|
| Status |
Public on Dec 02, 2023 |
| Title |
control-R-2 |
| Sample type |
SRA |
| |
|
| Source name |
limbal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary limbal stem cells
genotype: control
|
| Treatment protocol |
Cells were infected with lentiviruses expressing target genes.
|
| Growth protocol |
LSCs were grown in 1:1 DMEM/F-12 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 |
total RNA |
| Extraction protocol |
Total RNA were extracted by RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using NEBNext RNA first and second Strand Synthesis Module (NEB, USA) and KAPA Library Preparation Kit (KAPA Biosystem)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RORA_overexpression.xlsx
|
| Data processing |
trimmed reads were aligned to human hg19 reference genome with STAR software (version 2.6.1a) to acquire read counts within per gene.
TPM (Transcripts per million reads) values that represent gene expression were generated using RSEM tools (version v1.3.0).
Significantly differentially expressed genes with fold change ≥ 2 and FDR < 0.05 were determined by DESeq2 (version 1.20.0).
Assembly: hg19
Supplementary files format and content: Excel files containing the TPM value of each gene in control and RORA- and PITX1-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) |
| GSE248926 |
The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation [RNA-Seq] |
| GSE249150 |
The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation |
|
| Relations |
| BioSample |
SAMN38500435 |
| SRA |
SRX22681071 |
