run_metadata: 39773
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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 |
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| 39773 | SRR2136295 | SRX1125766 | SRS1017741 | SRP061855 | PRJNA291531 | Identification of qkia/c target genes | GSE71573 | Transcriptome Analysis | Quaking are RNA binding proteins which are known to regulate the expression of different genes at the post transcriptional level. Genetic interference with quaking a qkia and quaking c qkic leads to major myofibril defects during zebrafish development without xxx early muscle differentiation. In order to understand how qkia and qkic jointly regulate myofibril formation we performed a comparative analysis of the transcriptome of qkia/qkic qkia mutant injected with qkic morpholino versus control embryos. We show that Quaking activity is required for accumulation of the muscle specific tropomyosin 3 transcript tpm3.1. Whereas interference with tmp3.1 function disrupts myofibril formation reintroducing tpm3.1 transcripts into embryos with reduced Quaking activity can restore structured myofibrils. Thus we identify tropomyosin as an essential component in the process of myofibril formation and as a relay downstream of the regulator proteins Quaking. Overall design: Transcriptome of control versus qkia/qkic embryos at 24 26hpf. Biological triplicate were prepared for both condition 3x2 samples. | pubmed:28867488 | Qkiac 1 | GSM1838796 | tissue:trunk|Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino | Qkiac 1 | Before mapping poly N read tails were trimmed reads ≤40 bases were removed and reads with quality mean ≤30 were discarded. To obtain the counts on the exon features reads were then aligned against the genome using Bowtie version 0.12.9 with arguments n 2 l 34 e 70 k 2 best. To obtain the counts on the gene features reads were then aligned against the genome using STAR version 2.4.0j and Ensembl annotation v78. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression Danio rerio Zv9 GFF3 genome annotation version 78 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq count 0.5.3. To obtain the counts on the exon features we used the bowtie alignments excluding the junction reads. HTSeq count was used with arguments: genomictype=exon attributeid=Name stranded=no overlapmode=union removeambiguouscases=false. To obtain the counts on the gene features we used the STAR alignments including the junction reads. HTSeq count was used with arguments: genomictype=exon stranded=no overlapmode=union removeambiguouscases=false and attributeid=Alias where Alias was the corresponding parent gene ID. The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric Genome build: Danio rerio Zv9 Supplementary files format and content: tab delimited text files include normalized reads counts for each Sample using DESeq 1.8.3 with arguments: disp.est.method=pooled disp.est.sharing.mode=maximum disp.est.fit.type=parametric. | trunk | Zebrafish trunks at 24 26hpf were dissected removal of head and yolk flash frozen on dry ice and stored at 80°C until RNA extraction. | total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples. | Embryos resulting from crossing between qkia+/ fish were injected at a cell stage with qkic morpholino or control morpholino 0 6pmol. We let them develop until 24 26hpf stage where we could morphologically identify control embryos sibling qkia+/+ or qkia+/ with control morpholino and double qkia/c loss of function embryos qkia / with qkic morpholino. | Stage:embryo 24 26hpf|genotype:qkia / |injection:qkic morpholino | GSM1838796 | GSM1838796: Qkiac 1; Danio rerio; RNA Seq | GSM1838796 | 1 | total RNA was extracted using the RNeasy Plus Universal Mini kit Qiagen and treated with Dnase. Messenger polyA+ RNAs were purified from 0.7 µg of total RNA using oligodT. Libraries were prepared using the strand non specific RNA Seq library preparation TruSeq RNA Sample Prep v2 kit Illumina. Libraries were multiplexed by 6 on 2 flowcell lanes. A 50 bp read sequencing was performed on a HiSeq 1500 device Illumina. A mean of 27459238 ± 1611623 million passing Illumina quality filter reads was obtained for each of the 6 samples. | GEO Accession:GSM1838796 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 1500 | SRP061855 | Sample4_GCCAAT.fastq.bz2 | fastq | 2881827420.0 | 56506420.0 | GSM1838796 r1 | 0:51 | A:782512581;C:658453854;G:659856487;T:778195522;N:2808976 | 51 | 782512581 | 658453854 | 659856487 | 778195522 | 2808976 | SRX1125766 | SRS1017741 | SRA281148 | GEO | Plateforme transcriptome, Biologie, Ecole Normale Supérieure | 1 | 0.92629 | 0.08316 | 0.7276 | 0.47801 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | trueseq | bulk | bulk | bulk | France | 2015-07-30 | Pharyngula | Embryo | Trunk | Surface Structure |