title: Comprehensive Transcriptome Analysis of Cerebral Cavernous Malformation Across Multiple Species and Genotypes

status: Public on Dec 18 2018

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary:
Purpose: To determine important genes, functions, and networks contributing to the pathobiology of cerebral cavernous malformation (CCM) from transcriptomic analyses across 3 species and 2 disease genotypes.
Methods: Sequencing of RNA from laser microdissected  neurovascular units (NVUs) of 5 human surgically resected CCM lesions, mouse brain microvascular ECs (BMECs) and C. elegans with induced Ccm gene loss, and their respective controls, provided differentially expressed genes (DEGs). DEGs from mouse and C. elegans were annotated into human homologous genes. Cross-comparisons of DEGs between species and genotypes as well as network and Gene Ontology (GO) enrichment analyses were performed.
Results: Among hundreds of DEGs identified in each model, common genes and one GO term (GO:0051656 establishment of organelle localization) were commonly identified across the different species and genotypes. In addition, 24 GO functions were present in 4 out of 5 models and were related to cell-cell adhesion, neutrophil mediated immunity, ion transmembrane transporter activity, and responses to oxidative stress. We provide a comprehensive transcriptome library of CCM disease across species, and for the first time in Ccm1/Krit1 versus Ccm3/Pdcd10 genotypes
Conclusion: We provide examples of how results can be used in hypothesis generation or mechanistic confirmatory studies.

sample_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus

overall_design: 32 total RNA samples, including 8 laser microdissected  neurovascular units (NVUs) from 5 human cerebral cavernous malformations and 3 human brain autopsy contols, 12 mouse brain microvascular endothelium (3 Krit1 null, 3 Krit1 controls, 3 Pdcd10 null, 3 Pdcd10 controls), 12 C. elegans (3 Kri-1 null, 3 Kri-1 controls, 3 Pdcd10 null, 3 Pdcd10 controls)

first: Janne

last: Koskimäki

first: Romuald

last: Girard

first: Laleh

last: Saadat

first: Hussein

last: Zeineddine

first: Rhonda

last: Lightle

first: Thomas

last: Moore

first: Seán

last: Lyne

first: Kenneth

last: Avner

first: Robert

last: Shenkar

first: Ying

last: Cao

first: Changbin

last: Shi

first: Sean

last: Polster

first: Dongdong

last: Zhang

first: Julián

last: Carrión-Penagos

first: Sharbel

last: Romanos

first: Gregory

last: Fonseca

first: Miguel

last: Lopez-Ramirez

first: Eric

last: Chapman

first: Evelyn

last: Popiel

first: Alan

first: Amy

last: Akers

first: Pieter

last: Faber

first: Jorge

last: Andrade

first: Mark

last: Ginsberg

first: W

last: Derry

middle: L

last: Kahn

first: Douglas

last: Marchuk

first: Issam

last: Awad


title: Gene Expression Changes in Major Cell Types of the Glomerulus in a Mouse Model of Focal Segmental Glomerulosclerosis

status: Public on Dec 01 2018

city: Cincinnati

first: Andrew

last: Potter

state: OH

address: 240 Albert Sabin Way

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: We characterize the gene expression changes which occur in the mouse glomerular podocyte, mesangial, and endothelial cells between control mice and mutant mice which are missing two copies of Fyn-proto oncogene (Fyn) and one copy of CD2-associated protein (CD2AP) in a mouse model of FSGS.

overall_design: The glomeruli are purified by digestion with Collagenase A and sieving, a single cell suspension is generated via enzymatic dissociation; the single cell suspension is then FACS sorted based on GFP-fluorescence (targeting the glomerular endothelial, mesangial, and podocyte cells). Total RNA was purified using a column-based system. RNA was then quantitatively and qualitatively analyzed using an agilent bioanalynzer, cDNA libraries were generated using Nugen Ovation RNA-Seq V2, and the resulting libraries were ran on an Illumina HiSeq 2500. Data was analyzed using Strand NGS version 2.6.

middle: S

first: S

last: Brunskill


title: The pancreatic cancer stem cell marker CD44v6 affects transcription, translation and signaling: consequences on exosome composition and delivery III

status: Public on Aug 25 2018

city: Heidelberg

first: Jan

last: Provaznik

state: Baden-Wuerttemberg

address: Meyerhofstr. 1

department: Genomics Core Facility

country: Germany

institute: EMBL Heidelberg

summary:
The miRNA profile between EXO from different pancreatic adenocarcinoma cells (A818.4, Capan-1) and different colorectal carcinoma cells (SW948, HT-29).

The impact of a knockdown (kd) of function-relevant cancer stem cell markers (CD44v6, Tspan8, CD151, claudin7) on the EXO miRNA profile. The EXO kd cell miRNA profiles were compared with the wt cell EXO as well as between the different kd EXO miRNA profiles.

These analyses were important to elaborate joint miRNA in the EXO profile from different cell lines as a starting point to elaborate possible functional activities of EXO including therapeutic translation.

overall_design: miRNA profiling of exosomes in HT-29, SW-948 A818.4 and Capan-1 cells that are wildtype or Cld7 KD, CD151 KD, Tspan8 KD or CD44v6 KD.

first: Hanxue

last: Sun

first: Sanyukta

last: Rana

first: Zhe

last: Wang

first: Kun

last: Zhao

first: Martina

last: Schnölzer

first: Thilo

last: Hackert

first: Qingjie

last: Lv

first: Margot

last: Zöller


title: Genomic integrity safeguards pluripotency in embryonic stem cells

status: Public on Nov 01 2018

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

summary: Illumina BeadChip array analyses of mouse embryonic stem cell gene expression profiles in the presence of or upon knockdown of 4 candidate factors regulating genomic integrity -- Chek1, Ppm1g, Ppp2r1b and Bub1b. An ES complementation 'rescue' system was employed to measure the effects of knockdown (minus Dox). The 4 candidate factors are rescued to wildtype levels in the presence of Dox (plus Dox). A control rescue ES cell line, with a Luciferase-targeting shRNA, was also assessed.

overall_design: Total of 30 samples; Chek1_R (+/-Dox), Ppm1g_R (+/-Dox), Ppp2r1b_R (+/-Dox), Bub1b_R (+/-Dox), Control_R (+/-Dox); all performed in triplicates.

first: Dung

middle: F

last: Lee

first: Jie

last: Su

first: Yen

first: Xonia

last: Carvajal-Vergara

first: Betty

last: Chang

first: Ana

last: Sevilla

first: Ruiying

first: Christoph

last: Schaniel

first: Ihor

middle: R

last: Lemischka


title: Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings

status: Public on Nov 05 2018

city: Austin

first: Enamul

last: Huq

state: TX

address: NHB 2.616, Stop A5000 100 East 24th St.

department: Molecular Biosciences

institute: The University of Texas at Austin

summary:
Background: Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (e.g., HY5, HFR1, PAP1 and others) in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic bases for the constitutive photomorphogenic phenotypes of spaQ remain unknown.
Results: Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild type in the dark. Comparison of the RNAseq data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Moreover, a large number of genes (~2790) are predominantly regulated by SPA proteins and not by COP1, suggesting that SPA proteins might regulate many biological processes independently of COP1.
Conclusions: Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling expression of a large number of genes in concert with COP1, likely through regulating the abundance of downstream transcription factors in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and –independent manner in regulating many biological processes and developmental pathways in Arabidopsis.

overall_design: Total of 9 samples of  3 day dark-grown seedlings,  wild-type, cop1-4 mutant and spaQ mutant, each has three replicates

first: V

middle: N

last: Pham

first: Ute

last: Hoecker


title: Dynamic genetic regulation of gene expression during cellular differentiation

status: Public on Nov 10 2018

first: Reem

last: Elorbany

address: 920 E. 58th Street, CLSC 317

institute: University of Chicago

summary: The impact of genetic regulatory elements on gene expression can change during differentiation and across cell types and environments. We mapped expression quantitative trait loci (eQTLs) throughout differentiation to elucidate the dynamics of genetic effects and the associated cell type specific mechanisms. To do so, we generated high resolution time-series RNA-sequencing data, capturing differentiation from induced pluripotent stem cells to cardiomyocytes with 16 time points in 19 human cell lines. Genetic effects on gene regulation in these data show clear temporal structure. We identified hundreds of dynamic eQTLs that change significantly over time, with enrichment in enhancers of relevant cell types. We also found nonlinear dynamic eQTLs, which have effects only during intermediate stages of differentiation. These include a variant associated with body mass index, highlighting that transient genetic effects can contribute to disease.

overall_design: We obtained RNA-seq data for 19 Yoruba individuals at 16 time points each during the differentiation from iPSC to cardiomyocyte. There are a total of 297 samples.

first: Benjamin

middle: J

last: Strober

first: Katherine

last: Rhodes

first: Nirmal

last: Krishnan

first: Karl

last: Tayeb

first: Alexis

last: Battle

first: Yoav

last: Gilad


title: Transcriptional profiles of  Sox4 cKO, Sox11 cKO, and Sox4/11 dcKO mouse keratinocytes

status: Public on Oct 05 2018

city: Houston

first: Hoang

last: Nguyen

address: 1 Baylor Plaza

department: Center for Cell and Gene Therapy

institute: Baylor College of Medicine

summary: Transcriptional profiling of Sox4cKO, Sox11cKO, or Sox4/11dcKO  mouse keratinocytes as compared to their wild-type control keratinocytes, isolated from gender matched neonatal pairs. Goal was to identify the genes differentially expresssed in the conditional knockout keratinocytes vs the wild-type control.

overall_design: Two-condition experiments to compare gene expression profile of Sox4cKO, Sox11cKO, or Sox4/11 dcKO keratinocytes vs wild-type control. Biological replicates: 2 replicates for each comparison with color-swapping

first: Qi

last: Miao


title: Transcriptomic analyses of SLC5A8-deficient and wild-type mouse brains.

status: Public on Jul 27 2018

city: NICE

first: Laurent

last: SUISSA

state: (State)

address: 28, Avenue de Valombrose

country: France

institute: Faculté de Médecine

summary: We used transcriptomic analyses of whole brain homogenates from SLC5A8-deficient and wild-type mice at ages of 4 and 18 months to study the expression of genes encoding proteins that are involved in ketogenic amino acid and lipid catabolism.

overall_design: Four biological replicates were performed for each experimental condition.

last: Suissa

first: Thierry

last: Pourcher

first: Georges

last: Vassaux

first: Sabine

last: Lindenthal


title: Methylated microRNAs in Pancreatic cancer cell lines

city: Suita

first: Ayumu

last: Asai

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore micro RNAs containing methyated adenine in 4 pancreatic cancer cell lines, we tried to immunoprecipitation using anti-m6A antibdy. Imunoprecipitatted microRNA were isolated using  isolated using Hipure microRNA isolation kit and sequenced. This data showed that some microRNAs had methylated adenin in pancreatic cancer cell lines.

overall_design: RIP-sequence data using m6A Ab

first: Masamitsu

last: Konno

first: Jun

last: Koseki

first: Hideshi

last: Ishii


title: Mining the effector repertoire of the biotrophic fungal pathogen Ustilago hordei during host and non-host infection

status: Public on Jul 19 2018

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

summary:
The success of plant pathogenic fungi mostly relies on their arsenal of virulence factors that are expressed and delivered into the host tissue during colonization. The biotrophic fungal pathogen Ustilago hordei causes covered smut disease on both barley and oat. The biotrophic interaction of the fungus with its host plant starts with formation of appressorium and subsequent penetration of invasive hyphae into the plant cell, in which the plasma membrane of the infected cell gets invaginated and encases the penetrating hypha. After penetration, the fungus grows towards and in later stages along the vascular bundles, which contain assimilates and metabolites, representing a source of nutrients for the fungus. In this study, we combined cytological, genomics and molecular biological methods to achieve a better understanding of the molecular interactions in the U. hordei-barley pathosystem. This study focuses on the genome-wide Agilent Microarray-based transcriptome analysis of U. hordei during early stages (20 hpi, 40 hpi, 3 dpi, 6 dpi) of the biotrophic interaction in comparison to axenic culture growth. This should give insights into the molecular processes during these stages by the identification of regulated genes. Furthermore, the regulation of putative secreted enzymes and effector proteins can be studied. Transcriptome analysis of U. hordei at different stages of host infection revealed 273 effector gene candidates with differentially expressed transcript levels. Furthermore, U. hordei transcriptionally activates core-effector genes that may suppress even non-host early defense responses. It could be shown that about one half of the U. hordei open reading frames are differentially regulated during at least one of the analyzed stages. Based on the transcriptome data, some of them were identified to be involved in stage-specific processes, e.g. in the nutrient acquisition by the induction of carbohydrate transporters during the later stages of infection. Furthermore, a set of strongly induced genes was identified, which encode for secreted proteins.   The acquired datasets show a strong induction of stage-specific secreted effector proteins, whose functions remain unclear. Based on the expression values, a group of 16 promising candidates was chosen for functional characterization.
The success of plant pathogenic fungi mostly relies on their arsenal of virulence factors that are expressed and delivered into the host tissue during colonization. The biotrophic fungal pathogen Ustilago hordei causes covered smut disease on both barley and oat. The biotrophic interaction of the fungus with its host plant starts with formation of appressorium and subsequent penetration of invasive hyphae into the plant cell, in which the plasma membrane of the infected cell gets invaginated and encases the penetrating hypha. After penetration, the fungus grows towards and in later stages along the vascular bundles, which contain assimilates and metabolites, representing a source of nutrients for the fungus. In this study, we combined cytological, genomics and molecular biological methods to achieve a better understanding of the molecular interactions in the U. hordei-barley pathosystem. This study focuses on the genome-wide Agilent Microarray-based transcriptome analysis of U. hordei during early stages (20 hpi, 40 hpi, 3 dpi, 6 dpi) of the biotrophic interaction in comparison to axenic culture growth. This should give insights into the molecular processes during these stages by the identification of regulated genes. Furthermore, the regulation of putative secreted enzymes and effector proteins can be studied. Transcriptome analysis of U. hordei at different stages of host infection revealed 273 effector gene candidates with differentially expressed transcript levels. Furthermore, U. hordei transcriptionally activates core-effector genes that may suppress even non-host early defense responses. It could be shown that about one half of the U. hordei open reading frames are differentially regulated during at least one of the analyzed stages. Based on the transcriptome data, some of them were identified to be involved in stage-specific processes, e.g. in the nutrient acquisition by the induction of carbohydrate transporters during the later stages of infection. Furthermore, a set of strongly induced genes was identified, which encode for secreted proteins.The acquired datasets show a strong induction of stage-specific secreted effector proteins, whose functions remain unclear. Based on the expression values, a group of 16 promising candidates was chosen for functional characterization.

overall_design: One axenic culture of Ustilago hordei, four U. hordei infected barley leaf samples (at 20 hpi, 40 hpi, 3 dpi and 6 dpi) and one U. hordei infected maize leaf sample at 20 hpi. Three biological replicates were performed for each sample.

first: Bilal

last: Ökmen

first: Daniel

last: Mathow

first: Gunther

last: Doehlemann


title: Phytochrome B-SPA-COP1 regulation of red light induced gene expressions in Arabidopsis thaliana

status: Public on Jul 14 2018

first: Inyup

last: Paik

institute: UT Austin

summary: The mRNA expression profiles of the quadruple spa mutant spaQ and cop1-4 were analyzed in 1 hour red light treated condition. Under same condition, the gene expression changes in phyB-SPA1 interaction domain mutant was analyzed and compared with wild type.

overall_design: Total fifteen 1h red light treated Arabidopsis samples were used. These include three replicates of following genotypes: Col-0, cop1-4, spaQ, phyB C-terminal deletion, phyB full length. Total six additional samples were used for dark control. These include three replicates of following genotypes: phyB C-terminal deletion, phyB full length.

first: Vinh

last: Pham

first: Enamul

last: Huq


title: Expression data of candidates for prostate cancer active surveillance

status: Public on Sep 08 2018

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: GenomeDx

summary: The dataset consists of 266 NCCN very low/low or favorable-intermediate risk PCa patients who underwent diagnostic prostate biopsy between 2000 and 2014 and were treated with RP in six community or academic practices: University of Calgary, Cedars-Sinai, Spectrum Health, Cleveland Clinic, MD Anderson Cancer Center and Johns Hopkins. All patients had complete tumor pathology from biopsy and prostatectomy. Low risk PCa was defined as T1c or cT2a, and Gleason score (GS) ≤ 6, and PSA < 10ng/ml and favorable-intermediate risk was no greater than predominant GS 3 and percent positive biopsy cores < 50%, and either cT2b-cT2c or PSA 10-20ng/ml.

overall_design: A retrospective observational multi-institutional study

first: Hyung

last: Kim

first: Ping

last: Li

first: Huei-Chung

last: Huang

first: Samineh

last: Deheshi

first: Tara

last: Marti

first: Beatrice

last: Knudsen

first: Hatem

last: Abou-Ouf

first: Ridwan

last: Alam

first: Tamara

last: Lotan

first: Lucia

last: Lam

first: Marguerite

last: du Plessis

first: Neil

last: Fleshner

first: Brian

last: Lane

first: Ashley

middle: E

last: Ross

first: John

middle: W

last: Davis

first: James

last: Mohler

first: Bruce

last: Trock

first: Eric

middle: A

last: Klein

first: Jeffrey

last: Tosoian

first: M

last: Hyndman

first: Tarek

last: Bismar


title: Microarry and RNA-seq analysis of M. tuberculosis response to threonine auxotrophic starvation

status: Public on Aug 29 2018

city: Bronx

first: Erik

middle: James

last: Hasenoehrl

state: New York

address: 1301 Morris Park Ave. Price 569

department: Microbiology & Immunology

institute: Albert Einstein College of Medicine

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

platform_organism:
Mycobacterium tuberculosis
Mycobacterium tuberculosis H37Rv

overall_design: Refer to individual Series


title: RNA-seq analysis of Mycobacterium tuberculosis response to threonine auxotrophic starvation

summary: Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔthrB during threonine starvation

overall_design: RNA-Seq analysis of H37Rv∆thrB transcriptomic response during threonine starvation. Total RNA samples collected for extraction and analysis before starvation and at 1 and 2 days post starvation initiation.

first: Michael

last: Berney


title: Has-miRNA expression-based, the cells of SW480, SW480CSCs, SW480CSCs-NC and SW480CSCs-OCT4B1-shR groups

status: Public on Aug 31 2018

city: Zunyi

first: Kunming

last: Wen

address: 149 DaLian Road, Zunyi, Guizhou 563000, People's Republic of China

country: China

institute: The Affiliated Hospital of Zunyi Medical University

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 2571 has-miRNA in the cells OF SW480, SW480CSCs, SW480CSCs-NC and SW480CSCs-OCT4B1-shR groups

overall_design: We collected four groups of SW480, SW480CSCs, SW480CSCs-NC and SW480CSCs-OCT4B1-shR cells, showing the different miRNA expression folds of these four groups, and comparing the changes of miRNA expression induced by OCT4B1 gene.

first: K

first: J

last: Zhou


title: Quaking isoform depletion in C2C12 myoblasts; direct binding targets of Quaking RNA binding proteins

status: Public on Jul 11 2018

city: Galveston

first: W.

middle: Samuel

last: Fagg

address: 301 University Blvd, Department of Surgery, MRB5.150, L21875

department: Surgery/Biochemistry and Molecular Biology

institute: University of Texas Medical Branch


title: Genomewide analysis of Quaking isoform depletion in C2C12 myoblasts

summary: Identifying changes in RNA metabolism under depletion of Qk5 or Qk6/7 isoforms in mouse myoblasts

overall_design: RNAs regulated by either Qk isoform(s) or both Qk isoforms should change in abundance and splicing pattern under isoform-specific depletion strategy. Cultured myoblasts were treated with control, Qk5-specific, or Qk6/7-specific siRNAs, then RNA was extracted, purified, depleted of ribosomal RNA, and sequenced. Changes in abundance and splicing were measured.

first: W

first: Lily

last: Shiue

first: Sol

last: Katzman

first: Manuel

last: Ares


title: Genome-wide mapping of histone H3 in total sperm and HRCS

status: Public on Jul 26 2018

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

institute: RIKEN

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Majority of histones are replaced by protamine during spermatogenesis, but small amount of histones are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is important how histones are distributed on sperm genome. We have found that the swim-up sperm used in many studies contains about 10% of immature sperm which do not yet complete the histone-to-protamine replacement. We have developed the novel method to purify the histone replacement-completed sperm (HRCS), and to completely solubilize nucleosomes from cross-linked HRCS without MNase digestion. Here, we analyzed H3 binding profiles in total sperm and HRCS by Chromatin IP – sequencing (ChIP-seq) analysis, and DNA methylation profiles in swim-up sperm and HRCS by target bisulfite sequencing (TGSB).

overall_design: Identification of H3 binding sites in 2 fractions of mouse sperm samples.

first: Muratani

last: Masafumi


title: Transcriptional adaptation during starvation of Mycobacterium tuberculosis H37Rv ∆thrA

summary: Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔthrA during methionine starvation

overall_design: Two-condition experiment, before starvation vs. either 2 days, 4days or 6days after starvation. Biological replicates: 4, one dye swap


title: p53 binding and chromatin dynamics after etoposide treatment of primary lung fibroblast

status: Public on Jun 19 2018

city: Albany

first: Morgan

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: We report the chromatin modification dynamics at p53 binding sites afte 6 hours of treatment of etoposide (100 micromolar final) in IMR90 human lung fibroblasts using ChIP-seq , ATAC-seq, and polyA+ RNA-seq analyses. We assessed the genomewide occupancy of histone H3, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H4K16ac, RNA polymerase II, p53, and transposase-accessible chromatin (ATAC-seq) in response to etoposide treatment.

overall_design: ChIP-seq, RNA-seq, and ATAC-seq for histone modifications, p53, and RNA polymerase II after etoposide treatment in IMR90 fetal lung fibroblasts


title: A molecular signature for rejuvenation characterizes lesional and non lesional skin following Metvix treatment in Actinic Keratosis patients.

status: Public on Jun 15 2018

city: Sophia Antipolis

first: CORINNE

last: MENIGOT

address: 2400 route des colles

institute: GALDERMA R & D

summary: Actinic keratoses (AK) are proliferations of pre-neoplastic keratinocytes in the epidermis that are the result of cumulative ultraviolet (UV) radiations from sun exposure. Lesions are commonly found on sites of sun-exposed skin such as the face, balding scalp, and back of the hand. AKs may present on a patient as a few detectable lesions and 5-10% of them are susceptible to transform into SCC. In contrast, Organ Transplant Recipients (OTR) are of increasing risk at developing cancers as a consequence of long-term immunosuppressive therapy.  The molecular changes that occur in lesional and perilesional skin of OTR patients 18 weeks following of PDT with topical MAL treatment were investigated to better understand the effect of the therapeutic intervention on the AK lesions.  Our data show the complete normalization of the skin biology in the treated areas, i. e restoration of normal proliferation related gene profiles, and correction of aberrantly expressed cancer associated genes. We were also able to uncover a transcriptional signature of a rejuvenation effect induced by MAL-PDT in photodamaged skin opening new avenues in the use of PTD for treating photodamaged skin and field cancerized areas.

overall_design: Total of 35 chips. 7 patients : 5 biospies per patient: 1 in healthy skin areas (Buttock) before treatment, 1 in peri-lesional region  before treatment, 1 in lesional region  before treatment, 1 in perilesional region after 18 weeks of treatment and 1 in lesional region after 18 weeks fo treatment

first: F

last: Joly


title: Gene expression profiles of human mesenchymal stem cells exposed to surface water organic extracts

status: Public on Jun 01 2018

city: Dalian

first: Zhou

last: Zhang

state: Liaoning

address: Linggong Road 2

department: Environmental Science and Technology

institute: Dalian University of Technology

summary:
To assess the impact of surface water across the Hun River, several sampling sites located in the mainstream and the tributary were selected representative of pollution gradient and different pollution source. Human mesenchymal stem cells were exposed to organic extracts of surface water from six sites for 2 days.
Microarrays were used to measure the gene expression. And the gene expression profiles were used to evaluate the ability of determine the potential biological effects, to differentiate different pollution source, and to identify the toxic components.

overall_design: The gene expression of human mesenchymal stem cells were measured after 48h exposure to organic extracts of surface water from the Hun River. Culture medium with 0.1% DMSO was used as negative control. Three independent cultures were used for control group and each treatment.

first: Wei

last: Liu


title: JCAD/KIAA1462, a coronary artery disease-associated gene product, regulates endothelial function

status: Public on Aug 10 2018

city: Rochester

first: Suowen

last: Xu

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

summary: Recent genome-wide association studies (GWAS) have identified gene variants associated with coronary artery disease including ADAMTS7, PHACTR1, KIAA1462/JCAD (Junctional Protein Associated with Coronary Artery Disease) and many others. JCAD has been identified as a novel component of endothelial cell-cell junctions (Akashi et al., 2011, BBRC) and regulates angiogenesis (Hara et al, ATVB, 2017). In our study, we observed that JCAD is a 148-KDa protein identified by mass spectrometry, but display a band shift to around 180-200 KDa, suggesting that JCAD is subject to multiple post-translatinonal modification. We also observed that JCAD well colocalized with adheren junction VE-cadherin, tight junction ZO-1 and desmosome junction plakoglobin (also known as gamma-catenin). However,  the functional role of JCAD in endothelial function and the etiology of vascular disease remains unknown. In view of the critical role of junctional proteins in regulating endothelial function including vascular permeability, angiogenesis, and monocyte adhesion, we hypothesized that JCAD may play a crucial role in regulating endothelial function. To better understand the function of JCAD in endothelial cells, we performed RNA-sequencing based transcriptomic profiling in JCAD depleted (by transfection with by JCAD siRNA) human coronary artery endothelial cells, to identify critical genes and pathways associated with JCAD. We found that multiple atherosclerosis related genes and pathways are modulated by JCAD. Further studies are needed to characterize the biological function of JCAD in the pathogenesis of cardiometabolic diseases associated with endothelial dysfunction, such as diabetes, obesity, hypertension and atherosclerosis.

overall_design: Human Coronary Atery Endothelial Cells (HCAECs, passage 3 to passage 5) were seeded in 0.2% gelatin-coated dishes the day before experiment. The next day, 80% confluent HCAECs were transfected with 100 nM non-targetting siRNA control (siNC)  or JCAD siRNA (siJCAD, #GE Dharmacon, #D-026476-01) for 48 hours. After treatment, total RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN). High quality RNA samples (pre-assessed by Nanodrop measurements) were further processed in the Genome Research Center of the University of Rochester Medical Center. The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome. Sequenced reads were cleaned using Trimmomatic-0.32 before mapping some of to the human reference genome (GRCh38.p2) with STAR-2.4.2a. Raw read counts were obtained using HTSeq and gencode 23 human gene annotations. DESeq2-1.10.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05. Then, Cufflinks-2.0.2 Software was used with the gencode 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05.

first: Zheng

middle: G

last: Jin

first: John

middle: M

last: Ashton

first: Jason

last: Myers


title: Human proteins bound to RNA/DNA hybrid

status: Public on Aug 03 2018

city: Ann Arbor

first: Zhengwei

last: Zhu

address: 210 Washtenaw Ave

institute: University of Michigan

summary: RNA/DNA hybrids form when RNA hybridizes with its template DNA generating a three-stranded structure known as the R-loop.  Knowledge of how they form and resolve, and their functional roles are limited.  Here, we identified proteins that bind to RNA/DNA hybrids.

overall_design: We identified transcripts bound by SRSF1 using two independent methods PAR-CLIP and RNA-IP.  Then we characterized R-loop regions in human cells using DRIP-seq with the S9.6 antibody.

first: Isabel

middle: X

last: Wang

first: Vivian

last: Cheung

first: Markus

last: Hafner


title: Mandatory Role of HMGA1 in Human Airway Epithelial Normal Differentiation and Post-injury Regeneration

status: Public on Apr 04 2018

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Background: High mobility group AT-hook1 (HMGA1) is essential for airway basal cell mucociliary differentiation, barrier integrity and wound repair.  HMGA1 expression suppresses the abnormal basal cell differentiation to squamous, inflammatory and epithelial-mesenchymal transition phenotype commonly observed in association with cigarette smoking and chronic obstructive pulmonary disease (COPD).
Results: HMGA1 knockdown experiments indicate that when HMGA1 expression is suppressed, the airway basal cells cannot normally differentiate into a mucociliary epithelium, form an intact barrier, and repair following injury. Instead, airway basal cell differentiation was skewed to an abnormal squamous EMT-like phenotype associated with airway remodeling in COPD.
This study demonstrates that HMGA1 plays a key role in normal airway differentiation, regeneration of the normal airway epithelium following injury, and suppression of expression of genes related to squamous metaplasia, EMT and inflammation.

overall_design: [RNA-seq] Non-smoker large airway epithelium cells, large airway basal cells, small airway epithelial cells, small airway basal cells.  Smoker large airway basal cells, COPD smoker large airway basal cells,.

first: Haijun

first: Jing

last: Yang

first: Matthew

last: Walters

first: Michelle

last: Staudt

first: Jacqueline

last: Salit

last: Mezey

first: Renat

last: Shaykhiev

first: Ronald

last: Crystal


title: Mapping of histone-binding sites in histone replacement-completed spermatozoa

first: Keisuke

last: Yoshida

type: Methylation profiling by high throughput sequencing


title: Genome wide characterization of a STAT1-independent antiviral and immunoregulatory transcriptional program induced by IFNβ and TNFα reveals non-canonical STAT2 and IRF9 pathways

status: Public on Feb 28 2018

city: Montreal

first: Nathalie

last: Grandvaux

address: 2900, boul. Édouard-Montpetit

institute: University of Montreal

summary: Interferon (IFN) β and Tumor Necrosis Factor (TNF) α are key players in immunity against pathogens as well as in the development of autoinflammatory and autoimmune diseases. Accordingly, their molecular pathways have attracted much interest as therapeutic targets. Compelling evidence has shown that the antiviral and inflammatory transcriptional response induced by IFNβ is reprogrammed by crosstalk with TNFα. IFNβ typically induces interferon-stimulated genes by the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway leading to activation of the canonical ISGF3 transcriptional complex, composed of STAT1, STAT2 and IRF9. The signaling pathways engaged downstream of the combination of IFNβ and TNFα remain elusive, but previous observations suggested the existence of a response independent of STAT1. Here, using genome-wide transcriptional analysis by RNASeq, we observed a broad antiviral and immunoregulatory response initiated in the absence of STAT1 upon IFNβ and TNFα costimulation. Additional stratification of this transcriptional response with respect to the role of STAT2 and IRF9 revealed that they mediate the expression of a wide spectrum of genes. While a subset of genes was regulated by the concerted action of STAT2 and IRF9, other gene sets were independently regulated by STAT2 or IRF9. Collectively, our data supports a model in which STAT2 and IRF9 act through non-canonical parallel pathways to regulate distinct pool of genes in response to IFNβ and TNFα. This study provides novel insights into the molecular pathways leading to antiviral and immunoregulatory gene expression in conditions where elevated levels of both IFNβ and TNFα are present.

overall_design: To investigate the transcriptional program triggered by IFNβ and TNFα independently of STAT1, the human STAT1-deficient U3A cell line (derived from the 2ftGH fibrosarcoma cell line, McKendry R, et al.Proc Natl Acad Sci U S A. 1991;88(24):11455-9) were efficiently transfected with Control (Ctrl), STAT2 or IRF9 targeting RNAi and further left untreated or stimulated with a combination of IFNβ (1000U/ml) +TNFα (10ng/ml) for 24h. Total RNA was isolated and analyzed by RNA sequencing (n=3 for each group) on an Illumina HiSeq2500 platform. Bioinformatics analysis was performed to determine genes differentially regulated upon IFNβ and TNFα costimulation. Moreover, the role of STAT2 and IRF9 in the regulation of these genes was analyzed. Results of RNASeq were validated by qRT-PCR.

first: Mélissa

middle: K

last: Mariani

first: Pouria

last: Dasmeh

first: Audray

last: Fortin

first: Mario

last: Kalamujic

first: Elise

last: Caron

first: Sandra

last: Cervantes-Ortiz

first: Espérance

last: Mukawera

first: Adrian

last: Serohijos


title: Microarray profiling analysis of long non-coding RNAs expression in osteoarthritis

status: Public on May 11 2018

city: changsha

first: haibin

last: zhang

state: China

address: Xiangya Hospital, Central South University, Changsha

department: Department of Orthopedics

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

summary:
Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or <-2.0-fold change; p<0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, QPCR was used to validate chip results. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA.
OA cartilage were collected from 19 patients undergoing total knee joint replacement due to severe OA, and normal cartilage were collected from 11 patients (trauma, thromboangiities obliterans, or osteosarcoma, or limb amputation) without history of rheumatoid arthritis or OA

overall_design: Expression profiling of cartilage-normal (n=5) and cartilage-OA (n=5) samples.

first: Cheng

last: Chen

first: Haibin

last: Zhang


title: A Cross-Species Approach Identifies MELK as a Potential Therapeutic Target in Prostate Cancer

status: Public on Feb 05 2018

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

summary: Genetically engineered mouse models of cancer represent valuable biological tools that can be used to filter genome-wide expression datasets generated from human prostate tumours, and identify gene expression alterations that are functionally important to cancer development and progression.  In this study, we have generated RNASeq data from tumours arising in two established mouse models of prostate cancer, PB-Cre/PtenloxP/loxP and p53loxP/loxPRbloxP/loxP, and integrated this with published human prostate cancer expression data to pinpoint cancer-associated gene expression changes that are conserved between the two species. In order to identify potential therapeutic targets, we then filtered this information for genes that are either known or predicted to be druggable. Using this approach, we identified the serine/threonine kinase MELK as a potential therapeutic target in prostate cancer. MELK was overexpressed in both human and murine prostate cancers, and high expression of MELK was associated with biochemical recurrence in prostate cancer patients.

overall_design: 92 Samples

first: Sarah

last: Jurmeister

first: Antonio

last: Ramos-Montoya

first: Sérgio

last: Felisbino

first: David

last: Neal


title: Identification of MELK-regulated genes in prostate cancer cells using next-generation sequencing

summary: A cross-species analysis identified MELK as a potential therapeutic target in prostate cancer. To further elucidate the functional role of MELK in prostate cancer cells, we aimed to identify MELK-regulated genes. C4-2b cells were either treated with a small-molecule MELK inhibitor (OTSSP167), or transfected with siRNAs targeting MELK. Differentially expressed genes were identified using next-generation sequencing. Our results demonstrate that MELK promotes the expression of genes associated with tumour progression in prostate cancer cells.

overall_design: Gene expression profiles of C4-2b cells by RNA-Seq following silencing or inhibition of MELK. Four independent biological replicates were performed for each treatment condition. Two different siRNAs directed against MELK were used to account for potential off-target effects of the siRNAs. Negative controls were cells transfected with AllStars Negative Control siRNA, and cells treated with DMSO (vehicle for OTSSP167).


title: Genetic regulatory mechanisms of smooth muscle cells map to coronary artery disease risk loci

status: Public on Aug 09 2018

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

summary: Coronary artery disease (CAD) is the leading cause of death globally. Genome-wide association studies (GWAS) have identified more than 130 independent loci that influence CAD risk, most of which reside in non-coding regions of the genome. To interpret these loci, we generated transcriptome and whole-genome datasets using human coronary artery smooth muscle cells (HCASMC) from 52 unrelated donors, as well as ATAC-seq epigenomic datasets on a subset of 8 donors. Through systematic comparison with publicly available datasets from GTEx and ENCODE projects, we identify transcriptomic, epigenetic, and genetic regulatory mechanisms specific to HCASMC. We validate the relevance of HCASMC to CAD risk using transcriptomic and epigenomic level analyses. By jointly modeling eQTL and GWAS datasets, we identified five genes (SIPA1, TCF21, SMAD3, FES, and PDGFRA) that modulate CAD risk through HCASMC, all of which have biologically relevant functional roles in vascular remodeling. Comparison with GTEx data suggests that SIPA1 appears to influence CAD risk predominantly through HCASMC, while other annotated genes may have multiple cell targets. Together, these results provide new biological insights into the regulation of a critical vascular cell type associated with CAD in human populations.

overall_design: RNA-Seq and ATAC-seq on 52 lines of human coronary artery smooth muscle cells

first: Boxiang

last: Liu

first: Trieu

last: Nguyen

first: Victor

last: Castano

first: Ting

last: Wang

first: Sylvia

last: Nurnberg

first: Milos

last: Pjanic

first: Daniel

last: Rader

first: Stephen

middle: B

last: Montgomery

first: Clint

last: Miller


title: Eradiation of leukemia by effective reprogramming-associated cell elimination (ERACE)

status: Public on Feb 01 2018

city: Tianjin

first: Hui

last: Cheng

address: 288 Nanjing road

institute: Institute of Hematology

summary: We used microarrays to evaluate the global programming of gene expression after Dox inducible Yamanaka factors ectopic expression and identified distinct classes of genes during this biological process in vivo.

overall_design:
Leukemia cells were sorted from distinct groups at different time points. Microarray was performed at GMINIX in Shanghai.
To investigate the molecular mechanism for the elimination of leukemia cells after Dox inducible Yamanaka factors (Oct4,Sox2,Klf4,c-Myc) expression, we sorted GFP+ MLL-AF9 acute myeloid leukemia cells (AML) from leukemic mice and normal Lin-ckit+sca1+ cells (LKS) from 4F transgenic mice. We then performed microarray analysis of these samples before and after Dox-induced OSKM expression or treatment with reprogramming compound cocktail (VPA, CHIR, 616452, TCP) at 24h in vitro.

first: Tao

first: Yajie


title: Transcriptomic analysis of the HOTAIR-regulated genes

status: Public on Jan 01 2018

city: Wuhan

first: Xiong

last: Qian

state: Hubei

address: Donghu South Road 7, Wuhan 430072, People’s Republic of China

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

summary: An integrated RNA sequencing transcriptomic and quantitative proteomic analysis were employed to systematically explore the regulatory role of HOTAIR in HCC. A total of 673 transcripts and 298 proteins were identified to be dysregulated after HOTAIR inhibition.

overall_design: Examine the overall transcriptomic changes in HepG2 cells after HOTAIR knockdown by RNA sequencing, in triplicate, using Illumina Hiseq 2000 platform.

first: Qian

last: Xiong

first: Feng

last: Ge


title: The transcriptional regulator LysG of Mycobacterium tuberculosis activates lysE in a lysine-dependent manner

status: Public on Dec 31 2017

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Whole genome expression analysis showed that Rv1985c protein controlled gene expression of additional genes such as ppsB, ppsC and ppsD.

overall_design: To evaluate what genes are under the transcriptional control of LysG(Mt), a whole genome expression analysis of Wt Mt (Wt_Mtb) and ΔlysG(1985c) was done. Both were grown in a minimal medium supplemented with 5 mM lysine as sole nitrogen source.

first: F

middle: C

last: Bange

first: M

last: Schneefeld

first: R


title: Determination of direct binding targets of Quaking RNA binding proteins

first: W.

last: Fagg

summary: Identication of  RNA molecules directly bound by Quaking proteins in mouse myoblasts and myotubes

overall_design: Individual nucleotide resolution crosslinking immunoprecipitation of Qk proteins in either C2C12 myoblasts or 72h differentiated myotubes; control libraries were constructed using mouse anti-HA antibody from C2C12 myoblast cross-linked lysate, other libraries used either mouse anti-PanQk, mouse anti-Qk6, or mouse anti-Qk7 antibody

first: W

first: Lily

last: Shiue

first: Sol

last: Katzman

first: Manuel

last: Ares


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

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

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

overall_design: Human cell lines (PC3, C4-2, T24 and 786-O) were treated with miRNAs (miR-199-3p, miR-125b-1-3p, miR-532-5p, miR-532-3p, miR-140-5p and miR-140-3p), inihibitor (bisamide).

first: Yasutaka

last: Yamada


title: fruitENCODE: An encyclopedia of DNA elements for fruit ripening

status: Public on Jul 04 2018

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

institute: CUHK

summary: Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. The monocot banana used both, forming a unique dual-loop circuit. Genes in these circuits and their tissue-specific H3K27me3 mark could be traced back to both dry fruits and ethylene-independent fleshy fruits, suggesting that the ethylene-dependent ripening mechanisms evolved from pre-existing genetic and epigenetic pathways in the ancestral angiosperms. FruitENCODE provides a comprehensive annotation of functional elements for fleshy fruit crops and new insight into the origins of climacteric fruit ripening.

sample_organism:
Carica papaya
Citrullus lanatus
Cucumis melo
Cucumis sativus
Arabidopsis thaliana
Malus domestica
Prunus persica
Solanum lycopersicum
Oryza sativa
Vitis vinifera
Fragaria vesca
Musa acuminata AAA Group
Pyrus x bretschneideri

overall_design: Profiling of more than 300 transcriptome, more than 40 DNA methylome, more than 60 chromatin accessibility, more than 160 histone modification and bindings of several key ripening transcription factors in leaf, immature and ripe fruit tissues of 11 fleshy fruit bearing species. The raw data have beed deposited to SRA with Study accession number SRP102870 and Bioproject accession number PRJNA381300.


title: Ubiquitin-like processing of the conserved splicing regulator Sde2 promotes telomeric silencing and genome stability

status: Public on Sep 22 2017

city: Ithaca

first: Jeffrey

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary: Intron-containing gene expression in eukaryotes proceeds through the process of RNA splicing to generate protein-coding messenger RNAs (mRNAs). Herein a large and dynamic ribonucleoprotein complex — the spliceosome — removes non-coding introns from pre-mRNAs and joins exons. Spliceosomes must also ensure accurate and timely removal of diverse and highly prevalent introns. Here we show that Sde2 is a conserved splicing regulator, contains a ubiquitin fold, and supports splicing of a subset of pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Its orthologs in S. pombe and humans are synthesized as precursors harboring a ubiquitin fold, followed by an invariant GGKGG motif and an uncharacterized C-terminal domain (referred to as Sde2-C). The precursor must be cleaved at GG^K by the ubiquitin specific proteases Ubp5 and Ubp15 to produce the Sde2-C protein containing a lysine residue at its C-terminus, and is a substrate of the N-end rule pathway of proteasomal degradation. The truncated Sde2-C functions as a component of the spliceosome, and loss of Sde2-C results in inefficient splicing of selected introns from target genes having functions in DNA replication, transcription and telomeric silencing. Thus, the ubiquitin-like processing of Sde2 — associated with its regulation by the N-end rule pathway — contributes to genomic stability in S. pombe through specific pre-mRNA splicing events.

overall_design: Splicing sensitive microarrays for S. pombe (Agilent AMADID #: 027365) were used to monitor global changes in splicing in the background of temperature-sensitive variant of sde2 compared to wild type.


title: Functional redundancy of variant and canonical histone H3K9 modification in Drosophila

status: Public on Dec 25 2017

city: Chapel Hill

first: Taylor

last: Penke

state: NC

address: 3344 Genome Sciences Building, 250 Bell Tower Drive

department: Genetics and Molecular Biology

institute: University of North Carolina Chapel Hill

summary: To determine the relative functions of K9 modification on variant and canonical H3, we compared the phenotypes caused by engineering H3.3K9R and H3K9R mutant genotypes in Drosophila melanogaster. Whereas most H3.3K9R and a small number of H3K9R mutant animals are capable of completing development and do not have substantially altered protein coding transcriptomes, all H3.3K9R H3K9R combined mutants die soon after embryogenesis and display decreased expression of genes enriched for K9ac. These data indicate that the role of K9ac in gene activation during development can be provided by either H3 or H3.3. Conversely, we found that H3.3K9 is methylated at telomeric transposons, and this mark contributes to repressive chromatin architecture, supporting a role for H3.3 in heterochromatin that is distinct from that of H3. Thus, our genetic and molecular analyses demonstrate that K9 modification of variant and canonical H3 have overlapping roles in development and transcriptional regulation, though to differing extents in euchromatin and heterochromatin.

overall_design: FAIRE-seq was performed from imaginal wing discs from 3rd instar Drosophila larvae in triplicate on yw (WT) and three H3.3 mutants: 1) H3.3A null (H3.3A-null), 2) H3.3B with an endogenous K9R mutation (H3.3B-K9R), 3) and the double mutant of both 1 and 2 (H3.3-K9R). RNA-seq was performed on whole 1st instar larvae in triplicate on four genotypes: 1) endogenous histon_1e deletion mutant rescued by a 12x array of wild-type canonical histone genes (HWT), 2) endogenous histone deletion mutant rescued by a 12x array of canonical histone genes with a K9R mutation (H3.2-K9R), 3)  H3.3B K9R mutation in an H3.3A null and HWT background (H3.3-K9R_H3.2-HWT), 4) H3.3B K9R mutation in an H3.3A null and H3.2-K9R background (H3.3-K9R_H3.2-K9R).

last: Duronio


title: Myc and YAP roles in the control of the cell cycle [Liver ChIP-seq]

status: Public on Nov 22 2017

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

summary: ChIPseq analysis was performed on liver of  tet-YAP and tet-Myc  transgenic mice induced for 2 days (R26-mice)

first: Stefano

last: Campaner

first: Serena

last: De Fazio

first: Ottavio

last: Croci


title: A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence (miRNA-seq)

status: Public on Nov 18 2017

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary: Background: Senescence is a fundamental biological process implicated in various pathologies, including cancer. Regarding carcinogenesis, senescence signifies, at least in its initial phases, an anti-tumor response that needs to be circumvented for cancer to progress. Micro-RNAs, a subclass of regulatory, non-coding RNAs, participate in senescence regulation. At the subcellular level micro-RNAs, similar to proteins, have been shown to traffic between organelles influencing cellular behavior. The latter and the role of micro-RNAs in senescence biology, raises concurrent in situ analysis of coding and non-coding gene products in senescent cells as a necessity. However, technical challenges have rendered in situ co-detection unfeasible until now.  Results: In the present report we describe a methodology that bypasses these technical limitations achieving for the first time simultaneous detection of both a micro-RNA and a protein in the biological context of cellular senescence. The method was applied in a prototypical human non-malignant epithelial model of oncogene-induced senescence that we generated for the purposes of the study. This experimental setting has three advantages that are presented and discussed: i) it covers a “gap” in the molecular carcinogenesis field, as almost all corresponding in vitro models are fibroblast-based, even though the majority of neoplasms have epithelial origin, ii) it recapitulates the precancerous and cancerous phases of epithelial tumorigenesis within a short time frame under the light of natural selection and iii) it uses as an oncogenic signal, the replication licensing factor CDC6, implicated in both DNA replication and transcription when over-expressed, a characteristic that can be exploited to monitor RNA dynamics.  Conclusions: Consequently, we demonstrate that our model is optimal for studying the molecular basis of epithelial carcinogenesis shedding light in the tumor-initiating events. The latter may reveal novel molecular targets with clinical benefit. Besides, since this method can be incorporated in a wide range of low, medium or high-throughput image-based approaches, we expect it to be broadly applicable.

overall_design: miRNA-sequencing, 3 independent experiments, measured in 4 states ("OFF", 3rd day "ON", 6th day "ON" and "ESCAPED" as denoted in the orginal publication), with duplicates

first: Eirini-Stavroula

last: Komseli

first: Vassilis

last: Gorgoulis


title: Differential gene expression induced by anti-cancer agent plumbagin is mediated by androgen receptor in prostate cancer cells

status: Public on Sep 28 2017

city: San Diego

first: John

last: Welsh

state: California

address: 3030 Bunker Hill Street

institute: Vaccine Research Institute of San Diego

summary: Plumbagin treatment of mice harboring PTEN-P2 tumors in the prostate or on prostate tissue maintained in vivo results in tumor regression when coupled with androgen deprivation therapy. This suggested that dihydrotestosterone (DHT) production in the testes prevents tumor regression due to plumbagin treatment by an unknown mechanism. We performed RNA-seq analysis on cells treated with plumbagin, DHT, or both, and analyzed differential gene expression using RNA-seq. DHT and plumbagin synergize to differentially regulate many genes that are not differentially regulated by either agent alone. For many genes, increases in mRNAs caused by DHT are sharply down-regulated by plumbagin, and some transcripts increase or decrease in response to plumbagin in a DHT-dependent manner. We also observed that plumbagin causes extensive RNA damage independently of DHT. We also include data from a simple time course experiment in which gene expression in response to DHT was studied using RNA-seq.

overall_design: PTEN-P2 (Pten-/+) cells grown in culture were treated for 1 hour with 0, 0.5, or 4mM plumbagin dissolved in DMSO, with or without overnight and continued treatment with 10-8M DHT in DMSO, or mock treatment with DMSO. In addition, a time course experiment tracking gene expression due to DHT treatment in PTEN-P2 cells was performed. The DMSO concentration was constant between treatment conditions. After treatment, cells were harvested and RNA was purified using RNeasy. NGS sequencing libraries were prepared from using NEBNext for Illumina® using index primers. These libraries were sequenced, 6 index primers per lane, using the Illumina HiSeq platform. Reads were from 252-269 reads per lane.

first: Gaelle

last: Rondeau

first: Parisa

last: Abedinpour

first: Adrian

last: Chrastina

first: Jennifer

last: Pelayo

first: Per

last: Borgstrom


title: Cross-Species Approach Identifies MELK as a Potential Therapeutic Target in Prostate Cancer

first: Chandra

last: Chilamakuri

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression patterns in roots of Camelina sativa with enhanced salinity tolerance arising from growth in soil treated with plant growth promoting bacteria producing ACC deaminase or from expression of the corresponding acdS gene in transgenic lines

status: Public on Sep 12 2017

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary:
Gene expression patterns in roots of Camelina sativa with enhanced salinity tolerance arising from growth in soil treated with plant growth promoting bacteria producing 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) or from expression of the corresponding acdS gene in transgenic lines.
Salinity stress negatively affects crop production. However in camelina, grown in soils treated with PGPB producing 1-aminocyclopropane-1-carboxylate deaminase (acdS ) or transgenic lines expressing acdS exhibited increased salinity tolerance. AcdS reducing the level of stress ethylene to below the point where it is inhibitory to growth. Gene expression patterns in roots responding to salt stress was affected by the expression of acdS under the control of CaMV 35S or root-specific (rolD) promoters in transgenic lines, or by growth in soils treated with endophytic PGPB producing acdS indicate that the number of the genes were differentially expressed were more assigned to genome III in transgenic plants however in PGPB treated plants the number of the genes were differentially expressed were almost equally assigned to all three genomes. Different promoter may induce different set or even different homeologues genes in camelina with probably the same function in response to salt stress. Though root is not a photosynthetic tissue reduction of the ethylene in root cells has positive effect on plant photosynthetic machinery. The expression of the genes involved in minor CHO metabolism was up-regulated mainly in roots of acdS contain plants during salt stress. Moderate reduction in ethylene production has positive effect on root growth during salt stress but reduction of the ethylene higher than a certain level has negative effect on root growth due to reduction of the expression of the genes involved in root cell elongation. AcdS gene modulating the level of ROS in cells in the level that induce ROS signaling but preventing cellular damage by make a balance on up and down-regulation of the genes involved in oxidation-reduction process in root cells under salinity stress. The acdS containing PGPB (8R6) were mostly effected the ethylene signaling and ABA biosynthesis and signaling in positive way but transgenic line depends to the promoter affecting Auxin, JA and BR signaling or biosynthesis.

overall_design: Four experimental conditions were tested:  the parental Camelina (DH55), a transgenic with acdS contitutively expressed (35S::acdS), a transgenic with acdS most highly expressed in roots  (rolD::acdS), and DH55 exposed to a plant growth promoting bacteria expressing acdS (8R6).  Camelina roots (DH55, 35S::acdS, rolD::acdS, PGPB (8R6)) with salt treatment were analyzed.  3 replicates of each were compared.

first: Zohreh

last: Heydarian

first: Bernie

last: Glick

first: Margaret

last: Gruber

middle: D

first: Cathy

last: Coutu

first: Steven

last: Robinson


title: Changes in gene expression due to alpha-crystallin mutations cryaa-R49C and cryab-R120G in mutant knock-in mouse lenses

status: Public on Aug 20 2017

city: St. Louis

first: Usha

last: Andley

state: MO

address: 660 S. Euclid Avenue

department: Ophthalmology and Visual Sciences

institute: Washington University School of Medicine

summary: To investigate the relationship between histones, chaperone function, and cataracts, we performed RNA-seq, isothermal titration calorimetry (ITC), size-exclusion chromatography, and gel electrophoresis of histones. The RNA-seq of postnatal lenses from 2-day-old cryaa -R49C  mice revealed increased histone gene expression, suggesting that a α-crystallin mutation regulates histones via a transcriptional mechanism .

overall_design: RNA-seq studies on lenses of 2-day-old wild-type and 2-day-old cryaa-R49C heterozygous mutant and cryaa-R49C homozygous mutant knock-in mice; and 14-day old wild-type and 14-day-old cryab-R120G heterozygous mutant and cryab-R120G homozygous mutant knock-in mice


title: Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins

status: Public on Oct 25 2017

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

summary: We used RNA-seq to measure transcript levels in human cells with the PUM1 and PUM2 proteins knocked down; by analyzing the differences in transcript abundances between those conditions, we were able to identify 927 targets showing significant changes in the presence of the PUM knockdown.

overall_design: Comparative expression profiling via RNA seq between cells undergoing shRNA-mediated PUM knockdown and cells treated with a non-target control

first: Jen

last: Bohn

first: Peter

first: Aaron

last: Goldstrohm


title: Altered expression of genes in lncRNA-LBCS, hnRNPK and PTBP1 knockdown

status: Public on Aug 13 2017

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: We identify a lncRNA which low expresses and regulates self-renewal of bladder cancer stem cell. So we named it lncRNA-LBCS (low expresses in bladder cancer stem cell). Further study finds that lncRNA-LBCS bind to hnRNPK and PTBP1. To investigate the genes regulated by these, we knockdown lncRNA-LBCS, hnRNPK and PTBP1 by siRNA, respectively, and perform high-throughput sequence. So we identify a series of genes regulated by lncRNA-LBCS, hnRNPK and PTBP1, respectively.

overall_design: Bladder cancer cell line UM-UC-3 was transfected with the contol siRNA or lncRNA-LBCS, hnRNPK and PTBP1 siRNA for 48h, respectively. The RNA of the transfected cells was extracted and sequenced on an Illumina Hiseq 2500 platform and 100 bp paired-end reads were generated.

first: Tianxin

last: Lin

first: Jian

last: Huang


title: RNA-seq experiments of round spermatid deficient for Epc1/2

status: Public on Aug 14 2017

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: EPC1/TIP60-mediated histone acetylation facilitates spermiogenesis in mice

overall_design: Gene expression was analyzed using WT and deficient mice for both Epc1 and Epc2.

first: Yixin

last: Dong

first: Haruhiko

last: Koseki


title: Transcriptomic analysis of  fungus Penicillium oxalicum and its set2 deletion strains

status: Public on Nov 07 2017

city: Jinan

first: Yanan

last: Li

address: Shanda south road 27

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), and set2 knockout strain (Δset2) in different carbon sources. The deletion of set2 upregulated genes involved in oxidation- reduction process, extracellular region, and plasma membrane ATP synthesis coupled proton transport both with 2% glucose or 1% cellulose and 1% wheat bran as carbon sources. We find the expression levels of 20 secondary metabolism gene clusters were upregulated or downregulated under different carbon sources in Δset2. This study provides the information that SET2 function are required in conidiation and hydrolase activity of P. oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and set2 knockout mutant strains in 24h in modifeid Czapek culture medium with 2% glucose or 1% cellulose and 1% wheat bran as carbon sources.Three replicates were included for each samples.

first: Yuqi

last: Qin


title: Comparison of extracellular vesicles released from mouse WEHI-231 B cells under isotype or anti-CD24 antibody stimulation

status: Public on Aug 28 2017

city: Moncton

first: D. Craig

last: Ayre

state: New Brunswick

address: 35 rue Providence Street

institute: Atlantic Cancer Research Institute

summary: WEHI-231 extracellular vesicles, regardless of stimulation, predominantely contain 5S and  5.8S rRNA. No differentially expressed transcripts were identified, but CD24 induces an overall reduction in protein coding transcripts.

overall_design: Examination of the RNA in extracellular vesicles released by cells under 2 different stimulations

first: Sherri

middle: L

last: Christian


title: Quantitative Analysis of hippocampal transcriptomes form wild-type, control and Kdm5c mutant mice (KO and ifKO) through Next Generation Sequencing (RNA-Seq)

status: Public on Aug 18 2017

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary: RNA preparation for sequencing was performed as described in (Fiorenza et al., 2016). Hippocampi derived from three different animals were pooled together for each sample and three independent samples were sequenced. RNA-seq datasets from Kdm5c null mice and control littermates at their home cages (HC) and after 1 h of novelty exploration (NE) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus, where the configuration was in conditional samples paired-end and in conventional samples  single-end. RNA-Seq libraries were prepared from total RNA using poly(A) enrichment of the mRNA (mRNA-Seq). The libraries were stranded and multiplexed. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Library sizes can be found in Suppl Table 9 of the manuscript. RNA-Seq libraries were mapped to reference genome (Ensembl GRCm38) using STAR v2.5.0c (Dobin A. et al. 2013), and with corresponding gene model annotation (Mus_musculus.GRCm38.83.gtf). Samtools (v1.3) was used to further process BAM files (Li et al., 2009). For calling of differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2014) at gene level and count tables were analysed using DeSeq2 (v1.10.0) R-package (Love et al., 2014) and bioconductor v3.2. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 as indicated in the manuscript.

overall_design: mRNA profiles from adult mouse hippocampus from wild type, control, and Kdm5c mutant mice (KO and ifKO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Each sample was prepared by pooling hippocampal tissue from 3 idenpendent mice.

first: Jose

middle: P

last: Lopez-Atalaya

first: M

middle: T

last: López-Cascales

last: Scandaglia


title: Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [CAP-Seq]

status: Public on Aug 10 2017

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

institute: University of Oxford

summary: The human genome contains approximately 27,700 CpG islands (CGIs). Most are associated with promoters and their DNA is nearly always unmethylated. By contrast, CGIs lying within the bodies of genes usually become methylated during differentiation and development. CGIs also normally become methylated at X-inactivated and imprinted genes and abnormally methylated in genome rearrangements and in malignancy. In such circumstances, methylation of CGIs is often associated with RNA transcripts reading through these elements but the relationship of this RNA to methylation of CGIs is not clear. Here we investigated a previously described form of α-thalassemia caused by a genome rearrangement leading to abnormal transcription and DNA methylation of the CGI at the promoter of the α-globin gene. We show that transcription per se is responsible for DNMT3B-mediated methylation of the globin CGI, and that this is a general mechanism responsible for methylation of most intragenic CpG islands.

overall_design:
CapSeq was performed on day 7 in vitro differentiated EBs containing the human gene sequence of RHBDF1 with (RHBDF1+P; chr16:47,861-63,210, hg18) or without  (RHBDF1-P; chr16:47,911-60,819, hg18) its promoter in the a recombination mediated cassette exchange (RMCE) system established within the mouse α-globin locus (Lynch et al., 2012, DOI: 10.1038/emboj.2011.399 ) to map transcription initiation sites within the transgene.

Please note that the Cap-seq methods captures the 5’ end of any short RNA that was Capped, capturing both coding and non-coding RNA.

first: Danuta

last: Jeziorska

first: Jelena

last: Telenius

first: Douglas

middle: R

last: Higgs

first: Cristina

last: Tufarelli


title: Recovery of genomic stability by ZSCAN10 in induced pluripotent stem cells from aged donors

status: Public on Jul 31 2017

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Induced pluripotent stem cells (iPSC), which are generated from a patient’s own cells and used to produce transplantable tissues, may particularly benefit older patients who are more likely to suffer from degenerative diseases. However, iPSC generated from aged donors (A-iPSC) exhibit higher genomic instability, defects in apoptosis, and a blunted DNA damage response compared to iPSC generated from younger donors (Y-iPSC). This raises significant safety concerns, as transplantable tissues produced from A-iPSC may be functionally impaired and carry a higher risk of cancer development. When we consider the complex genomic and epigenetic variations that occur during aging, the genomic instability in A-iPSC is likely caused by multiple mechanims. Here, we introduce the first step toward unraveling this question with the discovery of a mechanism that contributes to A-iPSC instability. We demonstrated that A-iPSC exhibit excessive glutathione-mediated reactive oxygen species (ROS) scavenging activity, which blocks the DNA damage response and apoptosis and leads to genomic instability. We found that the pluripotency factor ZSCAN10 is poorly expressed in A-iPSC and addition of ZSCAN10 with the four Yamanaka factors (OCT4, SOX2, KLF4, and c-MYC) used in iPSC reprogramming normalizes ROS/glutathione homeostasis and the DNA damage response and recovers A-iPSC genomic stability. Restoring the genomic stability of A-iPSC will ultimately enhance our ability to produce histocompatible functional tissues from patient’s own cells that are safe for transplantation.

overall_design: Total RNA from Y-SC, A-SC, YiPSCS, AiPSCS, AiSPCS+Z and ESC  were labeled with Cy3. Samples were hybridized to a MouseRef-8 v2.0 Expression BeadChip (Illumina, San Diego, CA, http://www.illumina.com), according to the manufacturer’s protocol. Arrays were scanned with a BeadChip Reader (Illumina).

first: Maria

last: Skamagki

first: Kitai

last: Kim


title: Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs


title: Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [small RNA-seq]

overall_design: Total RNA samples was extracted from mouse embryonic stem (ES) cells carrying a transgene including human HBA2 either mantained undifferentiated (D0) in the presence of LIF or after 2 (D2), 4 (D4) and 6 (D6) days of embryoid bodies (EB) differentiation


title: Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [H3K36me3_ChIP-seq]

overall_design: One H3K36me3 ChIP-seq sample and its sonication input (no replicates)


title: Changes in relative transcript amounts caused by hydrogen sulfide treatment, calprotectin treatment, and deletion of CstR in Staphylococcus Aureus

status: Public on Jun 19 2017

city: Bloomington

first: David

middle: Peter

last: Giedroc

state: IN

address: 212 S. Hawthorne Drive

department: Chemistry

institute: Indiana University

summary: The Staphylococcus aureus strain Newman uses the dithiol-containing repressor CstR to sense sulfide stress via reactive sulfur species (RSS), allowing transcription of a mitochondrial-like sulfide oxidation system, the core of which is genetically linked to methicillin resistance determinants in MRSA strains. The cytoplasm maintains an excess of reduced relative to oxidized low molecular weight (LMW) thiols that are protective against oxidative stress and transition metal (Zn, Cd and Cu) toxicity, buffering these ions to low “free” concentrations via formation of coordination complexes. We hypothesize that unregulated H2S perturbs the LMW thiol pool by generating RSS; these, in turn, react with CstR cysteines (C31, C60), induce cst derepression, and are cleared by cst-encoded enzymes. These results show that sulfide stress induces the cst operon and a zinc starvation response, represses cysteine biosynthesis, and generally represses genes that are induced by acute oxidative stress; in addition, strong repression of the expression of staphylococcal virulence factors is observed in the ∆cstR strain.

overall_design: RNA for the sulfide experiment was prepared from cultures of wild-type and DcstR strains of Staphylococcus aureus strain Newman grown exponentially in HHWM media supplemented with thiosulfate and methionine at 37°C to OD600=0.2. At this point Na2S was added to treated cultures at a ﬁnal concentration of 0.2 mM for a 10 min exposure, then samples were collected from all conditions. For the calprotectin experiment, bacteria were grown in the presence and absence of 960mg/mL calprotectin in growth media containing 38% TSB/ 72% calprotectin buffer (20 mM Tris, pH 7.5, 100 mM NaCl, 3 mM CaCl2, 10 mM β-mercaptoethanol), supplemented with 1 µM Zn and 1 µM Mn Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Justin

last: Luebke

first: Kevin

middle: E

last: Bruce

first: Katherine

last: Edmonds

first: Thomas

last: Kehl-Fie

first: Lauren

last: Palmer

first: Yan

last: Guo

first: Mingsheng

last: Rusch

first: Eric

last: Skaar


title: Ethylene promotes root hair growth through coordinated EIN3/EIL1 and RHD6/RSL1 activity in Arabidopsis

status: Public on Dec 12 2017

city: Shenzhen

first: Bosheng

last: Li

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

summary: Root hairs are an extensive structure of root epidermal cells and are critical for nutrient acquisition, soil anchorage, and environ- mental interactions in sessile plants. The phytohormone ethylene (ET) promotes root hair growth and also mediates the effects of different signals that stimulate hair cell development. However, the molecular basis of ET-induced root hair growth remains poorly understood. Here, we show that ET-activated transcription factor ETHYLENE-INSENSITIVE 3 (EIN3) physically interacts with ROOT HAIR DEFECTIVE 6 (RHD6), a well-documented positive regulator of hair cells, and that the two factors directly coactivate the hair length-determining gene RHD6-LIKE 4 (RSL4) to promote root hair elongation. Transcriptome analysis further revealed the parallel roles of the regulator pairs EIN3/EIL1 (EIN3-LIKE 1) and RHD6/ RSL1 (RHD6-LIKE 1). EIN3/EIL1 and RHD6/RSL1 coordinately en- hance root hair initiation by selectively regulating a subset of core root hair (H) genes. Thus, our work reveals a key transcriptional complex consisting of EIN3/EIL1 and RHD6/RSL1 in the control of root hair initiation and elongation, and provides a molecular framework for the integration of environmental signals and in- trinsic regulators in modulating plant organ development.

overall_design: Col-0, ein3 eil1, rhd6 rsl1 and ein3 eil1 rhd6 rsl1 were grown vertically on MS medium for 6 d and then treated with or without ET at 10 ppm for 4 h. Two biological replicates were prepared for each condition. Library preparation and high-throughput sequencing were conducted in accordance with the manufacturers’ instructions. Root total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). Sequencing libraries were prepared using the TruSeq mRNA preparation kit (Illumina). RNA quality and library quality were examined by a Bioanalyzer 2100 instrument (Agilent), and paired-end, 100-bp deep sequencing was per-formed on an Illumina HiSeq 2000 platform.

first: Ying

last: Feng

first: Ping

last: Xu

first: Pengpeng

first: Xing

last: Wen

first: Fengying

last: An

last: Gong

first: Yi

last: Xin

first: Ziqiang

last: Zhu

first: Yichuan

last: Wang

first: Hongwei


title: A Long-Range cis-Regulatory Element for Class I Odorant Receptor Genes

status: Public on Jul 23 2017

first: Junji

last: Hirota

address: 4259-B63 Nagatsuta-cho

department: Center for Biological Resources and Informatics

institute: Tokyo Institute of Technology

summary:
Individual olfactory sensory neurons express a single odorant receptor (OR) gene from either class I genes residing in a single cluster on a single chromosome or class II genes spread over multiple clusters on multiple chromosomes.
Here, we identify an enhancer element for mouse class I genes, the J element, that regulates class I gene expression of a much larger number of genes and over a much greater genomic distance than known class II gene enhancers. Our data reveal an extraordinary long-range cis-regulatory element that governs the singular class I gene expression and has been phylogenetically preserved to retain a single cluster organization of class I genes in mammals.

overall_design: To comprehensively analyze the effects of deletion of J (ΔJ) on all the OR genes, we directly compared the gene expression profiles in the olfactory epithelia from six wild-type and six ΔJ littermate mice using microarray analysis.

first: Tetsuo

last: Iwata

first: Yoshihiro

last: Yoshihara


title: Transcriptional profiling of lung tumour cell lines with distinct p53 mutations in the absence or presence of WT p53

status: Public on Aug 09 2017

city: Belfast

first: Emma

last: Kerr

address: 97 Lisburn Rd

department: PGJCCR

institute: Queen's University Belfast

summary:
Microarray expression data generated to determine the impact of defined p53 mutations on lung cancer cell phenotypes, and on the tumour supressive responses induced by WT p53 restoration.
In murine models of lung cancer, the therapeutic benefit of WT p53 restoration has been demonstrated in p53-deficient tumours (Juntilla et al, 2010; Feldser et al, 2010). However, it remains unknown if the restoration of WT p53 function is beneficial in p53 mutant tumours. Thus, to determine the impact of p53-targeted therapy in mutant p53 lung cancer, we analysed cells from murine lung tumours of distinct p53 genotypes. Utilising the well characterised p53-ER allele (Christophorou et al, 2005; Martins et al, 2006; Juntilla et al, 2010) we carried out transcriptional profiling of KrasG12D/+ cell lines isolated from advanced lung tumours with defined p53 status: p53Fx/ER (null), p53R270H/ER and p53R172H/ER in the absence (p53 WT OFF) or presence (p53 WT ON) of 4-hydroxytamoxifen (4-OHT). The temporal specificity of p53-ER restoration allowed us to utilised two timepoints to determine both the immediate (2hr) and sustained (8hr) impact of WT p53 function.

overall_design: Murine tumour cell lines were isolated from independent advanced KrasG12D/+; p53Fx/ER (null), p53R270H/ER and p53R172H/ER lung tumours (minimum of 2 tumour mice/genotype used) 21-22 weeks post 5x106 PFU adenocre intranasal administration. Tumours were collected, homogenised and digested with 4mg/ml collagenase/dispase at 37oC for 2.5 hrs, before plating in DMEM/F12 media supplemented with 10% FBS and 2mM L-Glutamine. Epithelial tumour cells were isolated using differential detachment method and maintained in DMEM/F12; 10% FBS; 4mM L-Glutamine media.  Four independent tumour cell lines/genotype were cultured in 3D matrigel (3:2 Matrigel:Media)  before treatment with 4-OHT or ethanol (vehicle) for times indicated. Cell cultures were dissociated and RNA extracted, followed by Illumina Mouse WG-6 version 2.0 Expression BeadChip  microarray analysis. Data were analysed using R (R Development Core Team, 2010) and Bioconductor (Gentleman et al, 2004). Spatial artefacts were removed using BASH (Cairns et al, 2008) and HULK algorithms from the bead array package (Dunning et al, 2007). Data were log2 transformed and quantile normalised. Expression values were determined as average of two reads for each sample.

first: Frances

last: Turrell

first: Meiling

last: Gao

first: Shamith

last: Samarajiwa

first: Carla

last: Martins


title: Whole Plant Temperature Manipulation Affects Flavonoid Metabolism and the Transcriptome of Grapevine Berries

status: Public on Jun 14 2017

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

institute: University of Verona

summary: Among environmental factors, temperature is the one that poses serious threats to viticulture in the present and future scenarios of global climate change. In this work, we evaluated the effects on berry ripening of two thermal regimes, imposed from veraison to harvest. Potted vines were grown in two air-conditioned greenhouses with High Temperature (HT) and Low Temperature (LT) regimes characterized by 26 and 21°C as average and 42 and 35°C as maximum air daily temperature, respectively. We conducted analyses of the main berry compositional parameters, berry skin flavonoids and berry skin transcriptome on HT and LT berries sampled during ripening. The two thermal conditions strongly differentiated the berries. HT regime increased sugar accumulation at the beginning of ripening, but not at harvest, when HT treatment contributed to a slight total acidity reduction and pH increase. Conversely, growing temperatures greatly impacted on anthocyanin and flavonol concentrations, which resulted as strongly reduced, while no effects were found on skin tannins accumulation. Berry transcriptome was analyzed with several approaches in order to identify genes with different expression profile in berries ripened under HT or LT conditions. The analysis of whole transcriptome showed that the main differences emerging from this approach appeared to be more due to a shift in the ripening process, rather than to a strong rearrangement at transcriptional level, revealing that the LT temperature regime could delay berry ripening, at least in the early stages. Moreover, the results of the in-depth screening of genes differentially expressed in HT and LT did not highlight differences in the expression of transcripts involved in the biosynthesis of flavonoids (with the exception of PAL and STS) despite the enzymatic activities of PALs and UFGT being significantly higher in LT than HT. This suggests only a partial correlation between molecular and biochemical data in our conditions and the putative existence of post-transcriptional and post-translational mechanisms playing significant roles in the regulation of flavonoid metabolic pathways and in particular of anthocyanins.

overall_design: Grapevine (Vitis vinifera cv Sangiovese) samples were collected from vines grown in two different thermal regimes, low temperature (LT) and high temperature (HT). Berries were collected at four ripening stages, starting one week before véraison (stage 0, Controls), at véraison (stage 1) and 10 (stage 2), 20 (stage 3) and 32 (stage 4) days after véraison. Each sample comprised three biological replicates of about 10berry skins each, sampled from clusters of different grapevine plants, and from different position within the same cluster. The above-described procedure was followed for each stage and thermal regime, thus the experiment entailed the collection and the analysis of 27 berry skin samples (3 samples control + (2 thermal regimes X 4 stages X 3 replicates)).

first: Chiara

last: Pastore

first: Sara

last: Zenoni

first: Nushin

last: Mohaved

first: Gianluca

last: Allegro

first: Gabriele

last: Valentini

first: Ilaria

last: Filippetti

first: Giovanni Battista

last: Tornielli


title: Differential gene expression analysis of pediatric acute myeloid leukemia cell lines treated with azacytidine and panobinostat alone or in combination and compared to vehicle treated cells.

status: Public on Jul 01 2017

city: Wilmington

first: Sonali

last: Barwe

state: DE

address: 1701 Rockland Road

institute: Alfred I. duPont Hospital for Children

summary:
Pediatric AML cell lines (MV4;11, AML-193 and THP-1) were treated with DNA hypomethylating agent (azacytidine) and a pan histone deactylase inhibitor (panobinostat) alone or in combination. Treatment of AML cell lines with these epigenetic drugs synergistically suppresses cell viability in vitro and in xenograft models in vivo.
Data show differential regulation of gene expression in AML cell lines by epigenetic drugs at concentrations which retained cell viability  at a minimum of 75% even in the combination treatment.

overall_design: MV4;11 cells were treated with vehicle (0.1% DMSO), 0.5 uM azacytidine, 1.5 nM panobinostat or 0.5 uM azacytidine + 1.5 nM panobinostat for 48 h. AML-193 cells were treated with vehicle (0.1% DMSO), 5 uM azacytidine, 5 nM panobinostat or 5 uM azacytidine + 5 nM panobinostat for 48 h. THP-1 cells were treated with vehicle (0.1% DMSO), 3 uM azacytidine, 5 nM panobinostat or 3 uM azacytidine + 5 nM panobinostat for 48 h

first: Anilkumar

last: Gopalakrishnapillai

first: E

middle: A

last: Kolb

first: Suzanne

last: McCahan


title: Myc and YAP roles in the control of the cell cycle

status: Public on Nov 22 2017

city: milano

first: stefano

last: campaner

address: via adamello 16

institute: fondazione Istituto italiano di tecnologia

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

overall_design: Refer to individual Series


title: Expression data from fresh human embryonic lung epithelial tip and stalk cells and cultured organoids derived from tip and stalk.

status: Public on Jun 26 2017

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: We isolated the tip and stalk progenitors from four individual human embryonic lungs and used mRNAseq to profile their transcriptome. Tips and stalks from other individuals were subsequently cultured as organoids and their transcriptome profiled by mRNAseq in a separate sequencing run.

overall_design: Lung epithelial tip and stalk cells were microdissected before being lysed for RNA extraction. Organoids were removed from Matrigel prior to lysis.

first: Emma

last: Rawlins


title: Cell-type specific gene programs of the normal human nephron define kidney cancer subtypes

status: Public on Aug 07 2017

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

summary: Comprehensive transcriptome studies of cancers often rely on corresponding normal tissue samples to serve as a transcriptional reference. In this study we performed in-depth analyses of normal kidney tissue transcriptomes from TCGA and demonstrate that the histological variability in cellularity, inherent in the kidney architecture, lead to considerable transcriptional differences between samples. This should be considered when comparing expression profiles of normal and cancerous kidney tissues. We exploited these differences to define renal cell-specific gene signatures and used these as framework to analyze renal cell carcinoma (RCC) ontogeny. Chromophobe RCCs express FOXI1-driven genes that define collecting duct intercalated cells whereas HNF-regulated genes, specific for proximal tubule cells, are an integral part of clear cell and papillary RCC transcriptomes. These networks may be used as framework for understanding the interplay between genomic changes in RCC subtypes and the lineage-defining regulatory machinery of their non-neoplastic counterparts.

overall_design: Samples from different parts of the kidneys were procured using core-sampling from approximately 10 mm thick sections obtained from nephrectomized patients in surgery for renal neoplasms. Sampling was performed in the part of the kidney that was farthest from the tumor. Sections were thereafter embedded and hematoxylin-eosin stained allowing for approximation of the respective site in kidney from which the sample was obtained. In all cases a histologically normal kidney histology was confirmed. In all, 53 samples from 5 different renal specimens were included in the analysis.

first: Pontus

last: Eriksson

first: Krzysztof

last: Krawczyk

first: Srinival

last: Veerla

first: Jennifer

last: Hansson

first: Helen

last: Nilsson

first: Jonas

last: Sjölund

first: Mattias

last: Höglund

first: Martin

last: Johansson

first: Håkan

last: Axelson


title: A hydrogen cyanamide-responsive transcriptome of sweet cherry flower buds from endodormancy to flowering

status: Public on Jun 01 2017

city: Frederiksberg C

first: Irina

middle: Alexandra

last: Ionescu

address: Thorvaldsensvej 40

department: Department of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: Perennial plants, like fruit trees grown in temperate regions, are characterized by bud dormancy, a rest state that protects the bud from cold during winter. At the same time, these plants have developed a requirement for winter chill for correct flowering. However, winters are becoming increasingly warm in temperate regions, resulting in dramatic effects on the flowering output and therefore crop yield. A compound that successfully compensates for missing winter chill is hydrogen cyanamide, which has been used to synchronize and advance flowering time in a range of commercially important fruit crops. Hydrogen cyanamide also represents a unique tool for researchers to study controlled endodormancy release. Here, we treated dormant sweet cherry flower buds with hydrogen cyanamide, sampling flower buds at different time points after treatment. RNAseq revealed more than 6,000 hydrogen cyanamide-responsive genes. In accordance with these results, hydrogen cyanamide treatment increased the levels of jasmonoyl-isoleucine (JA-Ile) and the cytokinins trans-zeatin riboside (tZR), dihydrozeatin (DZ) and dihydrozeatin riboside (DZR). Furthermore, hydrogen cyanamide affected the expression of antioxidant- and cell wall loosening-associated transcripts. These results suggest a complex mechanism of action for hydrogen cyanamide-induced endodormancy release, including key roles for JA-Ile, zeatin-type cytokinins and hydrogen cyanide.

overall_design: 21 samples were analyzed in total, a day 0 sample (before treatment) and then day 1, 3 and 6 after treatment samples for both hydrogen cyanamide (2% Dormex) and control (water) treatment. Every sample was analyzed in three biological replicates.

first: Gregorio

last: López-Ortega

first: Meike

last: Burow

first: Almudena

last: Bayo-Canha

first: Alexander

last: Junge

first: Oliver

last: Gericke

first: Birger

last: Møller

first: Raquel

last: Sánchez-Pérez


title: RNA-seq analysis of blood transcriptomes from beluga whales in Bristol Bay, Alaska, USA

status: Public on May 11 2017

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

summary: Whole blood was collected as part of annual health assessments of beluga whales from the healthy Bristol Bay, Alaska stock during 2012-2014.  Gene expression from 24 animals (8 from each year) was analyzed to establish baseline information on the content and variation of the beluga whale blood transcriptome.

overall_design: Illumina based RNA-seq analyses were carried out on RNA from blood using a transcriptome assembled de novo in Trinity.  The data set was interrogated for transcripts exhibiting variablity between sexes or years.

first: Frances

last: Van Dolah

first: Kathy

last: Huntington

first: Caroline

last: Goertz


title: RNA-seq analysis of blood transcriptomes from managed bottlenose dolphins in Waikoloa, Hawaii, USA

status: Public on May 09 2017

summary: Whole blood was collected as part of monthly veterinary checkups of bottlenose dolphins housed at Dolphing Quest in Waikoloa, Hawaii, USA.  Gene expression from 5 samples was analyzed for comparison to the blood transcriptome of the beluga whale.

overall_design: Illumina based RNA-seq analyses were carried out on RNA from blood using a transcriptome assembled de novo in Trinity.  The data set was compared to a parallel analysis of the beluga whale blood transcriptome.

middle: S

first: Michelle

last: Campbell