run_metadata: 32137

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
32137	SRR29020078	SRX24545643	SRS21290020	SRP507567	PRJNA1111448	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267406	Transcriptome Analysis	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: We performed single cell RNA seq scRNA seq for shield stage embryos to compare gene expression between Mrbm24a and sibling embryos. Another purpose of this omic analysis is to examine possible cell populations that can be affected by the loss of maternal Rbm24a.				Zebrafish scRNAseq shield Mrbm24a 1	GSM8265293		source name:whole embryo\|tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:Mrbm24a\|geo loc name:missing\|collection date:missing	Zebrafish scRNAseq shield Mrbm24a 1	To remove any remaining biochemical reagents and primers from the post GEM reaction mixture silane magnetic beads were employed. The full length barcoded cDNAs were subsequently amplified by PCR to generate sufficient mass for library construction. During GEM incubation the molecules had R1 Read 1 primer sequence added to them. P5 P7 a sample index and R2 Read 2 primer sequence were added during library construction through processes such as End Repair A tailing Adaptor Ligation and PCR. The final libraries contained the P5 and P7 primers required for Illumina bridge amplification. The Single Cell three prime Protocol generated Illumina ready sequencing libraries. Each Single Cell three prime Library consisted of standard Illumina paired end constructs that began and ended with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI were encoded in Read 1 while Read 2 was utilized to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read. Read 1 and Read 2 corresponded to the standard Illumina® sequencing primer sites used in paired end sequencing. Assembly: GRCz10 Supplementary files format and content: Tab separated values files and matrix files	whole embryo		For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|cell line:shield stage\|cell type:embryonic cell\|genotype:Mrbm24a	GSM8265293	GSM8265293: Zebrafish scRNAseq shield Mrbm24a 1; Danio rerio; RNA Seq	GSM8265293 r1	GSM8265293	1	For the preparation of single cell suspensions a total of thirty three mutant embryos of Mrbm24a or wild type embryos at the shield stage were collected. These cellular suspensions were then loaded onto a 10X Genomics GemCode Single cell instrument which generates single cell Gel Bead In EMulsion GEMs. Libraries were generated and sequenced from the cDNAs using Chromium Next GEM Single Cell three prime Reagent Kits v3.1. Upon dissolution of the Gel Bead within a GEM primers containing an Illumina® R1 sequence Read 1 sequencing primer a 16 nt 10x Barcode a 10 nt Unique Molecular Identifier UMI and a poly dT primer sequence were released. These primers were mixed with the cell lysate and Master Mix. Full length barcoded cDNAs were then reverse transcribed from poly adenylated mRNA		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP507567			J23090495_R1_001.fastq.gz J23090495_R2_001.fastq.gz	fastq fastq	98193373500.0	327311245.0	GSM8265293 r1	0:150 1:150	A:27502195548;C:18458481431;G:18979601074;T:33252654514;N:440933	150	150			27502195548	18458481431	18979601074	33252654514	440933	SRX24545643	SRS21290020	SRA1866413	shao ming lab, school of life sciences, shandong university	shao ming lab, school of life sciences, shandong university	2	0.00149	0.9183	0.00037	0.14737	0.99947	0.79125	0.51851	0.50318	150	150	T	B	mate1 technical by mapping diff	illumina	nextseq	3prime	random_priming	unknown	sc	single_cell_droplet	10x		China	2024-05-14	Gastrula	Embryo	Whole Organism	All anatomical structures