|
| Status |
Public on Jul 07, 2021 |
| Title |
Primary lens cells - DMOG_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary lens cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Embryonic day 10 primary lens cells
strain: White leghorn
treatment: treated with 1mM DMOG for 4 hours
|
| Treatment protocol |
Primary lens cells were treated with the HIF1α activator dimethyloxalllyl glycine (DMOG, Santa Cruz Biotechnology, prod no: sc200755) (1 mM) for 4 hours at 37 °C
|
| Growth protocol |
Primary chick lens epithelial cell cultures were prepared from the lenses of Embryonic day 10 (E10) White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT). Briefly, primary lens cells were isolated from chicken lenses by trypsinization and agitation. Cells were plated onto dishes coated with mouse laminin (Invitrogen, prod no: 23017-015) and cultured in Medium 199 (Invitrogen, prod no: 11150) supplemented with 10% FBS (Invitrogen, prod no: 16140-071) and penicillin-streptomycin antibiotic mix (50 units/ml; Invitrogen, prod no: 15140-122)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from primary lens cells using TRIZOL® reagent (Invitrogen, prod no: 15593018) according to the manufacturer’s instructions
Libraries were prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DMOGvUntreated_RNAseq.txt
|
| Data processing |
Cutadapt was used to remove adaptor-contaminated reads, low quality bases and undetermined bases
Reads were mapped to galgal6 genome (ensemble version 96) using Bowtie2 and HISAT2
The mapped reads were assembled using StringTie
Comprehensive transcriptomes were generated using gffcompare and StringTie
The R package edgeR was used to estimate the expression levels of all transcripts and to identify differentially expressed genes (log2 fold change FPKM > 0.6 or <-0.6) with parametric F-test comparing nested linear models (p < 0.05)
Genome_build: galgal6
Supplementary_files_format_and_content: DMOGvUntreated_RNAseq.txt file: 526 genes were found to be differentially expressed in DMOG-treated primary lens cells relative to untreated primary lens cell samples
|
| |
|
| Submission date |
Feb 11, 2021 |
| Last update date |
Jul 07, 2021 |
| Contact name |
Marc Kantorow |
| E-mail(s) |
mkantoro@health.fau.edu
|
| Phone |
5612973806
|
| Organization name |
Florida Atlantic University
|
| Street address |
777 Glades Road
|
| City |
Boca Raton |
| State/province |
FL |
| ZIP/Postal code |
33431 |
| Country |
USA |
| |
|
| Platform ID |
GPL26853 |
| Series (2) |
| GSE166632 |
A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis [RNA-seq] |
| GSE166633 |
A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis |
|
| Relations |
| BioSample |
SAMN17868180 |
| SRA |
SRX10079879 |
