|
| Status |
Public on Dec 02, 2023 |
| Title |
control_H3K27AC_2 |
| Sample type |
SRA |
| |
|
| Source name |
limbal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary limbal stem cells
treatment: control
chip antibody: H3K27ac
|
| Treatment protocol |
Cells were infected with lentiviruses expressing target genes.
|
| Growth protocol |
LSCs were grown in DMEM/F-12 (1:1) medium containing 1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
chromatin was fixed with 1% formaldehyde for 10 min and sheared in a sonification buffer. Fragmented DNA was incubated with primary antibodies overnight at 4℃ and then with Protein A/G Dynabeads for 1 h. The beads were collected and washed sequentially with the following solutions: high-salt buffer, low-salt wash buffer, and TE buffer. Elution of the immunoprecipitated protein/DNA complexes was performed using elution buffer at 65℃ for 4 h. Next, the protein/DNA complexes were incubated with proteinase K (Invitrogen) and RNase A (Invitrogen) for 1 h. De-crosslinked DNA was purified using the PCR Purification Kit (Qiagen).
ChIP-seq DNA libraries were generated using VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RORA_OE_H3K27ac_differential_peaks.xlsx
|
| Data processing |
Reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software.
Duplicated reads were removed by Picard Markduplicates and only uniquely mapping reads were retained for further analysis.
MACS2 was used to call peak.
Assembly: hg19
Supplementary files format and content: Excel files containing differential H3K27ac, H3K4me3 and H3K27me3 peaks between control and RORA-overexpression groups. A BED file containing RORA binding sites in RORA-overexpressed LSCs.
|
| |
|
| Submission date |
Nov 29, 2023 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Mingsen Li |
| E-mail(s) |
lims3@mail2.sysu.edu.cn
|
| Organization name |
Sun Yat-sen University
|
| Department |
Zhongshan Ophthalmic Center
|
| Street address |
No. 7 Jinsui road Tianhe district
|
| City |
Guanzhou |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE248928 |
The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation [ChIP-seq] |
| GSE249150 |
The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation |
|
| Relations |
| BioSample |
SAMN38498833 |
| SRA |
SRX22700193 |
