run_metadata: 69934
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 69934 | SRR19178790 | SRX15244118 | SRS12977046 | 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 injected | GSM6135029 | tissue:whole larvae 48hpf|cell type:whole larvae 48hpf|genotype:WT|treatment:30 min 4sU injected|age:48hpf | larvae injected | 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 larvae injected with 5nl 4sU 100mM in 10 mM Tris•HCl pH 7.4 Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136 were incubated at 28°C for 30 minutes anesthesized on ice and homogenized 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 injected|age:48hpf | GSM6135029 | GSM6135029: larvae injected; Danio rerio; RNA Seq | GSM6135029 r1 | GSM6135029 | 1 | 10 larvae injected with 5nl 4sU 100mM in 10 mM Tris•HCl pH 7.4 Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136 were incubated at 28°C for 30 minutes anesthesized on ice and homogenized 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 | l_injected_R1.fastq.gz l_injected_R2.fastq.gz | fastq fastq | 1235050200.0 | 8233668.0 | GSM6135029 r1 | 0:120 1:30 | A:378943760;C:185923499;G:307183410;T:362956267;N:43264 | 120 | 30 | 378943760 | 185923499 | 307183410 | 362956267 | 43264 | SRX15244118 | SRS12977046 | SRA1419460 | Junker, Max-Delbrück-Center for Molecular Medicine | Junker, Max-Delbrück-Center for Molecular Medicine | 2 | 0.65413 | 0.25162 | 0.12157 | 0.25153 | 0.8757 | 0.99969 | 0.58973 | 0.66666 | 120 | 30 | B | T | mate2 technical by mapping diff | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | celseq | Germany | 2022-05-12 | Hatching | Embryo | Whole Organism | All anatomical structures |