|
| 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 |
