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Sample GSM7995007 Query DataSets for GSM7995007
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

Supplementary file Size Download File type/resource
GSM7995007_DSP-1001660011340-B-F03.dcc.gz 60.5 Kb (ftp)(http) DCC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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