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| Status |
Public on May 07, 2014 |
| Title |
Total cell small RNA preparation |
| Sample type |
SRA |
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| Source name |
Human cervical adenocarcinoma cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
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| Growth protocol |
HeLa cervical adenocarcinoma cells (CCL-2, ATCC) were maintained in DMEM supplemented with 10% FCS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Subcellular fractionation was carried out essentially as in Bai and Laiho (Efficient sequential recovery of nucleolar macromolecular components. Proteomics, 12, 3044-3048, 2012). Total RNA was extracted from whole cells and the isolated cellular compartments using the TRIzol. Approximately 400 µg RNA from each compartment was used to prepare cDNA libraries. Small RNAs (less than 200 nt) were isolated from the total RNA samples using mirVana Isolation Kit and separated on denaturing 15% polyacrylamide gel (15% PAA, 19:1 acrylamide/bis, 7 M urea) to purify RNAs in the approximate range of 10 - 40 nt. The sRNA size range was confirmed and the RNA was quantified using Bioanalyzer with Agilent Small RNA kit.
cDNA libraries were constructed using the Ion Torrent RNA-seq kit v1 for small RNA libraries, and their purity and concentration was confirmed using Bioanalyzer with the Agilent DNA kit. sRNA library sequencing was performed on a 314 chip on a Ion Torrent sequencing platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent PGM |
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| Description |
10-40 nt small RNA
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| Data processing |
Ion Torrent base calling with instrument-provided software, standard options
tmap version 0.1.3 alignment with default options
database: hg19
classification into miRNA, snoRNA, snRNA, and other
Genome_build: hg19
Supplementary_files_format_and_content: Xls files represent small RNA read distribution, annotation, identification of snoRNA-derived small RNA reads, and miRNAs present in subcellular compartments.
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| Submission date |
Aug 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marikki Laiho |
| Organization name |
The Johns Hopkins University School of Medicine
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| Department |
Department of Radiation Oncology and Molecular Radiation Sciences
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| Street address |
1550 Orleans Street, CRB II, Room 444
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE50057 |
Small RNA deep sequencing of cellular subcompartments |
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| Relations |
| BioSample |
SAMN02324152 |
| SRA |
SRX337521 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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