run_metadata: 54721

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
54721	SRR10136109	SRX6864201	SRS5401828	SRP222275	PRJNA566103	Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis	GSE137629	Other	We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group from uninjected fish 70fish/group and from cells in culture in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells		pubmed:31740783		27: Metastases3	GSM4083494		source name:PC 3M Pro4 injected fish\|tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	27: Metastases3	All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name ID reads and normalized comparision between each groups	PC 3M Pro4 injected fish		Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.	PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation 120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.	tissue:Metastases at zebrafish caudal hematopoietic tissue\|FISH strain:TGFli1a:EGFP\|age:8 dpf	GSM4083494	GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq	GSM4083494		1	Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at 80 ˚C. The whole process was finished within 30 min. 1000000 Cells in culture were lysized with TRIzol and stored at 80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina San Diego CA USA.	GEO Accession:GSM4083494	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP222275			ZFG-16-03_27_19265_CAGATC_L001_R1_001.fastq.gz	fastq	331816863.0	6506213.0	GSM4083494 r1	0:51	A:82933253;C:78905859;G:76570035;T:93218124;N:189592	51				82933253	78905859	76570035	93218124	189592	SRX6864201	SRS5401828	SRA963954	GEO	Institute of Biology, Leiden University	1	0.81726		0.07727		0.71928		0.47447		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		Netherlands	2019-09-18	Larval	Larval	Blood	Hematopoietic System