GSE54968
GSE GEOTranscriptomic analysis reveals novel long non-coding RNAs critical for vertebrate development [RNA-Seq]
Relations
Summary
Long non-coding RNAs (lncRNAs) have emerged as critical regulators of gene expression and chromatin modifications, with important functions in development and disease. Here we sought to identify and functionally characterize lncRNAs critical for vascular vertebrate development with significant conservation across species. Genome-wide transcriptomic analyses during human vascular lineage specification enabled the identification of three conserved novel lncRNAs: TERMINATOR, ALIEN and PUNISHER that are specifically expressed in pluripotent stem cells, mesoderm and endothelial cells, respectively. Gene expression profiling, alongside RNA immunoprecipitation coupled to mass spectrometry, revealed a wide range of new molecular networks and protein interactors related to post-transcriptional modifications for all three lncRNAs. Functional experiments in zebrafish and murine embryos, as well as differentiating human cells, confirmed a developmental-stage specific role for each lncRNA during vertebrate development. The identification and functional characterization of these three novel non-coding provide a comprehensive transcriptomic roadmap and shed new light on the molecular mechanisms underlying human vascular development.
Overall Design
Time course RNA-Seq analysis H1 ESCs differentiated into endothelial cells
Analysis (4 steps)
View Data Processing- Illumina Casava1.7 software used for basecalling.
- Reads were aligned to the human genome (hg19) with STAR (v2.2.0c) with default parameters.
- Only uniquely alignable reads were used for downstream analysis
- Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across the entire gene (both introns and exons)
Supplementary Files (1)
GEO Samples (6)
Dataset Citations (1)
SRA Experiments (6) and Runs (6)
Total: 66027 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1168494 | 90366017 | 16265883060 | 10709.05 | H1_D0_1.fq.gz, H1_D0_2.fq.gz, SRR1168494, SRR1168494.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1168495 | 86752934 | 15615528120 | 10357.25 | H1_D2_1.fq.gz, H1_D2_2.fq.gz, SRR1168495, SRR1168495.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1168496 | 94594307 | 17026975260 | 11325.01 | H1_D4_1.fq.gz, H1_D4_2.fq.gz, SRR1168496, SRR1168496.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1168497 | 96559954 | 17380791720 | 11567.73 | H1_D8_1.fq.gz, H1_D8_2.fq.gz, SRR1168497, SRR1168497.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1168498 | 82822721 | 14908089780 | 10155.2 | H_Endo_1.fq.gz, H_Endo_2.fq.gz, SRR1168498, SRR1168498.sralite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR1168499 | 97606136 | 17569104480 | 11913.18 | HUVEC_1.fq.gz, HUVEC_2.fq.gz, SRR1168499, SRR1168499.sralite | SRA |