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Status |
Public on Apr 28, 2010 |
Title |
G547N |
Sample type |
SRA |
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Source name |
normal cervix
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Organism |
Homo sapiens |
Characteristics |
diagnosis: normal tissue: normal cervix
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Treatment protocol |
not applicable
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Growth protocol |
not applicable
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Extracted molecule |
total RNA |
Extraction protocol |
Small RNA isolation was performed using mirVana miRNA isolation kit (Applied Biosystems/Ambion, Austin, TX). Purified small RNAs were ligated to the 3’-adaptor [“Linker-1”, IDT Inc., Coralville, IA] and 5’ adaptor [5’-ACGCTCTTCCGATCTv-3’ (uppercase, DNA; v=barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT Inc., Coralville, IA)] oligonucleotides. Products from the second ligation were gel-purified and reverse transcribed using the RT primer [5'-ATTGATGGTGCCTACAG-3’]. cDNA was amplified with 16-20 PCR cycles, using a forward primer 5'- GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5’-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG-3', to produce sequencing libraries that were subjected to Solexa/Illumina sequencing platform.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina Genome Analyzer |
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Description |
5' monophosphate dependent small RNA cloning aaa
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Data processing |
frequencies of known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)
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Submission date |
Apr 13, 2010 |
Last update date |
Jun 11, 2013 |
Contact name |
Sam Guoping Gu |
E-mail(s) |
ggu@dls.rutgers.edu
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Organization name |
Rutgers University
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Department |
Molecular Biology and Biochemistry
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Lab |
Sam Gu
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Street address |
Nelson Labs A125, 604 Allison Road
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City |
Piscataway |
State/province |
NJ |
ZIP/Postal code |
08854 |
Country |
USA |
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Platform ID |
GPL9052 |
Series (1) |
GSE20592 |
Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumors and matched controls |
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Relations |
BioSample |
SAMN02196143 |
Supplementary file |
Size |
Download |
File type/resource |
GSM532875_G547N.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
Processed data are available on Series record |
Raw data provided as supplementary file |
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