run_metadata: 43460
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 43460 | SRR5952025 | SRX3110519 | SRS2445612 | SRP115900 | PRJNA399133 | RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN | GSE102861 | Transcriptome Analysis | We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN. We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates. | pubmed:29765956 | IP HCtranslatome RNAseq rep1 | GSM2747292 | source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA | IP HCtranslatome RNAseq rep1 | Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample | Tgmyo6b:GFP 2A rpl10a 3xHA | Untreated | RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols | embryos were grown at 28 degrees C in E3 media until 5dpf | developmental stage:5dpf|tissue:hair cells enriched|antibody:HA | GSM2747292 | GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq | GSM2747292 | 1 | RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2747292 | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP115900 | RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz | fastq fastq | 5261113350.0 | 35074089.0 | GSM2747292 r1 | 0:75 1:75 | A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927 | 75 | 75 | 1356848229 | 1276483567 | 1260001700 | 1366757927 | 1021927 | SRX3110519 | SRS2445612 | SRA601675 | GEO | Department: Institute for Genome Sciences, University of Maryland in Baltimore | 2 | 0.66363 | 0.6599 | 0.15644 | 0.15316 | 0.76808 | 0.7725 | 0.48538 | 0.48933 | 75 | 75 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | trueseq | bulk | unknown | unknown | United States | 2017-08-21 | Larval | Larval | Embryo Imprecise | All anatomical structures |