run_metadata: 56673
This data as json
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| 56673 | SRR11035187 | SRX7687414 | SRS6113884 | SRP247522 | PRJNA605187 | miR 99 overexpression modulates neutrophil migration | GSE144873 | Transcriptome Analysis | We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils and RNAseq for identification of mRNA targets of miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA. | miR 99 1 | GSM4299821 | tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils | miR 99 1 | Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 " p Q 10". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts | miR 99 neutrophils | transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used. | tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc.. | zebrafish embryos were grow to 3 dpf in embryonic media | genotype/variation:overexpressing miR 99|cell type:neutrophils | GSM4299821 | GSM4299821: miR 99 1; Danio rerio; RNA Seq | GSM4299821 | 1 | tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc.. | GEO Accession:GSM4299821 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP247522 | 99-1_S19_L003_R1_001.fastq.gz 99-1_S19_L003_R2_001.fastq.gz | fastq fastq | 4160704056.0 | 27373053.0 | GSM4299821 r1 | 0:76 1:76 | A:1121170591;C:955488866;G:936977987;T:1146641997;N:424615 | 76 | 76 | 1121170591 | 955488866 | 936977987 | 1146641997 | 424615 | SRX7687414 | SRS6113884 | SRA1039054 | GEO | Department of Biological Sciences, Purdue University | 2 | 0.9007 | 0.89892 | 0.10574 | 0.10747 | 0.79312 | 0.79768 | 0.42626 | 0.42782 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | small_rna | unknown | sc | single_cell_plate | smartseq | United States | 2020-02-06 | Larval | Larval | Blood | Hematopoietic System |