run_metadata: 59194
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 59194 | SRR11773511 | SRX8326550 | SRS6646238 | SRP261174 | PRJNA631796 | Analysis of gene network branching during optic cup morphogenesis in zebrafish RNA Seq | GSE150346 | Transcriptome Analysis | We characterize transcriptomic landscape using RNA seq in isolated NR and RPE populations in zebrafish. Overall design: RNA seq profile of sorted zebrafish cell populations of retinal progenitors NR at 18 hpf NR at 23 hpf RPE at 18 hpf and RPE at 23 hpf | pubmed:34162866 | PG 2 | GSM4547295 | tissue:sorted retinal progenitor cells|cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP | PG 2 | Each sample was mapped against the index genome built from danRer10 assembly using Tophat v2.1.0 The aligned read BAM files were assembled into transcripts and their abundance was estimated by Cufflinks v2.2.1 Genome build: danRer10 Supplementary files format and content: txt file including the FPKM values for all genes in each eye domain | sorted retinal progenitor cells | Zebrafish cells were dissociated and prepared for FACS as described in Manoli and Driever 2012 | Total RNA was extracted by TRIzol Invitrogen following manufacturer’s protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina | Zebrafish embryos were raised in E3 medium at 28 °C | cell type:sorted retinal progenitor cells|developmental stage:16 hpf|transgenic line:tgvsx2.2:GFP | GSM4547295 | GSM4547295: PG 2; Danio rerio; RNA Seq | GSM4547295 | 1 | Total RNA was extracted by TRIzol Invitrogen following manufacturer's protocol. Possible DNA contamination was eliminated treating the RNA samples with with TURBO DNAse free Ambion. Ribo Zero® rRNA Removal Kit Illumina | GEO Accession:GSM4547295 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP261174 | PG16_2_R1.fastq.gz | fastq | 9860997500.0 | 78887980.0 | GSM4547295 r1 | 0:125 1:0 | A:2453379488;C:2434250915;G:2295560807;T:2677739557;N:66733 | 125 | 0 | 2453379488 | 2434250915 | 2295560807 | 2677739557 | 66733 | SRX8326550 | SRS6646238 | SRA1074492 | GEO | CABD | 1 | 0.88896 | 0.198 | 0.71356 | 0.48154 | 125 | B | usable mapping rate | illumina | hiseq_era | unknown | rrna_depletion | ribozero | bulk | unknown | unknown | Spain | 2020-05-11 | Segmentation | Embryo | Eye | Sensory System |