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run_metadata

648 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Tail"

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technology 7

devstage_curation 6

experiment.library_selection 3

devstage_curation_coarse 3

experiment.platform 2

experiment.library_strategy 2

tissue_curation_coarse 1

tissue_curation 1

  • Tail · 648 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 648 ✖

experiment.library_layout 1

  • PAIRED · 648 ✖
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
32781 32781 SRR29411985 SRX24925451 SRS21630866 SRP513930 PRJNA1124008 Cell state transitions are decoupled from cell division during early embryo development [II] GSE269848 Other Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…   pubmed:37546736   24 38 hpf and 48 hpf tails GSM8328864   source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing 24 38 hpf and 48 hpf tails Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f… embryo tail   Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.   tissue:embryo tail GSM8328864 GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER GSM8328864 r1 GSM8328864 1 Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513930     Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz fastq fastq fastq fastq 58603546956.0 505202991.0 GSM8328864 r1 0:86 1:8 2:8 3:14 A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340 86 8 8 14 13191204330 9162028793 9431065581 11662090182 1068340 SRX24925451 SRS21630866 SRA1899240 Harvard University Harvard University                       B   usable mapping rate illumina novaseq_era unknown other trueseq sc single_cell_droplet indrops   United States 2024-06-14 Multi-stage Embryo Tail Multi-system
32782 32782 SRR29411986 SRX24925451 SRS21630866 SRP513930 PRJNA1124008 Cell state transitions are decoupled from cell division during early embryo development [II] GSE269848 Other Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state informa…   pubmed:37546736   24 38 hpf and 48 hpf tails GSM8328864   source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing 24 38 hpf and 48 hpf tails Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section "Single cell RNA seq Data preprocessing" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary f… embryo tail   Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.   tissue:embryo tail GSM8328864 GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER GSM8328864 r1 GSM8328864 1 Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20µg/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513930     Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz fastq fastq fastq fastq 44072422880.0 379934680.0 GSM8328864 r2 0:86 1:8 2:8 3:14 A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152 86 8 8 14 9919784228 6894965731 7094749745 8764100624 782152 SRX24925451 SRS21630866 SRA1899240 Harvard University Harvard University                       B   usable mapping rate illumina novaseq_era unknown other trueseq sc single_cell_droplet indrops   United States 2024-06-14 Multi-stage Embryo Tail Multi-system
50874 50874 SRR8356798 SRX5167561 SRS4175446 SRP173971 PRJNA510841 Transcription factor induction of vascular blood stem cell niches in vivo [TOMO Seq] GSE124150 Other We report RNA tomography tomo seq gene expression data for the tail region of a 72 hpf zebrafish embryo. The portion of the tail containing the caudal hematopoietic tissue CHT was isolated by manual dissection snap froze and then cryosections 40 in total 8 µm thick were collected along the dorsal ventral axis. Each cryosection was placed into a tube and the RNA was exctracted and barcoded during a reverse trancription step prior to library synthesis and sequencing. Overall design: The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice. The RNA from individual cryosections was extracted using Trizol reagent and then barcoded during a reverse transcription step prior to library synthesis according to the previously published method Junker et al. 2014. parent bioproject:PRJNA510836     Tomo seq zebrafish tail at 72 hpf GSM3521717   source name:mpx:GFP transgenic zebrafish embryo wild type Casper background|tissue:tail|developmental stage:72 hpf Tomo seq zebrafish tail at 72 hpf Library strategy: RNA tomography tomo seq Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the Junker et al. 2014. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Mapping and demultiplexing were done as described in Grün et al. Validation of noise models for single cell transcriptomics Nature Methods 2014. The script needed to process the data is available in https://www.dropbox.com/sh/7s59vvocwtn2ct4/AAAR6pWte8xOzObCYONAFPvIa?dl=0 where script tomo.sh is an example for how to run the mapping scripts. Genome build: zv9 mpx:GFP transgenic zebrafish embryo wild type Casper background No treatment The total RNA from individual cryosections 40 in total each 8 µm thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014. mpx:GFP transgenic zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then euthanized by tricaine overdose. The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice. tissue:tail|developmental stage:72 hpf GSM3521717 GSM3521717: Tomo seq zebrafish tail at 72 hpf; Danio rerio; OTHER GSM3521717   1 The total RNA from individual cryosections 40 in total each 8 µm thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014. GEO Accession:GSM3521717 OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP173971         3762222874.0 24959737.0 GSM3521717 r1 0:75.36 1:75.37 A:1160852277;C:485683733;G:556965887;T:1558649449;N:71528 75 75     1160852277 485683733 556965887 1558649449 71528 SRX5167561 SRS4175446 SRA825234 GEO Oncology/Hematology, Boston Children's Hospital 2 0.20644 0.76788 0.14917 0.11551 0.98169 0.8382 0.50072 0.52728 76 76 T B mate1 technical by mapping diff illumina hiseq_era unknown other unknown sc single_cell_plate celseq   United States 2018-12-19 Larval Larval Tail Multi-system
52243 52243 SRR9050632 SRX5827023 SRS4754837 SRP198298 PRJNA542704 Thyroid hormone regulates distinct paths to maturation in pigment cell lineages GSE131136 Transcriptome Analysis Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.   pubmed:31140974;pubmed:33933422   Neural crest derived cells from 5 dpf euthyroid zebrafish tails GSM3764579   tissue:sox10:Cre+ cells from 5 dpf zebrafish tail tissue|cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.|treatment:Untreated Neural crest derived cells from 5 dpf euthyroid zebrafish tails Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files. sox10:Cre+ cells from 5 dpf zebrafish tail tissue Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms. cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.|treatment:Untreated GSM3764579 GSM3764579: Neural crest derived cells from 5 dpf euthyroid zebrafish tails; Danio rerio; RNA Seq GSM3764579   1 10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP198298   dangling references:treat as unmapped 5dpf_possorted_genome_bam.bam 10X Genomics bam file 6566978892.0 115210156.0 GSM3764579 r1 0:57 A:1984051591;C:1302406550;G:1514564296;T:1762601545;N:3354910 57       1984051591 1302406550 1514564296 1762601545 3354910 SRX5827023 SRS4754837 SRA886020 GEO Biology, University of Virginia 1 0.9291   0.194   0.81466   0.53116   57   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2019-05-13 Larval Larval Tail Multi-system
54735 54735 SRR10151942 SRX6877449 SRS5413231 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s383 GSM4087504   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s383 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087504 GSM4087504: lckgfp s383; Danio rerio; RNA Seq GSM4087504   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087504 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s383_R1.fastq.gz lckgfp_s383_R2.fastq.gz fastq fastq 234832600.0 1174163.0 GSM4087504 r1 0:100 1:100 A:73305400;C:48312945;G:46608604;T:66604424;N:1227 100 100     73305400 48312945 46608604 66604424 1227 SRX6877449 SRS5413231 SRA965286 GEO Stanford University 2 0.75941 0.76379 0.1177 0.1196 0.97948 0.9793 0.67812 0.67194 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54736 54736 SRR10151941 SRX6877448 SRS5413230 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s382 GSM4087503   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s382 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087503 GSM4087503: lckgfp s382; Danio rerio; RNA Seq GSM4087503   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087503 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s382_R1.fastq.gz lckgfp_s382_R2.fastq.gz fastq fastq 231321400.0 1156607.0 GSM4087503 r1 0:100 1:100 A:74109121;C:45769344;G:44284415;T:67157279;N:1241 100 100     74109121 45769344 44284415 67157279 1241 SRX6877448 SRS5413230 SRA965286 GEO Stanford University 2 0.71327 0.73209 0.11938 0.12294 0.98113 0.98121 0.67445 0.67189 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54737 54737 SRR10151940 SRX6877447 SRS5413229 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s381 GSM4087502   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s381 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087502 GSM4087502: lckgfp s381; Danio rerio; RNA Seq GSM4087502   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087502 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s381_R1.fastq.gz lckgfp_s381_R2.fastq.gz fastq fastq 245645600.0 1228228.0 GSM4087502 r1 0:100 1:100 A:73876655;C:46349996;G:46669257;T:78748704;N:988 100 100     73876655 46349996 46669257 78748704 988 SRX6877447 SRS5413229 SRA965286 GEO Stanford University 2 0.84889 0.85255 0.24599 0.25118 0.9584 0.9586 0.60851 0.60597 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54738 54738 SRR10151939 SRX6877446 SRS5413228 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s380 GSM4087501   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s380 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087501 GSM4087501: lckgfp s380; Danio rerio; RNA Seq GSM4087501   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087501 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s380_R1.fastq.gz lckgfp_s380_R2.fastq.gz fastq fastq 392055200.0 1960276.0 GSM4087501 r1 0:100 1:100 A:118333309;C:79802020;G:77119877;T:116798071;N:1923 100 100     118333309 79802020 77119877 116798071 1923 SRX6877446 SRS5413228 SRA965286 GEO Stanford University 2 0.78714 0.7986 0.11307 0.1166 0.94466 0.94505 0.72339 0.72034 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54739 54739 SRR10151938 SRX6877445 SRS5413227 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s379 GSM4087500   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s379 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087500 GSM4087500: lckgfp s379; Danio rerio; RNA Seq GSM4087500   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087500 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s379_R1.fastq.gz lckgfp_s379_R2.fastq.gz fastq fastq 1126607400.0 5633037.0 GSM4087500 r1 0:100 1:100 A:316942811;C:247242301;G:247434168;T:314982567;N:5553 100 100     316942811 247242301 247434168 314982567 5553 SRX6877445 SRS5413227 SRA965286 GEO Stanford University 2 0.90628 0.90945 0.2181 0.22037 0.97964 0.97958 0.47443 0.49146 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54740 54740 SRR10151937 SRX6877444 SRS5413226 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s378 GSM4087499   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s378 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087499 GSM4087499: lckgfp s378; Danio rerio; RNA Seq GSM4087499   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087499 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s378_R1.fastq.gz lckgfp_s378_R2.fastq.gz fastq fastq 337111400.0 1685557.0 GSM4087499 r1 0:100 1:100 A:98638322;C:70570254;G:69961020;T:97940105;N:1699 100 100     98638322 70570254 69961020 97940105 1699 SRX6877444 SRS5413226 SRA965286 GEO Stanford University 2 0.87386 0.87621 0.19517 0.19574 0.97443 0.97463 0.60077 0.60132 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54741 54741 SRR10151936 SRX6877443 SRS5413225 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s377 GSM4087498   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s377 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087498 GSM4087498: lckgfp s377; Danio rerio; RNA Seq GSM4087498   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087498 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s377_R1.fastq.gz lckgfp_s377_R2.fastq.gz fastq fastq 213595800.0 1067979.0 GSM4087498 r1 0:100 1:100 A:65929082;C:44373444;G:41959720;T:61332589;N:965 100 100     65929082 44373444 41959720 61332589 965 SRX6877443 SRS5413225 SRA965286 GEO Stanford University 2 0.63317 0.65413 0.48755 0.50508 0.96426 0.96317 0.67368 0.66493 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54742 54742 SRR10151935 SRX6877442 SRS5413224 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s376 GSM4087497   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s376 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087497 GSM4087497: lckgfp s376; Danio rerio; RNA Seq GSM4087497   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087497 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s376_R1.fastq.gz lckgfp_s376_R2.fastq.gz fastq fastq 88560200.0 442801.0 GSM4087497 r1 0:100 1:100 A:28243730;C:14191830;G:14708934;T:31415270;N:436 100 100     28243730 14191830 14708934 31415270 436 SRX6877442 SRS5413224 SRA965286 GEO Stanford University 2 0.71521 0.72283 0.5654 0.57182 0.92989 0.9317 0.531 0.52094 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54743 54743 SRR10151934 SRX6877441 SRS5413223 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s375 GSM4087496   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s375 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087496 GSM4087496: lckgfp s375; Danio rerio; RNA Seq GSM4087496   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087496 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s375_R1.fastq.gz lckgfp_s375_R2.fastq.gz fastq fastq 64991200.0 324956.0 GSM4087496 r1 0:100 1:100 A:22513291;C:12471508;G:11416691;T:18589412;N:298 100 100     22513291 12471508 11416691 18589412 298 SRX6877441 SRS5413223 SRA965286 GEO Stanford University 2 0.5963 0.62806 0.27588 0.2908 0.9754 0.975 0.44766 0.44857 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54744 54744 SRR10151933 SRX6877440 SRS5413222 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s374 GSM4087495   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s374 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087495 GSM4087495: lckgfp s374; Danio rerio; RNA Seq GSM4087495   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087495 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s374_R1.fastq.gz lckgfp_s374_R2.fastq.gz fastq fastq 176144200.0 880721.0 GSM4087495 r1 0:100 1:100 A:53180935;C:37108779;G:35845658;T:50007992;N:836 100 100     53180935 37108779 35845658 50007992 836 SRX6877440 SRS5413222 SRA965286 GEO Stanford University 2 0.76708 0.77852 0.13854 0.14107 0.98238 0.98283 0.66594 0.67246 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54745 54745 SRR10151932 SRX6877439 SRS5413221 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s373 GSM4087494   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s373 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087494 GSM4087494: lckgfp s373; Danio rerio; RNA Seq GSM4087494   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087494 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s373_R1.fastq.gz lckgfp_s373_R2.fastq.gz fastq fastq 139717800.0 698589.0 GSM4087494 r1 0:100 1:100 A:42519883;C:25961082;G:25907850;T:45328266;N:719 100 100     42519883 25961082 25907850 45328266 719 SRX6877439 SRS5413221 SRA965286 GEO Stanford University 2 0.75679 0.76819 0.28064 0.29002 0.97305 0.97273 0.56393 0.53945 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54746 54746 SRR10151931 SRX6877438 SRS5413220 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s372 GSM4087493   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s372 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087493 GSM4087493: lckgfp s372; Danio rerio; RNA Seq GSM4087493   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087493 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s372_R1.fastq.gz lckgfp_s372_R2.fastq.gz fastq fastq 446412600.0 2232063.0 GSM4087493 r1 0:100 1:100 A:128821576;C:93782508;G:93694322;T:130111961;N:2233 100 100     128821576 93782508 93694322 130111961 2233 SRX6877438 SRS5413220 SRA965286 GEO Stanford University 2 0.89125 0.89493 0.23701 0.24011 0.9697 0.97005 0.53362 0.53735 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54747 54747 SRR10151930 SRX6877437 SRS5413219 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s371 GSM4087492   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s371 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087492 GSM4087492: lckgfp s371; Danio rerio; RNA Seq GSM4087492   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087492 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s371_R1.fastq.gz lckgfp_s371_R2.fastq.gz fastq fastq 339631800.0 1698159.0 GSM4087492 r1 0:100 1:100 A:98594117;C:68506566;G:69103975;T:103425575;N:1567 100 100     98594117 68506566 69103975 103425575 1567 SRX6877437 SRS5413219 SRA965286 GEO Stanford University 2 0.84886 0.85388 0.19246 0.19436 0.95014 0.95012 0.54321 0.54848 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54748 54748 SRR10151929 SRX6877436 SRS5413218 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s370 GSM4087491   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s370 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087491 GSM4087491: lckgfp s370; Danio rerio; RNA Seq GSM4087491   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087491 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s370_R1.fastq.gz lckgfp_s370_R2.fastq.gz fastq fastq 87104400.0 435522.0 GSM4087491 r1 0:100 1:100 A:26443732;C:16935041;G:16826001;T:26899213;N:413 100 100     26443732 16935041 16826001 26899213 413 SRX6877436 SRS5413218 SRA965286 GEO Stanford University 2 0.82125 0.82733 0.31193 0.31596 0.97453 0.97433 0.60892 0.61117 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54749 54749 SRR10151928 SRX6877435 SRS5413217 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s369 GSM4087490   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s369 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087490 GSM4087490: lckgfp s369; Danio rerio; RNA Seq GSM4087490   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087490 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s369_R1.fastq.gz lckgfp_s369_R2.fastq.gz fastq fastq 581275000.0 2906375.0 GSM4087490 r1 0:100 1:100 A:164842289;C:120994794;G:122636896;T:172798268;N:2753 100 100     164842289 120994794 122636896 172798268 2753 SRX6877435 SRS5413217 SRA965286 GEO Stanford University 2 0.88299 0.88484 0.19686 0.19809 0.95436 0.95408 0.56675 0.57288 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 Larval Larval Tail Multi-system
54750 54750 SRR10151927 SRX6877434 SRS5413216 SRP222763 PRJNA572587 Characterization of T cells from the larval zebrafish tail via single cell RNAseq GSE137770 Transcriptome Analysis We report single cell RNA sequencing of cells from the Tglck:GFP larval zebrafish tail to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells in addition to canonical T and ubiquitous immune cell markers. Overall design: Single cells n=461 isolated from FACS of Tglck:GFP Danio rerio FITC+ were analyzed.   pubmed:32427565   lckgfp s368 GSM4087489   source name:Danio rerio tail|line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf lckgfp s368 STAR 2.5 Htseq 0.8.0 htseq count m intersection nonempty nonunique all Genome build: GRCz10 Supplementary files format and content: Raw counts of numbers of reads aligned to each feature for each cell in tab separated format lckgfp counts.txt Danio rerio tail Liberase TL 100 ug/mL and manual trituration was used to dissociate tail tissue. Cells were FACS sorted FITC+ Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018   line:Tglck:GFP|tissue:tail|devlopmental stage:15 dpf GSM4087489 GSM4087489: lckgfp s368; Danio rerio; RNA Seq GSM4087489   1 Lysis was performed as described in Schaum et al. Nature 2018 A Smart Seq2 based protocol was used for reverse transcription and cDNA amplification and a Nextera based protocol was used for library preparation as described in Schaum et al. Nature 2018 GEO Accession:GSM4087489 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP222763     lckgfp_s368_R1.fastq.gz lckgfp_s368_R2.fastq.gz fastq fastq 312312800.0 1561564.0 GSM4087489 r1 0:100 1:100 A:92531881;C:61673383;G:61568700;T:96537155;N:1681 100 100     92531881 61673383 61568700 96537155 1681 SRX6877434 SRS5413216 SRA965286 GEO Stanford University 2 0.82667 0.83385 0.29498 0.29709 0.97344 0.97366 0.54305 0.54647 100 100 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-09-20 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");;