run_metadata: 49739
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 49739 | SRR8009940 | SRX4840766 | SRS3905926 | SRP165180 | PRJNA495704 | Danio rerio strain:Tubingen Transcriptome or Gene expression | PRJNA495704 | Other | Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos. | Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos. | Danio rerio SMAR1 Morpholino mediated knockdown | SMAR1 Morpholino | strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal | RNA Seq of SMAR1 Morpholino injected Danio rerio Embryo | TB1 MO 2 | TB1 MO 2 | Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | NextSeq 500 | SRP165180 | 5229981040.0 | 34407770.0 | TB1 MO 2 R2.fastq.gz | 0:76 1:76 | A:1375946341;C:1255628851;G:1212656512;T:1382649755;N:3099581 | 76 | 76 | 1375946341 | 1255628851 | 1212656512 | 1382649755 | 3099581 | SRX4840766 | SRS3905926 | SRA792799 | Indian Institute of Chemical Biology|Chromatin and Disease Biology | Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad | 2 | 0.95547 | 0.95355 | 0.08995 | 0.08948 | 0.6799 | 0.68365 | 0.46004 | 0.46022 | 76 | 76 | B | B | biological fallback assumption | illumina | nextseq | unknown | random_priming | unknown | bulk | unknown | unknown | India | 2018-10-11 | Hatching | Embryo | Whole Organism | All anatomical structures |