run_metadata: 41011
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 |
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| 41011 | SRR3536536 | SRX1770315 | SRS1442798 | 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. | Protein injections | GSM2155530 | tissue:Single embryos|developmental stage:24h | Protein injections | For samples 1 32 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 Sample 33: WGS 1 We modified the genome sequence danRer10 by adding a sequence for the histone GFP fusion gene and removing chromosome five the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome. We use bwa mem to align the reads to this modified genome selected reads for which both mates align and remove duplicate reads. We bin these reads into bins of 1 000 bases Genome build: danRer10 modified as indicated above Supplementary files format and content: Abundance file of reads in each 1kb bin | Single embryos | Embryos were injected at the 1 cell stage with 1 nl Cas9 protein final concentration 1590 ng/ul in combination with an sgRNA targeting GFP final concentration 25 ng/μl sequence: GGTGTTCTGCTGGTAGTGGT. | RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. 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:24h | GSM2155530 | GSM2155530: Protein injections; Danio rerio; RNA Seq | GSM2155530 | 1 | RNA was extracted from homogenized zebrafish samples with TRIzol reagent Ambion. 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:GSM2155530 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP075286 | zfGFP4protein_AHG7CMBGXX_S11_L002_R1_001.fastq.gz zfGFP4protein_AHG7CMBGXX_S11_L002_R2_001.fastq.gz | fastq fastq | 114510782.0 | 753967.0 | GSM2155530 r2 | 0:75.98 1:75.90 | A:20684140;C:33805645;G:41313135;T:18471924;N:235938 | 75 | 75 | 20684140 | 33805645 | 41313135 | 18471924 | 235938 | SRX1770315 | SRS1442798 | SRA426643 | GEO | Max Delbrück Center | 2 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | small_rna | trueseq | sc | single_cell_plate | celseq | Germany | 2016-05-17 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |