GSE109423
GSE GEO Potentially relatedA transcriptome-wide divergence in protein translation scales with LIN28B expression
Relations
Summary
We report the mapping of LIN28B binding to RNA in HEK293A at various LIN28B expression levels using enhanced CLIP. We provide small RNA sequencing data regarding miRNA expression in HEK293A and those miRNAs bound by AGO2. We also profile the effect of LIN28B expression on transcriptome-wide ribosome occupancy in HEK293A via RNA-seq. Finally, we provide orthogonal regulatory data by profiling the effect of LIN28B expression on transcriptome-wide ribosome occupancy in NIH3T3 via RNA-seq.
Overall Design
Examination of LIN28B binding using enhanced CLIP via 2 biological replicates of RNA fragments derived from LIN28B immunoprecipitation and 2 control input replicates for 5 LIN28B expression conditions. X0 is lin28b knockout. X1 through X4 are increasing levels of lin28b expression (X1 < X2 < X3 < X4). X1 through X4 lie within the naturally occurring spectrum of lin28b expression from other cell types such as HepG2, NTera2 and iPSC. Examination of small RNAs expressed in HEK293A and those specifically bound by AGO2, in the presence or absence of LIN28B or transfected let-7a miRNA, single replicate. Examination of changes in transcriptome-wide ribosome occupancy in HEK293A via total RNA (2 replicates) and ribosome-bound RNA (2 replicates) for 5 different LIN28B expression conditions. Experimental design for examining changes in transcriptome-wide ribosome occupancy in NIH3T3 were the same as for HEK293A.
Analysis (6 steps)
View Data Processing- Library strategy: ribosome profiling
- Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
- Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences.
- Remaining reads were mapped to the appropriate genome build using STAR aligner
- RPKM values were calculated for all polysome and rnaseq samples.
- For eCLIP samples, read densities were calculated to identify eCLIP peaks. eCLIP peaks were identified using clipper
Supplementary Files (4)
GEO Samples (30)
Dataset Citations (2)
Potentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.
Data Files (10)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | b8p100_smallrnaseq_hek293_ko_l7_total_S23_L002_R1_001.… | ncRNA-Seq | 457.6 MB | link | |||
| — | b8p100_smallrnaseq_hek293_ko_wt_total_S21_L002_R1_001.… | ncRNA-Seq | 563.8 MB | link | |||
| — | b8p100_smallrnaseq_hek293_x3_l7_total_S24_L002_R1_001.… | ncRNA-Seq | 509.1 MB | link | |||
| — | b8p100_smallrnaseq_hek293_x3_wt_total_S22_L002_R1_001.… | ncRNA-Seq | 617.8 MB | link | |||
| — | b8p37_a9_polysome_let7_S6_L003_R1_001.fastq.gz | OTHER | 274.7 MB | link | |||
| — | b8p100_smallrnaseq_hek293_ko_l7_ip_S27_L002_R1_001.fas… | RIP-Seq | 335.9 MB | link | |||
| — | b8p100_smallrnaseq_hek293_ko_wt_ip_S25_L002_R1_001.fas… | RIP-Seq | 304.6 MB | link | |||
| — | b8p100_smallrnaseq_hek293_x3_l7_ip_S28_L002_R1_001.fas… | RIP-Seq | 241.0 MB | link | |||
| — | b8p100_smallrnaseq_hek293_x3_wt_ip_S26_L002_R1_001.fas… | RIP-Seq | 341.6 MB | link | |||
| — | b8p37_a9_input_let7_S1_L003_R1_001.fastq.gz | RNA-Seq | 857.6 MB | link |