title: Expression data from stomach biopsies with gastritis and intestinal metaplasia lesions

status: Public on Nov 23 2017

city: Ciudad de México

first: Yolanda

last: López-Vidal

state: Ciudad de México

address: Avenida Universidad 3000, Universidad Nacional Autónoma de México. C.U. Coyoacán

department: Departamento de Microbiología y Parasitología, Facultad de Medicina

institute: Universidad Nacional Autónoma de México

summary:
Helicobacter pylori is a well-recognized bacterium associated with the development of several histopathological lesions in the stomach. The chronic infection produces an inflammatory lesion known as gastritis. This lesion can later progress to more serious lesions such as intestinal metaplasia. Some attempts in the transcriptome of these conditions have been made; these however, have yielded limited information. Given the potential of high-throughput technologies for understanding biological processes altered and in the description of biomarkers of disease, we performed a genome-wide gene expression analysis in gastric biopsies. The aim of this study was to describe the altered molecular mechanism and potential biomarkers of follicular gastritis, chronic gastritis and intestinal metaplasia, through the identification of characteristic gene expression profiles in each histopathological lesion. The exploratory set comprised twenty-one biopsies from patients with follicular gastritis (n=7), chronic gastritis (n=7), and intestinal metaplasia (n=7), which were analyzed by whole-genome gene expression microarrays. The enrichment analyses and functional annotation of genes using computational tools were performed. The bioinformatics data of the same 21 biopsies were validated by real time PCR analysis while 79 FFPE samples were analyzed by immunohistochemistry.
Gene expression analyses showed profiles for each histopathological lesion. Follicular gastritis had an expression profile with marked enrichment of immunologically-related genes. In contrast, chronic gastritis was characterized by a deregulation of mitochondrial-related genes and a down regulation of genes associated with protection against oxidative stress. Meanwhile, intestinal metaplasia showed an over expression of gastrointestinal stem cell markers and molecules related to RNA metabolism. Our results provide a comprehensive and reliable gene expression analysis of follicular gastritis, chronic gastritis and intestinal metaplasia disorders. The gene expression patterns described established a clear difference between the three pathologies studied and allowed the identification of several potential biomarkers for each histological change.

overall_design: RNA from 21 biopsies from patients with follicular gastritis, chronic gastritis and intestinal metaplasia were analyzed by microarrays. Gene Set Enrichment Analysis, and differential expression analysis with subsequent functional annotation was performed for each group of histological lesions.

first: Stephanie

middle: E

last: Morales-Guerrero

first: Claudia

middle: I

last: Rivas-Ortiz

first: Sergio

last: de León Rosales

first: Armando

last: Gamboa-Dominguez

last: Rangel-Escareño

first: Luis

middle: F

last: Uscanga-Dominguez

first: Germán

last: Aguilar-Gutiérrez

first: David

last: Kershenobich-Stalnikowitz

first: Gonzalo

last: Castillo-Rojas


title: Endogenous Androgen Receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis

status: Public on Sep 05 2017

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Androgen Receptor (AR) is a key player in prostate cancer development and progression. Here, we applied immunoprecipitation mass spectrometry of endogenous AR in LNCaP cells to identify individual components of the AR transcription complex. In total, 66 known and novel AR interactors were identified in the presence of R1881, which were critically and selectively required in AR-driven prostate cancer cell proliferation. AR interactors required for LNCaP proliferation were profiled using ChIP-seq, identifying distinct genomic subcomplexes of AR interaction partners. Interestingly, three major subgroups of genomic subcomplexes were identified, where a selective gain-of-function for AR was identified in tumorigenesis, dictated by FOXA1 and HOXB13. Jointly, our study reveals subclasses of the AR transcription complex formation and composition, that is dictated by overexpression of AR-interactors, resulting in reprogramming of the AR cistrome and interactome in a genomic location-specific manner.

overall_design: AR, ARID1a, BRG1, FOXA1, HOXB13, TLE3, TRIM28 and WDHD1 binding to DNA was profiled by ChIP-seq (Chromatin Immunoprecipitation) genome-wide in prostate cancer cell line LNCaP.

first: Wilbert

last: Zwart


title: Direct Targets of pSTAT5 signalling in erythropoiesis

status: Public on Sep 06 2017

city: Melbourne

first: Kevin

middle: Robert

last: Gillinder

state: Victoria

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

type: Expression profiling by high throughput sequencing

summary: Identification of direct transcriptional targets of EPO-JAK2-STAT5 signalling in erythroid cells

overall_design: ChIP-seq and 4sU-labelled RNA-seq following EPO treatment of J2E cells

middle: R

first: Charles

middle: C

last: Bell

first: Hugh

last: Tuckey

first: Andrew

last: Perkins


title: Profiling of circulating microRNAs in patients with unstable angina pectoris

status: Public on Feb 08 2017

city: Tangshan

first: Yuntao

last: Zhou

state: Hebei

address: Wenhua Road, No.27

department: Clinical Laboratory Center

country: China

institute: Tangshan Gongren Hospital

summary: We profiled miRNA expression in the plasma from healthy subjects and patients with unstable angina pectoris to obtain differentially expressed plasma miRNAs. We randomly selected 25 samples from each group and combined into a sample pool. In this way we obtained 7 and 6 sample pools in control group and case group, respectively. miRNA levels in the plasma were detected with miRCURY LNATM microRNA Array, 6th gen -hsa, mmu & rno.

overall_design: 175 healthy subjects and 150 patients with unstable angina pectoris were enrolled in this study. We obtained 13 sample pools through randomly selected mixture of 25 plasma samples from each group into a sample pool.Total RNA was isolated from 0.2 mL pooled plasma sample for microarray detection.

first: Wei

last: Tian


title: Discovering the miR-26a/targetome in prostate cancer cells

status: Public on Apr 04 2017

city: Copenhagen

first: Francesco

last: Russo

address: Blegdamsvej 3b

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

summary: In this work, we showed that the re-expression of miR-26a in DU-145 prostate cancer cells restored the tumor suppressor activity of miR-26a. To discover the genes and pathways elicited by miR-26a re-expression, we used the miRNA pull out assay to capture and the Next Generation Sequencing to identify the miR-26a targets. Data showed that: i) miR-26a captured both non-coding and coding RNAs; ii) 46% of transcripts were putative miR-26a targets according to target prediction algorithms; iii) 21 pathways were significantly enriched and the “Pathway in Cancer” was among those comprising the largest number of genes, including BIRC5 that we experimentally validated. Accordingly, the detection of cell proliferation-related events showed that miR-26a exerted its tumor suppressor activity at several levels, by decreasing the survival, impairing the migration of tumor cells and by inducing both apoptosis and cell cycle block. In conclusion, we showed that the collection of miR-26a interacting transcripts (miR-26a/targetome) represented a fruitful platform to decipher the miR-26a-dependent gene expression networks. In perspective the availability of miRNA-specific and tumor-specific targetomes will allow the discovery of new druggable tumor genes and pathways.

overall_design: The miRNA pull out assay was performed modifying the protocol described by Orom et al. {Methods 43, 162-165, doi:S1046-2023(07)00097-7}. DU-145 were seeded into the wells of a 6-well at the density of 1.5 x105. After 24 hours from seeding, cells were transfected using lipofectamine (Thermo Fisher) with 60nM of either miR-26a duplex (ds-miR-26aCT) or a mix of 3’ biotin-tagged miR-26a 7tU (nucleotide 7 was a thiouridine) and miR-26a 17tU duplexes (ds-miR-26aBIO). The day after transfection, the cells were washed with PBS and irradiated with UV (365nm, 2J/cm2), using the Bio-Link crosslinking (BLX) (Ambrose Lourmat) with appropriate UV lamps, to induce cross-linking of tU nucleotides to RNA. Total RNA was extracted adding directly on adherent cells TRIzol reagent (Thermo Fisher) and following the instructions provided by the manufacturer. After DNAse treatment, 15 μg of RNA was incubated for 4 hrs at 4°C with 100 μl of streptavidin-conjugated beads (200 μl of Streptavidin Sepharose high performance, GE Healthcare) previously suspended in PO buffer (1M Tris pH8, 5M NaCl, 1M MgCl2, NP40 50 μl in 100 ml buffer). After 2 washes with PO buffer and 2 washes with DEPC-treated water, the RNA complexed with beads was recovered by adding 1 ml Trizol directly on the beads and then following the TRIzol RNA extraction protocol. We performed two biological replicates obtaining two miR-26aCT (control) and two miR-26aBIO (miR-26a) pull out samples. The RNA isolated after the miRNA pullout procedure from both miR-26aCT and miR-26aBIO samples was used for the construction of the cDNA libraries using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina) according to the manufacturer’s suggestions. cDNA libraries were sequenced by HiSeq2000 (Illumina) in single-reads mode (50bp) by IGA Technology Service, Udine, Italy, obtaining about 20 million of reads for each samples.

first: Milena

last: Rizzo

first: Gabriele

last: Berti

first: Sofia

last: Fazio

first: Monica

last: Evangelista

first: Romina

last: D'Aurizio

first: Marco

last: Pellegrini

first: Giuseppe

last: Rainaldi


title: DNase-SEQ analysis of whole leaf and bundle sheath tissues in Zea mays, Sorghum bicolor, Setaria italica and Brachypodium distachyon.

status: Public on Jul 24 2017

city: Cambridge

first: Steven

middle: James

last: Burgess

state: Cambridgeshire

address: Department of Plant Sciences, Downing College

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

summary: Photosynthesis supports life on Earth but the regulatory architecture associated with photosynthesis gene expression is poorly understood. Most crops use either C3 or C4 photosynthesis with the latter allowing significantly higher efficiencies as well as improved water and nitrogen use. Here we use DNAse-SEQ to define >1 million transcription factor binding sites in leaves of grasses that either operate C3 or C4 photosynthesis and that are consistent with significant differences in the modes of gene regulation between the kingdoms of life. Leaf samples were collected from seedlings to allow for comparison of regulatory interactions between species from the same (Zea mays and Sorghum bicolor) and different (Setaria italica) C4 lineages, as well as a C3 grass (Brachypodium distachyon) in order to investigate evolution of C4 photosynthetic gene expression. Additionally bundle sheath tissues were mechanically isolated from C4 species and analysed by DNAse-SEQ to identify DNA regulatory elements controlling cell-specific gene expression patterns.

sample_organism:
Setaria italica
Sorghum bicolor
Zea mays
Brachypodium distachyon

overall_design: Samples were collected from two tissue types (whole leaf and bundle sheath), with a minimum of two biological replicates per tissue resulting in a total of 17 samples.

middle: J

first: Ivan

last: Reyna-Llorens

first: Julian

middle: M

last: Hibberd


title: Term placenta syncytiotrophoblast transcriptome

status: Public on Jan 31 2017

city: Cincinnati

first: Mihaela

last: Pavlicev

state: OH

address: 3333 Burnet ave

department: Pediatrics

country: USA

institute: Cincinnati Children`s

summary: Placenta is an epitome of cell signalling, including the signalling between two semi-allogenic individuals, mother and fetus. We have studied the putative crosstalk by analyzing the expression of corresponding ligands and receptors on maternal fetal interface. This transcriptome represents one of the important cellular sources, namely the multinucleated fetal layer that is directly bathed in the maternal blood. It was collected by microdissection, as it is too large to be included in the single cell preparation. In combination with other compartments, whose transcriptomes are provided along with this one, we think this study provides a rich resource of gene expression profiles of term placenta.

overall_design: mRNA-seq of placental syncytiotrophoblast from term healthy pregnancies.

first: Louis

last: Muglia

first: Gunter

last: Wagner


title: RNA 5-methylcytosine modification is enriched and conserved at 5' UTRs in human and mouse

status: Public on Jul 11 2017

city: SuZhou

first: Zhen

last: Wei

address: 111 Ren'ai Road Suzhou Dushu Lake Science and Education Innovation District

institute: Xi'anJiaoTong Liverpool university

summary: Compared with the well-studied 5-methylcytosine (m5C) in DNA, the role of m5C in mRNA remains elusive as existing studies of RNA m5C are largely confined to rRNA and tRNA. Using bisulfite sequencing (BS-Seq) approach, we profiled transcriptome-wide m5C and found that RNA m5C modification is enriched and conserved at 5’UTRs in human and mouse. Through a comparative analysis of the mRNA and DNA methylome, we demonstrate that like DNA methylation, RNA m5C methylation exhibits a strong clustering. Surprisingly, mRNA Cytosine-5 methylation inversely correlates with DNA methylation under CpG context, which suggests a synergic regulatory effect. Importantly, comparison of the global RNA m5C methylome of breast cancer cells with normal mammary epithelial cells revealed that breast cancer methylome is predominantly hypomethylated and several breast cancer-related genes are differentially methylated. Despite global hypomethylation, 5’UTR of differentially methylated genes contain higher percentage of m5C. Taken together, this study provides a first-in-depth characterization of transcriptome-wide m5C modification.  Furthermore, our findings showing differential m5C methylation pattern in normal and cancer cells suggest a vital role m5C methylation may play in the post transcriptional regulation of key pro-tumorigenic genes.  Sample Preparation and RNA Bisulfite Sequencing: MCF10A and MDA-MB-468 (MDA468) cells were obtained from ATCC. Cells were cultured and maintained in DMEM media as per ATCC instructions. For BS-Seq total RNA was isolated from MCF10A and MDA_MB-468 cells and was enriched for polyA+ RNA using poly-A selection kits. The purified RNA is subjected to sodium bisulfite treatment at 60 degrees for 8 hours. The bisulfite-treated RNA was then reverse transcribed was subjected to deep-sequencing using Illumina RNA-Seq protocol.

first: Jia

last: Meng

first: Panneerdoss

last: Subbarayalu

first: Yidong

last: Chen

first: Manjeet

middle: K

last: Rao


title: Term placenta single cell transcriptome

summary: We provide single cell transcriptomes from the placental-uterine interface. Tissue was collected at term C-section (no labor) from two healthy pregnancies, from villous part of the placenta. Cells were disassociated and processed using Fluidigm technology. RNA-seq was performed on RNA from 33+54 single cells, at approx. 3.5 mio paired reads per cell. Clustering resulted in 4 trophoblast and a single immune cell clusters. As the placenta is an epitome of cell signaling, we combined the present cell-level transcriptomes with uterine cell transcriptomes to study the potential inter-cell communication. To this end, we inferred the cell-cell-interactome by assessing the gene expression of receptor-ligand pairs across cell types. We find among the signals transmitted a predominance of growth and immune signals, and suggest a delicate balance of enhancing and suppressive signals. Finally, this study provides a rich resource of gene expression profiles of term intravillous and extravillous trophoblasts.

overall_design: Single cell mRNA-seq of placenta from two term healthy pregnancies.

first: Helen

last: Jones


title: Term placenta transcriptomes

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

overall_design: Refer to individual Series


title: Diffuse large B-cell lymphoma (DLBCL) from primary sites and metastatic lymph nodes

status: Public on Jun 30 2017

city: Taoyuan

first: Yi-Ru

last: Pan

address: 5 Fu-Hsing Street, Kwei-Shan,

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

summary: Analysis of diffuse large B-cell lymphoma (DLBCL) from primary sites (named as S1, S2 and S3) and metastatic lymph nodes (named as L1, L2 and L3). Results provide insight into the targets involved in t DLBCL dissemination.

overall_design: DLBCL cell line HT cells were inoculated to the spleen of SCID/Beige mice. The tumor cells from primary sites (spleen) and metastatic sites (lymph node) were isolated.

first: Muh-Hwa

last: Yang


title: Term placenta tissue-level transcriptome

summary: We provide the tissue-level human placental transcriptomes from two term uncomplicated pregnancies. Tissue was collected at term C-section (no labor), from villous part of the placenta.

overall_design: mRNA-seq of placenta from two term healthy pregnancies.

first: Suhaz

last: Kallapur


title: Molecular analysis of endothelial and immune cells after anti-angiogenic cancer immunotherapy

status: Public on Apr 26 2017

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

summary:
Organism: Mus musculus

Experiment type: Gene expression profiling by high throughput sequencing

Summary: Pathological angiogenesis is a hallmark of cancer and therapeutic target. Vascular-endothelial growth factor-A (VEGFA) and angiopoietin-2 (ANGPT2/ANG2) sustain tumor angiogenesis and limit anti-tumor immunity. We show that combined ANGPT2 and VEGFA blockade by mono-specific antibodies (LC06 + B20) or a bi-specific antibody (A2V) provides synergistic anti-tumoral benefits in both transgenic and transplant tumor models. We further show that that combination of agonistic anti-CD40 or blocking anti-PD1 antibodies with ANGPT2/VEGFA blockade improves therapeutic response and induces pleiotropic immune mechanisms that facilitate tumor control.

overall_design:
Orthotopic MMTV-PyMT mammary tumors were generated as follows. Late stage, primary MMTV-PyMT tumor-derived cells were obtained from 14- to 15-week old female MMTV-PyMT mice, following tumor digestion with collagenase IV (0.2 mg/ml, Worthington), dispase (2 mg/ml, Lifetechnologies), and DNaseI (0.1 mg/ml, Lifetechnologies) treatment in IMDM medium for 30 min at 37°C. The cell suspensions were filtered using a cell strainer (70 μm) and washed in PBS containing 2 mM EDTA and 2% FBS. Tumor-derived cells were then cultured in 15-cm petri dishes for 48 h in IMDM supplemented with 10% FBS, 2 mM L-glutamine (Amimed) and a combination of 50 units/ml penicillin and 50 μg/ml streptomycin (Gibco). Non-adherent/dead cells and debris were then washed away, and 2x106 tumor-derived cells (in PBS) were orthotopically injected in the fourth mammary fat pad of 8-10–week-old female FVB/n mice. When tumors reached a size of 300 mm3, mice were injected i.p with the following monoclonal antibodies:
1) mouse IgG1 (clone MOPC-21, 20 mg/kg) + rat IgG2a (clone 2A3, 4 mg/kg), designated as “IgG”; or
2) anti-VEGFA/ANGPT2 (A2V, 20 mg/kg) + rat IgG2a (clone 2A3, 4 mg/kg), designated as “A2V”; or
3) anti-CD40 (clone FGK45, 4 mg/kg) + mouse IgG1 (MOPC21, 20 mg/kg), designated as “anti-CD40”; or
4) anti-VEGFA/ANGPT2 (A2V, 20 mg/kg) + anti-CD40 (clone FGK45, 4 mg/kg), designated as “A2V + anti-CD40”.
Five days later, mice were euthanized and tumors harvested and prepared for fluorescence-activated cell sorting (FACS). Cells were stained with CD45, CD8, CD4, CD31, CD11b, F480 and 7-AAD. After live-dead and single-cell discrimination, cell populations were discriminated according to the following markers:
Endothelial cells (ECs): CD45–CD31+;
Tumor associated macrophages (TAMs): CD45+CD11b+F480+.
CD8+ T cells: CD45+CD11b–CD8+;
CD4+ T cells: CD45+CD11b–CD4+.
Cell sorting was performed using FACS Aria II apparatus (BD). Each cell population (n=4) was isolated from an independent tumor. Typically, 2x104 to 2x105 cells were obtained for each cell population.

Citation(s):
Schmittnaegel M, et al. Dual angiopoietin-2 and VEGFA inhibition elicits antitumor immunity that is enhanced by PD-1 checkpoint blockade. Sci Transl Med 2017 Apr 12;9(385). PMID: 28404865

Kashyap AS, et al., Optimized antiangiogenic reprogramming of the tumor microenvironment potentiates CD40 immunotherapy. in press

first: Michele

last: De Palma


title: Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence (DamID-seq)

status: Public on Aug 17 2017

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

summary: Background. Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which cause Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement of chromatin reorganization, including the formation of senescence-associated heterochromatic foci (SAHF). The nuclear lamina (NL) is an important contributor to genome organization and has been involved in cellular senescence and organismal aging. It interacts with multiple regions of the genome called lamina-associated domains (LADs). Some LADs are cell type-specific, while others are conserved between cell types and are referred to as constitutive LADs. Here, we used DamID to investigate the changes in genome-NL interactions in a model of OIS triggered by the expression of the BRAFV600E oncogene.  Results. We found that OIS cells lose most of their constitutive LADs (cLADS), suggesting the loss of a specific mechanism that targets cLADs to the NL. In addition, multiple genes relocated to the NL. Unexpectedly, they were not repressed, implying the abrogation of the repressive activity of the NL during OIS. Finally, OIS cells displayed an increased association of telomeres with the NL.  Conclusions. Our study reveals that senescent cells acquire a new type of LAD organization and suggest the existence of as yet unknown mechanisms that tether cLADs to the NL and repress gene expression at the NL.

overall_design: Examination of gene expression in cycling cells, after oncogene induced senescence, and after quiescence

first: Christelle

last: Lenain

first: Ludo

last: Pagie

first: Bas

last: van Steensel

first: Daniel

last: Peeper


title: Gene Expression profiling in IGHV Unmutated vs mutated CLL

status: Public on May 29 2017

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

summary: In the present study, the gene expression profiling was carried out in 21 early stage CLL patients. A gene expression signature was generated for CLL patients as compared to normal controls; CLL patients were further seggregated into IGHV unmutated (n=10) and  IGHV mutated (n=11) subgroups. The expression pattern was confirmed using real time quantitative PCR and the results were correlated with clinical outcome.

overall_design: Gene expression profiling was carried out in 21 CLL samples and pooled samples (n=2) from 10 healthy subjects. The CLL cases were further divided into unmutated (n=11) and mutated subgroup (n=10) on the basis of IGHV mutation status.

first: Lata

last: Rani

first: Nitin

last: Mathur

first: Ajay

last: Gogia

first: Jaspreet

last: Dhanjal

first: Durai

last: Sundar

first: Lalit

last: Kumar

first: Atul

last: Sharma


title: Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence

type: Genome binding/occupancy profiling by genome tiling array


title: Gene expression and methylation profiling of IGHV Unmutated vs mutated CLL

type: Methylation profiling by genome tiling array


title: Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface

status: Public on Jan 25 2017

city: West Haven

first: Gunter

last: Wagner

state: CT

address: 300 Heffernan Drive, ISTC 108

department: Systems Biology Institute, EEB

institute: Yale University

summary: Organismal function is, to a great extent, determined by interactions among their fundamental building blocks, the cells. In?this work, we studied the cell-cell interactome of fetal placental trophoblast cells and maternal endometrial stromal cells, using single-cell transcriptomics. The placental interface mediates the interaction between two semiallogenic individuals, the mother and the fetus, and is thus the epitome of cell interactions. To study these, we inferred the cell-cell interactome? by assessing the gene expression of receptor-ligand pairs across cell types. Moreover, we find that the expression of G-protein coupled receptors is highly cell-type?specific, implying that ligand-receptor profiles could be a reliable tool for cell type identification. Furthermore, we find that uterine decidual cells represent a cell-cell interaction hub with a relatively large?number of potential incoming and outgoing signals. Decidual cells differentiate from their precursors, the endometrial stromal fibroblasts, during uterine preparation for pregnancy. We show that decidualization (even in vitro) enhances the ability ?to communicate with the fetus, as most of the receptors and ligands up-regulated during decidualization have their counterpart expressed in trophoblast cells. Among the signals transmitted, growth factors and immune signals dominate, suggesting a delicate balance of enhancing and suppressive signals. Finally, this study provides a rich resource of gene ?expression profiles of term intravillous and extravillous trophoblasts, including the transcriptome of the multinucleated syncytiotrophoblast.

overall_design: We sequenced mRNA from primary human endometrial stromal fibroblasts and in vitro human decidualized stromal fibroblasts.

first: Mihaela

last: Pavličev

first: Günter

middle: P

first: Arun

last: Chavan

first: Kathryn

last: Owens

first: Jamie

last: Maziarz

first: Caitlin

last: Dunn-Fletcher

first: Suhas

middle: G

first: Louis

last: Muglia

first: Helen

last: Jones


title: Identification of long non-coding RNAs associated with aberrant LKB1 signaling

status: Public on Dec 31 2016

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

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

summary: The LKB1 tumor suppressor gene is frequently mutated and inactivated in many cancers, particularly non-small cell lung carcinoma (NSCLC). LncRNAs are a novel class of gene regulators with newly discovered roles in cancer development and progression. LncRNA involvement in altered LKB1 signaling in lung cancer is currently unknown. To investigate whether lncRNAs contribute to loss of LKB1 tumor suppression in lung tumorigenesis and maintenance, we performed genome-wide lncRNA transcriptional profiling to identify lncRNAs associated with aberrant LKB1 signaling.

overall_design: We had 2 sets of experiments. (A) We compared lncRNA expression profiles in 2 groups of lung cancer cell lines, LKB1-null and LKB1-wt, and identified lncRNAs associated with loss of LKB1. LKB1-null (A549, H460) and LKB1-wt (H322, H3123) cells were harvested for isolation of RNA for microarray analysis. (B) We compared lncRNA expression profiles in three groups of cells by transducing LKB1-null A549 NSCLC cells with pBabe-based retroviruses harboring wild-type (wt) LKB1, LKB1 kinase-dead mutant (K78I), or vector control (Ctl). We then identified lncRNAs differentially regulated by LKB1-wt, or LKB1-K78I as compared with vector control cells. Two biological replicates for each sample group were prepared.

first: Zirong

last: Cheng

first: Jian

middle: L

last: Li


title: Expression data from WT and Cavin-3 knockout mice adipose tissue

city: Boston

first: Paul

last: Pilch

state: MA

address: 72 E. Concord

department: Biochemistry

institute: Boston University

summary: The cavins are a family of proteins associated with caveolae, cavin-1, -2 and -3 being widely expressed while cavin-4 is restricted to striated muscle.  Deletion of cavin-1 results in phenotypes including metabolic changes consistent with adipocyte dysfunction, and caveolae are completely absent.  Deletion of cavin-2 causes tissue-specific loss of caveolae. The consequences of cavin-3 deletion are less clear, as there are divergent data on the abundance of caveolae in cavin-3 null mice. Here we examine the consequences of cavin-3 deficiency in vivo by making cavin-3 knockout mice. Microarray analysis from adipose tissue shows that the changes in mRNA expression between cavin-3 null and wild type mouse are minimal.

overall_design: 3 each adipose tissue total RNA samples from WT and cavin-3 knockout mice (litter mates, 10-week old) were submitted to Boston University Microarray Resource Facility.


title: Transcript abundance of equine spermatozoa

status: Public on Nov 01 2016

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

summary: Microarray gene expression profiling of spermatozoa obtained from stallions

overall_design:
transcript abundance by season and by fertility
Type: 2-way ANOVA

first: Frank

last: Becker

first: Yara

last: Suliman

first: Siriluck

last: Ponsuksili


title: Methylation analysis of normal and adenocarcinoma lung tissues

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

institute: National Taiwan University

summary: Genome wide DNA methylation profiling of normal and adenocarcinoma lung tissues. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in lung adenocarcinoma samples.

overall_design: Bisulphite converted DNAs from the 88 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Hsin-Chieh

last: Lin


title: Ribosome profiling-guided depletion of an mRNA improves CHO cell growth and recombinant product titers

status: Public on Dec 21 2016

city: La Jolla

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: We present the first comprehensive genome-wide view of CHO translational activity during recombinant expression by the application of ribosome profiling. The distribution of translational power in CHO cells was analyzed in the context of the recombinant mRNAs and the endogenous mRNA pool. In an antibody-producing CHO cell line, the recombinant mRNAs were found to be the most abundant transcripts and also sequestered a substantial amount of translating ribosomes (up to 15%). The recombinant mRNAs were translated as efficiently as the endogenous mRNAs, and changes in translation and transcription of the recombinant mRNAs were directly reflected in changes in specific productivity. Interestingly, improvements in bioprocess quality attributes were achieved by depleting the highly expressed and translated inert NeoR mRNA by siRNA-mediated knock-down. This resulted in improved cellular growth, which was accompanied by an 18% increase in antibody titers. This study is the first to carefully map the translatome of the CHO cell to the nucleotide level and to demonstrate how recombinant expression affects the cell on the translational level.

overall_design: Examine translation of IgG at exponential phase (day3) and stationary phase (day6) in CHO cell

first: Thomas

middle: B

last: Kallehauge

first: Shangzhong

first: Lasse

last: Pedersen

first: Tae

last: Ha

first: Daniel

last: Ley

first: Mikael

last: Andersen

first: Helene

last: Kildegaard

first: Gyun

last: Lee


title: Transcriptome analysis of single cells from the mouse dentate gyrus

status: Public on Dec 12 2017

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet


title: An RNA binding polymer specifies nematode sperm fate

status: Public on Dec 30 2016

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Metazoan gamete development into sperm or oocytes requires specific programming cues. Many of these cues function through conserved proteins to regulate gene expression. In C. elegans, two proteins are the terminal regulators of the genetic regulatory network controlling sperm fate: FOG-1, a cytoplasmic polyadenylation element binding protein (CPEB), and FOG-3, a predicted Tob/BTG protein. Loss of either gene causes hermaphrodites or male germ cells to switch from making sperm to making oocytes. Characterized Tob/BTG proteins function as adaptor proteins, linking – in certain contexts –  deadenylases to mRNA via CPEB RNA motifs. Through crosslinking and sequencing, we confirmed FOG-3 binds to RNA directly and observed a preference for mRNA 3’UTRs. Our results bring together prior genetics and molecular biology data to propose a new molecular function in germ cell specification with a Tob protein. We discuss the potential for FOG-3 to function as an mRNA packaging protein to inhibit target genes, as well as the potential for the existence of other hidden protein polymers in biology.

overall_design: iCLIP was performed on 4 biological replicates of C. elegans L4 larvae expressing FLAG-tagged FOG-3 integrated into the genome. 4 biological replicates of control samples comprised the same worms processed by an identical protocol, except that the immunopurification did not include the antibody for the FLAG epitope, and, as a result, did not specifically purify FOG-3.

first: Scott

middle: T

last: Aoki

first: Aman

last: Prasad

first: A

last: Rohou

first: N

last: Grigorieff

first: M

last: Wickens

first: C

last: Bingman

first: J

last: Kimble


title: Transcriptome sequencing wide functional analysis of human mesenchymal stem cells

status: Public on Sep 19 2016

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

country: South Korea

institute: Hanyang Univ.

summary: Using RNA-seq, we report here that BM-MSC cells have a distinct transcriptomic signature and express a unique cluster of transcripts in response to 4 hrs LPS.

overall_design: Examination of effects of LPS-stimulated BM-MSCs, were generated by deep sequencing on an Illumina HiSeq 2000(101 cycles PE lane).

first: Young

first: Jin


title: Msn2 controls the yeast metabolic focus

status: Public on Oct 08 2016

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

summary: Msn2 is a transcription factor required for integration of environmental and metabolic signals. Msn2 is directly regulated by the carbon source sensing PKA and AMP pathways. Here we analyse the role of Msn2 for metabolic adjustment by using point mutants mimicking the dephosphorylated state.

overall_design: Yeast cells were grown in exponential phase and treated with 6nM  17ß-Estradiol  for 90 minutes to induce the expression of the Msn2A6 gene. Experiments were performed with 2 biological replicates. 0min refers to the untreated culture

first: Martin

last: Radolf

last: Schüller


title: Analysis of expression of genes involved in celiac disease

status: Public on Oct 31 2016

city: Leioa

first: Jose Ramon

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: Celiac disease (CD) is a chronic immune-mediated disorder with an important genetic component. We analyzed the expression of candidate genes in biopsies from duodenum.

overall_design: The sample set consisted of duodenal biopsies from 15 CD children at diagnosis (on a gluten-containing diet, with CD-associated antibodies, atrophy of intestinal villi and crypt hyperplasia), and the same patients in remission after being treated with gluten-free diet (GFD) for >2 years (asymptomatic, antibody negative, and normalized intestinal epithelium at that time), plus 15 tissue samples from non-celiac individuals not suffering from inflammation at the time of endoscopy, used as controls.

first: Koldo

last: Garcia-Etxebarria

first: Amaia

last: Jauregi-Miguel

first: Irati

last: Romero-Garmendia

first: Leticia

last: Plaza-Izurieta

first: Maria

last: Legarda

first: Iñaki

last: Irastorza

first: Jose


title: Genome wide DRIP-seq in E2 stimulated MCF7 cells

status: Public on Aug 23 2016

first: Karlene

middle: Anne

last: Cimprich

address: 318 Campus Drive

institute: Stanford University

summary: We mapped the location of RNA-DNA hybrids in hormone-starved MCF7 breast cancer cells treated with the hormone estradiol (E2.) E2 is a potent transcriptional activator, and causes proliferation in hormone starved cells. We find a significant induction of hybrids at genes known to be regulated by the estrogen receptor.

overall_design: Examination of RNA:DNA hybrid levels in MCF7 cells treated with two different time points of estradiol, and a mock control

first: Caroline

last: Stork

first: Michael

last: Bocek

first: Madzia

last: Crossley

first: Julie

last: Sollier

first: Lionel

last: Sanz

first: Frédéric

last: Chédin

first: Tomek

last: Swigut


title: HER2 expression identifies dynamic functional states within circulating breast cancer cells

status: Public on Aug 25 2016

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Circulating tumour cells in women with advanced oestrogen-receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer acquire a HER2-positive subpopulation after multiple courses of therapy. In contrast to HER2-amplified primary breast cancer, which is highly sensitive to HER2-targeted therapy, the clinical significance of acquired HER2 heterogeneity during the evolution of metastatic breast cancer is unknown. Here we analyse circulating tumour cells from 19 women with ER+/HER2- primary tumours, 84% of whom had acquired circulating tumour cells expressing HER2. Cultured circulating tumour cells maintain discrete HER2+ and HER2- subpopulations: HER2+ circulating tumour cells are more proliferative but not addicted to HER2, consistent with activation of multiple signalling pathways; HER2- circulating tumour cells show activation of Notch and DNA damage pathways, exhibiting resistance to cytotoxic chemotherapy, but sensitivity to Notch inhibition. HER2+ and HER2- circulating tumour cells interconvert spontaneously, with cells of one phenotype producing daughters of the opposite within four cell doublings. Although HER2+ and HER2- circulating tumour cells have comparable tumour initiating potential, differential proliferation favours the HER2+ state, while oxidative stress or cytotoxic chemotherapy enhances transition to the HER2- phenotype. Simultaneous treatment with paclitaxel and Notch inhibitors achieves sustained suppression of tumorigenesis in orthotopic circulating tumour cell-derived tumour models. Together, these results point to distinct yet interconverting phenotypes within patient-derived circulating tumour cells, contributing to progression of breast cancer and acquisition of drug resistance.

overall_design: Seventy-four single candidate CTCs from two representative ER+/HER2- patients (BRx-42 and BRx-82) and 14 triple negative patients were isolated via micromanipulation and subjected to single-cell RNA-sequencing. Thirteen candidate CTCs expressed PTPRC at a level higher than 10 reads-per-million, so were deemed potential White Blood Cells and therefore dropped from further consideration. Expression profiles of CTCs expressing ERBB2 at a level greater than 10 RPM were compared with those expressing ERBB2 at a level less than 10 RPM.

first: Nicole

middle: V

last: Jordan

middle: S

first: Aditya

last: Bardia

first: Cyril

last: Benes

first: Matteo

last: Ligorio

first: Yu

last: Zheng

first: Min

last: Yu

first: Tilak

last: Sundaresan

first: Rushil

last: Desai

first: Ryan

last: O’Keefe

first: Richard

middle: Y

last: Ebright

first: Thomas

last: Barber

first: Ravi

last: Kapur

first: Dennis

last: Sgroi

first: David

last: Ting

first: Sridhar

last: Ramaswamy

first: Mehmet

last: Toner

first: Wilhelm

last: Haas

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: Gene expression in TAMs

status: Public on May 12 2016

city: Chongqing

first: Hongming

last: Miao

state: Chongqing

address: Gaotanyan Street NO.30

department: Department of Biochemistry and Molecular Biology

institute: Third Military Medical University (Army Medical University)

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify different gene expression in normal or tumor-primed peritoneal macrophages

overall_design: Mouse peritoneal macrophages were extracted and treated with regular medium or CT-26 cell medium for 24 hours, and then subjected to microarray assays. Each group contain 3 samples.

first: Houjie

last: Liang


title: Expression data from 1499 cells, a mouse ADM/PanIN1-derived pancreatic ductal cell line, and the mouse pancreatic ductal adenocarcinoma (PDAC) AH375 cell line.

status: Public on May 10 2016

city: Montréal

first: Xavier

last: Deschênes-Simard

state: Québec

address: 3655 Sir William Osler

department: Medicine

country: Canada

institute: McGill University

summary: In a Kras-driven mouse model of multistage pancreatic cancer progression, decreased p-ERK levels correlate with tumor initiation. In cells derived from this model, transformed cells with low p-ERK levels express markers of pluripotency and demonstrate phenotypes of tumor initiating cells, such as formation of free-floating tumor spheres. Here, a comparison of gene expression from the 1499 cell line, which are premalignant cells isolated from mouse ADM (acinar-to-ductal metaplasia) and PanIN1 (pancreatic intraepithelial lesions), and the AH375 cell line, established from mouse PDAC, was performed.

overall_design: To establish the 1499 cell line, cells were isolated from premalignant pancreatic lesions (ADM and PanIN1) in a 9-week-old Pdx1-Cre;LSL-KRasG12D mouse. To establish the AH375 cell line, cells were isolated from PDAC in a 52-week-old Pdx1-Cre;LSL-KRasG12D mouse. These pancreatic ductal cells were propagated on surfaces coated with laminin and in a specific pancreatic medium. Total mRNA extracts were prepared in triplicates for both cell lines and sent to the Génome Québec Innovation Centre for RNA processing and data acquisition.

first: Nabeel

last: Bardeesy

first: Gerardo

last: Ferbeyre


title: Differentially expressed genes after miRNA or siRNA transfection in human cancer cell lines

status: Public on Apr 13 2016

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (microRNAs or siRNAs) in human cancer, several cell lines (bladder cancer, prostate cancer, hypopharyngeal cancer and lung squamous cell carcinoma) were subjected to Agilent whole genome microarrays.

overall_design: Human cancer cell lines (BOY, BOY-GFP, T24, PC3, FaDU, LNCap, DU145, EBC-1 and SK-MES-1 ) were treated with miRNAs (miR-218, miR-24, miR-144, miR-451, miR-221, miR-222, miR-224, miR-1, miR-133a and miR-452), siRNAs (si-LASP1 and si-FOXM1).


title: Transcriptional responses to i.v. administered I-131 in various mouse normal tissues underlie diurnal variation

status: Public on Mar 31 2016

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

institute: Sahlgrenska Academy at University of Gothenburg

summary:
Circadian rhythm study on transcriptional responses to i.v. administered 90 kBq iodine-131 after 24h in mouse kidney cortex and medulla, liver, lungs, spleen, and thyroid.
Female BALB/c nude mice (n=4/group) were i.v. injected with 90 kBq 131I at three different times of day, i.e. at 9.00 am, at 12.00 pm, or at 3.00 pm, and killed under anesthesia after 24h following treatment for excision of organs.
For each time of day, a control group (n=3-4/group) was i.v. injected with physiol. saline. The kidneys, liver, lungs, spleen, and thyroid were excised, flash-frozen, and stored at -80°C until extraction of total RNA.
Total RNA was extracted from homogenized tissue samples and subjected to expression analysis using RNA microarray technology.

overall_design: The study consisted of 6 groups in total, i.e. 3 groups (n=4/group) that were i.v. injected with 90 kBq 131I (at 9.00 am, 12.00 pm, or 3.00 pm) and 3 sham-treated control groups (n=3-4/group) that were i.v. injected with physiol. saline (at 9.00 am, 12.00 pm, or 3.00 pm); please note that the number of control animals varied between 3-4 animals per group, i.e. n=4 treated at 9.00 am, n=3 treated at 12.00 pm, and n=3 treated at 3.00 pm. Six tissues were analyzed per animal, i.e. kidney cortex, kidney medulla, liver, lungs, spleen, and thyroid.

first: Nils

last: Rudqvist

first: Toshima

middle: Z

last: Parris

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Neoadjuvant chemotherapy modulates T cell responses in high-grade serous ovarian cancer metastases

status: Public on Jul 27 2016

city: London

first: Oliver

last: Pearce

address: Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

summary: Our data suggest that neoadjuvant chemotherapy enhances anti-cancer responses of T cells in peritoneal metastases of patients with high-grade serous ovarian cancer but does not decrease levels of immune checkpoint molecules, providing a rationale for sequential chemo-immunotherapy.

overall_design: tRNA was isolated from 35 omental tissue samples of HGSOC metastases either pre or post NACT treatment. RNASeq was performed on poly-A selected mRNA fragments, 100 b.p paired end, and strand specific, on average 40 million reads per sample.

first: Steffen

last: Boehm

first: Probir

last: Chakravarty

first: Frances

last: Balkwill


title: Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation

status: Public on Feb 01 2016

city: Paris

first: PONTIS

last: Julien

address: 35, rue Hélène BRION

country: France

institute: UMR7216 CNRS

summary:
The histone 3 lysine 9 methyltransferase Setdb1 is essential for both stem cell pluripotency and terminal differentiation of different cell types. To shed light on Setdb1 roles in these mutually exclusive processes, we used mouse skeletal myoblasts as a model of terminal differentiation. Ex vivo studies on isolated single myofibres showed that Setdb1 is required for adult muscle stem cells expansion following activation. In vitro studies in skeletal myoblasts confirmed that Setdb1 suppresses terminal differentiation. Genomic binding analyses showed a release of Setdb1 from selected target genes upon myoblast terminal differentiation, concomitant to a nuclear export of Setdb1 to the cytoplasm. Both genomic release and cytoplasmic Setdb1 relocalisation during differentiation were dependent on canonical Wnt signalling. Transcriptomic assays in myoblasts unravelled a significant overlap between Setdb1 and Wnt3a regulated genetic programs. Together, our findings revealed Wnt-dependent subcellular relocalisation of Setdb1 as a novel mechanism regulating Setdb1 functions and myogenesis.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Profiling of Stem/Progenitor Cell Regulatory Genes of the Synovial Joint by Genome-wide RNASeq Analysis

status: Public on Jul 19 2018

city: New York

first: Christopher

last: Ricupero

state: NY

address: 630 West 168th Street VC12-2132

department: Center for Craniofacial Regeneration

institute: Columbia University Medical Center

summary: We report the application of RNA sequencing technology for high-throughput profiling of the articular and mature zones of the mandibular condyle in postnatal 7-day-old mice. Briefly, mandibular condyles of postnatal 7-day-old mice were frozen-sectioned with articular, mature zones idintified under a dissection microscope.  Cells from the articular zone (az), mature zone (mz) were isolated by laser capture microscopy. Total RNAs from each sample were polyA selected and single-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit (Illumina).  The samples were then sequenced using the Illumina HiSeq sequencer.  Total sequencing reads representing RNA transcripts were generated and were mapped to the NCBI mouse reference genome. Differential expressed genes were identified using DESeq, with <0.05 false discovery rate (FDR).  Fragments Per Kilobase of exon model per Million Mapped fragments (FPKM) were estimated for each gene in each sample.  Hierarchical clustering was also performed on log2FPKM values with Cluster 3.0.  Only genes with FDR<0.05 and ≥0.80 standard deviation were included. RNA comparison between articular and mature zones revealed distinctive gene expression profiles.

overall_design: Profiling of the articular and mature zones of postnatal 7-day-old mice mandibular condyle by RNA sequencing, in triplicate, using Illumina HiSeq sequencer.

first: Yue

last: Zhou

first: Mo

last: Chen

first: Ling

last: He

first: Jiaqian

last: Wu

first: Kenian

first: Richard

last: Friedman

first: Paolo

last: Guarnieri

first: Zuolin

last: Wang

first: Xuedong

first: Jeremy

last: Mao


title: Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation [ChIP-seq]

summary: The histone 3 lysine 9 (H3K9)-specific methyltransferase (KMT) Setdb1 is essential for both stem cell pluripotency and terminal differentiation of different cell types. To shed light on Setdb1 role(s) in these mutually exclusive processes, we used mouse skeletal myoblasts as a model of terminal differentiation. Ex vivo studies on isolated single myofibres showed that Setdb1 is required for muscle adult stem cells expansion following activation and in vitro studies on skeletal myoblasts confirmed that Setdb1 suppresses terminal myoblast differentiation. We used genome-wide analyses to identify Setdb1 direct target genes in myoblasts and observed a release of Setdb1 from the promoter of selected target genes upon myoblast terminal differentiation, concomitant to a nuclear export of Setdb1 to the cytoplasm. We demonstrated that both genomic release and cytoplasmic Setdb1 relocalisation during differentiation were dependent on canonical Wnt signalling. Taken together, our findings uncover a functional link between Setdb1 and canonical Wnt signalling in skeletal muscle cells, which affects the expression of a subset of Setdb1 target genes. We revealed Wnt-dependent subcellular relocalisation of Setdb1 as a novel mechanism regulating Setdb1 functions.

overall_design: ChIP-seq of Setdb1 and H3K9me3 in Myoblast cells (C2C12)

first: Julien

last: Pontis

first: Sophie

last: Beyer

first: Slimane

last: Ait-Si-Ali


title: Genotoxicity after adeno-associated virus (AAV) gene therapy is dependent upon dose, treatment age and enhancer-promoter selection (microRNA)

status: Public on Sep 01 2015

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: AAV gene therapy has recently been approved for clinical use and shown to be efficacious and safe in a growing number of clinical trials. However, the safety of AAV as a gene therapy has been challenged by a few studies that documented hepatocellular carcinoma (HCC) after AAV gene delivery in mice. The association between AAV and HCC has been difficult to reconcile and is the subject of intense debate because numerous AAV studies have not reported toxicity. Here, we report a comprehensive study of HCC in a large number of mice following therapeutic AAV gene delivery. Using a sensitive high-throughput integration site-capture technique and global expressional analysis, we found that AAV integration into the Rian locus and the over-expression of a proximal gene, Rtl1, were associated with HCC. In addition, we identify a number of genes with differential expression that maybe useful in the study, diagnosis and treatment of HCC. We demonstrate that AAV vector dose, enhancer-promoter selection, and the timing of gene delivery are the defining factors in AAV-mediated insertional mutagenesis. Our results help explain the AAV-mediated genotoxicity previously observed and have important implications for the design of both safer AAV vectors and gene therapy studies.

overall_design: To investigate the possibility that insertional mutagenesis by AAV contributed to the development of HCC, we collected normal and tumor tissues from adult mouse livers that received AAV injection at a neonatal stage.

first: R

last: Chandler

first: A

first: C

last: Venditti

first: Weiwei


title: Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances

status: Public on Jun 08 2016

city: Sydney

first: Rachel

last: Levin

state: New South Wales

address: UNSW

institute: University of New South Wales

summary: Using transcriptomics, we show that Symbiodinium acclimation to elevated temperature involves up-regulated expression of meiosis genes followed by up-regulated expression of numerous reactive oxygen species scavenging genes and molecular chaperone genes. Our study connects Symbiodinium transcriptional regulation with physiological heat stress responses as well as known bleaching responses of corals harboring these same Symbiodinium. By uncovering these critical links, we greatly advance understanding of the bleaching susceptibility of corals, which is a key process responsible for global coral reef health.

overall_design:
We analyzed gene regulation in response to heat stress by two Symbiodinium C1 populations with contrasting thermal tolerances and bleaching thresholds.
The thermo-sensitive South Molle (SM) Symbiodinium population and thermo-tolerant Magnetic Island (MI) Symbiodinium population were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). Light was provided at an intensity of 30 µmol quanta m^-2 s^-1 (Crompton 36W cool white fluorescent tubes, 4000 K) with a 12:12 h light:dark cycle. For this study, 50 ml (~1 x 10^6 cells/ml) of each population were added to eight replicate culture flasks per population (n=4 for each temperature treatment). Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C. After 10 days of acclimation, fresh media was supplied to the cultures. After an additional four days of acclimation (two weeks of acclimation total), two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C. Temperature and light intensity in the incubators were monitored with HOBO data loggers. Cultures remained in exponential growth phase, determined by the average of three replicate haemocytometer counts for each sample measured throughout the experiment. Transcriptomes were sampled on day -1 (pre-heating), 9, and 13.

SM_min250_nr.fasta: South Molle population de novo transcriptome, non-redundant transcripts (min transcript length 250 bp)

SM_transcriptome.fasta: preliminary South Molle population de novo transcriptome (min transcript length 150 bp)

MI_min250_nr.fasta: Magnetic Island population de novo transcriptome, non-redundant transcripts (min transcript length 250 bp)

MI_transcriptome.fasta: preliminary Magnetic Island population de novo transcriptome (min transcript length 150 bp)

Trinity_SM_min250nr_annotation_report.complete.5.xls: SM transcriptome annotation spreadsheet

Trinity_MI_min250nr_annotation_report.complete.5.xls: MI transcriptome annotation spreadsheet

day*nr.counts.txt: gene count matrix across samples

first: Victor

middle: H

last: Beltran

first: Ross

last: Hill

first: Staffan

last: Kjelleberg

first: Diane

last: McDougald

first: Peter

middle: D

last: Steinberg

first: Madeleine

last: van Oppen


title: Canonical Wnt signalling regulates nuclear export of Setdb1 during skeletal muscle terminal differentiation [RNA-seq]

first: PONTIS

last: Julien

summary: The histone 3 lysine 9 methyltransferase Setdb1 is essential for both stem cell pluripotency and terminal differentiation of different cell types. To shed light on Setdb1 roles in these mutually exclusive processes, we used mouse skeletal myoblasts as a model of terminal differentiation. Ex vivo studies on isolated single myofibres showed that Setdb1 is required for muscle adult stem cells expansion following activation. In vitro studies in skeletal myoblasts confirmed that Setdb1 suppresses terminal myoblast differentiation. Genomic binding  analyses showed a release of Setdb1 from the promoter of selected target genes upon myoblast terminal differentiation, concomitant to a nuclear export of Setdb1 to the cytoplasm. Both genomic release and cytoplasmic Setdb1 relocalisation during differentiation were dependent on canonical Wnt signalling. Together, our findings revealed Wnt-dependent subcellular relocalisation of Setdb1 as a novel mechanism regulating Setdb1 functions and adult myogenesis.

overall_design: RNA-seq of knockdown of Setdb1 in myoblast cells (C2C12).


title: Altered levels of circulating miRNAs are associated with Schistosoma japonicum infection in mice

status: Public on Sep 30 2015

city: Shanghai

first: Lihui

last: Zhu

state: Shanghai

address: 800 Dongchuang Road

department: School of Agriculture and Biology

institute: Shanghai Jiaotong University

summary:
miRNA profiling of  S. japonicum infected mouse plasma comparing control untreated mouse plasma.
Schistosomiasis, caused by dioecious flatworms in the genus Schistosoma, is torturing people predominantly in the developing countries. Knowledge on schistosome-host interaction and its parasitism may result in the development of novel strategies for schistosomiasis control. MicroRNAs (miRNAs) are involved in a wide range of biological processes including development, cell proliferation, metabolism ,signal transduction, et al. Circulating miRNAs are not only important biomarker associated the process of pathogenesis in many diseases and also are able to regulate target gene expression in recipient cells, just like hormones. In the present study, we investigated circulating miRNA profile associated with S. japonicum infection in mice using miRNA microarray.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Human betaherpesvirus 5
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Two-condition experiment, Control vs. S. japonicum infected. Biological replicates: 2 control, 2 transfected,  One replicate per array.

first: Guofeng

last: Cheng

first: Jin

last: Dao

first: Xiaoli

last: Du

first: Hao

last: Li

first: Ke

last: Lu


title: Regulatory T cells from colonic lamina propria [array]

status: Public on Jul 25 2015

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: The colonic lamina propria contains a distinct population of Foxp3+ T regulatory cells (Tregs) that modulate responses to commensal microbes. Analysis of gene expression revealed that the transcriptome of colonic Tregs is distinct from splenic and other tissue Tregs. Rorγ and Helios in colonic Tregs mark distinct populations: Rorγ+Helios- or Rorγ-Helios+ Tregs. We uncovered an unanticipated role for Rorγ, a transcription factor generally considered to be antagonistic to Foxp3. Rorγ in colonic Tregs accounts for a small but specific part of the colon-specific Treg signature.

overall_design: (1) Total colonic and splenic Foxp3+ Treg comparison: Lymphocytes were isolated from colonic lamina propria and spleens of Foxp3-ires-GFP mice, where GFP reports Foxp3 expression. TCRb+CD4+GFP+ cells were double sorted into Trizol. (2) Colonic Rorγ+ and Rorγ- Treg comparison: Foxp3-ires-Thy1.1 reporter mice were crossed to Rorc-GFP reporter mice to generate mice that report both Foxp3 and Rorγ expression. Rorγ+Foxp3+ Tregs (TCRb+CD4+Thy1.1+GFP+) and Rorγ-Foxp3+ Tregs (TCRb+CD4+Thy1.1+GFP-) from colonic lamina propria were double sorted into Trizol.To reduce variability and increase cell number, cells from multiple mice were pooled for sorting and at least three replicates were generated for all groups. RNA from 1.5-3.0 x104 cells was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays.

first: Esen

last: Sefik

last: Mathis

first: Christophe

last: Benoist


title: Transcriptome-wide Quantitative Analysis of XLPDR-derived human dermal fibroblasts with POLA1 deficiency

status: Public on Dec 09 2015

city: Dallas

first: Igor

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: The goal of this study is to analyzed transcriptome changes caused by POLA1 deficiency. Our data represents the first detailed analysis of molecular basis of XLPDR syndrome. We report than POLA1 deficiency leads to over-activation of IRF and NF-kB pathways with overexpression of typical markers of autoimmune syndromes.

overall_design: Wild type and XLPDR-derived dermal fibroblasts are analyzed under non-stimulated (basal) conditions, after TNF treatment (2 and 12 h, 1000 U/mL), and poly(dA:dT) stimulation (16h, 1 mkg/mL). Obtained data were confirmed using the cellular model of XLPDR - normal dermal fibroblasts pretreated with control or anti-POLA1 siRNA and stimulated in analogous way.

first: Petro

last: Starokadomskyy

first: Ezra

last: Burstein

first: Andrew

last: Zinn


title: Effects of the anti-microbial contaminant triclocarban on the reproductive function and ovarian transcriptome of the fathead minnow (Pimephales promelas)

status: Public on Jul 31 2015

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

summary: Triclocarban (TCC) is a widely used antimicrobial agent that is routinely detected in surface waters. The present study was designed to examine TCC’s efficacy and mode of action as a reproductive toxicant in fish. Reproductively mature Pimephales promelas were continuously exposed to either 1 or 5 μg TCC/L, 0.5 μg 17β-trenbolone (TRB)/L or a mixture (MIX) of 5 μg TCC and 0.5 μg TRB/L for 22 d and a variety of reproductive and endocrine-related endpoints were examined. The data were evaluated to answer several key questions: first, whether exposure to TCC could be linked with an ecologically-relevant adverse outcome, i.e., impaired reproduction; second, whether the present study provided additional support for augmentation of androgen action as an endocrine-disrupting mode of action for TCC; and third, whether there were any novel and/or plausible linkages between changes in the ovarian transcriptome and the apical responses observed in females that could support adverse outcome pathway development and/or further hypothesis-driven testing.

overall_design: Fathead minnows were randomly paired (one male, one female) and placed in tanks at a density of two pairs per tank with six replicate tanks per treatment. Pairs were separated by a water permeable mesh divider and each pair had its own breeding substrate. The fish were held in the test system, receiving UV-treated, filtered Lake Superior (control) water only, for a 21 d acclimation period during which the fecundity and fertility of each pair were assessed daily. After 21 d, exposures were initiated with pairs that had spawned successfully during acclimation. Fish were exposed continuously to target test concentrations of 0 (Lake Superior control), TCC (1 and 5 µg/L), TRB (0.5 μg/L), or a mixture of the two chemicals (5 μg TCC and 0.5 μg TRB/L) for 22 d.  Water concentrations of TCC and TRB were determined in stock solutions and all exposure tanks every two to three days. General water quality characteristics (mean ± SD) measured regularly over the course of the Experiment were: temperature, 24.8 ± 0.7 oC; pH, 7.87 ± 0.04; dissolved oxygen, 6.8 ± 0.35 mg/L. Ovary RNA samples from twenty four fish (n=5 for all treatments except TRB alone; n=4) were selected for microarray analysis.

first: Kathleen

last: Jensen

first: Jenna

middle: E

last: Cavallin

first: Elizabeth

middle: J

last: Durhan

first: Natàlia

last: Garcia-Reyero

first: Michael

last: Kahl

first: Richard

last: Leino

last: Makynen

first: Edward

last: Perkins

first: Leah

middle: C

last: Wehmas

first: Gerald

last: Ankley


title: Identification of the CREB-regulated transcriptional program in human mucoepidermoid carcinoma cells

status: Public on Oct 30 2015

city: Gainesville

first: Lizi

last: Wu

address: 2033 Mowry Road

institute: University of Florida

summary: Mucoepidermoid carcinomas (MEC) is the most common salivary gland malignancy.  To date, advanced and nonresectable MEC have poor prognosis and no effective treatment.  The CRTC1-MAML2 fusion oncogene, which is associated with more than 50% of MEC, consists of the N-terminal CREB-binding domain of the CREB transcriptional co-activator CRTC1 and the C-terminal transcriptional activation domain of the Notch transcriptional co-activator MAML2.  CRTC1-MAML2 fusion was found to interact with CREB and constitutively activate their transcriptional targets.  To investigate the contribution of the transcription factor CREB to mediate the fusion target gene expression, gene expression profiling analysis were performed in two salivary gland tumor cell lines (including fusion-positive H3118 MEC cells and fusion-negative HSY parotid adenocarcinoma cells) before and after CREB knockdown. This study demonstrated that CRTC1-MAML2 co-activation of CREB is a major mechanism underlying CRTC1-MAML2-mediated transcriptional regulation.

overall_design: Two salivary gland tumor cell lines were used in this study, including fusion-positive H3118 MEC cells and fusion-negative HSY parotid adenocarcinoma cells.  The CREB knock down was performed with three biological replicates for each group. Both fusion-positive MEC H3118 cells and fusion-negative parotid adenocarcinoma HSY cells were stably transduced with pLKO.1-based shRNA targeting luciferase gene (shLuc, control) or CREB (shCREB). The cells were independently cultured and RNAs were then harvested 72 hours after transduction for microarray analysis.


title: Activity-induced Nr4a1 regulates spine density and distribution pattern of excitatory synapses in pyramidal neurons

status: Public on Jan 13 2016

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

summary: Excitatory synapses occur mainly on dendritic spines, and spine density is usually correlated with the strength of excitatory synaptic transmission. We report that Nr4a1, an activity-inducible gene encoding a nuclear receptor, regulates the density and distribution of dendritic spines in CA1 pyramidal neurons. Nr4a1 overexpression resulted in elimination of the majority of spines; however, postsynaptic densities were preserved on dendritic shafts, and the strength of excitatory synaptic transmission was unaffected, showing that excitatory synapses can be dissociated from spines. mRNA expression profiling studies suggest that Nr4a1-mediated transcriptional regulation of the actin cytoskeleton contributes to this effect. Under conditions of chronically elevated activity, when Nr4a1 was induced, Nr4a1 knockdown increased the density of spines and PSDs specifically at the distal ends of dendrites. Thus, Nr4a1 is a key component of an activity-induced transcriptional program that regulates the density and distribution of spines and synapses.

overall_design: After 10 days in culture, dissociated mouse hippocampal neurons in 6-well plates were infected with lentivirus expressing either Flag-Nr4a1 or GFP and incubated for 6 days to allow for transgene expression. Total RNA was then isolated using RNeasy Plus kit (QIAGEN). Samples passing an mRNA quality check proceeded to quantitative analysis on Agilent-026655 4x44 Mouse Microarrays.

first: Joshua

first: Yelin

last: Chen

first: Morgan

last: Sheng


title: Gene expression profile of splenic p14 effector T cells eight days after LCMV infection

status: Public on Jun 01 2015

city: Aurora

first: Jens

last: Eberlein

state: CO

address: 1775 Aurora Court

department: Anesthesiology

institute: University of Colorado Denver

summary: Microarray analyses was employed to determine the gene expression profiles of LCMV-specific p14 CD8+ effector T cells eight days after an acute LCMV Armstrong infection providing a framework to compare and contrast effector function potential of distinct immune cell subsets to CD8+ effector T cells.

overall_design: Splenic CD90.1+ p14 effector T cells from congenic LCMV Armstrong-immune p14 chimeras were magnetically pre-enriched from individual p14 chimeras (n=3) 8 days after infection using an alpha-PE selection kit (EasySep, StemCell Technologies) and further purified by FACS-sorting of CD8+CD90.1+ cells (FACS Aria, BD Biosciences) achieving >99% purity.


title: Transcriptomic profiles of S. Typhimurium SL1344 parent strain and ΔrpoS and ΔrelAΔspoT and ΔrelAΔspoTΔrpoS mutant strains grown to various optical densities during late-log and stationary phase in LB aerobic batch culture

status: Public on May 31 2015

city: Norwich

first: Arthur

last: Thompson

address: Colney Lane

institute: Institute of Food Research

summary: S. Typhimurium SL1344 parental strain and isogenic ΔrpoS, ΔrelAΔspoT and ΔrelAΔspoTΔrpoS strains were grown to OD600=1.0, OD600=2.3, OD600=3.0 and OD600=4.2 in Luria-Bertani medium.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

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

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: 35 samples (parent, ΔrpoS, ppGpp^0 and ΔrelAΔspoTΔrpoS at late-log, early stationary, mid-stationary and late stationary growth phases and 3 biological replicates for each sample.


title: Time course analyses of aging antiviral CD8+ memory T cells

summary: The precise consequences for antiviral memory T cells (TM) generated early in life and allowed to age in the absence of pathogen persistence or potentially confounding heterologous infections remain to date largely unexplored. Here, we have employed microarray analyses to determine the gene expression profiles of LCMV-specific P14 CD8+ TM over a period of up to 400 days after an acute LCMV Armstrong infection.

overall_design: Congenic LCMV Armstrong-immune p14 chimeras were generated in a staggered fashion to allow for concurrent sample collection and processing of mice differing only in respect to the time after challenge (dpi: days post infection). Splenic CD90.1+ p14 TE (8 dpi) and TM (46, 156, 286 and 400 dpi) were magnetically pre-enriched from individual p14 chimeras (n=3-4) using an α-PE selection kit (EasySep, StemCell Technologies), and further purified by FACS-sorting of CD8+CD90.1+ cells (FACS Aria, BD Biosciences) achieving >99% purity.

first: Dirk

last: Homann


title: PDGF and FGF treatment in E13.5 MEPMs II

status: Public on May 07 2015

city: San Francisco

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

summary: PDGF and FGF treatment in E13.5 MEPMs.  4 hr PDGF treated MEPMs (3 replicates), 4 hr FGF treated MEPMs (3 replicates), 1 hr PDGF + PD325901 treated MEPMs (2 replicates), 4 hr PDGF + PD325901 treated MEPMs (2 replicates), 1 hr FGF + PD325901 treated MEPMs (2 replicates), 4 hr FGF + PD325901 treated MEPMs (2 replicates), 1 hr PDGF + LY294002 treated MEPMs (2 replicates), 4 hr PDGF + LY294002 treated MEPMs (2 replicates), 1 hr FGF + LY294002 treated MEPMs (2 replicates), 4 hr FGF + LY294002 treated MEPMs (2 replicates)

middle: N

first: Pierre

last: Mazot

first: Fenglei

last: He

first: Philippe

last: Soriano


title: Gender-specific post-natal demethylation and establishment of epigenetic memory

status: Public on May 03 2015

city: Jerusalem

first: Howard

last: Cedar

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation patterns are set up in a relatively fixed programmed manner during normal embryonic development and are then stably maintained.  Using genome-wide analysis, we have discovered a postnatal pathway involving gender-specific demethylation that occurs exclusively in the male liver.  This demodification is programmed to take place at tissue-specific enhancer sequences, and our data show that the methylation state at these loci is associated with and appears to play a role in the transcriptional regulation of nearby genes.  This process is mediated by the secretion of testosterone at the time of sexual maturity, but the resulting methylation profile is stable and therefore can serve as an epigenetic memory even in the absence of this inducer.  These findings add a new dimension to our understanding of the role of DNA methylation in vivo and provide the foundations for deciphering how environment can impact on the epigenetic regulation of genes, in general.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: DNA methylation profile of  male and female mouse and Human tissues was generated using the RRBS protocol followed by deep sequncing. Whole genome DNA methylation profile using deep sequencing was genereted for male and female mouse tissues. RNAseq was performed on male and female mouse tissues.

first: Yitzchak

last: Reizel

first: Adam

last: Spiro

first: Ofra

last: Sabag

first: Yael

last: Skversky

first: Merav

last: Hecht

first: Ilana

last: Keshet

first: Benjamin

middle: P

last: Berman


title: Characterization of TCF21 downstream target regions identifies a transcriptional network linking multiple independent coronary artery disease loci

status: Public on Apr 12 2015

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

summary: Recent meta-analyses of genome wide association studies (GWAS) have identified approximately 150 loci that are associated with coronary artery disease (CAD). To link the causal genes in these loci to functional transcriptional networks, we have used chromatin immunoprecipitation sequencing (ChIP-Seq) with human coronary artery smooth muscle cells (HCASMC) to investigate the cellular and molecular program downstream of one CAD associated transcription factor, TCF21. Analysis of the TCF21 downstream target genes for enrichment of molecular and cellular annotation terms identified processes relevant to CAD pathophysiology, including growth factor binding (PDGF, VEGF), matrix interactions (“integrin binding,” “cell adhesion”), and smooth muscle contraction (“actin filament-based processes,” “actin cytoskeleton”). Motif searches of peak sequences confirmed the canonical E-box CAGCTG as the likely binding sequence for TCF21, but also identified bZip motifs that coordinate binding of AP1 family transcription factors. Follow-up ChIP-Seq studies verified enriched binding of bZip factors JUN and JUND to TCF21 target loci. Importantly, analysis of the representation of CAD genes among TCF21 target loci showed highly significant enrichment. Further, expression quantitative trait variation mapped to target genes of TCF21 were significantly enriched among variants with low P-values in the GWAS analyses, and single nucleotide polymorphisms within TCF21 peaks were shown to be in linkage disequilibrium with CAD-associated SNPs, suggesting a functional interaction between TCF21 binding and causal variants in other CAD disease loci. Thus, data and analyses presented here provide evidence for a transcriptional regulatory network that links TCF21 function in smooth muscle cells with a number of other CAD-associated genes, and suggest that study of GWAS transcription factors may be a highly useful approach to identifying disease gene interactions and thus pathways that may be relevant to complex disease etiology.

overall_design: We did ChIP-Seq on human coronary artery smooth muscle cells grown in SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and FBS, but without antibiotics (Lonza, #CC-3182. We did immunoprecipitations with two antibodies (Sigma HPA013189 and Abcam 49475). We conducted two biological replicates for each antibody, and also did an IgG control for these studies. For these experiments, sequencing was done on an Illumina GAII, single end reads. In separate set of experiments we performed ChIP-Seq for JUN (Ab sc-1694) and JUND (Ab sc-74) with the same HCASMC cells under the same culture conditions. For these studies we did one replicate for each antibody, and also included an IgG control. Sequencing for the JUN and JUND studies was paired ends, on an Illumina HiSeq machine.

first: Olga

last: Sazonova

first: Milos

last: Pjanic


title: RNA polymerase binding sites revealed by ChIP-chip in S. Typhimurium wild-type, ΔrelAΔspoT (ppGpp0), and ΔdksA strains at early stationary phase (ESP) and late stationary phase (LSP)

first: Arthur

last: Thompson

type: Genome binding/occupancy profiling by array

summary: S. Typhimurium parent, ppGpp0 and dksA strains were grown to OD's of 2.3 (ESP) and 4.2 (LSP) and subjected to ChIP-chip analysis at 60 nt resolution.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: 38 samples (parent strain, ΔrelAΔspoT, ΔdksA grown to ESP or LSP, protein-DNA crosslinked and fragments immunoprecipitated with Ab against E.coli RNAP beta subunit (Neoclone, cat # WP023), or minus Ab as control. DNA fragments purified & labelled with dCTP-Cy5 and hybridised against Cy3-dCTP labelled gDNA on OGT 4 x 44K 60 mer S. Typhimurium SL1344 array).

first: Vinoy

last: Ramachandran


title: Transcriptional profiles of Salmonella Typhimurium 4/74 parent and  relA spoT,  rpoS and  dksA strains during stationary phase, and RNA polymerase distribution as determined by chromatin immunoprecipitation in parent,  relA spoT and  dksA strains

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

overall_design: Refer to individual Series


title: Effect of Crystalline Silica (CS) on murine (KrasLA1) lung tumors

status: Public on Apr 17 2015

city: Louisville

first: Venkatakrishna

middle: R

last: Jala

state: KY

address: 505 S Hancock Street # 323

department: Dept. Microbiology and Immunology

institute: University of Louisville

summary: Crystallline Silica induced inflammation in lungs

overall_design: Intra-trachial instilliation of CS or PBS into BLT1+/+, BLT1-/-, BLT1+/+KRasLA1 and BLT1-/-KRasLA1 mice.

first: Satpathy

last: Bodduluri


title: Prolyl hydroxylase P4HA1 is amplified, overexpressed in prostate cancer and enhances cancer invasion by altering MMP1 expression

status: Public on May 10 2015

city: Ann Arbor

first: Balabhadrapatruni

middle: Venkata Srinivasa Kalyana

last: Chakravarthi

state: Michigan

address: 2900 Huron Parkway, Suite 100

department: MCTP, Pathology

institute: Michigan Center for Translational Pathology

summary: Recent studies including next-generation sequencing have identified genomic events in prostate cancer including ETS gene fusions. However, it is critical to identify druggable targets for prostate cancer and their mechanism of action for therapeutic intervention. Here, we show that prolyl 4-hydroxylase, alpha polypeptide I (P4HA1) is overexpressed in aggressive prostate cancer and amplified in a subset of metastatic prostate cancer. This study provides mechanistic insights of P4HA1 regulation and its mode of action including its role in regulating MMP1. Importantly, P4HA1 mediated invasion in cancer cells could be reversed using MMP1 inhibitor, revealing therapeutic utility of targeting P4HA1 either directly or by inhibiting its downstream effectors.

overall_design: Two-color experiment, in duplicates.

first: Sooryanarayana

last: Varambally


title: Whole-genome expression analysis of melanoma tumor biopsies from a population-based cohort.

status: Public on Apr 01 2015

city: Lund

first: Göran

last: Jönsson

address: Scheelevägen 8

institute: Lund University

summary: Analysis of gene expression profiles in metastatic melanoma to validate prognostic signatures.

overall_design: Total RNA was extracted from fresh-frozen melanoma tumors and genome-wide expression profiling was performed using Illlumina Human HT-12V4.0 BeadChip arrays by standard methods. After removal of replicate samples there were 214 unique melanoma samples left.


title: DNA methylation profiling in the Carolina Breast Cancer Study

status: Public on Apr 07 2015

city: Chapel Hill

first: Kathleen

middle: Conway

last: Dorsey

state: NC

address: CB 7435, 2101 McGavran-Greenberg Hall

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 invasive breast tumors from the Carolina Breast Cancer Study (CBCS), a population-based study of invasive breast cancer.  Concensus clustering using methylation (β) values for the 167 most variant CpG loci defined 4 clusters differing most distinctly in hormone receptor (HR) status, intrinsic subtype (luminal versus basal-like) and p53 mutation status. Supervised analyses for HR status, subtype, and p53 status identified differentially methylated CpG loci with considerable overlap (n=266).  Concensus clustering also defined a hypermethylated luminal-enriched tumor cluster 3; gene ontology analysis of cluster 3 hypermethylated loci revealed enrichment for developmental genes, including homeobox domain genes (HOXB13, PAX6, IPF1, EYA4, DLK1, IHH, ISL1, TBX1, SOX1, SOX17). The hypermethylated luminal-enriched cluster 3 independently predicted poorer survival in multivariate Cox proportional hazard analysis, and this finding was confirmed in analysis of luminal A tumors.  This study demonstrates epigenetic heterogeneity among breast tumors of a single intrinsic subtype, and shows that epigenetic patterns are strongly associated with HR status, subtype, and p53 mutation status. Among HR+ tumors, a gene signature characterized by hypermethylation of developmental genes may have prognostic value. Genes differentially methylated between clinically-important tumor subsets have roles in differentiation, development, and tumor growth and may be critical to inducing and maintaining tumor phenotypes and clinical outcomes.

overall_design: 517 breast tumors, 9 normal breast tissues

last: Conway Dorsey

first: Sharon

last: Edmiston

first: Ryan

last: May

first: Pei

middle: F

last: Kuan

first: Haitao

last: Chu

first: Christopher

last: Bryant

first: Chiu-Kit

last: Tse

first: Theresa

last: Swift-Scanlan

first: Joseph

last: Geradts

first: Melissa

middle: A

last: Troester

first: Robert

last: Millikan


title: Transcriptomic profiles of S. Typhimurium SL1344 parent strain and ΔdksA and ΔrelAΔspoTΔdksA mutant strains grown to various optical densities during late-log and stationary phase in LB aerobic batch culture

first: Arthur

last: Thompson

summary: S. Typhimurium SL1344 parental strain and isogenic ΔrpoS, ΔdksA and ΔrelAΔspoT, ΔrelAΔspoTΔrpoS and ΔrelAΔspoTΔdksA strains were grown to OD600=1.0, OD600=2.3, OD600=3.0 and OD600=4.2 in Luria-Bertani medium.

overall_design: 30 samples (parent strain, ΔdksA, and  ΔrelAΔspoTΔdksA at late-log, early stationary, mid-stationary and late stationary growth phases and 3 or 5 biological replicates for each sample.


title: Fasting potentiates the anticancer activity of Crizotinib

status: Public on Jan 01 2016

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

country: Italy

institute: University of Trento

summary:
Background: Tyrosine kinase inhibitors (TKIs) are widely used for treating solid and hematologic malignancies. However, their efficacy is frequently short lived, warranting the search for safe potentiation strategies. Short courses of fasting were shown to sensitize cancer cells to chemo- and radiotherapy while increasing the resistance of healthy tissues to the same agents. The purpose of this study was to assess the potential of fasting to increase the efficacy of TKIs.

Methods: starvation-mimicking culture conditions were studied for their ability to potentiate the effects of Epidermal Growth Factor Receptor (EGFR), Human Epidermal Growth Factor Receptor 2 (HER2), Anaplastic Lymphoma Kinase (ALK) and multitarget TKIs in terms of cancer cell growth, signaling cascades inhibition, and changes in gene expression profile in TKI-sensitive cancer cells. In vivo, the activity of crizotinib or regorafenib, weekly cycles of fasting, or their combination was compared in tumor xenografts models.

Results: In vitro, starvation-mimicking culture conditions increased the ability of TKIs to block cancer cell growth and to inhibit the mitogen-activated protein kinase (MAPK) signaling pathway. At the gene expression profile level, starvation and crizotinib led to similar changes, but their combination strengthened Rb-, MYC-, and E2F-dependent transcription inhibition. In vivo, both TKIs and cycles of fasting slowed tumor growth, but, when combined, they were significantly more effective than either type of treatment alone.

Conclusions: Cycles of fasting or of specifically designed fasting-mimicking diets should be evaluated in clinical studies as a means to potentiate the activity of TKIs in clinical use.

overall_design: RNA was collected from H3122 cells in 4 different conditions: serum, starvation, treated with Crizotinib, starvation and treated with Crizotinib. Each condition was run in quadruplicate

first: Vito

last: D'Agostino

first: Irene

last: Caffa

first: Alessio

last: Nencioni

first: Patrizia

last: Damonte

first: Debora

last: Soncini

first: Alberto

last: Ballestrero

first: Patrizio

last: Odetti

first: Valter

last: Longo


title: Transcriptomic profiling study of canine degenerative mitral valve disease

status: Public on May 29 2015

city: Saint Louis

first: Qinghong

last: Li

state: MO - Missouri

address: 1 Checkerboard Square 2S

department: Basic Research

institute: Nestle Purina Research

summary: Degenerative mitral valve disease (DMVD) is the most common cardiac disease in dogs. Some signaling pathways have been implicated in DMVD, including the serotonin and TGF-beta pathways. We sought to identify additional molecular and metabolic pathways that contribute to DMVD using transcriptomic and metabolomic studies. RNA-seq gene expression evaluated on total RNA isolated from left ventricle (LV) and mitral valve (MV) identified 812 differentially expressed transcripts (DETs) in LV and 263 DETs in MV. Out of 15 transcripts selected for RT-qPCR validation, we confirmed 13. In addition, serum samples were collected for metabolomic evaluation. Endothelial nitric oxide synthase (eNOS) was significantly up-regulated in both LV and MV while the level of circulating asymmetrical dimethyl arginine (ADMA), an endogenous NOS inhibitor, was lower in DMVD. Expressions of matrix metalloproteinases (MMP) and their endogenous inhibitor tissue inhibitor of matrix metallopeptidases (TIMP) were altered. This study demonstrates transcript and metabolite differences consistent with increased nitric oxide (NO) and reactive oxygen species (ROS) production, impaired fatty acid transport and oxidation, and increased glucose uptake and glycolysis in DMVD. Our findings are consistent with metabolic conversion in the DMVD heart from oxidative metabolism to glycolysis along with an increased concentration of NO and ROS activity suggesting an alternative signaling effect. Alterations of redox-sensitive NO signaling may play a role in ECM (ECM) homeostasis via modulating MMP and TIMP expression.

overall_design: mRNA profiles of both left ventricle and mitral valve tissues from dogs with DMVD and healthy controls were generated by deep sequencing approach using Illumina HiSeq 2000 platform.


title: Expression data from benign and malignant pheochromocytomas and paragangliomas

status: Public on Mar 20 2015

city: Rotterdam

first: Esther

last: Korpershoek

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC University Medical Center Rotterdam

summary: Pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine, usually benign tumors. Currently, for these neoplasms the only reliable criterion of malignancy is the presence of metastases. The aim of the present study was to identify molecular markers that can distinguish malignant from benign PPGL.  An mRNA expression array was performed on 40 benign and 11 malignant PPGL. Genes showing a significantly different expression between benign and malignant PPGL with a ratio ? 4 were selected. Differentially expressed genes were confirmed by qRT-PCR and subsequently tested in an independent validation series (4 benign and 4 malignant) by qRT-PCR. Finally, immunohistochemistry was performed for the validated genes on Tissue Micro Arrays, which included 100 PPGL (87 benign and 13 malignant). Ten genes, which were significantly differentially expressed between benign and malignant tumors (False Discovery Rates <0.05), were selected from the mRNA expression array data. Differential expression of Interleukin 13 Receptor Alpha 2 and Contactin 4 was confirmed  (p<0.05) and validated by qRT-PCR. However, at the protein level, only Contactin 4 appeared to be significantly overexpressed in malignant tumors (58% in malignant versus 17% in benign; p<0.05). No difference in the immunohistochemical staining for Interleukin 13 Receptor Alpha 2 was observed between benign and malignant PPGL. Contactin 4 expression appears to be associated with malignancy in pheochromocytomas and paragangliomas, and may be predictive of malignant behavior.

overall_design: In totall, 40 benign pheochromocytoma/paraganglioma and 11 pheochromocytoma/paraganglioma by affymetrix mRNA expression arrays


title: Genotoxicity after adeno-associated virus (AAV) gene therapy is dependent upon dose, treatment age and enhancer-promoter selection

status: Public on Jan 01 2015

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: AAV gene therapy has recently been approved for clinical use and shown to be efficacious and safe in a growing number of clinical trials. However, the safety of AAV as a gene therapy has been challenged by a few studies that documented hepatocellular carcinoma (HCC) after AAV gene delivery in mice. The association between AAV and HCC has been difficult to reconcile and is the subject of intense debate because numerous AAV studies have not reported toxicity. Here, we report a comprehensive study of HCC in a large number of mice following therapeutic AAV gene delivery. Using a sensitive high-throughput integration site-capture technique and global expressional analysis, we found that AAV integration into the Rian locus and the over-expression of a proximal gene, Rtl1, were associated with HCC. In addition, we identify a number of genes with differential expression that maybe useful in the study, diagnosis and treatment of HCC. We demonstrate that AAV vector dose, enhancer-promoter selection, and the timing of gene delivery are the defining factors in AAV-mediated insertional mutagenesis. Our results help explain the AAV-mediated genotoxicity previously observed and have important implications for the design of both safer AAV vectors and gene therapy studies.

overall_design: To investigate the possibility that insertional mutagenesis by AAV contributed to the development of HCC, we collected normal and tumor tissues from adult mouse livers that received AAV injection at a neonatal stage.

first: R

last: Chandler

first: A

first: C

last: Venditti

first: Weiwei

last: Wu


title: Expression data from Pin1 KO and WT mice

status: Public on Mar 26 2015

city: Boston

first: Kun Ping

last: Lu

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary:
The prolyl isomerase PIN1 has been identified as a regulator of phosphorylation signalling that catalyses the conversion of specific phosphorylated motifs between the two completely distinct conformations in a subset of proteins. PIN1 regulates diverse cellular processes, including growth-signal responses, cell-cycle progression, cellular stress responses, neuronal function and immune responses.
We used microarrays to detail the global gene expression of mammary epithelial cells (MECs) and neuron cells (NCs) in Pin1 KO and WT mice

overall_design: Lin-MECs and NCs from two pairs of three month old Pin1 KO and WT littermates were analyzed. Microarray expression profiles were collected using Affymetrix GeneChip Mouse Expression Array 430A.

first: Man-Li

last: Luo

first: Kazuhiro

last: Nakamura

first: Hai

last: Hu

first: Kun


title: Gene expression in mouse DRG neurons at 2 or 5 days post-sciatic lesion in WT and Nfil3-KO

status: Public on Feb 25 2015

city: Amsterdam

first: Ronald

last: van Kesteren

address: De Boelelaan 1085

department: Center for Neurogenomics and Cognitive Research

institute: VU University Amsterdam

summary: Mice with a deletion of transcription factor Nfil3 show delayed functional regeneration after sciatic lesion compared to WT mice. To analyze differential gene expression, sciatic nerves were lesioned and nerve endings were coaptated. After two or 5 days, DRGs L4 and L5 were dissected out and gene expression was measured by microarray. Control tissue was taken from the non-injured side. We found that expression of classic regeneration associated genes was similar in WT and Nfil3 KO mice. We did identify a group of differentially expressed genes known for its role in olfactory signal transduction, but were not known as regeneration associated genes until now, which may explain the negative effects on functional recovery.

overall_design: Gene expression in DRGs L4 and L5 from WT and NFIL3 KO mice was analyzed at 2 and 5 days after receiving a sciatic nerve lesion. Control tissue was taken from the non-injured side. Four biological replicates were used per condition. Microarray chips were two color chips, but each channel was analyzed in single color fashion. Conditions were pseudo-randomized over chips in a balanced dye-swap setup.

first: Loek

last: van der Kallen

first: Ruben

last: Eggers

first: Erich

middle: M

last: Ehlert

first: Joost

last: Verhaagen

first: August

middle: B

last: Smit


title: Transcriptional responses of Medicago truncatula upon sulfur deficiency stress and arbuscular mycorrhizal symbiosis

city: Dijon

first: Leonardo

last: Casieri

address: 17, rue Sully

institute: INRA

summary: In this work we aimed to get a first overview on S-stress responses in leaf and root tissues of mycorrhized and non mycorrhized plants. Several hundred genes showed a significant different transcript accumulation. Their annotation and GO ID association allowed us to investigate the our data in order to identify biological processes and molecular functions preferentially affected, and to better understand in which terms the symbiotic relation avoid the plant to face deleterious S-deficiency effects.

overall_design: Four chips study, of leaves or roots from mycorrhized and non-mycorrhized Medicago plants grown in normal or S deficient conditions. Up to six biological repetitions per condition.

first: Daniel

last: Wipf

first: Gaëlle

last: Mongelard

first: Diederik

last: van Tuinen

first: Laurent

last: Gutierrez