run_metadata: 55938
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| 55938 | SRR10767281 | SRX7441199 | SRS5885526 | SRP238807 | PRJNA597725 | A Zebrafish JAK1 A634D Gain of Function Model Provides New Insights into the Pathogenesis of Familial Hypereosinophilia | GSE142599 | Transcriptome Analysis | JAK1 plays an important role during zebrafish development as hematopoietic regulator with a specific impact in the myeloid lineage from where the eosinophils arise. Several genes in the JAK STAT pathway are elevated in the transgenic mutants STAT1B SOCS3A SOCS3B PIAS2 as well as patways involved in hematopoiesis immunity response to interferon and response to biotic stimuli. Overall design: Total RNA from casper JAK1 WT and JAK1 A634D zebrafish embryos at 28 hpf and 36 hpf was extracted to characterize the transcriptomic effects of the JAK1 A634D gain of function mutation | 28 hpf JAK1 A634D transgenic rep 1 | GSM4232665 | tissue:whole embryo|genotype:Tgubi:cDNA JAK1 A634D p2A sfGFP|developmental stage:28 hpf embryo | 28 hpf JAK1 A634D transgenic rep 1 | Read trimming: the raw reads had the adapters “ATCACCGAC” removed and filtered by the quality of 20 with the Trim Galore v0.4.4. Read mapping: The reads passed through the two step mapping for RNA Seq data from Ion proton: first with STAR v2.7 and then mapping the unmapped reads from the first alignment using bowtie2. The two mapped files were merged with Picard tools v2.5.0. Read counting: The counts were extracted using HTSeq V0.9.1. Genome build: danRer11 Supplementary files format and content: read counts | whole embryo | Each total RNA sample was extracted from 30 50 zebrafish embryos by homogenizing them in 500 µL Trizol reagent Thermo Fisher Scientific 15596026 using 1 mL syringe and 22G needle. Lysates were centrifuged at 12 000 g at 4ºC for 5 minutes and the supernatant was transferred to Phasemaker Tubes Thermo Fisher Scientific A33248 and RNA was purified according to the Phasemaker Tubes protocol manual. Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number ≥8 were selected for library preparation. Poly A enrichment was performed from 20 µg of total RNA to enrich for mRNA Dyna beads mRNA direct micro Kit. 100ng of poly A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module RNA Seq V2 kit Life Technologies. The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA enriched RNA was used to prepare whole transcriptome library RNA seq V2. Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. Barcoded library was equally pooled and amplified onto Ion Sphere™ Particles ISPs from Ion Pi HiQ OT2 kit Life Technologies. ISPs enriched with template library were loaded onto Ion PI chip V3 and sequenced on Ion Proton from Thermo Fisher. | Zebrafish experiments and husbandry follows standard protocols in accordance with the standards of the University Committee on Laboratory Animals UCLA of Dalhousie University. Zebrafish embryos were maintained at 28.5 °C during development and as adults. Embryos were grown in egg water 1x E3 prepared from 60x E3 stock. | genotype:Tgubi:cDNA JAK1 A634D p2A sfGFP|developmental stage:28 hpf embryo | GSM4232665 | GSM4232665: 28 hpf JAK1 A634D transgenic rep 1; Danio rerio; RNA Seq | GSM4232665 | 1 | Each total RNA sample was extracted from 30 50 zebrafish embryos by homogenizing them in 500 µL Trizol reagent Thermo Fisher Scientific 15596026 using 1 mL syringe and 22G needle. Lysates were centrifuged at 12 000 g at 4ºC for 5 minutes and the supernatant was transferred to Phasemaker Tubes Thermo Fisher Scientific A33248 and RNA was purified according to the Phasemaker Tubes protocol manual. Total RNA samples were measured and analyzed for integrity on Agilent Tape Station. Samples with RNA integration number ≥8 were selected for library preparation. Poly A enrichment was performed from 20 µg of total RNA to enrich for mRNA Dyna beads mRNA direct micro Kit. 100ng of poly A enriched RNA was fragmented using RNase III and purified using magnetic bead clean up module RNA Seq V2 kit Life Technologies. The size distribution of the fragmented RNA was assessed on Agilent Tape Station using RNA HS screen tape assay and 50 ng of fragmented polyA enriched RNA was used to prepare whole transcriptome library RNA seq V2. Yield and size distribution of the library was analyzed on Agilent Tape Station using D1000 screen tape. Barcoded library was equally pooled and amplified onto Ion Sphere™ Particles ISPs from Ion Pi HiQ OT2 kit Life Technologies. ISPs enriched with template library were loaded onto Ion PI chip V3 and sequenced on Ion Proton from Thermo Fisher. | GEO Accession:GSM4232665 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ION_TORRENT | Ion Torrent Proton | SRP238807 | 28h_JAK1_A634D_1.fastq.gz | fastq | 2435214022.0 | 32006444.0 | GSM4232665 r1 | 0:76.09 | A:671766129;C:571275330;G:623388119;T:568784444;N:0 | 76 | 671766129 | 571275330 | 623388119 | 568784444 | 0 | SRX7441199 | SRS5885526 | SRA1016603 | GEO | Berman Lab, CHEO Research Institute/University of Ottawa | 1 | 0.70175 | 0.0702 | 0.74925 | 0.48275 | 136 | B | usable mapping rate | ion_torrent | ion_torrent | full_length | poly_a | unknown | bulk | unknown | unknown | Canada | 2019-12-26 | Pharyngula | Embryo | Whole Organism | All anatomical structures |