title: Sub-chronic pulmonary transcriptional response to a mixture of 4 PAHs in adult male MutaTMMouse.

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. The mice in this study were exposed to a mixture of 4 PAHs, benzo(a)pyrene, benz(a)anthracene, benzo(b)fluoranthene, and chrysene. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to this PAH mixture in the lung tissue. Adult male MutaTMMouse were exposed to three doses of the mixture of 4 PAHs or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary transcriptional response of male mice exposed to a 4PAH mixture for 28 days at three different doses, including D1 (12.5 mg BaP equivalents/kg-bw/day), D2 (25 mg BaP equivalents/kg-bw/day), and D3 (50 mg BaP equivalents/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total of 18 samples (arrays) from the lung included in the final analysis using a two-colour reference design.


title: Sub-chronic pulmonary transcriptional response to a mixture of 8 polycyclic aromatic hydrocarbons in adult male MutaTMMouse.

status: Public on Jan 01 2017

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

country: Canada

institute: Health Canada

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. The mice in this study were exposed to a mixture of 8 PAHs, benzo(a)pyrene, benz(a)anthracene, benzo(b)fluoranthene, benzo(ghi)perylene, benzo(k)fluoranthene, chrysene, dibenz(ah)anthracene, and indeno(123,cd)pyrene. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to this PAH mixture in the lung tissue. Adult male MutaTMMouse were exposed to three doses of the mixture of 8 PAHs or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary transcriptional response of male mice exposed to a 8PAH mixture for 28 days at three different doses, including D1 (15 mg BaP equivalents/kg-bw/day), D2 (30 mg BaP equivalents/kg-bw/day), and D3 (60 mg BaP equivalents/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total of 19 samples (arrays) from the lung included in the final analysis using a two-colour reference design.

first: Andrew

last: Williams

first: Sabina

last: Halappanavar


title: Expression data of adult digit tip of K14-CreER;Ctnnb1 cKO mouse

status: Public on Dec 31 2016

city: New York

first: Makoto

last: Takeo

state: NY

address: 522 First Ave.

country: USA

institute: New York University School of Medicine

summary: Removal of Ctnnb1 in epithelial cells results in the defect of nail differentiation as well as underlying digit bone maintenance. We have revealed that several osteoclastgenesis related genes are up-regulated in Ctnnb1 cKO digit.

overall_design: Whole digit tip of 8w old wildtype and Ctnnb1 cKO mice were harvested and processed to RNA extraction and hybridization on Affymetrix microarrays. We analyzed three control and three Ctnnb1 cKO samples.

first: Mayumi

last: Ito


title: ILF2 Regulates RNA Splicing of DNA Damage Response Genes to Confer Poor Prognosis in 1q21-Amplified Multiple Myeloma

city: Houston

first: Li

last: Zhang

state: TX

address: 1400 Pressler, unit 1410

department: Bioinformatics

institute: The University of Texas MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: To understand whether ILF2 is required to ensure the alternative splicing and processing of specific pre-mRNAs in Multiple Myeloma (MM), both in physiological and DNA damage conditions, we performed RNA sequencing (RNA-Seq) analysis of untreated or melphalan-treated ILF2-depleted JJN3 cells. Non-silencing or ILF2 shRNA transduced JJN3 cells were treated with melphalan for 10 hours.

overall_design:
Total RNA from untreated or melphalan-treated JJN3 cells transduced with a non-silencing or ILF2 shRNA (two independent replicates per condition) were isolated with the RNeasy Mini kit (Qiagen). Libraries were constructed using the Ovation RNA-Seq System V2 (Nugen) according to the manufacturer’s instructions.
Transcriptomic RNA-Seq was performed on the Illumina HiSeq 2000 platform using the standard paired-end protocol. In total, 60-160 million 76-bp reads were generated per sample. An initial sequence-level quality assessment was performed using FastQC (version 0.10.1, Simon Andrews). The RNA-Seq reads were then mapped to the reference human genome (GRCh37) using Tophat2, allowing a maximum of two mismatches per 76-bp sequencing end. Differential splicing was assessed by multivariate analysis of transcript splicing (MATS) using an FDR<0.05. Pathway enrichment analysis was performed with Pathway Studio.

first: Simona

last: Colla

first: Matteo

last: Marchesini


title: Gene expression during metabolism of polysaccharides and sugars by Alicyclobacillus acidocaldarius

city: Richland

first: Brady

last: Lee

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

summary:
The purpose of this study was to characterize carbon metabolism and gene regulation in Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and the effect of pentose and hexose sugars on gene expression
Chemostat studies and global transcriptome analysis were used to accomplish this goal.

overall_design: A three chip study using total RNA recovered from three sets of triplicate chemostat experiments using Alicyclobacillus acidocaldarius ATCC27009/DSM446 growing using wheat arabinoxylan (WAX) and glucose or xylose.  Each chip measures the expression level of 3,554 genes from Alicyclobacillus acidocaldarius ATCC27009/DSM446 with seven 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: William

last: Apel

first: Linda

last: DeVeaux

first: Peter

last: Sheridan


title: Expression profiling of small intestine neuroendocrine tumors identifies subclasses  with clinical relevance, therapeutic target and biomarkers for prognosis

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

summary: We sought to define the gene expression profiles of small intestine neuroendocrine tumors  (SI-NETs) in order to identify clinically relevant subgroups of tumors, prognostic markers  and novel targets for treatment.

overall_design: Genome-wide expression profiling was conducted on tumor biopsies from a cohort of 33  patients with metastatic SI-NETs and on 10 normal small intestine (SI)  mucosa (controls).

first: Ellinor

last: Andersson

first: Yvonne

last: Arvidsson

first: Christina

last: Swärd

first: Tobias

last: Hofving

first: Bo

last: Wängberg

first: Ola

last: Nilsson


title: Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross

status: Public on Jan 03 2017

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: We studied the cause-effect relationships between the transcriptomics and phenotypic outcomes within the CC-F1 population, which allowed us to identify novel genetic signatures. Our results indicate that Oas1b status as wild type or mutant, and overall Oas1b gene dosage, link with novel innate immune gene signatures that impact specific biological pathways for the control of flavivirus infection and immunity.

overall_design: Microarrays were performed on spleen samples from mice collected at days 2,4,7,12 post-infection with west nile virus or from mock-infected animals.

first: Richard

last: Green

first: Courtney

last: Wilkins

first: Sunil

last: Thomas

first: Aimee

last: Sekine

last: Gale Jr


title: Expression data from mouse kidney

status: Public on Dec 23 2016

city: Louisville

first: Gregory

last: Weber

state: KY

address: 500 S. Preston St., Rm 802

institute: University of Louisville

summary:
Hypertension is a major risk factor for chronic kidney disease (CKD) and renal inflammation is an integral part in this pathology.  Hydrogen sulfide (H2S) has been shown to mitigate renal damage through reduction in blood pressure and reactive oxygen species; however, the exact mechanisms are not clear.  While several studies have underlined the role of epigenetics in renal inflammation and dysfunction, the mechanisms through which epigenetic regulators play role in hypertension are not well defined.
We used microarrays to detail the global programme of gene expression underlying hypertension in the kidney and how hydrogen sulfide supplementation alleviates these effects.

overall_design: Wild-type mice were treated with Ang-II to induce hypertension for 28 days along with hydrogen sulfide, at the end of which kidneys were collected and processed for arrays.

first: Sathnur

last: Pushpakumar

first: Utpal

last: Sen


title: miRNAs involed in lactation of cow mammary gland

city: Haerbin

first: Chunmei

last: wang

address: 59 MuCai Street

country: China

institute: Northeast Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary:
We investigated miRNA expression in Holstein dairy cow of mammary gland with different producing quality milk using high-throughput sequence and qRT-PCR techniques. miRNA libraries were constructed from mammary gland tissues taken from a high producing quality milk and a low producing quality milk Holstein dairy cow, the small RNA digitalization analysis based on HiSeq high-throughput sequencing takes the SBS-sequencing by synthesis.The libraries included 4732 miRNAs. A total of 124 miRNAs in the high producing quality milk mammary gland showed significant differences in expression compared to low producing quality milk mammary gland (P<0.05).
Conclusion: Our study provides a broad view of the bovine mammary gland small RNA expression profile characteristics. Differences in types and expression levels of miRNAs were observed between high producing quality milk and a low producing quality milk Holstein dairy cow

overall_design: Examination of 3 group of different producing quality milk mammary gland of Holstein dairy cow,each group has 3 sample

last: Wang

first: Jie

first: Dan

last: Li

first: Qingzhang


title: Foxp3 DNA binding in HDAC6-KO vs wild type Regulatory T cells

status: Public on Dec 17 2016

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

type: Genome binding/occupancy profiling by genome tiling array

summary: We used NimbleGen Mouse ChIP-chip 3 × 720K RefSeq Promoter Arrays (NimbleGen Roche, Madison, WI). Briefly, we isolated three independent samples of gender and age matched HDAC6KO and WT control CD4+CD25+ Treg, isolated, cross-linked and processed genomic DNA as above. DNA-protein complexes were bound with Foxp3 mAb, and enriched through immunoprecipitation, which a control sample is retained without immunoprecipitation (input). Both input and Foxp3-IP enriched samples underwent whole-genome amplification or ligation mediated-PCR to obtain adequate amounts of DNA for labeling. Foxp3-IP enriched samples were labeled with Cy5, and input samples with Cy3, and the arrays submitted to NimbleGen for analysis. Data were analyzed using Partek GS (Partek Inc., St Louis, MO) and the Broad Institutes Interactive Genome Viewer (Version 2.3.32) (Robinson et al., 2011). Raw data underwent Loess normalization, and Student t-testing with a false discovery rate of 0.1 (p-value cutoff 0.0029). For visualization, we generated IGV files using NimbleGen mapping information from the SignalMap GFF files.

overall_design: Foxp3 ChIP in 8 week old male HDAC6-KO and wild type Regulatory T cells.

first: Liqing

first: Ulf

middle: H

last: Beier


title: Browning of White Adipose Tissue with Roscovitine Induces a Distinct Population of UCP1+ Adipocytes.

status: Public on Dec 13 2016

city: Boston

first: Stephen

middle: R.

last: Farmer

state: MA

address: 72 E. Concord

department: Biochemistry

institute: Boston University

summary: Analysis of FACS sorted UCP1+ adipocytes shows that the mRNA signature of brite adipocytes is distinct from beige adipocytes, which arise through catecholamine signaling.

overall_design: Total RNA samples of FACS-sorted adipocytes (3-4 each group) from UCP1/Tomato mice (8 to 10-week old) were analyzed by microarray at Boston University Microarray Resource Facility.

middle: R


title: The gene expression signatures of human normal, benign and PDAC pancreatic tisssues.

status: Public on Dec 09 2016

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

summary: To study the gene profile of 8 normal, 15 adjacent benign  and 27 PDAC pancreatic tissues of human, data was generated with Agilent G2565CA arrays. Results provide a global profile of over 56,000 genes in human normal, benign and tumorous pancreatic tissues, and comparison of the differentially expressed genes among these 3 groups.

overall_design: Gene expression was profiled and compared among human normal, benign and PDAC pancreatic tissue samples globally, using Agilent array with design ID 039714.

first: Daniel

last: Brackett

first: Jo

last: Vandesompele

first: Pieter

last: Mestdagh

first: Jinmai

last: Jiang


title: Transcriptional profiling of human ovarian cancer cells treated with ribonucleases

status: Public on Dec 08 2016

city: Girona

first: Maria

last: Vilanova Brugués

address: Maria Aurèlia Capmany  40

department: Biologia

country: Spain

institute: Universitat de Girona

summary: PE5 is a nuclear-directed human ribonuclease variant that exhibits selective cytotoxicity against cancer cells. Onconase is a natural cytotoxic ribonuclease that has reached advanced clinical trials for the treatment of different types of cancer. Onconase also posses established antiviral effects. In the present work, we have used global gene expression microarrays to study the effects caused by PE5 and onconase, and therefore elucidate the mechanism by which these ribonucleases induce cytotoxicity. Transcriptional profiling of human ovarian cancer cells treated with PE5 or onconase were compared with that of control untreated cells. The study were carried out with the multidrug resistance cell line NCI/ADR-RES and its parental cell line OVCAR8.

overall_design: Two loop-design microarray experiments were performed, one for NCI/ADR-RES cell line and one for OVCAR8 cell line. Each loop contained six hybridizations (samples A-F and G-L) and three experimental conditions (control, PE5 treatment, and onconase treatment). Each loop employed four independent biological replicates.

first: Anna

last: Vert

first: Jessica

last: Castro

first: Marc

last: Ribó

first: Antoni

last: Benito

last: Vilanova


title: Data from hepatocellular carcinoma PDX

status: Public on Dec 01 2016

city: Shanghai

first: hong

last: li

address: 320 Yueyang Road

institute: SIBS

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

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

overall_design: Refer to individual Series


title: SNP data from hepatocellular carcinoma PDX

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

summary:
Hepatocellular carcinoma samples were obtained after patients provided written informed consent and with the approval of the institutional research ethics board at the Liver Cancer Institute of Zhongshan Hospital, Fudan University (Shanghai, China). Fresh tumor tissues were implanted in NOD/SCID mice. Tumor lines were successfully maintained through multiple rounds of serial transplantation.
We used microarrays to evaluate the genotype similarity between patient tumor and patient-derived xenograft (PDX).

overall_design: PDX (F0, F2, F4) for DNA extraction and hybridization on Affymetrix microarrays.

first: Hong

first: Bo

last: Hu


title: Expression data from hepatocellular carcinoma PDX

summary:
Hepatocellular carcinoma samples were obtained after patients provided written informed consent and with the approval of the institutional research ethics board at the Liver Cancer Institute of Zhongshan Hospital, Fudan University (Shanghai, China). Fresh tumor tissues were implanted in NOD/SCID mice. Tumor lines were successfully maintained through multiple rounds of serial transplantation.
We used microarrays to evaluate the expression similarity between patient tumor and patient-derived xenograft (PDX).

overall_design: PDX (F0, F2, F4) for RNA extraction and hybridization on Affymetrix microarrays.

last: Li


title: Transcriptional changes in breast cancer cell lines associated with vascular mimicry

city: Portland

first: Rosalie

last: Sears

state: OR

address: 3720 SW Moody Ave

department: MMG

institute: Oregon Health & Science University

summary: The goal of this study was to determine the transcriptional changes associated with breast cancer cells undergoing vascular mimicry in a 3D assay.  Two breast cancer cell lines were plated on matrigel in the presence or absence of serum.  MDA-MB-231 cells undergo vascular mimicry on matrigel in the absence of serum, MDA-MB-453 cells do not.

overall_design: Four samples were analyzed.  MDA-MB-231 and MDA-MB-453 cells were plated for 24 hours on matrigel in the presence or absence of serum.  MDA-MB-231 cells undergo vascular mimicry when plated on matrigel in the absence of serum, while MDA-MB-453 cells do not.

first: Ellen

last: Langer


title: miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MDA-MB-231 cell line.

status: Public on Nov 17 2016

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

summary:
cancer spheroid has been widely used as in vitro model of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance. From the miRNA profile, miR-15b, miR-34a, miR-148a, miR-628 and miR-196b were shown to be involved in CSCs-associated signalling pathways in both models of spheroids which highlights the involvement of these miRNAs in maintaining the CSCs features. In addition, unique clusters of miRNAs namely miR-205, miR-181a and miR-204 were found in basal-like spheroid whereas miR-125, miR-760, miR-30c and miR-136 were identified in luminal-like spheroid. Our results highlight the roles of miRNAs as well as providing novel perspectives of the relevant pathways underlying spheroid-enriched CSCs in breast cancer.
Keywords: Breast

overall_design: miRNA profiles of MDA-MB-231 enriched CSCs spheroids and monolayer cultures were generated in triplicates by deep sequencing using TruSeq small RNA illumina

first: Lily

last: Boo

first: Wan

middle: Y

last: Ho

first: Norlaily

middle: M

last: Ali

first: Swee

middle: K

last: Yeap

first: Huynh

last: Ky

first: Kok

middle: G

last: Chan

first: Wai

middle: F

last: Yin

first: Dilan

middle: A

last: Satharasinghe

first: Woan

middle: C

last: Liew

first: Sheau

last: Tan

first: Han

last: Ong

first: Soon

last: Cheong


title: Gene expression profiling associated with knockdown of RNF20 in human normal and malignant lung epithelial cell lines

status: Public on Oct 20 2016

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: The experiment was designed to display differential gene expression profiling in one lung epithelial cell BEAS2-B, and three lung cancer cell lines A549, H1299, H460 cells upon knockdown of RNF20, by using RNAseq technology.

overall_design: RNF20 was first attenuated in duplicated normal lung epithelial cell BEAS2-B, and three lung cancer cell lines A549, H1299, H460 by siRNA-mediated knockdown. Total RNA was extracted from duplicated cancers cells transfected with two independent control siRNA (Ctrl1/2) and RNF20 specific siRNAs (RNF1/2) at 72h post-transfection for RNAseq analysis. Differentially expressed genes in RNF20-attenuated lung epithelial cells were identified in comparison to that in cells transfected with control siRNA.

first: Keqiang

last: Zhang

first: Xiwei

last: Wu

first: Jinhui

last: Wang

first: Lu

last: Yang

first: Dan

last: Raz


title: Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem

status: Public on Oct 15 2016

city: Tainan

first: Yao-Cheng

last: Lin

address: No. 59, Siraya Blvd., SinShih Dist.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary:
Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season.  Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area).
Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively.  The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction.  Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each.
Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize.

first: Dave

last: Berger


title: miRNA profile of lung adenocarcinoma cells treatment with monoclonal antibody NJ001 [miRNA_12h_24h_48h]

status: Public on Oct 29 2016

city: Nanjing

first: Yan

last: Cao

state: Jiangsu

address: NO.140 Hanzhong Road

department: Laboratory medicine

institute: Nanjing medical university

summary:
Previously, we developed a newly monoclonal antibody named NJ001 which selectively reacted to non-small cell lung cancer and exhibited anti-tumor activity both in vitro and in vivo by inhibiting proliferation, colony formation, apoptosis and so on. MiRNA ubiquitously regulates cell processes such as cell cycle regulation, invasion, differentiation and proliferation.
We used microarrays to detail the miRNA changes in the lung adenocarcinoma cell SPC-A1 after treatment with NJ001. These miRNA may have contribution to the effect of NJ001 on cancer cells.

overall_design: SPC-A1 cells treated with or without NJ001 were used as study group or control group respectively and everygroup has three biological repeats. Since we observed larges amounts of miRNA changes after NJ001treatment for 72h in SPC-A1. Another three time-points (12h, 24h, 48h) was added to find more earlier dynamic changes  expression levels of miRNA, which may be more important to the anti-tumor activity of NJ001.

first: Shiyang

last: Pan


title: Distinct small RNA populations act antagonistically in formation of heterosis

status: Public on Oct 24 2016

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

summary: This research reports the analysis of sRNAs in 14 and 7 inbred lines from a breeding population. We analyzed the contribution of sRNAs to the formation of heterosis via integrative association analysis with field data of 98 hybrids generated from the set of inbred lines. Our results indicate a contribution of sRNAs to heterosis. We were able to identify different sets of sRNAs associated with heterosis with distinct length and genome distribution patterns.

overall_design: Analysis of sRNA contribution to the formation of heterosis in maize by an association study in a breeding population.

first: Felix

last: Seifert

first: Alexander

last: Thiemann

first: Robert

last: Grant-Downton

first: Susanne

last: Edelmann

first: Matthias

last: Frisch

first: Albrecht

middle: E

last: Melchinger


title: Microarray analysis of Macrophages and Osteoclasts

status: Public on Sep 17 2016

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

summary: Comparaison of genes expression between bone marrow derived macrophages and osteoclasts in C57BL/6J mice

overall_design: 2 samples with 3 mice per sample.

first: I

last: Adamopoulos

first: Dennis


title: Probing Plasmodium falciparum sexual differentiation at the single cell level

status: Public on Mar 11 2017

city: Cambridge

first: Daniel

middle: E.

last: Neafsey

address: 415 Main St.

institute: Broad Institute

summary: Malaria parasites go through major transitions during their complex life cycle, yet the underlying differentiation pathways remain obscure. Here we apply single cell transcriptomics to unravel events that initiate sexual development in preparation for transmission of the parasite from human to mosquito. This proof-of-concept study provides a template to capture transcriptional diversity in heterogeneous parasite populations, with major implications for our understanding of parasite biology and the ongoing malaria elimination campaign.

overall_design: Plasmodium-infected human erythrocytes were single-cell sorted into 384-well plates at three separate time points after LysoPC depletion gametocyte induction (4, 8, 12 hours post induction). Two rows (total of 48 wells) of each 384-well plate were reserved for control samples (no induction). A total of 1152 wells were sequenced, with 144 control wells, and 1008 induced wells.

first: Nicolas

last: Brancucci

first: Mariana

last: De Niz

first: Timothy

middle: J

last: Straub

first: Deepali

last: Ravel

first: Eva

last: Hitz

first: Sylwia

middle: D

last: Boltryk

first: Igor

last: Niederwieser

first: Bruce

last: Birren

first: Till

middle: S

last: Voss

last: Marti


title: miRNA profile of lung adenocarcinoma cells treatment with monoclonal antibody NJ001 [miRNA_72h]

first: Yan

last: Cao

overall_design: SPC-A1 cells treated with or without NJ001 were used as study group or control group respectively and everygroup has three biological repeats. we observed this two groups at 72h to investigate changes in miRNA expression levels following this monoclonal antibody treatment.

first: Shiyang

last: Pan


title: Comparision of gene expression profiles between female germline stem cells and spermatogonia stem cells

status: Public on Sep 29 2016

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We used the microarray analysis to compare the globe gene expression profiles of female germ line stem cells (FGSCs) and spermatogonial stem cells (SSCs).

overall_design: The study is the first attempt to compare morphological and molecular characters (including comparing the globe gene expression profiles of FGSCs and SSCs)between FGSCs and SSCs. FGSCs and SSCs were isolated from ovaries of 3 days old mice and testes of 6 days old mice, respectively.

first: Wenhai

last: Xie


title: cGMP inducer effect on cell line Panc-1

status: Public on Sep 01 2016

city: Fukuoka

first: Motofumi

last: Kumazoe

state: Fukuoka

address: 6-10-1 Hakozaki, Higashi-ku

department: Department of Bioscience and Biotechnology

country: Japan

institute: Faculty of Agriculture, Kyushu University, Fukuoka

summary:
cGMP is well-known secound messanger involved in vascular homeostasis. However little is known the effect of cGMP inducer on mRNA expression in  cancer cells.
We performed microarrays to revealed the transcriptional change of a human pancreatic ductal adenocarcinoma (PDCA) cell line (Panc -1) to cGMP inducer Bay41-2272 in order to provide insight into impact of cGMP induction on Panc-1 cells.

overall_design: Panc-1 Human PDCA cells were treated with vehicle (DMSO) or 5 μM Bay41-2272 for 48 h and total RNA was extracted by using TRIzol Reagent. The microarray analysis was conducted on the Panc-1 cells expressing by using Agilent Microarray.

first: Mika

last: Takai

first: Hirofumi

last: Tachibana


title: Genome-wide identification of  Drought-responsive Regulatory Coding and Non-coding Transcripts from Oryza sativa L. by deep RNA sequencing

status: Public on Sep 06 2016

city: Seoul

first: Sun

last: Kim

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Abiotic environmental stresses cause serious economic losses in agriculture. These stresses include temperature extremes, high salinity and drought. To isolate drought-responsive novel coding and noncoding genes, we used the next generation sequencing method from three rice cultivars (wild type nipponbare, nipponbare AP2 transgenic plants, wild type vandana). 36 NGS data of mRNA-seq, small RNA-seq, riboZero-seq were analyzed. For the analyses of these data we constructed a TF-TG (Transcription Factor-Target Gene) network and an ap2 rooted cascading tree. Using these networks and tress we isolated lincRNAs, differentially expressed miRNAs and their targets. We identified several drought stress-related novel/function unknown coding transcripts (transcription factors and functional genes) and non-coding transcripts (small noncoding transcripts such as microRNA and long noncoding transcripts) from these database analyses and have constructed databases of drought stress-related coding and noncoding transcripts

overall_design: Identification of drought-responsive Regulatory Coding and Non-coding Transcripts from rice by deep RNA sequencing

first: Hawk-Bin

last: Kwon

first: Seon-Ju

last: Shin

first: Inuk

last: Jung

first: Hongryul

last: Ahn

first: Sungmin

last: Rhee


title: Expression Data from International C. elegans Experiment 1st (Agilent)

status: Public on Aug 31 2016

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

summary: The effect of microgravity on gene expression in C.elegans was comprehensively analysed by DNA microarray (Agilent).

overall_design: Mix staged C. elegans N2 was exposed microgravity for 10 days.

first: Toko

last: Hashizume


title: O-GlcNAc Aminidase is an RNA Pol II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1b

status: Public on Aug 29 2016

city: Bethesda

first: Brian

middle: Andrew

last: Lewis

state: MD

address: 9000 Rockville Pike

department: metabolism Branch

institute: National Cancer Institute-NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq shows that OGA and O-GlcNAc are found at promoters/TSS concomitantly with the known elongation factors SPT5 and TIF1b as well as RNA pol II.  There are gene body overlaps of various combinations of factors as well.

overall_design: ChIP-seq of the indicated factors from the human BJAB B-cell line

first: Bong-Hyun


title: The effect of FOXO3 knockdown and PDHA1 knockdown on PDAC cell line Panc-1

summary:
Little is known about the role of  FOXO3 and PDHA1 in PDAC. We performed microarrays to revealed the transcriptional change of a human pancreatic ductal adenocarcinoma (PDCA) cell line (Panc -1)
to scr-siRNA, FOXO3-siRNA and PDHA1-siRNA in order to provide insight into the role of PDHA1 and FOXO3 in Panc-1 cells.

overall_design: Panc-1 Human PDCA cells were treated with scr-siRNA, FOXO3-siRNA and PDHA1-siRNA for 48 h and total RNA was extracted by using TRIzol Reagent. The microarray analysis was conducted on the Panc-1 cells expressing by using Agilent Microarray.


title: miRNA profile of lung adenocarcinoma cells treatment with monoclonal antibody NJ001

first: Yan

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

overall_design: Refer to individual Series


title: DYRK2 regulates cancer stem cell population.

status: Public on Aug 23 2016

city: Tokyo

first: REI

last: MIMOTO

address: 3-25-8 Nishishinbashi, Minato-ku

institute: The Jikei University School of Medicine

summary: We used microarrays to  identified new factor that regulates cancer stem cell population in shRNA  DYRK2 cells using stable DYRK2 knockdown cells and mammosphere.

overall_design: We stably silenced DYRK2 in MCF-7 cells (shRNA-DYRK2 cells) using pSuper vector. For control, pSuper control cells were created. We obtained expression profiles from shRNA-DYRK2 cells and pSuper control cells. We also obtained RNA from  mammosphere which are stably expressing pSuper  vector or shRNA DYRK2.

first: Rei

last: Mimoto

first: Naoe

middle: N

last: Taira


title: Ethnicity-specific epigenetic variation in naïve CD4+ T cells and the susceptibility to autoimmunity

status: Public on Oct 01 2016

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: Background: Genetic and epigenetic variability contributes to the susceptibility and pathogenesis of autoimmune diseases. T cells play an important role in several autoimmune conditions, including lupus, which is more common and more severe in people of African descent. To investigate inherent epigenetic differences in T cells between ethnicities, we characterized genome-wide DNA methylation patterns in naïve CD4+ T cells in healthy African-Americans and European-Americans, and then confirmed our findings in lupus patients.  Results: Impressive ethnicity-specific clustering of DNA methylation profiling in naïve CD4+ T cells was revealed. Hypomethylated loci in healthy African-Americans were significantly enriched in pro-apoptotic and pro-inflammatory  genes. We also found hypomethylated genes in African-Americans to be disproportionately related to autoimmune diseases including lupus. We then confirmed that these genes, such as IL32, CD226, CDKN1A, and PTPRN2 were simi‑  larly hypomethylated in lupus patients of African-American compared to European-American descent. Using patch DNA methylation and luciferase reporter constructs, we showed that methylation of the IL32 promoter region reduces  gene expression in vitro. Importantly, bisulfite DNA sequencing demonstrated that cis-acting genetic variants within and directly disrupting CpG sites account for some ethnicity-specific variability in DNA methylation.

overall_design: A total of 66 healthy female individuals (21 African-Americans and 45 European-Americans) were recruited for our studies. There was no significant difference in age between the African-American (mean age = 39.3 years) and European-American (mean age  =  42.5  years) groups (P value = 0.34). All study participants signed an informed consent prior to enrollment into the study. The institutional review boards at the University of Michigan and the Henry Ford Health System approved this study. To validate the relevance of detected ethnicity-specific DNA methylation differences in an autoimmune disease, a group of age-matched 21 African-American and 42 European-American female lupus patients were studied. All patients met the American College of Rheumatology classification criteria for SLE.  This series includes only the healthy control samples.

first: Patrick

last: Coit

first: Amr

middle: H

last: Sawalha


title: Transcriptome analysis of granulosa cells after conventional vs long FSH-induced superstimulation in cattle

status: Public on Aug 01 2016

city: Saskatoon

first: Fernanda

last: Dias

address: 52 Campus Dr

institute: University of Saskatchewan

summary:
Conventional Superstimulation (group 1) vs. Long Superstimulation (group 3)
A genome-wide bovine oligo-microarray was used to compare the gene expression of granulosa cells collected from ovarian follicles after differing durations of the growing phase induced by exogenous FSH treatment. Cows were given a conventional (4-day) or long (7-day) superstimulatory treatment (25mg FSH im at 12-h intervals; n=6 per group), followed by prostaglandin treatment with last FSH and LH treatment 24 hr later. Granulosa cells were harvested 24 h after LH treatment. The expression of 416 genes was down-regulated and 615 genes was up-regulated in the long FSH group compared to the conventional FSH group. Quantification by RT-PCR of 7 genes (NTS, PTGS2, PTX3, RGS2, INHBA, CCND2 and LRP8) followed the same trend as in microarrays. Compared to the conventional group, the long FSH group responded to exogenous LH with down-regulation of mRNA for cyclinD2, lipoprotein receptorP8, CYP51A1, CYP19A1, CJA1, INHBA, SRPINE1, and up-regulation of Vannin, POSTN, GTPAse, Cysteine. Markers of fertility and follicle maturity were up-regulated in the long FSH group. We conclude that a prolonged FSH-induced growing phase is associated with transcriptomic characteristics of greater follicular maturity and may therefore be more appropriate for optimizing the superovulatory response and developmental competence of oocytes in cattle.

overall_design: straight comparison of Short Superstimulation group (the reference; group 1) versus a Long Superstimulation protocol ( the treatment; group 3) using 3 different animals (biological replicates) in each group and performed dye swap. For example on array 1: group 1 cow 1 versus group 3 cow 1 (cy3 vs cy5) and on array 4 is the dye swap group 3 cow 1 versus group 1 cow 1 (cy3 vs cy5).


title: miRNA expression of livers of liver-specific Hnf4a-null (Hnf4aΔH) mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Of 610 miRNAs, expression of 24 and 19 miRNAs was down-regulated or up-regulated more than 2-fold in Hnf4aΔH mice as compared to control (Hnf4af/f) mice

overall_design: In the study presented here, in order to identifiy the target genes for hepatic HNF4a, hepatic expression profiles of a total of 610 unique miRNA genes in Hnf4aΔH mice were investigated as compared with Hnf4af/f mice

first: Aoi

last: Morimoto

first: Mana

last: Kannari

first: Yuichi

last: Tsuchida

first: Chinatsu

last: Saito

first: Tsuyoshi

last: Matsuta

first: Shota

last: Sasaki

first: Tsukasa

last: Maeda

first: Takahiro

last: Nakamura

first: Masakiyo

last: Sakaguchi

first: Nobukazu

last: Nameki

first: Frank

last: Gonzalez

first: Yusuke

last: Inoue


title: BASP1 modifies the Tamoxifen response

city: Bristol

first: Andrew

middle: D.

last: Davidson

address: Faculty of Biomedical Sciences, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

summary: We report that WT1 transcriptional repressor protein BASP1 interacts with oestrogen receptor alpha (Erα), and interaction which in enhanced in the presence of Tamoxifen. We utilised RNASeq to identify common BASP1 and ERα target genes as well as Tamoxifen responsive genes that are altered in the absence of BASP1.

overall_design: Total mRNA sequencing analysis of MCF7 cells treated with either siRNA against BASP1 or negative control siRNA, with and without Tamoxifen treatment. Each experiment was performed in triplicate.

first: L

last: Marsh

first: A


title: TH2 cytokines promote tumor progression via regulating cathepsin secretion in tumor-associated macrophages

status: Public on Aug 17 2016

city: Philadelphia

first: Robert

last: Bowman

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

summary: Tumor-associated macrophages (TAMs) have emerged as prominent cells within the tumor microenvironment playing critical roles in extracellular matrix remodeling, tumor cell proliferation and invasion, angiogenesis, and metastasis.  Cathepsin proteases, produced by tumor cells and TAMs, have been demonstrated to mediate these processes, but it still remains unclear how these typically lysosomal enzymes are capable of executing their functions in the extracellular space. Here we identify a novel interaction between STAT6 and STAT3 that potently upregulates cathepsin secretion in macrophages in response to TH2 cytokine stimulation.  Systematic gene expression analyses reveal that the TH2 cytokine IL-4 synergizes with IL-6 or IL-10 to activate the IRE1α/ XBP1 axis of the unfolded protein response.  Pharmacological inhibition of the IRE1α axis blunts cathepsin secretion in macrophages and blocks macrophage-mediated tumor cell invasion.  Finally, we show that genetic ablation of either STAT6 or STAT3 signaling impairs tumor development and invasion.  Thus, these findings demonstrate that TH2 cytokine-mediated STAT6 and STAT3 activation in macrophages promotes a professional secretory phenotype capable of enhancing tumor cell invasion in a cathepsin-dependent manner.

overall_design: Murine bone marrow-derived macrophages (BMDMs) were cultured in DMEM + 10% FBS + CSF-1 (10 ng/ml) and  stimulated with IL-4 (n=5, 10 ng/ml), IL-6 (n=5, 10 ng/ml), IL-10 (n=3, 10 ng/ml), IL-4+IL-6 (n=5, 10 ng/ml each), IL-4+IL-10 (n=3 10 ng/ml each) or left unstimulated (n=8) for 24 hours.  RNA was then isolated and gene expression analyses were performed.

first: Johanna

last: Joyce


title: Identification of regulator of DYRK2

first: REI

last: MIMOTO

summary: We used microarrays to  identified new factor that regulates key factors in siRNA  DYRK2 cells.

overall_design: We  silenced DYRK2 in MCF-7 cells (siDYRK2 cells) using siRNA. For control, non-silencing siRNA was used. We obtained expression profiles from siDYRK2 cells and sControl cells.

first: Rei

last: Mimoto

first: Naoe

last: Taira

first: Yoshimi

last: Imawari


title: Effect of High-Fat Diet on Mouse Liver Gene Expression

status: Public on Jun 25 2016

city: Zurich

first: Zhibo

last: Gai

state: Schweiz

address: Wagistrasse 14

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zurich

summary: Global liver gene expression in mouse treated with either chow diet or high-fat diet was compared. Results provide insight into mechanisms underlying effects of high-fat diet on gene expression in mouse liver.

overall_design: Male C57/BJ mice aged 6 weeks were randomly assigned to a high-fat diet or control chow diet. All mice were sacrificed under anesthesia 20 weeks after treatment and livers were harvested. 3-4 total RNA samples per group were analyzed and gene expression was compared between groups.


title: Gene expression profiling of Salmonella enterica serovar Typhimurium exposed to subinhibitory concentrations of fosmidomycin and kanamycin

status: Public on Aug 28 2016

city: Flagstaff

last: Koppisch

state: AZ

address: PO Box 5698

department: Chemistry

institute: Northern Arizona University

summary: Expression profiling on a total of 4,391 genes was conducted to identify regulated S. typhimurium genes upon exposure to subinhibitory concentrations of the MEP pathway antibiotic fosmidomycin.  These results were subsequently compared to a similar gene expression analysis of subinhibitory exposures of S. typhimurium to the bactericide kanamycin

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: In this study, S. typhimurium cells in early stage logarithmic growth were exposed to subinhibitory concentrations of fosmidomycin or kanamycin and the expression profile was subsequently analyzed on a platform which assayed 4,391 unique genes.

middle: T

first: David

last: Fox


title: Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [H3K9me2]

status: Public on Jun 09 2016

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary:
ChIP-chip analyses of lysine 9 dimethylated histone H3 in Shelterin mutants.
Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation.

overall_design: Whole cell extract DNA and DNA recovered from H3K9 dimethylated chromatin of fission yeast were random-prime PCR amplified and labeled with Cy3 (whole cell extract) or Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

first: Martin

last: Zofall

first: Deborah

middle: R

last: Smith

first: Takeshi

last: Mizuguchi

first: Jothy

last: Dhakshnamoorthy

middle: I


title: Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [Rec12]

summary:
Occupancy profiling of Rec12 during  fission yeast meiosis.
Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation.

overall_design: Whole cell extract DNA and DNA recovered by Rec12 ChIP from fission yeast undergoing synchronous meiosis were random-prime PCR amplified and labeled with Cy3 (whole cell extract) or Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.


title: Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins


title: Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [BrdU]

summary:
BrdU profiling of replication activity in hydroxyurea treated synchronous  culture of fission yeast.
Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation.

overall_design: Cdc25-22 cells carrying thymidine kinase and human nucleoside transporter expression modules were arrested at the G2/M boundary. After release into the cell cycle in minimal medium supplemented with hydroxyurea and 5’-bromo-2’-deoxyuridine (BrdU) cells were collected at time corresponding to maximal septation index and fixed by treatment with sodium azide. BrdU labeled DNA was recovered by immunoprecipitation, amplified by random-primed PCR and after conjugation with Cy5 (IP) or Cy3 (input DNA) analyzed on Agilent 60mer array.


title: miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line

status: Public on May 10 2016

city: Cheras

first: norlaily

last: mohd ali

address: Universiti Tunku Abdul Rahman, Jln Sg Long

institute: Universiti Tunku Abdul Rahman

summary:
Intro: Spheroid culture especially on MCF-7 cell has been used as in vitro CSC model for anti-CSC drug discovery. The role of miRNAs in the regulation of mRNA specifically looking at the self-renewal capacity and the drug resistance of the spheroid-enriched CSCs models has not been evaluated. Therefore, a comprehensive profiling of the miRNAs will provide an insight into the regulatory mechanisms associated with breast cancer and CSCs.
Methods: Tumour spheroid of MCF-7 was generated and characterised for the biological features and CSCs characteristic comparing to the monolayer parental MCF-7 cells. Differential expression of miRNA between the spheroid and parental cells was evaluated using next generation sequencing (NGS). The differentially expressed miRNAs were then subjected to target genes predictions, followed pathway analyses to better understand the mechanism associated with spheroid-enriched CSCs.
Results: Spheroids generated from MCF-7 cell line under serum-free condition were found to be enriched with CSCs characteristics. miRNA-NGS analysis revealed 119 differentially expressed miRNAs between the spheroids and parental, with 24 up-regulated and 94 down-regulated. The gene ontology (GO) analysis showed that the predicted genes of the differentially expressed miRNAs were enriched in various biological processes. Pathway analysis revealed that the differentially expressed miRNAs and their target genes were associated with a variety of KEGG pathways, which could explain the self-renewal capability, and the higher drug resistance in spheroids when compared to parental.

overall_design: miRNA profiles of MCF-7 enriched CSCs spheroids and monolayer cultures were generated in triplicates by deep sequencing using TruSeq small RNA illumina

first: Lily

last: Boo

first: W

last: Y Ho

first: Norlaily

middle: M

last: Ali

first: Swee

middle: K

last: Yeap

first: Huynh

last: Ky

first: Kok

middle: G

last: Chan

first: Wai

middle: F

last: Yin

first: Dilan

last: Satharasinghe

first: Woan

last: Liew

first: Sheau

middle: W

last: Tan

first: Han

last: Ong

first: Soon

last: Cheong


title: Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [Taz1]

first: Shiv

last: Grewal

summary:
Occupancy profiling of Shelterin components in fission yeast.
Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation.

overall_design: Whole cell extract DNA and DNA recovered from Taz1 or Rif1-immunoprecipitated chromatin of fission yeast were random-prime PCR amplified and labeled with Cy3 (whole cell extract DNA) or with Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

first: Martin

last: Zofall


title: On the Origin and Evolutionary Consequences of Gene Body DNA Methylation

status: Public on Jul 11 2016

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

type: Methylation profiling by high throughput sequencing

summary: In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. salsugineum, indicating that CMT3 may be required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z and various histone modifications in E. salsugineum and Arabidopsis thaliana epiRILs turned up no evidence in support of any role for gbM in regulating transcription or affecting the composition and modifications of chromatin over evolutionary time scales.

sample_organism:
Arabidopsis thaliana
Brassica rapa
Brassica oleracea
Arabidopsis lyrata
Eutrema salsugineum
Capsella rubella

overall_design: Examination of DNA methylation, gene expression, and histone variant H2A.Z between Eutrema salsugineum, A. thaliana and methylation/histone modification mutants.


title: Gene expression data of two different strains of laying hens from a small group housing system

status: Public on Apr 30 2016

city: Hannover

first: Christin

last: Habig

state: lower saxony

address: Buenteweg 17p

institute: Institute for Animal Breeding and Genetics

summary: We used a chicken RNA microarray to identify differentially expressed genes in order to compare two layer lines kept in a small group housing system Eurovent Deutsch.

overall_design: Lohmann Selected Leghorn and Lohmann Brown

first: Ottmar

last: Distl


title: Short-term hypoxia synergizes with interleukin 15 priming in driving glycolytic gene transcription and supports human natural killer cell activities.

status: Public on May 09 2016

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Natural killer (NK) cells induce apoptosis in infected and transformed cells and produce immunoregulatory cytokines. At this, NK cells operate in inflammatory and tumor environments low in oxygen (hypoxic) and with immunosuppressive properties. In vitro studies of NK cells are, however, commonly performed in ambient air (normoxia).
We evaluated the immediate impact of short-term hypoxia on various intrinsic activities of resting and IL-15 primed NK cells and determined underlying transcriptional pathway regulations using a 2 × 2 factorial design. Hypoxia stimulated migration through extracellular matrix, supported secretion of specific chemokines, and shifted amounts of susceptible leukemia target cells toward late apoptosis. IL-15 was a powerful inducer of anabolic gene transcription. Associations of hypoxia with HIF-1 and glycolytic pathways were dependent on priming which represented the largest contrasts observed. Regulatory patterns and RT-PCR validated synergistic hypoxia-IL-15 interactions in upregulation of key glycolytic enzymes suggest an important function for anaerobic glycolysis in priming, underpinning the emerging role of glycolytic switching in driving NK cell function. Adaption to short-term hypoxia appeared however transitory. We conclude that control of oxygen in vitro can promote NK cell features desirable for adoptive transfer therapy.

overall_design: In five independent experiments, NK cells from healthy donors were enriched by immunomagnetic labeling and separation (negative selection, yielding >95% CD56+CD3-) and cultured in parallel under normoxia or hypoxia with or without IL-15 priming toward the end of the incubation.

first: Sonia

middle: Y

last: Velásquez

first: Doreen

last: Killian

first: Jutta

last: Schulte

first: Manfred

last: Thiel

first: Holger

middle: A

last: Lindner


title: High-throughput sequencing of eggplant small RNAs

status: Public on Apr 23 2016

city: Nanjing

first: Liu

last: Yang

address: Weigang No.1

institute: Nanjing Agricultural University

summary: MiRNAs are a class of non-coding, small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including eggplant (Solanum melongena L.). To identify miRNAs in eggplant and their response to Verticillium dahliae infection, a fungal pathogen for which effective cure methods and a clear understanding of its mechanisms are currently lacking, we deep-sequenced two small RNA (sRNA) libraries prepared from mocked and infected seedlings of eggplants. Specifically, 30,830,792 reads produced 7,716,328 unique small RNAs have been identified.

overall_design: Deep-sequenced two small RNA libraries prepared from mocked and Verticillium dahliae infected eggplant seedlings

first: Qing


title: Cyclic AMP-responsive element-binding protein (CREB) is critical in autoimmunity by promoting Th17 but inhibiting Treg differentiation

status: Public on Apr 19 2016

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

summary: The molecular mechanisms that govern differential T cell development into pro-inflammatory Th17 vs. regulatory T (Treg) cells remain unclear. Here, we show that selective deletion of CREB in T cells or Th17 cells impaired Th17 differentiation in vitro and in vivo, and led to resistance to autoimmune diseases. Mechanistically, CREB, activated by CD3-PKC-ϴ signaling, plays a key role in regulating Th17 differentiation, at least in part through directly binding to the Il17-Il17f gene locus. Unexpectedly, although dispensable for FOXP3 expression and for the homeostasis and function of thymus-derived Treg cells, CREB negatively regulates the survival of TGF-β-induced Treg cells, and deletion of CREB resulted in increased FOXP3+ Treg cells in the intestine and protection in a colitis model. Thus, CREB is critical in autoimmune diseases by promoting Th17 and inhibiting de novo Treg generation.

overall_design: Identification of CREB regulated genes in Th17 cells

first: Xiaohu

last: Wang

first: Lu

last: Ni

first: Chen

last: Dong


title: Transcriptional profiling of IL-10 producing vs non producing human TFR2 cells

status: Public on Apr 05 2016

city: canberra

first: Pablo

last: Fernandez De Canete Nieto

address: building 131 garran road

country: Australia

institute: JCSMR,ANU

summary:
Background information:
Antibody responses to most infectious and food protein antigens depend on help to B cells from specialised T follicular helper (Tfh) cells. A subset of Foxp3+ regulatory T cells (Tregs) has been described in mice, with a prominent role in repressing germinal center reactions that are critical for memory B cell formation and long-lived antibody responses. These specialised Tregs co-opt the Bcl-6-dependent Tfh differentiation pathway in order to access the B cell-rich follicles and have therefore been designated as T follicular regulatory (Tfr) cells.
Preliminary results:
We identified a unique Bcl-6-expressing follicular regulatory T cell in human secondary lymphoid tissue, designated hereafter as Tfr2 cells, that lacks Foxp3 expression and the thymic-imprinted Foxp3 methylation pattern, but shares expression of key Treg molecules. Interestingly, 25% of these cells are the predominant source of T cell-derived IL-10 in human tonsil, an important cytokine with immunomodulatory properties.
Aims of this study:
We performed transcriptional profiling using affymetrix microarrays to interrogate wether IL-10 producing vs non producing human Tfr2 cells were fundamentally different subsets.

overall_design: 2 cell types (IL-10+ vs IL10- TFR2 cell subsets) obtained from 3 different tonsil donors (biological replicates)

first: Rebecca

last: Sweet

first: Stephen

last: Ohms

last: Canete


title: 4C-seq data and Pho and Ph, H3K27me3 and Engrailed ChIP-seq data in wildtype and PRE-deleted third instar Drosophila larval brains and disks

status: Public on Apr 06 2016

city: North Bethesda

first: sandip

last: de

address: 6 center drive

department: rm 3B-331, bldg 6B

institute: NICHD/NIH

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

overall_design: Refer to individual Series


title: Pho and Ph, H3K27me3 and Engrailed ChIP-seq data in Drosophila third instar larval brains and disks

status: Public on Apr 01 2016

summary: Genome-wide binding profile of PcG proteins Pho and Ph, H3K27me3 and Engrailed in Drosophila third instar larval brains and disks, in duplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed.

overall_design: Drosophila third instar larval brains and disks were dissected and fixed with 2% HCHO before sonication. After sonication, chromatin immunoprecipitation using anti-Pho, -Ph, -H3K27me3, and -Engrailed antibodies was carried out.

first: Sandip

last: De

first: Judith

last: Kassis

first: Harold

last: Smith


title: tRNA-Derived Small Non-Coding RNAs in Response to Ischemia Inhibit Angiogenesis

status: Public on Mar 16 2016

city: Shanghai

last: Li

address: 600 YiShan Road

institute: Institute of Microsurgery on Extremities

summary: Ischemic injuries will lead to necrotic tissue damage, and post-ischemia angiogenesis plays critical roles in blood flow restoration and tissue recovery. Recently, several types of small RNAs have been reported to be involved in this process. In this study, we first generated a rat brain ischemic model to investigate the involvement of new types of small RNAs in ischemia. We utilized deep sequencing and bioinformatics analyses to demonstrate that the level of small RNA fragments derived from tRNAs was strikingly up-regulated in the ischemic rat brain. Among these sequences, tRNAVal- and tRNAGly-derived small RNAs account for the most abundant segments. The up-regulation of tRNAVal- and tRNAGly-derived fragments was verified through northern blot and quantitative PCR analyses. The levels of these two fragments also increased in a mouse hindlimb ischemia model and cellular hypoxia model. Importantly, the overexpression of tRNAVal- and tRNAGly-derived fragments in endothelial cells inhibited cell proliferation, migration and tube formation. Our results indicate that tRNA-derived fragments are involved in tissue ischemia, and we demonstrate for the first time that tRNAVal- and tRNAGly-derived fragments inhibit angiogenesis by modulating the function of endothelial cells.

overall_design: Examine small RNAs involved in post-ischemia angiogenesis

first: Yang


title: Effects of TLR4 ligands on inflammatory and lymphatic endothelial specific-cell gene expression in CD14+ PBMC

status: Public on Apr 22 2016

city: Springfield

first: Sophia

last: Ran

state: IL

address: 801 N. Rutledge St.

department: MMICB

institute: Southern Illinois University - School of Medicine

summary: Blood was donated by a healthy volunteer with no known illness or malignancies. Mononuclear cells were separated from the blood by density gradient and CD14+ cells were isolated using anti-CD14 IgG-conjugated magnetic beads and magnetic separation (Miltenyi Biotec). Cells were cultured for 7 days prior to treatment for 96 hours with one of three TLR4 ligands: LPS, HMGB1 or Nab-Paclitaxel. Total RNA was extracted and was analyzed via SYBR Green RT-qPCR. We used an in-house array to analyze the gene expression of a total of 150 targets including 33 cytokines, 34 cytokine receptors, 11 known TLR  targets, 64 other inflammation-related proteins, 31 endothelial related transcription factors, 12 myeloid associated genes, 12 genes expressed primarily in lymphatic endothelial cells, and 23 endothelial cell associated proteins. The results show a LPS, HMGB1 and Nab-Paclitaxel upregulated expression of lymphatic specific markers to varying degrees. LPS had the strongest induction of gene expression followed by HMGB1 and Nab-Paclitaxel, in general.

overall_design: CD14+ peripheral blood mononuclear cells (PBMC) were isolate and cultured. Cells were treated for 96 hours with one of three TLR4 ligands: LPS, HMGB1 or Nab-Paclitaxel. Transcript expression was analyzed by RT-qPCR for 150 targets, including inflammatory and lymphatic endothelial specific-cell genes.

first: Caitlin

last: Griggs

first: Kelly

last: Hall

first: Lisa

last: Volk-Draper


title: Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion (SCL-exo)

status: Public on Mar 04 2016

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

summary: We report the setup of a new method to map 5-hydroxymethylcytosine (5hmC) genome-wide at CpG resolution. The method combines selective chemical labeling by 5hmC b-glucosyltransferase and exonuclease digestion of the DNA molecules bound to streptavidin beads after biotinylation of the 5-glucosylmethylcytosines. Associated with a straightforward bioinformatic analysis, this new procedure provides a cost-effective and fast method for mapping 5hmC at high resolution.

overall_design: Genomic DNA from P19 mouse embryonal carcinoma (EC) cells treated with retinoic acid (RA) for 48hrs, or from undifferentiated E14 mouse embryonal stem cells, was extracted and submitted to the SCL-exo protocol. In parallel, a SCL reaction was run without exonuclease digestion for P19 cells. Reads were mapped to the mouse mm8 genome for P19 cells or mm9 genome for E14 cells and treated to extract a single-CpG signal file indicating the relative levels of hydroxymethylation.

first: Stéphane

last: Avner


title: Tra_Targets_Drosophila_Midgut_StemCells

status: Public on Feb 18 2016

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

summary:
Identification of midgut genes with sex-biased transcription and/or splicing under cell-autonomous control of transformer in adult intestinal stem cells
Sex differences in physiology are commonly attributed to developmental and/or hormonal factors, but there is increasing realisation that cell-intrinsic mechanisms play important and persistent roles. Here we use the Drosophila melanogaster intestine to investigate the activity and significance of intrinsic sex in an adult somatic organ in vivo. We find that the adult intestinal epithelium is a cellular mosaic of different sex differentiation pathways, and displays extensive sex differences in expression of genes with roles in growth and metabolism. Cell-specific reversals of the sexual identity of adult intestinal stem cells uncover its key roles in controlling organ size, its reproductive plasticity and susceptibility to tumours. Unlike previous examples of sexually dimorphic somatic stem cell activity, the sex differences in intestinal stem cell behaviour arise from intrinsic mechanisms, which control cell cycle duration and involve a new doublesex- and fruitless-independent branch of the sex differentiation pathway downstream of transformer. Together, our findings indicate that the plasticity of an adult somatic organ is reversibly controlled by its intrinsic sexual identity, imparted by a new mechanism that may be active in more tissues than previously recognised.

overall_design: Adult midgut transcriptomes of 15-day-old virgin females were generated by deep sequencing, in triplicate using a Hiseq2000 using paired end 100bp reads. Genotypes were: control, transformer mutant  and transformer mutant female in which transformer was re-introduced in adult intestinal stem cells.

first: Bruno

last: Hudry

first: Irene

last: Miguel-Aliaga


title: The sexual identity of adult intestinal stem cells controls organ size and plasticity.


title: Expression profiling individual DrosDel flies heterozygous for deletions of chromosome 2L in a hybrid background

status: Public on Jan 31 2016

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: In order to understand the effect of genetic background on the response to gene dose perturbation, we performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project, which have hybrid genetic background of OregonR/w1118.

overall_design: We performed RNA-Seq analysis of 417 single adult flies in duplicate or triplicate.  Flies are from 73 different genotypes. Differential gene expression was analyzed separately for each sex, gene expression from each genotype was compared to normalized mean of gene expression remaining 72 genotypes.

first: Hangnoh

last: Lee

first: Cale

last: Whitworth


title: Expression profiling pooled Drosophila melanogaster heterozygous for deletions on Chromosome 2L

summary: We performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project covering 68% of chromosome 2L, in order to understand how changes in gene copy number affect overall transcriptome.

overall_design: We performed RNA-Seq analysis on 396 pools of 15-25 adult flies each. Samples include males or females from 99 different genotypes in duplicate. Differential gene expression was analyzed separately for each sex, by comparing each genotype with the remaining 98.

first: Steve

last: Russell


title: BRD4 represses CBX5

status: Public on May 01 2016

first: Marianne

middle: Kwang-Hee

last: Kim

address: 10 Center Dr. 4B55

department: Women's Malignancies Branch

institute: NIH/NCI

summary:
BRD4 is amplified and/or up-regiulated in a subset of ovarian cancer which correlates with a poor survival
siRNA sensitization screens in the presence of CHK1 inhibitor, LY2606368, identify BRD4 as a therapeutic target in ovarian cancer. BRD4 suppression by either siRNA or using JQ1 increases CBX5 expression

overall_design:
(i) BRD4 knockdown by siBRD4 in Ovcar8, performed in 3 replicates.
(ii) BRD4 inhibition using JQ1 in Ovcar8, performed in 3 replicates.

first: Christina

last: Annunziata


title: Suppression of SWI/SNF component Arid1a promotes mammalian regeneration through chromatin remodeling

status: Public on Mar 30 2016

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

institute: shanghai jiao tong university


title: RhoE KD in U87 cells

status: Public on Jan 28 2016

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

institute: University of Birmingham

summary:
RhoE KD in U87 cells
Samples were collected at 24h or 48h after siRNA RHoE transfection or control siRNA (NSC) in U87 cells

overall_design: 3 replicates for control and 3 replicates for RhoE KD in U87 cells at 24h. 1 48h control and 1 48h RhoE KD.

first: Sarah

last: Durant

first: Neil

last: Hotchin

first: Francesco

last: Falciani


title: Global gene expression differences between blood- and lymphatic-specific human dermal microvascular endothelial cells

status: Public on Nov 01 2015

city: Seattle

first: Terri

last: DiMaio

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: We performed high throughput RNA-sequencing on blood and lymphatic HMVECs to identify differences in gene expression between these two cell types that may provide insight into their respective differentiation and roles in angiogenesis and lymphangiogenesis.

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

first: Michael

last: Lagunoff


title: In utero caffeine exposure alters DNA methylation patterns in adult hearts

status: Public on Dec 19 2015

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

type: Methylation profiling by genome tiling array

summary: Our previous research demonstrated that caffeine exposure on embryonic day (E) 8.5 increased body weight, altered cardiac morphology and function in adult male mice. However, these adverse effects were not observed in adenosine A1 receptor knockout (A1AR-/-) mice. Our hypothesis is that A1AR action mediates changes in DNA methylation patterns in mice exposed in utero to caffeine and that these changes in methylation lead to long-term effects in adult mice. To test this hypothesis, DNA Methylation 2.1M Deluxe Promoter Arrays (NimbleGen) were used to examine the methylation patterns of DNA isolated from adult left ventricles of the A1AR knockout line exposed to 20 mg/kg caffeine at E8.5 in utero. In A1AR+/+ mice, 4,896 hypermethylated and 2,823 hypomethylated regions were discovered in the left ventricles of the caffeine group compared to the normal saline group. In A1AR-/- mice, 1,024 hypermethylated and 1,757 hypomethylated regions were found in the caffeine group. The differentially methylated regions (DMRs) in the caffeine treated A1AR+/+ hearts mapped to 6,148 genes, 4,853 promoters, 4,111 primary transcripts, 816 CpG islands, and 98 miRNAs. Functional annotation clustering of genes revealed that many genes were involved in the development of hypertrophic cardiomyopathy and other heart diseases, which may explain our earlier findings of thickening of the left ventricular wall after in utero caffeine treatment. The methylation changes in several DMRs, mef2c, ins2, tnnt2, and myh6, were validated by bisulfite sequencing. In summary, in utero caffeine exposure caused DNA methylation changes in adult left ventricles and that these changes may be mediated by A1ARs.

overall_design: Pregnant mice were injected at embryonic day 8.5 with 0.9% NaCl (vehicle) or 20 mg/kg caffeine in vehicle i.p. Pups were born and raised until 8-10 weeks of age. Analysis was performed on the following groups vehicle A1AR+/+ (veh+/+), vehicle A1AR-/- (veh-/-), caffeine A1AR+/+ (caff+/+), and caffeine A1AR-/- (caff-/-). Genomic DNA from left ventricles of adult male mice was used. Two biological replicates were measured for each group.

first: Daniela

middle: L

last: Buscariollo

first: Huiling

last: Xue

first: Victoria

last: Greenwood

first: Scott

last: Rivkees

first: Christopher

middle: C

last: Wendler


title: Comparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation

status: Public on Oct 26 2015

city: Boston

first: Soohyun

last: Lee

state: MASSACHUSETTS

address: 10 Shattuck St.

department: Department of Biomedical Informatics

institute: Harvard Medical School

summary: The equivalency of human induced pluripotent stem cells (hiPSCs) with human embryonic stem cells (hESCs) remains controversial. Here, we devised a strategy to assess the contribution of clonal growth, reprogramming method and genetic background to transcriptional patterns in hESCs and hiPSCs. Surprisingly, transcriptional variation originating from two different genetic backgrounds was dominant over variation due to the reprogramming method or cell type of origin of pluripotent cell lines. Moreover, the few differences we detected between isogenic hESCs and hiPSCs neither predicted functional outcome, nor distinguished an independently derived, larger set of unmatched hESC/hiPSC lines. We conclude that hESCs and hiPSCs are transcriptionally and functionally highly similar and cannot be distinguished by a consistent gene expression signature. Our data further imply that genetic background variation is a major confounding factor for transcriptional comparisons of pluripotent cell lines, explaining some of the previously observed expression differences between unmatched hESCs and hiPSCs.

overall_design: Expression profiling of human embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and fibroblasts, mostly in triplicates.

first: Jiho

last: Choi

first: Kendell

last: Clement

first: William

last: Mallard

first: Guidantonio

last: Malagoli Tagliazucchi

first: Hotae

last: Lim

first: In-Young

last: Ferrari

first: Alexander

last: Tsankov

first: Ramona

last: Pop

first: Gabsang

first: John

last: Rinn

last: Meissner

first: Peter

middle: J

last: Park

first: Konrad

last: Hochedlinger


title: Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?

status: Public on Nov 04 2015

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD


title: Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? [RNA-Seq]

summary: The objective of this study was to examine the effect of the presence of a single or multiple embryo(s) on the transcriptome of the bovine oviduct. In Experiment 1, cyclic (non-bred, n = 6) and pregnant (artificially inseminated, n = 11) heifers were slaughtered on Day 3 after estrus, and the ampulla and isthmic regions of the oviduct ipsilateral to the corpus luteum were separately flushed. Oviductal epithelial cells from the isthmus region, in which all oocytes/embryos were located, were snap-frozen for microarray analysis. In Experiment 2, heifers were divided into cyclic (non-bred, n = 6) or pregnant (multiple embryo transfer, n = 10) groups. In vitro-produced presumptive zygotes were transferred endoscopically to the ipsilateral oviduct on Day 1.5 post estrus (n = 50 zygotes per heifer). Heifers were slaughtered on Day 3 and oviductal isthmus epithelial cells were recovered for RNA sequencing. Microarray analysis in Experiment 1 failed to detect any difference in the transcriptome of the oviductal isthmus induced by the presence of a single embryo. In Experiment 2, following multiple embryo transfer, RNA sequencing revealed 278 differentially expressed genes of which 123 were up- and 155 were down-regulated in pregnant heifers. Most of the down-regulated genes were related to immune function.

overall_design: Transcriptional profiles of oviductal isthmus epithelial cells from cyclic and pregnant heifers were generated by sequencing of total RNA on the Illumina HiSeq 2500 platform

first: Verónica

last: Maillo

last: Ó Gaora

first: Pat

last: Lonergan

first: Thomas

last: Spencer

first: Dimitrios

last: Rizos


title: Silencing of pericentric heterochromatin associated with SIRT6-dependent H3K18 deacetylation protects against mitotic errors and cellular senescence

status: Public on Apr 04 2016

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Pericentric heterochromatin silencing at mammalian centromeres is essential for mitotic fidelity and genomic stability. Defective pericentric silencing is observed in senescent cells, aging tissues, and mammalian tumors, but the underlying mechanisms and functional consequences of these defects are unclear. Here, we uncover a pivotal role of the human SIRT6 enzyme in pericentric transcriptional silencing, and this function protects against mitotic defects, genomic instability, and cellular senescence. At pericentric heterochromatin, SIRT6 promotes deacetylation of a new substrate, histone H3 lysine K18 (H3K18), and inactivation of SIRT6 in cells leads to H3K18 hyperacetylation and aberrant accumulation of pericentric transcripts. Strikingly, RNAi-depletion of these transcripts rescues the mitotic and senescence phenotypes of SIRT6-deficient cells. Together, our findings reveal a new function for SIRT6 and H3K18Ac regulation at heterochromatin, and demonstrate the pathogenic role of de-regulated pericentric transcription in aging- and cancer- related cellular dysfunction.

overall_design: H3K18ac, H3K9ac, H3K9me3, H3K56ac and Input ChIP-seq for U2OS cell

first: Luisa

last: Tasselli


title: Genomic DNA damage in oral potentially malignant disorders (OPMDs) and oral squamous cell carcinomas (OSCCs). Early detection of DNA aneuploidy and chromosomal aberrations in non dysplastic OPMDs.

status: Public on Oct 23 2015

city: Genova

first: Patrizio

last: Castagnola

state: GE

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS AOU San Martino - IST

type: Genome variation profiling by genome tiling array

summary: Oral potentially malignant disorders (OPMDs) may precede oral squamous cell carcinoma (OSCC). Early detection of OPMDs has a crucial role in OSCC prevention.  DNA aneuploidy and chromosomal aberrations are markers of genomic DNA damage and chromosomal instability (CIN), which is involved in cancer development. We explored the relationship among genomic DNA copy number aberrations (CNAs), histological diagnosis and DNA aneuploidy in OPMDs/OSCCs.   Samples from OPMDs and OSCCs were processed for high resolution DNA flow cytometry (hr DNA-FCM) to determine the relative DNA content expressed with the DNA index (DI). Additionally, on a subset of these samples, array-Comparative Genomic Hybridization (aCGH) analysis was performed on DNA obtained from diploid nuclei suspension or from aneuploid-enriched nuclei suspensions.

overall_design: DNA copy number aberrations were determined using high resolution arrays on 151 samples (2x105K, n=82 samples, and 4x180K, n=69 samples) (Agilent Technologies, Palo Alto, CA, USA). Labeling, hybridization, scanning and feature extraction were performed as previously described using the cross hybridization method previously described [Castagnola P, Malacarne D, Scaruffi P, Maffei M, Donadini A, et al. (2011) Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue. BMC Cancer 11: 445.].

first: Massimiliano

last: Monticone

first: Gabriele

last: Zoppoli

first: Monica

last: Pentenero

first: Davide

last: Malacarne

first: Gabriella

last: Cirmena

first: David

last: Brown

first: Cinzia

last: Aiello

first: Roberto

last: Marino

first: Walter

last: Giaretti

first: Sergio

last: Gandolfo


title: Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames

status: Public on Oct 14 2015

city: Lasuanne

last: Gatfield

address: UNIL CIG

department: CIG

institute: University of Lausanne

summary: Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around-the-clock and at high temporal and nucleotide resolution. Transcriptome-wide, we discovered extensive rhythms in ribosome occupancy, and identified a core set of ≈150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from non-oscillating transcripts revealed thus far unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of re-initiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ.

overall_design: A total of 48 mice were entrained under 12hours light:dark conditions for 2 weeks and also collected under 12hours light:dark. Mice were sacrificed every two hours during the 24 hours daily cycle. Two replicates per time point, each replicate is a pool of 2 livers.

first: Peggy

last: Janich

first: Alaaddin

middle: B

last: Arpat

first: Violeta

last: Castelo Székély


title: Defining the consequences of genetic variation on a proteome-wide scale

status: Public on Oct 06 2015

city: Bar Harbor

first: Steven

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Genetic variation governs protein expression through both transcriptional and post-transcriptional processes.  To investigate this relationship, we combined a multiplexed, mass spectrometry-based method for protein quantification with an emerging mouse model harboring extensive genetic variation from 8 founder strains. We collected genome-wide mRNA and protein profiling measurements to link genetic variation to protein expression differences in livers from 192 Diversity Outcross mice.

overall_design: Illumina 100bp single-end liver RNA-seq from 192 male and female Diversity Outbred 26-week old mice raised on standard chow or high fat diet. Each sample was sequenced in 2x technical replicates across multiple flowcells. Samples were randomly assigned lanes and multiplexed at 12-24x.

first: Joel

last: Chick

first: Petr

last: Simecek

first: Edward

last: Huttlin

first: Kwangbom

last: Choi

first: Daniel

last: Gatti

first: Narayanan

last: Raghupathy

first: Karen

last: Svenson

first: Gary

last: Churchill

middle: P

last: Gygi


title: The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation

status: Public on Sep 15 2015

city: New Haven

first: Susan

last: Kaech

state: CT

address: 300 Cedar St, TAC S640

department: Immunobiology

institute: Yale University

summary: T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during infection. We find that at high concentrations T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.

overall_design: Splenocyte derived CD8+ T cells from C57BL/6 mice with either a wildtype (WT) (GzmB-Cre Zeb2+/+) or GzmB-Cre Zeb2-fl/fl (Zeb2-/-) backgrounds, following 8 days post infection with LCMV-Armstrong, were subsetted into KLRG1-hi/IL-7R-lo populations (terminal effectors, TE) or KLRG1-lo/IL-7R-hi (memory precursors, MP) populations. Four experimental groups, each with 3 samples, comprised of TE+WT, MP+WT, TE+ZEB2-/-, and MP+ZEB2-/-, were profiled for gene expression utilizing a polyA RNA prep and hybridized to the Illumina microarray platform IlluminaWG-v2.0.

first: Robert

last: Amezquita


title: The Transcriptome Responses of Cardiomyocyte Exposed to Hypothermia

status: Public on Jul 28 2015

city: shenyang

first: huishan

last: wang

state: liaoning

address: No.83, Wenhua Road

department: Department of Cardiovascular Surgery

institute: General Hospital of Shenyang Military Area Command

summary: Hypothermia affects the body in positive and negative consequences. In cardiac, hypothermia depresses myocardial contraction, slows conduction, and decreases metabolic rate. However, little is known about the molecular mechanism. Here we compare the genes expression of human adult ventricular cardiomyocyte cells (AC16) treated with hypothermia, trying to find changes under different temperatures and then elucidate the candidate genes that may play important roles in the response to hypothermia. A total of 2413 differentially expressed genes (DEGs) were identified by microarray hybridization, which provided abundant data for further analysis. Gene Ontology enrichment analysis revealed that genes related to gene transcriptions, protein and lipid metabolic were significantly enriched. KEGG analysis showed that DEGs were significantly enriched in TGF-β pathway and cytokine-cytokine receptor interaction, which may play important roles in response to hypothermia. A set of TFs (CPBP, Churchill, NF-AT1, GKLF, SRY, ZNF333, ING4, myogenin, DRI1 and CRX) was recognized to be the functional layer of key nodes, which mapped the signal of hypothermia to transcriptome. These identified DEGs, pathways and predicted TF could facilitate further investigations of the detailed molecular mechanisms, making it possible to take advantage of the potential applications of hypothermia in broader ranger

overall_design: AC16 cell lines was treated by hypothermia (n=3) and control group (n=3) for 6 hours.

first: Huishan

last: Wang

first: Jian

last: Zhang

first: Xiaodong

last: Xue


title: Male_Female_Drosophila_Midgut

first: Sanjay

last: Khadayate

summary:
Drosophila adult midgut genes with sex-biased transcription and/or splicing
Sex differences in physiology are commonly attributed to developmental and/or hormonal factors, but there is increasing realisation that cell-intrinsic mechanisms play important and persistent roles. Here we use the Drosophila melanogaster intestine to investigate the activity and significance of intrinsic sex in an adult somatic organ in vivo. We find that the adult intestinal epithelium is a cellular mosaic of different sex differentiation pathways, and displays extensive sex differences in expression of genes with roles in growth and metabolism. Cell-specific reversals of the sexual identity of adult intestinal stem cells uncover its key roles in controlling organ size, its reproductive plasticity and susceptibility to tumours. Unlike previous examples of sexually dimorphic somatic stem cell activity, the sex differences in intestinal stem cell behaviour arise from intrinsic mechanisms, which control cell cycle duration and involve a new doublesex- and fruitless-independent branch of the sex differentiation pathway downstream of transformer. Together, our findings indicate that the plasticity of an adult somatic organ is reversibly controlled by its intrinsic sexual identity, imparted by a new mechanism that may be active in more tissues than previously recognised.

overall_design: Adult midgut transcriptomes of 15-day-old virgin female and males were generated by deep sequencing, in triplicate using a Hiseq2000 using paired end 100bp reads.

first: Bruno

last: Hudry

first: Irene

last: Miguel-Aliaga


title: Integrated Analysis of Dysregulated lncRNA and mRNA Expression profiles of myocardial sleevesof pulmonary veins in  atrial fibrillation

status: Public on Jan 16 2016

first: zhi

last: li

address: NO. 83 wenhua road

institute: the Shenyang Northern Hospital

summary:
Atrial fibrillation (AF) is currently the most prevalent arrhythmia worldwide.Recent clinical data implicate the additional contribution of non-coding RNAs in the pathogenesis of AF，which include microRNAs(miRNAs), endogenous small interfering RNAs, PIWIinteracting RNAs, and lncRNA. Notably, a growing number of lncRNAs have been implicated in disease etiology, although an association with AF has not been reported.
In the present study, we conducted an integrated analysis of dysregulated lncRNA and mRNA expression profiles in myocardial sleevesof pulmonary veins between the patients who develop AF and the patients who were in normal sinus rhythm, which was performed using a second generation lncRNA microarray，focusing specifically on the identification and characterization of lncRNAs and mRNA potentially involving in maintaining atrial fibrillation.

overall_design: We conducted an integrated analysis of myocardial sleeves of pulmonary veins（PVs）from 12 patients (6 non-AF and 6AF) in our center, of which hypertension, diabetes, smoking and alcohol abuse were excluded, using a second generation lncRNA microarray

first: Zhi

last: Li

first: Yuji


title: Remodeling of major genomic fabrics and their interplay in Capridine-treated DU145 classic human prostate cancer

status: Public on Aug 25 2015

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Our preclinical developmental program identified Capridine as a chemotherapeutic agent that had specificity towards prostate cancer with minimal bone marrow toxicity. In human prostate cancer xenograft studies both androgen responsive and non-responsive tumors were inhibited by a weekly therapeutic regimen Capridine. The minimal bone marrow toxicity as seen in rodent and dog preclinical studies is in line with its twenty-fold differential activity in prostate cancer cells vs. the promyelocytic leukemic cell line HL-60.   This differential activity was partly attributed to its activity on γH2AX modulation, which was considered as one of the targets.  Capridine structure is consistent with a classical DNA intercalating agent; however, its DNA intercalation property does not fully correlate with its anti prostate cancer specific activity. To identify the cellular targets of Capridine in a more comprehensive manner we analyzed its transcriptomic effects on androgen non-responsive DU145 cells. Agilent human gene expression microarray analysis indicated that expression of 97 unigenes genes was altered by Capridine. Our data confirm that, in addition to DNA intercalation, Capridine targets DNA transcription via histone modulation in a cell-specific manner.

overall_design: Two-conditions: DO = not treated, DA = Capridine-treated DU145 cells. Four biological replicates of each condition. Differently labeled biological replicates were cohybridized with each array. Results of similarly labeled different conditions were compared then averaged for the two fluorescent labels. For instance: DO1 & DO3 were compared with DA1 & DA3, DO2 & DO4 were compared  with DA2 & + DA4, and the results of the comparisons averaged. This design uses 100% of the resources, has a better normlaiztion and allows all possible comparisons among the conditions.

last: Suriano

first: Priyanka

last: Mukherjee

first: Tanay

last: Gupta

first: Anvita

first: Sanda

first: John

middle: T

last: Fallon

first: Jan

last: Geliebter

first: Abraham

last: Mittelman

first: Raj

last: Tiwari