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| Status |
Public on Jul 15, 2013 |
| Title |
RNAseq_Sucrose_Gradient_noarsenite_fraction1 |
| Sample type |
SRA |
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| Source name |
293S cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: no treatment (control)
cell line: 293S
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| Treatment protocol |
Where indicated, treated with 1 mM sodium arsenite for 30 minutes
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| Growth protocol |
293S cells were grown in DMEM + 10% FBS + penicillin/streptomycin, in adherent monolayer, to ~70% confluency.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol and NSR method
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
sucrose-gradient-fractionated total RNA
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| Data processing |
Basecalling with Illumina RTA 1.13.48
Reads were processed as for RNA-seq in subseries1-3, with an added initial mapping step to the ERCC spike-in sequences. ERCC scaling factors were calculated by linear regression of length-corrected counts for each ERCC RNA between samples. Non-ERCC reads were then mapped further as above. Exonic read counts were collapsed by gene, filtered for genes with 10 or more counts across all fractions for each condition (+/- arsenite), normalized to ERCC scaling factors, and further normalized to a total abundance of 1 across all fractions within a condition.
hg19
tab-delimited text file containing, per gene, normalized abundances in sucrose gradient fractions +/- arsenite, and the center-of-mass (COM) and COM shift upon arsenite
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| Submission date |
Feb 18, 2013 |
| Last update date |
Mar 04, 2023 |
| Contact name |
Fedor Karginov |
| E-mail(s) |
karginov@ucr.edu
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| Organization name |
UC Riverside
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| Department |
MCSB
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| Street address |
900 University Ave
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| City |
Riverside |
| State/province |
California |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platform ID |
GPL15433 |
| Series (2) |
| GSE44379 |
Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 4) |
| GSE44404 |
Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates |
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| Relations |
| SRA |
SRX241878 |
| BioSample |
SAMN01922235 |
| 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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