|
| Status |
Public on May 11, 2023 |
| Title |
#2 Non-inflamed |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Crohn's disease
endoscopic inflammation status: non-inflamed
sampling location: rectum
age (y): 14
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Intestinal biopsies were collected in wash buffer medium consisting of HBSS supplemented with antibiotics, FungizoneTM (Life Technologies) and HEPES (HyClone). Subsequently, enzymatic digestion with DNAse and Collagenase II was performed at 37° C under magnetic stirring. Cell suspension was filtered through a 40 μm cell strainer and rinsed with IMDM 10% FCS.
Samples were prepared using Chromium Single-Cell v2 3ʹ Reagents Kit (10x Genomics) according to manufacturer’s instructions. Samples were sequenced on a HiSeq4000 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Used the 10X Cell Ranger toolkit (v2.1.1) for filtering and aligning reads to human genome hg19 and counting barcodes and unique molecular identifiers (UMI)
Using Seurat (v3.2.3), cells with a percentage of mitochondria genes > 5% were considered as dead cells and were removed. Cells with < 200 genes and > 2500 numbers of detected genes were excluded. Genes detected in < 3 cells were excluded
Using Seurat (v3.2.3), raw unique molecular identifier counts were scaled and normalized through log transformation.
The top 2000 variable genes were selected for principle-component analysis. The top 10 principal components were selected for UMAP (Uniform Manifold Approximation and Projection) and clustering analysis with resolution 0.5 (for combined and non-inflamed) and 0.55 (for inflamed).
Seurat function FindAllMarkers (logFC threshold = 0.25) were used to find cluster- and sample-specific marker genes.
Genome_build: hg19
Supplementary_files_format_and_content: gene count text files generated using 10X Cell Ranger toolkit (v2.1.1)
|
| |
|
| Submission date |
Mar 18, 2021 |
| Last update date |
May 11, 2023 |
| Contact name |
Jenny Mjösberg |
| E-mail(s) |
jenny.mjosberg@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Medicine
|
| Lab |
Center for Infectious Medicine
|
| Street address |
Alfred Nobels allé 8
|
| City |
Huddinge |
| State/province |
Stockholm |
| ZIP/Postal code |
14152 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE169136 |
Single-cell RNA sequencing of ILCs and T cells reveals enrichment of NK-like T cells in pediatric and adult inflammatory bowel disease |
|
| Relations |
| BioSample |
SAMN18347767 |
