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| Status |
Public on Jun 02, 2016 |
| Title |
HTC116 |
| Sample type |
SRA |
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| Source name |
Cell culture
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HTC116
strain: ATCC CCL-247
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole cell total RNA was extracted using QIAZOL (QIAGEN), according to the manufacturers instructions, after which 15µg of total RNA per sample was subjected to native agarose gel electrophoresis and the LSU and SSU rRNA subsequently isolated and gel purified, using the NucleoSpin Gel and PCR Clean-up kit (MACHEREY-NAGEL) according to the manufacturers instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5'- phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 1.2.1
Mapping to rRNA reference sequence using Bowtie2 v. 2.1.0
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: gi|555853|gb|U13369.1|HSU13369 Human ribosomal DNA complete repeating unit with the following changes G1639-del, C1646-del and gi|555853|gb|U13369.1|HSU13369 Human ribosomal DNA complete repeating unit with the following changes A60G, C253G, G870C, G3192C, C3215G, G3216C, C4113G, G4454A
Supplementary_files_format_and_content: MS Excel files. Contains 5' and 3' read count over the rRNA sequence and the calculated RiboMeth-seq score
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| Submission date |
Dec 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolai Krogh |
| E-mail(s) |
nicolaikj@sund.ku.dk
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| Organization name |
University of Copenhagen
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| Department |
Department of Cellular and Molecular Medicine
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| Lab |
RNA Group - Prof. Henrik Nielsen
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| Street address |
Blegdamsvej 3B
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| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE76393 |
Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity |
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| Relations |
| BioSample |
SAMN04376637 |
| SRA |
SRX1507744 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1985880_R_2015_06_30_16_15_31_HTC116_RMS.xlsx |
1.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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