run_metadata: 76947

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
76947	SRR25386920	SRX21125092	SRS18391090	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR7b 4dpf osteoblasts P1 rep 5	GSM7656641		tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR7b 4dpf osteoblasts P1 rep 5	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression not to autofluorescence. De yolk buffer 4ml: 44µl NaCl 5M 14.4µl KCl 0.5M 5µl NaHCO3 1M Bidistillated water to make it up to 4ml. Dissection buffer 4ml: 1x HBSS buffer without xxx+2 and Mg+2 ions and phenol red free 10mM HEPES 0.5% 2mM EDTA 1% BSA Filter using 0 22µm filter and store at 4ºC. Digestion buffer 2ml: 1 8 ml filtered Dissection buffer 200µl TrypLeTM Select 10x Thermo Fisher Scientific Merelbeke Belgium 10µl Proteinase K 20µg/µl Thermo Fisher Scientific Merelbeke Belgium 10µl Collagenase 2 20mg/ml Thermo Fisher Scientific Merelbeke Belgium	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656641	GSM7656641: RR7b 4dpf osteoblasts P1 rep 5; Danio rerio; RNA Seq	GSM7656641 r1	GSM7656641	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794		loader:fastq load.py	RR7b-P1_NGS20-O038_HGLCNBGXG_S7_L001_R1_001.fastq.gz	fastq	351643397.0	4968808.0	GSM7656641 r1	0:70.77	A:105100153;C:66835699;G:69586761;T:108735482;N:1385302	70				105100153	66835699	69586761	108735482	1385302	SRX21125092	SRS18391090	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86068		0.33407		0.74511		0.6177		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown		Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element