|
| Status |
Public on Sep 12, 2023 |
| Title |
Human Tenon's fibroblasts, Control 2, Day1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Tenon's fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Human Tenon's fibroblasts
cell type: Conjunctival fibroblasts
genotype: WT
treatment: No treatment
|
| Treatment protocol |
HTFs were treated in triplicate wells with different concentrations of adrenaline (0%, 0.0005%, 0.01%) for 24 hours.
|
| Growth protocol |
Fibroblasts were cultured in complete media consisting of DMEM, 10% fetal calf serum, 100 U/mL streptomycin and 2 nM L-glutamine, and incubated at 37℃, 5% CO2 and 95% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a RNeasy mini kit (Qiagen, Crawley, UK).
For each sample, 500 ng of total RNA were processed using the KAPA mRNA HyperPrep Kit (Roche p/n KK8580).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Run data were demultiplexed and converted to fastq files using Illumina’s BCL Convert Software v3.75.
The unique molecular index was moved to the read header for downstream analysis.
Fastq files were then aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b.
Aligned reads were then UMI deduplicated using Je-suite (1.2.1), and reads per transcript were counted by FeatureCounts in order to produce a digital output of gene expression.
Differential expression was estimated using the BioConductor package SARTools, a DESeq2 wrapper.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text files
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Cynthia Yu-Wai-Man |
| E-mail(s) |
cynthia.yu-wai-man@kcl.ac.uk
|
| Organization name |
King's College London
|
| Street address |
Westminster Bridge Road
|
| City |
London |
| ZIP/Postal code |
SE1 7EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE213217 |
High concentration of adrenaline blocks key cell cycle genes and exhibits antifibrotic and vasoconstrictor effects in glaucoma surgery |
|
| Relations |
| BioSample |
SAMN30813829 |
| SRA |
SRX17537732 |
