|
| Status |
Public on Feb 16, 2024 |
| Title |
spatial transcriptomics ROI2 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney biopsy tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney biopsy tissue
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5-um thickness kidney biopsy sections were mounted on charged slides
Add PCR master mix and primer to transcripts samples, followed by PCR amplification. Combine each PCR product into a single microtube. Perform purification using AMPure magnetic beads and 80% ethanol. Obtain the libraries by elution in elution buffer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
FFPE spatial transcriptome analysis
|
| Data processing |
Fastq files were converted into DCC files by GeoMxNGSPipeline software
GeoMx DSP Analysis Suite (GEOMX-0094, v2.4.2.2) was utilized to analyze the spatial transcriptomic data. Target genes with 5% of the segment above the threshold were retained in the datasets and gene expressions with lower than the limit of quantitation were initially excluded.
Assembly: hg18
Supplementary files format and content: dcc
|
| |
|
| Submission date |
Dec 27, 2023 |
| Last update date |
Feb 16, 2024 |
| Contact name |
Minji Kang |
| E-mail(s) |
minzi@snu.ac.kr
|
| Organization name |
Seoul National University graduate school
|
| Department |
biomedical sciences
|
| Street address |
103 daehak-ro
|
| City |
Seoul |
| ZIP/Postal code |
03080 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE252137 |
Spatial transcriptome analysis unveils an innate immune activation signature of acute T cell-mediated rejection in kidney transplants |
|
| Relations |
| BioSample |
SAMN39152574 |
| SRA |
SRX23045285 |
