title: Glucose-mediated regulation of glycerol uptake in Rhodosporidium toruloides: Insights through transcriptomic analysis on dual substrate fermentation

status: Public on May 12 2016

city: Newcastle upon Tyne

first: Rajesh Reddy

last: Bommareddy

address: Ellision building

department: Health Sciences

institute: Northumbria University

summary: The goal of the study is to use Next generation sequencing (RNA-seq) to study the underlying regulation of glycerol metabolism in mixed culture fermentation (glucose and glycerol) of  Rhodosporidium toruloides. We  sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) with 2 replicates each. Transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3–phosphate dehydrogenase (GUT2) enzymes were not down-regulated in the presence of glucose at the transcriptional level. It also showed that this yeast has a different regulation compared to S.cerevisiae. Certain insights into lipid biosynthesis on these mixed cultures are provided at systems level. This analysis  provides interesting targets for metabolic engineering in this organism growing on glucose and glycerol.

overall_design: Total  4 phases (glucose-nitrogen excess, glucose-nitrogen limited, diauxic shift, glycerol growth) were choosen and 2 replicates for each phase were pair-end sequenced using Illumina True seq kit on Illumina Hiseq 2000 platform.

first: Rajesh

first: Wael

last: Sabra

first: An-Ping

last: Zeng


title: Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare

status: Public on Jun 23 2016

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

country: USA

institute: University of Maryland

type: Expression profiling by high throughput sequencing

summary: Beef represents a major diet component and source of protein in many countries. With an increment demand for beef, the industry is currently undergoing changes towards natural produced beef. Consumers not only concern about product quality, but also for the well-being of animals. Therefore, the consumption of grass-fed meat is continuously growing. However, the nutritional true differences between feeding systems are still unclear. The aim of this study was to examine latissimus dorsi muscle quality and animal welfare by transcriptome and metabolome profiles, and to identify biological pathways related to the differences between grass- and grain-fed Angus steers. By RNA-Seq analysis of latissimus dorsi muscle, we have recognized 241 differentially expressed genes (FDR < 0.1). The metabolome examination of muscle and blood revealed 163 and 179 altered compounds in each tissue (P-value < 0.05), respectively.  Accordingly, alterations in glucose metabolism, divergences in free fatty acids and carnitine conjugated lipid levels, and altered β-oxidation, have been observed. In summary, this study demonstrates a unique transcriptomic and metabolic signature in the muscle of grain and grass finished cattle. Results support the accumulation of anti-inflammatory n3 polyunsaturated fatty acids in grass finished cattle, while higher levels of n6 PUFAs in grain finished animals may promote inflammation and oxidative stress. Furthermore, grass-fed animals produce tender beef with lower total fat and higher omega3/omega6 ratio than grain fed animals, which could potentially benefit consumer health. Finally, blood cortisol levels strongly indicate that grass fed animals experience less stress than the grass fed individuals

overall_design: The steers came from a closed Wye Angus herd with very similar genetics. The grass-fed group was comprised of steers that received alfalfa and orchard grass hay, clover and orchard grass pasture, or orchard grass and alfalfa pasture. The grass-fed individuals consumed grazed alfalfa upon availability and bales during winter and were not exposed to any corn, any form of grain or feed by-products. The alfalfa and grass hay were harvested from land that has had minimal fertilizer and no application of pesticides or inorganic chemicals.  The control group was fed a conventional diet consisting of corn silage, soybean, shelled corn and minerals. The pastures were managed as organic lands–without fertilizers, pesticides or any chemical additives. At the slaughter plant, 10 ml whole blood sample from the jugular vein was collected in EDTA tubes and directly storage at -80°C. Then, a small piece of longissimus dorsi muscle was obtained from each hot carcass at the level of the 12th intercostal space and immediately frozen in dry ice for posterior analysis.

first: José

middle: A

first: Yanghua

last: He

first: Yaokun

last: Li

first: Richard

last: Erdman

first: Tad

last: Sonstegard

first: Jiuzhou

last: Song


title: Investigation of gene expression alterations of pancreatic cancer caused by Deferasirox administration

status: Public on May 13 2016

city: Ube

first: Hirofumi

last: Harima

state: Yamaguchi

address: Minami Kogushi 1-1-1

department: Department of Gastroenterology and Hepatology

country: Japan

institute: Yamaguchi University Graduate School of Medicine

summary: To investigate the genetic effect of Deferasirox in pancreatic cancer, we examined gene expression alternations in the removed tumors exposed to Deferasirox.

overall_design: Pancreatic cancer cells (BxPC-3) in culture were harvested and viable cells were injected subcutaneously into the backs of the mice. When tumor volumes reached 150 mm3, treatment began. The treatment group of mice received Deferasirox suspended in saline, which was administered by oral gavage every second day, with three treatments per week, over 21 days at concentrations of 200 mg/kg. The control mice were treated with the vehicle alone. At the end of the experiment, the mice were sacrificed and the tumors were excised and processed for genetic analyses. A total of 6 tumors were analyzed. Of these, 3 tumors were removed from vehicle-treated mice, and the other 3 tumors were removed from Deferasirox 200 mg/kg-treated mice.


title: microRNA expression profiling of human small cell lung cancer cell lines in the Molecular Pharmacology Branch, DTP, DCTD NCI collection of human cell lines

status: Public on May 01 2016

city: Bethesda

first: Eric

middle: C

last: Polley

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

institute: National Cancer Institute

summary: Characterization of ~ 68 cell lines derived from human sarcoma and 5 normal counterpart cells,  including drug sensitivity testing, gene expression profiling and microRNA expression profiling have been completed. Data and tools for searching these data will be made  publicly available through the NCI Developmental Therapeutics Program. The raw data (RCC files) are  provided through the GEO website. Sarcoma represents a variety of cancers at arise from cells of mesenchymal origin and have seen limited treatment advances in the last decade. Drug sensitivity data coupled with the transcription and microRNA profiles of a cohort of sarcoma cell lines may help define novel treatment paradigms.

overall_design: For each cell line, microRNA expression was measured on nCounter miRNA Expression Arrays (Nanostring Technologies), providing multiplexed, digital detection and counting of 800 human microRNA's.

first: A

last: Monks

first: E

first: B

last: Teicher


title: Comparative analysis on Corynebacterium glutamicum transcriptome in response to the change of dissolved oxygen in bioreactor

status: Public on Feb 03 2016

city: wuxi

first: Sun

last: Yang

address: lihu avenue

department: School of Biotechnology

country: China

institute: JIANGNAN UNIVERSITY

summary: Purpose: dissolved oxygen (DO) level is an important factor that could significantly influence microorganisms’ growth, maintenance, metabolism and product yield.  The goals of this study are to do comparative analysis on Corynebacterium glutamicum transcriptome in response to the change of dissolved oxygen in bioreactor, find the critical pathways and genes.

overall_design: Method: three batches of fermentation were conducted with different DO level separately (50%, 30%, 0%), and sampled on 20h of fermentation, the transcriptome of Corynebacterium glutamicum generated using Illumina hiseq 2000.

first: Liu

last: Xiuxia


title: NCI small cell lung cancer cell line panel

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: Yap and Taz regulate retinal pigment epithelial cell fate

status: Public on Aug 06 2015

city: Milwaukee

first: Brian

last: Link

state: WI

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

summary: The optic vesicle comprises a pool of bi-potential progenitor cells from  which the retinal pigment epithelium (RPE) and neural retina fates  segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE  maintenance and differentiation, but an understanding of the initial  fate specification and determination of this ocular cell type is lacking.  We show that Yap/Taz-Tead activity is necessary and sufficient for  optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive  transgene is expressed within the domain of the optic cup  from which RPE arises, and Yap immunoreactivity localizes to the  nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of  RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is  exacerbated in combination with taz (wwtr1) mutant alleles such that,  when Yap and Taz are both absent, optic vesicle progenitor cells  completely lose their ability to form RPE. The mechanism of Yap dependent  RPE cell type determination is reliant on both nuclear  localization of Yap and interaction with a Tead co-factor. In contrast to  loss of Yap and Taz, overexpression of either protein within optic  vesicle progenitors leads to ectopic pigmentation in a dosagedependent  manner. Overall, this study identifies Yap and Taz as key  early regulators of RPE genesis and provides a mechanistic  framework for understanding the congenital ocular defects of  Sveinsson’s chorioretinal atrophy and congenital retinal coloboma.

overall_design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample.  Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.

first: Joel

middle: B

last: Miesfeld

middle: S

last: Clark

first: Michael

last: Flinn


title: Cistrome of the Aldosterone-activated Mineralocorticoid Receptor in Human Renal Cells

status: Public on Jun 12 2015

city: Le Kremlin-Bicêtre

first: Florian

last: Le Billan

address: 63, Gabriel Péri street

country: France

institute: INSERM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aldosterone, the main mineralocorticoid hormone in Humans, has a major role in maintaining the hemo-electrolytique homeostasis, by acting in the distal part of nephron. This steroid hormone mainly acts through its binding to a ligand-induced transcription factor, the mineralocorticoid receptor (MR). MR binds to specific genomic sequences, where it recruits transcriptional coregulators, to activate or repress target gene transcription. The aim of this work was to access the whole aldosterone-dependand MR target genes, by comparing sequenced data from aldosterone or vehicle-treated samples.

overall_design: Anti-MR ChIP-seq in Human Kidney GFP-hMR cells treated with vehicle or Aldosterone.

first: Junaid

last: Khan

first: Khadija

last: Lamribet

first: Say

last: Viengchareun

first: Sophie

last: Lemoine

first: Juliette

last: Pouch

first: Jérôme

last: Bouligand

last: Fagart

first: Marc

last: Lombès


title: A simple method for generating high-resolution maps of genome wide protein binding

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.

first: Peter

middle: J

last: Skene

first: Steven


title: Transcriptome analysis of aging muscle progenitors (human myoblasts)

status: Public on Jun 01 2015

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

summary:
Although sarcopenia is evident from the fifth decade, mechanisms leading to this phenomenon start earlier, emphasizing the importance of defining biomarkers related to the onset of muscle weakness. To this aim, a transcriptome analysis will be performed on muscle cell cultures (myoblasts) obtained from adult donors of different ages. Any biomarkers identified by this analysis will be confirmed by western blot and immunostatining. We will then assess the role of those biomarkers in muscle aging.
Human myoblasts were extracted from the quadriceps of young (15-20 years old) and elderly (>70 years old) healthy subjects . The muscle cell population has been sorted using CD56 MACS beads. The myogenicity and the life span analysis of each muscle cell extract have been determined.

overall_design: We analysed the transcriptome (mRNA profiles) of the same cells at day 1 (baseline) and day 3 of differentiation (n=4 for the baseline (day1 ) group, and n=3 per day 3 group;  Young and aged adult). This should allow us to identify which pathway(s) are disregulated with aging, and help to answer the fundamental question: whether muscle stem cells progressively loose their potential to self re-new during ageing. We also, treated old myoblasts  with 5-AZA to demethylate the DNA - and did microarray expression profiling before and after treatment. We used HumanHT-12 v4 Expression BeadChips for the whole transcriptome analysis.

first: Stephanie

last: Duguez


title: Epigenome analysis of aging muscle progenitors

status: Public on May 01 2015

city: Paris

first: Stéphanie

state: France

address: UPMC Univ. Paris 6 / U974

department: Thérapie des maladies du muscle strié

institute: Institut de Myologie

summary: Genome wide DNA methylation profiling of muscle cells extracted from healthy donors at different ages. The Illumina Infinium Human Methylation 450 BeadChip was used to obtain DNA methylation profiles across > 485,000 methylation sites.  The muscle cells were extracted from young adults (18-40 years old) and elderly (>70 years old)(n=3 per group, 2 groups : Young and aged adult).

overall_design: Bisulphite converted DNA from the 6 samples were hybridized to the Illumina Infinium Human Methylation 450 BeadChip

first: Anne

last: Bigot

first: William

last: Duddy

first: Gisèle

last: Ouandaogo

first: Elisa

last: Negroni

first: Brennan

last: Harmon

first: Joe

last: Devaney

first: Gillian

last: Butler-Browne

first: Vincent

last: Mouly


title: Transcriptomic profiling of spleen in grass-fed and grain-fed Angus cattle

status: Public on Mar 14 2016

first: Jose

last: Carrillo

summary: The grass-fed cattle obtain nutrients directly from pastures containing limited assimilable energy but abundant amount of fiber; by contrast, grain-fed steers receive a diet that is comprised mainly of grains and serves as an efficient source of high-digestible energy. Besides energy, these two types of diet differ in a large number of nutritional components. Additionally, animals maintained on rich-energy regimen are more likely to develop metabolic disorders and infectious diseases than pasture raised individuals. Thus, we hypothesize that spleen–the main immune organ–may function differently under disparate regimes. The objective of this study was to find the differentially expressed genes in the spleen of grass-fed and grain-fed steers, and furtherly explore the potential involved biopathways. Through RNA sequencing (RNA-Seq), we detected 123 differentially expressed genes. Based on these genes, we performed an Ingenuity Pathway Analysis (IPA) and identified 9 significant molecular networks and 13 enriched biological pathways. Two of the pathways, Nur77 signaling in T lymphocytes and calcium-induced T lymphocyte apoptosis which are immune related, contain a pair of genes HLA-DRA and NR4A1 with dramatically altered expression level. Collectively, our results provided valuable insights into understanding the molecular mechanism of spleen under varied feeding regimens.

overall_design: We collected spleen samples from two randomly chosen animals per group, totaling four samples. The animals were born and raised at the Wye Angus farm, which has produced genetically similar progenies. The genetic resemblance among individuals permitted us to better control the variation between experimental individuals, constituting an excellent resource to perform scientific research. All animals included in this study received the same diet until weaning. Next, we assigned the animals to one certain diet at random, and exclusively raised them under that regimen until termination. The diet of grain-fed group consisted of soybean, shelled corn, corn silage and trace minerals. The grass-fed steers normally received alfalfa harvested from land without any fertilizers, pesticides or other chemicals; during wintertime, bailage was supplied. Grass-fed individuals ate no animal, agricultural or industrial byproducts and never consumed any type of grain. Grain-fed animals reached the market weight around 14 month-old; however, grass-fed steers needed approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD), a small piece of spleen was incised, washed and frozen at -80°C for posterior processing.

first: Yaokun

last: Li

first: José

first: Ding

last: Yi

first: YangHua

last: He

first: Chunping

last: Zhao

first: Jianan

last: Liu

first: Linsen

last: Zan

first: Jiuzhou

last: Song


title: Ruminal transcriptomic analysis of grass-fed and grain-fed Angus beef cattle

status: Public on Mar 31 2015

summary: Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle.

overall_design: Ruminal wall samples from two randomly chosen animals per group were obtained, totaling four samples. The animals were born, raised and maintained at the Wye Angus farm. This herd, which has been closed for almost 75 years and yielded genetically similar progenies, constitutes an excellent resource to perform transcriptomic analysis. The genetic resemblance among individuals permits us to better control the cause of variation between experimental clusters and individuals. The randomly chosen pairs of animals were part of larger sets of steers that received a particular treatment. All animals received the same diet until weaning. The grain group received conventional diet consisting of corn silage, shelled corn, soy bean and trace minerals. The grass fed steers consumed normally grazed alfalfa; during wintertime, bailage was utilized. The alfalfa has been harvested from land without any fertilizers, pesticides or other chemicals. The steers ate no animal, agricultural or industrial byproducts and never receive any type of grain. Then, the calves were randomly assigned to one diet and exclusively received that regimen until termination. Grain–fed animals reached the market weight around the age of 14 month-old, however, grass-fed steers required approximately 200 additional days to achieve the same weight. Immediately after termination at the Old Line Custom Meat Company (Baltimore, MD) a small piece of ruminal wall was excised, cleaned and preserved at -80°C for posterior processing.


title: Global gene expression differences between blood- and lymphatic-specific endothelial colony forming cells

status: Public on Jun 23 2014

first: Terri

last: DiMaio

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: The identification of circulating endothelial progenitor cells has led to speculation regarding their origin as well as their contribution to neovascular development. Two distinct types of endothelium make up the blood and lymphatic vessel system. However, it has yet to be determined whether there are distinct lymphatic-specific circulating endothelial progenitor cells. We isolated circulating endothelial colony forming cells (ECFCs) from whole peripheral blood. These cells are endothelial in nature, as defined by their expression of endothelial markers and their ability to undergo capillary morphogenesis in three-dimensional culture. A subset of isolated colonies express markers of lymphatic endothelium, including VEGFR-3 and Prox-1, with low levels of VEGFR-1, a blood endothelial marker, while the bulk of the isolated cells express high VEGFR-1 levels with low VEGFR-3 and Prox-1 expression. The different isolates have differential responses to VEGF-C, a lymphatic endothelial specific cytokine, strongly suggesting that there are lymphatic specific and blood specific ECFCs. Global analysis of gene expression revealed key differences in the regulation of pathways involved in cellular differentiation between blood and lymphatic-specific ECFCs. These data indicate that there are two distinguishable circulating ECFC types, blood and lymphatic, which are likely to have discrete functions during neovascularization.

overall_design: RNA was isolated from 2 blood-specific ECFC cell lines and 2 lymphatic-specific ECFC cell lines 3 separate times each

first: Michael

last: Lagunoff


title: Expression profiling in proliferative thyroid lesions of different histologies and normal thyroid tissue

status: Public on Feb 16 2015

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

summary:
Experiment a) Establishment of expression profiles in conventional papillary thyroid carcinomas (PTCs) with a BRAF mutation vs. PTCs without a BRAF mutation and using normal thyroid (TN) specimens as reference.
Experiment b) Establishment of expression profiles in follicular adenomas (FAs) of the thyroid and follicular variant of papillary thyroid carcinomas (FVPTCs).

overall_design: We extracted DNA from specimens and performed mutational analysis in malignant lesions and extracted RNA that was processed and hybridized to Affymetrix microarrays.

first: Sajjad

last: Karim


status: Public on Aug 01 2014

city: Suwon

first: Myung Ae

last: Lee

state: Gyeonggi-do

address: Woncheon-dong, Yeongtong-gu

country: South Korea

institute: ajou univ school of medicine 607

summary: Identification of genes modulated by Nurr1 overexpression in HB-1

overall_design: HB-1 cells overexpressing Nurr1

first: Myung


title: Human CLP1 mutations alter tRNA biogenesis affecting both peripheral and central nervous system function

status: Public on Dec 18 2013

city: New York

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

type: Non-coding RNA profiling by high throughput sequencing

summary: We elucidate a neurological syndrome affecting both the PNS and CNS defined by CLP1 mutations that impair tRNA splicing

overall_design: Identification and biochemical characterization of mutant CLP1 in human patients

first: Javier

last: Martinez

first: Thomas

last: Tuschl


title: MMP12 is induced by UVA1 in vivo in humans

status: Public on May 15 2014

city: London

first: Angela

last: Tewari

address: 9th Floor Tower Wing, Guys Hospital

department: St. John's Institute of Dermatology

country: United Kingdom

institute: King`s College London

summary: UVA1 makes up ~75% terrestrial ultraviolet radiation (UVR) is increasingly being used for the treatment for inflammatory skin disorders.  It is also the major UVR spectral source in tanning lamps, however we lack human data to understand its effects on gene expression and further consequences.  Using erythemally equivalent doses of UVA1 (50J/cm2) and UVB (30mJ/cm2) ~1MED (minimal erythema dose), this study examines time dependent whole genome expression, mRNA and protein changes in 12 skin types I/II individuals.  The top upregulated pathway at 6h is inflammation through IL17 signaling for UVA1 (p=1.16e-6) and UVB (p=2.1e-4).  At 24h the top upregulated pathway is extracellular matrix remodeling for UVA1 (p=5.5e-7) and UVB (p=2.9e-22).  We show key spectral differences with matrix metalloproteinases (MMP): UVB upregulates MMP1 mRNA (p=0.0062), MMP3 mRNA (p=0.0016), MMP10 mRNA (p=0.028) at 24h compared to UVA1, MMP12 mRNA is upregulated by UVA1 at 6h and not by UVB (p=0.02).  In a further 3 skin type I/II we show that MMP12 protein is formed by UVA1 (p=0.04) at 24h and that DQ™ collagen type IV(likely MMP12 activity) hydrolysis occurs by UVA1 (p=0.027) at 10h.  DQ™ collagen type I hydrolysis occurs predominantly by UVB at 24h (p=0.031).  Both UVA1 and UVB upregulate MMP1 at 10h and 24h. There is more MMP1 and MMP12 protein and activity in the epidermis than in dermis in all volunteers.   We conclude that the biological processes that occur after 24h in human skin in vivo in response to erythemally equivalent doses of UVA1 and UVB are similar however there are key spectral differences: UVB plays a larger role in upregulating key MMPs in the epidermis.  MMP12 is a UVA1 specific biomarker found predominantly in the epidermis and maybe useful as a marker of UVA1 exposure.  We hypothesise that its formation by UVA1 could be related to the ability of UVA1 to produce significantly more oxidatively generated DNA than UVB (8oxodG).

overall_design: 47 samples were processed. The RNA was isolated from human skin samples of individual donors pre- or post irradiation with UVA or UVB. Skin biopsies were taken either before, 6h post, or 24h post exposure. Different doses of UVA were applied. Each condition was available from five or nine individuals, as indicated in the samples description below.

first: Katarzyna

last: Grys

first: Robert

last: Sarkany

first: Anthony

middle: R

last: Young


title: Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Endoderm RNA-seq and ChIP-seq data sets]

status: Public on Nov 22 2013

city: Stanford

first: Kyle

middle: M.

last: Loh

state: CA

address: 265 Campus Drive

department: Department of Developmental Biology

institute: Stanford University School of Medicine

summary: Unraveling complex signaling programs animating developmental lineage-decisions is pivotal to differentiate human pluripotent stem cells (hPSC) into pure populations of desired lineages for regenerative medicine. Developmental signals are strikingly temporally dynamic: BMP and Wnt initially specify primitive streak (progenitor to endoderm) yet 24 hours later suppress endoderm and induce mesoderm. At lineage bifurcations we show mutually-exclusive embryonic lineages are segregated through cross-repressive signals: TGFβ and BMP/MAPK duel to respectively specify pancreas versus liver from endoderm. Unilateral endodermal differentiation requires blockade of alternative fates at every stage, revealing a universal developmental strategy for efficient differentiation and anterior-posterior patterning of diverse hPSC lines into highly-pure endodermal populations. This culminated in hPSC-derived hepatic progenitors that, for the first time, engraft long-term in genetically-unconditioned mouse livers and secrete human albumin. Finally, thirty transcriptional and chromatin state maps capturing endoderm commitment revealed endodermal enhancers reside in an unanticipated diversity of "pre-enhancer" chromatin states before activation.

overall_design: Endoderm RNA-seq and ChIP-seq data sets

middle: M

first: Lay

middle: T

last: Ang

first: Jingyao

last: Zhang

first: Vibhor

last: Kumar

first: Shyam

last: Prabhakar

first: Irving

middle: L

last: Weissman

first: Bing

last: Lim


title: Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells


title: Exon expression for NCI small cell lung cancer cell line panel

first: Eric

last: Polley

summary: Characterization of 63 small cell lung cancer (SCLC) cell lines and a comparator set of non-small cell lung cancer and normal counterpart cells, including drug sensitivity testing, gene expression profiling and microRNA expression profiling have been completed. Data and tools for searching these data will be made publicly available through the NCI Developmental Therapeutics Program at http://SCLC.cancer.gov. SCLC is an aggressive, recalcitrant cancer and have seen limited treatment advances in the last 30 years. Drug sensitivity data coupled with the transcription and microRNA profiles of a cohort of SCLC cell lines may help define novel treatment paradigms.

overall_design: For each cell line, exon expression was measured using Genechip Human Exon 1.0 ST arrays from Affymetrix, to provide comprehensive coverage of the entire genome at the exon and gene expression level.

first: Anne

last: Monks

first: Beverly

last: Teicher


title: ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition

status: Public on May 03 2012

city: Lausanne

first: Markus

middle: Volker

last: Kohnen

state: Vaud

address: Genopode Building

department: Center for Integrative Genomics (CIG)

country: Switzerland

institute: Université de Lausanne

summary: Phytochrome Interacting Factor 5 plays an important role in adaptive responses of plants to shaded environment collectively called shade avoidance syndrome. PIF 5 belongs to the bHLH transcription factor family and regulated gene expression in a low R/FR dependent fashion. In this experiment we investigate PIF5-DNA-binding genome wide to generate a candidate list of genes, which are directly regulated by PIF5.

overall_design: ChIP-Seq sample of whole seedlings treated with low R/FR light

first: Patricia

last: Hornitschek

first: Jacque

last: Rougement

first: Ioannis

last: Xenarios

first: Christian

last: Fankhauser


title: Suppression of the antiviral response by an influenza "histone mimic"

status: Public on Jul 01 2013

city: new york

first: ivan

last: marazzi

state: ny

address: 1230 York Avenue

institute: rockefeller univeristy

summary: Viral infection is commonly associated with virus-driven hijacking of host proteins. We describe a novel mechanism by which influenza virus impacts host cells through the interaction of influenza NS1 protein with the infected cell epigenome. We show that the NS1 protein of influenza A H3N2 target the transcription elongation PAF1 complex (hPAF1C). We demonstrate that binding of NS1 to hPAF1C results in suppression of hPAF1C-mediated transcriptional elongation.  In the following data sets, we show that NS1 colocalizes with hPAF1 on the chromatin of infected cells and that siRNA-mediated reduction of hPAF1 expression results in reduced recruitment of NS1 to the chromatin.

overall_design: Examination of  different histone modifications in infected cells and RNA-Seq and GRO-Seq transcript measurements.

first: Ivan

last: Marazzi

first: Jessica

last: Ho

first: Jaehoon

last: Kim

first: Balaji

last: Manicassamy

first: Scott

last: Dewell

first: Randy

last: Albrecht

first: Chris

last: Seibert

first: Uwe

last: Schaefer

first: Kate

last: Jeffrey

first: Rab

middle: K

last: Prinjha

first: Kevin

last: Lee

first: Adolfo

last: García-Sastre

first: Robert

last: Roeder

first: Alexander

last: Tarakhovsky


title: Analysis of global gene expression profiles of hPAF1 deficient A549 cells during infection with H1N1 influenza A virus or vesicular stomatitis virus (VSV)

status: Public on Feb 15 2012

summary:
Viral infection is commonly associated with virus-driven hijacking of host proteins. We describe a novel mechanism by which influenza virus impacts host cells through the interaction of influenza NS1 protein with the infected cell epigenome. We show that the NS1 protein of influenza A H3N2 targets the transcription elongation PAF1 complex (hPAF1C). We demonstrate that binding of NS1 to hPAF1C results in suppression of hPAF1C-mediated transcriptional elongation.
More importantly,in the following data sets, we show that hPAF1 plays a crucial role in the antiviral response.  Loss of hPAF1C reduces antiviral gene expression and reduces inducible transcription of target genes after stimulation with viral RNA analogue poly(I:C), vesicular stomatitis virus (VSV), exogenous recombinant IFN(beta) and influenza virus (H1N1). This study underscores the importance of hPAF1C in controlling inducible antiviral gene expression.
Untreated (no siRNA), control siRNA-treated and hPAF1 siRNA-treated A549 cells were stimulated with A/Puerto Rico/8/1934 influenza virus (H1N1) or vesicular stomatitis virus (VSV). Total RNA was isolated with the Qiagen RNeasy mini kit. 200ng of total RNA per sample was used to prepare biotin-labeled RNA using MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems) and hybridized to HumanHT-12 v4 Expression BeadChips (Illumina). Data analysis was performed using the GeneSpring GX11.0 software (Agilent Technologies).

overall_design: 3 biological replicates per condition


title: Analysis of global gene expression profiles of hPAF1 deficient A549 cells during stimulation with PR8/∆NS1 influenza virus, IFNβ1 or Poly(I:C)

summary:
Viral infection is commonly associated with virus-driven hijacking of host proteins. We describe a novel mechanism by which influenza virus impacts host cells through the interaction of influenza NS1 protein with the infected cell epigenome. We show that the NS1 protein of influenza A H3N2 targets the transcription elongation PAF1 complex (hPAF1C). We demonstrate that binding of NS1 to hPAF1C results in suppression of hPAF1C-mediated transcriptional elongation.
More importantly,in the following data sets, we show that hPAF1 plays a crucial role in the antiviral response.  Loss of hPAF1C reduces antiviral gene expression and reduces inducible transcription of target genes after stimulation with viral RNA analogue poly(I:C), vesicular stomatitis virus (VSV), exogenous recombinant IFN(beta) and influenza virus (H1N1). This study underscores the importance of hPAF1C in controlling inducible antiviral gene expression.
Untreated (no siRNA), control siRNA-treated and hPAF1 siRNA-treated A549 cells were stimulated with PR8/∆NS1 influenza virus (MOI 1), IFNβ1 (500U/mL) or Poly(I:C) (2ug/mL). Total RNA was isolated with the Qiagen RNeasy mini kit. 200ng of total RNA per sample was used to prepare biotin-labeled RNA using MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems) and hybridized to HumanHT-12 v4 Expression BeadChips (Illumina). Data analysis was performed using the GeneSpring GX11.0 software (Agilent Technologies).


title: Analysis of global gene expression profiles of hPAF1 deficient A549 cells

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

overall_design: Refer to individual Series


title: ChIP-chip of histone variants and modifications in S. pombe WT and various mutants

status: Public on Dec 01 2012

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

type: Genome binding/occupancy profiling by genome tiling array

summary: ChIP-chip of histone variants and modifications in A. thaliana WT and various mutants

overall_design: In Schizosaccharomyces pombe, H2AZ, H3, H3 acetylated, H3K36me3, H3K4me3 as well as RNAPII (along with associated DNA sequences) were immunoprecipitated. The ChIPs were performed in duplicate from WT cells as well as in few mutants as described below. The extracted DNA was hybridized to a DNA microarray containing an average of 4 probes per kilobase across the whole yeast genome. The combined datasets are available in the supplemental files of the related publication.

first: Viviane

last: Page

first: Pierre-Étienne

last: Jacques

first: Francois

first: Jason

last: Tanny


title: Analysis of global gene expression profiles of hPAF1 deficiency on unstimulated A549 cells

first: ivan

last: marazzi

summary:
Viral infection is commonly associated with virus-driven hijacking of host proteins. We describe a novel mechanism by which influenza virus impacts host cells through the interaction of influenza NS1 protein with the infected cell epigenome. We show that the NS1 protein of influenza A H3N2 targets the transcription elongation PAF1 complex (hPAF1C). We demonstrate that binding of NS1 to hPAF1C results in suppression of hPAF1C-mediated transcriptional elongation.
More importantly,in the following data sets, we show that hPAF1 plays a crucial role in the antiviral response.  Loss of hPAF1C reduces antiviral gene expression and reduces inducible transcription of target genes after stimulation with viral RNA analogue poly(I:C), vesicular stomatitis virus (VSV), exogenous recombinant IFN(beta) and influenza virus (H1N1). This study underscores the importance of hPAF1C in controlling inducible antiviral gene expression.
A549 cells were untreated (no siRNA) or treated with control siRNA-treated and hPAF1 siRNA. Total RNA was isolated with the Qiagen RNeasy mini kit. 200ng of total RNA per sample was used to prepare biotin-labeled RNA using MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems) and hybridized to HumanHT-12 v4 Expression BeadChips (Illumina). Data analysis was performed using the GeneSpring GX11.0 software (Agilent Technologies). These samples were then used for comparisons with stimulated cells (See series 1)

first: Ivan

last: Marazzi

first: Jessica

last: Ho

first: Jaehoon


title: Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping

status: Public on Oct 30 2013

first: Jie

last: Yao

address: 615 Westlake Ave N

institute: Allen Institute

summary: How gene positioning to the nuclear periphery regulates transcription remains largely unclear. We have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we have integrated high throughput DNA sequencing into the DNA adenine methyltransferase identification (DamID) assay, and have identified ~15, 000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts. These genomic regions range from a few kb to over 1 Mb and cover ~30% of the genome, and are spatially proximal to the nuclear lamina (NL). Active histone modifications such as H3K4me2, H3K9Ac, H3K36me3 and H3K79me2 are all localized away from the nuclear periphery microscopically, and distributed predominantly out of sLADs genome-wide. Therefore, the spatial compartmentalization of active histone modifications likely characterizes a major portion of chromatin at the nuclear periphery in mammalian cells. Genomic regions around transcription start sites of expressed sLAD genes display reduced associations with the NL and possess active histone modifications; in contrast, gene bodies of expressed sLAD genes possess very low levels of active histone modifications.  Our genome-wide analyses of NL-associated chromatin have enabled functional and mechanistic dissections of gene positioning on transcription regulation.

overall_design: generate DamID maps of genome-NL interaction for mouse 3T3 fibroblasts and C2C12 myoblasts with two control samples (*genomic DNA samples).

first: Feinan

last: Wu


title: Maternal Style Selectively Shapes Amygdalar Development and Social Behavior in Rats Genetically Prone to High Anxiety

status: Public on Oct 19 2016

city: Blacksburg

first: Sarah

middle: Megan

last: Clinton

state: Virginia

address: 1981 Kraft Dr., Integrated Life Sciences Building 0913

department: School of Neuroscience

institute: Virginia Polytechnic Institute and State University

summary:
The early-life environment critically influences neurodevelopment and later psychological health. To elucidate neural and environmental elements that shape emotional behavior, we developed a rat model of individual differences in temperament and environmental reactivity. We selectively bred rats for high versus low behavioral response to novelty and found that high-reactive (bred high-responder, bHR) rats displayed greater risk-taking, impulsivity and aggression relative to low-reactive (bred low-responder, bLR) rats, which showed high levels of anxiety/depression-like behavior and certain stress vulnerability. The bHR/bLR traits are heritable, but prior work revealed bHR/bLR maternal style differences, with bLR dams showing more maternal attention than bHRs. The present study implemented a cross-fostering paradigm to examine the contribution of maternal behavior to the brain development and emotional behavior of bLR offspring. bLR offspring were reared by biological bLR mothers or fostered to a bLR or bHR mother and then evaluated to determine the effects on the developmental gene expression in the hippocampus and amygdala. Genome-wide expression profiling showed that cross-fostering bLR rats to bHR mothers shifted developmental gene expression in the amygdala (but not hippocampus).
All samples were generated from Sprague-Dawley male rats selectively bred for high novelty response (HRs), low novelty response (LRs) or LRs that were crossfostered to either a LR dame or HR dame.

overall_design: Within each age and brain regions, the sample size of each group is 5 samples.

first: Matthew

middle: E

last: Glover

first: Joshua

last: Cohen

first: Chelsea

last: McCoy


title: To define the role of glycosylation in the interaction and metastatic behaviour of tumor cells

status: Public on Sep 06 2011

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: The aim of our study is to define the role of glycosylation in the interaction of pancreatic tumor cells with dendritic cells and/or in the metastatic behaviour of the tumor cells.

overall_design:
We want to examine two cell lines, established from the same primary human pancreatic tumor, which exhibit different grades of differentiation as well as a different potency to metastasize.
We believe that these cell lines represent a suitable model for study of glycosylation in the cell biology of human pancreatic adenocarcinoma.

first: Irma

last: Van Die

first: Alex

last: Moffit


title: Transcriptomic alterations in a myoblast cell line infected with four distinct strains of Trypanosoma cruzi

status: Public on Sep 23 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We examined the extent to which different Trypanosoma cruzi strains induce transcriptomic changes in cultured L6E9 myoblasts 72 hours or 48 hours after infection with four strains of the parasite [Brazil (TCI); Y, CL and Tulahuen (TC II) strains]. Expression of 6,289 distinct fully annotated unigenes was quantified with 27k rat oligonucleotide arrays in each of the four replicas of all control and infected RNA samples. Considering changes >1.5-fold and p-val<0.05, the Tulahuen strain was the most disruptive to host transcriptome, with (17% significantly altered genes), while in Y strain altered only 6% of the genes were altered. The significantly altered genes in the infected cells were largely different among the four strains, with only 21 genes changed in the same direction being similarly changed by all four strains. However, when expression ratios of all genes were compared, myoblasts infected with different strains showed proportional overall genbe expression alterations. These results indicate that infection with different parasite strains modulates similar but not identical pathways in the host cells.

overall_design: 20 µg total RNA extracted in Trizol from each of the 20 cell culture dishes containing control or infected with (Y, CL, Tulahuen or Brazil) Trypanosoma cruzi strains (4 dishes for each strain) was reverse transcribed in the presence of fluorescent Alexa Fluor®_647 or Alexa Fluor®_555-aha-dUTPs (Invitrogen, CA) to obtain labeled cDNAs. Red and green-labeled samples of biological replicas were then co-hybridized (“multiple yellow” strategy) overnight at 50°C with Operon v3.0 Rat 27k oligonucleotide arrays printed by Duke University (GPL9207). After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNA, each array was scanned with GenePix 4000B scanner (MDS, Toronto, Canada) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

first: Daniel

last: Adesse

first: Sanda

first: Luciana

last: Garzoni

first: Maria

middle: N

last: Meirelles

first: Herbert

last: Tanowitz

first: David

last: Spray


title: Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing in Neurospora crassa

status: Public on Apr 15 2020

city: Eugene

first: Elizabeth

middle: Toomey

last: Wiles

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

summary: Here we utilize a forward genetics approach in Neurospora crassa to identify novel effectors of Polycomb repression. We recovered several mutant alleles of a gene (NCU07505),which we deemed effector of Polycomb repression 1 (epr-1), encoding a protein with a bromo-adjacent homology (BAH) domain and plant homeodomain (PHD) finger. Although epr-1mutants display phenotypic and gene expression changes similar to strains lacking PRC2 components, H3K27 methylation is notably unaffected. We demonstrate that EPR-1 forms nuclear foci, reminiscent of Polycomb bodies {Pirrotta:2012br}, and its genomic distribution is limited to and dependent upon H3K27-methylated chromatin, which it recognizes through its BAH domain. Finally, we discover that EPR-1 homologs are widely distributed across eukaryotes, contrary to previous reports {LopezGonzalez:2014id, Li:2018kg}, suggesting an ancient role of EPR-1 homologs in Polycomb repression that was secondarily lost in select lineages.

overall_design:
ChIP-seq: We perform H3K27me2/3 ChIP-seq in ∆epr-1 strains to determine the effests of loss of epr-1 on H3K27me2/3 distribution. We perform GFP ChIP of GFP-tagged EPR-1 (WT, PHD, and BAH) to determine the genomic localization of EPR-1.
RNA-seq: We performed polyA-RNAseq on ∆epr-1 strains and compared gene expression levels to previously published data sets from wild type and ∆set-7 (in Series GSE82222).
DamID-seq: We performed DamID-seq on Dam tagged EPR-1 in a wild type and ∆eed background and a Dam tagged EPR-1 PHD mutatnt to determine the chromatin targets of EPR-1.

first: Kevin

last: McNaught

first: Gurmeet

last: Kaur

first: Jeanne

last: Selker

first: Tereza

last: Ormsby

first: L

last: Aravind

first: Eric

middle: U