|
| Status |
Public on May 16, 2023 |
| Title |
S18_HDM |
| Sample type |
SRA |
| |
|
| Source name |
LCs
|
| Organism |
Homo sapiens |
| Characteristics |
sample group: PatchTest_HDM
reponse: non-responing
experiment type: bulk RNA-seq
cell type: FACS sorted CD207+
|
| Treatment protocol |
in vivo 48h topical exposure to a control patch test or a patch test with HDM
|
| Growth protocol |
primary cells isolated by digestion from skin punch biopsies
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For bulk RNA-seq RNA was isolated using Direct-zol RNA micro prep (Zymo, UK) as per the manufacturer’s protocol.
For Bulk RNA-seq cDNA libraries were generated using SMART-Seq Stranded Library Preparation for Ultra Low Input according to the SMART-Seq Stranded Kit User Manual following the Ultra low input workflow (Takara Bio). Samples were pooled (12/batch) for library preparation. For Drop-seq High Sensitivity DNA Assay Nextera kit, Illumina, was used. For Constellation cDNA was aplified using targeted linear amplification (20 rounds) and further prepared using True-seq, Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Alignment bulk RNA: High-quality reads filtered at 15M depth across all samples were mapped to the human genome (GRCh38) using Kallisto
Normalisation bulk RNA: Raw counts from RNA-Seq were processed in Bioconductor package EdgeR (54) and SLEUTH
Alignment single cell RNA: Following demultiplexing, raw FASTQ files were aligned to the human genome (GRCh38), using kallisto-bustools
Filtering single cell RNA: Doublet detection and hashing demultiplexing was done using Solo. Empty barcodes and percentage of mitochondrial genes were checked within Scanpy.
Clean-up single cell RNA: CellBender was used to remove empty technical artefacts.
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV table with counts and TPM as estimated by Kallisto
|
| |
|
| Submission date |
Sep 21, 2021 |
| Last update date |
May 16, 2023 |
| Contact name |
Marta Ewa Polak |
| E-mail(s) |
m.e.polak@soton.ac.uk
|
| Phone |
2381205727
|
| Organization name |
University of Southampton
|
| Department |
Clinical and Experimental Sciences
|
| Lab |
Systems Immunology Group
|
| Street address |
Southampton General Hospital, Mailpoint 813, LE59,
|
| City |
Southampton |
| State/province |
Hampshire |
| ZIP/Postal code |
SO16 6YD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE184509 |
Transcriptomic analyses of cutaneous immune network in patiens with atopic dermatitis challenged with house dust mite (HDM) patch test |
|
| Relations |
| BioSample |
SAMN21531027 |
| SRA |
SRX12280711 |
