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| Status |
Public on Oct 01, 2019 |
| Title |
HD-HR3 |
| Sample type |
SRA |
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| Source name |
heart apex
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Lewis
recipient disease status: Healthy recipient
donor disease status: Healthy donor
tissue: heart apex
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| Treatment protocol |
To develop advanced CKD, rats underwent 2/3 bilateral ablation of renal mass by coagulating branches of both renal arteries under isoflurane anaesthesia (5% induction, 1.5–2% maintenance). All rats received an intramuscular injection of analgesia straight after and one day after surgery (Buprenorphine, 0.05 mg/kg). Subsequently, development of CKD was accelerated with L-NNA, a NO-synthase inhibitor (200 mg/L) in drinking water and animals were fed standard powdered chow (CRM-FG; Special Diet Services Ltd., Witham, Essex, UK) supplemented with 6% NaCl, until proteinuria reached 200 mg/24h at which point L-NNA and 6% NaCl were discontinued. CKD animals were included into the transplantation protocol when proteinuria reached 100 mg/24h (without L-NNA and without 6% NaCl) and, where applicable, were matched with healthy control rats with intact kidneys. We used orthotopic left kidney transplantation, with subsequent removal of the right native kidney 10-14 days after transplantation. Cold ischemia- and warm ischemia- times were 30 minutes each and all isografts were perfused and placed in organ preserving solution Viaspan (Bristol Meyers Squibb, Hoofddorp, Netherlands) prior to transplantation. Kidney transplantation was performed under isoflurane anaesthesia (5% induction, 1.5–2% maintenance) and analgesia was provided straight after and one day after surgery (Buprenorphine, 0.05 mg/kg i.m.). Six weeks after transplantation ts were sacrificed, perfused with 0.9% NaCl via the aorta, and tissues were collected and weighed. Transverse mid LV samples were fixed in 4% paraformaldehyde and the heart apexes were snap frozen and stored at -80°C.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA in the heart apex was isolated using Trizol and measured (NanoDrop spectrophotometer ND-1000, ThermoFischer Scientific Inc.). Polyadenylated mRNA fraction was isolated using Poly(A) Beads (NEXTflex).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
This sample is associated with two SRR at SRA. One contains the mapped reads and the other contains the unmapped reads.
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| Data processing |
RNA-sequencing reads were aligned to the rat reference genome RNO5.0 using STAR version2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups (v1.98). The BAM files are sorted with Sambamba v0.4.5 and transcript abundances are quantified with HTSeq-count version 0.6.1p1 using the union mode
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Raw read counts per gene
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| Submission date |
Oct 18, 2016 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Michal Mokry |
| E-mail(s) |
m.mokry@umcutrecht.nl
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| Organization name |
Wilhelmina Children's Hospital, University Medical Center Utrecht
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| Street address |
Lundlaan 6
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| City |
Utrecht |
| ZIP/Postal code |
3584 EA |
| Country |
Netherlands |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE88910 |
Transcriptomes of rat hearts after kidney transplantation in chronic kidney disease model |
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| Relations |
| BioSample |
SAMN05919523 |
| SRA |
SRX2250935 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2354230_13R25_htseq_counts.txt.gz |
97.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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