run_metadata: 41519
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 |
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| 41519 | SRR5004955 | SRX2336789 | SRS1790186 | SRP092907 | PRJNA352850 | Transcriptomics analysis of gene expressions m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos | GSE89655 | Other | RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels m6A enrichment levels m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells | pubmed:28869969 | mettl3 morphant zebrafish embryos input rep2 | GSM2386184 | source name:zebrafish embryos|genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk | mettl3 morphant zebrafish embryos input rep2 | Library strategy: MeRIP seq Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples | zebrafish embryos | For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. | genotype/variation:mettl3|cell type:embryos cells|age:28hpf|tissue:trunk | GSM2386184 | GSM2386184: mettl3 morphant zebrafish embryos input rep2; Danio rerio; RNA Seq | GSM2386184 | 1 | For MeRIP seq mRNA was isolated from the trunck region of zebrafish embryos at 28hpf. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. The RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina San Diego CA USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode creating reads with a length of 101 bp. | GEO Accession:GSM2386184 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 3000 | SRP092907 | mettl3-mo_input_rep2_1.fastq.gz mettl3-mo_input_rep2_2.fastq.gz | fastq fastq | 15677274742.0 | 77610271.0 | GSM2386184 r1 | 0:101 1:101 | A:4349575028;C:3553088246;G:3444690573;T:4326018819;N:3902076 | 101 | 101 | 4349575028 | 3553088246 | 3444690573 | 4326018819 | 3902076 | SRX2336789 | SRS1790186 | SRA491654 | GEO | Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS) | 2 | 0.9442 | 0.94896 | 0.12173 | 0.11299 | 0.70891 | 0.70094 | 0.52438 | 0.50498 | 101 | 101 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | China | 2016-11-08 | Pharyngula | Embryo | Trunk | Surface Structure |