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Analysis of Transcriptome in small intestine after radiation injury with treatment of pravastatin

ABSTRACT: This study is designed to understand whether Pravastatin (Pra) treatment alters the transcriptome of small intestine after radiation injury. RNA was extracted from 15 Gy abdominal irradiated Gottingen minipigs with PS treatment. A cDNA library was generated using a TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), and transcriptome sequencing was performed using a TruSeq 3000/4000 SBS kit and Illumina sequencer with 101 bp paired-end reads per sample (Macrogen, Seoul, Korea).

ORGANISM(S): Sus scrofa domesticus

PROVIDER: GSE182829 | GEO | 2021/08/29

REPOSITORIES: GEO

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Genome-wide methylation profiles of post-mortem tissue samples (human) 2

Project description:In this study, 60 post-mortem tissue samples comprising four tissue types (kidney, liver, and lung) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

2023-10-22 | GSE244994 | GEO

Genome-wide methylation profiles of post-mortem tissue samples (human) 1

Project description:In this study, 60 post-mortem tissue samples comprising three tissue types (blood, brain, and heart) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

2023-10-22 | GSE244993 | GEO

Genome-wide methylation profiles of post-mortem tissue samples (human) 3

Project description:In this study, 60 post-mortem tissue samples comprising four tissue types (dermis, epidermis, and muscle) were collected from autopsies of 20 Koreans aged 18 to 78. 250 ng of genomic DNA (gDNA) was employed to generate DNA methylation profiles utilizing the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA, USA) at Macrogen Inc. (Macrogen, Seoul, Korea).

2023-10-22 | GSE244995 | GEO

RNA-seq of mouse brain tissue after exposure to p-cresol glucuronide

Project description:In vivo work done to determine how p-cresol glucuronide (pCG) affects integrity of the blood-brain barrier. Wild-type male C57Bl/6 mice were injected with saline or pCG, and killed 2 h after injection. Mice were transcardially perfused with 0.9% saline at 4 °C to remove circulating blood, and brains were removed and collected into RNAlater. Whole brain total RNA was extracted using a PureLink RNA Mini Kit. RNA samples (n=6 pCG, n=6 control) were sent to Macrogen Inc. (Republic of Korea) where they were subject to quality checks (RIN analysis), library prep and sequencing [TruSeq Stranded mRNA LT Sample Prep Kit; paired-end (2x 100 nt) sequencing; Illumina HiSeq 4000].

2022-12-29 | E-MTAB-11340 | biostudies-arrayexpress

RNA-seq of mouse brain tissue to investigate the integrity of the blood brain barrier to trimethylamine N-oxide

Project description:In vivo work done to determine how trimethylamine N-oxide (TMAO) affects integrity of the blood-brain barrier. Wild-type male C57Bl/6 mice were injected with saline or TMAO (1.8 mg/kg in saline), and killed 2 h after injection. Mice were transcardially perfused with 0.9% saline at 4 °C to remove circulating blood, and brains were removed and collected into RNAlater. Whole brain total RNA was extracted using a PureLink RNA Mini Kit. RNA samples (n=3 TMAO, n=3 control) were sent to Macrogen Inc. (Republic of Korea) where they were subject to quality checks (RIN analysis), library prep and sequencing [TruSeq Stranded mRNA LT Sample Prep Kit; paired-end (2x 100 nt) sequencing; Illumina HiSeq 4000].

2020-12-19 | E-MTAB-9869 | biostudies-arrayexpress

RNA-seq of mouse brain tissue after exposure to p-cresol sulfate

Project description:In vivo work done to determine how p-cresol glucuronide (pCS) affects integrity of the blood-brain barrier. Wild-type male C57Bl/6 mice were injected with saline or pCS, and killed 2 h after injection. Mice were transcardially perfused with 0.9% saline at 4 °C to remove circulating blood, and brains were removed and collected into RNAlater. Whole brain total RNA was extracted using a PureLink RNA Mini Kit. RNA samples (n=5 pCS, n=5 control) were sent to Macrogen Inc. (Republic of Korea) where they were subject to quality checks (RIN analysis), library prep and sequencing [TruSeq Stranded mRNA LT Sample Prep Kit; paired-end (2x 100 nt) sequencing; Illumina HiSeq 4000]. Only R1 (forward strand) reads were analysed and have been uploaded to ArrayExpress.

2022-12-29 | E-MTAB-12326 | biostudies-arrayexpress

Expression data from pancreatic cancers patients and healthy controls

Project description:For the identification of miRNA biomarker of pancreatic cancer, total RNA containing miRNA was extracted from the serum samples using Affymetrix miRNA 4.0 and the serum miRNA purification kit (Genolution, Seoul, Korea)

2016-10-30 | GSE85589 | GEO

Analysis of gene expression patterns of arabidopsis whitening mutant wn1 and wild-type

Project description:This data analyzes gene expression patterns in Arabidopsis whitening mutants, wn1, with defects in chloroplast development. We found that wn1 was a T-DNA insertion line of Arabidopsis AtPTAC10/PAP3 (At3g48500) and exhibited a lethal, albino-like phenotype in the seedling stages. pTAC10 was known as a component of RNA polymerase complex called plastid-encoded RNA polymerase, PEP, in mature chloroplasts. Because wn1 mutants were lethal, we extracted RNA from cotyledons of 7-day-old seedlings from wn1 mutants and Col-0. RNA seq analysis was commissioned by NICEM in Seoul National University, Korea and transcriptome resequencing was confirmed in Macrogen, Korea. Through analysis, we compared gene expression patterns of wn1 mutant and Col-0 seedlings.

2017-04-02 | GSE90159 | GEO

Analysis of transcriptome of mouse melanoma cells co-cultured with HEK293T cells expressing mouse Siglec1.

Project description:To evaluate the effect of mouse Siglec1 on B16F10 melanoma we used co-culture methos where HEK293T cells were transiently transfected with plasmid containg mouse Siglec1 or empty plasmid (mock). These HEK293T cells were cultured with B16F10-GFP mouse melanoma cells for 18 hours in low binding plates. After 18 hours of incubation on 37°C, 5% CO2, melanoma cells were FACS sorted based on GFP expression and total RNA was isolated and used for TruSeq RNA library construction for transcriptome analysis. Samples were from 3 independent experiments. The library preparation and NGS data aquisition were performed by Macrogen (Macrogen, Inc., Korea)

2019-12-22 | GSE109077 | GEO

Overexpression of OsTZF8, a CCCH-Tandem Zinc finger, increases drought tolerance in rice by regulating stress related genes

Project description:Purpose: Next-generation sequencing (NGS) has been utilized for systems-based analysis of rice plants. The goals of this study were to compare the transcriptome between non-transgenic (NT) control and OsTZF8 overexpressing transgenic plants. Methods: Total RNAs were extracted from the whole plants of OsTZF8 overexpressing plants (T4 generation, line number #20) and non-transgenic (NT) plant using RNeasy plant mini kit (Qiagen, Germany) according to the manufacturer’s instruction. cDNA libraries were prepared from total RNAs using TruSeq RNA sample Prep kit (v2) (Macrogen, Korea). Two biological replicates were analyzed by RNA-sequencing analysis. Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). Conclusions: Our study has identified downstream candidate genes regulated by overexpression of OsTZF8.

2020-11-05 | GSE135940 | GEO

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