GSE39872
GSE GEOLIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (HTS)
Organism:
Homo sapiens
Platform:
GPL9052
Samples:
8
Experiment Types:
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Submitted:
Aug 03 2012
Last Updated:
May 15 2019
Status:
Public on Sep 10 2012
Contact:
Gene,,Yeo (UCSD)
Relations
SubSeries of: GSE39873
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA171939
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP014671
Summary
LIN28 is a conserved RNA binding protein implicated in pluripotency, reprogramming and oncogenesis. Previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through cross-linking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28 binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions.
Overall Design
CLIP-seq for LIN28-V5 in stable human Flp-In-293 cells, and LIN28 in hES cells; strand-specific mRNA-seq for uninfected, control KD, and LIN28 KD human H9 ES cells; and strand-specific smallRNA-seq for uninfected, control KD, and LIN28 KD human H9 ES cells.
Analysis (3 steps)
View Data Processing
Processing steps for GSE39872
- Read mapping from CLIP-seq experiments and data processing was performed as published (Polymenidou et al., 2011).
- Briefly, reads were processed and mapped to the human genome (hg18 http://genome.ucsc.edu; Bowtie version 0.12.2, with parameters -q -p 4 -e 70 -y -l 25 -n 2 -m 5 --best --strata) and assigned to 21,605 genes (as annotated previously (Yeo et al., 2009)).
- LIN28ES_CLIPseq_clusters.BED: hg18
Supplementary Files (1)
GSE39872_RAW.tar
Download
Dataset Citations (1)
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
PMID 22959275
· 2012
· Molecular cell
Melissa L Wilbert, Stephanie C Huelga, Katannya Kapeli, Thomas J Stark, Tiffany Y Liang, Stella X Chen, Bernice Y Yan, Jason L Nathanson, Kasey R Hutt, Michael T Lovci, Hilal Kazan, Anthony Q Vu, Katlin B Massirer, Quaid Morris, Shawn Hoon, Gene W Yeo
SRA Experiments (8) and Runs (9)
Total: 2796 MBGSM980593: LIN28ES CLIPseq; Homo sapiens; RNA-Seq
Sample: SRS352780
BioProject: PRJNA171939
BioSample: SAMN01096645
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer
Organism: Homo sapiens
Sample attributes
source_name: H9 human ES cells
cell line: H9
antibody: LIN28 (Abcam ab46020)
antibody manufactuer: Abcam
antibody catalog number: ab46020
Original files (1)
H9 human ES cells
GSM980594: LIN28V5 CLIPseq; Homo sapiens; RNA-Seq
Sample: SRS352781
BioProject: PRJNA171939
BioSample: SAMN01096646
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: human LIN28-V5 293 stable cells
cell line: HEK293
antibody: V5 (Sigma V8137)
antibody manufactuer: Sigma
antibody catalog number: V8137
Original files (1)
human LIN28-V5 293 stable cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531465 | 10992525 | 395730900 | 287.35 | SRR531465 | SRA |
GSM980595: uninfected H9 RNAseq; Homo sapiens; RNA-Seq
Sample: SRS352782
BioProject: PRJNA171939
BioSample: SAMN01096647
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: H9 human ES cells
cell line: H9
Original files (1)
H9 human ES cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531466 | 19413017 | 970650850 | 668.85 | SRR531466 | SRA |
GSM980596: LIN28KD H9 RNAseq; Homo sapiens; RNA-Seq
Sample: SRS352783
BioProject: PRJNA171939
BioSample: SAMN01096648
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: H9 human ES cells
cell line: H9
treatment: LIN28 shRNA (TRCN0000102579; Open Biosystems)
Original files (1)
H9 human ES cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531467 | 18347885 | 917394250 | 627.78 | LIN28KD_H9_rnaseq.fastq, SRR531467 | SRA |
GSM980597: ControlKD H9 RNAseq; Homo sapiens; RNA-Seq
Sample: SRS352784
BioProject: PRJNA171939
BioSample: SAMN01096649
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: H9 human ES cells
cell line: H9
treatment: GFP shRNA
Original files (1)
H9 human ES cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531468 | 14331910 | 716595500 | 501.08 | SRR531468 | SRA |
GSM980598: Flp-In-293 small NA; Homo sapiens; RNA-Seq
Sample: SRS352785
BioProject: PRJNA171939
BioSample: SAMN01096650
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: human Flp-In-293 cells
cell line: HEK293
treatment: Untreated Flp-In-293
Original files (1)
human Flp-In-293 cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531469 | 2845252 | 102429072 | 52.7 | SRR531469, SRR531469.sralite | SRA |
GSM980599: H9 small NA; Homo sapiens; RNA-Seq
Sample: SRS352786
BioProject: PRJNA171939
BioSample: SAMN01096651
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: H9 human ES cells
cell line: H9
treatment: Untreated H9 human ES cells
Original files (1)
H9 human ES cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531470 | 7184143 | 287365720 | 206.68 | SRR531470 | SRA |
GSM980600: LIN28V5-293 small NA; Homo sapiens; RNA-Seq
Sample: SRS352787
BioProject: PRJNA171939
BioSample: SAMN01096652
Platform: ILLUMINA
Instrument: Illumina Genome Analyzer II
Organism: Homo sapiens
Sample attributes
source_name: human LIN28-V5 293 stable cells
cell line: HEK293
treatment: LIN28 Flp-In-293
Original files (1)
human LIN28-V5 293 stable cells
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR531471 | 2293247 | 82556892 | 42.95 | SRR531471, SRR531471.sralite | SRA |
Linked Publications (1)
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012
Data Files (9)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | LIN28KD_H9_rnaseq.fastq | RNA-Seq | 627.8 MB | link | |||
| — | SRR531463 | RNA-Seq | 51.5 MB | link | |||
| — | SRR531464 | RNA-Seq | 357.0 MB | link | |||
| — | SRR531465 | RNA-Seq | 287.3 MB | link | |||
| — | SRR531466 | RNA-Seq | 668.8 MB | link | |||
| — | SRR531468 | RNA-Seq | 501.1 MB | link | |||
| — | SRR531469 | RNA-Seq | 52.7 MB | link | |||
| — | SRR531470 | RNA-Seq | 206.7 MB | link | |||
| — | SRR531471 | RNA-Seq | 42.9 MB | link |