|
| Status |
Public on Mar 31, 2022 |
| Title |
RNA-seq_Lens epithelial cells_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Lens epithelial cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Lens epithelial cells
developmental stage: Embryonic day 13
strain: White leghorn
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from biological triplicates of microdissected chick lens epithelial and fiber 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 |
| |
|
| 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 > 0.4 or <-0.4) with parametric F-test comparing nested linear models (p < 0.05)
Genome_build: galgal6
Supplementary_files_format_and_content: FibervEpi_RNAseq.txt file: 4,582 genes were found to be differentially expressed between lens epithelial cells relative to lens fiber cells
|
| |
|
| Submission date |
Feb 11, 2022 |
| Last update date |
Mar 31, 2022 |
| 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) |
| GSE196630 |
Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation [RNA-seq] |
| GSE196631 |
Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation |
|
| Relations |
| BioSample |
SAMN25871826 |
| SRA |
SRX14149350 |
