run_metadata: 62848

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
62848	SRR13402902	SRX9821929	SRS8004722	SRP301260	PRJNA691237	Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways	GSE164574	Other	The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage		pubmed:34737283		Zsphere scRNA	GSM5014336		tissue:Zebrafish embryos\|Stage:sphere	Zsphere scRNA	We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data	Zebrafish embryos		At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media	Stage:sphere	GSM5014336	GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq	GSM5014336		1	At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	GEO Accession:GSM5014336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP301260		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L001 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L001 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L001 R2 001.fastq.gz	GUG739A4_S2_L001_I1_001.fastq.gz GUG739A4_S2_L001_R1_001.fastq.gz GUG739A4_S2_L001_R2_001.fastq.gz	fastq fastq fastq	5235400170.0	24930477.0	GSM5014336 r1	0:8 1:101 2:101	A:1177347684;C:925887308;G:939712357;T:2191666659;N:786162	8	101	101		1177347684	925887308	939712357	2191666659	786162	SRX9821929	SRS8004722	SRA1182478	GEO	Bioinformatics, Bioinformatics, The Francis Crick Institute	1	0.91081		0.11647		0.78459		0.5629		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United Kingdom	2021-01-11	Blastula	Embryo	Embryo Imprecise	All anatomical structures