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| Status |
Public on May 21, 2020 |
| Title |
sKelm4L1 |
| Sample type |
SRA |
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| Source name |
Periaqueductal gray, brainstem
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Long Evans
tissue: Periaqueductal gray, brainstem
age: 8 months
genotype: WT
Sex: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were removed, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample as well as WGCNA data.
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| Submission date |
May 20, 2020 |
| Last update date |
May 21, 2020 |
| Contact name |
Cynthia A Kelm-Nelson |
| E-mail(s) |
cakelm@wisc.edu
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| Phone |
4144183662
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| Organization name |
University of Wisconsin- Madiso
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| Department |
Surgery
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| Street address |
1300 University Avenue, 416 Medical Sciences Center
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE150939 |
Gene expression within the periaqueductal gray in Pink1 knockout rats |
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| Relations |
| BioSample |
SAMN14984018 |
| SRA |
SRX8370421 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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