run_metadata: 31585

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
31585	SRR28471049	SRX24073984	SRS20864374	SRP498123	PRJNA1092581	Construction of Danio rerio Asymmetrical Maps DreAM	GSE262578	Transcriptome Analysis	Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references we implemented Palette to infer spatial gene expression from bulk RNA seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps DreAM. Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior AP axis and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally we difined a hox score and comprehensively demonstrated the spatial collinearity of Hox genes at single cell resolution during development. Overall design: Bulk RNA seq was performed on the serial cryosections taken along the left right axis of zebrafish embryos at 10 hpf 12 hpf and 16 hpf.				S10 slice 25	GSM8171961		source name:embryonic cells\|tissue:embryonic cells\|strain:AB\|age:10 hpf\|geo loc name:missing\|collection date:missing	S10 slice 25	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: rds files include count matrixes and slice position information post running the processing steps.	embryonic cells	Embedded embryos were cryosectioned at a thickness of 20 µm. Each slice was collected and placed on the PEN membrane slides. Then each slice was extracted from membrane slides through laser capture microdissection system and collected into a 1.5 mL Eppendorf tube.	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.	Zebrafish embryos were raised in 0.3x Danieau buffer and were then embedded in OCT at the required developmental stages of 10 hpf 12hpf and 16 hpf.	tissue:embryonic cells\|strain:AB\|age:10 hpf	GSM8171961	GSM8171961: S10 slice 25; Danio rerio; RNA Seq	GSM8171961 r1	GSM8171961	1	RNA was extracted using PicoPure™ RNA Isolation Kit following the standard protocol. Libraries were constructed using the Illumina's TruSeq™ Stranded mRNA LT Sample Prep Kit following the standard protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP498123		loader:fastq load.py	S10_2_25-R1.fq.gz S10_2_25-R2.fq.gz	fastq fastq	6912437288.0	23704050.0	GSM8171961 r1	0:144.17 1:147.45	A:1886377008;C:1583136289;G:1524973541;T:1917942644;N:7806	144	147			1886377008	1583136289	1524973541	1917942644	7806	SRX24073984	SRS20864374	SRA1834502	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk		China	2024-03-27	Gastrula	Embryo	Embryo Imprecise	All anatomical structures