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| Status |
Public on Oct 30, 2018 |
| Title |
knockout2 |
| Sample type |
SRA |
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| Source name |
whole embryonal mouse kidney
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: embryonal stage 16.5
genotype: DROSHA knockout
tissue: embryonal kidney
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| Extracted molecule |
total RNA |
| Extraction protocol |
kidneys were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
microRNA libraries were prepared for sequencing using standard BGI protocols
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
We use AASRA to map clean reads to reference genome and other sRNA database, except Rfam which was performanced by using cmsearch
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
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| Submission date |
Jul 25, 2018 |
| Last update date |
Oct 30, 2018 |
| Contact name |
Philip Kruber |
| Organization name |
University of Wuerzburg
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| Department |
Physiological Chemistry
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| Lab |
Developmental Biochemistry
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| Street address |
Am Hubland
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| City |
Wuerzburg |
| State/province |
Bayern |
| ZIP/Postal code |
97074 |
| Country |
Germany |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE117665 |
Loss or oncogenic mutation of DROSHA impairs kidney development and function, but is not sufficient for Wilms tumor formation |
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| Relations |
| BioSample |
SAMN09715167 |
| SRA |
SRX4457258 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3305845_knockout2exp.txt.gz |
28.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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