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| Status |
Public on Sep 27, 2017 |
| Title |
Treatment Shunt rep2 |
| Sample type |
SRA |
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| Source name |
TreatmentShunt
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| Organism |
Mus musculus |
| Characteristics |
genetic backround: (DBA/2J x C3HeB/FeJ)F1
genotype: MHC-cycD2 transgenic
treatment: Shunt
tissue: myocardium, left ventricle
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| Treatment protocol |
TAC Surgery: Surgery was done using a minimally invasive approach as described previously,(42) with the exception that the degree of aortic constriction was reduced to yield comparable survival in wild-type mice with TAC vs. Shunt. Briefly, 8 week old mice were anesthetized using intraperitoneal injections of ketamine and xylazine (100 mg/kg and 5 mg/kg, respectively). A horizontal incision at the jugulum was used to display the transverse aorta. A needle was tied against the aorta using a 5-0 non-absorbable suture. After removal of the needle, skin was closed and the mice were kept on a heating plate until recovered from anesthesia. Sham animals underwent the same procedure except banding of the aorta. DBA/2J x C3HeB/FeJ) F1 mice exhibit a pronounced gender-based difference in body weight at 8 weeks of age (29.6 +/- 0.8 vs. 23.3 +/- 0.4, males vs. females, n = 10 mice per gender). Because aortic dimension correlates with body weight,(43, 44) and because aortic dimensions influences the gradient, 25G needles were used to induced TAC in males and 26g needles were used in females. The resulting pressure gradients were measured by echocardiography, and comparable gradients were observed in male and female mice (Supplemental Figures 8 and 9).
Aortocaval Shunt: Surgery was done as described previously.(45) Briefly, 8 week old mice were anesthetized using isofluorane insufflation. A longitudinal abdominal incision was made and the vessels prepared. The aorta was clamped and punctured with a needle (23G) through the vena cava inferior. After removing the needle the external hole in the aorta was closed by a cyanoacrylate glue (Pattex, Düsseldorf, Germany). Successful shunt operation is immediately seen by inflow of oxygenated blood from the abdominal aorta into the vena cava. The abdomen was then closed and the mice were kept on a heating plate until full recovery from anesthesia. Sham animals underwent the same procedure except for the puncture of the vessels. In a previous analysis we showed that a decline of LVEDD after an initial increase is associated with a decrease in right ventricular oxygen saturation as an indicator of shunt closure. In the present study all animals after shunt surgery showed a persistent increase in LVEDD.
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated from left ventricular tissue using the RNeasy Fibrous Tissue Mini Kit (Qiagen) according to the manufacturer`s protocol.
Library preparation was conducted according to the instructions of the TruSeq RNA Sample Preparation v2 Kit from Illumina (Cat. N°RS-122-2002) using 1µg total RNA as starting material.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample IV2
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| Data processing |
[base-calling] Sequence images were transformed to bcl files with the software BaseCaller (Illumina), and then demultiplexed to fastq files with CASAVA v1.8.2. Quality checking was done via fastqc.
[alignment] Sequences were aligned to the genome reference sequence of Mus musculus (GRCm38/mm10). The Alignment was performed using the STAR alignment software (version 2.3.0e) 1 allowing for two mismatches within 50 bases.
[filtering] Subsequently, conversion of resulting SAM files to sorted BAM files, filtering of unique hits and counting were conducted with SAMtools (version 0.1.19) 2 and HTSeq (version 0.6.1p1) 3.
Data were preprocessed and analyzed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (version 1.8) 4.
Specifically, the data were normalized and tested for differentially expressed genes based on a generalized linear model likelihood ratio test assuming negative binomial data distribution. Candidate genes were filtered to a minimum of log2FC>1/-1 and a false discovery rate–corrected P-value < 0.05.
Genome_build: Gene annotation was performed using Mus musculus entries from Ensembl (www.ensembl.org) via the biomaRt package (version 2.18.0) 5.
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
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| Submission date |
Sep 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sara Khadjeh |
| E-mail(s) |
sara.khadjeh@med.uni-goettingen.de
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| Phone |
+49-(0)551-39 63633
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| Organization name |
University Medical Center Göttingen
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| Department |
Clinic for Cardiology and Pneumology
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| Lab |
Heart Research Center - Hasenfuß lab
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| Street address |
Robert-Koch-Str. 42a
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| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE103545 |
RNA-sequencing of MHC-cycD2 transgenic mice after Transverse Aortic Constriction and Aortocaval Shunt surgery |
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| Relations |
| BioSample |
SAMN07608153 |
| SRA |
SRX3163905 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2773424_Sample_r973sIV2TreatmentShunt_mm_rna_sr_Toischer_D_2_geneCounts.txt.gz |
142.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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