run_metadata: 67550
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 67550 | SRR17201124 | SRX13381108 | SRS11285137 | SRP350317 | PRJNA788011 | pharyngeal arch region in zebrafish embryos at 48 hpf | PRJNA788011 | Other | pharyngeal arch regions in wild type sibling and mutant zebrafish embryos at 48 hpf | homo 48h2 | strain:Tubingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf stage:not applicable|sex:not determined|tissue:pharyngeal arch|genotype:homozygotic mutant 2|BioSampleModel:Model organism or animal | RNA seq of Danio rerio: 48hpf homozygotic mutant pharyngeal arch 2 | homo 48h2 | homo 48h2 | Poly A RNA is purified from 1g total RNA using Dynabeads Oligo dT25 61005 Thermo Fisher CA USA using two rounds of purification. Then the polyA RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module NEB cat.e6150 USA under 94 5 7min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript II Reverse Transcriptase Invitrogen cat. 1896649 USA which were next used to synthesise U labeled second stranded DNAs with E. coli DNA polymerase I NEB cat.m0209 USA RNase H NEB cat.m0297 USA and dUTP Solution Thermo Fisher cat.R0133 USA. An A base is then added to the blunt ends of each strand preparing them for ligation to the indexed adapters. Each adapter contains a T base overhang for ligating the adapter to the A tailed fragmented DNA. Single or dual index adapters are ligated to the fragments and size selection was performed with AMPureXP beads. post the heat labile UDG enzyme NEB cat.m0280 USA treatment of the U labeled second stranded DNAs the ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8 cycles of denaturation at 98 for 15 sec annealing at 60 for 15 sec and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 30050 bp. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP350317 | homo_48h2_Clean_Data1.fq.gz homo_48h2_Clean_Data2.fq.gz | fastq fastq | 5736708800.0 | 20741445.0 | homo 48h2 Clean Data1.fq.gz | 0:138.30 1:138.28 | A:1509851615;C:1356120916;G:1368270971;T:1502443004;N:22294 | 138 | 138 | 1509851615 | 1356120916 | 1368270971 | 1502443004 | 22294 | SRX13381108 | SRS11285137 | SRA1341839 | Ocean University of China|School of Medicine and Pharmacy | Ocean University of China | 2 | 0.95037 | 0.95325 | 0.06985 | 0.06953 | 0.68763 | 0.68678 | 0.47361 | 0.46423 | 141 | 141 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-12-11 | Hatching | Embryo | Pharyngeal Arch | Multi-system |