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Sample GSM5934235 Query DataSets for GSM5934235
Status Public on May 11, 2022
Title RNA-Seq E5 RPE 2
Sample type SRA
 
Source name Retinal pigment epithelium
Organism Gallus gallus
Characteristics treatment: Development
Stage: E5
Treatment protocol For treated conditions, surgical retinectomy was performed. For FGF-treated samples, FGF2-containing heparain beads were delivered to the eye cup at the time of retinectomy.
Growth protocol White Leghorn chicken eggs obtained from Michigan State University were used. Eggs were incubated in a humidified, rotating incubator at 38 °C before performing experiments at Hamburger Hamilton stage 24 (E4) or 26 (E5).
Extracted molecule polyA RNA
Extraction protocol Biological samples were collected directly into 1X DNA/RNA Shield (Zymo, cat. R1200) on ice. RNA was isolated using the Quick-RNA Miniprep Kit (Zymo, cat. R1054) per manufacturer’s instructions, including 15 minutes of in-column DNase I treatment.
RNA libraries were constructed at the DNA Link, Inc. sequencing core (Los Angeles, CA, USA) using the TruSeq Stranded mRNA Library Prep kit (Illumina, cat. 20020594) with 580ng – 1ug of total RNA per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description E5_RPE_2
Data processing Low-quality bases and adapters were trimmed using Cutadapt and Trim Galore with the parameters --stringency 3 --length 36
Two-pass alignment with STAR was employed and the parameters --quantMode GeneCounts TranscriptomeSAM --readFilesCommand zcat --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate were used.
Gene counts were generated using Stringtie and Ensembl chicken gene annotation release 101
Differential expression testing was performed with DESeq2 with an expression filter of minimum raw counts 10 across all samples
Genome_build: GRCg6a
Supplementary_files_format_and_content: Normalized gene count matrix from DESeq2.
 
Submission date Mar 04, 2022
Last update date May 11, 2022
Contact name Katia Del Rio-Tsonis
E-mail(s) delriok@miamioh.edu
Organization name Miami University
Department Biology
Street address 700 E High St
City Oxford
State/province OH
ZIP/Postal code 45056
Country USA
 
Platform ID GPL26853
Series (2)
GSE197937 Gene expression (mRNA-seq) in the developing chicken retinal pigment epithelium
GSE197938 OTX2 regulatory network and maturation-associated gene programs are inherent barriers to RPE neural competency
Relations
BioSample SAMN26437428
SRA SRX14371552

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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