run_metadata: 69931

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
69931	SRR22318719	SRX18291978	SRS15783400	SRP374955	PRJNA837586	Labelling transcriptional response to dissociation using SLAMseq	GSE202880	Other	Transcriptional response to dissociation is known to cause artefacts in single cell data sets. We used 4sU to label newly made transcripts during dissociation in order to to later remove them from the data set Overall design: 10mM 4sU was added to the dissociation buffer while the samples were enzymatically dissociated for 30 min. A 4sU injected control was added to the zebrafish samples to identify high turnover genes	parent bioproject:PRJNA837863	pubmed:36573354		larvae cold dissociated rep 2	GSM6735817		tissue:whole larvae 48hpf\|cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	larvae cold dissociated rep 2	Demultiplexing bcl2fastq v2.19 CELseq barcodes demultiplexed using custom code https://github.com/anikaneuschulz/CELseq3 demultiplex mapping using STAR v2.7.3a aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code https://github.com/anikaneuschulz/MTglob pipeline genome build/assembly: dr11.95 processed data files format and content: Tab delimited mutation rates per gene	whole larvae 48hpf		10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		cell type:whole larvae 48hpf\|genotype:WT\|treatment:30 min 4sU during dissociation\|time:48hpf	GSM6735817	GSM6735817: larvae cold dissociated rep 2; Danio rerio; RNA Seq	GSM6735817 r1	GSM6735817	1	10 anesthetized larvae were washed twice in ice cold HBSS Life Technologies GmbH #14175095 and resuspended in 200µl psychrophilic protease mix 1x Native Bacillus licheniformis Protease Creative Enzymes #NATE 0633 in HBSS 10 mM 4sU and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip 25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA Sigma Aldrich; #A4503 before spinning down and resuspending the cells in TRIzol RNA was extracted using TRIzol Chloroform Isopropanol according to the manufacturer's instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 https://doi.org/10.1038/nmeth.4435. libraries for RNA seq were prepared following a CELseq protocol as published in Holler & Junker 2019 https://doi.org/10.1007/978 1 4939 9009 2 9. Sequencing adapters were switched – Insert is in read 1!		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP374955		assembly:dr11.95	l_cold_dissociated_2_R1.fastq.gz l_cold_dissociated_2_R2.fastq.gz	fastq fastq	2041072800.0	13607152.0	GSM6735817 r1	0:120 1:30	A:601835074;C:343437646;G:389096220;T:706671485;N:32375	120	30			601835074	343437646	389096220	706671485	32375	SRX18291978	SRS15783400	SRA1542250	Junker, Max-Delbrück-Center for Molecular Medicine	Junker, Max-Delbrück-Center for Molecular Medicine	2	0.77047	0.00385	0.20012	0.00362	0.83165	0.99985	0.52587	0.275	120	30	B	T	mate2 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq		Germany	2022-11-17	Multi-stage	Multi-stage	Whole Organism	All anatomical structures