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Mus musculus
22 Downloadable Samples
Illumina HiSeq 2500
Description
The dual leucine zipper kinase (DLK) is a mitogen-activated kinase kinase kinase that can activate the downstream cJun N terminal kinase (JNK) pathway (ref). We have previously reported that DLK is a positive regulator of the retrograde injury signaling and axon regeneration that unfolds after sciatic nerve injury (ref). Since DLK is required for activities of injury-associated transcription factors such as cJun and STAT3, we hypothesized that DLK is also necessary for the transcriptional responses to peripheral nerve injury. In the current study, we identify DLK-dependent transcriptome in dorsal root ganglion (DRG) neurons using a sciatic nerve injury paradigm. The DEG analysis reveals that DLK regulates regeneration/injury-associated genes in both basal and injured conditions. By performing gene ontology analysis, we suggest functional annotations and the involved genes as regulatory components of the axonal regeneration program. Finally, our comparative analysis indicates that DLK is required for a specific retrograde signaling pathway that regulates a regeneration program shared between PNS and CNS models.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 14 Downloadable Samples
- NextSeq 500
Description
we have compared the injury-induced transcriptomic changes between the regenerating proximal segment and the degenerating distal segment of a transected nerve, at different post-injury time points
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Rattus norvegicus
- 30 Downloadable Samples
Affymetrix Rat Expression 230A Array (rae230a), Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Gene expression profiling of the medial (MGE), lateral (LGE) and caudal (CGE) ganglionic eminence, and cerebral cortex (CTX) at various embryonic stages (E12.5, E14 and E16).
Publication Title
Comprehensive spatiotemporal transcriptomic analyses of the ganglionic eminences demonstrate the uniqueness of its caudal subdivision.
Sample Metadata Fields
Sex, Specimen part
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Global restriction of protein synthesis is a hallmark of cellular stress. Using hydrogen peroxide, we monitor the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analysed.
Publication Title
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.
Sample Metadata Fields
Sex, Compound
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
One common form of translational control is mediated by proteins that bind to the mRNA 5' cap-binding protein eIF4E. These proteins are collectively called 4E binding proteins (4EBPs). Saccharomyces cerevisiae possesses two 4EBPs that are encoded by non-essential genes called CAF20 and EAP1. To determine the impact of gene deletion on gene expression, we monitored the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes in wild-type, caf20 and eap1 cells. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analyzed.
Publication Title
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Compare m1A levels in the 16S (large) mitochondrial ribosomal RNA in TRMT61B knockdown cells and control.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 72 Downloadable Samples
- Illumina HiScanSQ
Description
we construct a comprehensive mouse transcriptomic BodyMap across 17 tissues of six-weeks old C57BL/6JJcl mice using RNA-seq. We find different expression patterns between protein-coding and non-coding genes. Liver and adrenal gland expressed the least complex transcriptome, whereas testis and ovary harbor more complex transcriptome than other tissues. We report a comprehensive list of tissue-specific genes across 17 tissues. Our study provides a unique resource of mouse gene-expression profiles, which is helpful for further biomedical research.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples
SRP072270- Mus musculus
- 50 Downloadable Samples
- Illumina HiSeq 2000
Description
To investigate the random X chromosome inactivation in vivo, we used allelic-specific RNA sequencing of single cells in mouse model. The intercross was between two genetically distant strains, C57BL/6 and PWK/Ph.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Cell line
View Samples- Glycine max
- 35 Downloadable Samples
- Illumina HiSeq 2000
Description
To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole genome RNA sequencing on salt-treatment soybean seedlings, on two tissues in a time-course experiment (0h, 1h, 2h, 4 h, 24h and 48h). This time series dataset enables us to identify important hubs and connection of gene expressions. We highlighted the analysis of phytohormone signaling pathways and their possible cross-talking. Gene expression regulation also controls adjustment of carbon and nitrogen metabolism. In general, the treated seedlings had turned off the photosynthetic mechanism and enhanced sugar catabolism to provide energy for survival. Primary nitrogen assimilation was shut down while re-distribution of nitrogen resources was activated. Genes for other protective mechanisms were also induced, including structural modification, ion-sequestering, and scavenging of reactive oxygen species.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Treatment
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Calcium acts as a universal second messenger to regulate gene expression in both developmental processes and responses to environmental stresses. Previous studies showed that a number of stimuli can induce calcium increases in the cytoplasm and nucleus, independently. However, the gene expression network deciphering [Ca2+]cyt and/or [Ca2+]nuc signaling pathway remain obscure.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples