|
| Status |
Public on Oct 16, 2023 |
| Title |
HiC, lens fiber, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
lens
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lens
cell type: fiber
genotype: CD-1
|
| Growth protocol |
HiC: v6.5 mESCs derived by Dr. Rudolph Jaenisch (gifted by Dr. Meelad Dawlaty) were used. Cells were grown under feeder-free conditions on 0.2% gelatin and supplemented with LIF (24 ng/mL). Each replicate contained ~2.0 x 106 cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC: Lenses were dissected at P0.5 and then micro-dissected into lens epithelium and lens fiber under a dissection microscope. Each replicate of lens tissue was comprised of either 30 lens epithelium, or 30 lens fiber samples. Samples were kept on dry ice for the duration of the micro-dissection process. Samples were then homogenized using a disposable pestle tissue grinder. Homogenized tissues were fixed in 2.0% formaldehyde for 10 mins at room temperature. Formaldehyde was quenched with 0.125 M glycine to stop the reaction. The crosslinking method for mESCs was the same. ChIP-seq: 200 P0.5 lenses were obtained from CD-1 mice, microdissected into lens epithelium and lens fibers and stored in liquid nitrogen prior the use as we described earlier (Sun et al. 2015).
The Hi-C library was generated using the Arima-HiC kit according to the manufacturers protocols (A510008) and performed by the NYU Langone Health Genome Technology Center. The ChIP-seq library was generated by Active Motif: Immunoprecipitation was performed on 6 µg chromatin from microdissected lens cells with 5 µl anti-CTCF antibody (ActiveMotif cat. # 61311, lot #11219006).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned with bwa. HiC: bwa-mem with default settings. ChIP-seq: bwa aln/samse with default settings.
HiC: contact maps were created from reads with MAPQ > 30 with a maximum resolution of 5kb with the ENCODE HiC pipeline (https://github.com/ENCODE-DCC/hic-pipeline), based on Juicer.
HiC: loops and topologically-associated domains (TADs) were called within the ENCODE pipeline using the HiCCUPs and Arrowhead algorithms, respectively.
HiC: A/B compartment analysis was performed using dcHiC to calculate, select, and normalize principal components of the Pearson correlation of the contact matrix at 10kb resolution
ChIP-seq: peaks were called with MACS2 using default settings.
Assembly: mm10
Supplementary files format and content: .hic (contact maps)
Supplementary files format and content: .bedpe (chromatin loops)
Supplementary files format and content: .bed (TADs)
Supplementary files format and content: .bedGraph (A/B compartment scores)
Supplementary files format and content: .bw (ChIP-seq read density)
Supplementary files format and content: .narrowPeak (ChIP-seq peaks)
|
| |
|
| Submission date |
Sep 22, 2023 |
| Last update date |
Oct 16, 2023 |
| Contact name |
William Chang |
| E-mail(s) |
william.chang@einsteinmed.edu, williamkurtischang@gmail.com
|
| Phone |
4107331644
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Ophthalmology
|
| Lab |
Cvekl
|
| Street address |
1301 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE243851 |
Nuclear Organization of Lens Epithelium and Fiber Cells in Newborn Lens |
|
| Relations |
| BioSample |
SAMN37519144 |
| SRA |
SRX21864961 |
