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SRP028570
Homo sapiens
32 Downloadable Samples
Illumina HiSeq 2000
Description
We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity. Overall design: Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.
Publication Title
Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.
Sample Metadata Fields
Cell line, Subject, Time
View Samples- Drosophila melanogaster
- 18 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
In most embryos, the mid-blastula transition is a complex process featuring maternal RNA degradation, cell cycle pause, zygotic transcriptional activation and morphological changes. The nucleocytoplasmic (N/C) ratio has been proposed to control the multiple events at MBT. To understand the global transcriptional response to the changes of the N/C ratio, we profiled wild type and haploid embryos using cDNA microarrays at three developmental stages.
Publication Title
Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaHiSeq2500
Description
To identify gene expression profile changes upon SNRNP40 depletion, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SNRNP40. Overall design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina HiSeq 2500.
Publication Title
Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
To identify MBNL1-dependent changes in gene expression, MDA-MB-231 cells expressing either control or MBNL1-targeting shRNAs were transcriptomically profiled. Overall design: MDA-MB-231 cells stably expressing a control or two independent MBNL1-targeting shRNAs were sequenced in biological duplicate.
Publication Title
Muscleblind-like 1 suppresses breast cancer metastatic colonization and stabilizes metastasis suppressor transcripts.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
- NextSeq500, IlluminaHiSeq2000
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA and ribosome-protected RNA fragments were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq500
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA(tt) and ribosome-protected RNA fragments (RPF) were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq500
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA(tt) and ribosome-protected RNA fragments (RPF) were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- NextSeq 500
Description
We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines Overall design: We followed the manufacturer's protocol: Cells were treated with cycloheximide (0.1 mg/ml) to inhibit translation; total RNA(tt) and ribosome-protected RNA fragments (RPF) were isolated and library preped for sequencing simultaneously.
Publication Title
Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HumanWG-6 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Extracellular metabolic energetics can promote cancer progression.
Sample Metadata Fields
Specimen part, Cell line, Time
View Samples- Homo sapiens
- 1 Downloadable Sample
- Illumina HumanWG-6 v3.0 expression beadchip
Description
miR-483-5p and miR-551a were over-expressed in a colon cancer cell-line LvM3b to identify genes that are down-regulated by the miRNAs over-expression.
Publication Title
Extracellular metabolic energetics can promote cancer progression.
Sample Metadata Fields
Specimen part, Cell line
View Samples