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GSE117294

GSE GEO
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Large-scale tethered function assays identify factors that regulate mRNA stability and translation

Organism: Homo sapiens
Platform: GPL20301
Samples: 118
Experiment Types:
Other Expression profiling by high throughput sequencing
Submitted: Jul 18 2018
Last Updated: Jul 02 2021
Status: Public on Aug 18 2020
Contact: En-Ching,,Luo (UCSD)

Relations

SuperSeries of: GSE117290 SuperSeries of: GSE117291 SuperSeries of: GSE117293 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA482133

Summary

This SuperSeries is composed of the SubSeries listed below.

Overall Design

Refer to individual Series

Analysis (5 steps)

View Data Processing
Processing steps for GSE117294
  1. RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i).
  2. Reads did not map to repetitive elements were then mapped to the human genome (hg19).
  3. Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
  4. Differential expression was calculated using DESeq2 version 1.10.1
  5. The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.

Supplementary Files (1)

GSE117294_RAW.tar Download
GEO Samples (118)
GSM3290512 GSM3290513 GSM3290514 GSM3290515 GSM3290516 GSM3290517 GSM3290518 GSM3290519 GSM3290520 GSM3290521 GSM3290522 GSM3290523 GSM3290532 GSM3290533 GSM3290534 GSM3290535 GSM3290536 GSM3290537 GSM3290538 GSM3290539 GSM3290540 GSM3290541 GSM3290542 GSM3290543 GSM3290544 GSM3290545 GSM3290546 GSM3290547 GSM3290548 GSM3290549 GSM3290550 GSM3290551 GSM3290552 GSM3290553 GSM3290554 GSM3290555 GSM3290556 GSM3290557 GSM3290558 GSM3290559 GSM3290560 GSM3290561 GSM3290562 GSM3290563 GSM3290564 GSM3290565 GSM3290566 GSM3290567 GSM3290568 GSM3290569 GSM3290570 GSM3290571 GSM3290572 GSM3290573 GSM3290574 GSM3290575 GSM3290576 GSM3290577 GSM3290578 GSM3290579 GSM3290580 GSM3290581 GSM4512262 GSM4512263 GSM4512264 GSM4512265 GSM4512266 GSM4512267 GSM4512268 GSM4512269 GSM4512270 GSM4512271 GSM4512272 GSM4512273 GSM4512274 GSM4512275 GSM4512276 GSM4512277 GSM4512278 GSM4512279 GSM4512280 GSM4512281 GSM4512282 GSM4512283 GSM4512284 GSM4512285 GSM4512286 GSM4512287 GSM4512288 GSM4512289 GSM4512290 GSM4512291 GSM4512292 GSM4512293 GSM4512294 GSM4512295 GSM4512296 GSM4512297 GSM4512298 GSM4512299 GSM4512300 GSM4512301 GSM4512302 GSM4512303 GSM4512304 GSM4512305 GSM4512306 GSM4512307 GSM4512308 GSM4512309 GSM4512310 GSM4512311 GSM4512312 GSM4512313 GSM4512314 GSM4512315 GSM4512316 GSM4512317

Dataset Citations (1)

Large-scale tethered function assays identify factors that regulate mRNA stability and translation.
PMID 32807991 · 2020 · Nature structural & molecular biology
En-Ching Luo, Jason L Nathanson, Frederick E Tan, Joshua L Schwartz, Jonathan C Schmok, Archana Shankar, Sebastian Markmiller, Brian A Yee, Shashank Sathe, Gabriel A Pratt, Duy B Scaletta, Yuanchi Ha, David E Hill, Stefan Aigner, Gene W Yeo

Linked Publications (1)

Large-scale tethered function assays identify factors that regulate mRNA stability and translation.
Nature structural & molecular biology · 2020