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| Status |
Public on Nov 16, 2018 |
| Title |
kidney sample 17 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney (glomerular and tubular portions)
disease state: Healthy
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| Extracted molecule |
total RNA |
| Extraction protocol |
Collected tissue was immersed in RNAlater solution at 4°C for several hours prior to being stored at -80°C in RNAlater. Tissue was thawed on ice, placed in RNAlater, and manually microdissected for glomerulus and tubule compartments.
RNA quality was assessed with the Agilent Bioanalyzer 2100. Only samples with RIN scores above 7 and a minimum total RNA of 100 ng were used for cDNA production. Non-strand specific, polyA+ selected RNA-seq libraries were generated using the Illumina TruSeq protocol. Libraries were sequenced to a median depth of 35 million 100-bp single end reads.
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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's CASAVA 1.8.2 was used for basecalling.
After first assessing sequence quality using FastQC and then trimming the adaptor and lower-quality bases using Trim-galore, RNA-seq reads were aligned to the human genome (hg19/GRCh37) using STAR (v2.4.1d) based on GENCODE v19 annotations.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include log2 (RPKM) for each Sample
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| Submission date |
May 30, 2018 |
| Last update date |
Nov 16, 2018 |
| Contact name |
Chengxiang Qiu |
| E-mail(s) |
cxqiu@uw.edu
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| Organization name |
University of Washington
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| Department |
Genome Sciences
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| Lab |
Jay Shendure
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| Street address |
William H. Foege Hall, 3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE115098 |
Kidney compartment specific eQTL studies highlight causal genes and pathways for renal disease development |
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| Relations |
| BioSample |
SAMN09282105 |
| SRA |
SRX4141439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3165136_sample_17.txt.gz |
327.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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