastq.gz Rad21-7-HET_S22_L001_R2_001.fastq.gz fastq fastq 3991372523.0 26445612.0 GSM7885879 r1 0:75.50 1:75.43 A:1041422592;C:951170399;G:942539955;T:1056130915;N:108662 75 75     1041422592 951170399 942539955 1056130915 108662 SRX22410942 SRS19443720 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.956 0.9592 0.07986 0.07892 0.71336 0.71407 0.45912 0.45547 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28839 28839 SRR26711857 SRX22410942 SRS19443720 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 3 GSM7885879   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885879 GSM7885879: rad21 heterozugous tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885879 r1 GSM7885879 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-7-HET_S22_L002_R1_001.fastq.gz Rad21-7-HET_S22_L002_R2_001.fastq.gz fastq fastq 4014736816.0 26600423.0 GSM7885879 r2 0:75.50 1:75.43 A:1047767788;C:956861322;G:947979944;T:1062023242;N:104520 75 75     1047767788 956861322 947979944 1062023242 104520 SRX22410942 SRS19443720 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95647 0.9597 0.07844 0.07753 0.71342 0.71449 0.45886 0.45627 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28840 28840 SRR26711858 SRX22410941 SRS19443719 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 3 GSM7885878   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885878 GSM7885878: rad21 homozygous tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885878 r1 GSM7885878 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-3-MUT_S21_L001_R1_001.fastq.gz Rad21-3-MUT_S21_L001_R2_001.fastq.gz fastq fastq 4087719740.0 27096477.0 GSM7885878 r1 0:75.47 1:75.39 A:1036209125;C:1001425527;G:987804368;T:1062147338;N:133382 75 75     1036209125 1001425527 987804368 1062147338 133382 SRX22410941 SRS19443719 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95988 0.9638 0.06968 0.06927 0.71407 0.7136 0.454 0.45623 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28841 28841 SRR26711859 SRX22410941 SRS19443719 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 3 GSM7885878   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885878 GSM7885878: rad21 homozygous tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885878 r1 GSM7885878 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-3-MUT_S21_L002_R1_001.fastq.gz Rad21-3-MUT_S21_L002_R2_001.fastq.gz fastq fastq 4118276880.0 27299338.0 GSM7885878 r2 0:75.47 1:75.38 A:1044090882;C:1009018215;G:995236418;T:1069786789;N:144576 75 75     1044090882 1009018215 995236418 1069786789 144576 SRX22410941 SRS19443719 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96038 0.96408 0.06924 0.06885 0.71405 0.71346 0.46106 0.46176 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28842 28842 SRR26711860 SRX22410940 SRS19443718 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 3 GSM7885877   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885877 GSM7885877: stag2b tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885877 r1 GSM7885877 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-3_S20_L001_R2_001.fastq.gz S2B-BIO-3_S20_L001_R1_001.fastq.gz fastq fastq 6393544263.0 42359569.0 GSM7885877 r1 0:75.52 1:75.42 A:1613857834;C:1576676813;G:1555975373;T:1646885701;N:148542 75 75     1613857834 1576676813 1555975373 1646885701 148542 SRX22410940 SRS19443718 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96254 0.96412 0.05789 0.05657 0.71928 0.71952 0.45598 0.4571 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28843 28843 SRR26711861 SRX22410940 SRS19443718 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 3 GSM7885877   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885877 GSM7885877: stag2b tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885877 r1 GSM7885877 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-3_S20_L002_R1_001.fastq.gz S2B-BIO-3_S20_L002_R2_001.fastq.gz fastq fastq 6434553541.0 42631351.0 GSM7885877 r2 0:75.52 1:75.42 A:1624553501;C:1586927728;G:1565855680;T:1657071521;N:145111 75 75     1624553501 1586927728 1565855680 1657071521 145111 SRX22410940 SRS19443718 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96161 0.96439 0.05708 0.057 0.71877 0.71885 0.45079 0.45162 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28844 28844 SRR26711862 SRX22410939 SRS19443717 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 3 GSM7885876   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885876 GSM7885876: stag2b tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885876 r1 GSM7885876 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-3_S19_L001_R2_001.fastq.gz S2B-3_S19_L001_R1_001.fastq.gz fastq fastq 5538483383.0 36711860.0 GSM7885876 r1 0:75.47 1:75.39 A:1435032372;C:1328594066;G:1316913430;T:1457777034;N:166481 75 75     1435032372 1328594066 1316913430 1457777034 166481 SRX22410939 SRS19443717 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95388 0.95759 0.06115 0.05971 0.72494 0.72437 0.45251 0.45094 75 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28845 28845 SRR26711863 SRX22410939 SRS19443717 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 3 GSM7885876   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885876 GSM7885876: stag2b tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885876 r1 GSM7885876 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-3_S19_L002_R2_001.fastq.gz S2B-3_S19_L002_R1_001.fastq.gz fastq fastq 5571956623.0 36933840.0 GSM7885876 r2 0:75.47 1:75.39 A:1444099757;C:1336600251;G:1324816524;T:1466267099;N:172992 75 75     1444099757 1336600251 1324816524 1466267099 172992 SRX22410939 SRS19443717 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95377 0.95715 0.06134 0.06056 0.72342 0.72399 0.45371 0.45229 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28846 28846 SRR26711864 SRX22410938 SRS19443716 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 3 GSM7885875   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885875 GSM7885875: Wild type tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885875 r1 GSM7885875 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-3_S18_L001_R2_001.fastq.gz WT-BIO-3_S18_L001_R1_001.fastq.gz fastq fastq 2907588427.0 19272780.0 GSM7885875 r1 0:75.47 1:75.39 A:744742520;C:704673544;G:696135407;T:761933560;N:103396 75 75     744742520 704673544 696135407 761933560 103396 SRX22410938 SRS19443716 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95667 0.96068 0.06758 0.06662 0.71654 0.71695 0.46152 0.46391 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28847 28847 SRR26711865 SRX22410938 SRS19443716 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 3 GSM7885875   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885875 GSM7885875: Wild type tailbud Wnt stimulation replicate 3; Danio rerio; RNA Seq GSM7885875 r1 GSM7885875 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-3_S18_L002_R2_001.fastq.gz WT-BIO-3_S18_L002_R1_001.fastq.gz fastq fastq 2928304522.0 19409983.0 GSM7885875 r2 0:75.47 1:75.39 A:750212329;C:709699732;G:701107247;T:767185941;N:99273 75 75     750212329 709699732 701107247 767185941 99273 SRX22410938 SRS19443716 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95734 0.96043 0.06712 0.06582 0.71764 0.71829 0.46986 0.46257 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28848 28848 SRR26711866 SRX22410937 SRS19443715 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 3 GSM7885874   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885874 GSM7885874: Wild type tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885874 r1 GSM7885874 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT3_S17_L001_R2_001.fastq.gz WT3_S17_L001_R1_001.fastq.gz fastq fastq 6706792771.0 44471190.0 GSM7885874 r1 0:75.45 1:75.37 A:1721256764;C:1618398945;G:1602221748;T:1764649478;N:265836 75 75     1721256764 1618398945 1602221748 1764649478 265836 SRX22410937 SRS19443715 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95476 0.95901 0.0654 0.06441 0.71821 0.71764 0.46826 0.46883 75 73 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28849 28849 SRR26711867 SRX22410937 SRS19443715 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 3 GSM7885874   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 3 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885874 GSM7885874: Wild type tailbud no treatment replicate 3; Danio rerio; RNA Seq GSM7885874 r1 GSM7885874 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT3_S17_L002_R1_001.fastq.gz WT3_S17_L002_R2_001.fastq.gz fastq fastq 6751557772.0 44768192.0 GSM7885874 r2 0:75.45 1:75.37 A:1732864650;C:1629248349;G:1613082990;T:1776088109;N:273674 75 75     1732864650 1629248349 1613082990 1776088109 273674 SRX22410937 SRS19443715 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95584 0.95991 0.0649 0.0638 0.71819 0.71855 0.47015 0.46826 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28850 28850 SRR26711868 SRX22410936 SRS19443714 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 2 GSM7885873   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885873 GSM7885873: rad21 heterozugous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885873 r1 GSM7885873 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-6-HET_S16_L001_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L001_R2_001.fastq.gz fastq fastq 10402910048.0 68936909.0 GSM7885873 r1 0:75.49 1:75.41 A:2678222257;C:2507951720;G:2508878864;T:2707580436;N:276771 75 75     2678222257 2507951720 2508878864 2707580436 276771 SRX22410936 SRS19443714 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95996 0.96303 0.07074 0.07121 0.7176 0.71977 0.46271 0.46279 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28851 28851 SRR26711869 SRX22410936 SRS19443714 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 2 GSM7885873   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885873 GSM7885873: rad21 heterozugous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885873 r1 GSM7885873 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-6-HET_S16_L002_R1_001.fastq.gz Rad21-BIO-6-HET_S16_L002_R2_001.fastq.gz fastq fastq 10457419135.0 69298126.0 GSM7885873 r2 0:75.49 1:75.41 A:2693018275;C:2521215208;G:2521858256;T:2721040335;N:287061 75 75     2693018275 2521215208 2521858256 2721040335 287061 SRX22410936 SRS19443714 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95978 0.962 0.07287 0.07218 0.71928 0.72015 0.4627 0.46327 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28852 28852 SRR26711870 SRX22410935 SRS19443713 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 2 GSM7885872   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885872 GSM7885872: rad21 homozygous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885872 r1 GSM7885872 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-2-MUT_S15_L001_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L001_R1_001.fastq.gz fastq fastq 7186685076.0 47626097.0 GSM7885872 r1 0:75.50 1:75.40 A:1840710532;C:1745543326;G:1746892421;T:1853340863;N:197934 75 75     1840710532 1745543326 1746892421 1853340863 197934 SRX22410935 SRS19443713 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96231 0.96418 0.06946 0.06881 0.71756 0.71873 0.46166 0.45998 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28853 28853 SRR26711871 SRX22410935 SRS19443713 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 2 GSM7885872   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885872 GSM7885872: rad21 homozygous tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885872 r1 GSM7885872 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-2-MUT_S15_L002_R2_001.fastq.gz Rad21-BIO-2-MUT_S15_L002_R1_001.fastq.gz fastq fastq 7224888168.0 47879502.0 GSM7885872 r2 0:75.50 1:75.40 A:1851188490;C:1754962659;G:1755894085;T:1862643357;N:199577 75 75     1851188490 1754962659 1755894085 1862643357 199577 SRX22410935 SRS19443713 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96174 0.96335 0.06858 0.06794 0.71624 0.71752 0.46477 0.46238 74 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28854 28854 SRR26711872 SRX22410934 SRS19443712 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 2 GSM7885871   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885871 GSM7885871: rad21 heterozugous tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885871 r1 GSM7885871 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-6-HET_S14_L001_R2_001.fastq.gz Rad21-6-HET_S14_L001_R1_001.fastq.gz fastq fastq 5920802946.0 39225537.0 GSM7885871 r1 0:75.52 1:75.42 A:1518148809;C:1443498311;G:1449929695;T:1509064332;N:161799 75 75     1518148809 1443498311 1449929695 1509064332 161799 SRX22410934 SRS19443712 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96404 0.96544 0.06392 0.06339 0.71825 0.71956 0.45911 0.44993 75 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28855 28855 SRR26711873 SRX22410934 SRS19443712 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 2 GSM7885871   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885871 GSM7885871: rad21 heterozugous tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885871 r1 GSM7885871 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-6-HET_S14_L002_R1_001.fastq.gz Rad21-6-HET_S14_L002_R2_001.fastq.gz fastq fastq 5948197274.0 39406919.0 GSM7885871 r2 0:75.52 1:75.42 A:1525770407;C:1450296537;G:1456334492;T:1515638367;N:157471 75 75     1525770407 1450296537 1456334492 1515638367 157471 SRX22410934 SRS19443712 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.9635 0.96517 0.06272 0.06248 0.71804 0.72202 0.45512 0.45879 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28856 28856 SRR26711874 SRX22410933 SRS19443711 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 2 GSM7885870   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885870 GSM7885870: rad21 homozygous tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885870 r1 GSM7885870 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-9-MUT_S13_L001_R2_001.fastq.gz Rad21-9-MUT_S13_L001_R1_001.fastq.gz fastq fastq 4731957733.0 31354997.0 GSM7885870 r1 0:75.51 1:75.41 A:1201221275;C:1160116117;G:1163056871;T:1207419408;N:144062 75 75     1201221275 1160116117 1163056871 1207419408 144062 SRX22410933 SRS19443711 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96425 0.96472 0.06588 0.06468 0.71687 0.71942 0.4434 0.44236 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28857 28857 SRR26711875 SRX22410933 SRS19443711 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 2 GSM7885870   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885870 GSM7885870: rad21 homozygous tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885870 r1 GSM7885870 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-9-MUT_S13_L002_R1_001.fastq.gz Rad21-9-MUT_S13_L002_R2_001.fastq.gz fastq fastq 4757933550.0 31527251.0 GSM7885870 r2 0:75.51 1:75.41 A:1208392417;C:1166483269;G:1169184243;T:1213729419;N:144202 75 75     1208392417 1166483269 1169184243 1213729419 144202 SRX22410933 SRS19443711 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96375 0.96493 0.06559 0.06422 0.71774 0.71922 0.44693 0.43358 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28858 28858 SRR26711876 SRX22410932 SRS19443710 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 2 GSM7885869   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885869 GSM7885869: stag2b tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885869 r1 GSM7885869 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-2_S12_L001_R1_001.fastq.gz S2B-BIO-2_S12_L001_R2_001.fastq.gz fastq fastq 3434334163.0 22753985.0 GSM7885869 r1 0:75.51 1:75.42 A:874466456;C:839309146;G:839975055;T:880508590;N:74916 75 75     874466456 839309146 839975055 880508590 74916 SRX22410932 SRS19443710 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96096 0.96302 0.06063 0.06064 0.71676 0.7177 0.45781 0.45685 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28859 28859 SRR26711877 SRX22410932 SRS19443710 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 2 GSM7885869   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885869 GSM7885869: stag2b tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885869 r1 GSM7885869 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-2_S12_L002_R1_001.fastq.gz S2B-BIO-2_S12_L002_R2_001.fastq.gz fastq fastq 3455106879.0 22891438.0 GSM7885869 r2 0:75.52 1:75.42 A:880118959;C:844367467;G:844856793;T:885694827;N:68833 75 75     880118959 844367467 844856793 885694827 68833 SRX22410932 SRS19443710 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96044 0.96247 0.06148 0.06124 0.71892 0.72019 0.45384 0.45979 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28860 28860 SRR26711878 SRX22410931 SRS19443708 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 2 GSM7885868   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885868 GSM7885868: stag2b tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885868 r1 GSM7885868 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-2_S11_L001_R1_001.fastq.gz S2B-2_S11_L001_R2_001.fastq.gz fastq fastq 3538294337.0 23437308.0 GSM7885868 r1 0:75.53 1:75.44 A:911440182;C:854797688;G:851200714;T:920789817;N:65936 75 75     911440182 854797688 851200714 920789817 65936 SRX22410931 SRS19443708 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95621 0.95881 0.06034 0.05969 0.71816 0.71892 0.45142 0.45093 75 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28861 28861 SRR26711879 SRX22410931 SRS19443708 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 2 GSM7885868   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885868 GSM7885868: stag2b tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885868 r1 GSM7885868 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-2_S11_L002_R1_001.fastq.gz S2B-2_S11_L002_R2_001.fastq.gz fastq fastq 3556484158.0 23557941.0 GSM7885868 r2 0:75.53 1:75.44 A:916293958;C:859339499;G:855534732;T:925247442;N:68527 75 75     916293958 859339499 855534732 925247442 68527 SRX22410931 SRS19443708 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95449 0.95714 0.05993 0.05895 0.7207 0.72174 0.44213 0.44014 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28862 28862 SRR26711880 SRX22410930 SRS19443709 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 2 GSM7885867   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885867 GSM7885867: Wild type tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885867 r1 GSM7885867 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-2_S10_L001_R1_001.fastq.gz WT-BIO-2_S10_L001_R2_001.fastq.gz fastq fastq 4962467069.0 32885292.0 GSM7885867 r1 0:75.49 1:75.41 A:1261895016;C:1212881283;G:1199367390;T:1288195310;N:128070 75 75     1261895016 1212881283 1199367390 1288195310 128070 SRX22410930 SRS19443709 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96086 0.96361 0.06058 0.05969 0.71679 0.71614 0.46741 0.47167 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28863 28863 SRR26711881 SRX22410930 SRS19443709 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 2 GSM7885867   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885867 GSM7885867: Wild type tailbud Wnt stimulation replicate 2; Danio rerio; RNA Seq GSM7885867 r1 GSM7885867 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-2_S10_L002_R1_001.fastq.gz WT-BIO-2_S10_L002_R2_001.fastq.gz fastq fastq 4987807658.0 33053054.0 GSM7885867 r2 0:75.50 1:75.41 A:1268585681;C:1219140011;G:1205507373;T:1294443086;N:131507 75 75     1268585681 1219140011 1205507373 1294443086 131507 SRX22410930 SRS19443709 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96019 0.96278 0.0598 0.05932 0.71837 0.71942 0.46581 0.46052 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28864 28864 SRR26711882 SRX22410929 SRS19443707 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 2 GSM7885866   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885866 GSM7885866: Wild type tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885866 r1 GSM7885866 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT2_S9_L001_R1_001.fastq.gz WT2_S9_L001_R2_001.fastq.gz fastq fastq 4886840867.0 32385548.0 GSM7885866 r1 0:75.49 1:75.41 A:1236862700;C:1194914216;G:1187547323;T:1267379660;N:136968 75 75     1236862700 1194914216 1187547323 1267379660 136968 SRX22410929 SRS19443707 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95919 0.96199 0.05896 0.0586 0.71555 0.71587 0.46036 0.46125 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28865 28865 SRR26711883 SRX22410929 SRS19443707 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 2 GSM7885866   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 2 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885866 GSM7885866: Wild type tailbud no treatment replicate 2; Danio rerio; RNA Seq GSM7885866 r1 GSM7885866 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT2_S9_L002_R1_001.fastq.gz WT2_S9_L002_R2_001.fastq.gz fastq fastq 4916008107.0 32579134.0 GSM7885866 r2 0:75.49 1:75.40 A:1244399521;C:1202192346;G:1194561433;T:1274714960;N:139847 75 75     1244399521 1202192346 1194561433 1274714960 139847 SRX22410929 SRS19443707 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.95906 0.9626 0.05798 0.05754 0.71502 0.71526 0.46094 0.45988 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28866 28866 SRR26711884 SRX22410928 SRS19443706 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 1 GSM7885865   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885865 GSM7885865: rad21 heterozugous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885865 r1 GSM7885865 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-5-HET_S8_L001_R1_001.fastq.gz Rad21-BIO-5-HET_S8_L001_R2_001.fastq.gz fastq fastq 3066593621.0 20312935.0 GSM7885865 r1 0:75.54 1:75.43 A:773539057;C:758309818;G:762855989;T:771829322;N:59435 75 75     773539057 758309818 762855989 771829322 59435 SRX22410928 SRS19443706 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.93814 0.93898 0.05206 0.05092 0.72403 0.72606 0.45323 0.45594 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28867 28867 SRR26711885 SRX22410928 SRS19443706 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud Wnt stimulation replicate 1 GSM7885865   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 heterozugous tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885865 GSM7885865: rad21 heterozugous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885865 r1 GSM7885865 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-5-HET_S8_L002_R1_001.fastq.gz Rad21-BIO-5-HET_S8_L002_R2_001.fastq.gz fastq fastq 3080824265.0 20407318.0 GSM7885865 r2 0:75.54 1:75.43 A:777565943;C:761729558;G:766237246;T:775229684;N:61834 75 75     777565943 761729558 766237246 775229684 61834 SRX22410928 SRS19443706 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.93811 0.93851 0.0524 0.05135 0.72403 0.72689 0.45207 0.46155 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28868 28868 SRR26711886 SRX22410927 SRS19443704 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 1 GSM7885864   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885864 GSM7885864: rad21 homozygous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885864 r1 GSM7885864 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-1-MUT_S7_L001_R1_001.fastq.gz Rad21-BIO-1-MUT_S7_L001_R2_001.fastq.gz fastq fastq 4788638898.0 31734845.0 GSM7885864 r1 0:75.51 1:75.38 A:1180996230;C:1208056992;G:1207225278;T:1192209164;N:151234 75 75     1180996230 1208056992 1207225278 1192209164 151234 SRX22410927 SRS19443704 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.971 0.97197 0.04922 0.04884 0.72342 0.72571 0.46723 0.46582 75 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28869 28869 SRR26711887 SRX22410927 SRS19443704 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud Wnt stimulation replicate 1 GSM7885864   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing rad21 homozygous tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant|treatment:Wnt signaling stimulation GSM7885864 GSM7885864: rad21 homozygous tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885864 r1 GSM7885864 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-BIO-1-MUT_S7_L002_R1_001.fastq.gz Rad21-BIO-1-MUT_S7_L002_R2_001.fastq.gz fastq fastq 4815323290.0 31911994.0 GSM7885864 r2 0:75.51 1:75.38 A:1187948393;C:1214824723;G:1213764297;T:1198630801;N:155076 75 75     1187948393 1214824723 1213764297 1198630801 155076 SRX22410927 SRS19443704 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.97042 0.97163 0.04919 0.04822 0.72575 0.72725 0.46784 0.46687 75 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28870 28870 SRR26711888 SRX22410926 SRS19443705 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 1 GSM7885863   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885863 GSM7885863: rad21 heterozugous tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885863 r1 GSM7885863 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-5-HET_S6_L001_R1_001.fastq.gz Rad21-5-HET_S6_L001_R2_001.fastq.gz fastq fastq 4731947877.0 31344805.0 GSM7885863 r1 0:75.54 1:75.42 A:1174667885;C:1187877616;G:1186233757;T:1183073645;N:94974 75 75     1174667885 1187877616 1186233757 1183073645 94974 SRX22410926 SRS19443705 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.97019 0.97104 0.04787 0.04709 0.72013 0.72157 0.45904 0.4534 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28871 28871 SRR26711889 SRX22410926 SRS19443705 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 heterozugous tailbud no treatment replicate 1 GSM7885863   source name:tailbud|tissue:tailbud|genotype:heterozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 heterozugous tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:heterozygous rad21 mutant GSM7885863 GSM7885863: rad21 heterozugous tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885863 r1 GSM7885863 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-5-HET_S6_L002_R2_001.fastq.gz Rad21-5-HET_S6_L002_R1_001.fastq.gz fastq fastq 4753935677.0 31490466.0 GSM7885863 r2 0:75.54 1:75.42 A:1180603224;C:1193421384;G:1191530186;T:1188281161;N:99722 75 75     1180603224 1193421384 1191530186 1188281161 99722 SRX22410926 SRS19443705 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96921 0.97138 0.04824 0.04771 0.72135 0.72253 0.4575 0.45266 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28872 28872 SRR26711890 SRX22410925 SRS19443703 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 1 GSM7885862   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885862 GSM7885862: rad21 homozygous tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885862 r1 GSM7885862 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-1-MUT_S5_L001_R1_001.fastq.gz Rad21-1-MUT_S5_L001_R2_001.fastq.gz fastq fastq 4118085890.0 27306618.0 GSM7885862 r1 0:75.47 1:75.34 A:1025300027;C:1029335773;G:1030828275;T:1032469485;N:152330 75 75     1025300027 1029335773 1030828275 1032469485 152330 SRX22410925 SRS19443703 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96791 0.96862 0.05188 0.0515 0.72013 0.72015 0.4522 0.4471 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28873 28873 SRR26711891 SRX22410925 SRS19443703 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   rad21 homozygous tailbud no treatment replicate 1 GSM7885862   source name:tailbud|tissue:tailbud|genotype:homozygous rad21 mutant|geo loc name:missing|collection date:missing rad21 homozygous tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous rad21 mutant GSM7885862 GSM7885862: rad21 homozygous tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885862 r1 GSM7885862 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py Rad21-1-MUT_S5_L002_R1_001.fastq.gz Rad21-1-MUT_S5_L002_R2_001.fastq.gz fastq fastq 4146986760.0 27498264.0 GSM7885862 r2 0:75.47 1:75.34 A:1032908199;C:1036610487;G:1037792727;T:1039516300;N:159047 75 75     1032908199 1036610487 1037792727 1039516300 159047 SRX22410925 SRS19443703 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96742 0.96892 0.05165 0.05113 0.71918 0.72068 0.45142 0.45319 76 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28874 28874 SRR26711892 SRX22410924 SRS19443702 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 1 GSM7885861   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885861 GSM7885861: stag2b tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885861 r1 GSM7885861 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-1_S4_L001_R2_001.fastq.gz S2B-BIO-1_S4_L001_R1_001.fastq.gz fastq fastq 2897013924.0 19254896.0 GSM7885861 r1 0:75.29 1:75.17 A:741141530;C:706870086;G:710814654;T:738037384;N:150270 75 75     741141530 706870086 710814654 738037384 150270 SRX22410924 SRS19443702 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96485 0.96632 0.05089 0.05075 0.72423 0.72638 0.46419 0.4639 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28875 28875 SRR26711893 SRX22410924 SRS19443702 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud Wnt stimulation replicate 1 GSM7885861   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing stag2b tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant|treatment:Wnt signaling stimulation GSM7885861 GSM7885861: stag2b tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885861 r1 GSM7885861 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-BIO-1_S4_L002_R1_001.fastq.gz S2B-BIO-1_S4_L002_R2_001.fastq.gz fastq fastq 2915617733.0 19378751.0 GSM7885861 r2 0:75.29 1:75.17 A:746370200;C:711440488;G:715102603;T:742552430;N:152012 75 75     746370200 711440488 715102603 742552430 152012 SRX22410924 SRS19443702 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96529 0.96741 0.05064 0.05044 0.72397 0.7259 0.47066 0.47479 75 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28876 28876 SRR26711894 SRX22410923 SRS19443701 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 1 GSM7885860   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885860 GSM7885860: stag2b tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885860 r1 GSM7885860 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-1_S3_L001_R1_001.fastq.gz S2B-1_S3_L001_R2_001.fastq.gz fastq fastq 4816347042.0 31912880.0 GSM7885860 r1 0:75.52 1:75.40 A:1186516295;C:1215887273;G:1212449212;T:1201357694;N:136568 75 75     1186516295 1215887273 1212449212 1201357694 136568 SRX22410923 SRS19443701 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96723 0.96949 0.03922 0.039 0.72417 0.72563 0.44797 0.44612 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28877 28877 SRR26711895 SRX22410923 SRS19443701 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   stag2b tailbud no treatment replicate 1 GSM7885860   source name:tailbud|tissue:tailbud|genotype:homozygous stag2b mutant|geo loc name:missing|collection date:missing stag2b tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:homozygous stag2b mutant GSM7885860 GSM7885860: stag2b tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885860 r1 GSM7885860 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py S2B-1_S3_L002_R1_001.fastq.gz S2B-1_S3_L002_R2_001.fastq.gz fastq fastq 4844499098.0 32099402.0 GSM7885860 r2 0:75.52 1:75.40 A:1193956975;C:1222998516;G:1219273844;T:1208134191;N:135572 75 75     1193956975 1222998516 1219273844 1208134191 135572 SRX22410923 SRS19443701 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.9673 0.96927 0.03901 0.03847 0.72265 0.7237 0.44466 0.44733 75 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28878 28878 SRR26711896 SRX22410922 SRS19443700 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 1 GSM7885859   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885859 GSM7885859: Wild type tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885859 r1 GSM7885859 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-1_S2_L001_R1_001.fastq.gz WT-BIO-1_S2_L001_R2_001.fastq.gz fastq fastq 5412178875.0 35866424.0 GSM7885859 r1 0:75.51 1:75.39 A:1366497169;C:1337079143;G:1340668569;T:1367824895;N:109099 75 75     1366497169 1337079143 1340668569 1367824895 109099 SRX22410922 SRS19443700 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96469 0.96636 0.05031 0.04926 0.71792 0.71985 0.46735 0.46003 76 76 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28879 28879 SRR26711897 SRX22410922 SRS19443700 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud Wnt stimulation replicate 1 GSM7885859   source name:tailbud|tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation|geo loc name:missing|collection date:missing Wild type tailbud Wnt stimulation replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type|treatment:Wnt signaling stimulation GSM7885859 GSM7885859: Wild type tailbud Wnt stimulation replicate 1; Danio rerio; RNA Seq GSM7885859 r1 GSM7885859 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT-BIO-1_S2_L002_R1_001.fastq.gz WT-BIO-1_S2_L002_R2_001.fastq.gz fastq fastq 5439582943.0 36048596.0 GSM7885859 r2 0:75.50 1:75.39 A:1374188816;C:1343757292;G:1347041961;T:1374478321;N:116553 75 75     1374188816 1343757292 1347041961 1374478321 116553 SRX22410922 SRS19443700 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96388 0.96569 0.04966 0.04871 0.71959 0.72141 0.46438 0.47241 76 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28880 28880 SRR26711898 SRX22410921 SRS19443699 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 1 GSM7885858   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885858 GSM7885858: Wild type tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885858 r1 GSM7885858 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT1_S1_L001_R2_001.fastq.gz WT1_S1_L001_R1_001.fastq.gz fastq fastq 4648127675.0 30828112.0 GSM7885858 r1 0:75.45 1:75.32 A:1143762350;C:1169301499;G:1170916895;T:1163919823;N:227108 75 75     1143762350 1169301499 1170916895 1163919823 227108 SRX22410921 SRS19443699 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96756 0.96895 0.03865 0.03806 0.73275 0.73521 0.4512 0.44878 74 74 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo Tail Multi-system
28881 28881 SRR26711899 SRX22410921 SRS19443699 SRP470622 PRJNA1036688 Cohesin composition and dosage independently affect early development in zebrafish GSE247246 Transcriptome Analysis Cohesin a chromatin associated protein complex with four core subunits Smc1a Smc3 Rad21 and either Stag1 or 2 has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2 but not rad21 mutants implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies. Overall design: RNA seq analysis was performed on tailbud samples from wild type zebrafish embryos as well as those with homozygous and heterozygous rad21 mutations and homozygous stag2b mutations. The dataset includes both baseline samples as well as samples treated with Wnt agonist 2.5 µM 6 bromoindirubin three prime oxime.   pubmed:38975838   Wild type tailbud no treatment replicate 1 GSM7885858   source name:tailbud|tissue:tailbud|genotype:wild type|geo loc name:missing|collection date:missing Wild type tailbud no treatment replicate 1 Cutadapt trimming adapter sequences HISAT2 and SAMtools read alignment FeatureCounts generating fragment count matrices The DESeq2 differential gene expression Assembly: GRCz11 Supplementary files format and content: CountMatrix tailbudRNAseq.tsv : a tsv containig counts for all 32 samples generated using FeatureCounts Supplementary files format and content: signDGE by genotype treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups tailbud 2.5 μM 6 bromoindirubin 3’ oxime in E3 media from 4 hpf till tailbud disection RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA E3 media 28 C tissue:tailbud|genotype:wild type GSM7885858 GSM7885858: Wild type tailbud no treatment replicate 1; Danio rerio; RNA Seq GSM7885858 r1 GSM7885858 1 RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit 74104; Qiagen Germany Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit Illumina USA and TruSeq RNA CD Index Plate Illumina USA   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP470622   loader:fastq load.py WT1_S1_L002_R1_001.fastq.gz WT1_S1_L002_R2_001.fastq.gz fastq fastq 4676143483.0 31014103.0 GSM7885858 r2 0:75.45 1:75.32 A:1151068941;C:1176347620;G:1177720113;T:1170778976;N:227833 75 75     1151068941 1176347620 1177720113 1170778976 227833 SRX22410921 SRS19443699 SRA1747076 Chromosome Structure and Development, Pathology, Otago University Chromosome Structure and Development, Pathology, Otago University 2 0.96645 0.96872 0.03855 0.03822 0.73486 0.73513 0.4505 0.4476 73 75 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified trueseq sc_generic single_cell_generic generic-scrnaseq-only   New Zealand 2023-11-07 Multi-stage Embryo 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

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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");;