|
| Status |
Public on May 30, 2024 |
| Title |
Hematopoetic_CD8T_32 |
| Sample type |
SRA |
| |
|
| Source name |
synovium
|
| Organism |
Mus musculus |
| Characteristics |
tissue: synovium
cell type: Hematopoietic cells (CD45+/CD8+/CD8-)
roi lot: collect slide 2
condition: Control
|
| Treatment protocol |
The slides were processedfollowing the NanoString protocols as documented in Manual Slide Preparation MAN-10150-01.The slides were stained with antibodies specific for human anti-CD8 (EPR21769, AbCam) and anti-CD45 (EM-05, Novus).
|
| Growth protocol |
Back paws were decalcified in 14% of EDTA for two weeks before being embedded in paraffin. Then, 4 um-thick parafin sections were stained with human anti CD45 and Human anti CD8 T cells. Stained slides were loaded and scanned onto a GeoMx instrument.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stained slides were loaded and scanned onto a GeoMx instrument.Seven Regions of interest (ROI) were selected based on the CD45 and CD8 fluorescent staining and auto-segmentation algorithm. RNA was isolated using Agilent RNA isolation kit with manufactured recommended protocol.
Photocleaved oligonucleotides from the ROI were collected and products were processed and sequenced on an Illumina NextSeq 2000. The ROI were selected based on the positive staining of CD8 and CD45
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
DSP-1001660011778-C-C05
|
| Data processing |
The resulting read count matrix was passed through robust QC procedure to remove ROIs of low surface area (<5000 µm2) or low perfect aligned reads (< 80%), and probes of low quality or identified as global or local outliers (fails Grubbs outlier test in ≥ 20% segments). Genes differentially expressed between groups of interest were detected using gene-wise linear modeling in R (limma, v3.50.3), with p-value adjusted for false discovery rate.
FASTQ files were decoded using a Nanostring GeoMx NGS pipeline app version 2.0.21
Assembly: HGR38
Supplementary files format and content: normalized matrix count
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
May 30, 2024 |
| Last update date |
May 30, 2024 |
| Contact name |
Soumyaroop Bhattacharya |
| E-mail(s) |
soumyaroop_bhattacharya@urmc.rochester.edu
|
| Phone |
5852764683
|
| Organization name |
University of Rochester
|
| Department |
Pediatrics
|
| Street address |
601 Elmwood Ave
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE268695 |
Spatial transcriptomic in synovial tissue of psoriasis (Ps) and psoriatic arthritis (PsA) humanized mice. |
|
| Relations |
| BioSample |
SAMN41603804 |
| SRA |
SRX24754511 |
