|
| Status |
Public on May 17, 2024 |
| Title |
Skin tissue, atopic-like model, treated with BP79, replicate 1_S10 |
| Sample type |
SRA |
| |
|
| Source name |
Skin tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skin tissue
treatment 1: atopic-like model
treatment 2: BP79
replicate: 1_S10
|
| Treatment protocol |
BP79 was topically applied onto the atopic-like skin disease models once every 24 h over 4 days.
|
| Growth protocol |
We developed a microfluidic two-organ chip setup which contained an atopic-like skin disease model that was co-cultivated with a 3D bronchial epithelial tissue model over four days on a dynamic organ chip platform that ensured media circulation and flow from the skin to the healthy lung tissue (Fig. 6 a, b). Activated CD4+ T cells were added to the circuit due to their role as direct TSLP effector cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
the total RNA was isolated using the Invitrogen PureLink™ RNA Mini Kit (ThermoFisher, Burnaby, BC, Canada) according to the manufacturer’s protocol.
Sample quality control was performed using the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Disease_Skin_BP79_1_S10
|
| Data processing |
Reads were demultiplexed using Illumina's BCL Convert and mapped to the genome using using the STAR aligner, v. 2.7.8.a.
For quality control, we used FastQC and MultiQC.
Read counts were collected using featureCounts. Features with fewer than a total of 10 counts or fewer than 5 samples with at least 3 counts were eliminated.
For differential gene expression analysis, we used the R package DESeq2, v. 1.30.1. Gene set enrichment testing was done with the CERNO algorithm implemented in the tmod package, v. 0.50.7.
with gene sets sourced from the MSigDB using the msigdbr package, v. 7.4.1.
Assembly: GRCh38, p7
Supplementary files format and content: tab-delimited text file containing raw counts for all samples
|
| |
|
| Submission date |
Apr 19, 2024 |
| Last update date |
May 17, 2024 |
| Contact name |
January 3rd Weiner |
| E-mail(s) |
january.weiner@gmail.com
|
| Phone |
030450543049
|
| Organization name |
Berlin Institute of Health, Charité Medical University of Berlin
|
| Department |
CUBI
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE264457 |
Disrupting TSLP - TSLP receptor interactions via small molecule inhibitors yields a novel and efficient treatment option for atopic diseases |
|
| Relations |
| BioSample |
SAMN41021587 |
| SRA |
SRX24313589 |
