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| Status |
Public on Jun 25, 2010 |
| Title |
HeLa Degradome 4 |
| Sample type |
SRA |
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| Source name |
HeLa cell
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| Organism |
Homo sapiens |
| Characteristics |
rnai treatment: xrn-1
data type: Degradome
cell line: HeLa
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| Extracted molecule |
total RNA |
| Extraction protocol |
Linker sequences were removed, requiring a match to at least five of the six most proximal linker nucleotides. After filtering out tags shorter than 20 nt, degradome tags were mapped to RNAs annotated in the ENSEMBL (http://www.ensembl.org/), requiring a perfect match. To find “multiple loci tags,” and tags that did not map to annotated RNAs, filtered tags were mapped to the human genome (hg18, http://genome.ucsc.edu/).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
PolyA selection
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| Data processing |
Linker sequences were removed, requiring a match to at least five of the six most proximal linker nucleotides. After filtering out tags shorter than 20 nt, degradome tags were mapped to RNAs annotated in the ENSEMBL (http://www.ensembl.org/), requiring a perfect match. To find “multiple loci tags,” and tags that did not map to annotated RNAs, filtered tags were mapped to the human genome (hg18, http://genome.ucsc.edu/).
sequence reads are summarized as frequency counts
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| Submission date |
Jun 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin-Wu Nam |
| E-mail(s) |
jwnam@wi.mit.edu
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| Organization name |
Whitehead Institute
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| Lab |
Bartel lab
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| Street address |
Nine Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE22068 |
Expanding the MicroRNA Targeting Code: A Novel Type of Site with Centered Pairing |
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| Relations |
| SRA |
SRX022201 |
| BioSample |
SAMN00015215 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM548633_HeLa_4_TagCount.processed.txt.gz |
4.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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