run_metadata: 41008

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
41008	SRR3996112	SRX1997147	SRS1598490	SRP075286	PRJNA321866	Massively parallel whole organism lineage tracing using CRISPR/Cas9 induced genetic scars	GSE81533	Other	A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many cells. Although impressive progress has been made in lineage tracing using imaging approaches analysis of vertebrate lineage trees has mostly been limited to relatively small subsets of cells. Here we present scar trace a strategy for massively parallel whole organism lineage tracing based on Cas9 induced genetic scars in the zebrafish. Overall design: Sequencing of CRISPR/Cas9 induced genetic scars was done by targeted PCR A Cas9 based method for massive genomic marker based lineage tracing in zebrafish. Plase note that the 'Barcodes zf1fin3.xlsx' annotates GSM2258256 GSM2258282 data.				dynamics RNA	GSM2258257		tissue:Single embryos\|developmental stage:48h	dynamics RNA	Align to h2afv GFP using bwa mem We only consider reads for which the left mate is mapped in the forward and reverse direction for which the left mate contains a correct barcode a list of barcodes can be found in the file cel seq barcodes.csv and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate. To identify different scars we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment combined with the 3’ location of the right mate. Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library and those sequences that make up at least 5% of all reads in its CIGAR class. Genome build: Custom Supplementary files format and content: Abundance file of each scar in each barcode present in the library	Single embryos	Embryos were injected at the 1 cell stage with 1 nl mRNA final concentration 300 ng/μl in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT.	TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.		developmental stage:48h	GSM2258257	GSM2258257: dynamics RNA; Danio rerio; RNA Seq	GSM2258257		1	TRIzol extraction GFP sequences were amplified by PCR with primers complementary to GFP including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup AMPure XP beads – Beckman Coulter. Finally sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.	GEO Accession:GSM2258257	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP075286			Philipp-dynamics-RNA_HKLJYBGXX_S8_L003_R1_001.fastq.gz Philipp-dynamics-RNA_HKLJYBGXX_S8_L003_R2_001.fastq.gz	fastq fastq	73436227.0	483449.0	GSM2258257 r3	0:75.98 1:75.92	A:13427325;C:21824372;G:26876634;T:11306254;N:1642	75	75			13427325	21824372	26876634	11306254	1642	SRX1997147	SRS1598490	SRA426643	GEO	Max Delbrück Center	2	2e-05	1e-05	0.0	0.0	0.99997	1.0	0.0		76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	small_rna	trueseq	sc	single_cell_plate	celseq		Germany	2016-08-03	Hatching	Embryo	Embryo Imprecise	All anatomical structures