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Status |
Public on May 23, 2024 |
Title |
Qiagen AllPrep DNA/RNA FFPE kit- Rep 8 |
Sample type |
SRA |
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Source name |
Cardiac Tissue
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Organism |
Macaca mulatta |
Characteristics |
method: Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE) tissue: Cardiac Tissue
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
rh2957 Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 8
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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
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Submission date |
May 16, 2024 |
Last update date |
May 23, 2024 |
Contact name |
Jin Sung Jang |
E-mail(s) |
jang.jin@mayo.edu
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Organization name |
Mayo Clinic
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Street address |
200 1st st sw
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City |
Rochester |
ZIP/Postal code |
55905 |
Country |
USA |
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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 |
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Relations |
BioSample |
SAMN41424196 |
SRA |
SRX24582859 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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