run_metadata: 53506

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
53506	SRR9879913	SRX6632434	SRS5202041	SRP217196	PRJNA558085	Zebrafish Danio rerio neural crest cell RNA sequencing	GSE135237	Transcriptome Analysis	RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.		pubmed:31495570		36hpfNCC rep1	GSM3996849		source name:Neural crest cells from larval trunk\|tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	36hpfNCC rep1	For data quality control FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20 the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations	Neural crest cells from larval trunk	36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C 1ml 1x Trypsin with 5% EDTA solution was added and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages	tissue:Neural crest cells from larval trunk\|transgene:Gtfoxd3:mCherry\|transgene:Tgsox10:mEGFP\|Stage:36 hpf	GSM3996849	GSM3996849: 36hpfNCC rep1; Danio rerio; RNA Seq	GSM3996849		1	Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing	GEO Accession:GSM3996849	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP217196			Sample1_S1_R1_001.fastq.gz Sample1_S1_R2_001.fastq.gz	fastq fastq	5567367667.0	18627261.0	GSM3996849 r1	0:149.46 1:149.42	A:1451891750;C:1299527629;G:1299734297;T:1515800229;N:413762	149	149			1451891750	1299527629	1299734297	1515800229	413762	SRX6632434	SRS5202041	SRA930488	GEO	Kucenas Lab, Biology, University of Virginia	2	0.70717	0.70612	0.10919	0.10754	0.83366	0.83875	0.55253	0.55519	149	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		United States	2019-08-01	Pharyngula	Embryo	Multi-tissue	Multi-system