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Mus musculus
10 Downloadable Samples
Illumina HiSeq 2000
Description
To study the function of E3 ligase Huwe1 knockdown on C2C12 proliferation and differentiation, we use mRNA-seq to compare gene expression profiles between control wild-type C2C12 myoblasts and two Huwe1 knockdown C2C12 cell lines generated by different shRNAs on differentiation Day 0 (proliferation medium) and Day 6 (differentiation medium for 6 days). To study the potential roles of Huwe1 in maintainance of muscle morphology, we use mRNA-seq to compare gene expression profiles between control and Huwe1 knockdown myotubes. To study whether downregulation of USP10 deubiquitinase is of functional significance during muscle differentiation, we compare gene expression profiles between control wildtype and USP10 overexpressing C2C12 cells on differentiation Day 6. Overall design: Control and Huwe1 knockdown C2C12 cells were collected on differentiation day 0, day 6 and day 8. Control and USP10 overexpressed C2C12 cells were collected on differentiation day 6. Subsequently, directional mRNA-seq expriments were performed with mRNAs purified from the collected cells.
Publication Title
A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to chromosomal regions bound by CTCF and cohesin. Enrichment for TAF3/CTCF/cohesin bound regions distinguishes TAF3-activated from TAF3-repressed genes. Our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions to safeguard the finely-balanced transcriptional programs that give rise to pluripotency. Overall design: Comparison of genome-wide expression patterns between TAF3-knockdown and WT embryonic stem cells using mRNA-Seq. Significantly differentially expressed protein-coding genes were identified by comparing control and knock-down samples at each timepoint (ES, embryoid body day 3 (EB3), EB6). Single and paired-end samples were combined at each timepoint, resulting in 3 tests for each gene (based on 8, 4, 4 independent measurements at ES ,EB3, EB6, respectively).
Publication Title
Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples- Mus musculus
- 11 Downloadable Samples
Description
Purpose: Characterize the role of the coactivator subunit TAF9b during differentiation of embryonic stem cells into motor neurons as well in mouse newborn spinal column tissues. Overall design: RNA-seq comparing WT and TAF9B KO mouse ES cells differentiated into motor neurons. RNA-seq comparing WT and TAF9B KO mouse newborn spinal column tissues. ChIP-seq mapping TAF9b and RNA Pol II binding sites in in vitro differentiated motor neurons.
Publication Title
Core promoter factor TAF9B regulates neuronal gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE13347- Mus musculus
- 3 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
C2C12 cells are mouse skeletal muscle cells. These cells were transfected with shRNA against FoxO1, FoxO3, and FoxO4. FoxO1, FoxO3, and FoxO4 are the known paralogues expressed in this cell line.
Publication Title
Codependent activators direct myoblast-specific MyoD transcription.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2000
Description
Brown adipose tissue (BAT) plays an essential role in metabolic homeostasis by dissipating energy via thermogenesis through uncoupling protein 1 (Ucp1). Previously, we reported that the TATA-binding protein Associated Factor 7L (Taf7l) is an important regulator of white adipose tissue (WAT) differentiation. Here, we show that Taf7l also serves as a molecular switch between brown fat and muscle lineages in vivo and in vitro. In adipose tissue, Taf7l containing TFIID complexes associate with PPAR? to mediate DNA looping between distal enhancers and core promoter elements. Our findings suggest that presence of the tissue-specific Taf7l subunit in TFIID functions to promote long-range chromatin interactions during BAT lineage specification. Overall design: mRNA-seq expression profiling wild type and Taf7l knockout interscapular brown adipose tissue (BAT)
Publication Title
TAF7L modulates brown adipose tissue formation.
Sample Metadata Fields
No sample metadata fields
View Samples GSE10553- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To study the function of BAF250 during ES cell self renewal and differentiation
Publication Title
ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Persistent severe asthma is associated with hyper-contractile airways and structural changes in the airway wall, including an increased airway smooth muscle (ASM) mass. This study used gene expression profiles from asthmatic and healthy airway smooth muscle cells grown in culture to identify novel receptors and pathways that potentially contributed to asthma pathogenesis.
Publication Title
Latrophilin receptors: novel bronchodilator targets in asthma.
Sample Metadata Fields
Sex, Disease, Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
To identify genes affected by mutant huntington protein, we performed mRNA-seq experiments with Striatal STHdh Q7/Q7, Q7Q111, and Q111/Q111 cells. We also tested the effect of Sp1 overexpression on rescuing gene expression in Q111/Q111 cells. Overall design: Striatal STHdh Q7/Q7, Q7/Q111 and Q111/Q111 cells were used for the mRNA-seq in replicates. After Sp1 transient overexpression in Q111/Q111 cells, cells were collected for mRNA-seq analysis.
Publication Title
Real-time imaging of Huntingtin aggregates diverting target search and gene transcription.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples