 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 09, 2018 |
| Title |
Active translatome profiling with RiboLace in MCF7 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes and associate RNAs by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to obtain a transcriptome-wide snapshot of active translation from eukaryotic in vitro and in vivo systems.
Keywords: translation, RiboLace, polysome profiling, RNA-seq, POL-seq, active translation
|
| |
|
| Overall design |
We performed RiboLace sequencing, polysomal RNA sequencing (POL-seq), total RNA sequencing (RNA-seq) and sequencing of the pull-down with mP-beads. Experiments were performed in duplicate on MCF7 cells in three conditions: control, serum starved (12h), serum starved and EGF treated (12h+4h).
|
| |
|
| Contributor(s) |
Clamer M, Tebaldi T, Viero G |
| Citation(s) |
30355487 |
| |
| Submission date |
Mar 24, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Toma Tebaldi |
| E-mail(s) |
t.tebaldi@unitn.it
|
| Organization name |
University of Trento
|
| Department |
Centre for Integrative Biology
|
| Street address |
via Sommarive n. 9
|
| City |
Povo |
| State/province |
Trento |
| ZIP/Postal code |
38123 |
| Country |
Italy |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (24)
|
| GSM3067233 |
mP beads, EGF treated MCF7 cells, rep 2 |
| GSM3067234 |
mP beads, serum starved MCF7 cells, rep 1 |
| GSM3067235 |
mP beads, serum starved MCF7 cells, rep 2 |
| GSM3067236 |
polysomal RNA, control MCF7 cells, rep 1 |
| GSM3067237 |
polysomal RNA, control MCF7 cells, rep 2 |
| GSM3067238 |
polysomal RNA, EGF treated MCF7 cells, rep 1 |
| GSM3067239 |
polysomal RNA, EGF treated MCF7 cells, rep 2 |
| GSM3067240 |
polysomal RNA, serum starved MCF7 cells, rep 1 |
| GSM3067241 |
polysomal RNA, serum starved MCF7 cells, rep 2 |
| GSM3067242 |
riboLace, control MCF7 cells, rep 1 |
| GSM3067243 |
riboLace, control MCF7 cells, rep 2 |
| GSM3067244 |
riboLace, EGF treated MCF7 cells, rep 1 |
| GSM3067245 |
riboLace, EGF treated MCF7 cells, rep 2 |
| GSM3067246 |
riboLace, serum starved MCF7 cells, rep 1 |
| GSM3067247 |
riboLace, serum starved MCF7 cells, rep 2 |
| GSM3067248 |
total RNA, control MCF7 cells, rep 1 |
| GSM3067249 |
total RNA, control MCF7 cells, rep 2 |
| GSM3067250 |
total RNA, EGF treated MCF7 cells, rep 1 |
| GSM3067251 |
total RNA, EGF treated MCF7 cells, rep 2 |
| GSM3067252 |
total RNA, serum starved MCF7 cells, rep 1 |
| GSM3067253 |
total RNA, serum starved MCF7 cells, rep 2 |
|
| Relations |
| BioProject |
PRJNA445552 |
| SRA |
SRP136387 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112295_MCF7_fpkm_table.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...