 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 31, 2022 |
| Title |
Bisulfite-seq_Lens epithelial cells_rep2 |
| 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 |
genomic DNA |
| Extraction protocol |
Lenses were isolated from White Leghorn embryonated chicken eggs (Charles River Laboratories, Storrs, CT) at embryonic developmental stage day 13 (E13). 25 lenses per biological replicate were microdissected into epithelial cells and fiber cells as previously described [217]. Microdissected epithelial and fiber cells from 25 lenses were pooled and stored in CryoStor CS10 cryopreservation media containing 10% DMSO (Stemcell, Vancouver, Canada) and stored at −80 °C as previously described [237].
Tissue in CryoStor media was thawed on ice, centrifuged at 800 x g for 5 mins and the CryStor removed. DNA was isolated using Qiagen Genomic-tip 20/G along with the Qiagen Genomic DNA buffer set according to the manufacturer’s instructions.
Bisulfite-seq was performed by Novogene (Sacramento CA) using an Illumina HiSeqTM2500/MiSeq platform using their standard protocols
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
CASAVA base calling and Trimmomatic read trimming and alignment to the galgal6 reference genome using Bismark software [238].
DSS analysis software based on beta-binomial distribution was used for the identification of DMRs as described previously [239,240] with consideration of the spatial correlation, read depth of the sites, and the variance among biological replicates. The parameters were smoothing = TRUE, smoothing.span = 200, delta = 0, p.threshold = 1 × 10−5, minlen = 50, minCG = 3, dis.merge = 100, and pct.sig = 0.5.
Genome_build: galgal6
Supplementary_files_format_and_content: mCG differentially methylated regions (DMR) text files: 7,621 differentially methylated mCG regions were identified between lens epithelial and fiber cells; file contains: bed coordinates, diff.methyl, and genomic loci of DMRs
|
| |
|
| 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 |
GPL19005 |
| Series (2) |
| GSE196629 |
Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation [Bisulfite-seq] |
| GSE196631 |
Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation |
|
| Relations |
| BioSample |
SAMN25871832 |
| SRA |
SRX14149477 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
