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| Status |
Public on Dec 15, 2021 |
| Title |
2_Tumor |
| Sample type |
SRA |
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| Source name |
Mammary tumor HIAC
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: High Inherent Aerobic Capacity (HIAC)
tissue: mammary tumor
gender: female
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary tumor, mammary gland (MG) and muscle were harvested and snap frozen in liquid nitrogen. RNA was isolated from MG and muscle using Qiazol reagent and RNeasy mini kit (Qiagen, Inc., USA). Mammary tumor RNA was isloated using the RNeasy mini-kit (Qiagen, Inc.) with addition of a proteinase K digestion step for 10 min at 55 °C between the lysis buffer and ethanol steps.
RNA libraries were prepared for sequencing using standard Illumina protocols (Nugen Universal mRNA kit, Tecan Genomics, Inc., Redwood City, CA, USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina Real-Time Analysis (RTA) software version 3.4.4 was used for
fastp version 0.20.0 used for sequence trimming and quality control
hisat2 version 2.1.0 used for genome alignment mapped to rnor6 using Ensembl IDs
featureCounts version 1.6.4 used for tabulating the number of reads per gene
Genome_build: rnor6
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Dec 13, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Henry J Thompson |
| E-mail(s) |
henry.thompson@colostate.edu
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| Organization name |
Colorado State University
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| Lab |
Cancer Prevention Laboratory
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| Street address |
1173 Campus Delivery
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| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523-1173 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE190840 |
The Renin-Angiotensin System, High Inherent Aerobic Capacity, and Low Breast Cancer Risk |
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| Relations |
| BioSample |
SAMN24011789 |
| SRA |
SRX13402608 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5732749_2_Tumor_Raw_Counts.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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