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SRP125709
Mus musculus
81 Downloadable Samples
Illumina HiSeq 2500
Description
This project examined the effects of substrate stress relaxation, stiffness, and adhesion ligand density on the D1 mouse MSC cell line. Cells were cultured in alginate hydrogels with low and high values for each of these material parameters for 40 hours before isolation and sequencing.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Rattus norvegicus
- 3 Downloadable Samples
- Illumina HiSeq 2000
Description
Gene expression profiling analysis reveals ?-3 polyunsaturated fatty acids attenuates a high fat diet induced fatty liver
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 1 Downloadable Sample
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
A long form (tRNase ZL) of tRNA 3' processing endoribonuclease (tRNase Z, or 3' tRNase) can cleave any target RNA at any desired site under the direction of artificial small guide RNA (sgRNA). We discovered in human kidney 293 cell extracts various new small noncoding RNAs (ncRNAs) including 5'-half-tRNAs and 28S rRNA fragments, co-immunoprecipitated with tRNase ZL, and demonstrated that two of these ncRNAs work as sgRNAs for tRNase ZL in vivo as well as in vitro. In order to find genuine mRNA targets of tRNase ZL guided by ncRNAs, we performed DNA microarray analysis for mRNAs from the 293 cells transfected with the tRNase ZL expression plasmid, and found that PPM1F and DYNC1H1 mRNAs are its genuine targets.
Publication Title
Modulation of gene expression by human cytosolic tRNase Z(L) through 5'-half-tRNA.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the biological activity of a Py-Im polyamide targeted to the sequence 5'-WGWWCW-3', which is found in a subset of ARE half-sites. This molecule reduces the growth of enzalutamide-resistant LREX' cells, both in vitro and in vivo. Gene expression changes associated with polyamide treatment in both settings are deposited here.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
VCaP cells were treated with 10uM of a Py-Im polyamided targeted to the DNA sequence 5''-WGWWCW-3'' for 24hrs. Gene expression changes are normalized to untreated VCaP cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq1000
Description
Superior frontal gyrus grey and white matter
Publication Title
Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Understanding host-pathogen interactions in tuberculosis is essential to d develop strategies and therapeutic tools to control Mycobacterium tuberculosis (Mtb). In this study, we performed the transcriptome analyses of macrophages infected with virulent Mtb strain H37Rv (Rv) or avirulent Mtb strain H37Ra (Ra).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 4000
Description
We present the RNA-seq datas of neuronal differentiation in mouse embryonic stem cell by all-trans retinoic acid.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples SRP098679- Drosophila melanogaster
- 3 Downloadable Samples
- Illumina HiSeq 2500
Description
Total RNA from Drosophila melanogaster head and thorax. Three biological replicates.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 823 Downloadable Samples
- Illumina HiSeq 2500
Description
Tumor recurrence and metastasis remain unavoidable due to a distinct tumor subpopulation known as cancer stem cells (CSCs). To explore the unique cell types contribute to colorectal cancer (CRC) progression, we profiled 831 single cells by simultaneous analysis of RNA sequencing (scRNA-seq) and telomere length in the same cell. Specific markers CD44, CD133 and LGR5 were used to enrich. We find small subpopulations with special features including quiescent CSCs, and epithelial lineage cancer cells (EPCs). Those quiescent CSCs have distinct features including higher level of pluripotency and Wnt signature, and shorter telomeres. Lineage tracing analysis showed that quiescent CSCs could plasticized and generate to epithelial lineage cancer cells with high proliferation and telomeres elongation, and these cells could also transform to each other. New marker genes for CSCs were identified including PROX1, TNFRSF19 and SMOC2. Survival analysis revealed that higher signatures of CSCs and EPCs predicts poor clinical outcome in CRC patients and could be a prognostic biomarkers. These findings provide insight into molecular classification of colorectal cancers and telomere function in CSCs.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples