title: Transcriptome alteration upon ZNF281 depletion in HCC cells

status: Public on Mar 07 2020

city: Beijing

first: Chenguang

last: Zhang

address: No.10 You An street, Fengtai district

department: Biochemistry and Molecular Biology

institute: Capital Medical University

summary:
To find potential target gene of ZNF281 in HCC cells, the transcriptome analyse (RNA-seq) were performed in HLE HCC cell lines with or with ZNF281 depletion using shRNAs in lentivirus vectors

Zinc finger protein 281 (ZNF281) has been implicated in the progression of several types of cancer. However, its functionality and transcriptional targets in hepatocellular carcinoma (HCC) remains elusive. In the present study, we discovered that the expression of ZNF281 was increased in tumor tissues and cell lines, and positively correlated with vessel invasion in HCC. We took RNA interference approach and constructed 2 shRNAs lentivirus vectors targeting different regions of ZNF281 which were named as ZNF281.kd1 and ZNF281.kd2 respectively. Knockdown of ZNF281 suppressed proliferation, migration and invasion of HCC cells. In searching for novel ZNF281 regulated genes, RNA-seq was performed on BGI-seq500 platform using the obtained stable cells of Con, ZNF281.kd1 and ZNF281.kd2 in HLE background (each in duplicate). The criteria of log2 FC (fold change) >1.5, and q value <0.001 was set for calling differentially expressed genes (DEGs). Besides, to minimize the off-target effect of single shRNAs, only DEGs that show consistent trend of alteration (up-regulated or down-regulated in both ZNF281.kd1 and ZNF281.kd2 groups against control shRNA group) were selected as potential ZNF281 targets. A list of potential targets was identified, including both up-regulated and down-regulated genes upon ZNF281 depletion. Further mechanistic studies were performed to uncover transcriptional regulation of ZNF281 on these genes. Our study was supposed to be helpful for understanding the molecular mechanism underpinning progression of HCC, and might also hold therapeutic potential for HCC treatment.

overall_design: The expression ZNF281 was knocked down with two shRNAs (ZNF281 kd.1 and ZNF281 kd.2, respectively) targeting different sites of the coding region, total RNAs of control and each knockdown group in duplicates were extracted, RNA-seq was performed to find differentially expressed gene between control and knockdown groups.

first: Liyong

last: Wang


title: Lifespan and healthspan benefits of FW1256,  a novel hydrogen sulfide donor compound, in C. elegans are independent from effects downstream of eat-2 mutation

status: Public on Mar 06 2020

city: Singapore

first: Jan

last: Gruber

address: Singapore

department: Science/Biochemistry

country: Singapore

institute: Yale-NUS College/National University of Singapore

type: Expression profiling by high throughput sequencing

summary: It has been suggested that hydrogen sulfide (H2S) may play a pivotal role in mediating some of these caloric restriction (CR)-associated benefits. We therefore explored whether a novel slow-releasing H2S donor compound, FW1256, mimics CR and reproduces CR-associated effects in normal feeding Caenorhabditis elegans. Using transcriptomics analysis via RNA sequencing, we determined sets of differentially expressed genes (DEG) for FW1256-exposed wild-type C. elegans and eat-2 mutants, a genetic model of CR in C. elegans,  relative to unexposed wild-type C. elegans.  We found that, while FW1256 affects some of the same downstream genes as eat-2 mutation, global gene expression changes are dissimilar between FW1256-exposed C. elegans and eat-2 mutants, suggesting that novel slow-releasing H2S donor compound, FW1256, does not mimic CR at the transcriptional level.

overall_design: Approximately 1000 of nematodes at age of day 6 were harvested and total RNA was extracted. Extracted RNA was thereafter sent for library prep and sequencing using Illumina HiSeq4000 sequencing platform. Wild-type C. elegans were treated with 500µM of FW1256 from L1 stage larvae . There were 12 samples in total, ie: unexposed wild-type C. elegans in quadruplicate, eat-2 mutants (DA1116) in quadruplicate, wild-type C. elegans exposed to FW1256 in quadruplicate.

first: Li

middle: T

last: Ng

first: Diogo

last: Barardo


title: Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins

status: Public on Aug 10 2020

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

country: USA

institute: Carnegie Institution/HHMI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb silencing represses gene expression and provides a molecular memory of chromatin state that is essential for animal development. We show that Drosophila female germline stem cells (GSCs) provide a powerful system for studying Polycomb silencing. GSCs have a non-canonical distribution of PRC2 activity and lack silenced chromatin, like embryonic progenitors. As GSC daughters differentiate into nurse cells and oocytes, nurse cells silence genes in traditional Polycomb domains and in generally inactive chromatin like embryonic somatic cells. Developmentally controlled expression of two Polycomb repressive complex 2 (PRC2)-interacting proteins, Pcl and Scm, initiate silencing during differentiation. In GSCs, abundant Pcl inhibits PRC2-dependent silencing globally, while in nurse cells Pcl declines and newly-induced Scm concentrates PRC2 activity on traditional Polycomb domains. Our results suggest that PRC2-dependent silencing is developmentally regulated by accessory proteins that either increase the concentration of PRC2 at target sites or inhibit the rate that PRC2 samples chromatin.

overall_design: RNAseq and ChIPseq of whole ovaries and purified germ cells and germ cell nuclei in wild type and Polycomb-group mutant flies

first: Steven

last: DeLuca


title: STAT5BN642H is a driver mutation for T-cell neoplasia

status: Public on Feb 24 2020

city: Wien

first: Ha T T

last: Pham

address: SCHWARZSPANIERSTR 17

country: Austria

institute: Ludwig Boltzmann Institute for Cancer Research

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: R-Roscovitine improves motoneuron function in mouse models for Spinal Muscular Atrophy.

status: Public on Jan 28 2020

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

country: Germany

institute: University Wuerzburg

summary: Neurotransmission defects and motoneuron degeneration are hallmarks of Spinal Muscular Atrophy, a monogenetic disease caused by the deficiency of the SMN protein. In the present study, we show that systemic application of R-Roscovitine - a Cav2.1 / Cav2.2 channel modifier and a Cyclin-dependent kinase 5 (Cdk-5) inhibitor - significantly improved survival of SMA mice. In addition, R-Roscovitine increased Cav2.1 channel density and sizes of the motor endplates. In vitro, R-Roscovitine restored axon lengths and growth cone sizes of Smn-deficient motoneurons corresponding to enhanced spontaneous Ca2+ influx and elevated Cav2.2 channel cluster formations independent of its capability to inhibit Cdk-5. Acute application of R-Roscovitine at the neuromuscular junction significantly increased evoked neurotransmitter release, the frequency of spontaneous miniature potentials, and lowered the activation threshold of silent terminals. These data indicate that R-Roscovitine improves Ca2+ signaling and Ca2+ homeostasis in Smn-deficient motoneurons which is generally crucial for motoneuron differentiation, maturation, and function.

overall_design:
Smn+/+;SMN2 (Smn_p_p) and Smn-/-;SMN2 (Smn_m_m)  motoneurons treated with R-Roscovitine (plus_R1-3) and controls (minus_R1-3).
Total number of samples is 12

first: Rocio

last: Tejero

first: Stefanie

last: Balk

first: Julio

last: Franco-Espin

first: Jorge

last: Ojeda

first: Luisa

last: Hennlein

first: Hans

last: Drexl

first: Benjamin

last: Dombert

middle: D

last: Clausen

first: Laura

last: Torres-Benito

first: Lena

last: Saal-Bauernschubert

first: Robert

last: Blum

first: Michael

last: Briese

first: Lucia

last: Tabares

first: Sibylle

last: Jablonka


title: Establishment and Characterisation by Expression Microarray of Patient Derived Xenograft Panel of Human Pancreatic Adenocarcinoma Patients

status: Public on Dec 12 2019

city: Dublin 9

first: Sandra

last: Roche

address: Glasnevin

country: Ireland

institute: Dublin City University

summary:
mRNA expression profiling of pancreatic cancer, comparing adjacent normal tissue, patient tumour and first generation patient derived xenograft tumours
Fresh tumour samples for human pancreatic adenocarcinoma patients were implanted in SCID mice. 70% of these pancreatic ductal adenocarcinoma patients grew as PDX tumours, confirmed by histopathology. Frozen samples from F1 PDX tumours could be later successful passaged in SCID mice to F2 PDX tumours. The human origin of the PDX was confirmed using human specific antibodies; however, the stromal component was replaced by murine cells. Cell lines were successfully developed from three PDX tumours. RNA was extracted from 8 PDX tumours and where possible, corresponding primary tumour and adjacent normal tissues. mRNA profiles of tumour vs F1 PDX and normal vs tumour were compared by Affymetric microarray analysis

overall_design: matched patient samples


title: Genome-wide TFBS (Transcription Factor Binding Site) map analysis in HepG2 cells

status: Public on Nov 27 2019

city: Huntsville

first: Eric

middle: M

last: Mendenhall

state: AL

address: 601 Genome Way Northwest

institute: HudsonAlpha Institute

summary: We performed Chip-Seq analysis of 208 Factors in HepG2, using ENCODE Consortium Data with 2 replicates and 2 controls for each factors, to study transcription factor landscape within single cell type.

overall_design:
ChipSeq data was produced by ENCODE Production Lab and submitted to ENCODE Data Coordination Center. Each of 208 TFs/DNA associated proteins included in this study were processed by the study group itself to generate only peaks passing IDR cutoff of 0.02 FDR(false discovery rate).
An alternative analysis of ENCODE data.

first: E

last: Partridge

first: Surya

middle: B

last: Chhetri

first: Richard

last: Myers


title: Strong correlation between air-liquid interface cultures and in vivo transcriptomics of nasal brush biopsy

status: Public on Jul 31 2020

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Air-liquid interface cultures are extensively used to model chronic respiratory diseases. Comparative transcriptomics between cultured cells and fresh nasal brushings from patients suggests a high degree of correlation.

overall_design: Total RNA sequencing was performed to compare the transcriptome of these nasal epithelial cells cultured at ALI for 6 weeks with the directly harvested brushed nasal epithelia.

first: Baishakhi

last: Ghosh

first: Debarshi

last: Bhowmik

first: Kristine

last: Nishida

first: Molly

last: Lauver

first: Nirupama

last: Putcha

first: Peisong

last: Gao

first: Murugappan

last: Ramanathan Jr

first: Nadia

last: Hansel

first: Shyam

last: Biswal

first: Venkataramana

last: Sidhaye


title: Induction of an alternative 5' leader enhances translation of Inpp5e and resistance to oncolytic virus infection

status: Public on Nov 30 2019

city: Ottawa

first: Tommy

last: Alain

state: Ontario

address: 401 Smyth Road

country: Canada

institute: Children's Hospital of Eastern Ontario Research Institute

summary: Residual cell-intrinsic innate immunity in cancer cells hampers infection with oncolytic viruses. Control of mRNA translation is an important feature of innate immunity, yet the identity of mRNA substrates that participate in host defences remain ill-defined. We characterized the translatome of resistant murine “4T1” breast cancer cells infected with three of the most clinically advanced oncolytic viruses: Herpes Simplex virus 1, Reovirus and Vaccinia virus. Common among all three infections were translationally de-repressed mRNAs including Inpp5e, encoding an inositol 5-phosphatase that modifies lipid second messenger signalling. We found that viral infection induced expression of an Inpp5e mRNA variant that lacks repressive upstream open reading frames (uORFs) within its 5’ leader and is efficiently translated. Furthermore, we show that INPP5E contributes to antiviral immunity by altering virus attachment. These findings uncover a role for translational control through alternative 5’ leader expression and assign an antiviral function to the ciliopathy gene INPP5E.

overall_design: Ribosome Profiling (RPF-Seq and RNA -Seq) of murine 4T1 breast cancer cells infected with different oncolytic viruses

first: Huy-Dung

last: Hoang

first: Tyson

middle: E

last: Graber

first: Seyed

last: Jafarnejad


title: TFEB-induced 5hmC and 5mC changes in AML cells [RRBS-seq]

status: Public on Jun 12 2020

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: We report reduced representation bisulfite-sequencing data after TFEBS211A overexpression in HL60 cell line.

overall_design: HL60 cells lines were transduced with either pRRL-EV-puro or pRRL-TFEBS211A-puro which inducibly overexpress TFEBS211A in doxycycline dependent manner. Then, reduced representation BS-seq was performed comparing TFEBS211A expressing cells vs. three other control groups. All samples were prepared as triplicate (biologically independent experiments).

first: John

middle: L

last: Cleveland

first: Seongseok

last: Yun


title: Single-cell atlas of the developing brain to investigate the cellular origins of pediatric brain tumors

status: Public on Nov 19 2019

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

summary: Gene expression is finely regulated during development, and deregulation can lead to disease. In pediatric brain tumors (PBT), disruption of neurodevelopmental gene regulation programs are suspected to drive oncogenesis. However, the transcriptional landscape and genetic regulation processes of the healthy developing brain are not fully characterized, limiting our investigation of these tumors. We used single-cell RNA-sequencing to generate a transcriptomic atlas of >65,000 cells in the developing forebrain and pons in human and mouse, two regions where PBT commonly arise. We projected bulk RNA-seq profiles for a cohort of 198 PBT onto these cell types, followed by focused analysis of three PBT subtypes by single-cell profiling: WNT medulloblastoma, embryonal tumors with multilayered rosettes (ETMR), and atypical teratoid/rhabdoid tumors (ATRT). Altogether, we pinpoint stalled differentiation during developmental programs as a common etiological mechanism of PBT, providing a valuable resource to aid modeling and therapeutics.

overall_design: The forebrains from 5 healthy mice at E12.5, E15.5, P0, P3, and P6; the hindbrain from a healthy mouse at E12.5;and the pons from healthy mice at E15.5, P0, P3, and P6 were processed for single-cell mRNA sequencing.

first: Selin

last: Jessa

first: Alexis

last: Blanchet-Cohen

first: Brian

last: Krug

first: Maria

last: Vladoiu

first: Marie

last: Coutelier

first: Damien

last: Faury

first: Brice

last: Poreau

first: Nicolas

last: De Jay

first: Steven

last: Hébert

first: Jean

last: Monlong

first: W

last: Farmer

first: Laura

middle: K

last: Donovan

first: Yixing

last: Hu

first: Melissa

last: McConechy

first: Florence

last: Cavalli

first: Leonie

middle: G

last: Mikael

first: Benjamin

last: Ellezam

first: Maxime

last: Richer

first: Andréa

last: Allaire

first: Alexandre

last: Weil

first: Jeffrey

last: Atkinson

first: Jean-Pierre

first: Roy

middle: W

last: Dudley

first: Valerie

last: Larouche

first: Louis

last: Crevier

first: Steffen

last: Albrecht

first: Mariella

last: Filbin

first: Hervé

last: Sartelet

first: Pierre-Eric

last: Lutz

first: Corina

last: Nagy

first: Gustavo

last: Turecki

first: Santiago

last: Constantino

first: Peter

last: Dirks

first: Keith

last: Murai

first: Guillaume

last: Bourque

first: Jiannis

last: Ragoussis

first: Livia

last: Garzia

first: Michael

last: Taylor

first: Nada

last: Jabado


title: Gene expression profiling of rat footpad skin in radiation dermatitis

status: Public on May 25 2019

city: Fuzhou

first: Yue

last: Zhicao

state: Fujian

address: Institute of Life Sciences, Fuzhou University

department: Institute of Life Sciences

country: China

institute: Fuzhou University

summary: Radiation dermatitis is a side effect in cancer radiotherapy, where ionizing radiation is delivered to eradicate cancer. Normal tissue such as the skin is also damaged by this treatment. We report here the gene expression change in a rat footpad model of this disease.

overall_design:
Rat footpad skin was irradiated at Day 1, Day 2, Day 4, Day 5 at 10Gy X 4 to mimic the fractioned delivery scheme used in clinic. The irradiation was performed using a Varian Clinac 23ex linear accelerator. Nine MeV electron beam was delivered at a dose rate of 500 cGy/min. Footpad skin from the hindlimb was collected at Day 0, Day 3, Day 6, Day 9, and total RNAs were extracted. After quality check, RNAs were processed for NGS in BGI, Shengzhen, China. The sequencing results were annotated according to a NCBI database.
Raw data were not saved and are therefore not available for these records.

first: Zhicao

last: Yue

first: Hao

last: Han


title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation

status: Public on Jul 27 2019

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

summary: Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. We performed ChIP sequencing to determine the genomic localization of CHD7 in human CD34+ and mouse HSPCs, revealing enrichment of binding motifs for hematopoietic transcription factors including Runx1 and GATA factors. CHD7 occupied regions are transcriptionally active and are near genes with hematopoietic function. Decreased Runx1 occupancy correlated with loss of CHD7 occupancy. Together, the physical and genetic interaction data support a model in which CHD7 interacts with and modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults. This represents a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.

overall_design: Analysis of CHD7 and RUNX1 binding in CBFV-MYH11 expressing hematopoietic progenitor cells, in replicate.

first: Nicola

last: Wilson

first: Victoria

last: Moignard

first: Fernando

last: Calero Nieto


title: Batf pioneers the reorganization of chromatin in developing effector T cells via Ets1-dependent recruitment of Ctcf

status: Public on Nov 04 2019

city: Birmingham

first: Min

last: Gao

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham


title: The NMDA receptor subunit GluN3A regulates a program of synaptic activity-induced and MEF2C-dependent transcription

status: Public on Jul 08 2019

city: Durham

first: Anne

last: West

state: NC

address: 311 research drive

department: Neurobiology

institute: Duke University

summary: N-methyl-D-aspartate type glutamate receptors (NMDARs) are key mediators of synaptic activity-regulated gene transcription in neurons, both during development and in the adult brain. Developmental differences in the GluN2 subunit composition of NMDARs determines whether NMDARs activate the transcription factor CREB. However, whether the developmentally-regulated GluN3A subunit also modulates NMDAR-induced transcription was unknown. Here we show that knocking down GluN3A in rat hippocampal neurons promotes the inducible transcription of a subset of NMDAR-sensitive genes. This enhancement is mediated by the accumulation of phosphorylated p38 MAP kinase in the nucleus, which drives the activation of the transcription factor MEF2C and promotes the transcription of a subset of synaptic activity-induced genes including Bdnf and Arc. Our evidence that GluN3A negatively regulates MEF2C-dependent transcription reveals a novel mechanism by which NMDAR subunit composition confers specificity on the program of synaptic activity-regulated gene transcription in developing neurons.

overall_design: Biological triplicate RNA-seq samples from cultured embryonic (E18.5) rat hippocampal neurons at 7 days in in vitro with Grin3a being knocked down by lentiviral shRNA or Ctrl lentiviral infection for comparison. There are 3 biological replicates per knockdown (kd) and 3 matched controls infected with the lentiviral vector (Ctrl) for each of two treatments (12 samples total). For each genetic condition (Ctrl or KD) there are two treatment conditions, either 1µm TTX for 48 hours (TTX) or 1µM TTX for 48 hours followed by 6 hours of TTX withdrawal (TTXwd).

first: Liang-Fu

last: Chen

first: Michelle

middle: R

last: Lyons

first: Fang

last: Liu


title: Batf pioneers the reorganization of chromatin in developing effector T cells via Ets1-dependent recruitment of Ctcf [Hi-C]

summary: We have examined mechanisms by which Batf acts to initiate gene transcription in developing effector CD4 T cells. We find that in addition to its pioneering function, Batf controls developmentally regulated recruitment of the chromatin architectural factor, Ctcf, to promote chromatin looping that is associated with transcription of lineage-specific genes. The chromatin organizing actions of Batf are largely Ets1-dependent, which appears to be indispensable for the Batf-dependent recruitment of Ctcf. Moreover, most of the Batf-dependent sites to which Ctcf is recruited lie outside of Ap-1–Irf composite elements (AICEs), indicating that direct involvement of Batf-Irf complexes is not required. Thus, we have identified a cooperative role for Batf, Ets1 and Ctcf in chromatin reorganization that underpins transcriptional programming of effector T cells.

overall_design:
Naïve CD4+ T cells isolated from spleen/lymph nodes were activated with anti-CD3 and anti-CD28 with or without IL-6 for 96 h.
D4 activated WT and BatfKO cells with or without IL-6.

first: Duy

last: Pham

first: Robin

last: Hatton

first: Casey

last: Weaver


title: Developmental trajectory of pre-hematopoietic stem cell formation from endothelium (scATAC-seq data set)

status: Public on Apr 27 2020

city: San Francisco

first: Qin

last: Zhu

state: CA

address: 600 Minnesota Street

institute: UCSF

summary: To examine the cell and molecular transitions between endothelial (E), hemogenic endothelial (HE), and intra-arterial clusters (IAC) cells,  we profiled ~1700 cells from the caudal arteries (dorsal aorta, umbilical, vitelline) of embryonic day (E) 10.5 mouse embryos by single-cell  ATAC sequencing  (scATAC-Seq). We found extensive cis--regulatory landscape change during the endothelial to hematopoietic transition (EHT).

overall_design: Single cell ATAC-seq profiles of cells involved in endothelial to hematopoietic transition (EHT) from mouse embryos at embryonic day 10.5

first: Kai

last: Tan

first: Nancy

middle: A

last: Speck


title: Batf pioneers the reorganization of chromatin in developing effector T cells via Ets1-dependent recruitment of Ctcf [ATAC-seq]

overall_design:
Naïve CD4+ T cells isolated from spleen/lymph nodes were activated with anti-CD3 and anti-CD28 with or without IL-6 or under Th17 culture conditions.
Naïve WT and BatfKO cells; D1 and D4 activated WT, BatfKO, and Irf4cKO (CD4 cKO) cells with or without IL-6 or under Th17 cell culture conditions; WT and BatfKO Tfh cells.


title: Genome-wide analysis of AR binding and transcriptomic analysis of mesenchymal subsets during prostate development

status: Public on Jun 30 2019

first: Claire

middle: Elizabeth

last: Nash

state: QC

address: 1001 Decarie Blvd

department: Urology

institute: Research Institute of McGill University Health Centre

summary: Prostate organogenesis is regulated by interactions between mesenchymal and epithelial cells, and via androgen signalling though androgen receptors (AR) expressed in mesenchymal cells. However, there is little knowledge of AR target genes and we have used high resolution genomic methods to examine AR function in subsets of mesenchyme during prostate development. Using ChIP-seq, we defined genomic AR binding sites (ARBS) in microdissected mesenchymal tissues of neonatal male and female rats during prostate growth. By comparing female tissue subsets (ventral mesenchymal pad and urethral smooth muscle) with male tissues (ventral prostate and dorsolateral prostate), we were able to identify sexually dimorphic ARBS.  Females had a distinct AR binding profile from males with enrichment of ARBS proximal to gene transcriptional start sites as well as binding to non-classical AR binding sequence motifs. Using both tissue RNA-sequencing and single-cell RNA-sequencing of the same mesenchymal subsets, we identified 128 differentially expressed transcripts between males and females. Comparison of these to ChIP-seq ARBS allowed us to define sexually dimorphic AR target genes.  Selected candidates were validated as sexually dimorphic at both the mRNA and protein level in both rat and human developing prostate tissues by qPCR and western blot. Response to testosterone stimulation was examined using ex vivo rat tissue organ cultures and qPCR. In single cell RNAseq data we observed subpopulations of mesenchymal cells in males and females as well as subpopulations common to both. The distribution of AR and target genes did not follow the subpopulation distribution, suggesting that AR action is not restricted by subset identity.Our study is the first to apply multiple transcriptomic approaches to prostate mesenchyme, and we have identified unique AR targets. We have identified sexually dimorphic, androgen responsive mesenchymal target genes that may underlie sexually dimorphic development of the prostate. We suggest that the analysis of transcription factor binding and transcriptomes in cell subsets will be informative when applied to tumour cells and stroma – since these show similar cellular heterogeneity and subset specific activity.

overall_design: Examination of AR binding profile and transcriptomics in developing rat urogenital sinus tissues.

first: Axel

last: Thomson


title: Transcriptomic Analysis in Renal T Lymphocytes Exposes Sodium-Independent Dietary Differences in Dahl Salt-Sensitive Rats

status: Public on Aug 26 2019

city: Milwaukee

first: Justine

last: Abais-Battad

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary:
Background. The Dahl salt-sensitive (SS) rat is an established model of salt-sensitive hypertension and renal damage. Recently, sodium-independent dietary effects were shown to be important in the development of the SS hypertensive phenotype. Compared to Dahl SS/JrHsdMcwi (SS/MCW) rats fed a purified diet (AIN-76A), grain-fed Dahl SS/JrHsdMcwiCrl rats (SS/CRL; Teklad 5L2F) were less susceptible to salt-induced hypertension and renal damage.
Methods. With the known role of the immune system in hypertension, the present study characterized the immune cells infiltrating SS/MCW and SS/CRL kidneys. To further identify distinct molecular pathways between SS/MCW and SS/CRL, transcriptomic analysis was performed via RNA sequencing in T-cells isolated from the blood and kidneys of low and high salt-fed rats.
Results. Following a 3-week high salt (4.0% NaCl) challenge, SS/CRL rats were protected from salt-induced hypertension (116.5±1.2 vs 141.9±14.4 mmHg) and albuminuria (21.7±3.5 vs 162.9±22.2 mg/day) compared to SS/MCW. Additionally, the absolute number of immune cells infiltrating the kidney was significantly reduced in SS/CRL. RNA-seq revealed >50% of all annotated genes in the entire transcriptome to be significantly differentially expressed in T-cells isolated from blood versus kidney. Pathway analysis of significant differentially expressed genes between SS/MCW and SS/CRL renal and circulating T-cells demonstrated salt-induced changes in genes related to inflammation in SS/MCW compared to metabolism-related pathways in SS/CRL.
Conclusions. These functional and transcriptomic T-cell differences between SS/MCW and SS/CRL show that sodium-independent dietary effects may influence the immune response and infiltration of immune cells into the kidney, ultimately impacting susceptibility to salt-induced hypertension and renal damage.

overall_design: 5 experimental groups; 4 pools/experimental group; 3 rats/pool

first: David

last: Mattson


title: MenSCs inhibit HCC growth through oncogenic pathway suppression via regulating 5-hmC in enhancer elements

status: Public on Jun 10 2019

city: Hangzhou

first: Yichen

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

department: College of Medicine

institute: Zhejiang University


title: ELP1 splicing correction reverses proprioceptive sensory loss in familial dysautonomia

status: Public on Mar 21 2019

city: Boston

first: Susan

last: Slaugenhaupt

state: MA

address: 185 Cambridge St

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Familial dysautonomia (FD) is a recessive neurodegenerative disease caused by a splice mutation in Elongator complex protein 1 (ELP1, also known as IKBKAP) which leads to variable skipping of exon 20 and to a drastic reduction of ELP1 levels in the nervous system. Clinically, many of the debilitating aspects of the disease are related to a progressive loss of proprioception, which leads to severe gait ataxia, spinal deformities and respiratory insufficiency due to neuromuscular incoordination. There is currently no effective treatment for FD and the disease is ultimately fatal. Development of a drug that targets the underlying molecular defect provides hope that the drastic peripheral neurodegeneration characteristic of FD can be halted. We demonstrate herein that the FD mouse, TgFD9; IkbkapΔ20/flox, recapitulates the proprioceptive impairment observed in individuals with FD, and we provide the in vivo evidence that postnatal correction of mutant ELP1 splicing promoted by the small molecule kinetin can rescue neurological phenotypes in FD. Daily administration of kinetin starting at birth improves sensory-motor coordination and prevents the onset of spinal abnormalities by stopping the loss of proprioceptive neurons. These phenotypic improvements correlate with increased levels of full length ELP1 mRNA and protein in multiple tissues including the peripheral nervous system (PNS). Our results show that postnatal correction of the underlying ELP1 splicing defect can rescue devastating disease phenotypes and is therefore a viable therapeutic approach for persons with FD.

overall_design: Both placebo and kinetin treatments were applied on six human FD fibroblast lines. Paired-end RNASeq was performed on these twelve fibroblast lines.

first: Elisabetta

last: Morini

first: Dadi

first: Connor

last: Montgomery

first: Monica

last: Salani


title: Batf pioneers the reorganization of chromatin in developing effector T cells via Ets1-dependent recruitment of Ctcf [ChIP-seq]

first: Min

last: Gao

overall_design:
Naive CD4+ T cells isolated from spleen/lymph nodes were activated with anti-CD3 and anti-CD28 with or without IL-6 or under Th17 culture conditions.
Naive WT and BatfKO cells; D1 and D4 activated WT, BatfKO, and Ets1cKO (CD4 cKO) cells with or without IL-6 or under Th17 cell culture conditions.


title: Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment

status: Public on Mar 26 2019

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

summary: Cancer stem cells (CSCs) have been proposed to underlie the hierarchical organization of Glioblastoma (GBM) causing resistance to treatment, however the identity of CSCs in solid tumors remains largely elusive. Here we find that GBM cells expressing cell membrane CSC-associated markers do not represent a clonal entity defined by distinct functional properties and/or transcriptomic profiles, but rather a plastic state that most cancer cells can adopt. We show that phenotypic heterogeneity arises from non-hierarchical, reversible state transitions that are instructed by the microenvironment. While all tested cancer cell subpopulations survive and adjust their phenotype in vivo, their speed of plasticity differs resulting in variable tumor growth rates. Thus CSC-associated phenotypic heterogeneity is a result of stochastic reversible plasticity and increased tumorigenic potential in vivo correlates with fast adapting cell states.

overall_design: Comparison of sorted tumor cells from 3 GBM patient-derived orthotopic xenografts (PDOX P3, P8 and P13) and 2 GBM stem-like cultures (NCH644, NCH421k). Additional subpopulations of NCH644 were further compared: subpopulation P2 (CD133+CD44-A2B5+CD15+) and subpopulation 6 (CD133+CD44+A2B5+CD15+). One sample per each tumor is available.

first: Anne

last: Dirkse

first: Anna

last: Golebiewska

first: Thomas

last: Buder

first: Petr

middle: V

last: Nazarov

first: Suresh

last: Poovathingal

first: Nicolaas

middle: H

last: Brons

first: Sonia

last: Leite

first: Nicolas

last: Sauvageot

first: Dzjemma

last: Sarkisjan

first: Mathieu

last: Seyfrid

first: Sabrina

last: Fritah

first: Daniel

last: Stieber

first: Alessandro

last: Michelucci

first: Christel

last: Herold-Mende

first: Rolf

last: Bjerkvig

first: Francisco

last: Azuaje

first: Alexander

last: Skupin

first: Andreas

last: Deutsch

first: Anja

last: Voss-Böhme

first: Simone

middle: P

last: Niclou


title: Leptin responsive neurons

status: Public on Apr 01 2019

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

summary: Genome wide association studies (GWAS) in obesity have identified a large number of noncoding loci located near genes expressed in the central nervous system. However, due to the difficulties in isolating and characterizing specific neuronal subpopulations, very few obesity-associated SNPs have been functionally characterized. Leptin responsive neurons in the hypothalamus are essential in controlling energy homeostasis and body weight. Here, we show that by combining FACS-sorting of leptin-responsive hypothalamic neuron nuclei with genomic approaches (RNA-seq, ChIP-seq, ATAC-seq), we can provide a comprehensive map of leptin-response specific regulatory elements, several of which overlap obesity-associated GWAS variants. Further demonstrating the robustness of our leptin-response neuron regulome, we functionally characterize a novel enhancer near Socs3, a leptin response-associated transcription factor. Combined, our results provide a comprehensive map of active genomic regions in leptin-responsive neurons and present a blueprint for functionally characterizing obesity-associated SNPs in the hypothalamus.

overall_design: RNA-seq, ChIP-seq and ATAC of LepR sorted neurons, treated with and without Leptin.

first: Nadav

last: Ahituv


title: Gloable gene expression is affected by loss of CSB function in the rat model for Cockayne syndrome

status: Public on Feb 05 2019

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Cockayne syndrome (CS) is a rare genetic neurodevelopmental disorder, characterized by a deficiency in the transcription-coupled nucleotide excision repair pathway. Mutation of Cockayne syndrome B (CSB) affects basal transcription which is considered a major cause of CS neurological dysfunction. Here, we generated a rat model by mimicking a nonsense mutation in the CSB(ERCC6) gene of CS-B patients. CSB-deficient rats exhibit the well-known CS repair characteristics: inability to resume RNA synthesis from stalled RNA polymerase II (RNAP II) and persistent gamma H2AX overexpression after UV damage. In contrast to that of the Csb-/- mouse models, the cerebella of the CSB-deficient rats are more profoundly affected. Both the molecular and the granular layers of the cerebellum cortex showed significant atrophy. The white matter of the cerebellum demonstrated high GFAP staining indicative of reactive astrogliosis. RNA-seq analysis of CSB-deficient rat cerebella revealed that even in the absence of UV damage, CSB affects the expression of hundreds of genes, many of which are neuronal genes, suggesting that transcription dysregulation could contribute to the neurological features in CSB rat models.

overall_design: Cerebellar mRNA profiles of CSBR571X/R571X, CSBR571X/- and WT rats were generated by deep sequencing, using Illumina HiSeq X Ten in paired-end mode.

first: Zhenzhen

last: Wu

first: Yingying

last: Xu

first: Lingyun

last: Liu


title: Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus [RRBS]

status: Public on Dec 31 2018

city: Los Angeles

first: Xia

last: Yang

address: 610 Charles E. Young Dr. East

institute: UCLA

summary: To investigate the effects of DHA (an omega-3 fatty acid) on brain dysfunction and metabolic disorders by sequencing the transcriptome (RNA-Seq) and epigenome (RRBS) in the hypothalamus and hippocampus of male SD rats.

overall_design: Male Sprague Dawley (SD) rats of 2 months old were randomly assigned to an omega-3 fatty acid diet containing DHA or a regular chow diet without DHA supplement for six weeks. The rats were sacrificed by decapitation. Hypothalamus and hippocampus were dissected out, flash frozen, and stored at -70 C for later transcriptome and DNA methylome sequencing experiments. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor's Animal Research Committee.

first: Q

last: Meng

first: F

last: Gomez-Pinilla

first: X


title: Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus

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

overall_design: Refer to individual Series


title: Genome-wide transcriptomic and epigenomic study of DHA in rat hypothalamus and hippocampus [RNA-seq]


title: Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair

status: Public on Dec 27 2018

city: CHICAGO

first: Shuang

last: Zhang

state: IL

address: 300 E. Superior St.

institute: Northwestern University

summary: Screening pathways that are affected in macrophages during efferocytosis

overall_design: primary peritoneal macrophages are cocultured with apoptotic cells or LPS for 5 hours; unengulfed apoptotic cells are rinsed off; macrophages are harvested and RNA was extracted for sequencing

first: Edward

last: Thorp


title: Analysis of cabazitaxel-resistant mechanism in human castration-resistant prostate cancer

status: Public on Aug 01 2018

city: Shinjuku-ku

first: Hiroshi

last: Hongo

state: Tokyo

address: 35, Shinanomachi

country: Japan

institute: Keio University School of Medicine

summary: To investigate cabazitaxel (CBZ) resistance in prostate cancer, we examined the changes in global gene expression before and after development of acquired CBZ resistance. Functional annotation clustering (FAC) analysis of DAVID showed cell division (GO: 0051301) and mitotic nuclear division (GO: 0007067) were the most enhanced clusters in DU145CR compared with DU145.

overall_design: DU145 and DU145CR cells were used for microarrays. DU145CR cells were newly established in our laboratory from DU145 cells as an acquired cabazitaxel resistant subline, which were grown and passaged upon reaching confluence in medium containing CBZ over a 18-month period.

first: T

last: Kosaka

first: H


title: Expression Profile of CHD7-Deficient Murine Long-term Hematopoietic Stem Cells

status: Public on Jul 01 2018

city: New York

first: Hsuan-Ting

last: Huang

state: NY

address: 550 First Ave, Smilow 1307

institute: NYU School of Medicine

summary:
Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Knockdown of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation in a cell autonomous manner in the embryo and adult. CHD7 chromatin immunoprecipitation in human CD34+ and mouse HSPCs revealed enrichment of binding motifs for hematopoietic transcription factors including Runx1 and GATA factors, and decreased Runx1 occupancy correlated with loss of CHD7 occupancy. CHD7 physically interacts with Runx1 and suppresses Runx1-induced expansion of HSPCs during development, providing both physical and genetic evidence for the Runx1-CHD7 interaction. CHD7 modulates Runx1 activity to provide proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults, representing a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.
We profiled expression of CHD7 wild-type and deficient adult mice bone marrow long-term hematopoietic stem cells and found genes from several hematopoietic lineages are upregulated.

overall_design: To examine hematopoietic gene expression in CHD7-deficient HSPCs, we purified 12-week adult mice bone marrow LT-HSCs (LSKCD48-CD150+) cells.  We compared the expression profile from Chd7f/f and Chd7f/f;Vav1-Cre mice.

first: Jingmei

last: Hsu

first: Shuqian

last: Yu


title: Analyses of long non-coding RNA and mRNA profiling in the spleen of diarrhea piglets caused by Clostridium perfringens type C

status: Public on Nov 01 2018

city: Lanzhou

first: y

middle: zun

last: qiang

state: Gansu Province

address: No. 1 Yingmen village, Anning District

institute: College of Animal Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed the transcriptome profiles of the spleen of piglets caused by Clostridium perfringens type Cens type C.
Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x109 CFU per ml. Then, 5 piglets were randomly selected as the control group (SC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (SS) and resistant group (SR), respectively. Finally, spleen were collected and sequenced for lncRNA and mRNA.
Results: RNA libraries constructed from spleen of piglets caused by Clostridium perfringens type C were sequenced. A total of 1,450,292,484 clean reads were generated. Among them, 2056 novel lncRNA transcripts corresponding to 1561 lncRNA genes were identified, including 1811 intergenic lncRNAs and 245 anti-sense lncRNAs. The identified spleen lncRNAs shared some characteristics, such as fewer exons and shorter length, with the lncRNAs in other animal. Notably, in pairwise comparisons between the libraries of spleen tissue at the different group, a total of 247 lncRNA and 2170 mRNA were differentially expressed (P < 0.05).    Function analyses indicated that these differentially expressed lncRNAs and mRNAs play roles in defensing Clostridium perfringens type C, which were enriched in immune-related biological processes, such as the antigen processing and presentation, TNF signaling pathway, NF-kappa B signaling pathway, B cell receptor signaling pathway and MAPK signaling pathway.
Conclusions: This study provides the information of spleen-related lncRNAs in swine diarrhea with Clostridium perfringens type C. We also analyzed all lncRNA’s genomic feature and expression. Bioinformatic analysis indicates that some lncRNAs participated in important biological processes associated with defeasing Clostridium perfringens type C, such as antigen processing and presentation, the MHC protein complex and regulation of autophagy.

overall_design: lncRNA and mRNA profiles of spleen in piglets were generated by deep sequencing,three group,five sample in each group,using Illumina

first: Zunqiang

last: Yan

first: Xiaoyu

first: Wenyang

last: Sun

first: Hairen

last: Shi

first: Qiaoli

first: Tiantuan

last: Jiang

first: Shenggui

last: Li

first: Pengfei

first: Shuangbao

last: Gun


title: Spec-seq sequencing data for CTCF [2018 series]

status: Public on Feb 10 2018

city: Palo Alto

first: Zheng

last: Zuo

address: Stanford

department: Genetics

institute: Stanford university

summary: We used Spec-seq method to quantifiy the in-vitro binding specificity of mouse CTCF insulator protein, particularly concerning its upstream motif. Our results confirmed the previously found "upstream motif“ with 5 or 6nt space to the core motif, which is conferred by CTCF's finger 10 and 11.

overall_design:
We used two recombinant proteins, mouse CTCF(F1-F11) and CTCF(F1-F9) to ran Spec-seq analysis on degereate libraries R1,R2,R2L, R3. As expected, only the F1-F11 verson of CTCF exhibited the upstream motif recognition, therefore we confirmed the recognition its relationship. Additionally, we showed that this upstream motif can only show up conditionally in the presence of strong core motif binding.

The experiment was redesigned and redone to include more variants and mutant in the updated series GSE188164


title: Impaired local translation of β-actin mRNA in Ighmbp2-deficient motoneurons: implications for spinal muscular atrophy with respiratory distress (SMARD1)

status: Public on Aug 21 2018

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

institute: University Wuerzburg

summary: Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a fatal motoneuron disorder in children with unknown etiology. The disease is caused by mutations in the IGHMBP2 gene, encoding a Super Family 1 (SF1)-type RNA/DNA helicase. IGHMBP2 is a cytosolic protein that binds to ribosomes and polysomes, suggesting a role in mRNA metabolism. Here we performed morphological and functional analyses of isolated Ighmbp2-deficient motoneurons to address the question whether the SMARD1 phenotype results from de-regulation of protein biosynthesis. Ighmbp2-deficient motoneurons exhibited only moderate morphological aberrations such as a slight increase of axonal branches. Consistent with the rather mild phenotypic aberrations, RNA sequencing of Ighmbp2-deficient motoneurons revealed only minor transcriptome alterations compared to controls. Likewise, we did not detect any global changes in protein synthesis using pulsed SILAC (Stable Isotope Labeling by Amino acids in Cell culture), FUNCAT (FlUorescent Non–Canonical Amino acid Tagging) and SUnSET (SUrface SEnsing of Translation) approaches. However, we observed reduced β-actin protein levels at the growth cone of Ighmbp2-deficient motoneurons which was accompanied by reduced level of IMP1/ZBP1, a known interactor of β-actin mRNA. Fluorescence Recovery after Photobleaching (FRAP) studies revealed translational down-regulation of an eGFP-myr- β-actin 3’UTR mRNA in growth cones. Local translational regulation of β-actin mRNA was dependent on the 3’ UTR but independent of direct Ighmbp2-binding to β-actin mRNA. Taken together, our data indicate that Ighmbp2 deficiency results in local but modest disruption of protein biosynthesis which might partially contribute to the motoneuron defects seen in SMARD1.

overall_design: Total number of samples is 6

first: Verena

last: Surrey

first: Caren

last: Zöller

first: Alicia

last: Lork

first: Mehri

last: Moradi

first: Stefanie

last: Balk

first: Benjamin

last: Dombert

first: Lena

last: Saal-Bauernschubert

first: Michael

last: Briese

first: Utz

last: Fischer

first: Sibylle

last: Jablonka


title: Unwinding the interplay between brain and liver in the pathophysiology of brain trauma

status: Public on Jul 13 2018

first: Xia

last: Yang

address: 610 Charles E. Young Drive East

summary: Although clinical evidence indicates that TBI has profound effects on peripheral metabolism, TBI research has primarily focused on the CNS. The liver plays a major role in control of homeostasis and pathogenesis, affecting synthesis of lipids and proteins used across the body and brain. Fructose consumption is common in the Western Society and a major cause of metabolic syndrome, diabetes, and obesity. Results showed that fructose consumption in rodents for 3 weeks, under the threshold for establishment of metabolic syndrome, exacerbates the deleterious effects of fluid percussion injury on glucose metabolism, inflammation, and cell energy homeostasis. These effects of TBI and fructose seem to engage the hypothalamic neuroendocrine axis by involving the growth hormone system with resulting effects on a metabolic/inflammatory cascade in the periphery. Fructose fed TBI animals had elevated markers of inflammation (TLR4), lipid peroxidation (4HNE), and reduced markers of cell energy homeostasis (uMitCK) as well as reduced insulin signaling proteins (InR, IRS1) and growth hormone signaling proteins (GHR, IGF-1) in the liver. Fructose also potentiated the action of TBI on hepatic lipid droplet accumulation involving lipid-promoting factors (FAS, LXRα, CD36, ABCA1).  Studies in cultured hepatocytes validated the action of growth hormone and fructose on the synthesis of FAS and CD36.  TBI affects the transcriptomic profiling in the hypothalamus and several differentially expressed genes that are primarily associated to lipid metabolism providing cues for peripheral alterations in TBI pathology.  These results reveal that the effects caused by TBI are not limited to the CNS, and that fructose promotes a stage of metabolic dysfunction that potentiates the effects of TBI on systemic metabolism.

overall_design: RNA samples of hypothalamus from Sham and TBI rats (n=5 per group ) were used for RNA-Seq sequenced in paired-end mode by HiSeq 4000 (Illumina Inc., CA, USA)

first: Shraddha

last: Rege

first: Fernando

last: Gomez-Pinilla


title: hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons

status: Public on Mar 06 2018

summary: Disturbed RNA processing and subcellular transport contribute to the pathomechanisms of motoneuron diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. RNA-binding proteins are involved in these processes, but the mechanisms how they regulate the subcellular diversity of transcriptomes, in particular in axons, are not understood. hnRNP R interacts with several proteins involved in motoneuron diseases. It is located in axons of developing motoneurons and its depletion causes defects in axon growth. Here, we used iCLIP to determine the RNA interactome of hnRNP R in motoneurons. We identified ~3,500 RNA targets, predominantly with functions in synaptic transmission and axon guidance. Among the RNA targets identified by iCLIP, the non-coding RNA 7SK was the top interactor of hnRNP R. We detected 7SK in the nucleus but also in the cytosol of motoneurons. In axons, 7SK localized in close proximity to hnRNP R and depletion of hnRNP R reduced axonal 7SK. Furthermore, suppression of 7SK led to defective axon growth that was accompanied by axonal transcriptome alterations similar to those caused by hnRNP R depletion. Using a series of 7SK deletion mutants we show that the function of 7SK in axon elongation depends on its interaction with hnRNP R but not with the pTEF-B complex involved in transcriptional regulation. These results propose a role of 7SK as essential interactor of hnRNP R to regulate its function in axon maintenance.

overall_design: Total number of samples is 33

first: Changhe

last: Ji

first: Hanaa

last: Ghanawi

last: Uhl

first: Rolf

last: Backofen

last: Sendtner


title: Gene expression profiles of liver and lung endothelial cells during normal and upregulation of Wnt/beta-catenin signaling

status: Public on Feb 25 2018

city: La Jolla

first: Richard

last: Daneman

address: 9500 Gilman Drive

institute: UCSD

summary: We genetically overexpressed a gain-of-function beta-catenin allele in liver and lung endothelial cells to identifiy the set of BBB genes regulated by the Wnt/beta-catenin pathway

overall_design: Gene expression profiles were generated by RNA sequencing from 4 biological samples from adult mice of each condition: liver and lung from control mice, liver and lung from mice with endothelial overexpression of activated-beta-catenin

first: Roeben

last: Munji


title: Spec-seq data for ZFY and its truncated variants

status: Public on Jan 12 2018

first: Zheng

last: Zuo

summary: We used previously developed method, Spec-seq, to characterize the protein-DNA interaction specificity of human and mouse Zinc Finger Y protein.

overall_design: In this data set, we included differently truncated versions of ZFY, i.e., human ZFY(F11-F13), human ZFY(F9-F13), human ZFY(F7-F13), mouse ZFY(F7-F13), human ZFY(F1-F11). With the same set of randomized dsDNA libraries used, we found the F12-F13 confered the highest specificity to GGCC motif, and the accessory finger bind to some extended secondary motif ----TAG---TTT--- in irregular way.


title: Expression data from human metastatic adrenocortical carcinoma

status: Public on Nov 24 2017

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary:
CXCR4 expression by metastatic adrenocortical carcinoma is heterogeneous among patients and among lesions
We used microarrays for 57 ACC metastases from 42 patients to evaluate gene expression in different lesions from same patients and over time, focusing on CXCR4 expression and other genes correlating with CXCR4 expression

overall_design: 57 ACC metastases from 42 patients were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain data on CXCR4 expression by ACC metastases. Multiple lesion samples were aquired for 9 of the patients, labeled a thru i. Single samples were aquired from the other subjects.

first: Joshua

last: Farber

first: Antonio

middle: T

last: Fojo

first: Ido

last: Weiss


title: Transcriptome profiling from adipose tissue during low-caloric diet reveals predictors of long-term weight and glycemic outcomes in obese, non-diabetic subjects

status: Public on Mar 01 2018

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

summary:
Background: Low-caloric diet (LCD) reduces fat mass excess, improves insulin sensitivity, and alters adipose tissue (AT) gene expression. Yet the relationship with long-term clinical outcomes remains unclear.

Objective: We evaluated transcriptome alterations in AT during LCD and association with weight and glycemic outcomes both at LCD termination and 6-month after the LCD.

Results: Upon LCD, we identified 1’173 genes differentially expressed; with 350 and 33 genes associated respectively with changes in BMI and Matsuda. Twenty-nine genes were associated with both endpoints. Pathway analyses highlighted enrichment in lipid and glucose metabolism. Models were constructed to predict weight maintainers. A model based on clinical baseline parameters could not achieve any prediction (validation’s AUC= 0.50 [0.36, 0.64]), while a model based on clinical changes during LCD yielded to good performance (AUC=0.73 [0.60, 0.87]). Incorporating baseline expression from the 18 genes outperformed the best clinical model (AUC=0.87 [0.77, 0.96], Delong’s p=0.012). Similar analyses were made to predict subjects with good glycemic improvements. Both baseline- and LCD-based clinical models yielded to similar performance (with best AUC=0.73 [0.60, 0.85]). Addition of expression changes during LCD improved substantially the performance (AUC=0.80 [0.69, 0.92], p=0.058).

Conclusions: This study investigated AT transcriptome alterations following LCD in a large cohort of obese, non-diabetic patients. The identified genes enabled to significantly improve clinical models and predict long-term clinical outcomes. These biomarkers may help clinicians understanding the large inter-subject variability and better predict the success of dietary interventions.

overall_design: Design: Using RNAseq, we analyzed transcriptome changes in AT from 191 obese, non-diabetic patients within a multi-center controlled dietary intervention. Expression changes were associated with outcomes after 8-week LCD (with 800-1000kcal/d) and 6-month after LCD. Results were validated using RT-qPCR in 350 subjects from the same cohort. Statistical models were constructed to predict subjects considered as weight maintainers or glycemic improvers 6-month after LCD.

first: Claudia

last: Armenise

first: Sophie

last: Bonnel

first: Jennifer

last: Bolton

first: Jérôme

last: Carayol

first: Nele

last: Gheldof

first: Patrick

last: Descombes

first: Dominique

last: Langin

first: Wim

last: Sarris

first: Arne

last: Astrup

first: Jorg

last: Hager

first: Nathalie

last: Viguerie

first: Armand

last: Valsesia


title: CCAR2 is required for proliferation and tumor maintenance in human Squamous Cell Carcinoma

status: Public on Feb 01 2017

first: Matthew

last: Ramsey

address: 77 Ave Louis Pasteur, HIM 668

department: Dermatology

institute: Brigham and Women's Hospital

summary: This study was designed to elucidate the role of CCAR2 in human Squamous Cell Carcinoma Cells.

overall_design: Total RNA from human Squamous Cell Carcinoma cell lines (SCC-13, HO1N1,and SCC-15) was isolated 48 hours after lentiviral infection with either control shRNA or shRNA directed against CCAR2


title: Ectopic overexpression of the SnRK1 interacting protein STOREKEEPER RELATED 1/GeBP affects growth and development of Arabidopsis thaliana and leads to a constitutive immune response

status: Public on Oct 06 2017

city: Erlangen

first: Weber

last: Simone

state: Bavaria

address: Ulmenweg 18

department: Medicine

summary: We show that the catalytic a subunits KIN10 and KIN11 of the Arabidopsis thaliana SnRK1 complex interact with the STOREKEEPER RELATED 1/G-element Binding Protein (STKR1) inside the plant cell nucleus. Overexpression of STKR1 in transgenic Arabidopsis plants led to reduced growth, a delay in flowering and strongly attenuated senescence. At the global transcriptome level, genes affected by STKR1 overexpression were broadly associated with systemic acquired resistance and transgenic plants showed enhanced resistance towards a virulent strain of the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2.

overall_design: For microarray analyses, leaf samples from mature source leaves were taken in triplicate from 4-weeks old wild type plants or 35S-STKR1 lines 1, 2, or 5 either after 6 h of illumination or after an extended dark period for 6 h and total RNA was extracted using the RNAeasy Kit (Qiagen). Transcriptome profiling was performed on ArrayXS Arabidopsis v2 (XS-5010) microarrays in the Agilent 8 × 60K format (Oaklabs GmbH, Hennigsdorf, Germany) that represent 30,541 Arabidopsis genes. The array design is described in GEO accession GPL19779.

first: Frederik

last: Börnke

first: Madlen

last: Nietzsche

first: Sophia

last: Sonnewald


title: Expression data in human young and old primary keratinocytes

status: Public on Jan 03 2018

city: Montreal

first: Simon-Pierre

last: Gravel

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

institute: University of Montreal

summary:
PGC-1s (PGC-1alpha and PGC-1beta) are transcriptional coactivators involved in mitochondrial biogenesis, metabolism, and antioxidant defense. Given the existing links between PGC-1s and aging, we wanted to investigate the contribution of PGC-1s to skin aging. Keratinocytes form a self-renewable layer that differentiate to generate full epidermis. Defects in keratinocyte metabolism related to aging or PGC-1s depletion could impair normal function of keratinocytes and contribute to skin thinning.
We used microarrays to detail the global gene expression changes shared by the aging process and the depletion in PGC-1s.

overall_design: We selected a pair of primary keratinocytes from human donors that were matched for gender (male), ethnicity (caucasian) and body site (back skin). Young cells were from a 28 y.o. donor, aged cells were from a 83 y.o. (55-year difference). Cells were cultured using the same media and grown at similar cell densities. RNA were extracted from subconfluent cultures 3 days post-treatment (siRNA control or siRNA PGC-1alpha+PGC1beta). Each condition has 2 biological replicates.

first: Youcef

last: Ben Khalifa

first: Stéphanie

last: Desbouis

first: Frédéric

last: Amaral

first: Damien

last: Benas

first: Lionel

last: Breton

first: Sybille

last: Jäger

first: Julie

last: St-Pierre


title: Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice

status: Public on Nov 10 2017

city: Irvine

first: Raquel

last: Chamorro-Garcia

address: 4351 Natural Sciences 2

institute: University of California Irvine

summary: Ancestral environmental exposures to non-mutagenic agents can exert effects in unexposed descendants, adding a layer of complexity to long-standing attempts to clarify the relationships between genotypic and phenotypic variations. Transgenerational inheritance of environmental exposures has significant implications for understanding disease etiology. The environmental obesogen hypothesis proposes that exposure to obesogenic chemicals can lead to increased adiposity, in vivo. Here we show that exposure of F0 mice to the obesogen tributyltin (TBT) throughout pregnancy and lactation predisposes unexposed F4 male descendants to obesity when dietary fat is increased. Analyses of body fat, plasma hormone levels, and visceral white adipose tissue DNA methylome and transcriptome collectively indicate that the TBT-dependent F4 obesity is consistent with a leptin resistant, "thrifty phenotype". We found that ancestral TBT exposure induced global changes in DNA methylation together with altered expression of metabolism-relevant genes when the animals were exposed to dietary challenges. Analysis of chromatin accessibility in sperm revealed significant differences between DMSO and TBT groups when guided by DNA sequence composition, a proxy for higher order chromatin organization. Taken together, these data establish an independent connection between ancestral TBT treatment and altered chromatin accessibility that may reflect changes in higher order chromatin organization transmissible through meiosis and mitosis.

overall_design:
We generated RNA-Seq data in gonadal adipose tissue from 33-week old F4 mice ancestrally exposed to DMSO (0.1%) or TBT (50 nM ) during in utero development and lactation. N=4 per treatment --> 8 RNA-seq samples in total
We generated MBD-seq data in gonadal adipose tissue from 33-week old F4 mice ancestrally exposed to DMSO (0.1%) or TBT (50 nM ) during in utero development and lactation. N=4 per treatment --> 8 RNA-seq samples in total
We generated ATAC-seq data in gonadal adipose tissue from F3 and F4 mice at 8 weeks of age ancestrally exposed to DMSO (0.1%) or TBT (50 nM ) during in utero development and lactation. N=6 per treatment --> 24 RNA-seq samples in total

first: Carlos

last: Diaz-Castillo

first: Bassem

last: Shoucri

first: Heidi

last: Käch

first: Ron

last: Leavitt

first: Toshi

last: Shioda

first: Bruce

last: Blumberg


title: Gene expression profiling of ovaries collected from rat treated with pregnant mare serum gonadotropins (PMSG) and without PMSG

status: Public on Jun 30 2017

city: Delhi

first: shah

middle: saddad

last: Hussain

state: Delhi

address: Chhatra marg

department: Zoology

country: India

institute: University of Delhi

summary: PMSG acts like LH in horses and mares but works like FSH in heterologous animals under certain circumstances.

overall_design:
Organism: Rattus norvegicus. Agilent Rat Gene expression 8x60k Array AMADID: 028279.
Ovaries from control rats or rats treated with PMSG. 4 replicates each.

first: Shah

middle: S

first: Kambadur

last: Muralidhar


title: Single-cell RNA-seq reveals disparate macrophage responses to intracellular Salmonella

status: Public on Sep 14 2016

first: Silke

last: Appenzeller

summary: Intracellular bacterial pathogens can exhibit large heterogeneity in growth rate inside host cells with major consequences for the infection outcome. If and how the host responds to this heterogeneity remains poorly understood. Here, we combined a fluorescent reporter of bacterial cell division with single-cell RNA-seq analysis to study the macrophage response to different intracellular states of the model pathogen Salmonella enterica serovar Typhimurium. The transcriptomes of individual infected macrophages revealed a spectrum of functional host response states to dividing and non-dividing bacteria. Intriguingly, macrophages harboring non-dividing Salmonella display hallmarks of the pro-inflammatory M1 polarization state and differ little from bystander cells, suggesting that non-dividing bacteria evade recognition by intracellular immune receptors. By contrast, macrophages containing dividing bacteria have turned into an anti-inflammatory, M2-like state, as if fast-growing intracellular Salmonella overcome host defense by reprogramming macrophage polarization. Additionally, our clustering approach reveals intermediate host functional states between these extremes. Altogether our data suggest that gene expression variability in infected host cells shapes different cellular environments, some of which may favor a growth arrest of Salmonella facilitating immune evasion and the establishment of a long-term niche; while others allow Salmonella to escape intracellular antimicrobial activity and proliferate.

overall_design: 60 samples

first: Antoine

last: Saliba

first: Lei

last: Li

first: Alexander

middle: J

last: Westermann

first: Daphne

last: Stapels

first: Leon

middle: N

last: Schulte

first: Sophie

last: Helaine

first: Joerg

last: Vogel


title: The cerebrovascular response to injury and disease

status: Public on Oct 03 2017

first: Roeben

last: Munji

state: California

address: 9500 Gilman Dr.

department: Pharmacology

institute: University of California San Diego

summary: RNAseq of purified CNS endothelial cells from health and disease.

overall_design: FACS purification of endothelial cells from different tissues during health, as well as CNS endothelial cells following different disease models

first: Richard

last: Daneman

first: Allison

last: Soung


title: Genomewide investigation of pre-invasive and invasive epithelial changes in human papillomavirus associated oropharyngeal carcinoma

status: Public on Nov 01 2015

city: Cambridge

first: Liam

last: Masterson

state: Cambridgeshire

address: Hills road

department: Pathology

institute: University of Cambridge

summary:
Background: The incidence of human papillomavirus (HPV) associated oropharyngeal carcinomas has increased rapidly over the last thirty years. These tumours behave as a distinct biological entity when compared to classical smoking- and alcohol-related disease. To gain more information regarding the pathway through pre-malignancy in HPV positive/HPV negative oropharyngeal carcinoma (OSCC), we investigated genomewide expression profiles in histopathologically confirmed tumour samples with site-matched normal epithelial controls.

Methods: Twenty-four patients with primary oropharyngeal squamous cell carcinoma (4 with stage III and 20 with stage IV disease) were included in this prospective clinical trial (UKCRN11945). The tumour tissues were each assessed by a histopathologist with HPV status and typing by p16INK4A, consensus PGMY PCR, type-specific HPV16 DNA & RNA PCR and DNA sequencing. Fresh tissue samples were subjected to whole transcriptome analysis using the Illumina Bead Array (~47,000 transcripts) and the results validated with quantitative Real Time-PCR (qRT-PCR). In a separate cohort of twelve OSCC patients, laser capture micro-dissection of formalin fixed paraffin embedded (FFPE) tissue allowed RNA extraction from regions of in situ malignant change (with matched normal and invasive SCC samples).

Results: The majority of OSCC patients (28/36) displayed evidence of high risk HPV positivity. Predictable fold changes of RNA expression in HPV-associated disease included multiple transcripts within the p53 oncogenic pathway (e.g. CDKN2A/CCND1). Other candidate transcripts found to have altered levels of expression in this study have not previously been established in HPV16 associated oropharyngeal cancer. These were involved in cell differentiation, proliferation and invasion and demonstrated considerable overlap with expression analysis data in other oncogenic pathways (SFRP1/CRCT1/DLG2/SYCP2/CRNN). SYCP2 showed the highest consistent fold change from baseline in both fresh frozen and FFPE tissue (qRT-PCR fresh frozen tissue [P<0.04]; FFPE tissue pre-invasive [P<0.01]; FFPE tissue invasive [P<0.01]), and aberrant expression of this meiosis-specific protein may contribute to genetic instability during HPV-associated cancer development.

Conclusion: Investigation of differentially expressed genes in HPV-positive tumours may reveal unique pathways that can explain their different natural history and biological properties. The data from this study reveal SYCP2 (amongst others) as a potential biomarker in HPV positive oropharyngeal carcinoma, and if corroborated on a larger scale, may facilitate the development of a non-invasive screening tool.

overall_design: Twenty four samples (12 matched invasive oropharyngeal carcinoma and normal epithelial controls).

first: Frederic

last: Sorgeloos

first: David

last: Winder

first: Alison

last: Marker

first: Shalini

last: Malhotra

first: Holger

last: Sudhoff

first: Piyush

last: Jani

first: Peter

last: Goon

first: Jane

last: Sterling


title: Subcellular whole transcriptome profiling reveals the RNA composition of motor axons

status: Public on Oct 13 2015

first: Silke

last: Appenzeller

summary: Most RNAs within polarized cells such as neurons are sorted subcellularly in a coordinated manner. Despite advances in the development of methods for profiling polyadenylated RNAs from small amounts of input RNA, techniques for profiling coding and non-coding RNAs simultaneously are not well established. Here, we optimized a transcriptome profiling method based on double-random priming and applied it to serially diluted total RNA down to 10 pg. Read counts of expressed genes were robustly correlated between replicates, indicating that the method is both reproducible and scalable. Our transcriptome profiling method detected both coding and long non-coding RNAs sized >300 bases. Compared to total RNA-seq using a conventional approach, our protocol detected 70% more genes due to reduced capture of ribosomal RNAs. We used our method to analyze the RNA composition of compartmentalized motoneurons. The somatodendritic compartment was enriched for transcripts with post-synaptic functions as well as for certain nuclear non-coding RNAs such as 7SK. In axons, transcripts related to translation were enriched including the cytoplasmic non-coding RNA 7SL. Our profiling method can be applied to a wide range of investigations including perturbations of subcellular transcriptomes in neurodegenerative diseases, and investigations of microdissected tissue samples such as anatomically defined fiber tracts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total number of samples is 43

first: Michael

last: Briese

first: Lena

last: Saal

first: Mehri

last: Moradi

first: Apoorva

last: Baluapuri

last: Sendtner


title: Transcript profiling upon ethanol-induced expression of Xcv type 3- effector xopB in A. thaliana

status: Public on Oct 01 2015

first: Weber

last: Simone

summary: The bacterial pathogen Xanthomonas campestris pv. vesicatoria 85-10 (Xcv) translocates about 30 type 3 effector proteins (T3Es) into pepper plants (Capsicum annuum) to suppress its immune responses. Among them is XopB which was previously shown to interfere with cell wall-bound invertase (CwInv) and sugar-mediated defence responses. Transgenic Arabidopsis thaliana lines expressing xopB under control of an ethanol inducible promotor were generated to investigate the in planta activity of this effector protein in more depth. The microarray analysis revealed that expression of the bacterial T3E XopB in A. thaliana plants causes immediate and massive reprogramming of transcription resulting in the alteration of the hormonal homeostasis and imbalances in signalling cascades. Further analyses unravelled that XopB modifies the pathogen associated molecular pattern (PAMP)-triggered calcium signature and inhibits the burst of reactive oxygen species (ROS).

overall_design: For microarray analyses, five week old transgenic plants (# 10, 12, 27) and wild-type plants were watered with 10 ml 1% (v/v) ethanol per pot after light has switch on in the climate chamber. Leaves from individual plants were harvested 4 h after treatment and immediately frozen in liquid nitrogen. Development of phenotypic changes was monitored and leaves of plants showing comparable phenotypes were pooled into 3 replicates.

first: Julia

last: Schuster

first: Stephen

last: Reid

first: Johannes

last: Priller

first: Sophia

last: Sonnewald


title: General retardation of mRNA degradation caused by speB 5’ UTR partial deletion in Streptococcus pyogenes

status: Public on Sep 10 2015

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

institute: University of Oklahoma Health Sciences Center

summary:
The speB gene of Streptococcus pyogenes has a long 5' UTR with unknown functions. Preliminary studies showed that the partial mutation of this region led to altered expression patterns of the speB gene and ropB, its upstream gene.
In this study, we used microarray to examine the effect of speB 5' UTR mutation on the S. pyogenes transcriptome.

overall_design: The speB ORF and a large portion of the speB 5’ UTR (-1 to -527 from ATG) was replaced with an erythromycin resistant cassette gene (ermAM) to generate a ΔIG mutant. Transcriptome profiles of the wild-type (WT) and ΔIG mutant in the mid-exponential phase and early stationary phase (ST) were examined with microarray analysis.

first: Zhiyun

last: Chen

first: Joseph

last: Ferretti


title: Development of gene expression profiles in human chronic kidney disease

status: Public on Aug 16 2015

city: Fukuoka

first: Satohiro

last: Masuda

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmacy

institute: Kyushu University Hospital

summary: A microarray analysis with renal biopsy specimens from CKD patients was conducted in order to identify the responsible genes associated with tubulointerstitial fibrosis and tubular cell injury in CKD. This study showed microarray profiles in total 53 biopsy specimens of CKD patients. In the discovery set, 554 down-regulated and 226 up-regulated signatures were identified. Then, the expressional changes of these genes were examined in the validation set.

overall_design: Gene expression profiles in human chronic kidney disease was explored using renal biopsy specimens. Two independent studies: discovery set and validation set were performed.

first: Shunsaku

last: Nakagawa

first: Kumiko

last: Nishihara

first: Hitomi

last: Miyata

first: Haruka

last: Shinke

first: Takeshi

last: Matsubara

first: Noriyuki

last: Iehara

first: Kazuo

first: Atsushi

last: Fukatsu

first: Motoko

last: Ynagita


title: Analysis of human, chimpanzee, macaque and mouse tissue transcriptomes using Next Generation Sequencing

status: Public on Sep 01 2015

city: Berlin

first: Jorge

last: Ruiz-Orera

state: Berlin

address: Robert-Rössle-Straße 10

institute: Max Delbruck Center for Molecular Medicine

summary: We performed deep strand-specific sequencing of poly-adenylated RNA (polyA+ RNAseq) from human, chimpanzee, macaque and mouse tissues, with the goal of detecting numerous non-annotated poorly expressed and antisense genes. We identified thousands of annotated and novel genes, especially in testis. We discovered that ~2% of the human and chimpanzee multiexonic genes were specific from such species.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus

overall_design: We generated RNA-Seq data (∼2.10 billion paired-end reads, 25-100 bp length) for the polyadenylated RNA fraction of brain (cerebral cortex), heart, liver and testis. In human and chimpanzee, we generated 2 samples per tissue corresponding to different individuals. In macaque, only 1 sample per tissue was generated. In mouse, considered as the evolutionary outgroup, we generated three pools of brain samples, and one pool of heart, liver and testis samples.  We generated an additional sample in Testis without including reverse transcriptase as a control of DNA contamination.

first: Jessica

last: Hernandez-Rodriguez

first: Tomàs

last: Marqués-Bonet

first: M

middle: M

last: Albà


title: Genome-wide analysis of gene expression to identify the probably functionally relevant pathways in cervical cancer progression

status: Public on Apr 02 2015

city: Kalyani

first: Sharmila

last: Sengupta

state: West Bengal

address: P.O.: N.S.S., Kalyani 741251 West Bengal, INDIA

institute: National Institute of Biomedical Genomics

summary: Identification of genes and pathways relevant to Cervical cancer pathogenesis. The study also aimed at identifying  probable mechanistic differences in the low and high HOTAIR expressing cervical cancers patients .

overall_design: Total RNA obtained from HPV negative histologically normal controls, HPV16 positive non-malignants and HPV16 positive cervical cancers having either low or high HOTAIR expression levels were compared to identify transcriptome level differences.

first: Sweta

last: Sharma

first: Paramita

last: Mandal


title: Multi-scale 3D genome rewiring during mouse neural development

status: Public on Oct 18 2017

city: Montpellier

first: Boyan

last: Bonev

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

summary: Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We mapped comprehensively 3D chromatin organization during mouse neural differentiation in vitro and in vivo, generating the highest resolution Hi-C maps available to date.  We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating topological domain (TAD) boundaries de novo. Additionally, we discovered long-range contacts between gene bodies of exon-rich, active genes in all cell types. During neural differentiation, contacts between active TADs become less pronounced while inactive TADs interact stronger. An extensive Polycomb network in stem cells is disrupted, while dynamic interactions between proneural transcription factors appear in vivo. Finally, cell-type specific enhancer-promoter contacts are established concomitant to gene expression. This work shows that multiple factors influence the dynamics of chromatin interactions in development.

overall_design: Hi-C, RNAseq, ChIPseq in mouse cortical development (in vitro and in vivo)

first: Netta

last: Mendelson Cohen

first: Quentin

last: Szabo

first: Lauriane

last: Fritsch

first: Giorgio

last: Papadopoulos

first: Yaniv

last: Lubling

first: Xiaole

last: Xu

first: Xiaodan

last: Lv

first: Jean-Philippe

last: Hugnot

first: Amos

last: Tanay

first: Giacomo

last: Cavalli


title: FC-IBC-02: A New in vitro-in vivo Model of Triple Negative Inflammatory Breast Cancer

status: Public on Sep 20 2012

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

summary: Inflammatory breast cancer (IBC) is the most aggressive type of advanced breast cancer and is associated with a poor prognosis. We have developed a new model of IBC derivated from the pleural effusion of a 49-year-old woman with metastatic secondary IBC. FC-IBC02 tumor cells were isolated from the pleural effusion and cultured under non-adherent conditions, resulting in the formation of spheroids or mammospheres. FC-IBC02 are triple negative (estrogen receptor negative, progesterone receptor negative and ErbB2 negative) and strongly positive for E-cadherin, beta-catenin and vimentin. FC-IBC02 cells developed breast tumors when they were injected into the mammary fat pad of SCID mice and characteristic tumor emboli were detected. Breast tumor xenografts were poorly differentiated triple negative carcinomas and all injected mice developed metastasis in the lungs and lymph nodes. These IBC tumor cells showed genomic alterations in all chromosomes, with the gains/amplifications more common than the deletions/losses. Duplicated regions were on 1q, 2p, 3q, 8q and 18p and chromosomes 7 and 9. The 8q chromosome arm where the MYC oncogene resides was amplified up to seven fold. Chromothripsis (local chromosome shattering) was observed on chromosome 11q and losses were found on 8p, 11q, 16q and 17p (location of TP53). FC-IBC-02 cells expressed the stem cell marker CD44, EpCAM and strongly expressed EGFR and ALK. In summary, this novel preclinical model demonstrated that IBC is a disease enriched for highly tumorigenic cells which harbor a stem cell phenotype. This IBC model is ideal for the study of the metastatic process and to evaluate targeting therapeutic modalities.

overall_design: Total RNA were isolated from IBC-02, IBC-02 in mammosphere growth, IBC3, SUM149, SUM190, MDA-MB231, and MDA-MB468 cell lines. Affymetrix Human U133 Plus 2.0 arrays were used for whole-genome gene expression assays. Duplicate samples were analyzed for each cell line.

first: Sandra

last: Fernandez

first: Khoi

last: Chu

first: Jianming

last: Pei

first: Lucy

last: Aburto

first: Katherine

last: Alpaugh

first: Zuejun

last: Zhang

first: Yu

last: Cao

first: Zaiming

last: Ye

first: Moisha

middle: C

last: Wright

first: Kimberly

last: Boley

first: Andres

last: Klein-Szanto

first: Kathy

middle: Q

last: Cail

first: Karthik

last: Devarajan

first: Fredika

last: Robertson

first: Massimo

last: Cristofanilli


title: Expression data from QdNOs treated Escherichia coli

status: Public on Jul 25 2012

city: WuHan

first: li

last: bei

address: Shizishan Street

institute: Huazhong Agricultural University

summary:
Cyadox(CYA), as a new species of Quinoxaline 1, 4-dioxides and olaquindox(OLA) both showed higher antibacterial activity under anaerobic incubation. Microarray was used for global gene expression studies, which were further confirmed by real-time PCR.
Cyadox and olaquindox mainly stimulated the expression of DNA repair genes as a response to the DNA damage. The induced gene sbmC was found to provide partial protection against the antibiotics of gyrase inhibitors like the quinolones and the ruvAB helped remove the topoisomerase IV-DNA cleavage complex caused by some type IIA topoisomerase poison antibiotics. It was inferred that the radical intermediate of cyadox reduction under anaerobic condition was responsible for the poison effect of IIA topoisomerases, which brought about DNA double stand breaks and other DNA damages in E. coli.

overall_design: We applied subinhibitory concentrations (concentrations that cause little growth inhibition) of two drus with the goal of observing antibiotic-specific primary expression profiles, and higher concentrations of drugs had been shown to cause a broader effect on cellular processes, thereby giving more complex response patterns and dose-specific effects could be examined.To the end, drugs were added to a final concentration of 0.5MIC(2) and MBC(3) for cyadox, and MIC(4) and MBC(5) for olaquindox, respectively. Control with 1% (vol/vol) DMSO(1) was grown in parallel.

first: Bei

last: Li

first: Menghong

last: Dai

first: Guyue

last: Cheng


title: Expression data SK-N-SH cells treated with risperidone

status: Public on Mar 22 2012

city: Barcelona

first: Sergi

last: Mas Herrero

state: Catalunya

address: Casanova 143

department: Pharmacology, School of Medicine

country: Spain

institute: University of Barcelona

summary:
We  performed a pharmacotranscriptomic analysis of a human neuroblastoma cell line (SK-N-SH) exposed to risperidone to identify molecular mechanisms involved in the cellular response to risperidone and thus identify candidate genes for pharmacogenetic studies.
This study is a part of a convergent functional genomic approach that plans to integrate the data presented here with: data from gene expression analysis of experimental animal brain under treatment with risperidone; and data from gene expression analysis of peripheral blood from first psychotic patients treated with risperidone.

overall_design: Gene expression was assessed by microarray (Human Genome U219 Array) in cells treated with risperidone 10 µM at 6, 24 and 48 h

last: Mas

first: Patricia

last: Gassò

first: Amalia

last: Lafuente


title: Mycobacterium smegmatis - Comparison of wild type SMR5 and amtR deletion strain YL1 under nitrogen surplus

status: Public on Jul 01 2011

first: Weber

last: Simone

summary:
In this approach, total transcript of the Mycobacterium smegmatis wild type was compared to a amtR deletion strain under nitrogen surplus. With this experiment, putative target genes of AmtR, a regulator protein of nitrogen metabolism, were identified.
Two biological replicates were analyzed.

overall_design: Nadja,Jessberger

first: Stephen

last: Reid

first: Sophia

last: Sonnewald

first: Johannes

last: Amon

first: Andreas

last: Burkovski


title: Mycobacterium smegmatis - Comparison of wild type SMR5 and glnR deletion strain MH1 under nitrogen starvation

summary:
In this approach, total transcript of the Mycobacterium smegmatis wild type SMR5 and a glnR deletion strain was compared under nitrogen starvation. Transcript levels of 6 genes were enhanced, 125 genes reduced in the mutant strain. This experiment confirmed GlnR as the global regulator of nitrogen metabolism in M. smegmatis.
Two biological replicates were analyzed.


title: Mycobacterium smegmatis - Comparison of wild type SMR5 under nitrogen surplus and starvation

summary:
In this approach, total transcript of the Mycobacterium smegmatis wild type SMR5 was compared under nitrogen surplus and starvation. This resulted in the change of transcript patterns of more than 500 genes due to nitrogen or general starvation response. Genes involved in uptake and assimilation of ammonium and alternative nitrogen sources showed enhanced transcript levels, genes involved in cell growth, protein biosynthesis etc showed reduced transcript levels.
Two biological replicates were analyzed.


title: Mycobacterium smegmatis - Comparison of glnR deletion strain MH1 under nitrogen surplus and starvation

summary: In this approach, changes in total transcript of a glnR deletion strain of Mycobacterium smegmatis due to nitrogen starvation were monitored. This is a control experiment for the comparison of wild type and glnR deletion strain resulting in putative nitrogen-related genes which are not controlled by GlnR.

overall_design: Two biological replicates were analyzed.

first: Nadja

last: Jessberger


title: Effect of intra-cytoplasmic sperm injection (ICSI) on gene expression and development of mouse preimplantation embryos

status: Public on Nov 10 2010

city: Reno

first: Gnanaratnam

last: Giritharan

state: Nevada

address: 645 Sierra Rose Drive, Suite 205

institute: Nevada Center for Reproductive Medicine

summary: Background: In vitro culture of preimplantation mouse embryos is associated with changes in gene expression.  It is however not known if the method of fertilization affects the global pattern of gene expression.   Method: We compared gene expression and development of mouse blastocysts produced by intra-cytoplasmic sperm injection and cultured in Whitten’s medium (ICSIWM) or KSOM medium with amino acids (ICSIKSOMaa) with control blastocysts flushed out of the uterus on post coital day 3.5 (In vivo). Global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip. In addition we compared gene expression in embryos generated in IVF or ICSI using WM.   Results: Blastocysts resulting from ICSI fertilization have a reduction in the number of trophoblastic and inner cell mass cells compared to in vivo generated embryos. Approximately 1000 genes are different between ICSI blastocyst and in vivo blastocysts; proliferation, apoptosis and morphogenetic pathways are the most common pathways altered after in vitro culture. Unexpectedly, only 41 genes were statistically different between embryo cultured in suboptimal conditions (WM) or optimal conditions (KSOMaa).  Conclusion: The method of fertilization plays a more important role in shaping the transcriptome of the developing mouse embryo than the culture media used.

overall_design: 16 samples were used in 4 treatment groups (4 replicate samples per treatment)

first: Paolo

middle: F

last: Rinaudo


title: Analyses of the GlnR- and AmtR- dependent nitrogen regulatory network of Mycobacterium smegmatis.

summary:
Total transcriptome analyses were carried out to investigate changes in transcript patterns in the Mycobacterium smegmatis wild type strain SMR5 due to nitrogen starvation and to expand the knowledge about the role of the two transcriptional regulators of nitrogen metabolism, namely GlnR and AmtR, in these processes. A first experiment revealed enhanced transcript levels of 284 genes and reduced transcripts of 231 genes in the wild type under nitrogen starvation compared to nitrogen surplus. When glnR deletion strain MH1 was compared to the wild type under nitrogen starvation, decreased transcript levels of 125 genes were detected, indicating that these are activated by GlnR due to nitrogen limitation. Comparing amtR deletion strain YL1 to the wild type under nitrogen starvation, enhanced transcript levels of 2 genes were found, indicating that they are repressed by AmtR under nitrogen surplus. A comparison of YL1 and wild type under surplus, as well as a comparison of YL1 under nitrogen surplus and starvation and of MH1 under nitrogen surplus and starvation were carried out as additional control experiments. It can be concluded that GlnR is the master regulator of nitrogen control in M. smegmatis and that AmtR fulfills only a small, subordinate role in the regulation of an operon.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Establishing a functional response of cardiomyocytes upon prorenin stimulation.

status: Public on Aug 31 2006

city: Rotterdam

first: Jasper

last: Saris

state: Zuid holland

address: Dr. Molewaterplein 50

country: Netherlands

institute: Erasmus Medical Center

summary:
Rat neonatal cardiomyocytes have been used to study the effect of (pro-) renin binding upon intracellular messenger systems, hypothesized via IGF2/mannoste 6 phosphate (M6P) -receptors and/or ATP6AP2/(pro)renin receptors, opposed to kidney cells. We have used DNA microarray technology to characterize and compare the expression of over 4800 genes in these cells. Gene expression differences were verified using RT-PCR and indicate the presence of cellular activation upon prorenin bindng, non-overlapping with AT-receptor activation. Exploration and follow-up will lead to further characterization of these pathways.
Keywords: loop design

overall_design: We analyzed 6 arrays in a loop design, including dye-swap with linear amplified RNA-pools of 5 different cardiomyocytes preparations, with the Compugen designed and Sigma-Genosys synthesised 65-mer oligo's spotted in triplicate on each slide.

first: PAC

last: 't Hoen


title: Substantial equivalence in transgenic barley

status: Public on Mar 03 2010

summary: In this study, possible adverse effects of transgene expression in field-grown barley were assessed in relation to the influence of genetic background and to the impact of interaction with arbuscular mycorrhiza fungi. The deposited microarray data originate from a parallel transcript profiling, metabolome profiling and metabolic fingerprinting approach with the wild type cultivars Golden Promise (GP) and Baronesse (B) as well as barley transgenics with i) seed-specific expression of (1,3-1,4)-ß-glucanase (GluB) being introgressed from the Golden Promise (GP) into the cultivar Baronesse (B) and ii) ubiquitous expression of codon-optimized Trichoderma harzianum endochitinase (ChGP).  Our conclusion from the results is that cultivar-specific differences and even the presence of few introgressed alleles exceed the effects on transcriptome and metabolome caused by transgene expression. Mycorrhization was shown to have more prominent effects on the metabolome than on the transcriptome.

overall_design: Hordeum vulgare plants were cultivated in the field in 2007 at Giessen Experimental station (165m elevation over NN, 1540h sunshine and 650mm precipitation per year in average) in replicated blocks, each consisted of eight 0.8 m × 0.5 m plots in which genotypes were randomly distributed and half of the plots were pretreated with Amykor® (containing the arbuscular fungi Glomus intraradices and Glomus mosseae). Ten pools of leaf material of at least 10 leaves per pool were sampled in the middle of the light period four months after planting. Two replicates of each genotype were subjected to microarray analysis.

first: Stefanie

last: Wisshak

first: Isabella

last: Zagorski

first: Alfred

last: Schmiedl

first: Jörg

last: Hofmann

first: Lars

last: Voll

first: Uwe


title: Mycobacterium smegmatis - Comparison of wild type SMR5 and amtR deletion strain YL1 under nitrogen starvation

summary:
In this approach, total transcript of the Mycobacterium smegmatis wild type was compared to a amtR deletion strain under nitrogen starvation. With this experiment, putative target genes of AmtR, a regulator protein of nitrogen metabolism, were identified.
Two biological replicates were analyzed.


title: Heterogeneity of Response to Chemotherapy and Recurrence-free Survival in Neoadjuvant Breast Cancer: Results from the I-SPY 1 TRIAL

status: Public on Jan 13 2012

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Introduction: The I-SPY 1 TRIAL was designed to evaluate complete pathologic response and tumor volume change, measured by magnetic resonance imaging (MRI), stratified by molecular subtypes and link response to 3-year recurrence free survival (RFS).Methods: Eligible patients had T =3 cm and received neoadjuvant chemotherapy with AC plus optional taxane.  Serial MRI, biopsy, and blood draws were conducted over the course of treatment, and a database of multiple molecular profiles was assembled.Results: A total of 221 patients were eligible for analysis: median tumor size was 6.0 cm and median age was 49 years.  The I-SPY 1 TRIAL patients had tumors with aggressive biology: 45% were estrogen receptor (ER) negative, 31% Her2+; and 91% high risk by the Netherlands Cancer Institute (NKI) 70-gene profile. After a median of 3.9 years, RFS was 77%.  HR/HER2 status improved predictability of RFS with the greatest difference between HR+/HER2- and triple-negative disease (hazard ratio 0.39).  Wound healing signature activation, p53 mutation, and Risk of Relapse (ROR) score were highly correlated and also significantly improved the accuracy of RFS predictions when added to stage. The rate of pathologic complete response (pCR) varied considerably from a low of 0-2% (NKI low risk, luminal A) to a high of 43-61% (17q Amplified, HER2 enriched, HR-/HER2+).  Both pCR and the more refined residual cancer burden (RCB) were significant predictors of RFS for all patients and even more predictive when analyzed within biomarker subsets.  Good risk (NKI low, ROR-S low risk, Wound Healing quiescent, p53 wild type) signatures were associated with significantly higher 3-year RFS than poor risk expression signatures (ROR-S high risk, Wound Healing Activated, p53 mutation, NKI high risk).Conclusion: Importantly, in this set of biologically poor prognosis tumors, pCR predicts for better outcome, especially when analyzed within breast cancer subsets.

Keywords: reference x sample

overall_design: reference x sample

first: LJ

last: Esserman

first: N

last: Hylton