title: Comparing miRNA Signature of Colon Cancer Primary Tumors to Metastases Formed in the Liver

status: Public on May 02 2017

city: Portland

first: Amiee

middle: Bell

last: Potter

state: OR

address: 3181 SW Sam Jackson Park Rd, Mail Code #L581

department: Integrated Genomics Laboratory

institute: OHSU

summary:
Genome wide miRNA expression profiling was performed using Affymetric miRNA v. 3.0 Array on 48 samples which included paired FFPE colon tuomor and metastisized liver and paired normal colon, normal liver). The data set was divided into two categories and identified by tissue source and patient demographics: Tissue (Colon, Liver), Source (Colon Tumor Liver Met, Colon Normal, Liver Normal), Sex (Male, Female), Patient Pair.
microRNAs (miRs) are frequently dysregulated in colorectal cancer (CRC) and subsets are correlated with advanced tumor stage and metastasis. Despite this, the development of prognostic biomarkers that predict metastatic potential remain limited. Our study was designed to identify, validate, and elucidate underlying biology imposed by a miR signature that defines and predicts metastatic disease. Genome-wide miR expression profiling was performed on fourteen patient-matched stage IV primary CRC tumors and corresponding liver metastases using microRNA array technology. Based on these results, this miR panel was then validated and evaluated in normal colon tissue (N = 5), early stage (I & II, N = 11) and late stage (Stage III & IV, N = 14) colorectal primary tumors via qRT-PCR.

overall_design: General study design included biological replicates and controls. miRNA was isolated from paired FFPE colon tumor and metastasized liver tumor samples derived from the same patient.  Controls were paired normal colon and liver samples from the same patients.  There were 42 samples total including: 28 paired patient colon tumor (14) and liver metastases (14), 14 paired normal colon (7) and normal liver (7).  Thus, biological replicates

first: Katherine

last: Kelley

first: Nicole

last: Wieghard

first: Yuki

last: Chin

first: Motomi

last: Mori

first: Christian

last: Lanciault

first: Melissa

last: Wong

first: Koei

first: Sudarshan

last: Anand

first: V

last: Tsikitis


title: Expression of inflammatory and structural matrix genes in synovial fluid following intra-articular administration of isoflupredone acetate to exercised horses

status: Public on May 03 2017

city: Davis

first: Heather

last: Knych

state: California

address: 620 W.  Health Sciencse Drive

department: CAHFS

country: USA

institute: University of California Davis

summary: In the current study, we use gene expression approach to assess the effects and duration of action of IPA on the expression levels of genes encoding pro and anti-inflammatory genes and structural proteins in an exercised horse model.Equine specific microarrays containing expression profiling of 25,923 genes were used.  Baseline samples collected the day prior to IPA administration were compared to those collected at 24 hours and on day 7 and samples from day 7 compared to 24 hours.  The volcano plots of differentially expressed abundant transcripts generated from microarray analysis are depicted in Figure 2.  Comparison of baseline samples to 24 hours revealed 855 differentially expressed genes with 632 genes up-regulated and 223 genes down regulated.  Comparison of baseline samples to those collected on day 7 showed 23,358 genes differentially expressed with 23,318 genes up-regulated and 40 down regulated.  When samples from day 7 were compared to 24 hours, 26,411 genes were differentially expressed with 26,409 genes up-regulated and 2 genes down regulated.  Based on the results of the microarray analysis (greatest fold change and statistical significance), 20 genes were chosen for further analysis to quantitate the change in expression levels, relative to baseline, at several time points post drug administration.

overall_design: Twelve university owned exercised adult Thoroughbred horses including 6 geldings and 6 mares age: 4-8 years; weight: 492-600 kg) were studied.  Horses did not receive corticosteroids or any other intra-articular medications for at least one year and any other medications for at least two weeks prior to commencement of the study.  This study was approved by the Institutional Animal Care and Use Committee of the University of California, Davis. Each horse was weighed the morning of drug administration and a 14- gauge catheter placed in the external jugular vein for blood sampling. Immediately prior to drug administration, the area over the right antebrachiocarpal joint was scrubbed with betadine solutionc and 70% isopropyl alcohol, the joint flexed and a total dose of 8 mg of IPA (Predef® 2X)d  or 0.9% saline administered aseptically into the right joint. Two days after synovial fluid collection, horses were allowed to freely exercise in a round pen.  Horses returned to their regular exercise regimen on day 3 post drug administration.  The IPA dose chosen for this study was based upon a published survey of the most commonly used dose by equine practitioners [ Ferris, D.J, 2009].

first: Linda

last: Harrison

first: Nadira

last: Chouicha

first: Philip

last: Kass


title: Transcriptional Analysis of Articular Cartilage in Knee Osteoarthritis: Relationship with Obesity

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

summary: Objective: To examine the changes in tibial plateau cartilage in relation to body mass index (BMI) in patients with end-stage osteoarthritis (OA).    Design: Knees were obtained from 23 OA patients (3 non-obese, 20 obese) at the time of total knee replacement. RNA prepared from cartilage was probed for differentially expressed (DE) gene transcripts using RNA microarrays and validated via real-time PCR. Differences with regard to age, sex, and between medial and lateral compartments were also queried.    Results: Microarrays revealed that numerous transcripts were significantly DE between non-obese and obese patients (≥1.5-fold) using pooled and separate data from medial and lateral compartments. Correlation analyses showed that 706 transcripts (459 positively, 247 negatively) were significantly correlated with BMI. Among these, HS3ST6, HSD17B12, and FAM26F were positively correlated while STAC3, PRSS21, and EDA were negatively correlated. Differentially correlated transcripts represented important biological processes e.g. cellular metabolic processes, anatomical structure morphogenesis and cellular response to growth factors. Although age and sex had some effect on transcript expression, most intriguing results were observed for comparison between medial and lateral compartments. Transcripts (MMP13, CLEC3A, MATN3, EPYC, SCARNA5, COL2A1) elevated in the medial compartment represented skeletal system development, cartilage development, collagen and proteoglycan metabolism, and extracellular matrix organization. Likewise, transcripts (SELE, CTSS, VSIG4, F13A1, and STEAP4) repressed in medial compartment represented host immune response, cell migration, wound healing, cell proliferation and response to cytokines. PCR data confirmed expression of DE transcripts.    Conclusions: This study supports molecular interaction between obesity and OA and implies that BMI is an important determinant of transcript-level changes in cartilage.

overall_design: Total RNA obtained from isolated from medial and lateral tibial plateau cartilage from patients undergoing total knee arthroplasty.

first: Muhammad

middle: F

middle: J

last: Sandell

first: Robert

middle: L

last: Barrack


title: Gene expression change by miR-17-92 in the dorsal root ganglion

status: Public on May 09 2017

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

summary: Gene expression profile of L5 DRG was examined to analyze a role of miR-17-92 in the DRG.

overall_design: Gene expression in the L5 DRG was measured in rats 7 days after injection of control or miR-17-92-expressing AAV vector (n = 4).

first: Fumihito

last: Saitow

first: Motoyo

last: Maruyama

first: Noriko

last: Miyake

first: Koichi

first: Takashi

last: Shimada

last: Okada

first: Hidenori

last: Suzuki


title: Expression data from subcutaneous adipose tissue of lean polycystic ovary syndrome (PCOS) and normoandrogenic women

city: Los Angeles

first: Daniel

last: Dumesic

state: CA

address: 10833 Le Conte Ave, CHS 22-222

department: Ob/Gyn

institute: UCLA

summary:
Lean polycystic ovary syndrome (PCOS) women have a greater proportion of android (abdominal) fat, increased numbers of small subcutaneous (SC) abdominal adipocytes and preferential intra-abdominal fat accumulation. This study examines whether abnormal gene expression of SC abdominal adipose stem cells (ASCs) from lean PCOS women underlies this altered abdominal adipose structure-function.
In this dataset, we include the expression data obtained from PCOS and NL subcutaneous adipose tissue. Differential expression of at least 1.5-fold change (P<0.05) were obtained in 120 genes (48 upregulated, 72 downregulated) of SC abdominal ASCs from PCOS versus NL women

overall_design: Julia,D,Phan

first: Vanessa

middle: K

last: Madrigal

first: Samantha

middle: C

last: Fisch

first: Annie

middle: A

last: Guedikian

first: Elizabeth

last: Wright

first: Ariela

last: Nikou

first: Xiangming

last: Ding

first: Xinmin

last: Li

first: Gregorio

middle: D

last: Chazenbalk


title: Denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary

city: Gulf Breeze

first: Jessica

middle: Anne

last: Lisa

state: FL

address: 1 Sabine Island Drive

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA.  Multivariate statistical analyses revealed three denitrifier assemblages and uncovered “generalist” and “specialist” archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 11-29% of the abundant NRE archetypes. Archetypes found in a particular site, “specialists”, were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe2+. A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H2S, respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among denitrifying communities and supports the essential role of individual community members in overall ecosystem function.

sample_organism:
synthetic construct
uncultured bacterium

overall_design: Two color array (Cy3 and Cy5): 90-mer oligonucleotide probe consisting of 70-mer archetype sequence and a 20-mer reference oligo is printed to the slide. Cy3 fluoresced environmental DNA sequences, within 15% of the 70-mer archetype, and the 20-mer, Cy5 fluoresced complementary reference oligo will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Two replicate arrays were run on duplicate targets.

first: Bess

last: Ward

first: Amal

last: Jayakumar

first: Bongkeun

last: Song


title: Acute and chronic treatment of trametinib plus lapatinib in patient-derived xenografts (PDX) of pancreatic adenocarcinoma (PDAC)

city: Charlottesville

first: Edik

middle: Matthew

last: Blais

state: Virginia

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

summary: Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease with limited effective treatment options. PDAC tumors frequently harbor the constitutively activated form of KRAS which drives proliferative signaling, but directly targeting KRAS has so far been unsuccessful. To overcome this limitation, combinatorial treatment strategies have been developed to inhibit upstream activators and downstream effectors of KRAS signaling. One such combination using trametinib, a MEK1/2 inhibitor, and lapatinib, an EGFR/HER2 inhibitor, substantially reduced tumor growth in a patient-derived xenograft (PDX) model of PDAC. Although trametinib and lapatinib are both known to inhibit the canonical MAPK signaling cascade, the effects of this combination on other important pathways in pancreatic cancer remains unclear. To investigate this, we analyze global gene expression profiles from PDX models of PDAC treated with trametinib, lapatinib, or their combination. Our results show that trametinib induces similar yet less significant expression changes compared to combination while lapatinib has little to no effect as a monotherapy in the acute treatment setting. In the chronic treatment setting, we show that tumors exposured to prolonged treatment with trametinib plus lapatinib eventually leads to adapative resistance. Expression analyses of resistant tumors revealed concominant gene expression changes in upstream receptor tyrosine kinases (RTKs).

overall_design: Patient-derived xenografts (PDX) from patients with pancreatic adenocarcinoma (PDAC) were explanted onto the pancreata of nude mice to evaluate the effects of trametinib (a MEK inhibitor), lapatinib (an EGFR/HER2 inhibitor) after acute (24 hours) exposure and chronic (3 months) exposure. In a factorial design, tripliate samples were obtained from T366, T608, and T738 tumors treated acutely with trametinib (3 mg/kg) plus lapatinib (65 mg/kg), trametinib (3 mg/kg) alone, lapatinib (65 mg/kg) alone, or vehicle controls.

middle: M

first: Sara

last: Adair

first: Dustin

last: Walters

first: James

last: Lindberg

first: Timothy

middle: E

last: Newhook

first: Matthew

middle: G

last: Mullen

first: Alex

last: Michaels

first: Jason

last: Papin

first: J

middle: T

last: Parsons

first: Todd

middle: W

last: Bauer


title: Liver progenitor cell response to human amniotic epithelial cell conditioned media

city: Clayton

last: Hodge

state: VIC

address: 246 Clayton Road

department: Gastroenterology and Hepatology Unit

country: Australia

institute: Monash Health

summary: To investigate the changes in liver progenitor cell (LPC) gene expression in response to human amniotic epithelial cell (hAEC) conditioned media. To find supporting evidence to indicate that hAEC conditioned media promotes proliferation and differentiation of LPC’s. To elucidate which pathways are up or down regulated in LPC’s in order to find potential mechanisms and candidate effector factors produced by hAEC’s.

overall_design: 8 Samples with 3 different medias

first: Alexander

first: William

last: Sievert

first: Rebecca

last: Lim


title: Expression data from C6 glioma and small molecule induced cells (SMiN)

city: Seoul

first: Jinsoo

last: Oh

address: Yonsei-ro, Shinchon-dong, Seodaemoon-gu

department: Neurosurgery

country: South Korea

institute: Yonsei University

summary:
Here we show that malignant glioma can be converted into fully differentiated neurons with no malignant characteristics through the combined action of two small molecules.
Gene ontology and gene expression profiles related to cell division, gliogenesis, and angiogenesis were significantly down-regulated in SMiNs.

overall_design: We investigated the various changes involving gene expression, cell-specific marker expression, signalling pathways, physiological characterization, and morphology in glioma after combination treatment with two small molecules (GSK3 inhibitor and cAMP activator).


title: Expression data from breast cancer cells MDA-MB-231

status: Public on May 01 2017

city: Beijing

first: Jie

last: Wu

address: #5, dongdan 3, dongcheng district

country: China

institute: Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science

summary:
CCCTC-binding factor (CTCF) is an important epigenetic regulator that has been implicated in multiple cellular processes including growth, proliferation, differentiation, and apoptosis. Deletion or mutation of CTCF is associated with human breast carcinogenesis. However, the exact role that CTCF plays in breast cancer has not been fully elucidated.
To investigate the biological functions of CTCF in breast cancer and the underlying mechanisms, we carried out microarray analysis comparing the gene expression of CTCF overexpressing and control MDA-MB-231 cells to screen the possible target genes and pathways that CTCF regulated.

overall_design: Total RNA from MDA-MB-231 cell infected with NC-lentivirus (n=3) or CTCF-OE-lentivirus (n=3) was extracted using Trizol reagents. NanoDrop 2000 and Agilent Bioanalyzer 2100 were used for detecting the RNA quantity and quality. The GeneChip PrimeView Human Gene Expression Array (Affymetrix) was used for microarray processing to determine gene expression profile depending on the manufacturer’s instruction.


title: Gene expression analysis of S. mutans wild type and lmrB mutant

city: Guangzhou

first: Jia

last: Liu

state: Guangzhou

address: 74 Zhong Shan Er Road,

institute: Sun Yat Sen University

summary: We used whole-genome microarrays to identify the global transcriptional changes upon lmrB deletion and also to investigate the molecular function of lmrB product

overall_design: S. mutans wild type cells and lmrB mutant cells at mid-log phase were collected for microarray analysis

first: Xi

last: Wei


title: The 11q-gain/loss aberration occurs recurrently in MYC-negative as well as MYC-positive Burkitt lymphoma and high grade B cell lymphoma

city: Warsaw

first: Beata

last: Grygalewicz

address: 15B Wawelska str

country: Poland

institute: Cancer Center and Institute of Oncology

type: Genome variation profiling by genome tiling array

summary: Detailed analysis of 11q aberrations consisted of duplication, terminal deletion and inversion performed by SNP/aCGH on 11 patients with BLL,11q; BL and HGBL,NOS diagnosis.

overall_design: Two color experiment, hybridization tumor sample vs normal (pooled), sex matched

first: Renata

last: Woroniecka


title: Human Yes Associated Protein (hYAP) expressing mouse liver

city: Bunkyo-ku

first: Hiroshi

last: Nishina

state: Tokyo

department: Department of Developmental and Regenerative Biology

institute: Medical Research Institute,Tokyo Medical and Dental University (TMDU)

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

overall_design: Refer to individual Series


title: SNP array data of multi regional colorectal carcinoma

city: FUKUOKA

first: RYUTARO

last: UCHI

state: FUKUOKA

institute: KYUSHUUNIVERSItY

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients’ ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease.

overall_design:
We isolated genomic DNA from geographically separated samples of eight series of colorectal carcinoma and matched normal mucosa to hybridise to the HumanOmniExpress BeadChip.
*** Raw data not provided for this record (because experiments were performed in other organization) ***

first: Ryutaro

last: Uchi

first: Yusuke

last: Takahashi

first: Atsushi

last: Niida

first: Teppei

last: Shimamura

first: Hidenari

last: Hirata

first: Keishi

last: Sugimachi

first: Genta

last: Sawada

first: Takeshi

last: Iwaya

first: Junji

last: Kurashige

first: Yoshiaki

last: Shinden


title: Wild type (WT), partial hepatectomy, and lncHand2 KO chip

status: Public on Apr 29 2017

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary:
To identify differential genes after partial hepatectomy, we performed gene chip analysis of livers from wild type (WT) mouse and PHx 36h mouse livers
To find differential genes regulated by lncHand2, we performed gene chip analysis from WT and lncHand2 deficiency livers.

overall_design: We used one wild type, one partial hepatectomy, and one lncHand2 knockout mice.

first: Zusen

last: Fan


title: Mapping the human DC lineage through the integration of high dimensional techniques

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type: Expression profiling by high throughput sequencing

summary: Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. The human DC population comprises two main functionally-specialized lineages, whose origins and differentiation pathways remain incompletely defined. Here we combine two high-dimensional technologies — single-cell mRNA sequencing and Cytometry by Time-of-Flight (CyTOF), to identify human blood CD123+CD33+CD45RA+ DC precursors (pre-DC). Pre-DC share surface markers with plasmacytoid DC (pDC) but have distinct functional properties that were previously attributed to pDC. Tracing the differentiation of DC from the bone marrow to the peripheral blood revealed that the pre-DC compartment contains distinct lineage-committed sub-populations including one early uncommitted CD123high pre-DC subset and two CD45RA+CD123low lineage-committed subsets exhibiting functional differences. The discovery of multiple committed pre-DC populations opens promising new avenues for the therapeutic exploitation of DC subset-specific targeting.

overall_design: single-cell RNA Seq of human dendritic cells

first: Peter

last: See

first: Charles-Antoine

last: Dutertre

first: Jinmiao

last: Chen

first: Patrick

last: Günther

first: Naomi

last: McGovern

first: Sergio

last: Irac

first: Merry

last: Gunawan

first: Marc

last: Beyer

first: Kristian

last: Händler

first: Kaibo

last: Duan

first: Hermi

middle: R

last: Sumatoh

first: Nicolas

last: Ruffin

first: Mabel

last: Jouve

first: Ester

last: Gea-Mallorquí

first: Raoul

last: Hennekam

first: Tony

last: Lim

first: Chan

last: Yip

first: Ming

last: Wen

first: Benoit

last: Malleret

first: Ivy

last: Low

first: Nurhidaya

middle: B

last: Shadan

first: Charlene

last: Fen

first: Alicia

last: Tay

first: Josephine

last: Lum

first: Francesca

last: Zolezzi

first: Anis

last: Larbi

first: Michael

last: Poidinger

first: Jerry

last: Chan

first: Qingfeng

first: Laurent

last: Renia

first: Muzlifah

last: Haniffa

first: Philippe

last: Benaroch

first: Andreas

last: Schlitzer

first: Evan

last: Newell

first: Florent

last: Ginhoux


title: Human Yes Associated Protein (hYAP) expressing mouse liver (set 2)

first: Hiroshi

last: Nishina

summary: To check the gene expression profiles on hYAP Wild-type (WT) or active-form (1SA) and (2SA) expressing mouse liver

overall_design: We analysed gene expression profiles in livers of mice expressing YAP (WT), YAP (1SA) or YAP (2SA) at 2 days after Hydrodynamic gene delivery.

first: Norio

last: Miyamura


title: The unique C-terminal and N-terminal sequences of MT3 on gene expression profiles of MCF-7 cells

city: Grand Forks

first: Donald

last: Sens

state: ND

address: 1301 North Columbia Road

department: Pathology

institute: University of North Dakota

summary: MCF-7 cells were transfected with various metallothionein gene constructs with contain the insertion or the removal of the unique MT3 C- and N-terminal domains. The goal of this study was to determine how the global gene expression of the unique C- and N- terminal domains of MT3 was correlated to phenotypic properties of the cells.

overall_design: Various gene constructs that were made by the alteration of the unqiue MT3 N- and C-terminal region have been stably transfected into the MCF-7 cells. Each gene construct was repeated in triplicate for array analysis.

first: Somji

last: Seema

first: Voels

last: Brent

first: Zhang

last: Kurt

first: Garrett

last: Scott


title: Exposure to Deepwater Horizon Oil and Corexit 9500 at Low Concentrations Induces Transcriptional Changes and Alters Immune Transcriptional Pathways in Sheepshead Minnows

city: Florence

first: Elizabeth

middle: R.

last: Jones

state: SC

address: 4822 E. Palmetto St.

department: Biology

institute: Francis Marion University

summary: To investigate molecular effects in fish following exposure to environmentally relevant concentrations of dispersants and DWH oil, we exposed adult sheepshead minnows (Cyprinodon variegatus) to Corexit 9500™ and two concentrations of high-energy water-accommodated fraction (HEWAF) or chemically enhanced water-accommodated fraction (CEWAF) for 7 and 14 days. Resulting changes in hepatic gene expression were measured using Agilent 8x15K microarrays. We observed significant changes to gene expression in all treatments (relative to controls), with Corexit and CEWAF having a greater effect on expression patterns in the liver than HEWAF treatments. Sub-network enrichment analysis of biological pathways revealed that the greatest number of altered pathways in high dose HEWAF and CEWAF treatments occurred following a 7-day exposure. Pathways related to immunity comprised the majority of pathways affected in each treatment, followed by pathways related to blood and circulation processes.

overall_design: Adult Sheepshead minnows were exposed to two doses of oil, dispersed oil, or a single dose of dispersant for 7 or 14 days.  Each  treatment consisted of four tanks with one individual sampled from each tank for this study.  After exposure, fish were sacrificed , liver tissue collected, and samples stored in RNA Later at -80  until further analysis. Total RNA was extracted, labeled with Cy3, and hybridized to Agilent  8 x 15k micorarrays to measure changes in gene expression.

first: Christopher

last: Martyniuk

first: Jeffrey

last: Morris

first: Michelle

middle: O

last: Krasnec

first: Robert

last: Griffitt


title: Human Yes Associated Protein (hYAP) expressing mouse liver (set 1)

summary: To check the gene expression profiles on hYAP Wild-type (WT), active-form (5SA) or inactive-form (5SA/TEAD*) expressing mouse liver

overall_design: We analysed gene expression profiles in livers of mice expressing YAP (WT), YAP (5SA) or YAP (5SA/TEAD*) at 2 days after Hydrodynamic gene delivery.


title: Mapping of mitotic gene conversion tracts associated with repair of a defined double-strand break (DSB) using SNP microarray

city: Durham

first: Yee Fang

last: Hum

state: NC

address: 381 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Mitotic recombination between homologous chromosomes can lead to loss-of-heterozygosity (LOH), which is an important contributor to human disease. In the current study, a defined double-strand break (DSB) on chromosome IV was used to initiate LOH in a yeast strain with sequence-diverged chromosomes. Associated gene conversion tracts, which reflect the repair of mismatches formed when diverged chromosomes exchange single strands, were mapped using microarrays. LOH events reflected two broken chromosomes, one of which was repaired as a crossover and the other as a noncrossover.

overall_design: To examine DSB-induced mitotic gene conversion tracts, an I-SceI cut site was inserted into one of the chromosome IVs of a diploid strain (by mating W303 and YJM789 haploid parents) and cleavage by I-SceI enzyme was induced with 45 or 90 minutes of incubation with 2% galactose. Twenty independent DSB-induced red white sectored colonies were analyzed using SNP microarrays specific for yeast chromosome IV. To determine the heterozygous versus homozygous status of SNPs in each event, DNA from individual red or white sectors was labeled with Cy5 and mixed with control parental DNA labeled with Cy3. Following competitive hybridization of the mixed samples to the microarray, the ratio of Cy5 to Cy3 hybridization to each oligo was determined. A hybridization ratio of ~1 to both W303- and YJM879-specific oligos signals heterozygosity for the corresponding SNP. A hybridization ratio >1.5 for a haploid-specific oligo indicates homozygosity for the corresponding SNP, while a ratio <0.5 for the alternative haploid specific indicates loss of the corresponding SNP.

first: Yee

middle: F

first: Sue

last: Jinks-Robertson


title: Gene expression analysis of GD9.25 vehicle- or cyclopamine-exposed mouse frontonasal prominence and ventral prosencephalon tissues

city: Madison

first: Joshua

middle: L

last: Everson

state: WI

address: 2015 Linden Drive, Rm 3217

department: Comparative Biosciences

institute: UW-Madison

summary: We sought to identify Hedgehog-regulated genes in the frontonasal process (FNP) and ventral prosencephalon at GD9.25 in mice, during the initial pathogenesis of cleft lip with or without cleft palate.

overall_design: Frontonasal process and underlying ventral prosencephalon tissues were microdissected from GD9.25 (20-24 somite pairs) mouse embryos exposed to vehicle or cyclopamine from GD8.25-9.25.  Tissues were pooled by litter to minimize intralitter variability.  N=6 vehicle and N=6 cyclopamine pooled litters were included in the analysis.

middle: J

last: Lipinski


title: Transcriptome signature of WT and C3ar1-/-C5ar1-/- splenic DCs in response to CpG

city: New York

first: Weijia

last: Zhang

state: NY

address: 1425 Madison Avenue

department: Department of Medicine

institute: Mount Sinai School of Medicine

summary: Our  group showed that DC-instrinsic C3ar1/C5ar1 signals are required for TLR-initiated DC maturation in vivo. To more broadly analyze how local complement signaling affects DC maturation process in response to TLR9 stimulation, WT  or C3ar1-/-C5ar1-/- mice were stimulated with CpG (i.v. 100 micrograms) or vehicle control. 4hrs later, splenic CD11c+DCs were isolated and RNAs from the cells were purified for microarray analyses.

overall_design: The experiment include samples from WT unstimulated DCs (n=2), WT CpG-stimulated DCs (n=3), C3ar1-/-C5ar1-/- unstimulated DCs (n=2), and C3ar1-/-C5ar1-/- CpG-stimulated DCs (n=3).

first: Joong

middle: H

last: Francis Sheen

first: Zhengzi

last: Li

first: Peter

middle: S

last: Heeger


title: Global gene expression changes between PTIP KO and control PerC B-1a cells

city: Copenhagen

first: Jeremy

middle: A

last: Daniel

address: Blegdamsvej 3b

country: Denmark

institute: NNF Center for Protein Research, University of Copenhagen

summary:
B cel receptor (BCR) signaling and downstream NF-kB activity are crucial for the generation and activation of innate-like B-1 and conventional B-2 B cells, yet the molecular requirements for these signaling pathways are not fully understood.
We used microarray analysis to detail the global gene expression differences underlying the developmental phenotype of B-1a cells associated with defciency in the PTIP chromatin regulator protein.

overall_design: B-1a cells were FACS sorted from 5-week-old CD19cre/+PTIPflox/flox mutant and CD19cre/+PTIP+/+ control mice.  After total RNA was extracted using the RNeasy Plus Micro kit (Qiagen) and assessing RNA quality using an Agilent Bioanalyzer with RIN numbers > 8, gene expression profiling was performed using 22 control and 29 mutant mice divided into 4 unique biological replicate samples for each genotype.


title: Transcriptome analysis of G protein-coupled receptors in distinct genetic subgroups of acute myeloid leukemia: identification of potential disease-specific targets

status: Public on Apr 28 2017

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Acute myeloid leukemia (AML) is associated with poor clinical outcome and the development of more effective therapies is urgently needed. G protein-coupled receptors (GPCRs) represent attractive therapeutic targets, accounting for approximately 30% of all targets of marketed drugs. Using next-generation sequencing, we studied the expression of 772 GPCRs in 148 genetically diverse AML specimens, normal blood and bone marrow cell populations as well as cord blood-derived CD34-positive cells. Among these receptors, 30 are overexpressed and 19 are downregulated in AML samples compared with normal CD34-positive cells. Upregulated GPCRs are enriched in chemokine (CCR1, CXCR4, CCR2, CX3CR1, CCR7 and CCRL2), adhesion (CD97, EMR1, EMR2 and GPR114) and purine (including P2RY2 and P2RY13) receptor subfamilies. The downregulated receptors include adhesion GPCRs, such as LPHN1, GPR125, GPR56, CELSR3 and GPR126, protease-activated receptors (F2R and F2RL1) and the Frizzled family receptors SMO and FZD6. Interestingly, specific deregulation was observed in genetically distinct subgroups of AML, thereby identifying different potential therapeutic targets in these frequent AML subgroups.

overall_design: Total healthy bone marrow was sorted to isolate distinct cell populations. RNA-Seq analysis was performed on sorted cells to determine gene expression profile of healthy bona marrow subpopulations.

first: Arhamatoulaye

last: Maiga

first: Sébastien

last: Lemieux

first: Caroline

last: Pabst

first: Vincent-Philippe

last: Lavallée

first: Michel

last: Bouvier

first: Josée

last: Hébert


title: Transcriptomic analysis of primary and metastatic Sonic Hedgehog subgroup medulloblastomas

city: Sioux Falls

first: Haotian

last: Zhao

state: SD

address: 2301 E. 60th St. North

department: Children's Health Research Center

institute: Sanford Research

summary: We report findings that illuminate a dynamic metastasis pathway in the common pediatric brain tumor medulloblastoma.

overall_design: We examined the transcriptomes of primary and metastatic medulloblastoma driven by ATOH1 in collaboration with aberrant Sonic Hedgehog (SHH) signaling, as well as those of medulloblastoma from Ptch1+/- animals .

first: Erliang

last: Zeng


title: Transcriptomic analysis of metastatic Sonic Hedgehog subgroup medulloblastomas

overall_design: We examined the transcriptomes of medulloblastoma driven by ATOH1 in collaboration with aberrant Sonic Hedgehog (SHH) signaling, as well as those of medulloblastoma from Ptch1+/- animals.


title: Long Noncoding RNA Moderates microRNA Activity to Maintain Self-Renewal in Embryonic Stem Cells

city: Chapel Hill

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Of the thousands of long non-coding RNAs expressed in embryonic stem (ES) cells, few have known roles and fewer have been functionally implicated in the regulation of self-renewal and pluripotency or reprogramming somatic cells to the pluripotent state. In ES cells, Cyrano is a stably expressed long intergenic non-coding RNA with no previously assigned role. We demonstrate that Cyrano contributes to ES cell maintenance, as its depletion results in loss of hallmarks of self-renewal. Delineation of Cyrano's network through transcriptomics revealed widespread effects on signaling pathways and gene expression networks that contribute to ES cell maintenance. Cyrano shares unique sequence complementarity with the differentiation-associated microRNA, mir-7, and mir-7 overexpression reduces expression of a key self-renewal factor to a similar extent as Cyrano knockdown. This suggests that Cyrano functions to restrain the action of mir-7. Altogether, we provide a view into the multifaceted function of Cyrano in ES cell maintenance.

overall_design: RNA-seq on mouse R1 embryonic stem (ES) cells with two biological replicates transfected with an shRNA knockdown of Cyrano and two biological replicates transfected with a non-targeting control vector.

first: Keriayn

last: Smith

first: Sarah

last: Miller

first: Praveen

last: Sethupathy

first: Terry

last: Magnuson


title: Sonic Hedgehog subgroup medulloblastomas

type: Genome binding/occupancy profiling by high throughput sequencing


title: S-adenosylmethionine (SAM) treatment attenuates breast cancer growth, invasion, metastasis

first: Niaz

last: Mahmood

state: Québec

address: 1001 Decarie Boulevard

institute: McGill University

summary:
This study examines the therapeutic plausibility of using universal methyl group donor S-adenosylmethionine (SAM) to block breast cancer development, growth, and metastasis. cancer.
Anti-tumor and anti-metastatic activity of SAM was evaluated through a series of studies in vitro using two different human breast cancer cell lines and in vivo using a MDA-MB-231 xenograft model of breast cancer. The data shown in this array is obtained from control and SAM-treated MDA-MB-231 cell lines.

overall_design: RNA from three different biological repeats from control and SAM-treated MDA-MB-231 cells were subjected to Human Gene 2.0 ST array.

first: David

last: Cheishvili

first: Ani

last: Arakelian

first: Imrana

last: Tanvir

first: Haseeb

last: Khan

first: Moshe

last: Szyf


title: The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci (Bisulfite-Seq)

city: Shanghai

first: Heng

last: Zhang

address: 3888 Chenhua Rd, Gate 3

department: Shanghai Center for Plant Stress Biology

institute: Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary:
Background: The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in noncoding RNA-directed DNA methylation in Arabidopsis thaliana.
Results: Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant.
Conclusions: PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the noncoding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences noncoding RNA production, DNA methylation and transcriptional silencing.

overall_design: BS-seq, mRNA-seq, and sRNA-seq in 2-week-old seedlings of WT, nrpd1-3, nrpe1-11 and pkl-1; mRNA-seq and sRNA-seq were performed with 3 biological replicates

first: Rong

last: Yang

first: Zhimin

last: Zheng

first: Huan

last: Huang

first: Daisuke

last: Miki

first: Jian-Kang

last: Zhu


title: The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci (miRNA-Seq)

type: Non-coding RNA profiling by high throughput sequencing

overall_design: small RNA sequencing in 2-week-old seedlings of WT, nrpd1-3, nrpe1-11 and pkl-1 with 3 biological replicates


title: Feeding Angptl4-/- mice trans fat promotes foam cell formation in mesenteric lymph nodes without leading to ascites

status: Public on Apr 27 2017

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: ANGPTL4 regulates plasma triglyceride levels by inhibiting lipoprotein lipase. Inactivation of ANGPTL4 decreases plasma triglycerides and reduces risk of coronary artery disease. Unfortunately, targeting ANGPTL4 for the therapeutic management of dyslipidemia and atherosclerosis is hampered by the observation that mice and monkeys in which ANGPTL4 is inactivated exhibit lipid accumulation in mesenteric lymph nodes. In mice these pathological events exclusively unfold upon feeding a high saturated fatty acid diet and are followed by an ultimately lethal pro-inflammatory response and chylous ascites. Here we show that Angptl4-/- mice fed a diet rich in trans fatty acids develop numerous lipid-filled giant cells in their mesenteric lymph nodes, yet do not have elevated serum amyloid and haptoglobin, do not exhibit ascites, and survive, unlike Angptl4-/- mice fed a saturated fatty acid-rich diet. In RAW264.7 macrophages the saturated fatty acid palmitate markedly increases markers of inflammation and the unfolded protein response, whereas the trans-unsaturated elaidate and the cis-unsaturated oleate have the opposite effect. In conclusion,  trans and saturated fatty acids have very distinct biological effects. Furthermore, lipid accumulation in mesenteric lymph nodes is uncoupled from activation of an acute-phase response and chylous ascites, suggesting that ANGPTL4 should not be fully dismissed as target for dyslipidemia.

overall_design: RAW264.7 macrophages were incubated with oleate, elaidate and palmitate for 6 hours and subjected to expression profiling.

first: Antwi

last: Oteng

first: Asmita

last: Bhattacharya

first: Susanne

last: Brodesser

first: Ling

last: Qi

first: Nguan

last: Tan

first: Sander

last: Kersten


title: Salivary lnc-PCDH9-13:1 and miR-664a-5p are Novel Hypersensitive and Specific Biomarkers in Diagnosis of Early Hepatocellular Carcinoma

first: Zijun

last: Xie

address: No.106,zhongshan 2nd round

institute: Guangdong General Hospital

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

summary: Sensitive and noninvasive biomarkers are essential for screening and treating hepatocellular carcinoma (HCC). We explored whether salivary lncRNAs and miRNAs could be robust biomarkers for HCC. Using Agilent microarray, lncRNAs and miRNAs were profiled from liver tissue with HCC and normal liver.

overall_design: Our study consisted of there stages. Candidate lncRNA and miRNA biomarkers were selected by microarray and bioinformatics analysis. The levels of the selected candidate biomarkers in tissue, plasma and saliva samples were measured by qPCR and analyzed by biostatistics. The diagnostic performances of the selected ncRNAs were validated in three cohorts.

first: Bin

last: Wu


title: Long noncoding RNA expression profile in HLE B-3 cells during TGF-β2-induced epithelial-mesenchymal transition

city: guilin

first: Bingyu

address: No.2 Around City North RD.109

institute: Guilin Medical University

summary: Recent evidences have showed that long noncoding RNA (lncRNAs) are involved in the process of epithelial-mesenchymal transition (EMT). To understand lncRNAs expression profile and potential functions in EMT of lens epithelial cells (HLE B-3), we investigated the lncRNA and mRNA expression in normal cells and TGF-β2 induced cells using microarray analysis.

overall_design: lens epithelial cells (HLE B-3): control vs. TGF-β2 induced cells. Biological replicates: 3 control replicates, 3 induced replicates.

first: Zhixiang

last: Ding


title: T. gondii Genome Wide CRISPR Screen for Fitness-Conferring Genes

city: Cambridge

first: Sebastian

last: Lourido

state: MA

address: 455 Main St.

institute: Whitehead Institute

summary: We provide examples of the next-generation sequencing results obtained after analyzing sgRNAs (single guide RNAs) isolated from an input library and from parasites three passages after transfection.

overall_design: sgRNAs were isolated from parasites that had been passaged in human foreskin fibroblasts three times after transfecting the sgRNA library. The abundances of the sgRNAs can be compared to those in the input library (also provided). sgRNAs that are lost over time are presumed to cleave genes that confer fitness.

first: Saima

last: Sidik

first: Diego

last: Huet


title: The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

first: Heng

last: Zhang

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

overall_design: Refer to individual Series


title: Immune response genes at the mRNA vaccine delivery sites and draining lymph nodes of rhesus macaques

status: Public on Apr 26 2017

city: Stockholm

first: Frank

last: Liang

address: Karolinska University Hospital Solna, L2:04

department: Dept. Medicine Solna

country: Sweden

institute: Karolinska Institutet

summary: mRNA vaccines are emerging as a powerful vaccine platform as they are well-tolerated and scalable. Modified non-replicating mRNA encoding Influenza hemagglutinin and encapsulated in lipid nanoparticles (LNP) induced robust antibody and CD4 T cell responses after intramuscular or intradermal delivery in rhesus macaques. We investigated the local innate immune responses modulating such vaccine-induced immunity at the sites of immunization (skeletal muscle and skin) and their draining lymph nodes (LNs).  Rapid mobilization of antigen presenting cells was found at the LNP/mRNA-injection sites and LNs. Dendritic cells efficiently internalized the LNPs, translated the mRNA cargo and upregulated co-stimulatory molecules. In addition, several type I interferon-inducible genes were expressed at the immunization sites and draining LNs. The innate immune activation was transient and resulted in priming of antigen-specific CD4+ T cells exclusively in the vaccine-draining LNs. Collectively, mRNA-based vaccines induce type I interferon-polarized innate immunity and antigen production by antigen presenting cells, which resulted potent vaccine-specific responses.

overall_design: Two groups of rhesus macaques (n=4/group) receiving either intramuscular (I.M.) or intradermal (I.D.) injection of lipid nanoparticle (LNP)-encapsulated mRNA vaccine plus a saline control injection given at a different site on the same animal. Injection site biopsies and draining lymph nodes from I.M. and I.D. group  were collected for gene expression analysis.

first: Josefine

last: Röhss

first: Hugh

last: Salter

first: Karin

last: Loré


title: Circularized Chromosome Conformation Capture (4C) for the genome-wide characterization of mammalian promoters with distal enhancer functions

city: Montpellier

first: David

last: Martin

address: 1919 route de Mende

country: France

institute: IGMM/CNRS

summary: We report the application of 4C technology for the identification of interaction points between the promoters of the RNF44 and FAF2 genes and their putative distal enhancers.

overall_design: Examination of 2 gene promoters for the interaction with putative distal promoters.

first: Charlotte

last: Andrieu-Soler

first: Eric

last: Soler

first: Salvatore

last: Spicuglia

first: Lan

last: Dao

first: Nicolas

last: Fernandez


title: Transcriptome analysis of Gerbera delavayi based on high-throughput sequencing technology

city: Kunming

first: Jing

last: Chen

address: No. 727 South Jingming Road

institute: Kunming University of Science and Technology

summary: Gerbera delavayi Franch. endemic to southwest China, is a rare fiber plant. In this study, the leaves of G. delavayi were sequenced based on Illumina Hi-Seq2500. The results showed that 108694 unigenes were found. N50 was 593.90bp, and the mean length was 912bp. By comparing with Nr and Swiss-prot database, 40915 unigenes were annotated, and 67779 unigenes were unannotated. In addition, 30 unigenes had homology with Ces family, 20 unigenes had homology with Cls family, and 11 unigenes had homology with SuSy. 11369 unigenes were assigned to 25 categories with COG database, and 21378 unigenes were divided into 52 GO terms. Function annotation against KEGG database obtained 8087 unigenes and 118 pathways. 47 unigenes were found at “phenylpropanoid biosynthesis” pathway. Furthermore, 4908 unigenes contained 5179 SSRs, 1 SSR occurred every 12.46kb. The largest number of SSR type was mono-nucleotide repeat, and its frequency was 54.37%; the next was di-nucleotide repeat and tri-nucleotide repeat, with the frequencies of 22.90% and 21.70%, respectively. These results greatly enriched the genetic information of G. delavayi, and provided basic data for genetic breeding and exploitation of this unique plant resource.

overall_design: Examination of Gerbera delavayi leaves samples.

first: Wei

last: Zheng


title: Immunohistochemical and transcriptional analysis uncover RasGRF2-mediated regulation of nestin-positive stem cell density and early neuronal differentiation in the dentate gyrus of the hippocampus of adult mouse

city: Salamanca

first: Carmela

last: Gómez

state: Salamanca

address: Paseo Universidad de Coimbra, Salamanca, España

country: Spain

institute: CSIC

summary: We used microarrays to investigate gene expression changes in olfactory bulb and hippocampus brain regions under RasGRF2 absence.

overall_design: Olfactory bulb and hippocampus from three GRF2 KO mice compared to olfactory bulb and hippocampus from three WT mice.

last: Jimeno

first: Alberto

last: Fernández-Medarde

first: Rósula

last: Navas

first: Nuria

last: Calzada

first: Eugenio

last: Santos


title: Post-infectious time-series DNA methylation analysis in gastric epithelial cells

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

type: Methylation profiling by genome tiling array

summary: Time-series comprehensive DNA methylation analysis after EBV infection in the immortalised normal gastric epithelial cell line, GES1, and low methylation gastric cancer cell line, MKN7. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 9 GES1 with and without EBV infection, 5 MKN7 with and without EBV infection, EBV+ gastric cancer cell and xenograft, SNU719 and KT, 2 normal gastric mucosae, 2 low-methylation gastric cancer cases, and 2 high-methylation gastric cancer cases.

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Infinium HumanMethylation450 BeadChip.

first: Keisuke

last: Matsusaka

first: Sayaka

last: Funata

first: Yasuyuki

last: Seto

first: Hiroyuki

last: Aburatani

first: Masashi

last: Fukayama

first: Atsushi

last: Kaneda


title: Gene expression of cardiac tissues in dietary obese mice administered with a dipeptidyl peptidase-4 inhibitor

city: Niigata

first: Masayoshi

last: Suda

address: 1-757 Asahimachi-dori, Chuo-ku

department: Department of Cardiovascular Biology and Medicine

institute: Niigata University

summary: Dipeptidyl peptidase-4 (Dpp4) inhibitors are used worldwide to combat diabetes, however, their roles in cardiovascular disorders are yet to be defined. Here we show that a DPP4 inhibitor, linagliptin, contributes for the suppression of capillary rarefaction in cardiac tissues of dietary obese mice model. Imposing a high fat diet into mice induced capillary rarefaction and cardiac dysfunction. These pathologies associated with high DPP4 level in circulation, and the administration of linagliptin into dietary obese mice suppressed the development of capillary rarefaction and ameliorated cardiac dysfunction. Early growth response protein 1 (EGR1), known as an angiogenic transcription factor, is significantly reduced in the cardiac tissue upon metabolic stress, and this suppression was inhibited by the administration of linagliptin.

overall_design: Total RNA of cardiac tissue was obtained from a normal chow- and  a high-fat diet-fed mice with or without a DPP-4 inhibitor. Mice were fed a high-fat diet or a normal chow for totally 8 weeks from 4 weeks age, and analyzed at 12 weeks of age.The DPP-4 inhibitor was administered within a water at the concentration of 10 mg/kg/day for 8 weeks since 4 weeks of age.

first: T

last: Minamino


title: Drought stress-mediated transcriptome profile in Populus davidiana (cv. Seogwang9)

city: Daegu

first: Sang-Uk

last: Lee

address: 80 Daehakro, Bukgu

institute: Kyungpook National University

summary: To understand the drought stress induced signaling mechanism in trees.

overall_design: 10min air-dried treatment to plant, Transcriptome profiling

first: Bong-Gyu

last: Mun

first: Hyun-Ho

last: Kim

first: Jae-Young

first: Adil

last: Hussain

first: Byung-Wook

last: Yun


title: Transcriptome-wide analysis of IL2RA enhancer activation by CRISPRa

city: Berkeley

first: Jacob

middle: Ellery

last: Corn

state: CA

address: 2151 Berkeley Way

department: Innovative Genomics Institute

institute: University of California, Berkeley

summary: We previously performed a tiling CRISPR activation (CRISPRa) screen in Jurkat T cells to discover enhancers controlling IL2RA expression. This screen identified six regions where recruitment of dCas9-VP64 was sufficient to drive increased expression of IL2RA. We named these putative enhancers CRISPRa Responsive Elements (CaREs). To examine transcriptome-wide consequences of dCas9-VP64 recruitment to IL2RA CaREs, we performed RNA-Seq on HuT78 cells stably expressing dCas9-VP64 and gRNAs targeting the IL2RA TSS, CaRE3, or CaRE4, or stimulated with anti-CD3/CD28 antibodies.

overall_design: RNA-Seq of HuT78 cells stably expression dCas9-VP64 and sgRNAs targeting the IL2RA TSS, CaRE3, or CaRE4, or non-targeting control sgRNA. Stimulated and unstimulated HuT78 cells stably expressing dCas9-VP64 but no sgRNA were also analyzed for comparison.

first: Alexander

last: Marson


title: Discovery of IL2RA and CD69 enhancers using CRISPRa

summary:
We performed tiling CRISPR activation (CRISPRa) screens in Jurkat T cells to discover enhancers controlling IL2RA and CD69 expression.  For each target gene, we constructed a pooled lentiviral library of sgRNAs that targeted sites at all Cas9 PAMs throughout the window starting 100 kb upstream of the transcription start site, extending through the gene body, and 25 kb downstream. A separate library was constructed for each gene, and a separate screen was performed for each gene. For each gene, Jurkat cells stably expressing the dCas9-VP64 transcriptional activator were transduced with the lentiviral sgRNA library. Cells were stained for the protein of interested and sorted by flow cytometry into four bins of expression. Distribution of sgRNAs in each of the sorted populations was compared to the unsorted population. Regions where dCas9-VP64 recruitment was sufficient to drive target gene expression were identified as putative enhancers.
The hg19 coordinates of the CD69 library window were chr12:9,880,082-10,013,497. The library contained 2,244 negative control sgRNAs taken from the CRISPRi/a libraries described in Gilbert et al., Cell 150, 647-661 (2014).
The hg19 coordinates of the IL2RA library window were chr10:6,027,657- 6,204,333. The library contained 2,244 negative control sgRNAs taken from the CRISPRi/a libraries described in Gilbert et al., Cell 150, 647-661 (2014).

overall_design: Targeted examination of the IL2RA and CD69 loci where recruitment of dCas9-VP64 was sufficient to drive transcription of the target gene.


title: Drought stress-mediated transcriptome profile in Populus davidiana (cv. Palgong2)


title: Drought stress-mediated transcriptome profile in Populus davidiana (cv. Palgong1)


title: Iron-Deficiency in Pregnancy: Effects on the Rat Hippocampus

city: Philadelphia

first: Rebecca

last: Simmons

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Whole-genome bisulfite sequencing on the rat hippocampus identifies DMRs near genes concerning neuronal development and plasticity which are affected by an iron-deficient diet in pregnancy.

overall_design: Hippocampus samples from three iron-sufficient rats, 3 iron-deficient rats are compared with whole-genome bisulfite sequencing.

first: Phu

middle: V

last: Tran

first: David

last: Condon

first: Jonathan

last: Schug

first: Yu

middle: C

last: Lein


title: Drought stress-mediated transcriptome profile in Populus davidiana (cv. Odae19)


title: DNA damage signaling mediates the functional antagonism between replicative senescence and terminal muscle differentiation

status: Public on Apr 25 2017

first: Alessandra

last: Dall'Agnese

address: 455 Main Street

summary: The molecular determinants of muscle progenitor impairment to regenerate aged muscles are currently unclear. We show that in a mouse model of replicative senescence, decline in muscle satellite cell-mediated regeneration coincides with activation of DNA damage response (DDR) and impaired ability to differentiate into myotubes. Inhibition of DDR restored satellite cell differentiation ability. Moreover, in replicative human senescentfibroblasts DDR precluded MYOD-mediated activation of the myogenic program. A DDR-resistant MYOD mutant could overcome this barrier by resuming cell cycle progression. Likewise, DDR inhibition could also restore MYOD ability to activate the myogenic program in human senescent fibroblasts. Of note, we found that cell cycle progression is necessary for DDR-resistant MYOD mutant to reverse senescence-mediated inhibition of the myogenic program. These data provide the first evidence of DDR-mediated functional antagonism between senescence and MYOD-activated gene expression, and indicate a previously unrecognized requirement of cell cycle progression for the activation of the myogenic program.

overall_design: RNASeq

first: Lucia

last: Latella

first: Pier

last: Puri


title: Identification of a human clonogenic progenitor with strict monocyte differentiation potential - a counterpart of mouse cMoPs

status: Public on Apr 24 2017

city: Bunkyo-ku

first: Shunsuke

last: Kawamura

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary: Monocytes and monocyte-derived macrophages cause a variety of inflammatory disorders. Kawamura and colleagues identified human cMoPs, a monocyte-restricted progenitor, in umbilical-cord blood and bone marrow, increasing our understanding of human monocyte differentiation and insight for therapies targeting cMoPs and monocytes.

overall_design: The PB-Mo (N=3), cMoP-Mo (N=3), preMo (N=3), cMoPs (N=3), rGMPs (N=3), and CMPs (N=3) were sorted from at least 20 UCB samples and pooled for one experiment.

first: Nobuyuki

last: Onai

first: Fuyuki

last: Miya

first: Taku

last: Sato

first: Tatsuhiko

last: Tsunoda

first: Kazutaka

last: Kurabayashi

first: Satoshi

last: Yotsumoto

first: Shoko

last: Kuroda

first: Katsuto

last: Takenaka

first: Koichi

last: Akashi

first: Toshiaki

last: Ohteki


title: Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (iSLKBac16WT ChIP-Seq)

city: Reno

first: Subhash

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

summary: The objective of this study was to identify the symmetric methylation sites on KSHV genome during latency and lytic reactivation

overall_design: KSHV infected iSLKBac16WT cells were induced with doxycycline for 24h to trigger the lytic reactivation, cells were crosslinked and subjected for chromatin isolation and sonication. ChIP assay was performed using specific antibodies.


title: Gene expression in non-adherent MDA-MB-468 subpopulation

status: Public on Apr 22 2017

city: Halle

first: Guido

last: Posern

address: Hollystrasse 1

department: Institute for Physiological Chemistry

institute: Martin Luther University Halle-Wittenberg

summary:
Plasticity between adhesive and less-adhesive states is important for mammalian cell behaviour. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of MDA-MB-468 breast carcinoma cells which grows in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices.
By transcriptome analysis, we aimed to identified the determinants of adhesion plasticity, and found downregulation of the focal adhesion protein tensin3 (Tns3).

overall_design: 6 samples: 3 independent RNA preparations of parental MDA-MB-468 cells (ctrl 1, ctrl2, ctrl3), and RNA preparations of 3 independently isolated MDA-MB-468 subpopulations (suspA, suspB, suspC)


title: Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (TREx Und 12h 24hInd ChIP-Seq)

overall_design: KSHV infected, TRExBCBL1-RTA or iSLKBac16WT cells were induced with doxycycline for 12h or 24h to trigger the lytic reactivation, cells were crosslinked and subjected for chromatin isolation and sonication. ChIP assay was performed using specific antibodies.


title: Expression profiling of colorectal cancer (CRC) tissue samples with microsatellite instability (MSI)

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: As part of a genomic profiling study of CRCs with MSI, we have performed genome-wide expression analyses of a consecutive patient series.

overall_design: This series consists of 34 CRC tissue samples with MSI analyzed on Affymetrix Human Transcriptome 2.0 Arrays, and is an amendment to a larger series of CRC analyzed for gene expression with exon-level resolution (GSE24550, GSE29638 and GSE69182).

first: Ina

last: Eilertsen

first: Ragnhild

last: Lothe


title: Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome

overall_design: Refer to individual Series


title: Single-cell profiling of tumor infiltrating T cells and macrophages [Nanostring]

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary:
Effective therapies for non-small cell lung cancer (NSCLC) remain challenging despite an increasingly comprehensive understanding of somatically altered oncogenic pathways. It is now clear that therapeutic agents with potential to impact the tumor immune microenvironment potentiate immune-orchestrated therapeutic benefit. Herein we evaluated the immunoregulatory properties of histone deacetylase (HDAC) and bromodomain inhibitors, two classes of drugs that modulate the epigenome, with a focus on key cell subsets that are engaged in an immune response. By evaluating human peripheral blood and NSCLC tumors, we show that the selective HDAC6 inhibitor ricolinostat promotes phenotypic changes that support enhanced T cell activation and improved function of antigen presenting cells. The bromodomain inhibitor JQ1 attenuated CD4+Foxp3+ T regulatory cell suppressive function and synergized with ricolinostat to facilitate immune-mediated tumor growth arrest, leading to prolonged survival of mice with lung adenocarcinomas. Collectively, our findings highlight the immunomodulatory effects of two epigenetic modifiers that, together, promote T cell-mediated anti-tumor immunity and demonstrate their therapeutic potential for treatment of NSCLC.
6 Kras-mutant/p53-deficient lung tumors T cells and macrophages were analyzed wth Nanostring mouse PanCancer immune module

overall_design: Gene expression analyses of tumor-infiltrating T cells and macrophages in lung tumor-bearing mice treated with Vehicle (control), ricolinostat (HDAC inhibitor), or JQ1 (Bromodomain inhibitor)

first: Dennis

last: Adeegbe

first: Liu

last: Yan


title: DNA methylation changes in blood leukocytes following an omega-3 fatty acid supplementation

city: Quebec

first: Bénédicte L.

last: Tremblay

state: Quebec

address: Pavillon des Services, 2440 Hochelaga Blvd

department: School of Nutrition

institute: Institute of Nutrition and Functional Foods (INAF), Laval University

summary: The objective is to investigate, using genome-wide DNA methylation analyses, methylation changes following an n-3 FA supplementation in overweight and obese subjects and to identify specific biological pathways potentially altered by the supplementation.

overall_design: A total of 36 non-smokers subjects, aged between 18 and 50 with a BMI between 25 and 40 kg/m2 were recruited. They received 3g of n-3 Fas (1.9-2.2g of EPA and 1.1g of DHA) per day for 6 weeks. Blood samples were taken before and after the supplementation period. Genomic DNA was extracted from blood leukocytes using GenElute Blood Genomic DNA kit (Sigma-Aldrich, USA) for the 72 samples: 36 sampels before and 36 samples after the supplementation. Three samples (one before and two after supplementation) were excluded from microarray analysis following quality control steps. Differences in methylation levels before and after the supplementation were tested using the Illumina Custom model in GenomeStudio software.

first: Bénédicte

first: Frédéric

last: Guénard

first: Iwona

last: Rudkowska

first: Simone

last: Lemieux

first: Patrick

last: Couture

first: Marie-Claude

last: Vohl


title: Circulating miRNAs for gestational diabetes mellitus

city: He fei

first: yan

middle: fu

last: Wang

address: 443 huangshan road

institute: University of Science and Technology of China

summary: We compared the plasma miRNA expression profiles between healthy and GDM women by microarray analysis.Our study offers new insights into circulating biomarkers of GDM and thus provides a valuable resource for future investigations.

overall_design: Plasma from 4 pregnant women (2 from normal controls and 2 from GDM patients) were used for microarray analysis using the SurePrint human miRNA microarray

first: Fuyan

first: Ming

last: Zhao

first: Xi

last: Wu

first: Yisheng

last: Zhang

first: Shizhong

last: Bu


title: A tumor suppressor role for Bank1 in B cell precursor acute lymphoblastic leukemia (BCP-ALL)

status: Public on Apr 21 2017

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: We used microarrays to investigate gene expression changes in BM leukemic Bank1+/- + Pax5+/- cells

overall_design: Bone marrow leukemic cells of six Bank1+/- + Pax5+/- mice compared with bone marrow proB and preB cells of three WT mice and bone marrow leukemic cells of six Pax5+/- mice.

first: Franziska

last: Auer

first: Alberto

last: Martín-Lorenzo

first: Idoia

last: García-Ramírez

first: Inés

last: González-Herrero

first: Guillermo

last: Rodríguez-Hernández

first: Oscar

last: Blanco

first: Diego

last: Alonso-López

first: Javier

last: De Las Rivas

first: Rafael

last: Jiménez

first: Francisco

last: Javier García Criado

first: María

last: Begoña García Cenador

first: Carolina

last: Vicente-Dueñas

first: Arndt

last: Borkhardt

last: Sánchez-García

first: Julia

last: Hauer


title: Genome-wide transcriptome analysis of chickens during dietary methionine restriction reveals compromised immune competency

city: Athens

first: Samuel

middle: E

last: Aggrey

state: GA

address: 110 Cedar Street

department: Poultry Science

institute: University of Georgia

summary:
The goal of this study was to compare next-generation sequencing (NGS)-derived liver and pectoralis major transcriptome profilings (RNA-seq) of chicken fed control diet to treatment birds fed methionine restriction diet.
We sequenced mRNA from 10 Gallus gallus males fed either control (L-Methionine) or L-Methionine-deficient diet (5 control and 5 treatment) from 3-5 weeks of age. We sequenced both liver and the pectoralis major muscle.

overall_design: Examination of mRNA levels in liver and pectoralis major of male Gallus gallus fed either regular (L-Methionine) or L-methionine-deficient diet.


title: Bovine granulocytes gene expression profiles reflect the aberration of liver functions

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: Liver takes multifunctional important roles and the prediction of its function is hard issue. Detecting methods of gene expression profiles like microarray provide functional information of tissues. Liver and peripheral white blood cells (PBLs) were collected from two different feeding conditioned Holstein cows; estrus cycle and middle of gestation. Also PBLs were fractionated with gradient cells separation. The RNA was applied to oligo-microarray and qRT-PCR. It revealed a group of stable bovine liver genes in constant physiological feeding condition. When they applied to different cows fed in different status, the profiles of some specific genes in liver coincided with those in PBLs. Microarray data were applied to a principal component analysis (PCA). It was found that the liver gene expression profiles were more coincided those in granulocytes than other PBLs fraction by PCA. The relationship between gene profiles in liver and granulocytes was confirmed by qRT-PCR and Hierarchical cluster analysis. Granulocytes gene profile is more reliable than those in mononuclear cells in reflection of liver metabolic function. These results suggest that expressed genes in PBLs, especially granulocytes, may be convenient bio-indicators for diagnosis of clinical disorder and/or detecting aberration of liver function in different feeding condition of cows.

overall_design: Bovine liver, peripheral blood granulocytes and mononuclear cells were obtained from estrous cycle (n=4) and mid gestation (n=4) of Holstein cows.


title: Drought stress-mediated transcriptome profile in Populus davidiana (cv. Seogwang15)

first: Sang-Uk

last: Lee

overall_design: 10min air-dried treatment to plant, Transcriptome profiling

first: Bong-Gyu

last: Mun

first: Hyun-Ho

last: Kim

first: Jae-Young

first: Adil

last: Hussain

first: Byung-Wook

last: Yun


title: Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-small Cell Lung Cancer.

first: Ruben

last: Dries

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


title: The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (ChIRP-seq)

status: Public on Mar 29 2017

city: Cambridge

first: Juan

last: Alvarez-Dominguez

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Enhancer-derived RNAs are thought to contribute locally to their parent enhancers’ functions. Whether large domains of clustered enhancers (super-enhancers, SEs) also produce cis-acting RNAs, however, remains unclear. Unlike typical enhancers, SEs form large spans of robustly transcribed chromatin, amassing capped and polyadenylated RNAs that are sufficiently abundant to sustain trans functions. Here, we show that one such RNA, alncRNA-EC7/Bloodlinc, is transcribed from a SE of the erythroid membrane transporter SLC4A1/BAND3 but diffuses beyond this site. Bloodlinc localizes to trans-chromosomal loci encoding critical regulators/effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor HNRNPU. Inhibiting Bloodlinc or Hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing Bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. Thus, Bloodlinc represents a novel type of trans-acting SE RNA that potentiates red blood cell development.

overall_design: Bloodlinc ChIRP-seq in MEL cells, harvested after 5 days of 2% DMSO-induced differentiation, generated by deep sequencing using the Illumina HiSeq2000 platform.


title: The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans


title: Identification of the Sulfolobus acidocaldarius small RNome and L7Ae-RNA interactome

status: Public on Feb 10 2017

city: Marburg

first: Michael

last: Daume

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Prokaryotic Small RNA Biology

institute: Max Planck Institute for Terrestrial Microbiology

summary: Small RNAs and L7Ae co-immunoprecipitated RNA were isolated from the thermophilic archaeon Sulfolobus acidocaldarius and subjected to Illumina sequencing. The sRNome revealed a high abundance of C/D box sRNAs and CRISPR RNAs. The L7Ae-RNA interactome showed enrichment of all known interactors of the L7Ae protein, i.e. C/D box sRNAs, H/ACA box sRNAs, RNaseP, rRNA. A high abundance of reads for the SRP RNA was found, suggesting L7Ae´s interaction with this universal RNA. Many mRNA reads were enriched, several of them comprise binding sites for the L7Ae protein.

overall_design: A S. acidocaldarius small RNA isolate and RNA that was co-immunoprecipitated with L7Ae were subjected to Illumina sequencing.

first: Lennart

last: Randau


title: Genome-wide maps of chromatin state in neurosphere cells and breast cancer cells

status: Public on Feb 23 2017

city: Stanford

first: Mark

last: Zarnegar

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: We report the validation of a new epigenetic profiling technique for high-throughput profiling of histone modifications, targeted chromatin ligation (TCL), applicable to low cell numbers, that produces data comparable to ChIP.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of four different histone marks using two cell types

last: Clarke


title: Microarray analysis of TNFα indcued senescence in Human umbilical vein endothelial cells

city: Barcelona

first: Renuka

last: Kadhaya Pillai

state: Barcelona

address: Passeig Vall d’Hebron

department: Aging Basic Research Group, Molecular Biology and Biochemistry Research Center for Nanomedicine

institute: CIBBIM-Nanomedicine

summary: Cellular senescence is a key cell-fate program that leads to an essentially irreversible proliferative arrest in potentially damaged cells. Cytokine production and signaling play a significant role in senescence. Tumor necrosis factor-alpha (TNFα), an important pro-inflammatory cytokine secreted by some senescent cells, can induce senescence in mouse and human cells. However, downstream signaling pathways and key regulatory genes linking inflammation to senescence are not fully characterized. Using human umbilical vein endothelial cells (HUVECs) as a model, we show TNFα induces permanent growth arrest and increased senescence markers such as p21, p16, and senescence-associated β-galactosidase (SA-β-gal), accompanied by persistent DNA damage and ROS. By gene expression profiling and pathway analysis, we identify the crucial involvement of inflammatory networks, an interferon signature, and persistent activation of the Janus kinase (JAK) /signal transducer and activator of transcription (STAT) pathway in TNFα-mediated senescence. TNFα initiates a STAT-dependent autocrine loop leading to sustained inflammation, DNA damage, and expression of interferon response genes to lock cells into senescence. Further, we show STAT1/3 activation is necessary for cytokine and ROS production during TNFα-induced senescence. However, inhibition of STAT1/3 did not rescue cells from TNFα-mediated senescence. Rather, blockade of STAT activation accelerated senescence, suppressed genes that control the cell cycle, and modulated TNFα-induced senescence. Our findings suggest a positive feedback mechanism via a STAT pathway that sustains cytokine production and reveal a reciprocal regulatory role of JAK/STAT in TNFα-mediated senescence.

overall_design:
Human umbilical vein endothelial cells (HUVECs) were untreated or treated TNFα (5ng/ml) continously for 26 days or (Passage 2 -Passage 8/ Passage 3- Passage9)//until cells exhibit senescent morphology. Gene expression of TNFα treated/senescenced cells were compared to corresponding passaged untreated or control cells.

Three samples (GSM2590763, GSM2590764 and GSM2590765) are missing CEL files due to storage failure.

first: Francesc

last: Miro-Mur

first: Simo

last: Schwartz Jr


title: Coordinated regulation of acid resistance in Escherichia coli

status: Public on Jan 12 2017

first: James

last: Galagan

address: 44 Cummington Mall

department: Biomedical Engineering

institute: Boston University

summary: We report regulatory interactions on four E. coli transcription factors in relation to the acid resistance systems by using a combination of ChIP-Seq and gene expression analysis

overall_design: Performed chromatin immunoprecipitation and total RNA extraction on WT strains cloned with inducible TFs in E. coli K-12 MG1655. Sequences were generated with an Illumina GAIIx

first: Patricia

last: Aquino

first: Brent

last: Honda

first: Suma

last: Jaini

first: Anna

last: Lyubetskaya

first: Krutika

last: Hosur

first: Joanna

middle: G

last: Chiu

first: Iriny

last: Ekladious

first: Dongjian

last: Hu

first: Lin

last: Jin

first: Marianna

middle: K

last: Sayeg

first: Arion

middle: I

last: Stettner

first: Julia

last: Wang

first: Brandon

last: Wong

first: Winnie

first: Stephen

last: Alexander

first: Cong

last: Ba

first: Seth

last: Bensussen

first: David

last: Bernstein

first: Dana

last: Braff

first: Susie

last: Cha

first: Daniel

last: Cheng

first: Jang

last: Cho

first: Kenny

last: Chou

last: Chuang

last: Gastler

last: Grasso

first: John

last: Greifenberger

first: Chen

last: Guo

last: Hawes

first: Divya

last: Israni

first: Saloni

last: Jain

first: Jessica

first: Junyu

last: Lei

first: Hao

last: Li

first: Qian

first: Christopher

middle: P

last: Mancuso


title: Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy

status: Public on Dec 31 2016

city: Nijmegen

first: Till

middle: Sebastian Manuel

last: Mathan

state: Gelderland

address: Geert Grooteplein 26-28

department: Tumor Immunology

institute: Radboud Institute for Molecular Life Sciences

summary: Effective stimulation of immune cells is crucial for the success of cancer immunotherapies. Current approaches to evaluate the efficiency of stimuli activating immune cells are mainly defined by known flow cytometry-based cell activation or cell maturation markers. This method however does not give a complete overview of the achieved activation state and may leave important side effects unnoticed. Here, we used an unbiased RNA sequencing (RNA-seq)-based approach to compare the capacity of four clinical-grade dendritic cell (DC) activation stimuli used to prepare DC-vaccines composed of various types of DC subsets; the already clinically applied GM-CSF and Frühsommer meningoencephalitis (FSME) prophylactic vaccine and the novel clinical grade adjuvants protamine-RNA (pRNA) complexes and CpG-P. We found that GM-CSF and pRNA have similar effects on their target cells, whereas pRNA and CpG-P induce stronger tType I interferon (IFN) expression than FSME. In general, the pathways most affected by all stimuli were related to immune activity and cell migration. GM-CSF stimulation, however, also induced a significant increase of genes related to nonsense-mediated decay, indicating a possible deleterious effect of this stimulus. Taken together, all novel stimuli appear to be promising alternatives. Our study demonstrates how RNA-seq based investigation of changes in a large number of genes and gene groups can be exploited for fast and unbiased, global evaluation of clinical-grade stimuli, as opposed to the general limited evaluation of a pre-specified set of genes, by which one might miss important biological effects detrimental for vaccine efficacy.

overall_design: mRNA profiles of CD1c+ mDCs and pDCs, MACS isolated from 3 healthy volunteers and stimulated with 4 clinical grade stimuli, were generated by deep RNA sequencing using HiSeq 2000 System (TruSeq SBS KIT-HS V3，Illumina)

first: Johannes

last: Textor

first: Annette

last: Sköld

first: Inge

last: Reinieren-Beeren

first: Tom

last: van Oorschot

first: Mareke

last: Brüning

first: Sonja

last: Buschow

first: Ghaith

last: Bakdash

first: I

last: de Vries


title: Incomplete MyoD-induced transdifferentiation is mediated by chromatin remodeling deficiencies [Dnase-Seq]

status: Public on Jan 07 2017

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

summary: MyoD is known to transdifferentiate fibroblasts into muscle-like cells. Despite phenotypic resemblance and expression of myogenic marker genes in transdifferentiated cells, our global gene expression data suggests that ~100 genes, many involved in muscle development and function, remain non-reprogrammed. To understand this incomplete reprogramming, we characterized genome-wide chromatin accessibility and MyoD binding in human primary myoblasts and in MyoD-induced skin fibroblast cells. Our analyses revealed thousands of sites with incomplete chromatin reprogramming.Combined analyses of gene expression and epigenetic profiles revealed that many myogenic genes not upregulated during the transdifferentiation process have undergone MyoD-dependent chromatin remodeling, but to a significantly lower extent than reprogrammed genes. Our findings suggest that incomplete MyoD-induced transdifferentiation is due to chromatin-remodeling deficiencies, and that additional factors are required to transdifferentiate cells into a state more similar to myoblasts.

overall_design: Fibroblast cells were transduced with a vector carrying human MyoD gene and induced by tetracycline for expression. Dnase-seq, ChIP-seq and RNA-seq were used to identify transcription factors binding, differential chromtin structural change, and differential expression at on-target and off-target sites.

first: Dinesh

last: Manandhar

first: Lingyun

last: Song

first: Ami

last: Kabadi

first: Lee

last: Edsall

first: Melanie

last: Ehrlich

first: Koji

last: Tsumagari

first: Charles

last: Gersbach

first: Raluca

last: Gordan


title: DNA methylation profile of triple negative breast cancer specific genes (study)

city: New Lambton Heights

first: Kelly

last: Avery-Kiejda

state: NSW

address: Kookaburra Circuit

department: Medical Genetics

institute: Hunter Medical Research Institute

summary:
Purpose Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with no targeted treatment available. Our previous study identified 38 TNBC-specific genes with altered expression in tumour samples compared to normal samples. This study aimed to identify whether DNA methylation contributed to these gene expression changes in the same breast cancer cohort. Additionally, we aimed to identify a whole genome methylation profile that contributes to the progression from primary breast tumour to lymph node metastasis.  Methods We used the DNA of 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues to perform 450K Illumina methylation arrays. The results were validated in an independent cohort of 70 primary TNBC samples.  Results The gene expression of 16/38 TNBC-specific genes was associated with significantly altered methylation. Furthermore, altered methylation of 18 genes associated with lymph node metastasis was identified and validated in an independent cohort. Additionally, novel methylation changes between primary tumours and lymph node metastases, as well as those associated with survival were identified.  Conclusion This study has shown that DNA methylation plays an important role in altered gene expression patterns of TNBC-specific genes and is the first study to perform whole genome DNA methylation analysis that includes matched lymph node metastases in this breast cancer subtype. This novel insight into the progression of TNBC to secondary cancers may provide potential prognostic indicators for this hard-to-treat breast cancer subtype.
study cohort

overall_design: Methods We used the DNA of 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues (3 pools and one single) to perform 450K Illumina methylation arrays. The results were validated in an independent cohort of 70 primary TNBC samples

first: Andrea

last: Mathe

first: Michelle

last: Wong-Brown

first: Warwick

last: Locke

first: Clare

last: Stirzaker

first: Stephen

last: Braye

first: John

last: Forbe

first: Susan

last: Clar

last: Avery-Kiejd

first: Rodney

last: Scott


title: Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the methylome

status: Public on Feb 15 2017

city: Richmond

first: Edwin

last: van den Oord

address: 1112 East Clay Street

department: Center Biomarker Research and Precision Med

institute: Virginia Commonwealth University

summary: Methylome-wide association studies (MWAS) are typically performed using microarray technologies that assay only a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is the use whole genome bisulfite sequencing, but this approach is not yet practically feasible with the sample sizes required for adequate statistical power. We argue for revisiting methylation enrichment methods that, provided optimal protocols are used, enable comprehensive, adequately powered, and cost-effective genome-wide investigations of the methylome. To support our claim we use data showing that enrichment methods approximate the sensitivity obtained with the whole genome bisulfite methods with slightly better specificity. However, this performance is achieved at <5% of the reagent costs. Furthermore, because many more samples can be sequenced simultaneously, projects can be completed about 15 times faster. A potential drawback of our approach to assay CG methylation (the dominant form of methylation in the vast majority of somatic tissues). is the relatively large amount of genomic DNA (ideally >1 ug) required to obtain high quality data. Biomaterials are typically expensive to collect, provide a finite amount of DNA, and may simply not yield sufficient starting material. Thus, any possibility to use low amounts of DNA will increase the breadth and number of the studies that can be conducted. Therefore, we further adapted the enrichment step of the protocol. With this low starting material protocol, the assay performed generally equal well or better than the ample starting material protocol requiring >1 ug.

overall_design:
To validate the enrichment methods we calculated the sensitivity (proportion of methylated loci correctly detected by enrichment methods), specificity (proportion of non-methylated loci correctly identify by enrichment methods) and the overall agreement (proportion of times the enrichment methods arrived at the same conclusion regarding the methylation status as the bisulfite data).

Please note that GSM2486673-GSM2486686 samples are discussed in the 'Nucleic Acids Res' publication and that GSM2486673-GSM2486678, GSM2593327-GSM2593338 are discussed in another manucript (pending manuscript review). Since the two papers are closely related, all samples were grouped under one Series.

first: Karolina

last: Aberg

first: Robin

last: Chan


title: Incomplete MyoD-induced transdifferentiation is mediated by chromatin remodeling deficiencies

first: Gregory

last: Crawford

overall_design: Refer to individual Series


title: Transcription and chromatin profiling in differentiating THP-1 monocytes and THP-1 derived macrophages

city: Palo Alto

first: Kevin

last: Van Bortle

address: 3165 Porter Dr

department: Genetics

summary: Here we profile nascent transcription, RNA polymerase III occupancy, chromatin accessibility, and H3K27ac levels in THP-1 monocytes and THP-1 derived macrophages after 72 hr exposure to phorbol myristate acetate (PMA).

overall_design: Biotin-capture of nascent transcription, ChIP-seq against RNA polymerase III subunit RPC4 (POLR3D), histone H3K27 acetylation (H3K27ac), CCCTC-binding factor (CTCF), and MAF1, and ATAC-seq in THP-1 monocytes and THP-1 derived macrophages after 72 hr exposure to PMA.

first: Douglas

last: Phanstiel

first: Michael

last: Snyder


title: The Schizophrenia Risk Gene Product Satb2 Regulates miRNAs Expression and Long-Term Memory in Adult CNS

status: Public on Dec 12 2016

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary:
(i)  The hippocampal transcriptome was analyzed in mice that lack the SatB2 gene
(ii)  Satb2 binds to active promoters of protein-coding and non-coding loci and determines the levels of a large cohort of miRNAs in the CA1 hippocampal field that are implicated in synaptic plasticity and/or memory formation.

overall_design:
(i) RNA was isolated from the hippocampal CA1 region of mice that lack the SatB2 gene from the adult forebrain and subjected to RNA-sequencing
(ii) Mapping the genomic localization of Satb2 in mouse primary hippocampal neurons.

first: Galina

last: Apostolova

first: Farahnaz

last: Sananbenesi

first: Georg

last: Dechant

first: Dietmar

last: Rieder


title: Characterization of chromatin and gene expression changes during fasting in mouse liver [ChIP-Seq]

status: Public on Dec 20 2016

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: During fasting transcriptional programs lead to glucose and ketone production. The major TFs, their crosstalk and the enhancers driving it are unknown. We show that fasting massively reorganizes liver chromatin to expose 'fasting enhancers'. By tracking TF footprints, we implicated the major TFs regulating fuel production by two modules. The ketogenic module is executed by a temporally-organized TF cascade. Conversely, in the gluconeogenic module glucocorticoid receptor (GR) augments cAMP-response element-binding protein (CREB) activity in an enhancer-selective manner. Using genomics and single-molecule tracking, we show that GR enhances the number of bound CREB molecules and the quantity, intensity and accessibility of CREB binding sites; leading to synergistic gene expression and glucose production. Our findings reveal that TFs dynamically and cooperatively respond to environmental signals to restore homeostasis.

overall_design: characterization of liver transcription factor binding and histone acetylation during fasting using chromatin immunoprecipitation

first: Ido

last: Goldstein

first: Gordon

last: Hager


title: Methylation, expression, and SNP data of multi regional colorectal carcinoma

status: Public on Nov 30 2016

city: FUKUOKA

first: RYUTARO

last: UCHI

state: FUKUOKA

institute: KYUSHUUNIVERSItY


title: DNA methylation profile of triple negative breast cancer specific genes

first: Kelly

last: Avery-Kiejda


title: Wounds That Never Heal?  Stem Cell Lineage Infidelity at the Crossroads of Wound-Repair and Cancer

status: Public on Mar 30 2017

city: New York

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: Tissue stem cells govern tissue regeneration and wound-repair.  Tumors often hijack these normal cellular programs and exploit them for malignancy.  Here, we identify such a phenomenon in skin, where stem cells of the epidermis and hair follicle remain faithfully restricted to fueling their own tissue during homeostasis. They lose lineage fidelity during tumorigenesis. Moreover, breakdown of stem cell lineage confinement – granting privileges associated with both fates – is not only a hallmark, but also obligatory for malignancy. Intriguingly, we find that lineage plasticity is also critical in wound-repair, where it functions transiently to redirect fates. Probing mechanism, we show that irrespective of cellular origin, lineage infidelity occurs in wounding when stress-responsive enhancers are activated and override the normal enhancers that govern lineage-specificity. In cancer, stress-responsive transcription factor levels rise, causing lineage commanders to reach excess. When lineage and stress factors collaborate, they activate new oncogenic enhancers that distinguish cancers from wounds.

overall_design: Open chromatin regions bound by TFs typically exhibit higher accessibility than otherwise closed regions. Since ATAC-seq technology can be applied on small numbers of SCs, we could use this approach to delineate open chromatin states across homeostatic, wound-induced and tumorigenic SC populations in vivo. Importantly, by complementing these data with transcriptional profiling, we could predict the TF binding sites that are functional for each cellular state

first: Elaine

last: Fuchs


title: Gene expression of myeloma cell line (U266) transduced with Scr or shKDM3A cultured in normoxia or hypoxia

status: Public on Apr 01 2017

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

summary: By using a myeloma cell line U266 transduced Scrumbled shRNA or shKDM3A, we conducted whole genome gene screening against the cells that were subjected by chronic hypoxia condition.

overall_design: We performed comprehensive gene expression analysis on the shKDM3A transduced U266 cell line and extracted several genes that have increased expression in hypoxia and downregulated by siKDM3A

first: Hiroyuki

last: Tagawa


title: Characterization of chromatin and gene expression changes during fasting in mouse liver


title: Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas

status: Public on Nov 23 2016

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan


title: Global reduction in H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas

summary: A subgroup of  Posterior fossa ependymomas show reduced H3K27me3, global DNA hypomethylation, are more invasive, exhibit poor prognosis and epigenetically deregulated genes converge on radial glial factors, suggesting developing cerebellar radial glia as candidate cells-of-origin.

overall_design: RNA-sequencing was performed  in 5 posterior fossa (PF) and three supratentorial (ST) ependymoma samples. All 5 PF samples show low H3K27me3 and designated PF_H3K27me3-ve; all 3 ST ependymoma samples show high H3K27me3 and desginated ST_H3K27me3+ve

first: Marcin

last: Cieslik


title: Pluripotent Reprogramming of Human AML Resets Leukemic Behavior and Models Therapeutic Targeting of Subclones [methylation]

status: Public on Nov 14 2016

first: Andrew

last: Gentles

address: 1201 Welch Road

summary: Understanding the contribution of abnormal genetic and epigenetic programs to acute myeloid leukemia (AML) is necessary for the integrated design of targeted therapies. To investigate this, we determined the effect of epigenetic reprogramming on leukemic behavior by generating induced pluripotent stem cells (iPSCs) from AML patient samples harboring MLL rearrangements. AML-derived iPSCs (AML-iPSCs) retained leukemic mutations, but reset leukemic DNA methylation/gene expression patterns and lacked leukemic potential. However, when differentiated into hematopoietic cells, AML-iPSCs reacquired the ability to give rise to leukemia in vivo and reestablished leukemic methylation/gene expression patterns, including an aberrant MLL signature, indicating that epigenetic reprogramming was insufficient to eliminate leukemic behavior. In one case, we identified distinct AML-iPSC KRAS mutant and wildtype subclones that demonstrated differential growth properties and therapeutic susceptibilities, predicting KRAS wildtype clonal relapse due to increased cytarabine resistance. Increased cytarabine resistance was further observed in a cohort of KRAS wildtype MLL-rearranged AML samples, demonstrating the utility of AML-iPSCs in predicting subclonal relapse and facilitating clonal targeting in AML.

overall_design: DNA methylation array profiling of normal and leukemic differentiated and iPSC populations

first: Mark

last: Chao