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| Status |
Public on Sep 29, 2013 |
| Title |
K6C miRNA-Seq |
| Sample type |
SRA |
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| Source name |
kidney cancer tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney cancer
tumor stage: T1N0M0
pathology: renal clear cell
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ccRCC and normal adjacent tissues by TRIZOL reagent (Invitrogen, US) according to the manufacture¡¯s protocol. In breif, 50mg tissue was milled in liquid nitrogen and lysised in 1 ml TRIZOL reagent. Adding 0.2 ml of chloroform, vortexing, centrifuging,and transfering upper aqueous phase to a fresh tube following precipitating by isopropyl alcohol and washing with 75% ethanol.Then, tatal RNA was air-dryed and dissolved in DEPC-treated water.
5μg of total RNA was used in miRNA sequencing. In short, after ligation of both 5’adapter and 3’adapter, Reverse transcription by Superscript II was performed at 42℃ for 1 h and 70℃ for 15 min. A separate-15-cycles reaction was run using the following program: 98℃ 30 sec, followed by 15 cycles of 98℃ for 10 sec, 72℃ for 15 sec, and then 72℃ for 10 min. The PCR products were run on a 6% PAGE gel and the ~92bp DNA band was excised and purified using Spin-X filter column ethanol precipitation. Finally, miRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer Ⅱ following the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
small RNA
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| Data processing |
miRNA analysis was performed using RNAFold software version 1.7.1 using the following criteria:
miRNA:
1.the sequences of tags which don't include "N" was reserved, for example,"ATGTCGTNACT" was filtered.
2.the length of tags should between 18-30 nt.
3.there could not have more than 6 bases which are smaller than Q13 in a tag.
version of genome annotations used is hg19
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| Submission date |
Sep 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
JACK LI |
| E-mail(s) |
[email protected]
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| Organization name |
beijing genomics insititute
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| Street address |
beishangongyequ
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| City |
shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE24457 |
miRNA sequencing of 10 pairs samples between kidney normal tissues and cancer tissue |
| GSE24952 |
Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma |
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| Relations |
| SRA |
SRX029302 |
| BioSample |
SAMN00116710 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM602584_K6Cmatch_hairpin.aln.txt.gz |
94.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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