{"database": "metadata", "table": "run_metadata", "rows": [[54717, "SRR10136113", "SRX6864203", "SRS5401830", "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", null, "pubmed:31740783", null, "23: PBS injected fish2", "GSM4083496", null, "source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf", "23: PBS injected fish2", "All RNAseq libraries 150\u2013750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 \u00d7 50 nucleotides single end reads according to the manufacturer\u2019s 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", "PBS injected fish", null, "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 \u02daC. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 \u02daC. 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\u2019s 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 \u02daC incubator for 6 days.", "tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf", "GSM4083496", "GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq", "GSM4083496", null, "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 \u02daC. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 \u02daC. 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:GSM4083496", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222275", null, null, "ZFG-16-03_23_18844_CGATGT_L001_R1_001.fastq.gz", "fastq", 178603683.0, 3502033.0, "GSM4083496 r1", "0:51", "A:43615081;C:43303795;G:41835813;T:49795688;N:53306", 51, null, null, null, 43615081, 43303795, 41835813, 49795688, 53306, "SRX6864203", "SRS5401830", "SRA963954", "GEO", "Institute of Biology, Leiden University", 1, 0.9227, null, 0.06923, null, 0.72547, null, 0.45761, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Netherlands", "2019-09-18", "Larval", "Larval", "Blood", "Hematopoietic System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["54717"], "units": {}, "query_ms": 11.567549001483712}