title: Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

status: Public on Apr 19 2015

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

summary: We developed a method for genome-wide mapping of DNA excision repair named XR-seq (eXcision Repair-seq). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating a ~30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells, cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts ((6-4)PPs). In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern, and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bi-directional eRNA production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.

overall_design: We have performed XR-seq for two types of UV-induced damages (CPD and (6-4)PP) in three different cell lines: NHF1, XP-C (XP4PA-SV-EB, GM15983)), and CS-B (CS1ANps3g2, GM16095). Two biological replicates were performed for each experiment, in which independent cell populations were UV treated and subjected to XR-seq.

first: J

last: Hu

first: S

first: C

middle: P

last: Selby

last: Lieb

first: A

last: Sancar


title: Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development

status: Public on Feb 22 2017

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

country: China

institute: Nanjing University

type: Expression profiling by high throughput sequencing

summary: Through analyzing RNA-seq datasets in zfpm1 mutant embryo (36hpf) and maturing heart (21 dpf), we characterized the effects of loss of zfpm1 on the transcriptomic landscape.

overall_design: Using RNA-seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.

first: Xin

last: Lou


title: Guselkumab (interleukin-23-specific monoclonal antibody) demonstrates clinical and molecular response in moderate-to-severe psoriasis

status: Public on May 14 2014

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

country: USA

institute: Janssen R&D

summary:
A gene expression profiling study was conducted in which skin biopsy samples were collected for RNA extraction and hybridization to microarrays from patients with moderate-to-severe psoriasis who participated in the phase 1, guselkumab first-in-human randomized, double-blind, placebo-controlled trial.
At week 12, significant reductions in psoriasis gene expression were observed in guselkumab-treated patients.

overall_design: Skin biopsy samples (n=59, LS: lesion, NL: non-lesion) were collected at baseline, weeks 1 and 12 following guselkumab treatment from patients with moderate-to-severe psoriasis for RNA extraction and microarray analysis.

first: Howard

last: Sofen

first: Stacy

last: Smith

first: Robert

middle: T

last: Matheson

first: Craig

middle: L

last: Leonardi

first: Cesar

last: Calderon

first: Carrie

last: Brodmerkel

first: Katherine

first: Kim

last: Campbell

first: Stanley

middle: J

last: Marciniak Jr

first: Yasmine

last: Wasfi

first: Yuhua

last: Wang

first: Philippe

last: Szapary

first: James

middle: G

last: Krueger


title: RNA sequencing analysis of decidua tissues from unexplained recurrent spontaneous abortion patients and controls with induced abortions

status: Public on Jul 12 2018

first: Mingming

last: Yu

address: NO.818 Tianyuan East Road, Jiangning District

department: School of public health

institute: Nanjing Medical University

summary: Recurrent spontaneous abortion (RSA), defined as the failure of two or more consecutive clinical pregnancies before 20 weeks of gestation, affects approximately 1% of couples attempting to conceive. However, the underlying mechanisms of 50% of cases are unknown. The decidua plays a crucial role during pregnancy, which can provide a delicate balance between immune tolerance and defense to maintain the pregnancy.We performed RNA-seq to identify gene expression alterations in the deciduas of RSA patients and controls. RNA-seq was done using TruSeq Stranded mRNA Library Preparation. Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000. After quality control, sequence data were processed with STAR to generate read alignments with hg19. Raw read counts for annotated genes were obtained with featureCounts with default settings, normalized and analyzed using DEseq2.

overall_design: Intact RNA isolated from 6 human decidua tissues was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 2000.

first: Guizhen

last: Du