{"database": "metadata", "table": "run_metadata", "rows": [[59135, "SRR11684028", "SRX8244831", "SRS6592466", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo csf1rdm 2", "GSM4512720", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo csf1rdm 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512720", "GSM4512720: 5mo csf1rdm 2; Danio rerio; RNA Seq", "GSM4512720", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_csf1rdm_2_R2.fastq.gz 5mo_csf1rdm_2_R1.fastq.gz", "fastq fastq", 9868898870.0, 48855935.0, "GSM4512720 r1", "0:101 1:101", "A:2841225530;C:2066572676;G:2116298647;T:2844775713;N:26304", 101, 101, null, null, 2841225530, 2066572676, 2116298647, 2844775713, 26304, "SRX8244831", "SRS6592466", "SRA1072140", "GEO", "Erasmus MC", 2, 0.89516, 0.87542, 0.18501, 0.18252, 0.764, 0.77293, 0.47581, 0.47272, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"]], "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": ["59135"], "units": {}, "query_ms": 9.196184008033015}