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| Status |
Public on May 23, 2024 |
| Title |
Qiagen AllPrep DNA/RNA FFPE kit- Rep 4 |
| 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 |
r15089
Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization(Method QE)-Rep 4
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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 |
SAMN41424201 |
| SRA |
SRX24582854 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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