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| Status |
Public on Dec 20, 2011 |
| Title |
Cyt footprints |
| Sample type |
SRA |
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| Source name |
HEK293_Cyt_footprints
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
sample fraction: Purified cytoplasm
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| Treatment protocol |
Detergent fractionation of cytosol and ER
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| Growth protocol |
Clutured in DMEM + 10% FBS at 37C, 5% CO2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome footprints were generated by nuclease treatment of polyribosomes. The mRNA footprints were purified by centrifugation. In parallel, mRNAs were enriched by treatment of total RNA with RiboMinus, then treated with Rnase III. Each library was generated according to standard SOLiD library preparation. Briefly, primers were ligated onto RNAs and then cDNA was generated by reverse transcription. cDNA was purified by gel electrophoresis, amplified, then emusified to beads and sequenced.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| Description |
small RNA
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| Data processing |
Mapped to Refseq genes using Bowtie; mRNAs >10 RPKM were considered.
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| Submission date |
Aug 19, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
David Reid |
| Organization name |
Duke University
|
| Department |
Biochemistry
|
| Lab |
Nicchitta
|
| Street address |
436 Nanaline Duke Bldg., Box 3709 DUMC
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE31539 |
Ribosome footprinting in the cytosol and endoplasmic reticulum |
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| Relations |
| SRA |
SRX093609 |
| BioSample |
SAMN00714438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM782788_NACF-mapped.map.gz |
31.8 Mb |
(ftp)(http) |
MAP |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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