|
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 |