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run_metadata: 29167

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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
29167 SRR27180615 SRX22861015 SRS19836055 SRP477408 PRJNA1051145 laser captured chondrocyte transcriptomes from cranial base GSE249932 Transcriptome Analysis similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes   pubmed:38117077   Z1 WT GSM7967331   source name:laser captured cartilage without xxx from cranial base in occipital region|tissue:cartilage|age:6dpf|genotype:wild type|geo loc name:missing|collection date:missing Z1 WT The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples laser captured cartilage without xxx from cranial base in occipital region N/A RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc.. standard conditions EM filled dishes at 28.5C tissue:cartilage|age:6dpf|genotype:wild type GSM7967331 GSM7967331: Z1 WT; Danio rerio; RNA Seq GSM7967331 r1 GSM7967331 1 RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP477408     Z1_R1.fastq.gz Z1_R2.fastq.gz fastq fastq 9727948522.0 48158161.0 GSM7967331 r1 0:101 1:101 A:2710612972;C:2124743635;G:2101950141;T:2787702029;N:2939745 101 101     2710612972 2124743635 2101950141 2787702029 2939745 SRX22861015 SRS19836055 SRA1767043 3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan 3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan 2 0.92553 0.92633 0.25474 0.25434 0.83362 0.83615 0.76464 0.75351 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Canada 2023-12-11 Larval Larval Bone or Cartilage Skeletal Element