{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\", technology = \"celseq\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[50874, "SRR8356798", "SRX5167561", "SRS4175446", "SRP173971", "PRJNA510841", "Transcription factor induction of vascular blood stem cell niches in vivo [TOMO Seq]", "GSE124150", "Other", "We report RNA tomography tomo seq gene expression data for the tail region of a 72 hpf zebrafish embryo. The portion of the tail containing the caudal hematopoietic tissue CHT was isolated by manual dissection  snap froze  and then cryosections 40 in total  8 \u00b5m thick were collected along the dorsal ventral axis. Each cryosection was placed into a tube and the RNA was exctracted and barcoded during a reverse trancription step prior to library synthesis and sequencing. Overall design: The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice. The RNA from individual cryosections was extracted using Trizol reagent and then barcoded during a reverse transcription step prior to library synthesis according to the previously published method Junker et al.  2014.", "parent bioproject:PRJNA510836", null, null, "Tomo seq zebrafish tail at 72 hpf", "GSM3521717", null, "source name:mpx:GFP transgenic zebrafish embryo wild type  Casper background|tissue:tail|developmental stage:72 hpf", "Tomo seq zebrafish tail at 72 hpf", "Library strategy: RNA tomography tomo seq Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the Junker  et al.  2014. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Mapping and demultiplexing were done as described in Gr\u00fcn et al.  Validation of noise models for single cell transcriptomics  Nature Methods  2014. The script needed to process the data is available in https://www.dropbox.com/sh/7s59vvocwtn2ct4/AAAR6pWte8xOzObCYONAFPvIa?dl=0   where script tomo.sh is an example for how to run the mapping scripts. Genome build: zv9", "mpx:GFP transgenic zebrafish embryo wild type  Casper background", "No treatment", "The total RNA from individual cryosections 40 in total  each 8 \u00b5m thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al.  2014.", "mpx:GFP transgenic zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then euthanized by tricaine overdose. The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice.", "tissue:tail|developmental stage:72 hpf", "GSM3521717", "GSM3521717: Tomo seq zebrafish tail at 72 hpf; Danio rerio; OTHER", "GSM3521717", null, "1", "The total RNA from individual cryosections 40 in total  each 8 \u00b5m thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al.  2014.", "GEO Accession:GSM3521717", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP173971", null, null, null, null, 3762222874.0, 24959737.0, "GSM3521717 r1", "0:75.36 1:75.37", "A:1160852277;C:485683733;G:556965887;T:1558649449;N:71528", 75, 75, null, null, 1160852277, 485683733, 556965887, 1558649449, 71528, "SRX5167561", "SRS4175446", "SRA825234", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.20644, 0.76788, 0.14917, 0.11551, 0.98169, 0.8382, 0.50072, 0.52728, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2018-12-19", "Larval", "Larval", "Tail", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 1, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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, 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=celseq&tissue_curation_coarse=Multi-system", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&technology=celseq&tissue_curation_coarse=Multi-system", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&technology=celseq&tissue_curation_coarse=Multi-system&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&technology=celseq&tissue_curation_coarse=Multi-system", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 1, 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