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| Status |
Public on Sep 21, 2019 |
| Title |
Female.CLK.PT.3 |
| Sample type |
SRA |
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| Source name |
Proximal tubule
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| Organism |
Mus musculus |
| Characteristics |
gender: Female
age: Wk12
disease state: contralateral kidney (healthy control)
tissue: Proximal tubule
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| Extracted molecule |
total RNA |
| Extraction protocol |
[TRAP-seq protocol] Kidneys were removed and decapsulated after perfusion with iced-cold PBS. Renal cortex was rapidly dissected and minced on ice. Samples were then transferred to 1 ml of ice-cold extraction buffer for homogenization. Streptavidin Dyanbeads, which were freshly coated with monoclonal anti-GFP antibodies (clone 19C8 and clone 19F7) through biotinylated Protein L, were added to the kidney postmitochondrial supernatants and incubated at 4°C under end-over-end rotation for 4 hours for immunoprecipitation. After that, beads were collected on a magnetic rack, and the unbound fraction of samples were taken. Collected beads were then washed 4 times by high-salt washing buffer. Bound fractions of samples were then extracted by Qiagen RNeasy lysis buffer. All of the bound and unbound fractions of RNA were then purified by RNeasy MinElute Cleanup Kit with in-column DNase digestion
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
TRAP-seq
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| Data processing |
Sequencing reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was accessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: Ensembl release 76 assembly
Supplementary_files_format_and_content: Raw counts, RPKMs.
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| Submission date |
Jan 13, 2019 |
| Last update date |
Sep 21, 2019 |
| Contact name |
Haojia Wu |
| E-mail(s) |
haojiawu@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Renal Division/Internal Medicine
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| Lab |
Humphreys Lab
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| Street address |
600 S Euclid Ave
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| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
MO 63110 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE125015 |
Translational profiling of proximal tubule in fibrotic kidney |
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| Relations |
| BioSample |
SAMN10737091 |
| SRA |
SRX5245673 |
| 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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