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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The transcriptome-wide CPSF6-induced APA alterations in HCC cells

ABSTRACT: In this study, we showed that CPSF6 promoted HCC cell growth, migration and metastasis in vitro and in vivo. In order to understand the underlying mechanisms of CPSF6, we aimed to perform a APA profiling analysis in hepatocyte and hepatoma carcinoma cells under different CPSF6 expression conditions using 3T-seq method.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Tan Sheng

PROVIDER: E-MTAB-9458 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The transcriptome-wide CPSF6-induced APA alterations in gastric cancer cells

Project description:In this study, we showed that knockdown of CPSF6 inhibited GC cell growth and promoted apoptosis in vitro and in vivo. In order to understand the underlying mechanisms of CPSF6, we performed an APA profiling analysis in wild-type and CPSF6-knockdown AGS cells, using 3T-seq method.

2021-07-31 | E-MTAB-9980 | biostudies-arrayexpress

RNA and cell free miRNA in one family of Kallmann's syndrome

Project description:Kallmann Syndrome (KS) is a rare human genetic disorder characterized by the hypogonadotropic hypogonadism with the reduction or absence of olfactory sense. The mutations on the multiple genes including Chemokine Prokineticin-2 (PROK2) were considered to contribute to the abnormal migration of gonadotropin-releasing hormone (GnRH) neurons in embryonic stage. Here, we submit RNA-seq of the peripheral blood and the cell free miRNA-seq in the serum of one family, in which the KS patient has the same mutation of PROK2 (c.223-4C>A) with his mother, and the genetic phenotype of his father is normal. The sexual development and function of his parents are normal.

2020-05-01 | E-MTAB-8919 | biostudies-arrayexpress

Expression analysis of effect of Intestine-specific knockdown of KLF5 on radiation induced intestinal injury

Project description:The objective was to determine the role of Krüppel-like factor 5 (KLF5) in radiation-induced intestinal injury. Mice with intestinal-specific knockdown of KLF5 (Cre+ mice) were generated and their response to radiation was compared with controls (Cre- mice). Mice were given 15 Gy total body irradiation (TBI). The mice intestines were harvested at 6h post TBI and screened for differentially expressed genes by microarray analysis. We identified 11,004 and 2,466 differentially expressed genes in non-irradiated and irradiated mice at 6h post TBI, respectively. KLF5 knockdown down-regulated genes related to DNA damage repair pathways such as nucleotide excision repair, mismatch repair, non-homologous end joining and the Fanconi anemia pathway, which may suggest a novel function of KLF5. A four chip study using total RNA recovered from four pooled intestine tissues of four experimental groups. The four experimental groups respectively were the 6h-cre+ group, 6h-cre- group, con-cre+ group and con-cre- group. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group. One pooled sample in every group were tested with one chip. Each chip measures the expression level of 44,170 genes from C57BL/6 mouse (background) with three 60-mer probe pairs per gene.

2015-03-10 | E-GEOD-66655 | biostudies-arrayexpress

Site-specific protein modification by 3-n-butylphthalide in primary hepatocytes: covalent protein adducts diminished by glutathione and N-acetylcysteine

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2022-10-22 | PXD029480 | Pride

RNA-seq of human with nonalcoholic fatty liver disease against untreated controls

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2022-12-19 | E-MTAB-12445 | biostudies-arrayexpress

shRNA Screening Identifies JMJD1C as being required for Leukemia Maintenance

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2013-08-22 | E-GEOD-50048 | biostudies-arrayexpress

Proteomic analysis of mycelial exudate of Ustilaginoidea virens

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2021-04-08 | PXD019861 | Pride

Targeting of SMARCA4 bromodomain selectively inhibits leukemic cell proliferation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-07-12 | E-GEOD-67924 | biostudies-arrayexpress

Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins (expression data)

Project description:Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA. Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states. Comparison of Brd2 and HP1b shRNA knockdown HEK293 cells to control knockdown HEK293 cells.

2012-07-30 | E-GEOD-39580 | biostudies-arrayexpress

Expression analysis in pancreatic and liver tissues of diabetic db/db mice in response to dietary supplementation with selenate

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2014-03-07 | E-GEOD-55636 | biostudies-arrayexpress

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