title: The piRNA Response to Retroviral Invasion of the Koala Genome

status: Public on Oct 12 2019

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

summary: Antisense piRNAs guide silencing of established transposons during germline development, and sense piRNAs drive ping-pong amplification of the antisense pool, but how the germline responds to genome invasion is not understood. The KoRV-A gammaretrovirus infects the soma and germline and is sweeping through wild koalas by a combination of horizontal and vertical transfer, allowing direct analysis of retroviral invasion of the germline genome. Gammaretroviruses produce spliced Env mRNAs and unspliced transcripts encoding Gag, Pol and the viral genome, but KoRV-A piRNAs are almost exclusively derived from unspliced genomic transcripts and are strongly sense strand biased. Significantly, selective piRNA processing of unspliced proviral transcripts is conserved from insects to placental mammals. We speculate that bypassed splicing generates a conserved molecular pattern that directs proviral genomic transcripts to the piRNA biogenesis machinery, and that this “innate” piRNA response suppresses transposition until antisense piRNAs are produced, establishing sequence-specific adaptive immunity.

sample_organism:
Mus musculus
Phascolarctos cinereus

platform_organism:
Mus musculus
Phascolarctos cinereus

overall_design: DNAseq, RNAseq and small RNAseq data for koala testes, livers and brains; RNAseq and small RNAseq data for different strains of mouse.

first: Birgit

last: Koppetsch

first: Zhiping

last: Weng

first: William

middle: E

last: Theurkauf

first: Chappell

last: Keith

first: Luban

last: Jeremy


title: Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [WGBS]

status: Public on Dec 11 2019

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: Endocrine therapy resistance invariably develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine resistant breast cancer cells and that the differential interactions are enriched for genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. Importantly, new 3D chromatin interactions often occur coincidently with hypermethylation and loss of ER binding. Additionally, alterations in active (A-type) and inactive (B-type) chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer.

overall_design: Hi-C, WGS, WGBS, ChIP-seq and RNA-seq were conducted in endocrine-sensitive breast cancer cells (MCF7) and its two endocrine-resistant derivatives - tamoxifen-resistant (TAMR) cells and fulvestrant-resistant (FASR) cells.


title: Alzheimer's disease DNA (hydroxy) methylome in the brain: OXT methylation as a preclinical marker.

status: Public on Dec 09 2019

city: Göttingen

first: Roy

last: Lardenoije

address: Robert-Koch-Str. 40

country: Germany

institute: University Medical Center Göttingen

type: Methylation profiling by genome tiling array

summary: The present study investigated the DNA methylome and hydroxymethylome, as well as unmodified cytosine in relation to Alzheimer’s disease (AD). We identified epigenetic differences between AD patients and age-matched controls in the middle temporal gyrus, in genomic regions associated with genes such as OXT, ACSL1, RHBDF2, C3, and MIR9-3HG. Interestingly, we found that OXT methylation in the blood of aged, non-demented individuals is also associated with conversion to AD dementia. The current GEO records concerns the middle temporal gyrus (ox)BS-processed Illumina 450K dataset of this study.

overall_design: (Oxidative) Bisulphite converted DNA from 82 samples were hybridised to the Illumina HumanMethylation450 BeadChip.

first: Daniël

middle: L

last: van den Hove


title: A developmental landscape of 3D-cultured human pre-gastrulation embryos

status: Public on Nov 26 2019

city: Kunming

first: Tianqing

last: Li

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

country: China

institute: Kunming University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: Knowledge detailing human pre-gastrulation embryonic development including spatial self-organization and cell type ontogeny remains limited by available twodimensional technological platforms that do not recapitulate the in vivo condition. Here, we report a three-dimensional (3D) blastocyst-culture system, which enables human blastocyst development through primitive streak anlage (PSA) formation. These 3D-embryos mimic in vivo developmental landmarks and 3D-architectures, including embryonic disc, amnion, basement membrane, primary and primate unique secondary yolk sac, anterior-posterior polarity formation and PSA. Using single cell transcriptome profiling, we delineate ontology and regulatory networks underlying epiblast, hypoblast and trophoblast segregation. Compared to epiblast, the grown amniotic epithelium shows unique and characteristic phenotypes. After implantation, specific pathways and transcription factors trigger differentiation of cytotrophoblasts, extravillous cytotrophoblasts and syncytiotrophoblasts. Epiblast undergoes pluripotency transition upon implantation and maintains its transcriptome until PSA generation as coordinated by different pluripotent factors. Using our 3D-culture approach, our findings elucidate the molecular and morphogenetic developmental landscape during early human embryogenesis.

overall_design: Using 3D-culture approach, to elucidate the molecular and morphogenetic developmental landscape during early human embryogenesis.

first: Yun

last: Zheng


title: scRNAseq of immune cells from young and aged mouse bladders

status: Public on Apr 30 2020

city: St. Louis

first: Indira

middle: U

last: Mysorekar

state: MO

address: 425 S. Euclid Ave, OB/GYN, BJCIH 10th Floor, Attn: Mysorekar Lab

department: OB/GYN

country: USA

institute: Washington University in St. Louis School of Medicine

summary: Aging has multifaceted effects on the immune system, but how aging affects tissue-specific immunity is not well-defined. Bladder diseases characterized by chronic inflammation are highly prevalent in older women, but mechanisms by which aging promotes these pathologies remain unknown. Tissue transcriptomics of unperturbed, young, and aged bladders identified a highly altered immune landscape as a fundamental feature of the aging female bladder. Detailed mapping of immune cells using single cell RNA- sequencing revealed novel subsets of macrophages and dendritic cells and unique changes to the immune repertoire in the aged bladder. B and T cells are highly enriched in aged bladders and spontaneously form organized bladder tertiary lymphoid tissues (bTLTs).

overall_design: 3 young (3 mo) and 1 aged (18 mo) C57BL6J mouse bladders

first: Marianne

middle: M

last: Ligon


title: MYOD Gene Expression Regulation during Myogenic Conversion of Fibroblasts

status: Public on Sep 10 2019

city: Cambridge

first: Alessandra

last: Dall'Agnese

address: 455 Main Street

institute: Whitehead Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We provide here gene expression profile of IMR90 fibroblasts expressing or not MYOD culured in GM for 1 day or GM for 1 day and DM for 3 days

overall_design: Integration of RNASeq and ChIPSeq

first: Pier

last: Puri


title: Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans

status: Public on Jul 29 2019

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [human scRNA-seq]

summary: In response to various stimuli, vascular smooth muscle cells (SMCs) can de-differentiate, proliferate and migrate in a process known as phenotypic modulation. However, the phenotype of modulated SMCs in vivo during atherosclerosis and the influence of this process on coronary artery disease (CAD) risk have not been clearly established. Using single cell RNA sequencing, we comprehensively characterized the transcriptomic phenotype of modulated SMCs in vivo in atherosclerotic lesions of both mouse and human. We performed CITE-seq in mouse atherosclerotic lesions using antibodies directed against several macrophage surface markers. In the mice, we also performed SMC-specific knockout of TCF21, a causal CAD gene, to determine the effect of this gene on SMC phenotypic modulation. Finally, we performed ChIP-seq for the transcription factor TCF21 in a pooled DNA sample comprised of 52 different human coronary artery smooth muscle cell (HCASMC) lines to determine TCF21 target genes.

overall_design: We performed single-cell RNAseq of cells from atherosclerotic human coronary arteries, obtained from explanted hearts of patients undergoing heart transplantation. The proximal-to-mid RCA was used for these studies. Debris was removed and cells were positively selected for viability using FACS. Cells were then processed by a 10X Chromium instrument using 3’ reagents (version 2 chemistry).

first: Robert

middle: C

last: Wirka

first: Dhananjay

last: Wagh

first: David

middle: T

last: Paik

first: Milos

last: Pjanic

first: Trieu

last: Nguyen

first: Clint

last: Miller

first: Ramen

last: Kundu

first: Manabu

last: Nagao

first: John

last: Coller

first: Tiffany

last: Koyano

first: Robyn

last: Fong

first: Y

middle: J

last: Woo

first: Boxiang

last: Liu

first: Stephen

middle: B

last: Montgomery

first: Joseph

last: Wu

first: Kuixi

last: Zhu

first: Rui

last: Chang

first: Melissa

last: Alamprese

first: Michelle

middle: D

last: Tallquist

first: Juyong

last: Kim


title: mRNA changes induced by Unfolded protein response

status: Public on Dec 31 2019

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

summary: We report the results NGS based of mRNA profiling in human bronchial epithelial cells (16HBE14o-) up on ER stress induction with Tunicamycin (2.5ug/ml) and ALLN (100uM)

overall_design: mRNA profiles of 16HBEs exposed to UPR (2h; 4h; 6h; 9h)

first: Rafa


title: Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [mouse scRNA-seq]

first: Thomas

last: Quertermous

overall_design: We performed single-cell RNAseq (scRNAseq) of cells from the aortic root and ascending aorta (up to the level of the brachiocephalic artery) in ApoE-/- mice. All mice contained the Myh11-Cre and ROSA tdTomato (tdT) alleles for smooth muscle cell (SMC) lineage tracing. Some mice also contained a floxed Tcf21 allele and are termed ‘KO’. Mice with the wild-type Tcf21 allele are termed ‘WT’. All mice underwent gavage with tamoxifen at 7 weeks of age, prior to the onset of high-fat diet feeding. Mice were then sacrificed at baseline (approximately 72 hours post gavage), after 8 weeks of high-fat diet (HFD) feeding or after 16 weeks of HFD feeding. Single-cell suspensions from these mice were separated by FACS into tdT-positive (‘SMC’) and tdT-negative (‘nonSMC’) populations and processed by a 10X Chromium instrument using 3’ reagents (version 2 chemistry).

first: Robert

last: Wirka

first: Dhananjay

last: Wagh

first: David

last: Paik

first: Milos

last: Pjanic

first: Trieu

last: Nguyen

first: Clint


title: Mitigating antagonism between transcription and proliferation allows near-deterministic cellular reprogramming (Single Cell)

status: Public on Jul 24 2019

first: Kate

last: Galloway

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary: RNA sequencing analysis of Hb9::GFP mouse embryonic fibroblasts infected with control or reprogramming transcription factors at 4 dpi, and Hb9::GFP+ mouse induced motor neurons generated using transcription factor overexpression. The goal of this study is to examine the transcriptional path of reprogramming cells to identify molecular mechanisms and populations of highly efficient reprogramming.

overall_design:
Transcriptional profiling of cells during the process of direct reprogramming of mouse embryonic fibroblasts to induced motor neurons (iMNs) and at the terminal stage at 17 dpi. Samples include Hb9::GFP+ sorted iMNs generated with  six factors (6F), 6FDD (e.g. 6F with p53DD), or 6FDDRR (6F with p53DD, hRASG12V, RepSox) as well as MEFs and samples at 4 dpi in conversion for 6F and 6FDDRR for both bulk and CFSE-low populations.
The 6F are Ascl1, Brn2, Myt1l, Ngn2, Isl1, Lhx3.

first: Justin

middle: K

last: Ichida


title: DNA-methylation of GGCC motifs via M.Ssp6803II is linked to DNA repair in the cyanobacterium Synechocystis sp. PCC 6803 [sll0729 mutant]

status: Public on Jul 02 2019

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: DNA methylation plays a crucial role for gene regulation among eukaryotes, but its regulatory function is less understood in bacteria. In the cyanobacterium Synechocystis sp. PCC 6803 five DNA methyltransferases have been identified. Among them, M.Ssp6803II is responsible for the specific methylation of the first cytosine in the frequently occurring motif GGCC, leading to N4-methylcytosine (GGm4CC). The mutation of the corresponding gene sll0729 led to a strong phenotype, including a lowered chlorophyll/phycocyanin ratio, impaired growth, and alterations of the expression of two genes encoding hypothetical proteins. However, prolonged cultivation revealed instability of the initially obtained phenotype, with colonies showing normal pigmentation and wild-type-like growth appearing regularly and in high frequencies on agar plates. These colonies represent suppressor mutants, since the sll0729 gene was still completely inactivated and the GGCC sites remained un-methylated. Two suppressor clones were further characterized and showed a smaller cell size and lowered DNA content per cell. Moreover, they exhibited a decreased tolerance against UV stress compared to wild type. Proteomics revealed the reduction of DNA topoisomerase in suppressor mutant cells. Collectively, these results indicate that GGm4CC methylation is involved in the regulation of gene expression, in the fine-tuning of DNA replication, and DNA repair mechanisms.

overall_design: We analyzed gene expression in various mutant strains of Synechocystis sp. PCC 6803 compared to WT.

first: Katrin

last: Gärtner

first: Satoru

last: Watanabe

first: Stefan

last: Mikkat

first: Ingeborg

last: Scholz

first: Wolfgang

middle: R

last: Hess

first: Martin

last: Hagemann


title: DNA-methylation of GGCC motifs via M.Ssp6803II is linked to DNA repair in the cyanobacterium Synechocystis sp. PCC 6803


title: Young and aged mouse bladders

first: Indira

last: Mysorekar


title: Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [pooled TCF21 ChIPseq]

first: Thomas

overall_design: TCF21 ChIPseq with total 65 primary human coronary artery smooth muscle cell (HCASMC) lines

last: Miller

first: Ramen

last: Kundu

first: Manabu

last: Nagao

first: John

last: Coller

first: Tiffany

last: Koyano

first: Robyn

last: Fong

first: Y

last: Woo

first: Boxiang

last: Liu

first: Stephen

last: Montgomery

first: Joseph

last: Wu

first: Kuixi

last: Zhu

first: Rui

last: Chang

first: Melissa

last: Alamprese

first: Michelle

last: Tallquist

first: Juyong

last: Kim


title: DNA Methylation (EPIC) from the Grady Trauma Project

status: Public on Jun 06 2019

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

summary: Childhood and cumulative exposure to trauma increases an individual's lifetime risk for psychiatric and stress-related disorders. This study evaluates DNA methylation in whole blood, with the goal of identifying associaitons between peripheral DNA methylation and psychiatric symptoms.

overall_design: DNA methylation was assessed in whole blood from participants of the Grady Trauma Project. Blood was collected in EDTA vacuum tubes prior to extraction. DNA methylation was interrogated for each sample using the MethylationEPIC BeadChip (Illumina).

first: Varun

last: Kilaru

first: Seyma

last: Katrinli

first: Kerry

last: Ressler


title: Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response

status: Public on May 03 2019

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital


title: Long noncoding RNA signatures induced by TLR7 and type I IFN signaling in activated human plasmacytoid dendritic cells

status: Public on Mar 21 2019

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: Using genome-wide sequencing approaches we viewed the contributions of Toll-like receptor 7 (TLR7) and type I interferon (IFN-I) in the regulation of coding and noncoding RNA expression in CAL-1 pDC treated with R848 or IFNβ. Functional enrichment analysis revealed both the unique and synergistic roles of TLR7 and IFN-I signaling in the orchestration of pDC function.

overall_design: Total RNA-seq profiling was performed on CAL-1 cells (1 million cells/mL) were cultured in 0.1% FBS CAL-1 media in triplicate in a 12-  well tissue culture plate for 6 hours prior to stimulation with 1,000 U/mL recombinant human  IFN-β (PBL Interferon Source) or 1ug/mL R848 (Invitrogen) or 1ug/mL R848 (Invitrogen) +  1ug/mL recombinant vaccinia virus B18R protein (Thermo Fisher Scientific) or mock  stimulation. Total RNA was harvested 12 hours post stimulation

first: Rochelle

last: Joslyn

first: Adriana

last: Forero

first: Snehal

last: Ozarkar

first: Chia

middle: H

last: Lee

first: Lomon

last: So

first: Richard

last: Green

first: Ram

last: Savan


title: Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response I

summary: The purpose of this study was to define biomarkers of  sensitivty and mechanisms of resistance to the KDM1A/LSD1 inhibtor SP-2509 (HCI-2509) in Ewing sarcoma cell lines. We report that regardless of drug sensitivity all cell lines engage the UPR and ER-stress response following treatment with SP-2509 resulting in apoptotic cytotoxicity. In addition hypersentsitive cell lines shared a common basal transcriptnomic profile, with hypersensitive cell lines signficantly inducing ETS1  which was not observed in sensitive cell  lines.

overall_design: 6 Ewing sarcoma cell lines were treated with either vehicle control (DMSO) or the reversible LSD1/KDM1A inhibitor SP-2509 (2uM) for 48hrs. Three SP-2509 hypersensitive (IC50< 300nM)(A673, TC32, TC252) and three SP-2509 sensitive (IC50>900nM) (EWS-502, ES-2 and TC71) cell lines were investigated. Paired RNA from three indpendent experiments per cell line was analyzed.

first: Kathleen

middle: I

last: Pishas

first: Stephen

last: Lessnick


title: Association between gut microbiota and global DNA methylation pattern in subjects with obesity

status: Public on Jun 07 2019

city: Malaga

first: Isabel

last: Moreno-Indias

state: Malaga

address: Virgen de la Victoria Hospital

country: Spain

institute: IBIMA

summary: In this study we demonstrate that the DNA methylation status in both blood and adipose tissue is highly associated to gut microbiota composition in obese subjects

overall_design: Gut microbiota composition was analyzed in DNA stool samples from a cohort of obese subjects by 16S rRNA gene sequencing. 20 patients were selected based on their Bacteroidetes-to-Firmicutes ratio (BFR): HighBFR group (BFR>2.5, n=10); LowBFR group (BFR<1.2, n=10). Genome-wide analysis of DNA methylation pattern in both whole blood and visceral adipose tissue of these selected patients was performed with an Infinium EPIC BeadChip array-based platform.

first: Bruno

last: Ramos-Molina

first: Francisco

last: Tinahones


title: Liver transcriptome of statin-treated patients

status: Public on May 15 2019

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

country: France

institute: Inserm

summary:
Background: Clinical data identified an association between the use of HMG-CoA reductase inhibitors (statins) and incident diabetes in patients with underlying diabetes risk factors such as obesity, hypertension and dyslipidemia. The molecular mechanisms however are unknown.
Methods: An observational cross-sectional study included 910 severely obese patients, mean (SD) body mass index 46.7 (8.7), treated with or without statins (ABOS cohort: a biological atlas of severe obesity). Data and sample collection took place in France between 2006 and 2016. Transcriptomic signatures of statin treatment in human liver obtained from genome-wide transcriptomic profiling of five different statin drugs using microarrays were correlated to clinico-biological phenotypes and also assigned to biological pathways and mechanisms.
Results: We determined the hepatic, statin-related gene signature from genome-wide transcriptomic profiling in severely obese patients with varying degrees of glucose tolerance and cardio-metabolic comorbidities. Patients on statin treatment showed higher diabetes prevalence (OR=2.67; 95%CI, 1.60-4.45; P= 0.0002) and impairment of glucose homeostasis. This phenotype was associated with molecular signatures of increased hepatic de novo lipogenesis (DNL) via activation of sterol regulatory element-binding protein-1 (SREBP1) and concomitant upregulation of the expression of key genes in both fatty acid and triglyceride metabolism.
Conclusions: DNL gene activation profile in response to statins was associated with insulin resistance and the diabetic status of the patients. Identified molecular signatures thus suggest that statin treatment increases the risk for diabetes in humans at least in part via induction of DNL.

overall_design: Total RNA from liver samples of 910 patients was extracted for Affymetrix microarray analysis from 30 mg frozen liver biopsies using Trizol reagent (Thermo Fisher Scientific) followed by a purification step on RNeasy columns (Qiagen). RNA purity and quantity was assessed using a Nanodrop spectrometer (Thermo Fisher Scientific). RNA integrity was quantified using the Agilent RNA6000 Nano assay and an Agilent 2100 BioAnalyzer. Nine hundred and ten samples complying with Affymetrix QC standards and a RNA integrity number (RIN) value of 5 to 7 were randomized for further processing and 300 ng RNA per sample was amplified using the Affymetrix WT amplification kit. Fragmented sscDNA was labelled using the Affymetrix WT Terminal Labeling Kit. Labeled DNA was then hybridized to Human Transcriptome Arrays 2.0 (Affymetrix) for 16 to 18 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix). These high-resolution arrays contain >6 million distinct oligonucleotide probes (25-mers) covering coding and non-coding transcripts, enabling the identification and analysis of differential expression at the gene and exon level. After washing, arrays were scanned with the GeneChip Scanner 3000 7G (Affymetrix), controlled by the Affymetrix software GeneChip Operating System (GCOS) v1.4. Quality controls (pm_mean / background_mean, pos_vs_neg_auc, all_probeset_mad_residual_mean), hybridization controls (bioB, bioC, bioD and cre) and polyA controls (lys, phe, thr and dap) were performed according to the Affymetrix quality criteria using the Expression Console software (Affymetrix).

first: Daniel

last: Margerie

first: Philippe

last: Lefebvre

first: Céline

last: Gheeraert

last: Derudas


title: microRNA expression profiling of papillary thyroid carcinoma (PTC) and matched adjacent normal thyroid tissues

status: Public on Mar 06 2019

city: Changsha, China

first: Xia

last: Fada

address: NO. 87, Xiangya Road

institute: Central South university

summary: We profiled the microRNA expression of 5 pairs of PTC and normal thyroid tissues. All the tissues were immediately snap-frozen in liquid nitrogen and confirmed as papillary thyroid carcinoma by expert pathologists. Numerous deregulated mature microRNAs were identified comparing PTC tissues versus normal thyroid tissues. Details about the clinical-pathological characteristics of the samples are also provided.

overall_design: Total RNA was extracted from the ten tissues. We measured the microRNA expression with Agilent Human microRNA Microarray Slides (Release 21.0) probed with 2549 human microRNAs.

first: Xinying

last: Li

first: Fada

last: Xia


title: MYOD Remodeling of the Genome Architecture during Myogenic Conversion of Somatic Cells

first: Alessandra

last: Dall'Agnese

summary: We provide here an unprecedented analysis of the three-dimensional re-organization of the genome during cellular reprograming of one cell type into another by the ectopic expression of one single transcription factor. By integrating Hi-C analysis with ChIPseq-based detection of MYOD genome-wide binding and RNAseq profiling of gene expression, we discovered that MYOD causes profound alterations in the high order chromatin structure during fibroblast reprogramming into skeletal muscle cells. We also used CTCF ChIPSeq in IMR90 GSE31477 (GSM935404); CTCF ChIPSeq in human myoblasts (hMB) GSE29611 (GSM733762);  CTCF ChIPSeq human myotubes (hMT) GSE29611 (GSM733783); H3K27Ac in IMR90 GSE43070 (GSM1055818); H3K27Ac in hMB GSE29611 (GSM733755); H3K27Ac in hMT GSE29611 (GSM733666) Same number of reads was used for H3K27Ac ChIP comparison. ChIPSeq p300 IMR90 GSE43070 (GSM1055812). We also used RNASeq from GSE90895 (GSM2417196, GSM2417197, GSM2417198, GSM2417204, GSM2417203)

overall_design: Integration of RNASeq, ChIPSeq and HiC experiments to characterize the 3D regulatory mechanisms for the myogenic conversion of fibrobalsts. For this project we used CTCF ChIPSeq in IMR90 GSE31477 (GSM935404); CTCF ChIPSeq in human myoblasts (hMB) GSE29611 (GSM733762);  CTCF ChIPSeq human myotubes (hMT) GSE29611 (GSM733783); H3K27Ac in IMR90 GSE43070 (GSM1055818); H3K27Ac in hMB GSE29611 (GSM733755); H3K27Ac in hMT GSE29611 (GSM733666) Same number of reads was used for H3K27Ac ChIP comparison. We also used RNASeq from GSE90895 (GSM2417196, GSM2417197, GSM2417204, GSM2417203)

first: Pier

last: Puri


title: Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [mouse CITE-seq]

first: Thomas

last: Quertermous

first: Robert

last: Wirka

first: Dhananjay

last: Wagh

first: David

last: Paik

first: Milos

last: Pjanic

first: Trieu

last: Nguyen

first: Clint

last: Miller

first: Ramen

last: Kundu

first: Manabu

last: Nagao

first: John

last: Coller

first: Tiffany

last: Koyano

first: Robyn

last: Fong

first: Y

last: Woo

first: Boxiang

last: Liu

last: Montgomery

first: Joseph

last: Wu

first: Kuixi

last: Zhu

first: Rui

last: Chang

first: Melissa

last: Alamprese

first: Michelle

last: Tallquist

first: Juyong

last: Kim


title: Targeted sequencing based maternal whole blood expression changes with gestational age and labor in normal pregnancy

status: Public on Feb 04 2019

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Maternal plasama colected longitudinally were profiled using targeted sequencing (DriverMap™) (https://www.cellecta.com) to evaluate changes with gestational age and with labor in normal pregnancy.

overall_design: The study included normal pregnancies with (TIL) (n=8) and without (TNL) (n=8) spontaneous labor at term.  Half of the women in each group had 3 longitudinal samples taken from 12.1-40.3 weeks of gestation, while the other half of women had only one sample taken at term before delivery, for a total of 32 samples.  Note that Sample_26 was considered contaminated and hence data for that sample was not included in downstream analyses.

first: Roberto

last: Romero

first: Nardhy

last: Gomez-Lopez

first: Sonia

middle: S

last: Hassan

first: Alex

last: Chenchik


title: Sequencing based maternal whole blood expression changes with gestational age and labor in normal pregnancy

summary: Maternal plasama colected longitudinally were profiled using paired-end Illumina RNA-Seq with globin reduction to evaluate changes with gestational age and with labor in normal pregnancy.

overall_design: The study included normal pregnancies with (n=8) and without (n=8) spontaneous labor at term.  Half of the women in each group had 3 longitudinal samples taken from 12.1-40.3 weeks of gestation, while the other half of women had only one sample taken at term before delivery, for a total of 32 samples.


title: Maternal whole blood expression changes with gestational age and labor in normal pregnancy [array]

summary: Maternal plasama colected longitudinally were profiled using Affymetrix Human Transcriptome Arrays to evaluate changes with gestational age and with labor in normal pregnancy.


title: Cytokine Stimulation of ADAR-deleted B16 murine melanoma cells

status: Public on Dec 30 2018

first: Kathleen

middle: Brosnahan

last: Yates

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

summary: ADAR was deleted from the B16 murine melanoma line using CRISPR/Cas9. The loss-of-function phenotype was assessed in vitro with cytokine stimulation or vehicle control.

overall_design: In order to determine the effect of an interferon sensitivity phenotype caused by ADAR deletion, B16 murine melanoma cancer cells were transiently transfected with plasmids encording Cas9 and guide RNA (sgRNA) against Adar or a non-targeting sequence. Cells were then subcloned and assessed for Adar deletion. Once verified, the Adar-null cells  were treated with vehicle control (PBS with 0.1% BSA), interferon-beta (IFNb), or interferon-gamma (IFNg), and transcriptionally profiled by directional, paired-end RNAseq after a 36 hour stimulation.

first: Jeffrey

last: Ishizuka


title: Re-Wiring 3D Nuclear Architecture by a Single Transcription Factor during Somatic Cell Reprogramming

first: Alessandra

last: Dall'Agnese

overall_design: Refer to individual Series


title: Genome-wide analysis of placental gene expression in severe preterm preeclampsia

summary: Analysis of genome-wide gene expression in placentas from women with preterm severe preeclampsia, with or without HELLP syndrome, compared to gestational age-matched controls. The hypothesis tested in the present study was that placental transcriptomic changes in preeclampsia are considerably different from controls. The results provide important information on placental transcriptomic changes in preeclampsia.

overall_design: Total RNA was obtained from placentas taken from patients in the following groups: 1) preterm preeclampsia  (n=6); 2) preterm preeclampsia with HELLP syndrome (n=6); and 3) preterm controls (n=5).

first: Gaurav

last: Bhatti

first: Katalin

last: Eder

first: Andras

last: Falus

first: Nandor

middle: G

last: Than

first: Tibor

last: Varkonyi


title: Genome-wide analysis of gene expression in BeWo cells treated with ZNF554 siRNA

summary: Analysis of the effect of ZNF554 knock-down on genome-wide gene expression in BeWo trophoblast-like cells. The hypothesis tested in the present study was that ZNF554 regulates the expression of genes involved in key functions of trophoblastic cells. The results provide important information on the functions of ZNF554 in BeWo trophoblast-like cells.

overall_design: Total RNA was obtained from BeWo cells subjected to either ZNF554 (n=3) or scrambled (n=3) siRNA treatment.

first: Susan

last: Land

first: Yi

last: Xu


title: IFN lambda modulates dendritic cells to facilitate T cell immunity during influenza virus infection

status: Public on Dec 28 2018

first: Michael

last: Gale

summary: Type I and type III interferon (IFN) are important in regulating responses to viral infection. Type I IFN signaling is know to contribute to dendritic cell (DC) function, but the contribution of type III IFN remains unknown. To determine changes in migratory dendritic cell gene expression during influenza A virus (IAV) in the presence or absence of type I or type III (IFN) receptors, C57Bl/6 (WT) mice, mice lacking the type I IFN receptor (Ifnar-/-), and mice lacking the type III IFN receptor (Ifnlr-/-) were infected intranasally with 40 plaque forming units (PFU) IAV H1N1 strain A/PR/8/34 or mock infected. On day 4, lung-draining lymph nodes (dLN) were harvested, conventional DC were isolated, and mRNA sequencing (mRNAseq) was performed.

overall_design: DCs were enriched from dLN of WT, Ifnar-/-, and Ifnlr-/- mice on day 4 following intranasal mock or infection with 40 PFU A/PR/8/34. These enriched DCs were then FACS sorted to isolate conventional DC (lineage-/MHCII+/CD11b-/CD11c+). cDNA was amplified and mRNA sequencing was performed.

first: Emily

last: Hemann

first: Richard

last: Green

first: Ryan

last: Langlois

first: Ram

last: Savan

last: Gale Jr


title: RSC Defines MNase-sensitive Promoter Architecture in Yeast

status: Public on Dec 22 2018

city: Omaha

first: Sandipan

last: Brahma

state: NE

address: 985805 Nebraska Medical Center, DRCI 6054

institute: University of Nebraska Medical Center

summary: The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently challenged by contradictory reports as to whether a distinct set of wider (≳150 bp) NDRs instead contain unusually unstable Micrococcal Nuclease-sensitive “fragile” particles, thought to be nucleosomal because of their size. To determine the composition of fragile particles we introduce CUT&RUN.ChIP, in which targeted nuclease cleavage and release is followed by chromatin immunoprecipitation. We find that fragile particles represent the occupancy and action of the RSC nucleosome remodeler acting on dynamically unwrapped nucleosomal intermediates. We also find that general regulatory factors (GRFs) bind to partially unwrapped nucleosomal intermediates at NDRs. We propose that RSC-engagement and its action cause nucleosomes to unravel, and subsequent binding of GRFs constitute a dynamic cycle of nucleosome deposition and clearance at the subset of wide Pol II promoter NDRs.

overall_design: We used Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing, followed by chromatin immunoprecipitation (ChIP).

first: Steven

last: Henikoff


title: Mitigating antagonism between transcription and proliferation allows near-deterministic cellular reprogramming

first: Kate

middle: E

last: Galloway

summary: This SuperSeries is composed of the SubSeries listed below.


title: Kidney compartment specific eQTL studies highlight causal genes and pathways for renal disease development

status: Public on Nov 16 2018

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Expression quantitative trait loci (eQTL) analyses were conducted separately on the glomerular and tubular portions of healthy human kidney samples obtained from subjects of European descent.

overall_design: We aimed to define genotype driven gene expression changes in the glomerular and tubular compartments of human kidneys, identifying genetic variants (eVariants) that influence the expression of genes (eGenes). Later, we integrated this information with genotype and phenotype association studies (GWAS) to identify genes for which expression in the kidney shows differences in patients with GWAS variants.

last: Susztak


title: Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma

status: Public on Dec 05 2018

city: Los Angeles

first: Willy

last: Hugo

state: California

address: 10833 Le Conte Ave

department: Medicine

institute: University of California, Los Angeles

summary: Glioblastoma is the most common primary malignant brain tumor in adults and associated with poor survival. Standard-of-care chemotherapy and radiation confer a median overall survival of under two years. The Ivy Foundation Early Phase Clinical Trials Consortium conducted a randomized, multi institution clinical trial to evaluate immune responses and survival following neoadjuvant and/or adjuvant therapy with pembrolizumab, a programmed cell death protein 1 (PD-1) monoclonal antibody, in 35 patients with recurrent, surgically resectable glioblastoma. Patients who were randomized to receive neoadjuvant pembrolizumab, with continued adjuvant therapy following surgery, had significantly extended overall survival compared to patients that were randomized to receive adjuvant, post-surgical PD-1 blockade alone (hazard ratio = 0.39; P = 0.04, log-rank test). Neoadjuvant PD-1 blockade was associated with upregulation of T cell and interferon-γ-related genes, but downregulation of cell cycle related genes within the tumor, which was not seen in patients that received adjuvant therapy alone. Focal induction of programmed death-ligand 1 (PD-L1) in the tumor microenvironment was observed more frequently in the neoadjuvant group than in tumors obtained from patients treated only in the adjuvant setting. Similarly, neoadjuvant pembrolizumab was associated with clonal T cell expansion and the overlap of T cell receptors between tumor and blood, decreased PD-1 expression in T cells and a decreasing peripheral monocytic population. These findings suggest that the neoadjuvant administration of PD-1 blockade enhances the local and systemic anti-tumor immune response and may represent a more efficacious approach to the treatment of this uniformly lethal brain tumor. This trial was registered with ClinicalTrials.gov under the identifier NCT02852655 (https://clinicaltrials.gov/ct2/show/NCT02852655).

overall_design: This dataset contains the transcriptomes of recurrent glioblastoma with either neoadjuvant (1 dose) or adjuvant pembrolizumab treatment

first: Timothy

middle: F

last: Cloughesy

first: Aaron

middle: Y

last: Mochizuki

first: Joey

last: Orpilla

first: Alexander

last: Lee

first: Tom

last: Davidson

first: Anthony

last: Wang

first: Benjamin

last: Ellingson

first: Julie

last: Rytlewski

first: Catherine

last: Sanders

first: Eric

last: Kawaguchi

first: Lin

last: Du

first: Gang

last: Li

first: William

last: Yong

first: Sarah

last: Gaffey

first: Adam

middle: L

last: Cohen

first: Ingo

last: Mellinghoff

first: Eudocia

middle: Q

first: David

last: Reardon

first: Barbara

last: O’Brien

first: Nicholas

last: Butowski

first: Phioanh

last: Nghiemphu

first: Jennifer

last: Clarke

first: Isabel

last: Arrillaga-Romany

first: Howard

last: Colman

first: Thomas

last: Kaley

first: John

last: de Groot

first: Linda

last: Liau

first: Patrick

last: Wen

first: Robert

last: Prins


title: Differentially expressed genes in human brest cancer specimens

status: Public on Aug 15 2018

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes in human brest cancer specimens were subjected to Agilent whole genome microarrays.

overall_design: Human breast cancer specimens　divided with the state of receptor tyrosine kinase and estrogen receptor.

first: Yasutaka

last: Yamada


title: The Stat3-Fam3a axis promotes muscle stem cell myogenic lineage progression by inducing mitochondrial respiration

status: Public on Mar 19 2019

first: Alessandra

last: Dall'Agnese

institute: Whitehead Institute

summary: Metabolic reprogramming is an active regulator of stem cell fate choices, and successful stem cell differentiation in different compartments requires the induction of oxidative phosphorylation. However, the mechanisms that promote mitochondrial respiration during stem cell differentiation are poorly understood. Here we demonstrate that Stat3 promotes muscle stem cell myogenic lineage progression by stimulating mitochondrial respiration. We identify Fam3a, a cytokine-like protein, as a major Stat3 downstream effector in muscle stem cells. We demonstrate that Fam3a is required for muscle stem cell commitment and skeletal muscle development. We show that myogenic cells secrete Fam3a, and exposure of Stat3-ablated muscle stem cells to recombinant Fam3a in vitro and in vivo rescues their defects in mitochondrial respiration and myogenic commitment. Together, these findings indicate that Fam3a is a Stat3-regulated secreted factor that promotes muscle stem cell oxidative metabolism and differentiation, and suggests that Fam3a is a potential tool to modulate cell fate choices.

overall_design: To assess whether MYOD was a direct regulator of Fam3a expression, we performed ChIP-seq analysis in myogenically converted IMR90 cells. IMR90 fibroblast were electroporated with a plasmid enconding for MYOD, and MYOD expression was induced by doxycycline treatment. Cells were then cultured in growth media (myoblasts) or in differentiation media to induce the formation of myotubes. Myoblasts and Myotubes were used to analyze MYOD binding to the FAM3A promoter.

last: Sala

last: Sacco

first: Lorenzo

last: Puri


title: Gene expression profile of DLBCL cells emerged in  Cg1-Cre Spi1 KO mice

status: Public on Jul 26 2018

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

institute: Kumamoto university of Medicine

summary: We performed RNA-seq analysis and compared the differences in gene expression between tumor cells from Cγ1-Cre Spi1 KO mice and B cells from PU.1-loxP mice.

overall_design: We performed RNA-seq analysis of tumor cells from Cγ1-Cre Spi1 KO mice and B cells from PU.1-loxP mice. We analyzed DLBCL cells from three Cγ1-Cre Spi1 KO mice and splenic B cells from two Cγ1-Cre Spi1 KO mice with mild splenomegaly. We also analyzed B cells from spleen of two PU.1-loxP mice. B220+ cells were purified using B220 magnetic beads (Miltenyi Biotec) and RNAs were extracted using Trizol reagent (Thermo Fisher Scientific) and RNeasy Mini Kit (Qiagen). We next compared the differences in gene expression between tumor cells from Cγ1-Cre Spi1 KO mice and those from Spi1-loxP mice.

first: Shinya

last: Endo

first: Nao

last: Nishimura

first: Hiromichi

last: Yuki

first: Matsuoka

last: Masao


title: miRNA changes induced by Unfolded protein response

first: Rafal

last: Bartoszewski

institute: Medical University of Gdansk

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the results NGS based of miRNA profiling in human bronchial epithelial cells (16HBE) up on ER stress induction with Tunicamycin (2.5ug/ml) and ALLN (100uM)

overall_design: mRNA profiles of 16HBEs exposed to UPR and or silecning of PIWIL proteins genes were generated by deep sequencing.


title: Maternal whole blood expression changes with gestational age and labor in normal pregnancy

first: Adi

last: Tarca


title: FD and vegetative development

status: Public on Dec 22 2017

city: College Park

first: Cecile

last: Parmentier-Line

address: Baltimore avenue

institute: University of MD

summary: Perennial plants alternate between periods of active growth and periods of dormancy. Prerequisite to bud dormancy is the formation of an apical bud. Short day photoperiod in the fall induces bud formation in poplar. Transgenic plants overexpressing the bZIP transcription factor FD do not stop growing and do not form a bud. In order to better understand the molecular events leading to bud formation, we used microarrays to compare the transcriptomes of shoot tips of poplars overexpressing FD and wild type plants (1) grown under long day conditions and (2) collected after 3 weeks under short day conditions

overall_design: Shoot tips of poplar plants were collected under LD and after 3 weeks under SD when bud forms in wild type plants. Shoot tips were collected from 4 plants and pooled. 3 replicates/genotype/time point

first: Gary

last: Coleman


title: RNA-seq from human meningioma samples

status: Public on Nov 27 2017

city: San Francisco

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

summary: We performed RNA-seq on 42 meningioma samples isolated from human patients to characterize the transcriptome of these tumors

overall_design: Poly A selected RNA-seq from 42 meningioma samples

middle: N

first: David

last: Raleigh


title: RNA-seq analysis of swine reproductive tissues including endometrium, oviduct and ovary through the estrous

status: Public on Apr 18 2018

city: Wanju

first: Jun-Mo

last: Kim

state: Jeollabuk-do

address: 1500, Kongjwipatjwi-ro

department: Animal Genomics and Bioinformatics

country: South Korea

institute: National Institute of Animal Science

summary: The underlying genomic regulation of the tissue synchronization is poorly understood. To understand this better we investigated the transcriptomes of the porcine ovary, endometrium, and oviduct at days 0, 3, 6, 9, 12, 15, or 18 of the oestrous cycle. We analysed the transcriptome profiles of the individual tissues.

overall_design: The tissues of gilts were collected on days 0 (the onset of oestrous behaviour), 3, 6, 9, 12, 15, or 18 of the oestrous cycle by hysterectomy. In total, whole mRNA sequencing profiles of 67 samples from 23 female pigs (23 profiles for Endometrium, 22 profiles for Oviduct and 22 profiles for Oviduct tissues).

first: Kyung-Tai

last: Lee

first: Hakhyun

last: Ka


title: Cytokine Stimulation of PTPN2-deleted cancer cells

status: Public on Jul 31 2017

city: Cambridge

first: Kathleen

last: Yates

summary: PTPN2 was deleted from a selection of murine and human cancer cells using CRISPR/Cas9. The loss-of-function phenotype was assessed in vitro with cytokine stimulation or vehicle control.

overall_design:
In order to determine the effect of PTPN2-inhibition of interferon signalling, Cas9-expressing murine (B16 melanoma) and human (A375, A549, HT29, MelJuSo) cancer cells were infected with lentivirus containing guide RNA (sgRNA) against Ptpn2 or a non-targeting sequence. After Ptpn2 deletion was verified, the cell lines were treated with vehicle control (PBS with 0.1% BSA), interferon-beta (IFNb), interferon-gamma (IFNg), or tumor necrosis factor (TNFa), alone or in combination, and transcriptionally profiled by directional, paired-end RNAseq after a 48 hour stimulation.!Series_overall_design = Please note that 'Bro3' and 'Bro4'  refer to non-targeting guides provided by the Broad Institute.

Please note that 'Bro3' and 'Bro4'  refer to non-targeting guides provided by the Broad Institute.

first: Robert

last: Manguso


title: A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma [RNA-Seq]

status: Public on Oct 22 2017

first: Kirsten

last: Johnson

state: Ohio

address: The Research Institute, WA5110, 700 Childrens Drive

department: Childhood Cancer and Blood Disorders

institute: Nationwide Childrens Hospital

summary: Ewing sarcoma usually expresses the EWS/FLI fusion transcription factor oncoprotein. EWS/FLI regulates myriad genes required for Ewing sarcoma development.  EWS/FLI binds GGAA-microsatellite sequences in vivo and in vitro, and these sequences provide EWS/FLI-mediated activation to reporter constructs, suggesting that they function as EWS/FLI-response elements.  Genomic GGAA-microsatellites are highly variable and polymorphic.  Current data suggest that there is an optimal “sweet-spot” GGAA-microsatellite length (of 18-26 GGAA repeats) that confers maximal EWS/FLI-responsiveness to target genes, but the mechanistic basis for this was not known.  We now demonstrate the absolute necessity of an EWS/FLI-bound GGAA-microsatellite in regulation of the NR0B1 gene, as well as for Ewing sarcoma proliferation and oncogenic transformation.  Biochemical studies, using recombinant Δ22 (a version of EWS/FLI containing only the FLI portion) demonstrated a stoichiometry of one Δ22-monomer binding to every two consecutive GGAA-repeats on shorter GGAA-microsatellite sequences.  Surprisingly, the affinity for Δ22 binding to GGAA-microsatellites significantly decreased, and ultimately became unmeasureable, when the size of the GGAA-microsatellite was increased to the “sweet-spot” length.  In contrast, a fully-functional EWS/FLI mutant (Mut9) that retains approximately half of the EWS portion of the fusion showed low affinity for smaller GGAA-microsatellites, but instead significantly increased its affinity at “sweet-spot” microsatellite lengths.  Single-gene ChIP and genome-wide ChIP-seq and RNA-seq studies extended these findings to the in vivo setting.  Taken together, these data demonstrate the absolute requirement of GGAA-microsatellites as EWS/FLI activating response elements in vivo and reveal an unsuspected novel role for the EWS portion of the EWS/FLI fusion in binding to optimal-length GGAA-microsatellites.

overall_design: The treatments applied to our RNA-seq A673 samples were for EWS/FLI knockdown/rescue experiments. Briefly, A673 cells were stably infected and selected for expression of a control Luc-RNAi or the EF-2-RNAi to knock-down EWS/FLI. Following 4 days of selection, cells were infected with either an empty pMSCV-hygro vector or vector expressing full length type IV EWS/FLI, the Ä22 EWS/FLI mutant, or mut9 EWS/FLI mutant to rescue EWS/FLI (or respective mutant EWS/FLI) expression in these cells.

middle: M


title: A Mouse Model of Chronic West Nile Virus Infection

status: Public on Jun 01 2016

first: Michael

last: Gale

institute: University of Minnesota

summary: Here, we characterize the RIX line CC(032x013)F1, which serves as a mouse model of chronic WNV infection. While studies using C57BL/6 mice have shown that WNV RNA can persist in the CNS up to 3 months post infection in a limited fraction of mice (Appler et al., 2010), to date there is a lack of a robust mouse model of chronic West Nile virus infection that can be used to elucidate the immune responses associated with this viral persistence and chronicity of symptoms described in human patients. Here, we characterize this line in comparison with lines showing either no disease symptoms or significant disease, and suggest a mechanism by which WNV infection can become chronic through alterations in immune responses.

overall_design: Microarrays were performed on spleen samples from mice collected at days 7,12,21,28 post-infection with west nile virus or from time-matched mock-infected animals.

first: Jessica

middle: B

last: Graham

last: Swarts

first: Courtney

last: Wilkins

first: Richard

last: Green

last: Mooney

first: Shannon

last: McWeeney

last: Gale Jr

first: Jennifer

last: Lund


title: A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma

overall_design: Refer to individual Series


title: Human Transcriptome Array 2.0 (HTA) in matched colorectal cancer and normal colonic mucosa and in widely used cancer cell lines

status: Public on Dec 31 2016

city: Catania

first: Daniele

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

summary: We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines (Caco-2, HT-29,HCT-116), one human breast adenocarcinoma cell line (MCF-7) and one human prostate adenocarcinoma cell line (PC3) were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis.

overall_design: 37 tumoral bioptic samples, deriving from 27 patients, were collected directly after surgical resection. The mean age was 66.61 years (SD 16.31) for 18 male patients and 68.67 (SD 15.63) for 9 female patients. In 9 patients, two samples were taken at arbitrary positions in the tumor area, separated by at least 1 cm (double-sampling pairs, indicated as tumoral sample 1 or 2). In one patient a sample from a synchronous colorectal adenocarcinoma was also collected (tumoral sample 3). In 19 cases biopsies of adjacent normal mucosa (at distance of 3-6 cm from the tumor) were also collected (matched tumor/mucosa pairs). 18 tumoral samples and 12 normal colonic mucosa samples were analyzed in duplicate arrays (indicated as array 1 or 2).

first: Vincenza

last: Barresi

first: Angela

last: Trovato

first: Giorgia

last: Spampinato

first: Giovanna

last: Valenti

first: Nicolo'

last: Musso


title: Strong Vaccine-Elicited Th1-Biased CD4 T cell Response Abrogates SIV Vaccine Efficacy

status: Public on Mar 01 2018

summary: Results from the Step trial in humans and studies in non-human primates highlighted a role for heightened activated CD4 T cell response in promoting HIV/SIV acquisition. However, the contribution of vaccine-specific CD4 T cell response in influencing protection is not known. Here, using the macaque model, we show that vaccine-induced Th1-biased CCR5+ CD4 T cell response in blood and mucosal tissue above a certain thresh¬old is detrimental for vaccine-mediated protection against pathogenic mucosal SIV infections.

overall_design: 10 vaccinated animals that acquired SIV infection within the first two challenges (early SIV acquirers) and 12 vaccinated animals that acquired SIV infection after 6 challenges (late SIV acquirers). We performed microarray analysis on whole blood samples for both set of animals at multiple days after the 1st DNA vaccine (Wk0), 1st MVA boost (Wk16), 2nd MVA boost (Wk32) and 1st rectal challenge.

first: Venkateswarlu

last: Chamcha

first: Sunil

last: Kannanganat

first: Zeeshan

last: Khaliq

first: Fredrik

last: Barrenäs

first: Jan

last: Komorowski

first: Guido

last: Silvestri

first: Francois

last: Villinger

first: Rama

last: Amara


title: Expression data of Cohesin-deficient, human cord blood-derived, hematopoietic CD34 cells

status: Public on Mar 17 2016

city: Lund

first: Roman

last: Galeev

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary:
Decreased levels of Cohesin proteins increases the amount of primitive hematopoietic stem and progenitor cells in an in vitro setting.
We used microarrays to detail the changes in global transcription programme to understand the underlying mechanisms behind this phenotype. Of note, we discover that hematopoietic stem cell-specific genes are upregulated in cells with decreased Cohesin levels.

overall_design: CD34 positive cells were isolated from human cord blood (not older than 24h), lentivirally transduced with shRNA targeting different members of the Cohesin complex. In order to focus on immediate changes, transduced cells were sorted 36 hours post transduction and analyzed.

first: Jonas

last: Larsson


title: Changes in gene expression and splicing associated with pregnancy, labor and regions of human adipose tissue.

status: Public on Dec 31 2015

first: Adi

last: Tarca

summary:
This is the expression dataset for two studies: 1) Characterization of visceral and subcutaneous adipose tissue transcriptome and biological pathways in pregnant and non-pregnant women: Evidence for pregnancy-related regional-specific differences in adipose tissue and 2) Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: Implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition.
The studies compare expression profiles and exon usage between adipose tissue regions and groups of women (pregnant vs non-pregnant) and in labor vs not in labor.

overall_design: Paired design for regional differences within groups of women (identified by Subject _# in the title), and unpaired design between groups of women.

first: Shali

last: Mazaki-Tovi

first: Edi

last: Vaisbuch

first: Juan

middle: P

last: Kusanovic

first: Nandor

last: Than

first: Tinnakorn

last: Chaiworapongsa

first: Zhong

last: Dong

first: Sonia

last: Hassan

first: Roberto

last: Romero


title: Genome-wide analysis of gene expression in HTR8/SVneo cells treated with ZNF554 siRNA

status: Public on Dec 30 2018

summary: Analysis of the effect of ZNF554 knock-down on genome-wide gene expression in trophoblastic cells. The hypothesis tested in the present study was that ZNF554 regulates the expression of genes involved in trophoblastic cell migration and invasion. The results provide important information on the functions of ZNF554 in trophoblastic cells.

overall_design: Total RNA was obtained from HTR8/SVneo cells subjected to either ZNF554 (n=3) or scrambled (n=3) siRNA treatment.

first: Gaurav

last: Bhatti

first: Susan

last: Land

first: Yi

last: Xu


title: Comparison between two different Pinus pinaster provenances

status: Public on Nov 04 2015

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: The transcriptome of needles from plants propagated by cuttings and cultured in the same condictions at SERIDA’s greenhouse at Villaviciosa (Asturias, Spain) were analyzed.

overall_design: The cuttings are from two different provenances of Pinus pinaster; Leiria (Portugal) and Tamrabta (Morocco). Their transcriptomes were analyzed using one color microarrays.

first: Concepción

last: Ávila

first: Francisco

last: Cánovas


title: Vitamin D receptor (VDR) regulates epidermal stem cells and cutanous wound healing

status: Public on Jul 31 2015

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

summary: This SuperSeries is composed of the SubSeries listed below.


title: A Transcriptomic Analysis of the Development of Skeletal Muscle Atrophy in Cancer-Cachexia in Tumor-Bearing Mice

status: Public on Oct 08 2018

city: Fayetteville

first: Nicholas

middle: P.

last: Greene

state: Arkansas

address: 308 HPER Building

department: Health, Human Performance and Recreation

institute: University of Arkansas

summary: We recently demonstrated mitochondrial degenerations precede muscle wasting in time course progression of CC. However, the extent of muscle perturbations prior to wasting in CC is unknown. Therefore, we performed global gene expression analysis in CC-induced muscle wasting to enhance understanding of intramuscular perturbations across the development of CC.

overall_design: Lewis Lung Carcinoma (LLC) was injected into the hind-flank of C57BL6/J mice at 8 wks age with tumor allowed to develop for 1, 2, 3, or 4 wks and compared to PBS injected control. Muscle wasting was evident at 4 wks LLC. Animals were anesthetized using isoflourane and gastrocnemius muscles were collected for analysis.  Conclusions: Current findings present novel evidence of transcriptomic shifts and altered cellular pathways in CC-induced muscle wasting.


title: Vitamin D receptor (VDR) regulates epidermal stem cells and cutanous wound healing [VDR KO]

summary: The vitamin D receptor (VDR) regulates cell proliferation and differentiation including epidermal keratinocytes by modulating transcription of its target genes. We are investigating the role of VDR in epidermal stem cells and their progenies in the regeneration process of epidermis and hair in the skin. VDR null mice are utilized in which VDR is specifically deleted in keratin 14 (K14) expressing keratinocytes by Cre-lox strategy. The impact of VDR deletion was evaluated by comparison of VDR null mice with no cre littermate control mice. The VDR was abundantly expressed in potential epidermal stem cells including basal cells in interfollicular epidermis (IFE), and in CD34 expressing bulge keratinocytes in hair follicles. Gene expression profiles and subsequent pathway analysis of stem cell enriched keratinocyte populations revealed that the VDR deletion significantly suppressed β-catenin signaling as well as VDR signaling. The role of VDR in epidermal stem cells was studied during hair follicle cycling and wound healing processes. The epidermal stem cells were not appropriately stimulated by hair depilation, and did not reinitiate anagen in the hair follicles resulting in a failure of hair regrowth. In addition, the stem cells were not fully activated after full thickness wounds were generated in VDR null skin under a low calcium diet to suppress compensation pathways. Cell proliferation was not fully induced in potential stem cells located in both IFE and hair follicles near the wounding edges, and re-epithelialization rate was delayed in VDR null skin. Gene expression profiling of the wounded skin (3 days after injury) indicated that β-catenin signaling was not fully induced in VDR null skin comparable to that observed in β-catenin null mice.  The β-catenin target genes including Axin2 and cell cycle regulators involved in epidermal stem cell function were not induced in the edges of the wound of VDR null skin. These results demonstrated that VDR plays an essential role in hair cycling and wound healing processes through regulation of β-catenin signaling in epidermal stem cells and their progenies.

overall_design: n=3 CON and KO (each sample contain RNA isolated from wounded or nonwounded skins excised from 3 mice)

first: Thai

last: Nguyen

first: Daniel

middle: D

last: Bikle


title: Genome-wide analysis of DNA methylation in drug-tolerant cancer cell subpopulations

status: Public on May 26 2015

city: New Haven

first: Kohei

last: Kume

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: Cancer relapse after curative treatment is thought to originate from drug-tolerant and invisible cancer cell subpopulations. Using cancer cell colonies emerging in the presence of drugs (drug-tolerant colonies, DTCs), we found that the drug-tolerant properties of DTCs are lost through a reversible mechanism. To examine whether epigenetic regulation is responsible for the phenotypic changes in DTCs, we performed a genome-wide analysis for relative CpG methylation between the DTCs and untreated colonies derived from MKN45 by NimbleGen Human Meth 385K Prom Plus CpG Arrays. Global changes in the methylation levels were evident in a chromosomal location-dependent manner. The methylation status of the upstream regions of the transcription start sites of the pluripotency-inducing genes showed good agreement with the qRT-PCR data. These results suggest that reversible drug-tolerant properties in DTCs are epigenetically regulated and associated with transcriptional regulation, including pluripotency-inducing factors.

overall_design: Comparison of untreated colonies v.s. DTCs derived from MKN45 cells.

first: Satoshi

last: Nishizuka


title: Transcriptional profiling of drug-tolerant cancer cell subpopulations

status: Public on Jan 30 2015

summary: Cancer relapse occurs even after curative treatment, suggesting the existence of undetectable cancer cell subpopulations and their drug-tolerant potential. We found that the number of drug-tolerant colonies (DTCs) was significantly suppressed by an RNA polymerase II (RNAPII) inhibitor, alpha-amanitin (alpha-AMA). To identify potential molecular target of alpha-AMA, we performed transcriptional profiling by  Agilent-028004 SurePrint G3 Human GE 8x60K Microarray using untreated colonies and DTCs derived from MCF7. Among the top 2.5% of specifically induced genes in DTCs, we focused on TAF15 gene because its gene product binds RNAPII. A subsequent colony formation assay revealed that TAF15 knockdown suppressed the emergence of both DTCs and untreated colonies, suggesting that TAF15 is a crucial target of alpha-AMA in the context of DTC suppression.

overall_design: Total RNA was extracted from two biological replicates of bulk untreated MCF7 colonies and MCF7 DTCs emerged in the presence of 0.8 µM CIS. For identification of the TAF15 gene, gene ontology analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) software tools (http://david.abcc.ncifcrf.gov/).


title: Neurocognitive impairment at 18-24 months in children born preterm may originate in utero: a microarray study

status: Public on Jan 21 2015

first: Adi

last: Tarca

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: To characterize the molecular profile of the chorioamniotic membranes of preterm neonates with and without neurocognitive impairment at 18-24 months and (2) to determine if neonates who developed neurocognitive impairment can be identified at birth.

overall_design: Paired two-group design

first: Athina

last: Pappas


title: Mutual reinforcement of pathophysiological host-microbe interactions that maintain steady state conditions of disease

status: Public on Jul 12 2014

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

summary:
Chronic diseases arise when pathophysiological processes achieve a steady state by self-reinforcing. Here, we explored the possibility of a self-reinforcement state in a common condition, chronic constipation, where alterations of the gut microbiota have been reported. The functional impact of the microbiota shifts on host physiology remains unclear, however we hypothesized that microbial communities adapted to slow gastrointestinal transit affect host functions in a way that reinforces altered transit, thereby maintaining the advantage for microbial self-selection. To test this, we examined the impact of pharmacologically (loperamide)-induced constipation (PIC) on the structural and functional profile of altered gut microbiota. PIC promoted changes in the gut microbiome, characterized by decreased representation of butyrate-producing Clostridiales, decreased cecal butyrate concentration and altered metabolic profiles of gut microbiota. PIC-associated gut microbiota also impacted colonic gene expression, suggesting this might be a basis for decreased gastrointestinal (GI) motor function. Introduction of PIC-associated cecal microbiota into germ-free (GF) mice significantly decreased GI transit time. Our findings therefore support the concept that chronic diseases like constipation are caused by disease-associated steady states, in this case, caused by reciprocating reinforcement of pathophysiological factors in host-microbe interactions.
We used microarrays to detail the global gene expression profile in the proximal colon smooth muscle tissues of germ-free, conventionalized, or specific pathogen free mouse

overall_design: C57Bl/6 female and male specific pathogen free (SPF) mice were bred and housed in the animal care facility at the University of Chicago. Mice of 8–10 weeks of age were treated with 0.1% loperamide in the drinking water for 7 days. Age matched, germ-free (GF) C57Bl/6 mice were gavaged orally with cecal luminal contents harvested from control or loperamide-treated C57Bl/6 donor mice. Recipient mice were sacrificed 4 weeks post-colonization.

first: Ketrija

last: Touw

first: Yunwei

last: Wang

first: Vanessa

last: Leone

first: Gianrico

last: Farrugia

first: Eugene

last: Chang


title: Developmental gene expression in Gaspe in response to nitrate

status: Public on Sep 27 2014

city: Urrbrae

first: Darren

last: Plett

state: South Australia

address: Hartley Grove Road

department: ACPFG

institute: University of Adelaide

summary: Elucidation of the gene networks underlying the response to N supply and demand should facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both NO3- provision and to development-based N demand changes across the entire lifecycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the lifecycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire lifecycle, however the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3- responsive gene expression.

overall_design: Gaspe Flint maize was grown hydroponically for the entire lifecycle on 0.5 or 2.5 mM NO3-. Shoot and root tissues were harvested from three biological replicates at seven time points during the lifecycle, RNA was extracted, fluorescently labled cRNA was synthesised and hybridised to a 4x44K microarray.


title: Transcriptome Analysis of the Basal Chordate Botryllus schlosseri Reveals a Set of Genes Associated with Fertility

status: Public on Jan 12 2015

city: Santa Barbara

first: Delany

last: Rodriguez

state: CA

address: Biological Science Building  RM1201 University of California Santa Barbara

department: Molecular Cellular and Developmental Biology

institute: University of California Santa Barbara

summary: Background: Gonad differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. The colonial ascidian, Botryllus schlosseri is a chordate model organism which offers two unique traits that can be utilized to characterize the genes underlying germline development: a colonial life history and variable fertility. These properties allow individual genotypes to be isolated at different stages of fertility and gene expression can be characterized comprehensively.  Results: Here we characterized the transcriptome of both fertile and infertile colonies throughout blastogenesis (asexual development) using differential expression analysis. We identified genes (as few as 7 and as many as 647) regulating fertility in Botryllus at each stage of blastogenesis. Several of these genes appear to drive gonad maturation, as they are expressed by follicle cells surrounding both testis and oocyte precursors. Spatial and temporal expression of differentially expressed genes was analyzed by in situ hybridization, confirming expression in developing gonads.   Conclusion: We have identified several genes expressed in developing and mature gonads in B. schlosseri. Analysis of genes upregulated in fertile animals suggests a high level of conservation of the mechanisms regulating fertility between basal chordates and vertebrates.

overall_design: mRNA profiles of seven infertile stages from infertile Botryllus schlosseri colonies (each in triplicates) and seven stages of fertile Botryllus schlosseri colonies (each in triplicates) using Illumina deep sequencing and analyzed for differential expression between each stage.

first: Erin

last: Sanders

first: Kelsea

last: Farell

first: Adam

last: Langenbacher

first: Daryl

last: Taketa

first: Michelle

middle: R

last: Hopper

first: Morgan

last: Kennedy

first: Andrew

last: Gracey

first: Anthony

middle: W

last: De Tomaso


title: IL-1B signaling in dendritic cells induces antiviral interferon responses

status: Public on Jan 12 2018

city: Minneapolis

first: Michael

last: Gale

address: 689 23rd Ave SE

summary: Activation of interferon-stimulated gene (ISG) responses is critical for control of viral infection.  We recently identified that stimulation of the NLRP3 inflammasome and mobilization of the inflammatory cytokine IL-1β act as critical host restrictive pathways against West Nile virus (WNV) in a mechanism dependent on the regulation of ISGs. In order to define the mechanism by which IL-1β regulates these antiviral immune programs, we utilized global transcriptome analysis in myeloid cells, known targets of WNV replication to define gene signatures required for IL-1β driven antiviral responses. Surprisingly, we found IL-1β dependent activation of interferon-beta (IFN-β) and ISGs at late times following IL-1β treatment. Expression of these antiviral innate immune genes was found to be dependent on activation of IRF3 and appears to reflect a general shift in IL-1β signaling from an inflammatory response early following treatment to an anti-inflammatory type-I IFN mediated response at later times post-treatment. These data demonstrate that inflammatory and antiviral signals integrate to control viral infection. Strategies to co-opt these cytokine activated antiviral signatures can act as novel targeted therapeutic strategies tailored specifically to individual pathogens.

overall_design:
WT or IL-1R KO BMDCs were either mock-treated or pre-treated with 100 ng IL-1b for 24 hours. Cells were then either mock-infected or infected with WNV at an MOI of 2.5. Both mock and WNV-infected samples were harvested at 24 and 48 hours. WT BMDCs were also treated with IL-1b for 24 or 48 hours before harvest. All samples were run in triplicate. Total RNA was run on Agilent 4x44 mouse microarray

Please note that the sample titles represent pre-treatment and infection status as following;
sample group - pre-treatment - infection
KO_MK_*hr - mock - mock
KO_WNV_*hr - mock - WMV
WT_IL1b_*hr - IL-1b - mock
WT_MK_*hr - mock - mock
WT_WNV_*hr - mock - WMV
The *hr represents the time after infection.

first: Lauren

last: Aarreberg

first: Courtney

last: Wilkins

first: Hilario

middle: J

last: Ramos

first: Richard

last: Greena

last: Davis

first: Kwan

last: Chow

last: Gale Jr


title: Vitamin D receptor (VDR) regulates epidermal stem cells and cutanous wound healing [keratinocytes]

first: Yuko

last: Oda

overall_design: n=3 CON and KO (each sample contain RNA extracted from keratinocytes, which is isolated from VDR KO and littermate control skins excised from 3 mice)

first: Thai

last: Nguyen

first: Daniel

last: Bikle


title: High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain

status: Public on Aug 02 2013

city: Houston

first: James

last: Lupski

address: One Baylor Plaza, 604B

institute: Baylor College of Medicine

type: Genome variation profiling by genome tiling array

overall_design: Refer to individual Series


title: High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 2)

summary: The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

overall_design: We designed a tiling-path oligonucleotide microarray spanning 4.0 Mb surrounding the MECP2 region on Xq28. The custom 4x44k Agilent Technologies microarray was designed using the Agilent earray website. We selected 22,000 probes covering ChrX: 150,400,000-154,400,000 (NCBI build 35), including the MECP2 gene, which represents an average distribution of 1 probe per 500 bp. Each patient sample was run once using this array; hybridization was done using a gender-matched reference sample.

first: Claudia

last: Carvalho

first: Davut

last: Pehlivan


title: Integrated extracellular microRNA profiling for ovarian cancer screening

status: Public on Oct 23 2018

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

summary: A serum miRNA combination could be a powerful classifier for the detEsophageal Cancertion of patients with ovarian cancer.

overall_design: Serum microRNA profiles of 4046 woman samples, which consist of 333 of ovarian cancers, 66 of borderline ovarian tumors, 29 of benign ovarian diseases, 2759 of non-cancer controls, and 859 of the other solid cancers.

first: Akira

last: Yokoi

first: Juntaro

last: Matsuzaki

first: Yusuke

last: Yamamoto

first: Kenta

last: Takahashi

first: Hanako

last: Shimizu

first: Takashi

last: Uehara

first: Mitsuya

last: Ishikawa

first: Shun-ichi

last: Ikeda

first: Junpei

last: Kawauchi

first: Yoshiaki

last: Aoki

first: Shumpei

last: Niida

first: Hiromi

last: Sakamoto

first: Ken

last: Kato

first: Tomoyasu

first: Takahiro

last: Ochiya


title: Brisbane Systems Genetics Study

status: Public on Dec 11 2013

city: Brisbane

first: Joseph

last: Powell

state: Qld

address: St lucia

department: Queensland Brain Institute

institute: University of Queensland

summary:
Brisbane Systems Genetics Study comprises of a total of 862 individuals from 374 families.
Families consist of combinations of both MZ and DZ twin pairs, their siblings and for 72 families their parents.

overall_design: Whole blood for expression profiling was collected directly into PAXgene tubes and total RNA was extracted using the WB gene RNA purification kit. RNA from all samples was run on an Agilent Bioanalyzer to assess quality.

first: Grant

last: Montgonery

first: Peter

last: Visscher


title: High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 1)

first: James

last: Lupski

overall_design: We designed a tiling-path oligonucleotide microarray spanning 4.6 Mb surrounding the MECP2 region on Xq28. The custom 4x44k Agilent Technologies microarray was designed using the Agilent earray website. We selected 22,000 probes covering ChrX: 150,000,000-154,600,000 (NCBI build 36), including the MECP2 gene, which represents an average distribution of 1 probe per 209 bp. Each patient sample was run once using this array; hybridization was done using a gender-matched reference sample.

first: Claudia

last: Carvalho

first: Davut

last: Pehlivan


title: Expression data from F344N rats in long and short photoperiods

status: Public on Feb 21 2012

city: Aberdeen

first: Alexander

middle: William

last: Ross

state: Aberdeenshire

address: Ashgrove Road West

country: United Kingdom

institute: University of Aberdeen

summary:
Rats were housed in either long day (LD, 16:8 hours, light:dark) or short day (SD, 8:16 hours, light dark) photoperiods for 3, 14 and 28 days and brains removed, frozen on dry ice and then hypothalamic arcuate nucleus tissue blocks cut for RNA extraction.
At each time point 4 rats were used in each photoperiod giving 24 rats in total.

overall_design: RNA from each rat was used on separate affymetrix rat 230 2.0 arrays, using 24 in total. Comparison of expression of genes were made between rats from each photoperiod at 3, 14 and 28 day timepoints.

first: Laura

last: Russell

first: Gisela

last: Helfer

first: Lynn

last: Bell

last: Morgan


title: Fetal blood transcriptome in maternal anti-fetal rejection

status: Public on Apr 01 2012

city: Detroit

first: Adi

last: Tarca

summary: Both the fetus and the mother who are involved in maternal anti-fetal rejection during pregnancy show distinct alterations in the peripheral blood transcriptome

overall_design: Total RNA isolated from umbilical cord blood and maternal blood was compared between cases without (Normal) and with maternal anti-fetal rejection  (FIRS2) using whole genome DASL assay.

first: Joo

middle: H

last: Lee

first: Roberto

last: Romero

first: Zhong

last: Dong

first: Yi

last: Xu

first: Juan

last: Kusanovic

first: Tinnakorn

last: Chaiworapongsa

first: Sonia

middle: S

last: Hassan

first: Chong

last: Kim


title: A Comparative Analysis of the Transcriptome of Hypoxia and Inflammation in Swan 71 Human Trophophoblast Cells: Its Implications in Preeclampsia

status: Public on Nov 15 2011

summary: Chemical hypoxia by CoCl2 treatment and pro-inflammatory cytokines induced distinct changes in the transcriptome of Swan 71 human trophoblasts.

overall_design: Not Paired. Samples were treated with control treatments (PBS) as well as with CoCl2, IL-1β, and TNFα.

first: Joon

last: Hong

first: Francesca

last: Gotsch

first: Gaurav

last: Bhatti

first: John

last: Hotra

first: Deug

middle: C

first: Nandor

middle: G

last: Than

first: Yeon


title: Genomic Run-On (GRO): determination of the nascent transcriptional rate and mRNA amount in Xrn1 mutants

status: Public on May 22 2013

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin - preferentially ~30bp upstream of transcription start-sites - and directly stimulate transcription initiation and elongation. Hence, the decaysome has a dual role in maintaining mRNA levels. Significantly, proper import of some decaysome components seems to play a key role in coupling the two functions. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected.

overall_design: This study focuses on the transcriptional activity of RNA pol II in 6035 S. cerevisiae ORFs. S. cerevisiae cells grown in YPD to exponential phase were subjected to Genomic Run-On. Data were normalized using gDNA hybridized on the same array and by the software ArrayStat. Home-made macroarrays containing 6035 ORFs were used.

first: José

middle: E

last: Pérez-Ortín

first: Daniel

last: Medina

first: Mordechai

last: Choder


title: Amniotic microRNA profile of normal delivery at term

status: Public on Sep 01 2011

first: Adi

last: Tarca

state: MI

summary: Amnion is a vital structure for human parturition, and it is anatomically compartmentalized into the placental amnion and the reflected amnion. microRNA expression was profiled to determine the expression pattern and its significance in the placental amnion and the reflected amnion in association with spontaneous labor at term.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: placental and reflected amnion tissue from two groups of women (term in labor and term no labor)

first: Sun

middle: Y

first: Roberto

middle: L

first: JoonHo

last: Lee

first: ChongJai


title: Treatment of prostate cancer cells with S-adenosylmethionine leads to genomewide alterations of transcription profiles

status: Public on Jul 18 2015

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The analysis investigates the impact of methyl donor S-adenosylmethionin on transcription and methylation profiles of prostate carcinoma cells.

overall_design: PC-3 cells (Prostate carcinoma cells) were treated with 160 micromolar S-adenosylmethionine or vehicle

first: Thomas

last: Schmidt

last: Lingner

last: Salinas-Riester


title: Temporal Analysis of Platelets as Cytotoxic Mediators in Sepsis-induced Acute Lung Injury (ALI)

status: Public on Feb 02 2008

city: Binghamton

first: Eric

last: Hoffman

state: NY

address: PO Box 6000

department: Pharmaceutical Sciences

institute: Binghamton University - SUNY

summary:
ALI is one of the most common disease processes in adult and pediatric intensive care units and results in significant morbidity and mortality. The pathophysiology of ALI begins with a massive pro-inflammatory response likely mediated by as yet uncharacterized platelet/endothelium interactions with macrophage activation. This leads to a cytokine/chemokine cascade producing endothelial disruption. Neutrophilic infiltration of the alveolar wall and alveolar space with a concomitant procoagulant state develops. Despite the fact that inadequate understanding of ALI pathophysiology remains a barrier to effective treatment, novel therapeutics including ventilatory manipulations and anti-inflammatory molecules are beginning to improve the morbidity and mortality associated with this disease process.
Keywords: Time Series Design, ALI - acute lung injury, ARDS - acute respiratory distress syndrome

overall_design: Acute Lung Injury (ALI) represents a spectrum of critical pulmonary illness in which inflammatory processes lead to varying degrees of alveolar damage and respiratory failure. ALI is a common disease process in the intensive care unit (ICU) with high morbidity and mortality. Based on new insights into the molecular processes of lung injury, we hypothesize that a temporal analysis of cells of innate immunity and thrombosis will demonstrate changes in mRNA and protein expression that are significantly associated with progression of ALI. Additionally, the analysis of the resulting datasets will lead to an unprecedented understanding of the pathogenesis of ALI.

first: Robert

last: Freishtat


title: Methylome of Fetal and Maternal Monocytes and Macrophages at the Feto-Maternal Interface

summary: Maternal and fetal monocytes and tissue macrophages (decidual macrophages, Hofbauer cells) at the feto-maternal interface have different methylome.

overall_design: Paired and balanced design.  We compared maternal blood monocytes (MB) vs. cord blood monocytes (CB), maternal blood monocytes (MB) vs. decidual macrophages (Deci), cord blood monocytes (CB) vs placental macrophages (villi) and decidual macrophages (Deci) vs. placental macrophages (villi).

last: Kim

last: Romero

first: Chong

first: Amelia

last: Elsey

first: Gabor

middle: N

first: Gyeong

last: Kang

first: Jung


title: IRF5 and IRF3 regulate distinct immune programs in plasmacytoid dendritic cells

status: Public on Dec 27 2017

first: Michael

last: Gale

state: Minnesota

department: Microbiology and Immunology

institute: University of Minnesota

summary: Transcriptomic analyses of pDCs show that the partitioning of TLR/IRF5 and RLR/IRF3 pathways confers differential gene expression and immune cytokine production in pDCs, linking IRF5 with immune regulatory and proinflammatory gene expression.

overall_design: mRNA-seq profiling of plasmacytoid dendritic cells treated with TLR7/8 agonist R848 vs. vehicle; also PAMP (pU/UC) and controls (xRNA) vs. no RNA

first: Kwan

middle: T

last: Chow

first: Courtney

last: Wilkins

first: Richard

last: Green

first: Connor

last: Driscoll

last: Gale Jr