title: mTOR has distinct functions in generating versus sustaining humoral immunity

status: Public on Sep 20 2016

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary: Little is known about the role of mTOR signaling in plasma cell differentiation and function. Furthermore, for reasons not understood, mTOR inhibition reverses antibody-associated disease in a murine model of systemic lupus erythematosus. Here, we have demonstrated that induced B-lineage specific deletion of the gene encoding RAPTOR, an essential signaling adaptor for the rapamycin-sensitive mTOR complex 1 (mTORC1) abrogated the generation of antibody-secreting plasma cells in mice. Acute treatment with rapamycin recapitulated the effects of RAPTOR deficiency, while both strategies led to the ablation of newly formed plasma cells in the spleen and bone marrow while also obliterating pre-existing germinal centers. Surprisingly, although perturbing mTOR activity caused a profound decline in serum antibodies that were specific for exogenous antigen or DNA, frequencies of long-lived bone marrow plasma cells were unaffected. Instead, mTORC1 inhibition led to decreased expression of immunoglobulin binding protein (BiP) and other factors needed for robust protein synthesis. Consequently, blockade of antibody synthesis was rapidly reversed after termination of rapamycin treatment. We conclude that mTOR signaling plays critical but diverse roles in early and late phases of antibody responses and plasma cell differentiation.

overall_design: B6.BLIMP1 +/GFP mice were untreated or treated with rapamycin. RNA isolated from FACS-sorted B220-negative Blimp1-positive bone marrow plasma cells was subjected to microarray analysis. Five mice were used per group.

first: Derek

middle: D

last: Jones

middle: T

first: Joel

middle: R

last: Wilmore

first: Irene

last: Chernova

first: Alexandra

last: Bortnick

first: Brendan

last: Weiss

last: Allman


title: Next generation sequencing reveals potential for the development of insecticide resistance and cross-resistance in Drosophila suzukii (Diptera: Drosophilidae)

status: Public on Sep 23 2016

city: Athens

first: Ruchir

last: Mishra

state: GA

address: 120 Cedar St

department: Entomology

country: USA

institute: University of Georgia

type: Expression profiling by high throughput sequencing

summary:
The goal of this study is to proactively assess the risk of insecticide resistance development by determining susceptibility of field-collected D. suzukii and their response to insecticide treatment at the transcriptome level using next-generation sequencing technology.
Methods:LC50 values were calculated for zeta-cypermethrin, spinosad, malathion treated D. suzukii field-collected and lab-reared populations. LC50 dosage survived and untreated (10 individuals per replicate)  field-collected and lab reared D.suzukii transcript profiles were generated by RNA sequencing, in triplicate, using Illumina NextSeq 500. The 24 samples (paired-end reads, including  replicates) were independently mapped onto the D. suzukii genome (SpottedWingFlybase v.1) by using TopHat followed by Cufflinks to estimate the expression values of the transcripts in FPKM (Fragments Per Kilobase per Million mapped reads) with the Cuffdiff 2 default geometric normalization. Differentially expressed genes (FDR < 0.05 after Benjamini-Hochberg correction for multiple-testing) were identified for insecticide-treated or untreated control for either (1) lab-reared populations or (2) field-collected populations.
Results: As an approach to proactively assess the risk of insecticide resistance development, we determined the LC50 (lethal concentration, 50%) values of commonly used insecticides zeta-cypermethrin, spinosad, and malathion against laboratory-reared and field-collected D. suzukii populations. The LC50 values were significantly higher in field-collected populations when compared to lab-reared populations, indicating that field populations are less susceptible to these insecticides. Furthermore, we used RNA sequencing to analyze the response of D. suzukii at the transcriptome level upon treatment with the same three insecticide classes that are used in our bioassays. We identified differentially expressed genes (DEGs) in D. suzukii that survived LD50 doses of zeta-cypermethrin, spinosad, and malathion and gene classes that are overrepresented in DEGs. We observed that a high number of significantly DEGs are involved in detoxification and reduced cuticular penetration, especially in field population, thus providing potential molecular mechanisms for the higher LC50 values for field-collected population.
Conclusion: Our study identified a high number of metabolic detoxification genes that are induced in field-collected D. suzukii upon insecticide treatment and a high degree of overlap when examining the lists of genes that are induced when D. suzukii is treated with three commonly used insecticides. Based on our results, we conclude that there is a substantial risk of insecticide resistance and cross-resistance development in D. suzukii in the field.

first: Joanna

middle: C

last: Chiu

first: Gang

last: Hua

first: Michael

middle: J

last: Adang

first: Ashfaq

middle: A

last: Sial


title: Microarray analysis of PIN lesions from APT121 mouse prostate

status: Public on Sep 09 2016

city: Austin

first: James

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

summary: High grade prostate intraepithelial neoplasia (HGPIN) is a precursor lesion for prostate cancer. The APT121 mouse is a model of early stage prostate cancer that develops PIN lesions that progress to adenocarcinoma over a period of 6 months.  At 12 wks of age APT121 mouse prostate contains mostly high grade PIN lesions.  We compared the transcript profile of RNA from the anterior prostate of age- and genetic background matched wild type and APT121 mice using Affymetric microarrays.

overall_design: Wild-type and APT121 mice were fed semi-purified AIN93G diets from weaning to 12 wks of age. Their genetics is a mixed C57BL/6J and DBA/2 background (F3 generation). 8 APT121 mice and 16 wild type mice were used. At 12 wks of age mice were killed and the anterior prostate was harvested directly into liquid nitrogen.RNA was isolated using the SV Total RNA isolation kit (Promega); prostates were crushed under liquid nitrogen and added to the kit lysis buffer to prevent RNA degradation. Genomic DNA was removed by digestion with RNAase free DNAse and RNA was repurified with the RNAeasy mini kit. After quantification, equal amounts of RNA from two mice were pooled to make 4 pooled APT121 and 8 pooled wild type samples. Profiling was done using the GeneChip Mouse Gene 1.0 ST array (affymetrix). Data from the 12 chips was normalized with RMA. Differential expression was determined using Significance Analysis for Microarrays (SAM) at 5% FDR.  Functional analysis was determined using GeneGo/Metacore.


title: Expression data of HepG2 cells treated with AP000770.1-1 siRNAs

status: Public on Sep 06 2016

city: Yuzhong distict

first: Li

last: Chuanwei

state: Chongqing

address: Changjiang road 10th

department: Department of cardiology

country: China

institute: The third military university

summary:
In our study, we found the expression of the novel long coding RNA (AP000770.1-1) was positively associated with cholesterol levels in human samples and HepG2 cells.
The Affymetrix GeneChip Human Gene 1.0 ST Array were used to analyze the expression profile of mRNAs in l AP000770.1-1 knockdown HepG2 cells and control by siRNA methods.

overall_design: Human hepatocellular carcinoma cell lines (HepG2) were purchased from the Institute of Biochemistry and Cell Biology of the Chinese Academy of Sciences (Shanghai, China). The cells were cultured in Dulbecco's Modified Eagle Medium (DMEM，Gibco, U.S. ), supplemented with 10% fetal bovine serum (FBS, Gibco, U.S.) as well as 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen , U.S.) and maintained at 37°C with 5% CO2. For transient transfections, cells were plated at 1 × 10^5 cells ml−1 for 24 hours  before transfection  with antibiotic free medium. Transfections (50 nM) were conducted with siRNA (targeting pool) against AP000770.1-1 (GenePharma, China) or nontargeting controls (GenePharma, China) according to the manufacturer’s protocol for 48 hours.


title: Gene expression analysis reveals the concurrent activation of pro-apoptotic and antioxidant-defensive mechanisms in Flavokawain B and FIH-treated cervical cancer HeLa cells

status: Public on Sep 15 2016

city: Serdang

first: Nadiah

last: Abu

state: Selangor

address: Animal Tissue Culture Lab

department: Faculty of Biotechnology

country: Malaysia

institute: Universiti Putra Malaysia

summary: To examine the difference in gene expression of HeLa cells after 48 hours of treatment with 7 µg/mL FKB and 15 µg/mL FIH after 48 hours

overall_design: 3 sets of sample were prepared; the untreated HeLa cells, 7 µg/mL FKB-treated HeLa cells after 48 hours, 15 µg/mL of FIH-treated HeLa cells after 48 hours

first: Abu

last: Nadiah


title: Expression profiles of the aquatic midge larvae (Chironomus tentans) under the sublethal-dose of chlopyrifos and atrazine exposure

status: Public on Sep 29 2016

city: Stoneville

first: JIANXIU

last: YAO

state: Mississippi

address: 141 Experiment station Rd

institute: USDA-ARS

summary: The aquatic midge, Chironomus tentans, is a keystone species in aquatic ecosystem and used as a model organism to assess chemicals toxicity in aquatic environment. To characterize midge’s cellular and molecular responses to pesticides, we established cDNA library with 10,000 cDNA elements representing 2,456 C. tentans unique genes. Blast2go identified 49 genes potentially involved in xenobiotics metabolism, including 24 cytochrome p450s (CYPs), 14 esterases (ESTs) and 11 glutathione-s-transferases (GSTs). Based on 2,456 unique genes, a cDNA microarray was developed to monitor gene expression profiles in 4th instar larvae under chlopyrifos (0.1 µg/L and 0.5 µg/L) and 1000 µg/L atrazine 48-hr exposure. We identified 149, 435 and 244 genes were significantly differentially expressed (p-value ≤0.05 with expression ratios ≥2.0) after 0.1 µg/L, 0.5 µg/L chlopyrifos, and 1000 µg/L atrazine application, respectively. Sixteen insect detoxification genes (11 CYPs, 3 GSTs and 2 esterases) were validated by qPCR and their expressions were significantly either up- or down-regulated under chlorpyrifos and atrazine exposure, especially the expression of 10 CYPs were significantly induced after chlopyrifos and atrazine exposure. The up-regulated CYPs might be involved in xenobiotic activation and/or degradation. Furthermore, we also found 5 differentially expressed hemoglobin genes. The expression changes of hemoglobins might be an adaption mechanism of C. tentans to hypoxic condition caused by xenobiotic exposure. This study provides a platform for further functional studies of pesticide-insect interactions in C. tentans.

overall_design: Chironmous tentans 4th instar larvae were exposed to chlopyrifos (0.1 µg/L and 0.5 µg/L) and 1000 µg/L atrazine 48-hr, respectively. The gene expression of whole body after exposure were monitored by custome designed cDNA microarray. Four independent experiments were performed using five insect whole body samples.

first: Guanghui

last: Tang

first: Jianxiu

last: Yao

first: Kun

middle: Y

last: Zhu


title: Widespread shortening of 3’ untranslated regions and increased exon inclusion characterize the human macrophage response to infection [miRNA]

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Changes in gene regulation have long been known to play important roles in both innate and adaptive immune responses. However, post-transcriptional mechanisms involved in mRNA processing have been poorly studied despite emerging examples of their role as regulators of immune defenses. We sought to investigate the role of mRNA processing in the cellular responses of human macrophages to live bacterial infections.

overall_design: miRNAs profiles for infected and non-infected samples at multiple time points.

first: Athma

last: Pai

first: Golshid

last: Baharian

first: Ariane

last: Pagé Sabourin

first: Yohann

last: Nédélec

first: Jean-Christophe

last: Grenier

first: Katherine

last: Siddle

first: Anne

last: Dumaine

first: Vania

last: Yotova

first: Christopher

middle: B

last: Burge


title: Genetic ancestry and natural selection drive population differences in immune responses to pathogens in humans

summary: Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. 12% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 569 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting eQTL. Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are central to coping with infection.

overall_design: Transcriptomic profiles of 503 infected (Listeria and Salmonella) and non-infected samples at 2hr time point.

first: Joaquin

last: Sanz-Remon

first: Aaron

last: Sams

first: Alain

last: Pacis

first: Steven

last: Hebert

first: Roger

last: Pique-Regi

first: Ran

last: Bleckman

first: Jenny

last: Tung


title: Widespread shortening of 3’ untranslated regions and increased exon inclusion characterize the human macrophage response to infection [mRNA]

first: Luis

last: Barreiro

overall_design: Transcriptomic profiles of 198 infected (Listeria and Salmonella) and non-infected samples at multiple time points.


title: Transcriptome profiling of 15 conditions for Escherichia coli selected from optimal experiment design, and targeted experimentation to increase functional coverage in omics dataset

status: Public on Sep 03 2016

city: davis

first: Ilias

last: Tagkopoulos

state: CALIFORNIA

address: 2063 kemper hall, 1 shields avenue

institute: university of california at davis

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

overall_design: Refer to individual Series


title: Foxo3 drives pathogenic Th1 differentiation

status: Public on Sep 01 2016

city: Toulouse

middle: S

last: Dejean

state: Haute-Garonne

address: Hopital Purpan

country: France

institute: INSERM

summary:
We showed that the transcription factor Foxo3 played a specific role in the polarization of CD4+ T cells towards pathogenic Th1 cells producing both interferon-γ (IFN-γ) and granulocyte monocyte colony stimulating factor (GM-CSF).
To understand the molecular mechanisms whereby Foxo3 controls CD4+ T cell differentiation, unbiased analysis of genes differentially expressed in Foxo3-deficient vs. Foxo3-sufficient CD4+ T cells was achieved using both resting and activated CD4+ T cells obtained following 12 or 24 hours of stimulation with anti-CD3 mAbs.

overall_design: Gene expression analysis were performed on purified naive CD4+ T cells from Foxo3-/- (n=4) or WT (n=4) littremate controls either unstimulated (T0) or stimulated with 2 μg/ml of anti-CD3 mAbs for 12 (T12) or 24 (T24) hours

first: Caroline

last: Stienne

first: Michaël

middle: F

last: Michieletto

first: Yannick

last: LIPPI


title: Transcriptomes of FA1090,, FA1090cpxA::kan, FA1090cpxR::erm mutant strains of Neisseria gonorrhoeae in late log phase

city: Indianapolis

first: Dharanesh

last: Gangaiah

state: Indiana

address: 635 Barnhill drive, MS 420

department: Department of Microbiology and Immunology

institute: Indiana University School of Medicine

summary: To better understand the role of Neisseria gonorrhoeae CpxRA in controlling virulence determinants, here we defined genes potentially regulated by CpxRA by using RNA-Seq. We identified approximately 139 genes differentially expressed between cpxA (Cpx system active) and cpxR (Cpx system inactive) mutants. A large number of the differentially expressed genes encode envelope-localized proteins.

overall_design: RNA of Neisseria gonorrhoeae wildtype, cpxA and cpxR mutants were collected at late log phase of growth, in quadruplicate.

first: Stanley

middle: M

last: Spinola


title: Transcriptome Sequencing and Assembly of Canna indica Flower

city: Guangzhou

first: Xueyi

last: Tian

state: Guangdong

address: No.723, Xingke Road, Tianhe District

institute: South China Botanical Garden, CAS

summary: Canna indica L. is an ornamental plant with petaloid staminodes and only a half fertile stamen in its flowers. The genetic basis for petaloid androecium remains unclear. In order to get comprehensive transcriptome data for further studies, RNA-Seq analysis were carried out. Two libraries from flower primordia and differentiated flowers of Canna indica were constructed and sequenced respectively, and totally 118,869 unigenes were assembled. The unigenes were aligned to the protein databases NR, NT, Swiss-Prot, KEGG, COG and GO (e-value<0.00001), and totally 67,299 unigenes were annotated. Our data constitute a preliminary basis for further studies on flower development of Canna indica.

overall_design: The two samples from flower primordium and differentiated flower were sequenced for transcriptome assembly, and gene expression information of the two stages was also obtained from these data.

first: Huanfang

last: Liu

first: Jingping

last: Liao


title: Expression profile from murine acute myeloid leukemia cells C1498 with or without PARP-1 inhibition

status: Public on Aug 31 2016

city: Jinan

first: Lingbo

last: Wang

address: No.107, Wen Hua Xi Road

institute: Qilu Hospital of Shandong University

summary:
Poly(ADP-ribose) polymerase 1 (PARP-1) is abnormally expressed in a wide variety of tumors. Emerging evidence suggests that PARP-1 plays key roles in multiple biologic behaviors of tumors, such as modulation of chromatin structure, regulation of gene transcription, tumor proliferation, apoptosis, and angiogenesis, by acting on different molecular pathways. PARP-1 inhibition can achieve a beneficial outcome in tumor treatment. But the specific mechanism of PARP-1 in acute myeloid leukemia (AML) is still to be discovered.
We used microarrays to detail the global gene expression in C1498 with and without PARP-1 inhibition and profile differentially expressed genes that might be involved in PARP-1 regulation in AML.

overall_design: Murine acute myeloid leukemia cells C1498 was from ATCC and cultured in complete Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were treated with 20μM PARP-1 inhibitor PJ34 or control PBS for 48 h. Then total RNA was extraction and hybridization on Affymetrix microarrays. Each sample was conducted in triplicate.

first: Mingxiang

last: Zhang

first: Chunyan

last: Ji


title: Widespread shortening of 3' untranslated regions and increased exon inclusion characterize the human macrophage response to infection


title: Ｇene expression profiles of skeletal musucles in response to GDE5 overexpression

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

summary: Transcriptional profiling of mouse skeletal muscles. The objective of this study is to explore gene expression profiles of skeletal muscles in response to GDE5 overexpression by DNA microarray data analysis.

overall_design: C57BL/6 mice: GDE5 transgenic mice

first: Noriyuki

last: Yanaka

first: Yuri

last: Okazaki


title: Dynamics of chromatin maturation after genome replication

status: Public on Aug 25 2016

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

institute: CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Replication of the eukaryotic genome occurs in the context of chromatin, a nucleoprotein packaging state consisting of repeating nucleosomes. Chromatin is commonly thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture that occur during genomic replication. Here, we sought to directly measure a key aspect of chromatin structure dynamics during replication – how rapidly nucleosome positions are established on the newly-replicated daughter genomes. By isolating newly-synthesized DNA marked with the nucleotide analogue EdU, we characterize nucleosome positions on both daughter genomes of budding yeast during a time course of chromatin maturation. We find that nucleosomes rapidly adopt their mid log positions at highly-transcribed genes, and that this process was impaired upon treatment with the transcription inhibitor thiolutin, consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in the Hir1Δ background reveal a role for HIR in nucleosome spacing. Using strand-specific EdU libraries, we characterize nucleosome positions on the leading and lagging strand daughter genomes, uncovering differences in chromatin maturation dynamics between the two daughter genomes at hundreds of genes. Our data define the maturation dynamics of newly-replicated chromatin, and support a role for transcription in sculpting the chromatin template.

overall_design: We have mapped changes in nucleosome positions on newly replicated DNA in a timecourse after genome replication. We have used Micrococcal Nuclease footprinting of cross linked chromatin to determine nucleosome positions and EdU (ethylene deoxy uridine) to mark nascent DNA strands. EdU incorporated into nascent DNA strands was biotinylated with Click chemistry and nascent DNA strand fragments were subsequently isolated using Streptavidin coated magnetic beads.

first: Pauline

last: Vasseur

first: Saphia

last: Tonazzini

first: Rahima

last: Ziane

first: Alain

last: Camsses

first: Oliver

last: Rando


title: Affymetrix SNP array data for NSCLC samples

city: Uppsala

first: Patrick

last: Micke

address: Rudbeck laboratory

country: Sweden

institute: Uppsala University

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

summary:
Non-small cell lung cancer (NSCLC) presents a notoriously genomically unstable cancer type, with numerous large scale and focal genomic aberrations resulting in gene copy number variations across the whole genome. The relations of these gene copy number changes to subsequent mRNA levels are only fragmentarily understood. The aim of this study was an integrated analysis of gene copy number changes and corresponding gene expression in a large clinically annotated NSCLC patient cohort. Fresh frozen tumor sample from 190 resected NSCLC patients were subjected to SNP arrays and gene expression array analysis resulting 39788 tested copy number/ RNA expression pairs. Correlation analysis using an externally centered correlation coefficient (ECCC) revealed that gene expression of 19058 genes was significantly influenced by gene copy number changes (FDR < 0.05). However, only 440 probe sets demonstrated high correlations (ECCC > 0.7) that were mostly due to few cases with high gene copy number gains. These gene copy number dependent genes were clustered in only few chromosomal hot spot regions and classical oncogenes (e.g. EGFR, MDM2, KRAS) are overrepresented among these genes. In a meta-analysis, including 1585 NSCLC patients, gene expression levels from 70 of 440 (16%) gene-copy-number-dependent genes were associated with survival.
In conclusion, the genome-wide analysis indicates that gene copy number aberrations influence directly gene expression levels in a distinct subset of genes. The concrete illustration of these molecular relations help to interpret the impact of gene copy number changes and may serve as starting points to identify new cancer drivers in NSCLC.

overall_design:
Affymetrix Gene Chip Human Mapping 250K Nsp I arrays wer performed according to the manufacturer's directions with genomic DNA extracted from fresh frozen lung cancer tissue.
Copy number analysis of Affymetrix 250 K arrays was performed on DNA from 190 NSCLC patients. These data sets belongs to the previous described cohort of 100 cases (Micke et al. 2011, GSE28582). Thus altogether the cohort used in the comprehensive gene copy number analysis comprised 190 patients.

first: Johan

last: Botling

first: Verena

last: Jabs

first: Helena

last: König

first: Karolina

last: Edlund

first: Birte

last: Hellwig

first: Marianna

last: Grinberg

first: Katrin

last: Madjar

first: Jörg

last: Rahnenführer

first: Simon

last: Ekman

first: Michael

last: Bergkvist

first: Katja

last: Ickstadt

first: Jan

middle: G

last: Hengstler


title: Transcriptome Analysis of floral organ in Canna indica by RNA-Seq

first: Xueyi

last: Tian

summary: In Canna indica L, 3-4 (occasionally 5) petaloid staminodes and a one-theca stamen with a petaloid appendage constitute the androecium. In order to find out the genetic basis of petaloid development of androecium members, RNA-Seq analysis of petal (P),  petaloid staminode (PS), anther (A) and petaloid appendage (PA) were carried out.

overall_design: P-PS comparison was carried out to find the differences between the two kinds of petal-like organ, and A-PA comparison was conducted to reveal the mechanism for the differentiation of these two parts within stamen.

first: Huanfang

last: Liu

first: Jingping

last: Liao


title: Gene expression profiling of infrequently and frequently dividing cells in the mouse epidermis

city: Kumamoto

first: Aiko

last: Sada

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: International Research Center for Medical Sciences (IRCMS)

institute: Kumamoto University

summary: Infrequently (LRCs) and frequently (non-LRCs) dividing cells in the mouse epidermis are moleculary distinct.

overall_design: Fluorescence activated cell sorting (FACS) from back skin cells of quadruple-transgenic mice harboring K5-tTA, pTRE-H2B-GFP, K14-CreER and Rosa-tdTomato transgenes.

first: Tudorita

last: Tumbar


title: Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy

status: Public on Aug 15 2016

city: Chuncheon

first: Bong-seok

last: Jo

address: Kangwon university street 1

country: South Korea

institute: Kangwon national university

type:
Expression profiling by array
Methylation profiling by array


title: Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus

city: Guiyang

first: zuo-yi

state: Guizhou

address: Jinzhu road

department: Guizhou academy of Agricultural Sciences

institute: Aspergillus cristatus

summary: The purpose of this study is to find the differently expressed genes in Aspergillus cristatus at different osmotic pressure.

overall_design: Examination of 3 transcriptomes in different osmotic pressure to find their different gene expression style.

first: Yongyi

last: Ge

first: Zuoyi


title: Dynamics of nucleosome positioning maturation following genomic replication

first: Marta

last: Radman-Livaja

summary: Replication of the eukaryotic genome occurs in the context of chromatin, a nucleoprotein packaging state consisting of repeating nucleosomes. Chromatin is commonly thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture that occur during genomic replication. Here, we sought to directly measure a key aspect of chromatin structure dynamics during replication – how rapidly nucleosome positions are established on the newly-replicated daughter genomes. By isolating newly-synthesized DNA marked with the nucleotide analogue EdU, we characterize nucleosome positions on both daughter genomes of budding yeast during a time course of chromatin maturation. We find that nucleosomes rapidly adopt their mid log positions at highly-transcribed genes, and that this process was impaired upon treatment with the transcription inhibitor thiolutin, consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in the Hir1-delta background reveal a role for HIR in nucleosome spacing. Using strand-specific EdU libraries, we characterize nucleosome positions on the leading and lagging strand daughter genomes, uncovering differences in chromatin maturation dynamics between the two daughter genomes at hundreds of genes. Our data define the maturation dynamics of newly-replicated chromatin, and support a role for transcription in sculpting the chromatin template.

overall_design: Gene expression array.

first: Pauline

last: Vasseur

first: Saphia

last: Tonazzini

first: Rahima

last: Ziane

first: Alain

last: Camasses

first: Oliver

last: Rando


title: TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene

city: New Orleans

first: HUA

last: LU

state: LA

address: 1430 Tulane Ave

department: Biochemistry and Molecular Biology

institute: TULANE UNIVERSITY

summary:
Investigation of whole genome gene expression level changes in human colon cancer cell lines in response to p53 activation by Inauhzin (INZ), and identification of novel p53 target genes.
Part of the data has been described in our publication: Liao, J. M., Zeng, S. X., Zhou, X. & Lu, H. Global effect of inauhzin on human p53-responsive transcriptome. PloS one 7, e52172, doi:10.1371/journal.pone.0052172 (2012).

overall_design: HCT116 p53+/+ and HCT116 p53-/- cells were treated with DMSO or 4μM INZ and harvested at 18 hours post treatment. Cells were then homogenized in TriZol reagents. Triplicates were included for each sample. Total RNA was extracted by following the manufacturer’s standard instructions (Invitrogen).

first: J

first: H

last: Lu


title: Murine Pancreatic Cancer Cells: KLF10 wild type vs KLF10 knockout

status: Public on Aug 22 2016

city: Chiayi

first: Weng

middle: Ching

last: Chieh

address: No.168, Sec. 1, University Rd., Minhsiung

department: Department of Biomedical Sciences

country: Taiwan

institute: National Chung Cheng University

summary: Transcriptional profiling of mouse pancreatic cancer cells comparing Pdx-1Cre LSL-KrasG12D P53L/L cells with Pdx-1Cre LSL-KrasG12D KLF10L/L P53L/L cells, and to determine the effects of KLF10 deficiency on murine PDAC gene expression.

overall_design: Two-condition experiment, Pdx-1Cre LSL-KrasG12D P53L/L cells vs. Pdx-1Cre LSL-KrasG12D KLF10L/L P53L/L cells: 3 KLF10 wild type replicates, 3 KLF10 knockout replicates.

first: Ching-Chieh

last: Weng

first: Kuang-Hung

last: Cheng

first: Li-Tzong

last: Chen


title: Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy (mRNA)

first: Bong-seok

summary: Alterations in DNA methylation and gene expression have been implicated in the development of human dilated cardiomyopathy (DCM). In this study, we analyzed DNA methylomes (Infinium 450K HumanMethylation BeadChip) and transcriptomes (Infinium HT-12 v4) to characterize differentially methylated probes (DMPs) and differentially expressed genes (DEGs) between the left and right ventricles of human DCM.

overall_design: Illumina 450K array and HT-12 v4 array for the left, right ventricles

first: Bong-Seok

first: In-Uk

last: Koh

first: Jae-Bum

last: Bae

first: Ho-Yeong

last: Yu

first: Eun-Seok

last: Jeon

first: Hae-Young

last: Lee

first: Jae-Joong

last: Kim

first: Murim

last: Choi

first: Sun-Shim


title: Gene expression analysis of human haploid cells (HAP1) depleted of SMARCB1 and SMARCA4

city: stanford

first: Rajat

last: Rohatgi

state: California

address: 279 campus drive

department: Biochemistry

institute: Stanford University School of Medicine

summary: The aim of this study is to analyze the change in genome wide expression levels in HAP1 cells upon loss of SMARCB1, SMARCA4 or both these genes together.  The SMARCB1 and SMARCA4 genes were the hits from a genome wide screen involving genetrap mutagenesis to find new players that are involved in sensitivity to Doxorubicin (Dox). It was found that loss of SMARCB1 and SMARCA4 genes impart resistance in HAP1 cells to Dox. To validate this, the genes were knocked out in HAP1 cells with CRISPR-Cas9 technology. Gene expression levels in SMARCB1 null, SMARCA4 null and SMARCB1-SMARCA4 double null cells were compared to wildtype HAP1 cells using RNAseq. From these experiments it was found that SMARCB1 loss caused several fold increase in ABCB1 gene levels. ABCB1 is an efflux pump in cells responsible for flushing out many small-molecule drugs. Further analysis of this gene confirmed that ABCB1 was the main factor responsible for Dox resistance upon SMARCB1 loss.

overall_design: In total there are four different cell types with two replicates for each cell type. Therefore, 8 samples in total.

first: Ramin

last: Dubey

first: Andres

last: Lebensohn

first: Zahra

last: Bahrami-Nejad

first: Caleb

last: Marceau

first: Branimir

middle: I

last: Sikic

first: Jan

last: Carette


title: Gene expression profile for SMYD3 knockdown in esophageal squamous carcinoma cell

status: Public on Aug 11 2016

city: shantou

first: Enmin

last: Li

state: guangdong

address: 22 Xinling Road

institute: Shantou university, medical college

summary:
SET (Su) and MYND (myeloid-Nervy-DEAF-1) domain-containing protein (SMYD) is a methyltransferase family, including five members of which SMYD1, SMYD2, SMYD3 and SMYD4, has been found to play critical roles in human carcinogenesis. It has been demonstrated that the altered expression of SMYD3 is associated with the progression of several solid tumors, including bladder cancer, glioma, gastric cancer, prostate cancer and colorectal cancer. Several trials have explored the effects of SMYD3 overexpression on proliferation, viability, cancer cells migration and invasion. The series of elegant experiments suggested that SMYD3 could serve as a potential biomarker for clinically aggressive disease and an attractive therapeutic target.
In our previous study (PMID: 26980013), we found SMYD3 expression is frequently upregulated in human esophageal squamous cell carcinoma (ESCC) clinical tissues, correlating with overall survival of ESCC patients. RNAi-mediated knockdown of SMYD3 suppressed ESCC cell proliferation, migration and invasion in vitro, and inhibited local tumor invasion in vivo. To  identify genes and biological pathways associated with SMYD3 functions and mechanism, SMYD3 was knockdowned bypGLV3/H1/GFP/+Puro Vector in ESCC cell line KYSE150 with an empty plasmid as a control, these two cells were applied for mRNA expression profile analyses to find the differentially expressed genes using GeneChip® PrimeView™ Human Gene Expression Array.

overall_design: shRNA sequences targeting SMYD3 was ligated into the pGLV3/H1/GFP/+Puro Vector and transfected into ESCC cell line KYSE150 with an empty plasmid as a control. The mRNA expression profiles of SMYD3 knockdown was analyzed by GeneChip® PrimeView™ Human Gene Expression Array (Affymetrix, USA). The knockdown of SMYD3 was confirmed by QRT-PCR and Western blot. Total RNAs from SMYD3 knockdown cells and control cells were extracted for GeneChip® PrimeView™ Human Gene Expression Array.

first: Ying

last: Zhu

first: Mengxiao

first: Bingli

last: Wu

first: Liyan

last: Xu


title: An arginine sensing pathway in Leishmania induces a Mitogen-Activated Protein Kinase 2-mediated response during macrophage invasion

status: Public on Aug 01 2016

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: Protozoa of the genus Leishmania are the causative agents of leishmaniasis in humans. These parasites cycle between promastigotes in the sand fly mid-gut and amastigotes in phagolysosome of mammalian macrophages. During infection, host up-regulate nitric oxide synthase and parasite induce host arginase expression, both of which use arginine as a substrate. These elevated activities deplete macrophage arginine pools, a situation that invading Leishmania must overcome since it is an essential amino acid. Leishmania donovani imports exogenous arginine via a mono-specific amino acid transporter (AAP3) and utilizes it primarily through the polyamine pathway to provide precursors for trypanothione biosynthesis.  Here we report the discovery of a pathway whereby promastigote and amastigote forms of the Leishmania sense the lack of environmental arginine and respond with rapid up-regulation in AAP3 expression and activity, as well as several other transporters. Significantly, this arginine deprivation response is also activated in parasites during macrophage infection. Phosphoproteomic analyses of L. donovani promastigotes have implicated a Mitogen-Activated Protein Kinase 2 (MPK2)-mediated signaling cascade in this response and L. mexicana mutants lacking MPK2 are unable to respond to arginine deprivation. In this study, we established that Leishmania cells sense the absence of arginine in their environment; both in culture (axenic promastigotes and amastigotes) and in macrophages during infection (amastigotes). This study describes the first amino acid deprivation sensing mechanism and the pathway that transduce this response, and reveals a novel host-pathogen metabolic interplay.

overall_design: Total RNA from Ten Leishmania donovani samples were analyzed using RNA-Seq. Cells from two life stages (promastigotes and amastigotes) were grown in axenic culture in the presence and absense of arginine. For each condition two biological replicates were grown and analyzed. In addition two macrophage grown amastigotes were analyzed.

first: Adele

last: Goldman-Pinkovich

first: Caitlin

last: Balno

first: Rona

last: Strasser

first: Michal

last: Zeituni-Molad

first: Keren

last: Bendelak

first: Doris

last: Rentsch

first: Moshe

last: Ephros

first: Martin

last: Wiese

first: Armando

last: Jardim

first: Peter

last: Myler

first: Dan

last: Zilberstein


title: Study of microbial functional structure in Xiangjiang River sediment

status: Public on Aug 02 2016

city: Changsha

first: Shiqi

last: Jie

state: Hunan

address: Lushan South Road 932

institute: Central South University

summary: Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Three groups of samples, A, B and C. Every group has 3 replicates.

first: Jie

last: Shiqi

first: Zhu

last: Jianyu


title: Comparative analysis of gene expression in HAT4-nulls and HAT2-heterozygous knockout cells, versus wild type Leishmania donovani cells

status: Public on Jul 31 2016

city: New Delhi

first: Swati

last: Saha

state: Delhi

address: Benito Juarez Raod

department: Microbiology

country: India

institute: University of Delhi

summary: Histone acetylations are known to impact gene transcription. Here, we have attempted to examine the role of Leishmania donovani histone acetyltransferases HAT4 and HAT2 in regulating global gene expression. The transcriptome of HAT4-null promastigotes (Samples 2A, 2B) and HAT2-heterozygous knockout promastigotes (Samples 3A, 3B) have been compared with the transcriptome of wild-type Leishmania promastigotes (Samples 1A, 1B) and fold change in gene expression with respect to the control wild-type has been determined.

overall_design: DNA microarray analysis was carried out with biological replicates, using RNA isolated from logarithmically growing promastigotes in two separate experiments. Bioanalyzer profiles of the isolated RNA samples were used to assess purity and integrity of the isolated RNA. Samples 1A and 1B: analyses carried out using RNA isolated from wild-type Leishmania donovani promastigotes. Samples 2A and 2B: analyses carried out using RNA isolated from HAT4-null promastigotes. Samples 3A and 3B: analyses carried out using RNA isolated from HAT2-heterozygous knockout promastigotes.

first: Aarti

last: Yadav

first: Udita

last: Chandra


title: Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy (methylation)

first: Bong-seok

last: Jo

summary: Alterations in DNA methylation and gene expression have been implicated in the development of human dilated cardiomyopathy (DCM). In this study, we analyzed DNA methylomes (Infinium 450K HumanMethylation BeadChip) and characterize differentially methylated probes between the left and right ventricles

first: Bong-Seok

first: In-Uk

last: Koh

first: Jae-Bum

last: Bae

first: Ho-Yeong

last: Yu

first: Eun-Seok

last: Jeon

first: Hae-Young

last: Lee

first: Jae-Joong

last: Kim

first: Murim

last: Choi

first: Sun-Shim


title: SMAD2/3 mediated transcripts in A549 cells

status: Public on Aug 10 2016

first: Mengfeng

last: Li

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

institute: Sun Yat-sen University

summary: This experiment is designed to evaluate gene expression alteration following silencing SMAD2/3 and overexpressing CCT6A in A549 lung cancer cells.

overall_design: Total RNA were extraced from indicated stable cell lines treated with or with out TGF-β

first: Zhe

last: Ying

first: Han

last: Tian


title: Lectin-type oxidized LDL receptor 1 defines population of polymorphonuclear myeloid-derived suppressor cells in cancer patients

status: Public on Jul 22 2016

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) are important regulators of immune responses and promoters of tumor progression in cancer1,2. The heterogeneity of these cells as well as their distinction from neutrophils hampers the progress in understanding of the biology and clinical significance of these cells. PMN-MDSC had a distinct gene signature from neutrophils isolated from the same patients with most prominent changes in genes associated with endoplasmic reticulum (ER) stress response. Surprisingly, low-density lipoprotein (LDL) was one of the most enriched gene regulators and oxidized LDL receptor 1 (OLR1) was one of the most overexpressed genes in PMN-MDSC. Lectin-type oxidized LDL receptor 1 (LOX-1) encoded by OLR1 was expressed in only 0.7% of neutrophils in peripheral blood of healthy donors, whereas 5-15% of neutrophils in cancer patients and 15-50% of neutrophils in tumor tissues were LOX-1+. In contrast to their LOX-1- counterparts, LOX-1+ neutrophils had gene signature, biochemical and functional characteristics of PMN-MDSC. Induction of ER stress in neutrophils from healthy donors up-regulated LOX-1 expression and converted these cells to suppressive PMN-MDSC. Thus, PMN-MDSC have distinct gene signature and LOX-1 can define this population of cells, which may provide new insight to the biology and clinical evaluation of these cells.

overall_design: Examination of LOX1+/LOX1- and PMN/MDSC cells in cancer patient samples

first: D

last: Gabrilovich

first: T

last: Condamine


title: Expression data of Brain CD11b+ cells from WT and DP1 knockout mice infected with rJ2.2

status: Public on Jul 23 2016

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

summary: PGD2 is the most abundant prostaglandin in the brain. PGD2/DP1 signaling thus has a mulitple roles in regulating the CNS immune response.

overall_design: We used 4 mice in each group.

first: Stanley

last: Perlman


title: Comparative effect of DON and plant or microbial biotransformation of DON on gene expression of piglets jejunal explants

status: Public on Jul 20 2016

city: Toulouse

first: Alix

last: Pierron

address: 180 chemin de Tournefeuille

institute: INRA

summary: Deoxynivalenol (DON) is a frequent mycotoxin in grains, produced by Fusarium fungi, which demonstre multiple side effects such as modulation of immune responses, reduced feed intake and weight gain or impairment of the intestinal barrier function. Among animal species, pigs are the best model for humans and are very sensitive to DON. In wheat, DON can be conjugated to glucose to form DON-3-β-D-glucoside (D3G). Some bacteria isolated from digestive tracts or soil, are also able to de-epoxydize or epimerize DON to metabolites such as deepoxy-deoxynivalenol (DOM-1) or 3-epi-deoxynivalenol (epi-DON). The toxicity of these DON metabolites is poorly documented. By the way of ingestion, the intestine is the first organ exposed to these molecules and so constitute a relevant model. The aim of this study was to compare the intestinal toxicity of three DON metabolites (D3G, DOM-1 and epi-DON) with the one of DON. Intestinal explants from 6 pigs were treated with 10mM DON, D3G, DOM-1 or epi-DON for 4 hours and transcriptomic analysis was performed using an “Agilent Porcinet 60K”.

overall_design: Jejunal explants from 4 piglets aged of 5 weeks were sampled and exposed in vitro to differents molecules (DON, D3G, DOM-1 & 3-epi-DON) at 10µM during 4h. Then RNA was extracted.

first: Sabria

last: Mimoun

first: Leticia

last: Murate

first: Yannick

last: Lippi

first: Anna-Paula

last: Loureiro-Bracarense

first: Delphine

last: Payros

first: Nicolas

last: Loiseau

first: Laurence

last: Liaubet

first: Gerd

last: Schatmayr

first: Ting

last: Zhou

first: Franz

last: Berthiller

first: Dieter

last: Moll

first: Isabelle

middle: P

last: Oswald


title: Expression data of Brain CD11b+ cells from WT and DP1I knockout mice


title: Quantitative mRNA profile of eif3e (yin6, int6) deleted S. pombe cells

status: Public on Jul 29 2016

city: La Jolla

last: Wolf

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation & Maintenance Program

institute: Sanford-Burnham-Prebys Medical Discovery Institute

summary: Int6/yin6 encodes the eIF3e subunits of the eukaryotic translation initiation factor 3 complex (eIF3). To assess the impact of eIF3e on the global transcriptome, RNA seq of total mRNA was performed.

overall_design: Total RNA was prepared from wildtype S. pombe (h- ura4-D18 leu1-32) and cells deleted for eif3e (int6, yin6, SPBC646.09c;  h- int6::kanMX6 ura4-D18 leu1-32). Following rRNA depletion and library construction, samples were sequenced on the SOLID4 platform. Two replicates were analyzed and statistical analysis was performed to identify significant differences in mRNA levels.

first: Feng

last: Qi

first: Judith

last: Scheliga


title: The gene expression profile of Helicobacter pylori exposed to 0.25μg/ml (2×MIC) Clarithromycin (CLA) stress

status: Public on Jul 19 2016

city: Jinan

first: Yundong

last: Sun

state: Shandong

address: Wenhua xi road NO.44

department: Medicine

institute: Shandong university

summary: Analysis of Helicobacter pylori strain 26695 after 20 minutes of 0.25μg/ml Clarithromycin. Results provide insight into the mechanisms employed by the bacterium that help it adapt to Clarithromycin stress

overall_design: In the study presented here, we compared the gene expression profile between H.pylori without CLA treatment and H.pylori treated with 0.25μg/ml Clarithromycin.


title: Changes in Gene Expression Profiles in Patients with Pulmonary Arterial Hypertension Associated with Scleroderma Treated with Tadalafil

status: Public on Aug 26 2016

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: The study looked at changes in gene expression profiles in subjects with Pulmonary Arterial Hypertension and Scleroderma (PAH-SSc) before and after treatment with Tadalafil. A total of ten subjects were enrolled and various clinical assessments including 6-minute walk tes, cardiac MRI and right heart catheterization were done in addition to gene expression study.

overall_design: An open label study with subjects who have pulmonary arterial hypertension and scleroderma treated with tadalafil and their gene expression profiles were analyzed before and after tadalafil treatment

first: Fei-Ying

last: Cheong

first: Harrison

middle: W

last: Farber


title: Molecular Signatures Underlying Selective Regional Vulnerability to Alzheimer's Disease

status: Public on Aug 19 2016

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration as a result of abnormal neuronal loss. To elucidate the molecular systems associated with AD, we characterized the gene expression changes associated with multiple clinical and neuropathological traits in 1,053 postmortem brain samples across 19 brain regions from 125 persons dying with varying severities of dementia and variable AD-neuropathology severities.

overall_design: 125 human brains were accessed from the Mount Sinai/JJ Peters VA Medical Center Brain Bank (MSBB). This brain resource was assembled after applying stringent inclusion/exclusion criteria and represents the full spectrum of clinical and neuropathological disease severity in the absence of discernable non-AD neuropathology. RNA samples from 19 brain regions isolated from the 125 MSBB specimens were collected and profiled using Affymetrix Genechip microarrays. There were 50 to 60 subjects per brain region with varying degrees of AD pathological abnormalities.

first: Minghui

last: Wang

first: Panos

last: Roussos

first: Katsel

last: Pavel

first: Vahram

last: Haroutunian


title: WT and AUF1 KO satellite cell RNA-sequencing

status: Public on Jul 21 2016

city: NY

first: Devon

last: Chenette

address: 450 East 29 Street

institute: NYU School of Medicine

summary:
Following skeletal muscle injury, muscle stem cells (satellite cells) are activated, proliferate, and differentiate to form myofibers.  We show that mRNA decay protein AUF1 regulates satellite cell function through targeted degradation of specific mRNAs.  AUF1 targets certain mRNAs containing 3  AU-rich elements (AREs) for rapid decay.  Auf1-/- (KO) mice undergo accelerated skeletal muscle wasting with age and impaired muscle repair following injury.  Satellite cell mRNA analysis and regeneration studies demonstrate that auf1-/- satellite cell self-renewal is impaired due to increased stability and overexpression of ARE-mRNAs. Control of ARE-mRNA decay by AUF1 and potentially other ARE-binding proteins represents a mechanism for adult stem cell regulation and is implicated in human muscle wasting diseases.
We report the RNA transcript expression profiles from sorted satellite cells isolated from wild type (WT) and AUF1-null (KO) mice hindlimb muscles

overall_design:
Examination of RNA transcript expression from satellite cells of two genotypes
Please note that mice are bred through a C57BL/6 strain of 129 background.

first: Robert

last: Schneider


title: microRNA-like RNAs exploring and expression profile in plant pathogenic fungus Fusarium oxysporum f. sp. niveum

status: Public on Jul 15 2016

city: Danzhou

first: Hanqing

last: Cong

state: Hainan

address: Baodaoxincun

department: Tropical Crops Genetic Resources Institute

institute: Chinese Academy of Tropical Agricultural Sciences

summary: To explore the presence of milRNA in Fusarium oxysporum f. sp. niveum (Fon) and evaluate their expression at different propagules, two categories of sRNAs were identified from Fon hyphae and microconidia by using illumina sequencing. A total of 650,960 and 561,114 unique sRNAs were obtained from the hyphae and microconidia samples. With a previously constructed pipeline to search for microRNA, we then identified 74 and 56 miRNA-like small RNAs (milRNAs) candidates in hyphae and microconidia based on the short hairpin structure analysis, respectively. Global expression analysis showed an extensively differential expression of sRNAs between two propagules. Altogether, 78 significantly differently expressed milRNAs were identified in two libraries. Target prediction revealed 2 interesting genes involved in trichothecene and necrosis and ethylene-inducing peptide 1 (NEP1) biosynthesis predicted to be down regulated by Fon-miR7696a-3p and Fon-miR6108a. These two milRNAs were further validated by qRT-PCR and showed a well consistency with sequencing. The negative correlation expression levels between these two milRNAs and their targets genes imply that they might play a role in trichothecene and NEP1 biosynthesis, and this negative regulation for toxin related gene expression are more specific in microconidia. The present study provides the firstly large-scale characterization of milRNAs in Fon and the comparison between hyphae and microconidia propagules gives a clue on how milRNAs involves in toxin biosynthesis.

overall_design: microRNA-like RNAs in hyphae and microconidia were identified and compared

first: Fei

last: Qiao


title: Genomic features shaping the landscape of meiotic double-strand break hotspots in maize [ChIP-Seq]

status: Public on Jul 08 2016

city: Ithaca

first: Wojciech

last: Pawlowski

address: Bradfield Hall, Room 403

department: Plant Breeding and Genetics

institute: Cornell University

summary: To generate the double-strand break (DSB) hotspot map in maize, we used a chromatin immunoprecipitation (ChIP) approach, in which chromatin from flowers containing zygotene meiocytes was enriched in fragments associated with RAD51.

overall_design: To identify sites occupied by RAD51, we compared the genomic distribution of RAD51 ChIP-seq reads to (i) Illumina-sequenced meiotic input chromatin that was not subjected to ChIP, (ii) ChIP products generated by using pre-immune IgG, instead of the anti-RAD51 antibody, on meiotic chromatin, and (iii) ChIP products generated using the anti-RAD51 antibody on leaf tissue chromatin. RAD51 ChIP-seq was also performed on the meiotic chromatin of a POOR HOMOLOGOUS SYNAPSIS1 (phs1) mutant.

first: Yan

last: He


title: Genomic features shaping the landscape of meiotic double-strand break hotspots in maize [MNase-Seq]

status: Public on Jul 13 2016

summary: We report the application of next generation sequencing techonology to study nucleosomal occupancy in flowers containing zygotene meiocytes. The results show DSB enrichment in nucleosome depleted regions associated with RAD51

overall_design: To identify distribution characters of nucleosomal occupancy, we compared the genomic distribution of MNase-Seq reads to Illumina-sequenced meiotic input


title: Protective monocytes in cerebral ischemia

first: Josef

last: Anrather

address: 407 East 61st Street

department: BMRI

institute: Weill Cornell Medical College

summary: Stroke is a highly prevalent and devastating disease with limited therapeutic options. Most efforts to develop treatments for stroke have thus far met with limited success in large clinical trials. The brain has an enormous capacity for self-preservation, and elucidating how the brain protects itself may provide novel insights into stroke treatment. Ischemic tolerance (IT), a phenomenon in which application of sub-lethal stress [preconditioning (PC) stimulus; PC] induces a state of tolerance to a subsequent ischemic insult, represents an example of endogenous neuroprotection. IT can be induced in brain by systemic administration of the Toll-like receptor-4 ligand lipopolysaccharide (LPS). Different populations of immune cell could potentially play a role in PC induced by LPS. In particular, monocytes, which are the main target of LPS, can exert a powerful protective effect either directly or by modulating the immune system.

overall_design: C57Bl/6 male mice (8-12 weeks old) were treated with 0.5 mg/kg LPS i.p. (experimental) or saline (control). Twentyfour hours later mice were transcardially perfused with cold PBS and brains were harvested. Brains from 3-4 mice were pooled and enzymatically digested with Liberase DH (Roche Diagnostics) and 50 U/ml DNase I (Worthington Biochemical) at 37°C for 45 min in an orbital shaker at 160 rpm. Mononuclear cells were harvested from digested brains after fractionation over a discontinuous Percoll gradient. Nonspecific binding was blocked by incubation for 10 min at 4 °C with anti–CD16-CD32 antibody (BioLegend, clone 93, 5 ng/μl) and stained with the appropriate antibodies for 15 min at 4 °C. The following antibodies were used for extracellular staining: CD45 (clone 30F-11, 0.5 ng/μl), CD115 (clone AFS98, 0.5 ng/µl), Ly6G (clone 1A8, 2 ng/μl), and Ly6C (clone HK1.4, 0.5 ng/μl). Inflammatory monocytes (CD45highCD115+Ly6ChighLy6G–) were sorted on a FACSVantage cytometer (BD Biosciences) and collected in Trizol LS (Invitrogen).

first: Lidia

last: Garcia-Bonilla


title: Mouse Lewis lung carcinoma cell line treated with single or fractionated ionizing radiation doses nated ionizing radiation doses

status: Public on Jul 07 2016

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

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

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

overall_design: Refer to individual Series


title: miR expression profiles of human miRs in glioma spheres

city: Chicago

first: Shiyuan

last: Cheng

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University

summary: In this study, we performed miRNA profiles analysis of 84, 17, 20, 83, 718, 1123, 528 and 816 glioma spheres compared to normal progenitor sample (16wf) using microarray to evaluate their potential role in regulation of the biological properties of proneural and mesenchymal glioma spheres

overall_design: miRNA profiling analysis of the 9 samples including 8 patient-derived samples including glioma sphere samples (84, 17, 20, 718, 816, 528, 83 and 1123), as well as one normal progenitor sample (16wf).

first: Tianzhi

last: Huang

first: Angel

last: Alvarez

first: Rajendra

last: Pangeni

first: Craig

last: Horbinski

first: Songjian

last: Lu

first: Sung-Hak

last: Kim

first: C

last: James

first: Jeffery

last: Raizer

first: John

last: Kessler

first: Cameron

last: Brenann

first: Erik

last: Sulman

first: Gaetano

last: Finocchiaro

first: Ming

last: Tan

first: Ryo

last: Nishikawa

first: Xinghua

first: Ichiro

last: Nakano

first: Bo

last: Hu

first: Shi-Yuan


title: Replication timing of control and suv4-20h (KO and inducible mutant) cells

status: Public on Jul 01 2016

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

type: Genome variation profiling by genome tiling array

summary: Although histone modifications have been implicated in many DNA-dependent processes, their precise role in DNA replication remains poorly understood. Here, we show that the regulation of histone H4-K20 methylation states, in particular for the trimethylation, is a critical determinant of licensing and time activation of replication origins in mammalian cells.

overall_design: WT cells  versus suv4-20h KO cells, and non-induced cells versus induced cells

first: Julien

last: Brustel

first: Stanimir

last: Dulev

first: Nina

last: Kirstein

first: Fanny

last: Izard

first: Charlotte

last: Grimaud

first: Chrystelle

last: Cayrou

first: Gunnar

last: Schotta

first: Marcel

last: Mechali

first: Giuseppe

last: Baldacci

first: Claude

last: Sardet

first: Nizar

middle: N

last: Batada

first: Aloys

last: Schepers

first: Eric

last: Julien


title: Analysis of the Argonaute 4-associated non-coding RNA in Arabidopsis thaliana sheds novel insights into gene regulation through RNA-directed DNA methylation

city: Granville

first: Phil

middle: Chi Khang

last: Au

state: New South Wales

address: 10/23 Elizabeth Street

country: Australia

institute: CSIRO

summary:
RNA-directed DNA methylation (RdDM) is a de novo DNA methylation mechanism in plants that plays a fundamental role in plant defence against invasive DNA and in maintaining genome stability by silencing transposons and repetitive sequences.
Using nuclear RNA immunoprecipitation, we constructed a highly enriched library and obtained sequences of ncRNAs specifically associated with Argonaute 4 (AGO4), a key component of RNA-directed DNA methylation.
A negative immunoprecipation (IP) library was prepared using IP RNA from tissues that don't express the target protein. A nuclear RNA library was also prepared using nuclei isolated RNA.

overall_design: Three libraries (1X FLAGAGO4 IP, 1X negative IP, 1X nuclear RNA). RNA-IP or nuclear RNA seq cDNA libraries were prepared using the template-switch cDNA library preparation method derived from Zhao et al (2010), and subjected to Illumina GAIIx single end sequencing (100bp)

first: Liz

last: Dennis

first: Ming-Bo

last: Wang


title: Oncoscan for HER2 copy number assessment

city: Hannover

first: Doris

middle: Johanna

last: Steinemann

department: Institute of Human Genetics

country: Germany

institute: Hannover Medical School

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

summary: Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

overall_design: Copy number analysis using Affymetrix Oncoscan arrays was performed for 29 primary breast cancers

first: Jana

last: van Luttikhuizen

first: Matthias

last: Christgen

first: Hans

last: Kreipe


title: Striatal gene expression profile of the YAC 128 mouse

city: London

first: Andrew

last: Pitsilides

address: Royal College Street

department: Comparative Biomedical Sciences

country: United Kingdom

institute: The Royal Veterinary College

summary:
The Yeast Artificial Chomosome (YAC) 128 model of Huntington's disease shows substantial deficits in motor, learning and memory tasks and alterations in its transcriptional profile.
We examined the changes in the transcriptional profile in the YAC 128 mouse model of HD at 6, 12, and 18 weeks

overall_design: Brain striatal tissue from Wild Type and YAC 128 mice were sampled at the three age groups

first: Lesley

last: Jones

first: Zubeyde

last: Bayram-Weston


title: LSD1 promotes castration-resistant prostate cancer progression

status: Public on Jun 30 2016

city: Ann Arbor

first: Armand

last: Bankhead

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: University of Michigan


title: LNCaP LSD1 knockdown and SP-2509 treatment ChIP-seq data

summary: LSD1 (also known as KDM1A) is a histone demethylase and a key regulator of gene expression in embryonic stem cells and cancer.1,2 LSD1 was initially identified as a transcriptional repressor via its demethylation of active histone H3 marks (di-methyl lysine 4 [2MK4]).1  In prostate cancer, specifically, LSD1 also co-localizes with the AR and demethylates repressive 2MK9 histone marks from androgen-responsive AR target genes, facilitating androgen-mediated induction of AR-regulated gene expression and androgen-induced proliferation in androgen-dependent cancers.   We report here that the LSD1 protein is universally upregulated in human CRPC and promotes survival of CRPC cell lines. This effect is explained in part by LSD1-induced activation of cell cycle and embryonic stem cell gene sets—gene sets enriched in transcriptomal studies of lethal human tumors. Importantly, despite the fact that many of these genes are direct LSD1 targets, we did not observe histone methylation changes at the LSD1-bound regions, demonstrating non-canonical histone demethylation-independent mechanisms of gene regulation.   This ChIP-seq dataset included H3K4me2 and H3K9me2 ChIP-seq data for siRNA target against LSD1 and non-targeting control, as well as SP2509 inhibition of LSD1 and mock treatment

overall_design: 4 conditions: siRNA against LSD1, siRNA against luciferase (non-targeting control); SP2509 inhibition of LSD1, mock treatment. There are 2 replicates per condition.

first: Joshi

last: Alumkal

first: Yuliang


title: Iodine-131 Biomarker Identification in the Rat Thyroid Gland

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

institute: Gothenburg university

summary: Introduction  Iodine-131 (131I) is frequently used in nuclear medicine. Unbound or released 131I accumulate in the thyroid gland and may be detrimental to normal thyroid function. The aim of the present study was to identify biomarkers for 131I exposure in rat thyroid tissue and to assess the effect on thyroid function.    Methods   Thirty six male Sprague Dawley rats were i.v. injected with 150 µl saline solution containing 9.0, 88, 170, 260, 340, 760, 1300, or 4700 kBq (group A-H) 131I, or mock-treated with 150 µl saline solution only, and killed at 24 h after injection. Total RNA was extracted from individual thyroid tissue samples thyroids and mRNA levels were determined with the Agilent microarray platform.     Results   Estimated absorbed doses in treatment groups A-H was 0.0058, 0.057, 0.11, 0.17, 0.22, 0.5 Gy, 0.8 Gy, and 3 Gy. Totally, 429 transcripts were identified with a fold change fold change ≥ 1.5 and adjusted p-value ≤ 0.01. A trend with downregulation of thyroid hormone biosynthesis associated genes (e.g. thyroglobulin, thyroid peroxidase, the sodium-iodine symporter) was identified, but only statistically significant after 0.0058 and 0.22 Gy. Three transcripts coding for isoform 1 of the DBP protein showed a pattern with monotonous decrease in downregulation with absorbed dose between 0.0058-0.22 Gy. Changes in Dbp expression were not statistically significant between 0.5-3 Gy. However, a trend with downregulation at 0.5 and 0.8 Gy and upregulation and 3 Gy was identified. Previously, 131I (0.85-17 Gy) and 211At (0.023-32 Gy) exposure resulted in upregulation of Dbp in mice thyroid tissue 24 h after administrations. Additionally, a monotonous decrease in Dbp downregulation has been identified of in mouse kidney tissue at 8 and 12 months after 177Lu-octreotate administrations.     Conclusion  Conclusively, the Dbp gene is a promising candidate biomarker gene for exposure to 131I and possibly other internal radiation emitters. Further studies should be performed to establish how Dbp expression vary with dose-rate, absorbed dose, time after administration, different radiation qualities, and the function of Dbp.

overall_design: Total RNA was isolated from fresh-frozen individual thyroid tissue samples (Sprague Dawley rats). Each sample was run once. Four rats received the same treatment. Control samples (from non-irradiated rats) are included.

first: Johan

last: Spetz

first: Emil

last: Schüler

first: Toshima

middle: Z

last: Parris

first: Britta

last: Langen

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: KSHV LANA upregulates the expression of EGFL7 proteins in BJAB cells

status: Public on Jun 09 2016

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

institute: University of Nevada, Reno

summary: The objective of this study was to determine the effects of LANA on the expressions of the cellular genes.

overall_design: BJAB cells were transduced with lentiviral vector expressing LANA or the control vector, total RNA was extracted for the detection of relative expression of cellular genes in LANA expressing cells.


title: Degree of H4-K20me defines distinct subsets of replication origins in active and silent chromatin domains of mammalian cells

first: Jean-Charles

last: Cadoret

sample_organism:
Homo sapiens
Mus musculus


title: Promoter H3K4 methylation reveals the dynamic reinforcement of activation-induced pathways in human CD4 T cells with differential kinetics in naïve and memory cells (RNA-Seq)

status: Public on Jun 01 2016

first: Ryan

middle: Conrad

last: Thompson

address: 1 Gustave L. Levy Place

department: Charles Bronfman Institute for Personalized Medicine

summary: The epigenetic determinants driving the rapid responses of memory CD4 T cells to antigen are currently an area of active research.  While much has been done to characterize various Th subsets and their associated genome-wide epigenetic patterns, the dynamics of histone modifications during CD4 T cell activation and the differential kinetics of these epigenetic marks between naïve and memory T cells have not been evaluated.  In this study we have detailed the dynamics of genome-wide promoter H3K4me2 and H3K4me3 over a time course during activation of human naïve and memory CD4 T cells.  Our results demonstrate that changes to H3K4 methylation predominantly occur relatively late after activation (120 hours) and reinforce activation-induced upregulation of gene expression affecting multiple pathways important to T cell activation, differentiation, and function.  The dynamics and mapped pathways of H3K4 methylation are distinctly different in memory cells. Memory CD4 have substantially more promoters marked by H3K4me3 alone, and that is influenced by promoter CpG content, reinforcing their more differentiated state.  Our study provides the first data examining genome-wide histone modification dynamics during T cell activation, providing insight into the cross-talk between H3K4 methylation and gene expression, and underscoring the impact of these marks upon key pathways integral to CD4 T cell activation and function.

overall_design: RNA-Seq of naïve and memory CD4 T cells at rest and at 3 time points after activation with anti-CD3/CD28.

first: Sarah

last: LaMere

first: Kiyomi

last: Komori

first: Adam

last: Mark

first: Daniel

middle: R

last: Salomon


title: Genome-wide analysis of uterine natural killer cell gene expression from lean and obese women in early pregnancy

status: Public on Jun 15 2016

city: Vancouver

first: Alexander

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

country: Canada

institute: The University of British Columbia

summary: Analysis of gene expression in uterine natural killer (NK) cells purified from either lean (control) or obese pregnanct women. The studys' aim is to identify differentially expressed genes and pathways in natural killer cells that are affected by maternal obesity. Results provide mechanitic insight into gene pathways altered in the condition of obeisty.

overall_design: Total RNA obtained from immuno-magnetic bead purified natural killer cells from uterine decidual mucosa from 7 to 10 week old pregnancies from 13 lean (BMI 20-24.9) and 11 obese (BMI >30) women. All women were between 19 and 35 years of age. In addition to BMI, blood serum CRP (hsCRP), a measure of inflammation, was measured via ELISA.


title: Analysis of differential gene expression during Bacillus subtilis spore outgrowth in high-salinity environments using RNA sequencing

status: Public on May 09 2016

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Overall, salt stress seemed to slow down the complex molecular reorganization processes (‘ripening’) of outgrowing spores by exerting detrimental effects on vegetative functions such as amino acid metabolism.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: 3 conditions 4 time points

first: Katja

last: Nagler

first: Antonina

middle: O

last: Krawczyk

last: de Jong

first: Kazimierz

last: Madela

first: Tamara

last: Hoffmann

first: Michael

last: Laue

first: Oscar

last: Kuipers

first: Erhard

last: Bremer

first: Ralf

last: Moeller


title: Genomic features shaping the landscape of meiotic double-strand break hotspots in maize

status: Public on Jul 14 2016

first: Wojciech

last: Pawlowski


title: Mkx overexpression effect in C3H10T1/2 cells

status: Public on May 11 2016

city: Bunkyo-ku

first: Ryo

last: Nakamichi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

institute: Tokyo Medical and Dental University

summary: Analysis of C3H10T1/2 cells overexpressing Mkx. This microarray results show that Mkx has the potential ability to promote differentiation to tendon, ligament and annulus fibrosus cells.

overall_design: DNA microarray analysis was performed using Affymetrix mouse genome 430 2.0 array. RNA samples were obtained from C3H10T1/2, C3H10T1/2 overexpressing Venus and C3H10T1/2 overexpressing Venus-Mohawk.

first: R

first: Y

last: Ito

first: H

last: Asahara


title: Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells

first: Ryan

last: Thompson

institute: Icahn School of Medicine at Mount Sinai


title: Metabolite and transcript profiling of VvERF045 OE transgenic lines elucidate the role of this transcription factor in the grapevine ripening physiology

city: San Michele all'Adige

first: Carmen

last: Leida

address: E. Mach, 1

country: Italy

institute: Fondazione E. Mach

summary: We report the transcriptomic profile of L15, a transgenic line overexpressing VvERF045, and the WT as a reference. The main aim is to understand the function of this transcription factor in the  overall plant though the differences in the transcript abundance (RNA-seq)  and metabolite production. Total RNA from L15 and WT was sequenced with an average genome coverage of more than 100X.  Transcripts representing very different biological processes were grouped into ten major categories: protein phosphorilation, wax biosynthesis process, response to andogenous stimulus, cotyledonal vascular tissue/pattern formation, drug transmembrane transport stress, jasmonic acid biosynthesis, response to salt stress, defense response to bacterium, negative regulation. This transcription factor regulates genes involved in many different responses such as drought, sanility and defense suggesting it covers a key role into the plant, moreover into those processes also typical in ripening.

overall_design: Total RNA profile of WT and overexpressing VvERF045 transgenic line were generated by deep sequencing, in triplicate paired end with IlluminaHiSep2000. Each biological replicate is derived from pools from five independent in vitro grapevine plants.

first: Paolo

last: Sonego

first: Claudio

last: Moser


title: Genome-wide maps of Topoisomerase IV binding and cleavage sites in E. coli

status: Public on Apr 21 2016

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

institute: College de France

summary: We report binding of Topoisomerase IV  on the E. coli genome. We report the cleavage sites of Topoisomerase IV on the E. coli genome

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: 7 ChIP-seq samples and 3 NorflIP-seq samples were included.

first: Ludovic

last: le Chat

first: Hafez

last: el Sayyed


title: Gene expression data of mRNA from skeletal muscle sample of pig breed Duroc and Pietrain with malignant hyperthermia syndrome homozygous negative

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: 47,880 probe-sets were screened, in the first part of this study, they were analysed for differential expression between different breeds (Duroc and Pietrain) at adult stage.

overall_design: RNAs of skeletal muscle from Duroc and Pietrain at adult stage were hybridized to Affymetrix Porcine Snowball Array.

first: Klaus

last: Wimmers


title: Master transcription factors in corneal epithelial cells [OVOL2 Knock-down]

status: Public on Apr 11 2016

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

institute: Kyoto Prefectural University of Medicine

summary: In development, embryonic ectoderm differentiates into several lineages including neuroectoderm and surface ectoderm, through the mechanism largely unclear. Here we report that OVOL2 is required for the transcriptional program of corneal epithelium cell(CEC)s, a derivative of surface ectoderm, and it might regulates the differential transcriptional programs between the two lineages. By a functional screening, we identified transcription factors (TFs) maintaining human CECs. OVOL2 was necessary to maintain the transcriptional program in CECs, particularly through repressing expression of mesenchymal genes. OVOL2 combined with several TFs were able to activate the transcriptional program of CECs in fibroblasts, accompanied by induction of chromatin landscape. Moreover, our analysis revealed that neuroectoderm derivatives express some of mesenchymal genes. In fact, OVOL2 alone was able to induce the transcriptional program of CECs in neural progenitor cells (NPCs) through repression of mesenchymal genes as well as activation of epithelial genes. Our data suggest that the difference between the transcriptional programs of surface ectoderm-derivatives and neuroectoderm-derivatives is regulated in part by the reciprocally-repressive mechanism between epithelial and mesenchymal genes that is seen in epithelial-to-mesenchymal transition.

overall_design: OVOL2 knock-down effects in human CEC were detected by microarray analysis

first: Shigeru

last: Kinoshita

first: Shinji

last: Masui


title: Global gene expression in ocular isolates of Escherichia coli with potential to form biofilm

status: Public on Apr 29 2016

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

institute: Centre for Cellular and Molecular biology

summary: The results of this study would unravel the identity of genes that are differentially regulated during biofilm formation and establish whether the differentially regulated genes are related to increased resistance to antimicrobials and or virulence.

overall_design: The results indicate that ocular biofilm E. coli cells differ from non-biofilm E.coli cells in genes related to biofilm formation, cell adhesion, antimicrobial efflux pumping, stationary phase related and virulence exhibition which were all up-regulated. The findings also include upregulation of several genes encoding for toxin production and secretions (sat, yjgK, chpS, chpB and ygjN), pointing towards the virulence behaviour in E. coli L-1216/2013 biofilm cells.

first: S

last: Shivaji

first: K

last: Ranjit

first: G

last: Reddy

first: Sharma

last: Savitri


title: Specific Inflammatory Stimuli Lead to Distinct Platelet Responses in mice and Humans

status: Public on May 13 2016

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

institute: Boston University

summary:
Different inflammatory stimuli contribute to the formation of atherosclerosis. It is hypothesized that although the end result is the same - plaque formation in arterial vessels - the pathogenesis is dependent on the etiology. In particular, platelets will respond differently depending on the inflammatory stimuli and timepoint.
Using a microarray and platelet inflammatory function studies, we identified the transcriptional and functional changes that occur early and late with different inflammatory stimuli.

overall_design: ApoE-/- C57BL/6 mice were left untreated (control) or administered oral P. gingivalis (Pg) or intranasal C. pneumoniae (Cp) for 3 weeks, and sacrificed either 1 day (early timepoint) or 9 weeks (late timepoint) after this 3-week period.  A separate group of animals was fed a Western Diet (WD) for 9 weeks and then sacrificed.  Whole blood samples were collected from each animal into citrate solution and serially centrifuged to produce a pure platelet population.  RNA was extracted and pooled from each experimental group and hybridized to Affymetrix Mouse Gene 1.0 ST microarrays.

first: Lea

last: Beaulieu

first: Jane

middle: E

last: Freedman


title: Master transcription factors in corneal epithelial cells [ATAC-Seq]

overall_design: ATAC-Seq protocol performed on: Human primary CECs; N=4,  6TFs transduced fibroblasts; N=4,  fibroblasts; N=4


title: Master transcription factors in corneal epithelial cells [ChIP-seq]

overall_design: OVOL2 binding sites were detected by ChIP analysis


title: Master transcription factors in corneal epithelial cells [6TFs transduced experimental samples]

overall_design: Human in vivo samples; N=4, 6TFs transduced experimental samples; N=10, OVOL2 transduced experimental samples; N=4


title: Eicosapentaenoic and docosahexaenoic acid - enriched high fat diet delays skeletal muscle degradation in mice

status: Public on May 31 2016

city: Gothenburg

first: Nikulkumar

middle: Kirtilal

last: Soni

state: Vastra Gotaland

address: Kemivagen 10

department: Department of Biology and Biological Engineering

institute: Chalmers University of Technology

summary: Effects of EPA/DHA enriched high fat diets (HFD) compared to HFD-Corn oil after 8 weeks intervention on age/obesity induced skeletal muscle degradation. Results provides novel information on the signalling pathways regulated by EPA and DHA enriched HFD in delaying the onset of muscle degradation in C57Bl/6J mice compared with HFD-Corn oil.

overall_design: Four mice representing each diet group on the basis of body weight, plasma triglyceride and plasma cholesterol levels were selected for RNA isolation and microarray analysis. Total RNA from skeletal muscle of these selected animals was purified using the RNeasy® Plus Universal Mini kit (Qiagen Nordic, Sollentuna, Sweden) by following the manufacturer?s instruction carefully. The extracted RNA was quantified by NanoDrop 2000c UV-Vis Spectrophotometer (Thermo Scientific, USA) and the quality of the RNA was estimated by RNA 6000 Nano LabChip for Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).


title: Expression data 550cGy vs 0cGy KSL

status: Public on Apr 05 2016

city: Los Angeles

first: Xiao

last: Yan

address: 615 Charles E. Young Dr. S

department: Medicine

institute: UCLA

summary: Precise study of HSCs during regeneration has been impeded by the rarity of the HSC population and depletion of phenotypic HSCs early following genotoxic stresses, such as total body irradiation (TBI).  We isolated bone marrow (BM) ckit+sca-1+lin- (KSL) cells, which are enriched for HSCs, from adult C57Bl6 mice before and at several time points following TBI, as a means to map the dynamic molecular response of HSC regeneration.

overall_design: We isolated BM KSL cells and myeloid progenitor cells (c-kit+sca-1-lin- cells) at day +14 after irradiation and compared the gene expression profile of regenerating HSCs versus steady state HSCs (non-irradiated) and committed progenitor cells.


title: LNCaP and C42B LSD1 knockdown microarray gene expression data and C42B androgen (DHT) stimulation microarray gene expression data

first: Armand

last: Bankhead

summary: LSD1 (also known as KDM1A) is a histone demethylase and a key regulator of gene expression in embryonic stem cells and cancer.1,2 LSD1 was initially identified as a transcriptional repressor via its demethylation of active histone H3 marks (di-methyl lysine 4 [2MK4]).1  In prostate cancer, specifically, LSD1 also co-localizes with the AR and demethylates repressive 2MK9 histone marks from androgen-responsive AR target genes, facilitating androgen-mediated induction of AR-regulated gene expression and androgen-induced proliferation in androgen-dependent cancers.3,4  Recently, it was shown that treatment with high doses of androgens (e.g.10-fold higher doses than those required for induction of expression of androgen-activated genes such as PSA) recruits LSD1 and AR to an enhancer within the AR; this AR and LSD1 recruitment represses AR transcription.5 Thus, LSD1 appears to play a role in mediating both the proliferative and repressive phases of the biphasic androgen dose-response curve. For these reasons, we hypothesized that LSD1 might be important for maintenance of AR signaling in castration-resistant prostate cancer (CRPC) tumors. However, in this report, we describe a distinct role of LSD1 as a driver of proliferation and survival of prostate cancer cells, including CRPC cells, irrespective of androgens or even AR expression. Specifically, LSD1 activates expression of cell cycle, mitosis, and embryonic stem cell maintenance pathways that are enriched in lethal prostate cancers – pathways not activated by androgens. Finally, we observe that treatment with a new LSD1 inhibitor potently and specifically suppresses LSD1 function and suppresses CRPC growth and survival in vitro and in vivo. Our data place LSD1 as a key driver of androgen-independent survival in lethal prostate cancers and demonstrate the potential of LSD1-directed therapies in the near-term.

overall_design: The enclosed files are from microarrays experiments after suppressing LSD1 with RNAi or stimulating cells with the androgen agonist dihydrotestosterone (DHT).

first: Joshi

last: Alumkal


title: Master transcription factors in corneal epithelial cells

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

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: microRNA profiling of multiple myeloma bone marrow

city: Bethesda

first: Weixin

last: Wang

state: MD

address: 9000 Rockville Pike

department: DLM/CC

institute: NIH

summary: Bone marrow microenvironment in MM contains a unique miR signature, which is partially present and detectable in the peripheral blood. A subset of miRs (let-7i, miR-106b, miR-15a, and miR16) shows aberrant expression in the precursor lesion of MGUS, while aberrant expression of other miRs (let-7a, miR-15a/b, miR-19b, miR-20a, miR-21, miR-223, and miR-361) is associated with cell proliferation and disease progression.

overall_design: miRNA profiling was performed using Agilent miRNA array platforms with RNAs isolated from the bone marrow supernatant of multiple myeloma.

first: Meghan

last: Corrigan-Cummins

first: Adriana

last: Zingone

first: Irene

last: Ghobrial

first: Ola

last: Landgren

first: Katherine

last: Calvo


title: miRNA profiles in livers with different mass deficits after partial hepatectomy and miR-106b~25 cluster accelerating hepatocyte proliferation in rats

status: Public on Apr 06 2016

city: Hangzhou

first: Zhikun

last: Liu

address: Qingchun Road 79#

institute: Zhejiang University

summary: To query the relationship between miRNA profiles and deficits in liver mass after PH and the miRNAs linked to liver regeneration, we compared the miRNA expression profile after 2/3 PH, a standard procedure that leads to robust DNA synthesis, with that after 1/3 PH, a procedure that causes minimal replication. The patterns and dynamics of miRNA profiles after PH were featured, providing a rich resource of miRNAs underlying mechanisms of liver regeneration.

overall_design: We generated miRNA profiles from normal and remnant livers at 6, 12, 24, and 36 hours after 1/3 or 2/3PH using microarrays. Two or three rats were used at each time.

last: Xu

first: Shusen

last: Zheng


city: New York

first: Ryan

last: Thompson

overall_design: ChIP-Seq for H3K4me2, H3K4me3, and H3K27me3 in naïve and memory CD4 T cells at rest and at 3 time points after activation with anti-CD3/CD28.

first: Sarah

middle: A

last: LaMere

first: Kiyomi

last: Komori

first: Adam

last: Mark

first: Daniel

last: Salomon


title: ChIP-sequencing of prostate cancer cells

status: Public on Mar 29 2016

city: Tampa

first: Nupam

last: Mahajan

state: FL

address: 10902 Magnolia Dr

department: Drug Discovery Program

institute: Moffitt Cancer Center

summary: Chromatin from LNCaP-C4-2B cells was immunoprecipitated using pY88-H4 or IgG antibodies, followed by sequencing of the ChIP-DNA

overall_design: Examination of the distribution of pY88-H4 epigenetic marks in CRPC cell line


title: Expression data in human esophageal squamous carcinoma cell line KYSE150 with LOXL2 delta 72 over-expression

status: Public on Mar 28 2016

city: Shantou

first: Haiying

last: Zou

state: Guangdong

address: 22 Xinling Road

department: Department of Biochemistry and Molecular Biology

institute: Shantou University Medical College

summary:
We have identified a new novel spliced variant of Lysyl Oxidase-like 2 (LOXL2), termed LOXL2 delta72, in human oesophageal carcinoma cells (ESCC). To explore the biological function of this variant, the cDNA microarrays was perform to assess the genes expression induced by its over-expression in ESCC KYSE150.
We used microarrays to detail the global programmed of genes expression when LOXL2 delta72 over-expressed in KYSE150 cells compared with wild-type LOXL2.

overall_design: KYSE 150 cells were transfected with vector, pcDNA3.1 LOXL2 WT or pcDNA3.1 LOXL2 delta72, respectively. After 48 hours transfection, RNA extractions were carried out, and the expressions of LOXL2 were examined by RT-PCR. The samples were sent to perfor hybridization on Affymetrix microarrays.

first: Guoqing

last: Lv


title: Effects of Escherichia coli global gene expression due to microfluidic processing

status: Public on Apr 01 2016

city: Edinburgh

first: Senthil

last: Gandi

address: 49 Little France Crescent

department: Division of Infection and Pathway Medicine

institute: University of Edinburgh

summary: Investigation in bacterial transcriptomics is widely used to investigate gene regulation, bacterial susceptibility to antibiotics, host-pathogen interactions, and pathogenesis. Transcriptomics is crucially dependent on suitable methods to isolate and detect bacterial RNA. Microfluidic approaches offer ways of creating integrated point-of-care systems, analysing a sample from preparation, RNA isolation through to detection. Critical for on-chip diagnostics to deliver on their promise is that mRNA expression is not altered through the use microfluidic sample processing. Here, we investigate the impact on the use of a microfluidic sample processing system based on hydrodynamic separation upon RNA expression of bacteria isolated from blood to prove its suitability for further microfluidic test development.

overall_design: A 10 array study using total RNA recovered from bacteria isolated using the microfluidic device and total RNA recovered from bacteria that were not separated using the device were compared. Arrays were performed in 5 biological replicates from each condition

first: David

last: Watson

first: Maïwenn

last: Kersaudy-Kerhoas

first: Marc

last: Desmulliez

first: Till

last: Bachmann

first: Helen

last: Bridle


title: KDM5 Lysine Demethylases Are Involved in Maintenance of 3'UTR Length [ChIP-Seq]

status: Public on Mar 23 2016

city: new haven

first: Zongzhi

last: Liu

state: CONNECTICUT

address: 310 Cedar Street

institute: yale university

summary: We discovered that the Saccharomyces cerevisiae lysine demethylase, Jhd2 (also known as KDM5), recruits 3'UTR processing machinery and promotes alteration of 3'UTR length in a demethylase-dependent manner. Interaction of Jhd2 with both chromatin and RNA suggests that Jhd2 affects selection of polyadenylation sites through a transcription-coupled mechanism.

overall_design: Wild-type yeast or yeast with JHD2 deleted were grown to mid-log phase.  ChIP analysis performed for H3K4me3, Pol2, IgG.

first: Lauren

last: Blair

first: Qin

last: Yan


title: Histamine footprint on the human exercise transcriptome

status: Public on Mar 21 2016

city: Eugene

first: John

last: Halliwill

state: OR

address: 1370 Franklin Blvd

institute: University of Oregon

summary: Transcriptome wide analysis of the skeletal muscle response to exercise in humans. Subjects performed one 60-min bout of moderate-intensity single-leg knee-extension exercise, and samples were obtained by biopsy of the vastus lateralis muscle before, immediately after, and at 3 hr post-exercise. Eight subjects were control (no drug), and eight received combined H1/H2-histamine receptor blockade prior to exercise.

overall_design:
Three time-points in each of 8 control and 8 histamine-blockade subjects. Time points are before exercise, immediately after exercise, and at 3 hrs post-exercise.

Note: Alignments were re-run using an updated piece of software and the results are reported in PMID 29455450. The following supplementary files contain information on the differentially expressed genes that were identified by the new analysis of the data:

GSE71972_Differential_Expression_Tables_Updated_20160830.xlsx
GSE71972_Protein_Coding_Full_Counts_Updated_20160830.xlsx

first: Steven

last: Romero

first: Doug

last: Turnbull


title: KDM5 Lysine Demethylases Are Involved in Maintenance of 3'UTR Length


title: Tumor Cell-Derived Periostin Regulates Cytokines That Maintain Breast Cancer Stem Cells

status: Public on Mar 07 2016

first: Boston University

last: Microarray and Sequencing Resource

state: MA

department: Microarray and Sequencing Resource

summary: Basal-like breast cancer (BLBC) cells share phenotypic similarities with cancer stem cells (CSCs) but the underlying molecular basis for this connection remains elusive. We hypothesized that BLBC cells are able to establish a niche permissive to the maintenance of CSCs and found that tumor cell-derived periostin (POSTN), a component of the extracellular matrix, as well as a corresponding cognate receptor, integrin αvβ3, are highly expressed in a subset of BLBC cell lines as well as in cancer stem cell-enriched populations. Furthermore, we demonstrated that an intact periostin-integrin β3 signaling axis is required for the maintenance of breast CSCs. POSTN activates the ERK signaling pathway and regulates NF-κB-mediated transcription of key cytokines, namely IL6 and IL8, which in turn mediate downstream activation of STAT3. In summary, these findings suggest that BLBC cells have an innate ability to establish a microenvironmental niche supportive of CSCs.

overall_design: RNA was isolated from three biological replicates of the indicated SUM159 cell lines.  SUM159 shGFP cells express a control shRNA plasmid directed at GFP while the two other lines carry shRNA plasmids directed at POSTN or ITGB3.

first: Arthur

last: Lambert

first: Sam

last: Thiagalingam


title: KDM5 Lysine Demethylases Are Involved in Maintenance of 3'UTR Length [RNA-Seq]

overall_design: For 3'READs analysis, wild-type yeast or yeast with JHD2 deleted were grown to mid-log phase and RNA was extracted as mentioned above.  cDNA libraries enriched for 3'UTRs were prepared as previously published and as noted in Figure 4a [28].  Samples were then subjected to RNA sequencing on the Illumina Hiseq 2000 using 50bp single end reads.  Data was analyzed as previously [Hoque M] with the following modifications:   The adapter sequences were trimmed off the single-ended reads.  The remaining reads longer than 15 bp were mapped to yeast genome SacCer3 using bowtie2 [Langmead B 2012] with the setting '-5 4 --local', trimming off 4bp from 5' and allowing soft clipping (S) at both ends.  The alignments were then filtered by 1) MAPQ>=10, 2) mismatches <= 5%, 3) unaligned 5' Ts >=2 to get the PASS reads. The last aligned positions of the PASS reads were grouped to pA clusters with a clustering size of 24 bp.  Each pA cluster was assigned to one of the genes defined by SGD [Cherry JM].  The 3' end of a gene was extended 1000bp from the end of CDS until it overlaps with another gene in the same direction.  The pA Clusters were then filtered by contains 1) >= 3 PASS reads 2) >= 5% of all PASS reads mapped to the gene.

first: Dinghai

last: Zheng

first: Bin

last: Tian


title: Genome-wide gene expression in Dupuytren’s disease

status: Public on Mar 01 2016

city: Cologne

first: Kerstin

last: Becker

address: Weyertal 115b

institute: Cologne Center for Genomics

summary: We compared the whole-genome expression profiles of primary tissue samples from Dupuytren patients and controls. The aim was to identify differential expressed genes in the disease tissue and to identify pathways and networks altered in Dupuytren´s disease.

overall_design: Total RNA was obtained from disease and control primary tissue samples. Twelve Dupuytren Samples were compared with 12 samples from age and gender matched controls for genome-wide differential expression.

first: Hans

last: Hennies