|
| Status |
Public on Jan 29, 2014 |
| Title |
HeLa_total_PAL_only |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
|
| Treatment protocol |
RNA-seq: Cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation. Ribosome profiling: Cell extracts were processed as described in Subtelny et al., 2014 (GSE52809). PAL-seq: Polyadenylated ends in total RNA were ligated to a biotinylated adaptor, then partially digested with RNase T1. The resulting fragments were size-selected (104-750 nt), captured on streptavidin beads, and used for library preparation.
|
| Growth protocol |
Each sample was grown or maintained in accordance with standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
PAL-Seq
processed data file: HeLa_total.txt
processed data file: HeLa_total_PAL_norm_intensities.txt.gz
processed data file: HeLa_total_PAL_raw_intensities.txt.gz
|
| Data processing |
Raw read files were stripped of adaptor and mapped to the appropriate species' genome and/or transcriptome.
RNA-seq and ribosome profiling reads mapping within the coding sequence of an annotated gene, excluding the first 50 nucleotides of the coding sequence, were assigned to that gene and used to calculate its RPKM value. Poly(A)-tail length measurements were generated using PAL-seq tags that mapped within the 3' UTR of an annotated gene.
Genome_build: Human: hg18; Mouse: mm9; Zebrafish: danRer7; Drosophila: dm3; Arabidopsis: tair10; S. cerevisiae: sacCer3; S. pombe: Spombe1; Xenopus: Unigene
Supplementary_files_format_and_content: One set of processed data files contains abundance and poly(A)-tail length measurements for each gene. Another set contains raw fluorescence intensities for each base for each cycle of sequencing-by-synthesis and streptavidin flow-in for each sequencing cluster. Another set contains normalized streptavidin fluorescence intensities for each sequencing cluster.
|
| |
|
| Submission date |
Jan 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Eichhorn |
| E-mail(s) |
eichhorn@wi.mit.edu
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Department |
Biology
|
| Lab |
Bartel
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE52809 |
Poly(A)-tail profiling reveals an embryonic switch in translational control |
|
| Relations |
| BioSample |
SAMN02598799 |
| SRA |
SRX451690 |
