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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 24, 2016 |
| Title |
db/db glom rep 1 |
| Sample type |
SRA |
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| Source name |
Kidney Glomeruli
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| Organism |
Mus musculus |
| Characteristics |
phenotype: Type 2 diabetic
genotype: homozygous mutation in Leptin receptor (db)
age: 25 weeks
tissue: Kidney Glomeruli
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| Treatment protocol |
n/a
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| Growth protocol |
All animal studies were conducted according to the “Principles of Laboratory Animal Care” (NIH publication No. 85023, revised 1985) and the guidelines of the IACUC of The University of Texas MD Anderson Cancer Center/Texas A&M Institute of Biosciences and Technology (IBT). Diabetic db/db mice and their control littermates, db/m, were obtained from Jackson Laboratories (Strain: BKS.Cg-Dock7m+/+Leprdb/J, Bar Harbor, ME). All mice used in experiments were male. Ages of mice are reported in figure legends or denoted in figure panels. Mice were 25 weeks old at the time of sacrifice. All animals were maintained on a normal chow diet and housed in a room with a 12:12-hour light/dark cycle and an ambient temperature of 22° C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
After placing mice under a surgical plane of anesthesia, mice were perfused by insertion of a butterfly needle into the left ventricle. Cold Perfusion solution consisted of 200ul of Dynabeads M-450 Tosylactivated (Life Technologies) diluted in 40 ml of Hank's Balanced Salt Solution (HBSS). After perfusion, kidneys were harvested on ice, minced and chemically digested. Dynabead perfused glomeruli were retreived by magnetic isolation and RNA extracted by Trizol Reagent, purified over PureLink RNA Easy mini columns (Life Tech)
The Illumina compatible libraries were prepared using Illumina’s TruSeq RNA Sample Prep kit v2, as per the manufacturer’s protocol. In brief, Poly-A RNA was enriched using Oligo-dT beads. Enriched Poly-A RNA was fragmented to a median size of 150bp using chemical fragmentation and converted into double stranded cDNA. Ends of the double stranded cDNA were polished, 5′-phosphorylated, and 3’-A tailed for ligation of the Y-shaped indexed adapters. Adapter ligated DNA fragments were PCR amplified, quantified and validated by qPCR, and sequenced on Illumina’s HiSeq 2000 in a paired-end read format for 76 cycles.
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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 |
The raw data quality was assessed using FastQC software.
Adaptor presence was tested using Trimmomatic. Reads from each sample were aligned to the NCBI mouse reference genome build 37.2 using Tophat2 v2.0.4.
Transcript quantification, normalization and assembly were carried out using Cufflinks.
Genome_build: mm9
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| Submission date |
Feb 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn Samson Badal |
| Organization name |
MD Anderson Cancer Center
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| Department |
Nephrology
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| Lab |
Danesh
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| Street address |
2121 W. Holcombe Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE77717 |
RNA-Seq of Kidney Glomeruli from Type 2 diabetic (db/db) and non-diabetic mice |
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| Relations |
| BioSample |
SAMN04481406 |
| SRA |
SRX1567659 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2057620_dbdb_1_genes.fpkm_tracking.withGeneName.txt.gz |
838.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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