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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 28, 2013 |
| Title |
2P-Seq fraction 1 |
| Sample type |
SRA |
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| Source name |
3T3 cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: 3T3 cells
treatment: 2P protocol and sucrose gradient fractionation
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| Extracted molecule |
total RNA |
| Extraction protocol |
2P-Seq, barcoded
sucrose gradient fractionation, poly(A)-selected RNA
2P-Seq: partial digested with RNase T1, poly(A)-primed reverse transcription, circularization, PCR and sequencing from putative poly(A) tail
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were aligned the mouse mm9 genome using Bowtie. 3P-Seq reads were used to annotate poly(A) sites. Reads within +/- 20 nt of these annotated poly(A) sites were combined when calculating read totals for 2P-Seq datasets.
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file: poly(A) site annotations, reads, half-lives, translation rates per poly(A) site
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| Submission date |
Feb 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Noah Spies |
| Organization name |
Stanford University
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| Department |
Pathology
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| Lab |
Arend Sidow
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| Street address |
300 Pasteur Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE44698 |
Global analyses of how 3' UTR-isoform choice influences mRNA stability and translational efficiency |
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| Relations |
| SRA |
SRX246090 |
| BioSample |
SAMN01931915 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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