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To detect full-length transcript of ts-ARFGEF1 in MCF-7 cell [captureRNA]

ABSTRACT: To detect full-length transcript of ts-ARFGEF1 in MCF-7 cell [captureRNA]

PROVIDER: PRJNA809825 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18119793_1.fastq.gz	Fastqsanger.gz

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To detect full-length transcript of ts-ARFGEF1 in MCF-7 cell [captureRNA]

Project description:Analysis of high-throughput transcriptome sequencing (RNA-seq) data often observed numerous 'non-co-linear' (NCL) transcripts, which may originate from genetic rearrangements (gene fusion) indicated the importance of fusion events and circRNAs in carcinogenesis; however, the role of ts-RNAs remains largely uninvestigated. Here we developed a hybrid sequencing pipeline ("NCLscan-hybrid"), which integrated different types of short (Illumina-based) and extra-long (PacBio-based) RNA-seq data to eliminate potential false positives from experimental artifacts, fusion events, and circRNAs. We applied NCLscan-hybrid to investigate of ts-RNAs in human breast cancer, the most malignant tumors diagnosed in women worldwide. Through multiple experimental validation steps, we confirmed that the intragenic ts-RNA, ts-ARFGEF1, was highly expressed in breast cancer cells but absent in normal breast cells. Furthermore, we experimentally validated that ts-ARGEF1 can contribute to cell proliferation and apoptosis. Analysis of xenograft in nude mice showed that disruption of ts-ARFGEF1 expression can significantly attenuate tumor growth. Microarray analysis revealed that ts-ARFGEF1 knockdown could trigger PERK/ATF4/CHOP signaling pathway, implying the function of ts-ARFGEF1 in ER homeostasis. Taken together, our findings provide an in-depth view of the true complexity of intragenic NCL events and, for the first time, show further insight into the potential roles of intragenic ts-RNAs in tumor cell development.

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To detect full-length genome of intron 19 of ARFGEF1 [intron19arfgef1]

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To detect full-length genome of intron 19 of ARFGEF1 [intron19arfgef1]

Project description:To detect full-length genome of intron 19 of ARFGEF1 [intron19arfgef1]

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H3K27me3 profiles along the length of the X chromosome in trophoblast stem (TS) cells, ChIP-chip

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H3K27me3 profiles along the length of the X chromosome in trophoblast stem (TS) cells showing inverted X-inactivation profiles, ChIP-chip

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H3K27me3 profiles along the length of the X chromosome in trophoblast stem (TS) cells, ChIP-chip

Project description:This analysis includes H3K27me3 profiles along the length of the X-chromosome in male (F2) and female (K4) TS cells and in female TS cells showing local reversals of imprinted X-chromosome inactivation (K4GFP). Data also includes H3K27me3 ChIP-chip profiles in Eed-/- mutant male and female TS cells obtained from Magnuson laboratory (Kalantry S. et al., Nat Cell Biol, 2006). Analysis of H3K27me3 profiles in five different cell populations. Three independent biological replicates for each wild-type female cell population and two independent biological replicates for the wild-type male cell population are provided. The ChIP-chip analysis was also carried out in Eed-/- male and female TS cells lacking H3K27me3 for comparison (one replicate). The array includes approx. 162,5 Mb of the X chromosome and approx. 14,6 Mb of chromosome 17 as a control.

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Project description:This analysis includes H3K27me3 and H3K4me2 profiles along the length of the X-chromosome in male (F2) and female (F3) TS cells and in male (GHP7/7) and female (GHP7/9) XEN cells.

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TS-seq

Project description:TS-seq

| PRJNA847608 | ENA