NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8272277 Query DataSets for GSM8272277
Status Public on May 23, 2024
Title CELLDATA RNAstorm FFPE RNA Extraction Method-Rep 2
Sample type SRA
 
Source name Cardiac Tissue
Organism Macaca mulatta
Characteristics method: CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)
tissue: Cardiac Tissue
Extracted molecule total RNA
Extraction protocol Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)
Illumina Stranded Total RNA-seq kit, Ligation
Total RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 12075_B
CELLDATA RNAstorm FFPE RNA Extraction Kit with protocol modifications on the lysis step(Method BL)-Rep 2
Data processing FASTQ files were uploaded into Partek Flow software (Partek Inc., USA) for primary QC. The STAR (2.7.8a) aligner was used to align reads to the Macaca mulatta (Mmul_10) reference genome. The generated BAM files were quantified using Partek E/M algorithm (Xing et al, Nucleic Acids Res. 2006;34(10):3150–60) by Ensembl annotations (Ensembl Transcripts release 110) and then normalized using Median of ratios method (M Love, Genome Biol. 2014 15:550). The BAM files were also used for rRNA quantification, calculated using the percentage of the total mapped reads using Partek E/M algorithm.
Assembly: Mmul_10
Supplementary files format and content: xlsx, raw gene counts
 
Submission date May 16, 2024
Last update date May 23, 2024
Contact name Jin Sung Jang
E-mail(s) jang.jin@mayo.edu
Organization name Mayo Clinic
Street address 200 1st st sw
City Rochester
ZIP/Postal code 55905
Country USA
 
Platform ID GPL27943
Series (1)
GSE267659 Optimizing RNA Extraction Methods for High Throughput Transcriptome Sequencing of Fresh Frozen and Formalin-Fixed Paraffin-Embedded Cardiac Tissues Specimens
Relations
BioSample SAMN41424207
SRA SRX24582848

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap