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| Status |
Public on Apr 18, 2019 |
| Title |
FS_1157.2_Saline |
| Sample type |
SRA |
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| Source name |
MUC1 kidney disease mouse_saline_kidney
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| Organism |
Mus musculus |
| Characteristics |
strain: MUC1 kidney disease mouse model
age: 8 month-old
Sex: male
treatment: saline (vehicle) daily for 7 days
tissue: Kidney
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| Treatment protocol |
BRD4780 (50mg/kg) or vehicle control were applied to 8 month old male knock-in mice daily during 7 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from a sagittal section of a half-kidney. Kidney tissue was homogenized using tissue homogenizer in 1 mL of TRIzol™ Reagent. Following 5 min incubation, 0.2 mL chloroform was added, and samples were vigorously mixed for 30 sec, then centrifuged at 12,000 x g at 4°C for 15 min. The upper aqueous phase containing RNA was then vigorously mixed with 0.5 mL of isopropanol for 30 sec. After 10 min incubation at RT, the samples were centrifuged at 12,000 x g at 4°C for 10 min. The pellet was resuspended in 1 mL of 75% ethanol and centrifuged at 12,000 x g 4°C for 5 min. The RNA pellet was then air dried for 15 min, dissolved in 50 μL of Nuclease-Free Water, treated with DNase I, Amplification Grade following the manufacturer’s protocol and assessed for yield and purity by NanoDrop™ 2000.
Concentrations of purified RNA were measured with the QuantiTTM RiboGreen® RNA Assay Kit and normalized to 5 ng/μL. An automated variant of the Illumina TruSeqTM Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA. This method preserves strand orientation of the RNA transcript and uses oligo dT beads to select mRNA from the total RNA sample. Following cDNA synthesis and enrichment, cDNA libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina HiSeq2500 sequencing system (2x101 Bp Reads) software used for basecalling. The provided data from Sequencing platform are de-multiplexed and aggregated Picard Bam files.
Bam files received from sequencing platform were reverted to fastq files followed by alignment of paired end reads to the mm10 mouse or hg19 human reference genome using STAR v2.5.2b.
Quality Control metrics were obtained using RNA-SeQC v2.3.1.
Expression levels were estimated by running RSEM v1.3.0 with default parameters on these alignments.
Genome_build: mm10
Supplementary_files_format_and_content: Raw expression levels produced by RSEM
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| Submission date |
Apr 17, 2019 |
| Last update date |
Apr 18, 2019 |
| Contact name |
Moran Dvela Levitt |
| E-mail(s) |
[email protected]
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| Organization name |
Broad Institute
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| Lab |
Greka Lab
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE129941 |
RNA sequencing in kidneys of MUC1 Kidney Disease mouse model with and without treatment |
| GSE129971 |
Small molecule targets TMED9, promotes lysosomal degradation to reverse proteinopathy |
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| Relations |
| BioSample |
SAMN11446122 |
| SRA |
SRX5702792 |
| 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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