|
| Status |
Public on Apr 01, 2024 |
| Title |
Pre-Treatment Non-Lesional |
| Sample type |
SRA |
| |
|
| Source name |
Skin punch biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skin punch biopsy
|
| Growth protocol |
Three to four millimeter skin punch biopsies were obtained from pre- and post-treatment lesional and non-lesional psoriatic skin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within5 minutes of devascularization.10-µm cryosections were mounted onto the ST arrays (10X Visium) where reverse transcription of cellular transcripts took place in situ after tissue permeabilization.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing output and the histology images were processed using space ranger software (10X Genomics). The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FATSQ files to human genome (hg38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Jul 19, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Shruti Naik |
| Organization name |
NYU Langone Health
|
| Department |
Pathology
|
| Lab |
Naik Lab
|
| Street address |
435 E 30th St
|
| City |
NYC |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE237771 |
Epithelial-Immune Metabolic Codependency Fuels Inflammatory Disease [Spatial Transcriptomics] |
| GSE237772 |
Epithelial-Immune Metabolic Codependency Fuels Inflammatory Disease |
|
| Relations |
| BioSample |
SAMN36620615 |
| SRA |
SRX21081442 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7648698_pre_NL_aligned_fiducials.jpg.gz |
1.1 Mb |
(ftp)(http) |
JPG |
| GSM7648698_pre_NL_barcodes.tsv.gz |
3.9 Kb |
(ftp)(http) |
TSV |
| GSM7648698_pre_NL_detected_tissue_image.jpg.gz |
1.7 Mb |
(ftp)(http) |
JPG |
| GSM7648698_pre_NL_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM7648698_pre_NL_matrix.mtx.gz |
1.1 Mb |
(ftp)(http) |
MTX |
| GSM7648698_pre_NL_scalefactors_json.json.gz |
173 b |
(ftp)(http) |
JSON |
| GSM7648698_pre_NL_tissue_hires_image.png.gz |
2.8 Mb |
(ftp)(http) |
PNG |
| GSM7648698_pre_NL_tissue_lowres_image.png.gz |
325.2 Kb |
(ftp)(http) |
PNG |
| GSM7648698_pre_NL_tissue_positions_list.csv.gz |
59.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
