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Mus musculus
12 Downloadable Samples
Illumina HiSeq 2000
Description
The goals of this study are to comprehensively identify genes controlled by Jmjd6 in the thymic stroma, and to identify a novel alternative splicing mechanism. Methods: Samples were WT and Jmjd6-/- fetal thymus organ culture with (2 samples for each category) or without (1 sample for each category) RANKL stimulation for 4 days under 2-DG. One µg of total RNA was used for library construction with TruSeq RNA Sample Prep Kit v2. THe ligated products were amplified using 8 cycles of PCR to generate RNA-seq library. Library integrity was verified by Bioanalyzer DNA1000 assay. Sequencing was performed in 101-bp paired-end mode using an Illumina HiSeq.Technical duplicate has done. Results: A total of 177,060,020 reads were obtained for 6 samples. Filtered reads were mapped to the UCSC mm10 using the TopHat program(v2.0.10) with the default parameters. The Cufflinks program (v2.1.1) was then used to assemble 22,448 transcripts and to calculate the fragments per kilobase of exon per million mapped fragments(FPKM) values, which are normalized measurement of gene expression levels(= genes-FPKM file).To identify differentially expressed genes, the ratio of the maximum FPKM to the minimum FPKM was compared among 6 samples. When the ratio was more than 3, the gene was regarded as being significantly altered in expression level. We added 0.1 to the FPKM value to avoid division by zero. This led us to identify 3212 genes with differential expression. Among these, the expression levels of 2536 genes were significantly associated with the RANKL treatment or Jmjd6 expression ( P value <0.05). Analysis for intron retention was performed as follows. According to the current gene annotation ("known genes" in UCSC mm10), there are 188,208 introns in total. As intron retention events should be observed in the genes with relatively high expression, we only focused on the genes with the maximum FPKM value more than 10 at least in one of the six samples. As a result, we obtained 84,708 introns. The reads mapped to these intronic regions were counted by the intersectBed program in the BEDTools utilities with -c option, and the counts are converted into the FPKM values for each intron (intronic FPKM). There are 1051 introns with intronic FPKM more than 10 in at last on of the six samples, and the degree of intron retention was calculated by dividing intronic FPKM value by conventional FPKM value for each gene (intron-FPKM file). Overall design: Samples were WT and Jmjd6-/- fetal thymus organ culture with (2 samples for each category) or without (1 sample for each category) RANKL stimulation for 4 days under 2-DG. One µg of total RNA was used for library construction with TruSeq RNA Sample Prep Kit v2. THe ligated products were amplified using 8 cycles of PCR to generate RNA-seq library. Library integrity was verified by Bioanalyzer DNA1000 assay. Sequencing was performed in 101-bp paired-end mode using an Illumina HiSeq.Technical duplicate has done.
Publication Title
Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
The mechanisms that activate some genes while silencing others are critical to ensure precision in lineage specification as multipotent progenitors become restricted in cell fate. During neurodevelopment, these mechanisms are required to generate the wide variety of neuronal subtypes found in the nervous system. Here we report interactions between basic helix-loop-helix (bHLH) transcriptional activators and the transcriptional repressor PRDM13 that are critical for these processes during specification of dorsal spinal cord neurons. PRDM13 inhibits gene expression programs for the excitatory neuronal lineages in the dorsal neural tube while also suppressing a battery of genes that determine ventral neural tube fates including Olig1, Olig2 and Prdm12. PRDM13 does this via recruitment to chromatin by multiple neural bHLH factors to restrict gene expression in specific neuronal lineages. Together these findings highlight the function of PRDM13 in repressing bHLH transcriptional activators that together are required to achieve precise neuronal specification during development. Overall design: RNA-seq analysis performed on GFP+ cells sorted by FACS from Prdm13GFP/+ or Prdm13GFP/GFP mouse E11.5 neural tubes to identify gene expression in the presence and absence of PRDM13.
Publication Title
Repression by PRDM13 is critical for generating precision in neuronal identity.
Sample Metadata Fields
Subject
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GSE1886- Mus musculus
- 18 Downloadable Samples
Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Diethylstilbestrol (DES) inhibits the differentiation of female reproductive tracts during fetal and neonatal days . We examined global gene expressions in the oviduct, uterus and vagina in newborn mice with or without DES. These results suggest understanding the mechanism of the differentiation of female reproductive tracts.
Publication Title
Gene expression change in the Müllerian duct of the mouse fetus exposed to diethylstilbestrol in utero.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Estrogen induce organ-specific cell proliferation and development in female reproductive organs, though the reproductive differentiation, sex maturation, implantation and lactation. However, the mechanism of organ-specific estrogen responsive genes is unknown. Thus, we examined early estrogen responsive genes in mouse uterus, vagina and mammary gland.
Publication Title
Comparison of estrogen responsive genes in the mouse uterus, vagina and mammary gland.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 36 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: To identify transcriptional changes by RNA-seq in tumor samples, before bevacizumab combination treatment and after bevacizumab combination treatment in both responding and non-responding recurrent glioblastoma patients Overall design: Three comparison analyses were further performed: 1.) Paired analysis of pre- and post-treated samples from responding patients; 2.) Comparison of pre-treated samples of responders vs. non-responders; 3.) Paired analysis of pre- and post-treated samples from non-responding patients The sample ''characteristics: batch'' represents a combination of the RNA-extraction date and the library-preparation date for each sample.
Publication Title
Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients.
Sample Metadata Fields
Sex, Disease, Disease stage, Subject, Time
View Samples- Homo sapiens
- 6 Downloadable Samples
- IonTorrentProton
Description
To investigate the roles of TAZ in lung fibroblasts, we compared the expression profiles of a lung fibroblast cell line, HFL-1, transfected with control siRNA and siTAZ. Overall design: We collected RNA from HFL-1 cells transfected with control siRNA and siTAZ. Two kinds of TAZ siRNAs (siTAZ #1 and siTAZ #2) were used. Two biological replicates (rep1 and rep2) were used for each condition.
Publication Title
TAZ contributes to pulmonary fibrosis by activating profibrotic functions of lung fibroblasts.
Sample Metadata Fields
No sample metadata fields
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