run_metadata: 59120

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
59120	SRR11684010	SRX8244813	SRS6592450	SRP259988	PRJNA630160	Zebrafish embryonic mpeg+ macrophages	GSE149786	Transcriptome Analysis	We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates	parent bioproject:PRJNA630158	pubmed:32367800		csf1r doubleknockout2 28hpf	GSM4512702		tissue:whole embryos\|developmental stage:28 hpf\|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	csf1r doubleknockout2 28hpf	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 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 embryos		35 embryos 28 hpf wt 50 hpf wt 28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. 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	developmental stage:28 hpf\|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP\|cell type:mpeg GFP+ cells	GSM4512702	GSM4512702: csf1r doubleknockout2 28hpf; Danio rerio; RNA Seq	GSM4512702		1	35 embryos 28 hpf wt 50 hpf wt 28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. 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:GSM4512702	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP259988		intentional duplicate	csf1r_doubleknockout2_28hpf.bam	bam	2908203540.0	19226046.0	GSM4512702 r1	0:75.97 1:75.30	A:812002267;C:642558682;G:646762399;T:792733574;N:14146618	75	75			812002267	642558682	646762399	792733574	14146618	SRX8244813	SRS6592450	SRA1072139	GEO	Erasmus MC	2	0.92454	0.93402	0.10684	0.11073	0.78238	0.78224	0.44909	0.44853	76	76	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cdna_unspecified	trueseq	sc	single_cell_plate	smartseq		Netherlands	2020-05-04	Pharyngula	Embryo	Whole Organism	All anatomical structures