|
| Status |
Public on Aug 08, 2023 |
| Title |
Kidney cortex biopsy_baboon_male_15058 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney cortex biopsy
|
| Organism |
Papio hamadryas |
| Characteristics |
animal id: 15058
sample name: slc_rna_seq_34_S44
diet: low salt control chow
Sex: male
age: 7
colony: Southwest national primate research center
collection: Ultrasound guided biopsy into liquid nitrogen
surgery anesthetic: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.
tissue: Kidney cortex biopsy
|
| Treatment protocol |
None
|
| Growth protocol |
Animals were maintained on a low salt chow diet their whole life leading up to the study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from kidney biopsy samples using the Direct-zol RNA Miniprep Plus Kit (Zymo Research). Tissue was homogenized in 600 μL of TRI reagent (Zymo Research) using a BeadBeater for 3 x 30 sec with RNA purification according to the Direct-zol RNA Miniprep Plus Kit instructions. RNA was quantified by Qubit RNA BR Assay Kit (Invitrogen) and RIN was determined by with an RNA ScreenTape Kit on the Tapestation 2200 (Agilent).
cDNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Roche). Libraries were quantified by Qubit dsDNA Assay Kit (Invitrogen) and quality was determined by with a DNA ScreenTape Kit on the Tapestation 2200 (Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
20210119_Males_Transcripts_GEO.csv
|
| Data processing |
Female and male transcripts were processed together in Partek Flow with an average read length of 93.58± 1.52 (minimum=25) and an average Phred score of 36.46 ± 0.54 (minimum=30).
Reads were aligned to the olive baboon genome (papAnu2.0; March 2012) with 57,005 transcripts represented by an average of 11,161,874 ± 3,684,392 total reads and 5.80 ± 1.88% coverage and 16.23 ± 2.71 depth.
Transcripts were excluded where the sum was less than or equal to 5 among all samples and normalized using TMM with a +1 offset to eliminate zeros for downstream analyses.
The full transcript list generated in Partek Flow was imported into Partek Genomics Suite for principal component analysis (PCA) (Partek®, Inc).
Transcripts were filtered for expression values totaling <17 among all samples and filtered based on coefficient of variation for values equal to 0 prior to sex-specific WGCNA.
The R package WGCNA was run as a Pearson’s correlation with default settings as described by Langfelder and Horvath34.
Genome_build: papAnu2.0
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from male samples.
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from female samples.
|
| |
|
| Submission date |
Feb 06, 2021 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Laura A Cox |
| E-mail(s) |
laurcox@wakehealth.edu
|
| Organization name |
Wake Forest School of Medicine
|
| Department |
Internal Medicine
|
| Street address |
1 Medical Center Blvd
|
| City |
Winston Salem |
| State/province |
NC |
| ZIP/Postal code |
27103 |
| Country |
USA |
| |
|
| Platform ID |
GPL25014 |
| Series (1) |
| GSE166295 |
RNA-Seq of baboon kidney cortex biopsies |
|
| Relations |
| BioSample |
SAMN17823191 |
| SRA |
SRX10043128 |
