metadata: run_metadata: 66 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue

66 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation = "Tail"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	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.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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36147	36147	SRR33446914	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-4_S18_L001_R1_001.fastq.gz	fastq	392062720.0	5158720.0	GSM8970925 r1	0:76	A:111393933;C:84178440;G:86759120;T:109728583;N:2644	76		111393933	84178440	86759120	109728583	2644	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36148	36148	SRR33446915	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-4_S18_L002_R1_001.fastq.gz	fastq	382539160.0	5033410.0	GSM8970925 r2	0:76	A:108549273;C:82135694;G:84877971;T:106974218;N:2004	76		108549273	82135694	84877971	106974218	2004	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36149	36149	SRR33446916	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-4_S18_L003_R1_001.fastq.gz	fastq	390689020.0	5140645.0	GSM8970925 r3	0:76	A:110921885;C:83926202;G:86538209;T:109300187;N:2537	76		110921885	83926202	86538209	109300187	2537	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36150	36150	SRR33446917	SRX28687233	SRS24954089	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 4	GSM8970925	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970925	GSM8970925: SB 431542 treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970925 r1	GSM8970925	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-4_S18_L004_R1_001.fastq.gz	fastq	385026032.0	5066132.0	GSM8970925 r4	0:76	A:109282089;C:82666299;G:85291625;T:107783812;N:2207	76		109282089	82666299	85291625	107783812	2207	SRX28687233	SRS24954089	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36151	36151	SRR33446918	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-3_S17_L001_R1_001.fastq.gz	fastq	242078544.0	3185244.0	GSM8970924 r1	0:76	A:70805011;C:50935537;G:52720022;T:67616569;N:1405	76		70805011	50935537	52720022	67616569	1405	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36152	36152	SRR33446919	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-3_S17_L002_R1_001.fastq.gz	fastq	236879840.0	3116840.0	GSM8970924 r2	0:76	A:69118193;C:49900432;G:51722708;T:66137243;N:1264	76		69118193	49900432	51722708	66137243	1264	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36153	36153	SRR33446920	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-3_S17_L003_R1_001.fastq.gz	fastq	241246952.0	3174302.0	GSM8970924 r3	0:76	A:70493049;C:50814403;G:52594412;T:67343618;N:1470	76		70493049	50814403	52594412	67343618	1470	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36154	36154	SRR33446921	SRX28687232	SRS24954088	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 3	GSM8970924	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970924	GSM8970924: SB 431542 treated / uncut tail replicate 3; Danio rerio; RNA Seq	GSM8970924 r1	GSM8970924	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-3_S17_L004_R1_001.fastq.gz	fastq	238296936.0	3135486.0	GSM8970924 r4	0:76	A:69600911;C:50177666;G:51934697;T:66582348;N:1314	76		69600911	50177666	51934697	66582348	1314	SRX28687232	SRS24954088	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36155	36155	SRR33446922	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-2_S16_L001_R1_001.fastq.gz	fastq	293546884.0	3862459.0	GSM8970923 r1	0:76	A:86721485;C:61000183;G:63592308;T:82231012;N:1896	76		86721485	61000183	63592308	82231012	1896	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36156	36156	SRR33446923	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-2_S16_L002_R1_001.fastq.gz	fastq	287313668.0	3780443.0	GSM8970923 r2	0:76	A:84719789;C:59732524;G:62422596;T:80437282;N:1477	76		84719789	59732524	62422596	80437282	1477	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36157	36157	SRR33446924	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-2_S16_L003_R1_001.fastq.gz	fastq	293081612.0	3856337.0	GSM8970923 r3	0:76	A:86491724;C:60944765;G:63551581;T:82091805;N:1737	76		86491724	60944765	63551581	82091805	1737	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36158	36158	SRR33446925	SRX28687231	SRS24954087	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / uncut tail replicate 2	GSM8970923	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured SB431542 treated	GSM8970923	GSM8970923: SB 431542 treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970923 r1	GSM8970923	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	White-2_S16_L004_R1_001.fastq.gz	fastq	289340284.0	3807109.0	GSM8970923 r4	0:76	A:85390241;C:60135471;G:62741618;T:81071340;N:1614	76		85390241	60135471	62741618	81071340	1614	SRX28687231	SRS24954087	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36159	36159	SRR33446926	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-4_S15_L001_R1_001.fastq.gz	fastq	293676616.0	3864166.0	GSM8970922 r1	0:76	A:85055525;C:61514402;G:62951777;T:84153135;N:1777	76		85055525	61514402	62951777	84153135	1777	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36160	36160	SRR33446927	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-4_S15_L002_R1_001.fastq.gz	fastq	287550712.0	3783562.0	GSM8970922 r2	0:76	A:83130155;C:60249305;G:61817163;T:82352632;N:1457	76		83130155	60249305	61817163	82352632	1457	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36161	36161	SRR33446928	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-4_S15_L003_R1_001.fastq.gz	fastq	293005460.0	3855335.0	GSM8970922 r3	0:76	A:84798214;C:61435286;G:62865004;T:83905146;N:1810	76		84798214	61435286	62865004	83905146	1810	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36162	36162	SRR33446929	SRX28687230	SRS24954086	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 4	GSM8970922	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970922	GSM8970922: SB 431542 treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970922 r1	GSM8970922	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-4_S15_L004_R1_001.fastq.gz	fastq	289004668.0	3802693.0	GSM8970922 r4	0:76	A:83595831;C:60570265;G:62006632;T:82830364;N:1576	76		83595831	60570265	62006632	82830364	1576	SRX28687230	SRS24954086	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36163	36163	SRR33446930	SRX28687229	SRS24954085	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 3	GSM8970921	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970921	GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970921 r1	GSM8970921	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-3_S14_L001_R1_001.fastq.gz	fastq	300231768.0	3950418.0	GSM8970921 r1	0:76	A:88106516;C:61818857;G:65466450;T:84838096;N:1849	76		88106516	61818857	65466450	84838096	1849	SRX28687229	SRS24954085	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36164	36164	SRR33446931	SRX28687229	SRS24954085	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 3	GSM8970921	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970921	GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970921 r1	GSM8970921	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-3_S14_L002_R1_001.fastq.gz	fastq	293677452.0	3864177.0	GSM8970921 r2	0:76	A:86015379;C:60508410;G:64229226;T:82922956;N:1481	76		86015379	60508410	64229226	82922956	1481	SRX28687229	SRS24954085	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36165	36165	SRR33446932	SRX28687229	SRS24954085	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 3	GSM8970921	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970921	GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970921 r1	GSM8970921	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-3_S14_L003_R1_001.fastq.gz	fastq	299518280.0	3941030.0	GSM8970921 r3	0:76	A:87800455;C:61713738;G:65389216;T:84612972;N:1899	76		87800455	61713738	65389216	84612972	1899	SRX28687229	SRS24954085	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36166	36166	SRR33446933	SRX28687229	SRS24954085	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 3	GSM8970921	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970921	GSM8970921: SB 431542 treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970921 r1	GSM8970921	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-3_S14_L004_R1_001.fastq.gz	fastq	295680204.0	3890529.0	GSM8970921 r4	0:76	A:86636984;C:60930934;G:64539123;T:83571354;N:1809	76		86636984	60930934	64539123	83571354	1809	SRX28687229	SRS24954085	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36167	36167	SRR33446934	SRX28687228	SRS24954084	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 2	GSM8970920	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970920	GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq	GSM8970920 r1	GSM8970920	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-2_S13_L001_R1_001.fastq.gz	fastq	266233396.0	3503071.0	GSM8970920 r1	0:76	A:78387833;C:55246603;G:58347116;T:74250158;N:1686	76		78387833	55246603	58347116	74250158	1686	SRX28687228	SRS24954084	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36168	36168	SRR33446935	SRX28687228	SRS24954084	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 2	GSM8970920	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970920	GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq	GSM8970920 r1	GSM8970920	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-2_S13_L002_R1_001.fastq.gz	fastq	260317404.0	3425229.0	GSM8970920 r2	0:76	A:76487964;C:54052872;G:57202492;T:72572684;N:1392	76		76487964	54052872	57202492	72572684	1392	SRX28687228	SRS24954084	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36169	36169	SRR33446936	SRX28687228	SRS24954084	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 2	GSM8970920	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970920	GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq	GSM8970920 r1	GSM8970920	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-2_S13_L003_R1_001.fastq.gz	fastq	265513676.0	3493601.0	GSM8970920 r3	0:76	A:78116084;C:55123773;G:58227738;T:74044386;N:1695	76		78116084	55123773	58227738	74044386	1695	SRX28687228	SRS24954084	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36170	36170	SRR33446937	SRX28687228	SRS24954084	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		SB 431542 treated / cut tail replicate 2	GSM8970920	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated\|geo loc name:missing\|collection date:missing	SB 431542 treated / cut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision SB431542 treated	GSM8970920	GSM8970920: SB 431542 treated / cut tail replicate 2; Danio rerio; RNA Seq	GSM8970920 r1	GSM8970920	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Red-2_S13_L004_R1_001.fastq.gz	fastq	262010532.0	3447507.0	GSM8970920 r4	0:76	A:77058783;C:54402656;G:57452833;T:73094822;N:1438	76		77058783	54402656	57452833	73094822	1438	SRX28687228	SRS24954084	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36171	36171	SRR33446938	SRX28687227	SRS24954083	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 4	GSM8970919	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970919	GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970919 r1	GSM8970919	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-4_S24_L001_R1_001.fastq.gz	fastq	334535736.0	4401786.0	GSM8970919 r1	0:76	A:104303278;C:67025244;G:65441286;T:97763807;N:2121	76		104303278	67025244	65441286	97763807	2121	SRX28687227	SRS24954083	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36172	36172	SRR33446939	SRX28687227	SRS24954083	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 4	GSM8970919	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970919	GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970919 r1	GSM8970919	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-4_S24_L002_R1_001.fastq.gz	fastq	325405780.0	4281655.0	GSM8970919 r2	0:76	A:101185453;C:65289632;G:63869692;T:95059316;N:1687	76		101185453	65289632	63869692	95059316	1687	SRX28687227	SRS24954083	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36173	36173	SRR33446940	SRX28687227	SRS24954083	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 4	GSM8970919	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970919	GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970919 r1	GSM8970919	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-4_S24_L003_R1_001.fastq.gz	fastq	333272540.0	4385165.0	GSM8970919 r3	0:76	A:103781471;C:66831319;G:65274288;T:97383334;N:2128	76		103781471	66831319	65274288	97383334	2128	SRX28687227	SRS24954083	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36174	36174	SRR33446941	SRX28687227	SRS24954083	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 4	GSM8970919	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970919	GSM8970919: DMSO treated / uncut tail replicate 4; Danio rerio; RNA Seq	GSM8970919 r1	GSM8970919	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-4_S24_L004_R1_001.fastq.gz	fastq	328778432.0	4326032.0	GSM8970919 r4	0:76	A:102340372;C:65917125;G:64384673;T:96134375;N:1887	76		102340372	65917125	64384673	96134375	1887	SRX28687227	SRS24954083	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36175	36175	SRR33446942	SRX28687226	SRS24954082	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 2	GSM8970918	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970918	GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970918 r1	GSM8970918	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-2_S23_L001_R1_001.fastq.gz	fastq	254273428.0	3345703.0	GSM8970918 r1	0:76	A:73868437;C:53712396;G:55649268;T:71041836;N:1491	76		73868437	53712396	55649268	71041836	1491	SRX28687226	SRS24954082	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36176	36176	SRR33446943	SRX28687226	SRS24954082	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 2	GSM8970918	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970918	GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970918 r1	GSM8970918	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-2_S23_L002_R1_001.fastq.gz	fastq	247479256.0	3256306.0	GSM8970918 r2	0:76	A:71749772;C:52269437;G:54304263;T:69154447;N:1337	76		71749772	52269437	54304263	69154447	1337	SRX28687226	SRS24954082	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36177	36177	SRR33446944	SRX28687226	SRS24954082	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 2	GSM8970918	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970918	GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970918 r1	GSM8970918	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-2_S23_L003_R1_001.fastq.gz	fastq	252975424.0	3328624.0	GSM8970918 r3	0:76	A:73431938;C:53451559;G:55422676;T:70667726;N:1525	76		73431938	53451559	55422676	70667726	1525	SRX28687226	SRS24954082	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36178	36178	SRR33446945	SRX28687226	SRS24954082	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 2	GSM8970918	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 2	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970918	GSM8970918: DMSO treated / uncut tail replicate 2; Danio rerio; RNA Seq	GSM8970918 r1	GSM8970918	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-2_S23_L004_R1_001.fastq.gz	fastq	249310400.0	3280400.0	GSM8970918 r4	0:76	A:72326303;C:52679056;G:54605938;T:69697722;N:1381	76		72326303	52679056	54605938	69697722	1381	SRX28687226	SRS24954082	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36179	36179	SRR33446946	SRX28687225	SRS24954081	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 1	GSM8970917	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970917	GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq	GSM8970917 r1	GSM8970917	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-1_S22_L001_R1_001.fastq.gz	fastq	270570108.0	3560133.0	GSM8970917 r1	0:76	A:78499185;C:56484520;G:59318322;T:76266342;N:1739	76		78499185	56484520	59318322	76266342	1739	SRX28687225	SRS24954081	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36180	36180	SRR33446947	SRX28687225	SRS24954081	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 1	GSM8970917	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970917	GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq	GSM8970917 r1	GSM8970917	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-1_S22_L002_R1_001.fastq.gz	fastq	263995348.0	3473623.0	GSM8970917 r2	0:76	A:76492301;C:55131794;G:58036716;T:74333178;N:1359	76		76492301	55131794	58036716	74333178	1359	SRX28687225	SRS24954081	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36181	36181	SRR33446948	SRX28687225	SRS24954081	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 1	GSM8970917	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970917	GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq	GSM8970917 r1	GSM8970917	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-1_S22_L003_R1_001.fastq.gz	fastq	269322036.0	3543711.0	GSM8970917 r3	0:76	A:78091756;C:56257589;G:59094882;T:75876132;N:1677	76		78091756	56257589	59094882	75876132	1677	SRX28687225	SRS24954081	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36182	36182	SRR33446949	SRX28687225	SRS24954081	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / uncut tail replicate 1	GSM8970917	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured\|geo loc name:missing\|collection date:missing	DMSO treated / uncut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Uninjured	GSM8970917	GSM8970917: DMSO treated / uncut tail replicate 1; Danio rerio; RNA Seq	GSM8970917 r1	GSM8970917	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Pink-1_S22_L004_R1_001.fastq.gz	fastq	265691820.0	3495945.0	GSM8970917 r4	0:76	A:77002713;C:55467944;G:58293660;T:74926013;N:1490	76		77002713	55467944	58293660	74926013	1490	SRX28687225	SRS24954081	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36183	36183	SRR33446950	SRX28687224	SRS24954080	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 4	GSM8970916	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970916	GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970916 r1	GSM8970916	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-4_S21_L001_R1_001.fastq.gz	fastq	349029392.0	4592492.0	GSM8970916 r1	0:76	A:99839652;C:73943935;G:76249851;T:98993782;N:2172	76		99839652	73943935	76249851	98993782	2172	SRX28687224	SRS24954080	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36184	36184	SRR33446951	SRX28687224	SRS24954080	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 4	GSM8970916	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970916	GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970916 r1	GSM8970916	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-4_S21_L002_R1_001.fastq.gz	fastq	340876568.0	4485218.0	GSM8970916 r2	0:76	A:97335332;C:72249777;G:74668638;T:96621097;N:1724	76		97335332	72249777	74668638	96621097	1724	SRX28687224	SRS24954080	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36185	36185	SRR33446952	SRX28687224	SRS24954080	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 4	GSM8970916	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970916	GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970916 r1	GSM8970916	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-4_S21_L003_R1_001.fastq.gz	fastq	347633196.0	4574121.0	GSM8970916 r3	0:76	A:99370315;C:73701054;G:75983700;T:98575995;N:2132	76		99370315	73701054	75983700	98575995	2132	SRX28687224	SRS24954080	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36186	36186	SRR33446953	SRX28687224	SRS24954080	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 4	GSM8970916	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 4	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970916	GSM8970916: DMSO treated / cut tail replicate 4; Danio rerio; RNA Seq	GSM8970916 r1	GSM8970916	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-4_S21_L004_R1_001.fastq.gz	fastq	343592352.0	4520952.0	GSM8970916 r4	0:76	A:98157486;C:72839122;G:75134528;T:97459296;N:1920	76		98157486	72839122	75134528	97459296	1920	SRX28687224	SRS24954080	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36187	36187	SRR33446954	SRX28687223	SRS24954079	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 3	GSM8970915	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970915	GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970915 r1	GSM8970915	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-3_S20_L001_R1_001.fastq.gz	fastq	304693500.0	4009125.0	GSM8970915 r1	0:76	A:89126862;C:63666599;G:66255160;T:85642963;N:1916	76		89126862	63666599	66255160	85642963	1916	SRX28687223	SRS24954079	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36188	36188	SRR33446955	SRX28687223	SRS24954079	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 3	GSM8970915	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970915	GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970915 r1	GSM8970915	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-3_S20_L002_R1_001.fastq.gz	fastq	297396892.0	3913117.0	GSM8970915 r2	0:76	A:86844888;C:62174886;G:64844462;T:83531083;N:1573	76		86844888	62174886	64844462	83531083	1573	SRX28687223	SRS24954079	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36189	36189	SRR33446956	SRX28687223	SRS24954079	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 3	GSM8970915	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970915	GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970915 r1	GSM8970915	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-3_S20_L003_R1_001.fastq.gz	fastq	303170840.0	3989090.0	GSM8970915 r3	0:76	A:88574880;C:63384769;G:65999210;T:85210123;N:1858	76		88574880	63384769	65999210	85210123	1858	SRX28687223	SRS24954079	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36190	36190	SRR33446957	SRX28687223	SRS24954079	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 3	GSM8970915	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 3	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970915	GSM8970915: DMSO treated / cut tail replicate 3; Danio rerio; RNA Seq	GSM8970915 r1	GSM8970915	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-3_S20_L004_R1_001.fastq.gz	fastq	299538876.0	3941301.0	GSM8970915 r4	0:76	A:87486058;C:62643433;G:65200414;T:84207227;N:1744	76		87486058	62643433	65200414	84207227	1744	SRX28687223	SRS24954079	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36191	36191	SRR33446958	SRX28687222	SRS24954078	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 1	GSM8970914	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970914	GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq	GSM8970914 r1	GSM8970914	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-1_S19_L001_R1_001.fastq.gz	fastq	356071020.0	4685145.0	GSM8970914 r1	0:76	A:101990320;C:75361307;G:78194540;T:100522661;N:2192	76		101990320	75361307	78194540	100522661	2192	SRX28687222	SRS24954078	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36192	36192	SRR33446959	SRX28687222	SRS24954078	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 1	GSM8970914	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970914	GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq	GSM8970914 r1	GSM8970914	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-1_S19_L002_R1_001.fastq.gz	fastq	349258684.0	4595509.0	GSM8970914 r2	0:76	A:99883376;C:73952042;G:76902800;T:98518682;N:1784	76		99883376	73952042	76902800	98518682	1784	SRX28687222	SRS24954078	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36193	36193	SRR33446960	SRX28687222	SRS24954078	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 1	GSM8970914	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970914	GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq	GSM8970914 r1	GSM8970914	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-1_S19_L003_R1_001.fastq.gz	fastq	355553156.0	4678331.0	GSM8970914 r3	0:76	A:101770613;C:75287760;G:78157774;T:100334741;N:2268	76		101770613	75287760	78157774	100334741	2268	SRX28687222	SRS24954078	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36194	36194	SRR33446961	SRX28687222	SRS24954078	SRP583344	PRJNA1259437	Inhibition of TGF beta signalling during zebrafish larval tail regeneration.	GSE296469	Transcriptome Analysis	This study investigates the role of TGF beta signalling during tail regeneration in 72 hpf 96 hpf zebrafish. The inhibitor SB431542 was used to inhibit TGF beta signalling with and without xxx tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes xxx post injury; TGF beta dependent injury regulated DEGs; TGF beta dependent DEGs in the absence of injury; and TGF beta independent injury dependent DEGs. Overall design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap approximately 200um from the end of the tail at 72 hpf. 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used at 0.1%.		DMSO treated / cut tail replicate 1	GSM8970914	source name:Larval tail\|tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision\|geo loc name:missing\|collection date:missing	DMSO treated / cut tail replicate 1	demultiplexed using the BlueBee tool Illumina Assembly: GRCz11 Ensembl Supplementary files format and content: count matrix.tsv is the gene counts file	Larval tail	SB431542 treatments were at 50uM and were from 72 90hpf. DMSO was used as vehicle control at 0.1%.	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit	Zebrafish embryos were raised until 72hpf at 28.5C. Fish were anesthetised in 40 μg/ml Tricaine 3 amino benzoic acidethylester in E3. A scalpel was used to remove the end of the tail using the pigment gap as a reference	tissue:Larval tail\|genotype:Wild type\|treatment:Tail excision	GSM8970914	GSM8970914: DMSO treated / cut tail replicate 1; Danio rerio; RNA Seq	GSM8970914 r1	GSM8970914	1	100 tails were processed for each sample. These were put in 1ml of TRI Reagent Merck using a plastic pestle to dissociate the tissue. Following the TRI Reagent procedure the RNA was further purified by LiCL precipitation. Lexogen QuantSeq three prime FWD library kit		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP583344	Orange-1_S19_L004_R1_001.fastq.gz	fastq	351537316.0	4625491.0	GSM8970914 r4	0:76	A:100573823;C:74441165;G:77263744;T:99256707;N:1877	76		100573823	74441165	77263744	99256707	1877	SRX28687222	SRS24954078	SRA2124571	University of Sheffield	University of Sheffield							B	usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	United Kingdom	2025-05-06	Larval	Larval	Tail	Multi-system
36478	36478	SRR527835	SRX171222	SRS352108	SRP014596	PRJNA171539	Transcriptomic analysis of zebrafish during development and homeostasis	GSE39703	Transcriptome Analysis	Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail	pubmed:23684812	tail	GSM977960	tissue:entire adult tail\|genotype:Wild type\|strain:AB\|Stage:adult tail	tail	Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: .count file are the output of Htseq reads quantification. .fpkm files are the output of cufflinks quantification	entire adult tail		Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions		genotype:Wild type\|strain:AB\|Stage:adult tail	GSM977960	GSM977960: tail; Danio rerio; RNA Seq	GSM977960 1	GSM977960: tail	1		GEO Accession:GSM977960	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP014596			534897504.0	14858264.0	GSM977960 r1	0:36	A:144900139;C:122639505;G:130189210;T:136990883;N:177767	36		144900139	122639505	130189210	136990883	177767	SRX171222	SRS352108	SRA056408	GEO	ITG	1	0.89933	0.04578	0.71254	0.41668	36	B	usable mapping rate	illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Unknown	2012-07-27	Adult	Adult	Tail	Multi-system
38049	38049	SRR1519899	SRX657112	SRS662299	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		sih3	GSM1439473	tissue:tail derived cells\|genotype/variation:sih\|embryonic stage:28 hpf	sih3	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:sih\|embryonic stage:28 hpf	GSM1439473	GSM1439473: sih3; Danio rerio; RNA Seq	GSM1439473		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439473	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP044634	JGZ-06.fastq.gz	fastq	1416036978.0	26222907.0	GSM1439473 r1	0:54	A:342287675;C:370618836;G:361870457;T:341179934;N:80076	54		342287675	370618836	361870457	341179934	80076	SRX657112	SRS662299	SRA175990	GEO	IGBMC	1	0.96217	0.03055	0.76869	0.44925	54	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38050	38050	SRR1519898	SRX657111	SRS662291	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		WT3	GSM1439472	tissue:tail derived cells\|genotype/variation:WT\|embryonic stage:28 hpf	WT3	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:WT\|embryonic stage:28 hpf	GSM1439472	GSM1439472: WT3; Danio rerio; RNA Seq	GSM1439472		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439472	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP044634	JGZ-05.fastq.gz	fastq	1787680692.0	33105198.0	GSM1439472 r1	0:54	A:442553431;C:457003567;G:446438405;T:441598672;N:86617	54		442553431	457003567	446438405	441598672	86617	SRX657111	SRS662291	SRA175990	GEO	IGBMC	1	0.96318	0.03918	0.75371	0.4423	54	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38051	38051	SRR1519897	SRX657110	SRS662290	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		sih2	GSM1439471	tissue:tail derived cells\|genotype/variation:sih\|embryonic stage:28 hpf	sih2	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:sih\|embryonic stage:28 hpf	GSM1439471	GSM1439471: sih2; Danio rerio; RNA Seq	GSM1439471		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439471	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP044634	JGZ-04.fastq.gz	fastq	1813069386.0	33575359.0	GSM1439471 r1	0:54	A:462594376;C:449896725;G:440482879;T:460019095;N:76311	54		462594376	449896725	440482879	460019095	76311	SRX657110	SRS662290	SRA175990	GEO	IGBMC	1	0.95859	0.05282	0.74199	0.47244	54	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38052	38052	SRR1519896	SRX657109	SRS662289	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		WT2	GSM1439470	tissue:tail derived cells\|genotype/variation:WT\|embryonic stage:28 hpf	WT2	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:WT\|embryonic stage:28 hpf	GSM1439470	GSM1439470: WT2; Danio rerio; RNA Seq	GSM1439470		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439470	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP044634	JGZ-03.fastq.gz	fastq	1866194316.0	34559154.0	GSM1439470 r1	0:54	A:483946414;C:453986455;G:443561481;T:484623941;N:76025	54		483946414	453986455	443561481	484623941	76025	SRX657109	SRS662289	SRA175990	GEO	IGBMC	1	0.95615	0.06195	0.73594	0.47144	54	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38053	38053	SRR1519895	SRX657108	SRS662288	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		sih1	GSM1439469	tissue:tail derived cells\|genotype/variation:sih\|embryonic stage:28 hpf	sih1	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:sih\|embryonic stage:28 hpf	GSM1439469	GSM1439469: sih1; Danio rerio; RNA Seq	GSM1439469		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439469	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP044634	JGZ-02.fastq.gz	fastq	1451212470.0	26874305.0	GSM1439469 r1	0:54	A:368354355;C:360129390;G:353350795;T:369317437;N:60493	54		368354355	360129390	353350795	369317437	60493	SRX657108	SRS662288	SRA175990	GEO	IGBMC	1	0.94911	0.04509	0.74604	0.46107	54	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
38054	38054	SRR1519894	SRX657107	SRS662287	SRP044634	PRJNA255636	mRNA sequencing of embryonic tails of sih mutants at 28 hpf	GSE59563	Transcriptome Analysis	We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf		WT1	GSM1439468	tissue:tail derived cells\|genotype/variation:WT\|embryonic stage:28 hpf	WT1	Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id Gene name and one column for each sample containing the normalized read counts	tail derived cells	sih embryos lack heart contraction	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	Embryos were grown in normal conditions	genotype/variation:WT\|embryonic stage:28 hpf	GSM1439468	GSM1439468: WT1; Danio rerio; RNA Seq	GSM1439468		1	RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “mRNA sequencing sample preparation guide” part #1004898 Rev.D with some modifications. Briefly mRNA was purified from 2 µg total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94°C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801 Beckman Coulter Inc with the SPRI TE instrument Beckman Coulter Inc. Briefly in this system double stranded cDNA fragments were blunted phosphorylated and ligated to indexed adapter dimers and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98°C; [10 sec at 98°C 30 sec at 60°C 30 sec at 72°C] x 13 cycles; 5 min at 72°C then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.	GEO Accession:GSM1439468	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP044634	JGZ-01.fastq.gz	fastq	1583485146.0	29323799.0	GSM1439468 r1	0:54	A:405051413;C:391145102;G:382645289;T:404569188;N:74154	54		405051413	391145102	382645289	404569188	74154	SRX657107	SRS662287	SRA175990	GEO	IGBMC	1	0.94743	0.05464	0.73156	0.46572	54	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	France	2014-07-18	Pharyngula	Embryo	Tail	Multi-system
41312	41312	SRR4199307	SRX2148087	SRS1679265	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	NICD rep3	GSM2306087	source name:dissociated embryo tails\|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	NICD rep3	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	GSM2306087	GSM2306087: NICD rep3; Danio rerio; RNA Seq	GSM2306087		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306087	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617	mutant3.fastq.gz	fastq	1706861931.0	33467881.0	GSM2306087 r1	0:51 1:0	A:400027681;C:444926525;G:399939257;T:461913972;N:54496	51	0	400027681	444926525	399939257	461913972	54496	SRX2148087	SRS1679265	SRA464955	GEO	Stowers Institute for Medical Research	1	0.75848	0.06958	0.73616	0.47901	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41313	41313	SRR4199306	SRX2148086	SRS1679264	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	NICD rep2	GSM2306086	source name:dissociated embryo tails\|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	NICD rep2	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	GSM2306086	GSM2306086: NICD rep2; Danio rerio; RNA Seq	GSM2306086		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306086	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617	mutant2.fastq.gz	fastq	1745551857.0	34226507.0	GSM2306086 r1	0:51 1:0	A:414724753;C:449494336;G:403529006;T:477747391;N:56371	51	0	414724753	449494336	403529006	477747391	56371	SRX2148086	SRS1679264	SRA464955	GEO	Stowers Institute for Medical Research	1	0.77355	0.08842	0.71674	0.48589	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41314	41314	SRR4199305	SRX2148085	SRS1679263	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	NICD rep1	GSM2306085	source name:dissociated embryo tails\|strain:TgcldnB:GFP; TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	NICD rep1	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd\|tissue:dissociated embryo tails\|age:36 hpf	GSM2306085	GSM2306085: NICD rep1; Danio rerio; RNA Seq	GSM2306085		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306085	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617	mutant1.fastq.gz	fastq	1606289064.0	31495864.0	GSM2306085 r1	0:51 1:0	A:383363329;C:409816147;G:373853062;T:439205035;N:51491	51	0	383363329	409816147	373853062	439205035	51491	SRX2148085	SRS1679263	SRA464955	GEO	Stowers Institute for Medical Research	1	0.80199	0.09405	0.71382	0.48651	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41315	41315	SRR4199304	SRX2148084	SRS1679262	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	WT rep3	GSM2306084	source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep3	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306084	GSM2306084: WT rep3; Danio rerio; RNA Seq	GSM2306084		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306084	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617	WT3.fastq.gz	fastq	1621399650.0	31792150.0	GSM2306084 r1	0:51 1:0	A:394689371;C:400826196;G:384059217;T:441773624;N:51242	51	0	394689371	400826196	384059217	441773624	51242	SRX2148084	SRS1679262	SRA464955	GEO	Stowers Institute for Medical Research	1	0.87053	0.08236	0.7218	0.4831	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41316	41316	SRR4199303	SRX2148083	SRS1679261	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	WT rep2	GSM2306083	source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep2	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306083	GSM2306083: WT rep2; Danio rerio; RNA Seq	GSM2306083		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306083	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617	WT2.fastq.gz	fastq	1626903774.0	31900074.0	GSM2306083 r1	0:51 1:0	A:394214874;C:407655291;G:379120984;T:445859413;N:53212	51	0	394214874	407655291	379120984	445859413	53212	SRX2148083	SRS1679261	SRA464955	GEO	Stowers Institute for Medical Research	1	0.81975	0.09539	0.70869	0.4872	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41317	41317	SRR4199302	SRX2148082	SRS1679260	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.	pubmed:28085667	WT rep1	GSM2306082	source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep1	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306082	GSM2306082: WT rep1; Danio rerio; RNA Seq	GSM2306082		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306082	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617	WT1.fastq.gz	fastq	1646867622.0	32291522.0	GSM2306082 r1	0:51 1:0	A:400030238;C:412959654;G:377713613;T:456111038;N:53079	51	0	400030238	412959654	377713613	456111038	53079	SRX2148082	SRS1679260	SRA464955	GEO	Stowers Institute for Medical Research	1	0.81411	0.10419	0.70621	0.48075	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system
41418	41418	SRR4423118	SRX2245302	SRS1745860	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development			Adult FT Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Adult\|sex:female\|tissue:tail\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: Adult female tail	172 5	172 5	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP091534	femaletailRID0172BC05smallZF.fastq	fastq	491055734.0	7690105.0	femaletailRID0172BC05smallZF.fastq	0:63.86	A:114732043;C:132287469;G:130972143;T:113064079;N:0	63		114732043	132287469	130972143	113064079	0	SRX2245302	SRS1745860	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.82246	0.13521	0.91303	0.63226	43	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Adult	Adult	Tail	Multi-system
41419	41419	SRR4423117	SRX2245301	SRS1745860	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development			Adult FT Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Adult\|sex:female\|tissue:tail\|BioSampleModel:Model organism or animal									RNA Seq of Zebrafish: Adult female tail	172 3	172 3	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP091534	femaletailRID0172BC03largeZF.fastq	fastq	1414932187.0	9757587.0	femaletailRID0172BC03largeZF.fastq	0:145.01	A:343007105;C:362895564;G:422320111;T:286709407;N:0	145		343007105	362895564	422320111	286709407	0	SRX2245301	SRS1745860	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.96057	0.21796	0.95177	0.76663	141	B	usable mapping rate	ion_torrent	ion_torrent	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Adult	Adult	Tail	Multi-system
63892	63892	SRR14213374	SRX10579919	SRS8684387	SRP314470	PRJNA721381	RNA Seq from zebrafish adult tissues	GSE171906	Transcriptome Analysis	The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.	pubmed:34556579	Tail3	GSM5237143	source name:zebrafish tail\|genotype:wild type\|tissue:tail\|strain:TLAB	Tail3	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM	zebrafish tail		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:tail\|strain:TLAB	GSM5237143	GSM5237143: Tail3; Danio rerio; RNA Seq	GSM5237143		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM5237143	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP314470	Tail3.fastq	fastq	1351349800.0	13513498.0	GSM5237143 r1	0:100	A:344334043;C:321881505;G:312915864;T:372166616;N:51772	100		344334043	321881505	312915864	372166616	51772	SRX10579919	SRS8684387	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93634	0.09976	0.75521	0.48801	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Tail	Multi-system
63893	63893	SRR14213373	SRX10579918	SRS8684386	SRP314470	PRJNA721381	RNA Seq from zebrafish adult tissues	GSE171906	Transcriptome Analysis	The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.	pubmed:34556579	Tail2	GSM5237142	source name:zebrafish tail\|genotype:wild type\|tissue:tail\|strain:TLAB	Tail2	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM	zebrafish tail		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:tail\|strain:TLAB	GSM5237142	GSM5237142: Tail2; Danio rerio; RNA Seq	GSM5237142		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM5237142	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP314470	Tail2.fastq	fastq	1669271300.0	16692713.0	GSM5237142 r1	0:100	A:422977972;C:402400334;G:387344093;T:456484890;N:64011	100		422977972	402400334	387344093	456484890	64011	SRX10579918	SRS8684386	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93177	0.10145	0.75532	0.47775	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Tail	Multi-system
63894	63894	SRR14213372	SRX10579917	SRS8684385	SRP314470	PRJNA721381	RNA Seq from zebrafish adult tissues	GSE171906	Transcriptome Analysis	The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.	pubmed:34556579	Tail1	GSM5237141	source name:zebrafish tail\|genotype:wild type\|tissue:tail\|strain:TLAB	Tail1	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 102. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM	zebrafish tail		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|tissue:tail\|strain:TLAB	GSM5237141	GSM5237141: Tail1; Danio rerio; RNA Seq	GSM5237141		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM5237141	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP314470	Tail1.fastq	fastq	2117983600.0	21179836.0	GSM5237141 r1	0:100	A:534692684;C:517420692;G:497313091;T:568475177;N:81956	100		534692684	517420692	497313091	568475177	81956	SRX10579917	SRS8684385	SRA1217576	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93316	0.11572	0.74951	0.48824	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2021-04-12	Undetermined	Undetermined	Tail	Multi-system

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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");;