metadata: run_metadata: 56 rows where technology = "smartseq", tissue_curation = "Endothelium" and tissue_curation

56 rows where technology = "smartseq", tissue_curation = "Endothelium" and tissue_curation_coarse = "Cardiovascular System"

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.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
49040	49040	SRR7633494	SRX4497225	SRS3618225	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G2 endo 03	GSM3317066	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G2 mRNA	G2 endo 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G2 mRNA	GSM3317066	GSM3317066: G2 endo 03; Danio rerio; RNA Seq	GSM3317066		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317066	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S18_trimmed.fastq.gz	fastq	950344310.0	18847513.0	GSM3317066 r1	0:50.42 1:0	A:270135652;C:209210468;G:202674675;T:268256430;N:67085	50	0	270135652	209210468	202674675	268256430	67085	SRX4497225	SRS3618225	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89759		0.1428		0.69132		0.4729		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49041	49041	SRR7633493	SRX4497224	SRS3618224	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G2 endo 02	GSM3317065	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G2 mRNA	G2 endo 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G2 mRNA	GSM3317065	GSM3317065: G2 endo 02; Danio rerio; RNA Seq	GSM3317065		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317065	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S17_trimmed.fastq.gz	fastq	1635110054.0	32380584.0	GSM3317065 r1	0:50.50 1:0	A:462134552;C:361057634;G:349465446;T:462337205;N:115217	50	0	462134552	361057634	349465446	462337205	115217	SRX4497224	SRS3618224	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.80201		0.12711		0.70471		0.44427		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49042	49042	SRR7633492	SRX4497223	SRS3618223	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G2 endo 01	GSM3317064	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G2 mRNA	G2 endo 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G2 mRNA	GSM3317064	GSM3317064: G2 endo 01; Danio rerio; RNA Seq	GSM3317064		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317064	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S16_trimmed.fastq.gz	fastq	1302352614.0	25794210.0	GSM3317064 r1	0:50.49 1:0	A:370194702;C:286011167;G:276758200;T:369297736;N:90809	50	0	370194702	286011167	276758200	369297736	90809	SRX4497223	SRS3618223	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89468		0.15745		0.69447		0.47938		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49043	49043	SRR7633491	SRX4497222	SRS3618222	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G0 endo 03	GSM3317063	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G0 mRNA	G0 endo 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G0 mRNA	GSM3317063	GSM3317063: G0 endo 03; Danio rerio; RNA Seq	GSM3317063		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317063	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S15_trimmed.fastq.gz	fastq	1248556473.0	24725241.0	GSM3317063 r1	0:50.50 1:0	A:350256976;C:280431139;G:270771772;T:347009294;N:87292	50	0	350256976	280431139	270771772	347009294	87292	SRX4497222	SRS3618222	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.90514		0.13266		0.69236		0.47977		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49044	49044	SRR7633490	SRX4497221	SRS3618221	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G0 endo 02	GSM3317062	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G0 mRNA	G0 endo 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G0 mRNA	GSM3317062	GSM3317062: G0 endo 02; Danio rerio; RNA Seq	GSM3317062		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317062	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S14_trimmed.fastq.gz	fastq	372093672.0	7456111.0	GSM3317062 r1	0:49.90 1:0	A:113486766;C:74400549;G:71245468;T:112935661;N:25228	49	0	113486766	74400549	71245468	112935661	25228	SRX4497221	SRS3618221	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89644		0.12968		0.70658		0.47231		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49045	49045	SRR7633489	SRX4497220	SRS3618220	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	G0 endo 01	GSM3317061	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G0 mRNA	G0 endo 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G0 mRNA	GSM3317061	GSM3317061: G0 endo 01; Danio rerio; RNA Seq	GSM3317061		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317061	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S13_trimmed.fastq.gz	fastq	1450133780.0	28705598.0	GSM3317061 r1	0:50.52 1:0	A:407543677;C:323333189;G:313321100;T:405835253;N:100561	50	0	407543677	323333189	313321100	405835253	100561	SRX4497220	SRS3618220	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.8994		0.13347		0.6942		0.47759		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49046	49046	SRR7633488	SRX4497219	SRS3618219	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	control endo 03	GSM3317060	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:control	control endo 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:control	GSM3317060	GSM3317060: control endo 03; Danio rerio; RNA Seq	GSM3317060		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317060	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S12_trimmed.fastq.gz	fastq	1720199608.0	34019943.0	GSM3317060 r1	0:50.56 1:0	A:474252335;C:393152371;G:382256277;T:470417173;N:121452	50	0	474252335	393152371	382256277	470417173	121452	SRX4497219	SRS3618219	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.90252		0.11709		0.69668		0.47424		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49047	49047	SRR7633487	SRX4497218	SRS3618218	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	control endo 02	GSM3317059	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:control	control endo 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:control	GSM3317059	GSM3317059: control endo 02; Danio rerio; RNA Seq	GSM3317059		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317059	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S11_trimmed.fastq.gz	fastq	322327295.0	6605687.0	GSM3317059 r1	0:48.80 1:0	A:109722776;C:53179948;G:51091267;T:108312123;N:21181	48	0	109722776	53179948	51091267	108312123	21181	SRX4497218	SRS3618218	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.8922		0.1261		0.72811		0.46128		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49048	49048	SRR7633486	SRX4497217	SRS3618217	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2	pubmed:31158233	control endo 01	GSM3317058	tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:control	control endo 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:control	GSM3317058	GSM3317058: control endo 01; Danio rerio; RNA Seq	GSM3317058		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317058	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992		BA_S10_trimmed.fastq.gz	fastq	1484074935.0	29385409.0	GSM3317058 r1	0:50.50 1:0	A:411414710;C:336260838;G:326730208;T:409563857;N:105322	50	0	411414710	336260838	326730208	409563857	105322	SRX4497217	SRS3618217	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.88777		0.11462		0.70102		0.47353		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
58567	58567	SRR11420478	SRX7998914	SRS6376277	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL E3 endo Danio	GSM4432625	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL E3 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432625	GSM4432625: Smartseq2 AXL E3 endo Danio; Danio rerio; RNA Seq	GSM4432625		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432625	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-E3_HHVK7CCXY_L3_1.clean.fq.gz AXL-E3_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1568068200.0	5226894.0	GSM4432625 r1	0:150 1:150	A:437547051;C:305827667;G:317225931;T:507380843;N:86708	150	150	437547051	305827667	317225931	507380843	86708	SRX7998914	SRS6376277	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.90556	0.91298	0.73969	0.74743	0.94888	0.95061	0.47195	0.48203	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58568	58568	SRR11420477	SRX7998913	SRS6376276	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL E2 endo Danio	GSM4432624	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL E2 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432624	GSM4432624: Smartseq2 AXL E2 endo Danio; Danio rerio; RNA Seq	GSM4432624		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432624	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-E2_HHVK7CCXY_L3_2.clean.fq.gz AXL-E2_HHVK7CCXY_L3_1.clean.fq.gz	fastq fastq	1506462600.0	5021542.0	GSM4432624 r1	0:150 1:150	A:419138482;C:294375706;G:306403925;T:486460081;N:84406	150	150	419138482	294375706	306403925	486460081	84406	SRX7998913	SRS6376276	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.90958	0.91859	0.78806	0.79513	0.96327	0.96477	0.45808	0.46876	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58569	58569	SRR11420476	SRX7998912	SRS6376275	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL E1 endo Danio	GSM4432623	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL E1 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432623	GSM4432623: Smartseq2 AXL E1 endo Danio; Danio rerio; RNA Seq	GSM4432623		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432623	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-E1_HHVK7CCXY_L3_1.clean.fq.gz AXL-E1_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1583815800.0	5279386.0	GSM4432623 r1	0:150 1:150	A:440756401;C:310619619;G:322228450;T:510122285;N:89045	150	150	440756401	310619619	322228450	510122285	89045	SRX7998912	SRS6376275	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.91047	0.91678	0.69764	0.70328	0.95217	0.95349	0.46044	0.44698	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58570	58570	SRR11420475	SRX7998911	SRS6376274	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL D3 endo Danio	GSM4432622	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL D3 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432622	GSM4432622: Smartseq2 AXL D3 endo Danio; Danio rerio; RNA Seq	GSM4432622		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432622	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-D3_HHVK7CCXY_L3_1.clean.fq.gz AXL-D3_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1602725100.0	5342417.0	GSM4432622 r1	0:150 1:150	A:454250175;C:320141617;G:330588624;T:497655411;N:89273	150	150	454250175	320141617	330588624	497655411	89273	SRX7998911	SRS6376274	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.82435	0.83275	0.22763	0.23084	0.88716	0.89023	0.75529	0.75251	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58571	58571	SRR11420474	SRX7998910	SRS6376273	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL C3 endo Danio	GSM4432621	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL C3 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432621	GSM4432621: Smartseq2 AXL C3 endo Danio; Danio rerio; RNA Seq	GSM4432621		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432621	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-C3_HHVK7CCXY_L3_1.clean.fq.gz AXL-C3_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1574724600.0	5249082.0	GSM4432621 r1	0:150 1:150	A:435586693;C:313192449;G:325059370;T:500799470;N:86618	150	150	435586693	313192449	325059370	500799470	86618	SRX7998910	SRS6376273	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.91247	0.91968	0.66959	0.67559	0.94515	0.94734	0.47277	0.49142	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58572	58572	SRR11420473	SRX7998909	SRS6376272	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL C2 endo Danio	GSM4432620	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL C2 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432620	GSM4432620: Smartseq2 AXL C2 endo Danio; Danio rerio; RNA Seq	GSM4432620		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432620	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-C2_HHVK7CCXY_L3_1.clean.fq.gz AXL-C2_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	918029400.0	3060098.0	GSM4432620 r1	0:150 1:150	A:247708437;C:197427436;G:203244315;T:269598842;N:50370	150	150	247708437	197427436	203244315	269598842	50370	SRX7998909	SRS6376272	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.85585	0.86096	0.18376	0.1852	0.91352	0.91571	0.44329	0.55709	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58573	58573	SRR11420472	SRX7998908	SRS6376270	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL C1 endo Danio	GSM4432619	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL C1 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432619	GSM4432619: Smartseq2 AXL C1 endo Danio; Danio rerio; RNA Seq	GSM4432619		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432619	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-C1_HHVK7CCXY_L3_1.clean.fq.gz AXL-C1_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1500775500.0	5002585.0	GSM4432619 r1	0:150 1:150	A:432671655;C:289434226;G:302125698;T:476460891;N:83030	150	150	432671655	289434226	302125698	476460891	83030	SRX7998908	SRS6376270	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.67663	0.68022	0.32993	0.33204	0.86841	0.87373	0.55098	0.55286	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58574	58574	SRR11420471	SRX7998907	SRS6376271	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL B2 endo Danio	GSM4432618	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL B2 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432618	GSM4432618: Smartseq2 AXL B2 endo Danio; Danio rerio; RNA Seq	GSM4432618		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432618	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-B2_HHVK7CCXY_L3_1.clean.fq.gz AXL-B2_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	989060100.0	3296867.0	GSM4432618 r1	0:150 1:150	A:274301021;C:196555336;G:203736274;T:314412137;N:55332	150	150	274301021	196555336	203736274	314412137	55332	SRX7998907	SRS6376271	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.9149	0.92243	0.73373	0.73884	0.95296	0.95426	0.47934	0.47668	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58575	58575	SRR11420470	SRX7998906	SRS6376269	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL B1 endo Danio	GSM4432617	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL B1 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432617	GSM4432617: Smartseq2 AXL B1 endo Danio; Danio rerio; RNA Seq	GSM4432617		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432617	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-B1_HHVK7CCXY_L3_1.clean.fq.gz AXL-B1_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	2099031600.0	6996772.0	GSM4432617 r1	0:150 1:150	A:583452672;C:414863616;G:430728068;T:669871636;N:115608	150	150	583452672	414863616	430728068	669871636	115608	SRX7998906	SRS6376269	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.82207	0.82952	0.63293	0.64238	0.94602	0.94828	0.49299	0.49862	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58576	58576	SRR11420469	SRX7998905	SRS6376268	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL A3 endo Danio	GSM4432616	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL A3 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432616	GSM4432616: Smartseq2 AXL A3 endo Danio; Danio rerio; RNA Seq	GSM4432616		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432616	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-A3_HHVK7CCXY_L3_1.clean.fq.gz AXL-A3_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	932495100.0	3108317.0	GSM4432616 r1	0:150 1:150	A:258055487;C:185801372;G:192600723;T:295985361;N:52157	150	150	258055487	185801372	192600723	295985361	52157	SRX7998905	SRS6376268	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.91666	0.92212	0.7484	0.75372	0.94826	0.95018	0.50494	0.50846	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58577	58577	SRR11420468	SRX7998904	SRS6376267	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL A2 endo Danio	GSM4432615	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL A2 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432615	GSM4432615: Smartseq2 AXL A2 endo Danio; Danio rerio; RNA Seq	GSM4432615		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432615	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-A2_HHVK7CCXY_L3_1.clean.fq.gz AXL-A2_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1474053600.0	4913512.0	GSM4432615 r1	0:150 1:150	A:409235463;C:294510014;G:304366926;T:465858337;N:82860	150	150	409235463	294510014	304366926	465858337	82860	SRX7998904	SRS6376267	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.89481	0.90098	0.57187	0.57596	0.91045	0.91366	0.46573	0.46566	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
58578	58578	SRR11420467	SRX7998903	SRS6376266	SRP254020	PRJNA615175	A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction	GSE147526	Other	A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here we report a zebrafish based orthotopic GBM xenograft model in which GBM cells from different species and even patients can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain	pubmed:35199829	Smartseq2 AXL A1 endo Danio	GSM4432614	tissue:endothelial cells\|strain:flk:GFP\|cell tye:endothelial cells	Smartseq2 AXL A1 endo Danio	ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM	endothelial cells		1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.		strain:flk:GFP\|cell tye:endothelial cells	GSM4432614	GSM4432614: Smartseq2 AXL A1 endo Danio; Danio rerio; RNA Seq	GSM4432614		1	1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle. 2. For GBM cells zebrafish were injected with GBM U251 mCherry cells and allowed to form widespread tumor invasion for xxx 5 days. At that point the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37°C for 30min. post digestion a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.	GEO Accession:GSM4432614	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP254020		AXL-A1_HHVK7CCXY_L3_1.clean.fq.gz AXL-A1_HHVK7CCXY_L3_2.clean.fq.gz	fastq fastq	1017985800.0	3393286.0	GSM4432614 r1	0:150 1:150	A:297904574;C:190252853;G:199665607;T:330106549;N:56217	150	150	297904574	190252853	199665607	330106549	56217	SRX7998903	SRS6376266	SRA1059261	GEO	Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University	2	0.82827	0.84942	0.55392	0.56701	0.89029	0.89394	0.61422	0.61422	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	China	2020-03-25	Larval	Larval	Endothelium	Cardiovascular System
69580	69580	SRR18927184	SRX15004844	SRS12753556	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	GSM6068604	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068604	GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq	GSM6068604 r1	GSM6068604	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_03_S9_L001_R1_001.fastq.gz	fastq	744134237.0	10221322.0	GSM6068604 r1	0:72.80 1:0	A:200415459;C:170890467;G:175699158;T:196451943;N:677210	72	0	200415459	170890467	175699158	196451943	677210	SRX15004844	SRS12753556	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93677		0.0458		0.76144		0.51338		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69581	69581	SRR18927185	SRX15004844	SRS12753556	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	GSM6068604	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068604	GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq	GSM6068604 r1	GSM6068604	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_03_S9_L002_R1_001.fastq.gz	fastq	713336563.0	9806369.0	GSM6068604 r2	0:72.74 1:0	A:192232089;C:164110978;G:167926911;T:188411430;N:655155	72	0	192232089	164110978	167926911	188411430	655155	SRX15004844	SRS12753556	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93575		0.0459		0.7628		0.52271		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69582	69582	SRR18927186	SRX15004844	SRS12753556	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	GSM6068604	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068604	GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq	GSM6068604 r1	GSM6068604	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_03_S9_L003_R1_001.fastq.gz	fastq	718617566.0	9871758.0	GSM6068604 r3	0:72.80 1:0	A:193895503;C:165112470;G:169254039;T:189730714;N:624840	72	0	193895503	165112470	169254039	189730714	624840	SRX15004844	SRS12753556	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.9355		0.04598		0.76459		0.5158		73		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69583	69583	SRR18927187	SRX15004844	SRS12753556	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	GSM6068604	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068604	GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq	GSM6068604 r1	GSM6068604	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_03_S9_L004_R1_001.fastq.gz	fastq	727564590.0	9976511.0	GSM6068604 r4	0:72.93 1:0	A:196363760;C:167163486;G:171092104;T:192383180;N:562060	72	0	196363760	167163486	171092104	192383180	562060	SRX15004844	SRS12753556	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93595		0.04601		0.76353		0.51732		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69584	69584	SRR18927188	SRX15004843	SRS12753555	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	GSM6068603	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068603	GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq	GSM6068603 r1	GSM6068603	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_02_S8_L001_R1_001.fastq.gz	fastq	697802741.0	9548738.0	GSM6068603 r1	0:73.08 1:0	A:187922068;C:160061203;G:164649390;T:184626878;N:543202	73	0	187922068	160061203	164649390	184626878	543202	SRX15004843	SRS12753555	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93586		0.05129		0.76424		0.52169		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69585	69585	SRR18927189	SRX15004843	SRS12753555	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	GSM6068603	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068603	GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq	GSM6068603 r1	GSM6068603	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_02_S8_L002_R1_001.fastq.gz	fastq	662903444.0	9078930.0	GSM6068603 r2	0:73.02 1:0	A:178605669;C:152357709;G:156008633;T:175409889;N:521544	73	0	178605669	152357709	156008633	175409889	521544	SRX15004843	SRS12753555	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93653		0.05146		0.7628		0.51778		74		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69586	69586	SRR18927190	SRX15004843	SRS12753555	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	GSM6068603	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068603	GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq	GSM6068603 r1	GSM6068603	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_02_S8_L003_R1_001.fastq.gz	fastq	668311097.0	9143688.0	GSM6068603 r3	0:73.09 1:0	A:180289485;C:153373494;G:157331239;T:176839110;N:477769	73	0	180289485	153373494	157331239	176839110	477769	SRX15004843	SRS12753555	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93696		0.05225		0.7637		0.51732		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69587	69587	SRR18927191	SRX15004843	SRS12753555	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	GSM6068603	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068603	GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq	GSM6068603 r1	GSM6068603	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_02_S8_L004_R1_001.fastq.gz	fastq	680968806.0	9296775.0	GSM6068603 r4	0:73.25 1:0	A:183838465;C:156195225;G:160056448;T:180449193;N:429475	73	0	183838465	156195225	160056448	180449193	429475	SRX15004843	SRS12753555	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93695		0.05036		0.76394		0.52148		55		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69588	69588	SRR18927192	SRX15004842	SRS12753554	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	GSM6068602	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068602	GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq	GSM6068602 r1	GSM6068602	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_01_S7_L001_R1_001.fastq.gz	fastq	860623909.0	11793192.0	GSM6068602 r1	0:72.98 1:0	A:231785480;C:197544026;G:202920509;T:227621795;N:752099	72	0	231785480	197544026	202920509	227621795	752099	SRX15004842	SRS12753554	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93103		0.0562		0.76179		0.51243		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69589	69589	SRR18927193	SRX15004842	SRS12753554	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	GSM6068602	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068602	GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq	GSM6068602 r1	GSM6068602	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_01_S7_L002_R1_001.fastq.gz	fastq	829335984.0	11372967.0	GSM6068602 r2	0:72.92 1:0	A:223480519;C:190755977;G:194990382;T:219387236;N:721870	72	0	223480519	190755977	194990382	219387236	721870	SRX15004842	SRS12753554	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93059		0.05558		0.76106		0.51174		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69590	69590	SRR18927194	SRX15004842	SRS12753554	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	GSM6068602	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068602	GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq	GSM6068602 r1	GSM6068602	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_01_S7_L003_R1_001.fastq.gz	fastq	834710665.0	11441037.0	GSM6068602 r3	0:72.96 1:0	A:225104441;C:191764824;G:196384217;T:220771605;N:685578	72	0	225104441	191764824	196384217	220771605	685578	SRX15004842	SRS12753554	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93233		0.05582		0.76159		0.51481		74		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
69591	69591	SRR18927195	SRX15004842	SRS12753554	SRP372368	PRJNA832312	Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2	GSE201611	Transcriptome Analysis	The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition	pubmed:35531980	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	GSM6068602	source name:Endothelium\|tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1	Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output	Endothelium		Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147	Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage	tissue:Endothelium\|transgenic line:Tgfli1a:egfp\|genotype:WT\|developmental stage:15 somite stage	GSM6068602	GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq	GSM6068602 r1	GSM6068602	1	Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP372368		fliegfp_01_S7_L004_R1_001.fastq.gz	fastq	851008802.0	11646797.0	GSM6068602 r4	0:73.07 1:0	A:229587437;C:195482220;G:199880005;T:225397616;N:661524	73	0	229587437	195482220	199880005	225397616	661524	SRX15004842	SRS12753554	SRA1410588	Department of Anatomy & Physiology, The University of Melbourne	Department of Anatomy & Physiology, The University of Melbourne	1	0.93162		0.05617		0.76195		0.51057		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Australia	2022-04-26	Segmentation	Embryo	Endothelium	Cardiovascular System
75610	75610	SRR24740771	SRX20518083	SRS17828039	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf wnt7aa MO 4	GSM7429341	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf wnt7aa MO 4	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted	GSM7429341	GSM7429341: PHBC endothelial cells 30 hpf wnt7aa MO 4; Danio rerio; RNA Seq	GSM7429341 r1	GSM7429341	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	F4_MO_wnt7aa_R1.fastq.gz F4_MO_wnt7aa_R2.fastq.gz	fastq fastq	3410657071.0	22888059.0	GSM7429341 r1		A:930255790;C:774998735;G:770566602;T:932969311;N:1866633			930255790	774998735	770566602	932969311	1866633	SRX20518083	SRS17828039	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.9278	0.9295	0.13464	0.13259	0.75345	0.75694	0.50275	0.49844	74	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75611	75611	SRR24740772	SRX20518082	SRS17828038	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf wnt7aa MO 3	GSM7429340	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf wnt7aa MO 3	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted	GSM7429340	GSM7429340: PHBC endothelial cells 30 hpf wnt7aa MO 3; Danio rerio; RNA Seq	GSM7429340 r1	GSM7429340	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	F3_MO_wnt7aa_R1.fastq.gz F3_MO_wnt7aa_R2.fastq.gz	fastq fastq	2844102685.0	19087245.0	GSM7429340 r1		A:753836724;C:664365246;G:664895731;T:759443497;N:1561487			753836724	664365246	664895731	759443497	1561487	SRX20518082	SRS17828038	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.87882	0.88191	0.10969	0.10713	0.79397	0.79557	0.52306	0.52523	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75612	75612	SRR24740773	SRX20518081	SRS17828037	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf wnt7aa MO 2	GSM7429339	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf wnt7aa MO 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted	GSM7429339	GSM7429339: PHBC endothelial cells 30 hpf wnt7aa MO 2; Danio rerio; RNA Seq	GSM7429339 r1	GSM7429339	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	F2_MO_wnt7aa_R1.fastq.gz F2_MO_wnt7aa_R2.fastq.gz	fastq fastq	3003877741.0	20155237.0	GSM7429339 r1		A:806731621;C:691626094;G:690105872;T:813757253;N:1656901			806731621	691626094	690105872	813757253	1656901	SRX20518081	SRS17828037	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.88411	0.88628	0.15488	0.15267	0.77654	0.77891	0.5348	0.5414	73	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75613	75613	SRR24740774	SRX20518080	SRS17828036	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf wnt7aa MO 1	GSM7429338	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf wnt7aa MO 1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:wnt7aa MO\|treatment:photoconverted	GSM7429338	GSM7429338: PHBC endothelial cells 30 hpf wnt7aa MO 1; Danio rerio; RNA Seq	GSM7429338 r1	GSM7429338	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	F1_MO_wnt7aa_R1.fastq.gz F1_MO_wnt7aa_R2.fastq.gz	fastq fastq	2134056620.0	14319615.0	GSM7429338 r1		A:574764769;C:489478372;G:488808981;T:579820041;N:1184457			574764769	489478372	488808981	579820041	1184457	SRX20518080	SRS17828036	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.90992	0.91125	0.15485	0.15169	0.77126	0.77352	0.52889	0.52569	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75614	75614	SRR24740775	SRX20518079	SRS17828035	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf reck MO 4	GSM7429337	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf reck MO 4	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted	GSM7429337	GSM7429337: PHBC endothelial cells 30 hpf reck MO 4; Danio rerio; RNA Seq	GSM7429337 r1	GSM7429337	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	E4_MO_reck_R1.fastq.gz E4_MO_reck_R2.fastq.gz	fastq fastq	2600213337.0	17457111.0	GSM7429337 r1		A:711797268;C:588127202;G:584757641;T:714124587;N:1406639			711797268	588127202	584757641	714124587	1406639	SRX20518079	SRS17828035	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.90425	0.905	0.13217	0.13087	0.74245	0.74692	0.47354	0.48629	74	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75615	75615	SRR24740776	SRX20518078	SRS17828034	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf reck MO 3	GSM7429336	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf reck MO 3	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted	GSM7429336	GSM7429336: PHBC endothelial cells 30 hpf reck MO 3; Danio rerio; RNA Seq	GSM7429336 r1	GSM7429336	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	E3_MO_reck_R1.fastq.gz E3_MO_reck_R2.fastq.gz	fastq fastq	1741572044.0	11687076.0	GSM7429336 r1		A:472997022;C:397732899;G:395569364;T:474320408;N:952351			472997022	397732899	395569364	474320408	952351	SRX20518078	SRS17828034	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.93581	0.93755	0.1129	0.11226	0.7559	0.75801	0.48017	0.47999	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75616	75616	SRR24740777	SRX20518077	SRS17828033	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf reck MO 2	GSM7429335	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf reck MO 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted	GSM7429335	GSM7429335: PHBC endothelial cells 30 hpf reck MO 2; Danio rerio; RNA Seq	GSM7429335 r1	GSM7429335	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	E2_MO_reck_R1.fastq.gz E2_MO_reck_R2.fastq.gz	fastq fastq	2671658198.0	17928556.0	GSM7429335 r1		A:725812218;C:610551715;G:606842688;T:726993096;N:1458481			725812218	610551715	606842688	726993096	1458481	SRX20518077	SRS17828033	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.92509	0.92531	0.13119	0.13003	0.74487	0.74854	0.47968	0.48136	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75617	75617	SRR24740778	SRX20518076	SRS17828032	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf reck MO 1	GSM7429334	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf reck MO 1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:reck MO\|treatment:photoconverted	GSM7429334	GSM7429334: PHBC endothelial cells 30 hpf reck MO 1; Danio rerio; RNA Seq	GSM7429334 r1	GSM7429334	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	E1_MO_reck_R1.fastq.gz E1_MO_reck_R2.fastq.gz	fastq fastq	2779576944.0	19473447.0	GSM7429334 r1		A:818491725;C:569735041;G:564250518;T:825468450;N:1631210			818491725	569735041	564250518	825468450	1631210	SRX20518076	SRS17828032	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.60589	0.60513	0.08903	0.0878	0.80093	0.80391	0.50318	0.48591	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75618	75618	SRR24740779	SRX20518075	SRS17828031	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf TF MO 4	GSM7429333	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf TF MO 4	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted	GSM7429333	GSM7429333: PHBC endothelial cells 30 hpf TF MO 4; Danio rerio; RNA Seq	GSM7429333 r1	GSM7429333	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	D4_MO_TF_R1.fastq.gz D4_MO_TF_R2.fastq.gz	fastq fastq	3262028321.0	21890211.0	GSM7429333 r1		A:876880120;C:749366908;G:748032046;T:885943266;N:1805981			876880120	749366908	748032046	885943266	1805981	SRX20518075	SRS17828031	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.90243	0.90467	0.15799	0.15728	0.77218	0.77524	0.54673	0.54717	75	74	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75619	75619	SRR24740780	SRX20518074	SRS17828030	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf TF MO 3	GSM7429332	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf TF MO 3	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted	GSM7429332	GSM7429332: PHBC endothelial cells 30 hpf TF MO 3; Danio rerio; RNA Seq	GSM7429332 r1	GSM7429332	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	D3_MO_TF_R1.fastq.gz D3_MO_TF_R2.fastq.gz	fastq fastq	911957449.0	6119680.0	GSM7429332 r1		A:240966620;C:213588458;G:213137469;T:243759752;N:505150			240966620	213588458	213137469	243759752	505150	SRX20518074	SRS17828030	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.88163	0.88298	0.13578	0.13347	0.77977	0.7837	0.53317	0.5412	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75620	75620	SRR24740781	SRX20518073	SRS17828029	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf TF MO 2	GSM7429331	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf TF MO 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted	GSM7429331	GSM7429331: PHBC endothelial cells 30 hpf TF MO 2; Danio rerio; RNA Seq	GSM7429331 r1	GSM7429331	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	D2_MO_TF_R1.fastq.gz D2_MO_TF_R2.fastq.gz	fastq fastq	2828207009.0	18989270.0	GSM7429331 r1		A:742830477;C:672427123;G:669193099;T:742200169;N:1556141			742830477	672427123	669193099	742200169	1556141	SRX20518073	SRS17828029	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.8578	0.86018	0.08003	0.07945	0.8016	0.80359	0.47591	0.47619	74	73	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75621	75621	SRR24740782	SRX20518072	SRS17828028	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf TF MO 1	GSM7429330	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf TF MO 1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:TF MO\|treatment:photoconverted	GSM7429330	GSM7429330: PHBC endothelial cells 30 hpf TF MO 1; Danio rerio; RNA Seq	GSM7429330 r1	GSM7429330	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	D1_MO_TF_R1.fastq.gz D1_MO_TF_R2.fastq.gz	fastq fastq	3219964468.0	21606481.0	GSM7429330 r1		A:865281524;C:741783926;G:739687813;T:871436747;N:1774458			865281524	741783926	739687813	871436747	1774458	SRX20518072	SRS17828028	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.90355	0.9049	0.12506	0.12473	0.76469	0.76891	0.5213	0.51875	72	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75622	75622	SRR24740783	SRX20518071	SRS17828027	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf gpr124 MO 4	GSM7429329	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf gpr124 MO 4	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted	GSM7429329	GSM7429329: PHBC endothelial cells 30 hpf gpr124 MO 4; Danio rerio; RNA Seq	GSM7429329 r1	GSM7429329	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	C4_MO_gpr124_R1.fastq.gz C4_MO_gpr124_R2.fastq.gz	fastq fastq	2735180426.0	18351837.0	GSM7429329 r1		A:727609254;C:631295729;G:635633455;T:739158077;N:1483911			727609254	631295729	635633455	739158077	1483911	SRX20518071	SRS17828027	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.87574	0.88067	0.18017	0.17428	0.81091	0.81345	0.51599	0.50175	72	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75623	75623	SRR24740784	SRX20518070	SRS17828026	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf gpr124 MO 3	GSM7429328	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf gpr124 MO 3	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted	GSM7429328	GSM7429328: PHBC endothelial cells 30 hpf gpr124 MO 3; Danio rerio; RNA Seq	GSM7429328 r1	GSM7429328	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	C3_MO_gpr124_R1.fastq.gz C3_MO_gpr124_R2.fastq.gz	fastq fastq	2832145279.0	19001125.0	GSM7429328 r1		A:742506972;C:669366817;G:669405672;T:749307010;N:1558808			742506972	669366817	669405672	749307010	1558808	SRX20518070	SRS17828026	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.86374	0.86649	0.12603	0.12479	0.78699	0.78971	0.53138	0.53587	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75624	75624	SRR24740785	SRX20518069	SRS17828025	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf gpr124 MO 2	GSM7429327	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf gpr124 MO 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted	GSM7429327	GSM7429327: PHBC endothelial cells 30 hpf gpr124 MO 2; Danio rerio; RNA Seq	GSM7429327 r1	GSM7429327	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	C2_MO_gpr124_R1.fastq.gz C2_MO_gpr124_R2.fastq.gz	fastq fastq	2095742074.0	14058965.0	GSM7429327 r1		A:525622879;C:516816905;G:520123702;T:532027251;N:1151337			525622879	516816905	520123702	532027251	1151337	SRX20518069	SRS17828025	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.88042	0.88475	0.10515	0.10178	0.81245	0.81759	0.54948	0.54823	75	74	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75625	75625	SRR24740786	SRX20518068	SRS17828024	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf gpr124 MO 1	GSM7429326	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf gpr124 MO 1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:gpr124 MO\|treatment:photoconverted	GSM7429326	GSM7429326: PHBC endothelial cells 30 hpf gpr124 MO 1; Danio rerio; RNA Seq	GSM7429326 r1	GSM7429326	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	C1_MO_gpr124_R1.fastq.gz C1_MO_gpr124_R2.fastq.gz	fastq fastq	2767627147.0	18597154.0	GSM7429326 r1		A:759461761;C:625145665;G:619178577;T:762309844;N:1531300			759461761	625145665	619178577	762309844	1531300	SRX20518068	SRS17828024	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.67422	0.67595	0.085	0.08394	0.78817	0.79119	0.4915	0.4887	75	73	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75626	75626	SRR24740787	SRX20518067	SRS17828023	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf WT 4	GSM7429325	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf WT 4	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted	GSM7429325	GSM7429325: PHBC endothelial cells 30 hpf WT 4; Danio rerio; RNA Seq	GSM7429325 r1	GSM7429325	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	B4_WT_R1.fastq.gz B4_WT_R2.fastq.gz	fastq fastq	2924689332.0	19639070.0	GSM7429325 r1		A:809211667;C:649768099;G:647294872;T:816789532;N:1625162			809211667	649768099	647294872	816789532	1625162	SRX20518067	SRS17828023	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.90556	0.90777	0.20579	0.20449	0.76836	0.77234	0.55234	0.55251	74	71	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75627	75627	SRR24740788	SRX20518066	SRS17828022	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf WT 3	GSM7429324	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf WT 3	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted	GSM7429324	GSM7429324: PHBC endothelial cells 30 hpf WT 3; Danio rerio; RNA Seq	GSM7429324 r1	GSM7429324	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	B3_WT_R1.fastq.gz B3_WT_R2.fastq.gz	fastq fastq	2556876101.0	17158306.0	GSM7429324 r1		A:674099968;C:605785858;G:602757969;T:672809126;N:1423180			674099968	605785858	602757969	672809126	1423180	SRX20518066	SRS17828022	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.93764	0.93809	0.09995	0.09895	0.76976	0.77181	0.47357	0.47232	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75628	75628	SRR24740789	SRX20518065	SRS17828021	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf WT 2	GSM7429323	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf WT 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted	GSM7429323	GSM7429323: PHBC endothelial cells 30 hpf WT 2; Danio rerio; RNA Seq	GSM7429323 r1	GSM7429323	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	B2_WT_R1.fastq.gz B2_WT_R2.fastq.gz	fastq fastq	2719619180.0	18253304.0	GSM7429323 r1		A:737514407;C:623462360;G:618552838;T:738582283;N:1507292			737514407	623462360	618552838	738582283	1507292	SRX20518065	SRS17828021	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.92769	0.92835	0.12021	0.11953	0.74852	0.75116	0.48883	0.49108	75	74	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75629	75629	SRR24740790	SRX20518064	SRS17828020	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	PHBC endothelial cells 30 hpf WT 1	GSM7429322	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted\|geo loc name:missing\|collection date:missing	PHBC endothelial cells 30 hpf WT 1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:PHBC endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:photoconverted	GSM7429322	GSM7429322: PHBC endothelial cells 30 hpf WT 1; Danio rerio; RNA Seq	GSM7429322 r1	GSM7429322	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	B1_WT_R1.fastq.gz B1_WT_R2.fastq.gz	fastq fastq	3264716585.0	21921700.0	GSM7429322 r1		A:879625441;C:754137197;G:748183608;T:880983333;N:1787006			879625441	754137197	748183608	880983333	1787006	SRX20518064	SRS17828020	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.82107	0.82113	0.12446	0.12391	0.78007	0.7847	0.48973	0.48394	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75630	75630	SRR24740791	SRX20518063	SRS17828019	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	Endothelial cells 30 hpf negative 3	GSM7429321	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:Endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:Non photoconverted\|geo loc name:missing\|collection date:missing	Endothelial cells 30 hpf negative 3	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:Endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:Non photoconverted	GSM7429321	GSM7429321: Endothelial cells 30 hpf negative 3; Danio rerio; RNA Seq	GSM7429321 r1	GSM7429321	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	A3_Neg_controls_R1.fastq.gz A3_Neg_controls_R2.fastq.gz	fastq fastq	2754470229.0	18487768.0	GSM7429321 r1		A:707439749;C:673922384;G:669885592;T:701717257;N:1505247			707439749	673922384	669885592	701717257	1505247	SRX20518063	SRS17828019	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.95585	0.9557	0.05025	0.04999	0.7837	0.78693	0.40771	0.40943	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75631	75631	SRR24740792	SRX20518062	SRS17828018	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	Endothelial cells 30 hpf negative 2	GSM7429320	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:Endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:Non photoconverted\|geo loc name:missing\|collection date:missing	Endothelial cells 30 hpf negative 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:Endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:Non photoconverted	GSM7429320	GSM7429320: Endothelial cells 30 hpf negative 2; Danio rerio; RNA Seq	GSM7429320 r1	GSM7429320	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	A2_Neg_controls_R1.fastq.gz A2_Neg_controls_R2.fastq.gz	fastq fastq	2820835655.0	18927799.0	GSM7429320 r1		A:731665823;C:680271247;G:678251388;T:729095004;N:1552193			731665823	680271247	678251388	729095004	1552193	SRX20518062	SRS17828018	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.92704	0.92685	0.08579	0.0849	0.78597	0.79091	0.45975	0.46663	74	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular System
75632	75632	SRR24740793	SRX20518061	SRS17828017	SRP439616	PRJNA976345	An organ specific angiogenic control mechanism for endothelial tailoring	GSE233488	Transcriptome Analysis	To address the role of endothelial Wnt/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß catenin signaling: Morpholino mediated knock down of gpr124 reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/ß catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124 reck or wnt7aa. Prior to CNS vascular invasion 30 hpf PHBC endothelial cells expressing the Kaede fluorescent protein were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition each containing photoconverted PHBC endothelial cells of 80 embryos.	pubmed:38570687	Endothelial cells 30 hpf negative 1	GSM7429319	source name:Vascular endothelium\|tissue:Vascular endothelium\|cell line:Endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:Non photoconverted\|geo loc name:missing\|collection date:missing	Endothelial cells 30 hpf negative 1	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts	Vascular endothelium		RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		tissue:Vascular endothelium\|cell line:Endothelial cells\|Stage:30 hpf\|cell type:Endothelial cells\|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8\|genotype:WT\|treatment:Non photoconverted	GSM7429319	GSM7429319: Endothelial cells 30 hpf negative 1; Danio rerio; RNA Seq	GSM7429319 r1	GSM7429319	1	RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP439616	loader:fastq load.py	A1_Neg_controls_R1.fastq.gz A1_Neg_controls_R2.fastq.gz	fastq fastq	3578902225.0	24014303.0	GSM7429319 r1		A:937280207;C:855762487;G:851738460;T:932155139;N:1965932			937280207	855762487	851738460	932155139	1965932	SRX20518061	SRS17828017	SRA1644604	MPI for heart and lung research	MPI for heart and lung research	2	0.95371	0.95422	0.08678	0.08593	0.7709	0.77364	0.46937	0.46998	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	Germany	2023-05-25	Pharyngula	Embryo	Endothelium	Cardiovascular 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");;