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| Status |
Public on Apr 15, 2013 |
| Title |
Kidney Frozen 2 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue storage: Frozen
tissue: Kidney
histology: Clear Cell Carcinoma
Sex: F
age: 67
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| Treatment protocol |
Eight paired human malignant tissue samples were received. Remnant surgical tissues were taken after diagnostic samples were secured from patients.Surgical specimens were transported from the operating rooms to Tissue Procurement, examined under a pathologist’s supervision and preserved within 5 to 57 recorded minutes. Paired tissue samples selected for research were either immediately snap frozen in liquid nitrogen and placed in a -80 °C freezer for monitored storage or fixed in 10% buffered formalin for up to 24 hours and then processed into a paraffin embedded block and stored at room temperature .
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from FFPE samples were extracted using Recover All Total Nucleic Acid Isolation Kit (Life Technologies Corporation, Carlsbad, CA). The microRNA samples from the fresh frozen samples were extracted using PureLink™ miRNA Isolation Kit (Life Technologies Corporation, Carlsbad, CA).
Small RNAs from FFPE and fresh frozen samples were prepared for SOLiD sequencing as follows: the total RNA samples were processed by the flashPAGE fractionator (Ambion) and flashPAGE Clean-Up Kit (Ambion). The enriched small RNA was then processed according to the SOLiD Small RNA Expression Kit protocol (Applied Biosystems). The purified small RNAs were ligated with 5' and 3' adapter mix using RNA ligase. The ligated products (40–60 bases in length) were reverse transcribed and purified on Novex 10% TBE-Urea gel. Subsequently, 15–18 cycles of PCR were performed by amplifying the purified cDNA with barcoded PCR primer sets provided in the kit, which differed by a unique 6-nucleotide sequence. The amplified products were loaded on Novex 6% TBE gel (Invitrogen) and the gel bands containing 110 to 130bp fragments were excised. The amplified products were purfied from excised gel band, amplified by emulsion PCR, then loaded on Applied Biosystems SOLiD 4 next generation high throughput sequencing system for data acquisition. The quality of the samples and libraries were verified on the Agilent Bioanalyzer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
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| Data processing |
The linker sequences of small RNA libraries were removed using cutadapt software (http://code.google.com/p/cutadapt/) under default parameters.
After removing linker sequences and filtrating by different small RNA databases, reads were mapped with miRBase V16.
All reads of each sample were aligned against miRBase and the hg19 reference genome using SOLiD™ small RNA Analysis pipeline (http://solidsoftwaretools.com), and were normalized as reads per million (RPM).
Sequences with expression value below 5 RPMs were considered not detected.
Genome_build: miRBase version 16
Supplementary_files_format_and_content: txt file contained 250 microRNA expression information
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| Submission date |
Apr 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
wei meng |
| E-mail(s) |
wei.meng@osumc.edu
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| Organization name |
The Ohio State University
|
| Department |
Radiation Oncology
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| Street address |
400 W12 street
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| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE45740 |
Comparison of MicroRNA deep sequencing of matched formalin-fixed paraffin-embedded and fresh frozen cancer tissues |
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| Relations |
| SRA |
SRX259631 |
| BioSample |
SAMN01997772 |
| 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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