run_metadata: 44123

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
44123	SRR6250327	SRX3357250	SRS2656332	SRP123526	PRJNA416939	Single cell RNAseq SMART seq2 of wild type TLAB and MZoep tz57 zebrafish embryos at 50% epiboly stage	GSE106466	Transcriptome Analysis	SMART seq2 was performed on single cells isolated from visually staged zebrafish embryos. Overall design: Samples were all sequenced in one batch. Some were generated with a five prime' UMI tagged method and others are full length SMART seq2.	parent bioproject:PRJNA417291	pubmed:29700225		wt p2 S11	GSM2838413		tissue:Embryonic cell\|developmental stage:50% epiboly\|library preparation batch:p2\|genotype:Wild type TLAB	wt p2 S11	Bases 1 8 the UMI and template switch were trimmed from the remaining reads trimmed stretches of polyA or polyT longer than 6bp and removed any reads that were shorter than 15 bp post trimming. We identified and depleted mtRNA and rRNA reads from the remaining reads by using Bowtie2 to align all reads against a transcriptome of mtRNA and rRNA using the parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed no unal. Remaining reads were then aligned to a modified version of the Ensembl Zv10 release 81 zebrafish transcriptome using Bowtie2 with parameters q phred33 N 1 I 1 X 2000 k 200 score min L 3.36 0.617 no discordant no mixed. The transcriptome start site of each gene was padded by 100bp to increase alignment rates since reads were generated from the 5’ end of the transcript and not all transcripts had correct annotations for their 5’ end. Additionally pseudogenes were removed from the transcriptome as they sometimes interfered with real genes given our 5’ coordinate selection described below. We chose the best alignment per read as the read with the most 5’ alignment coordinate to a transcript among those that aligned to the correct strand and had an alignment score of no more than 4 below the best alignment score overall. We then iteratively collapsed pairs of UMIs if the sum of the minimum Phred quality scores across non matching bases was at most 30 to account for mis matched bases that were likely due to sequencing errors. A collapsed pair was represented for future comparisons by the UMI with a larger prior number of aligned reads unless the other UMI had at least 75% as many reads aligned and had equal or better UMI quality scores for those alignments evaluated as the softmin over aligned reads of the softmax over quality scores for the UMI bases in an aligned read. post collapsing the number of transcripts observed per gene was calculated. This value was then adjusted based on the probability of a collision the drawing at random of the same UMI multiple times which was calculated from the number of UMIs not detected for a given gene. The full length fragmented reads without xxx’ enrichment or UMI were aligned using RSEM against a reference transcriptome which is depleted of mtRNA rRNA and pseudogenes as described above. The command ‘rsem calculate expression’ was used with parameters p 4 paired end seed length 24 for performing the alignment. The resulting gene levels in FPKM was used to build the expression matrix. Genome build: GRCz10 dr81 Supplementary files format and content: Tab delimited text files include gene levels UMI counts or FKPM for each sample.	Embryonic cell		50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for 5’ enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.	Fish of each genotype were incrossed and embryos were collected. Embryos were dechorionated and allowed to grow at 28°C in standard fish water containing methylene blue till 50% epiboly stage.	developmental stage:50% epiboly\|library preparation batch:p2\|genotype:Wild type TLAB	GSM2838413	GSM2838413: wt p2 S11; Danio rerio; RNA Seq	GSM2838413		1	50% epiboly embryos were manually deyolked and mechanically dissociated. Single cells were manually picked under a dissecting microscope and flash frozen on dry ice in 4uL lysis buffer. Libraries were prepared using a SMART seq2 protocol Picelli et al. 2014 with custom TSO oligos and indexing adapters Satija et al. 2015. Reaction volumn for tagmentation steps were reduced to 15% of the volumn indicated in the protocol. 88 MZoep libraries were built with customized indices for five prime enriched transcripts with unique molecular identifiers UMIs. The remaining libraries were built without xxx and contained fragments along full length transcripts.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP123526			wt_p2_S11.R1.fastq.gz wt_p2_S11.R2.fastq.gz	fastq fastq	40102944.0	716124.0	GSM2838413 r1	0:24 1:32	A:10511641;C:9360932;G:9463806;T:10731533;N:35032	24	32			10511641	9360932	9463806	10731533	35032	SRX3357250	SRS2656332	SRA627905	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	2	0.78698	0.83686	0.21254	0.22573	0.85985	0.86011	0.67858	0.67878	24	32	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_plate	smartseq		United States	2017-11-02	Gastrula	Embryo	Embryo Imprecise	All anatomical structures