run_metadata: 49327
This data as json
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| 49327 | SRR7886608 | SRX4724260 | SRS3809034 | SRP162288 | PRJNA492363 | Genetic control of cellular morphogenesis in Müller glia | GSE120275 | Transcriptome Analysis | How the various cell types of the body achieve their specific shapes is fundamentally unknown. Here we explore this issue by identifying genes involved in the elaboration of the complex yet conserved cellular morphology of Müller glial MG cells in the retina. Using genomic based strategies in zebrafish we found more than 40 candidate genes involved in specific aspects of MG morphogenesis. The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided. GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage | pubmed:30924555 | 48MGS2 | GSM3397442 | source name:48hpf GFAP:GFP Positive|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive | 48MGS2 | Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts Rsubread limma DESeq2 DEFormats org.Dr.eg.db EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis | 48hpf GFAP:GFP Positive | Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer’s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions | age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive | GSM3397442 | GSM3397442: 48MGS2; Danio rerio; RNA Seq | GSM3397442 | 1 | Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions | GEO Accession:GSM3397442 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP162288 | dangling references:treat as unmapped | 48MGS2.bam | bam | 3253082750.0 | 26024662.0 | GSM3397442 r1 | 0:125 | A:860727696;C:787565434;G:719641544;T:885087745;N:60331 | 125 | 860727696 | 787565434 | 719641544 | 885087745 | 60331 | SRX4724260 | SRS3809034 | SRA780762 | GEO | University of Cambridge | 1 | 0.70949 | 0.06764 | 0.79251 | 0.56599 | 125 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | nextera | bulk | unknown | unknown | United Kingdom | 2018-09-20 | Hatching | Embryo | Eye | Sensory System |