run_metadata: 47743
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 47743 | SRR6848346 | SRX3803616 | SRS3055249 | SRP135898 | PRJNA438687 | Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos | GSE111963 | Transcriptome Analysis | We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf | pubmed:30006544 | hhex mutant rep1 | GSM3045713 | tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells | hhex mutant rep1 | The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak | FACS sorted endothelial cells | For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. | genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells | GSM3045713 | GSM3045713: hhex mutant rep1; Danio rerio; RNA Seq | GSM3045713 | 1 | For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28°C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer® Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup. | GEO Accession:GSM3045713 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP135898 | Sebastien_Mut_1_R1.fastq.gz | fastq | 2492708175.0 | 34527636.0 | GSM3045713 r1 | 0:72.19 1:0 | A:555859455;C:702003394;G:740775583;T:493818885;N:250858 | 72 | 0 | 555859455 | 702003394 | 740775583 | 493818885 | 250858 | SRX3803616 | SRS3055249 | SRA667127 | GEO | MPI for heart and lung research | 1 | 0.93924 | 0.25343 | 0.81889 | 0.6311 | 75 | B | usable mapping rate | illumina | nextseq | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | Germany | 2018-03-16 | Hatching | Embryo | Endothelium | Cardiovascular System |