title: A NAFLD Model Created By Endoplasmic Reticulum Stress Response-Associated Steatosis in Human Induced Pluripotent Stem Cell-Derived Hepatocytes

status: Public on Sep 13 2018

city: Orlando

first: Maddalena

last: Parafati

state: FL

address: 6400 Sanger rd

department: Conrad Prebys Center for Chemical Genomics

institute: SBPMRI

summary: Our study reports a phenotypic approach to model hepatic steatosis in induced pluripotent stem cell-derived hepatocytes

overall_design: hiPSCs, differentiated into functional hepatocytes that exhibited classic hepatocyte-associated bio-functions, were subjected to lipid overload and challenged with acute induced-ER stress developed a steatotic phenotype used to model hepatic steatosis in vitro. The quantification of lipid induction was performed by fluorescent high-content imaging.

first: Malany

last: Siobhan


title: DNA methylome of pineapple

status: Public on Sep 27 2018

city: Fuzhou

first: Haifeng

last: Wang

state: Fujian

address: Shangxia dian

country: China

institute: Fujian Agriculture and Forestry University

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Bisulfite treatment libraries were made to characterize the DNA methylome of pineapple

overall_design: Genome-wide methylome was done by Illumina TruSeq preparation kits followed by high-throughput sequencing with Illumina HiSeqX-ten


title: Exploring the landscape of transcriptome 3’ end diversity (TREND) by applying TRENDseq

status: Public on Dec 14 2018

city: San Francisco

first: Anton

last: Ogorodnikov

state: CA

address: 513 Parnassuss Ave

department: Rheumatology

country: USA

institute: UCSF

summary: Purpose: To identify key drivers of transcriptome 3’end diversity (TREND) in neuroblastoma in a genome wide scale. To develop and apply TRENDseq – a tailored method for genome-wide interrogation of the TREND landscape in highly multiplexed libraries.  Methods: RNA from BE(2)-C cells transfected with control or specific siRNA’s against indicated TREND regulator were processed according to TRENDseq protocol and sequenced using Illumina HiSeq 2500 or NextSeq 500. Raw data was aligned to human genome hg38 and processed using TRENDseq analysis pipeline. BE(2)-C differentiation samples were processed using the 3’READS protocol (Hoque M et al. 2014, PMID 24590784)  Conclusions:   We analyzed the diversity of the transcriptome 3’end in response to depletion of 174 potential TREND regulators by RNAi. TRENDseq is capable to deconvolute the dynamics of TREND from highly multiplexed libraries. The screening revealed regulators of various levels of gene expression control (e.g. transcription, splicing, mRNA turnover, etc.) to play an important role in the diversification of the transcriptome 3’ end, affecting over 3600 genes altogether.   Data types:  1 – 198 siRNA depletion experiments including 174 knockdowns of putative TREND regulators and 24 mock control samples.  2 – Biological replicates of top TREND regulators depletion and TRENDseq with and without PCF11 co-depletion  3 – Additional independent replicates of PCF11 knockdown  4 – BE(2)-C 3’READS upon differentiation

overall_design: 174 functional RNAi depletions in BE(2)-C neuroblastoma cells. Additional independent knockdown and TRENDseq were performed for selected key regulators of TREND. BE(2)-C neuroblastoma cells were differentiated by all-trans retinoic acid administration and analyzed using 3’READS (Hoque M et al. 2014, PMID 24590784).

first: Michal

last: Levin

first: Mainul

last: Hoque

first: Bin

last: Tian

first: Sven

last: Danckwardt


title: Next Generation Sequencing of CELF6-HA/YFP Crosslinking Immunoprecipitation Samples and Controls

status: Public on Aug 17 2018

city: St. Louis

first: Michael

middle: A

last: Rieger

state: MO

address: 660 S. Euclid, Box 8232

department: Genetics

institute: Washington University in St. Louis

summary:
Purpose: This study was performed to determine the RNA binding targets of the RNA binding protein CELF6 in the mouse brain.
Method: 4 pools of CELF6-HA/YFP brains (cortices & cerebella removed) were snap frozen in liquid nitrogen, powdered, crosslinked (254 nm, 400 J/cm^2, 3 pulses), and homogenized and immunoprecipitated with anti-EGFP antibodies. Control samples consistent of input RNA from immunoprecipitates as well as anti-EGFP immunoprecipitates of wild-type (WT, HA/YFP negative) tissue. Sequencing libraries were prepared from harvested RNA with 9-mer unique molecular identifiers (UMIs). Procedure uses Trimmomatic to catalog UMIs as well  as trim low quality bases, STAR to align to mm10 reference genome, Fulcrum Genomics FGBio to annotate BAM files with UMI information, Picard Tools to remove PCR duplicates, and Subread featureCounts to count reads mapping to features in a GTF in a strand specific manner. GTFs were prepared to contain annotated: 3'UTRs, 5'UTRs, CDS, as introns+/-10 bp overlap into surrounding exons. Additionally, BAMs were counted against features in a GTF corresponding to peaks identified by Piranha. To do this, an example BAM file (merge of all HA/YFP+ samples) was windowed using Bedtools, counted in a strand-specific manner using Subread featureCounts, and converted to BED format for peak calling with Piranha. The final called peaks were edited to a width of of 100 bp around significant maxima, and compiled into a GTF. This GTF was used for recounting individual sample files for immunoprecipitates and controls. Final counts were tested for significant enrichment in the HA/YFP-immunoprecipitated sample compared to (a) input samples, and (b) WT controls using edgeR. Samples were sequenced on 4 lanes of an 2xruns on an Illumina NextSeq, and BAMs were prepared on data for each lane separately and then merged across lanes by sample before counting.
Results: Features showing nominal edgeR p values <0.05 in both YFP vs. Input and YFP vs. WT comparisons, as well as positive log2 fold change in YFP vs. Input and YFP vs. WT input comparison showed a predominance of significant comparisons falling in counts from 3'UTR regions. This was also true when restricting to only high confidence targets which showed FDR <0.05 by Benjamini-Hochberg. This was the case whether testing across sums under Piranha peaks in YFP vs. controls, as well as summing all counts across annotated 3'UTR, 5'UTR, introns, and CDS regardless of the presence of a called peak.
Conclusions: CELF6 shows enriched binding in 3'UTR regions in YFP+ samples vs. controls. Nominally bound regions were used downstream to validate findings and explore the consequence of CELF6 associate in a massively parallel reporter assay. This is the first exploration of the binding targets of this RNA binding protein, linked to behavioral changes in knock-out mice (Dougherty et al. J. Neurosci 2013)

overall_design: Differential enrichment analysis in CELF6 CLIP samples vs. input & non-target control samples.

first: Joseph

middle: D

last: Dougherty


title: Differentially expressed genes in normal gastric mucosa and gastric cancer tissues

status: Public on Aug 23 2018

city: Shanghai

first: Zhongyin

last: Yang

address: NO.197 Ruijin er road

department: Department of Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary:
To identify the differentially expressed genes in normal gastric mucosa and gastric cancer tissues, we employed the microarray profiling analysis. Genes with greater than 2-fold change and P-value ＜0.05 were identified as differentially expressed genes.
From this dataset, we obtained differentially expressed genes by cluster analysis and enriched GOs was identified by Gene set enrichment analysis (GSEA) analysis, microtubule GO was one of the most enriched GOs, and the gene KIF14 was selected to go on to the next step in the study.

overall_design: 10 paired of total samples were analyzed. Genes with an FDR 0.25 and a fold-change ≥2 were selected. Pathway and GO analysis was used for the next step analysis.

first: Qinlong

last: Gu


title: Molecular signature of Aluminum hydroxide adjuvant in ovine PBMCs by integrated mRNA and microRNA transcriptome sequencing

status: Public on Oct 30 2018

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

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

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine peripheral blood mononuclear cells (PBMCs) [RNA-Seq]

summary: We report the application of RNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep.  We mapped about 52 million sequence reads per sample to the sheep genome (build Oar3.1) and identified 21,274 genes in the PBMCs of sheep treated with commercial vaccines or with the adjuvant alone. A total of 2473, 2980 and 429 differentialy expressed genes were identified in the vaccine tf VS vaccine t0, adjuvant tf VS adjuvant t0 and adjuvant tf VS vaccine tf comparisons, respectively. Previously reported genes related to alterations caused by aluminium adjuvant were found differentially expressed, namely: NLRP3, IL1B, IL8, TNF, NFKB2, RELA and RELB. In addition, most of the genes related to apoptosis were up-regulated in both group after treatment. In contrast, other genes related to immune response, inflammatory response and cell-cell signalling were up-regulated in Vac-injected sheep and whereas down-regulated in Adj-injected animals. Taken together, our analysis provides characterization of alterations in the transcriptome caused by the aluminium adjuvant and identifies increased expression of inflammatory cytokines, NF-KB family genes and apoptotic genes.

overall_design: PBMCs Total RNA profiles of six age-matched Rasa sheep before and after inoculation (t0 and tf) of nine different commercial vaccines based of aluminium hydroxide (the vaccine group composed of 3 animals) or with the aluminium adjuvant alone in an equivalent dose (the adjuvant group composed of 3 animals) were generated by deep sequencing on an Illumina HiSeq2000 sequencer. In total, the study is composed of three biological replicates per group and thirteen libraries were sequenced (there was a tecnical replicate of a sample at the end of the experiment and two other samples where sequenced in two different sequencing runs).

first: Endika

last: Varela

first: Naiara

last: Abendaño

first: Javier

last: Asín

first: Maialen

last: Sistiaga

first: Marta

last: Pérez

first: Ramsés

last: Reina

first: Damián

last: de Andrés

first: Lluís

last: Luján


title: The transcription factor Myb enhances CD8+ T cell stemness and antitumor immunity

status: Public on Nov 01 2018

city: Bethesda

first: Luca

last: Gattinoni

state: MD

address: 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: Stem cells are maintained by transcriptional programs promoting self-renewal and repressing differentiation. Here, we show that the transcription factor Myb is essential for generating and maintaining stem cells within the CD8+ T-cell memory compartment. We found that, following viral infection, CD8+ T cells lacking Myb underwent terminal differentiation and exhibited impaired capacity to form CD62L+ stem cell-like memory cells. Myb acted both as a transcriptional activator of Tcf7 to enhance the development of memory cells and as a repressor of effector differentiation through Zeb2 suppression. Myb mutants’ complementation revealed that the Myb transactivation domain was necessary to restrain terminal differentiation, whereas the negative regulatory domain was critical for cell survival. Conversely, Myb overexpression enhanced CD8+ T-cell memory formation, polyfunctionality, and recall responses promoting curative antitumor immunity. These findings identify Myb as a pivotal regulator of CD8+ T-cell stemness and highlight the therapeutic potential of increasing Myb activity in CD8+ T cells.

overall_design: We compared the gene expression profiles of Myb-defiecient CD8+ T cells  with those of Myb-sufficient CD8+ T cells

first: Yun

last: Ji


title: The host response to influenza virus infection

status: Public on Jul 12 2018

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary: In this study, we performed a cross-species gene expression study of the peripheral blood from the Collaborative Cross (CC) mouse population after Influenza virus (IV).

overall_design: Blood was taken for RNA isolation at different time points after virus infection (day 3, 5 and 8) and mock infection (day 3 post sterile phosphate-buffered saline infection). Body weight was measured until the day of sample collection. For every treatment and day post infection (pi), 3-5 mice per CC strain were analyzed.


title: Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia

status: Public on Dec 18 2018

city: Tampere

first: Saara

last: Laukkanen

address: Arvo Ylpön Katu 34

country: Finland

institute: University of Tampere

summary: Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal, and proliferative features. We sought to identify the transcription factors exhibiting altered and subtype-specific expression patterns in B-ALL and report here that SOX11, a developmental and neuronal transcription factor, is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. We show that a high expression of SOX11 leads to alterations of gene expression that are typically associated with cell adhesion, migration, and differentiation. A high expression is associated with DNA hypomethylation at the SOX11 locus and a favorable outcome. The results indicate that SOX11 expression marks a group of patients with good outcomes and thereby prompts further study of its use as a biomarker.

overall_design: mRNA expression profiles were generated from three different B-ALL cells in three biological replicates after 48h of SOX11 or control siRNA treatment.

first: Toni

last: Grönroos

first: Artturi

last: Mäkinen

first: Juha

last: Mehtonen

first: Atte

last: Nikkilä

first: Laura

last: Oksa

first: Samuli

last: Rounioja

first: Yanara

last: Marincevic-Zuniga

first: Jessica

last: Nordlund

first: Virva

last: Pohjolainen

first: Timo

last: Paavonen

first: Merja

last: Heinäniemi

first: Olli

last: Lohi


title: Histone H3 T11 phosphorylation by Sch9 and CK2 regulates lifespan by controlling the nutritional stress response

status: Public on Jun 25 2018

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

type: Genome binding/occupancy profiling by high throughput sequencing


title: Histone H3 T11 phosphorylation by Sch9 and CK2 regulates lifespan by controlling the nutritional stress response [RNA-seq]

status: Public on Jun 26 2018

summary: We report mRNA expression changes upon nutritional stress condition in WT strains and Histone H3T11 phosphorylation defective mutants.

overall_design: Three replicates each comparing RNA expression levels between wild type, cka1 mutant in various stress conditions.

first: Seunghee

last: Oh


title: Histone H3 T11 phosphorylation by Sch9 and CK2 regulates lifespan by controlling the nutritional stress response [ChIP-seq]

summary: We report the changes of Histone H3 T11 phosphorylation (H3pT11) signal upon nutritional stress (YP with 3% glycerol).

overall_design: Two replicates each of H3pT11 ChIP in YPD (YP media with 2% glucose) and YPglycerol (YP with 3% glycerol) as well as corresponding H3 IP samples (used as controls).


title: Alterations in Sperm DNA Methylation, Non-coding RNA and Histone Retention Associate with DDT Induced Epigenetic Transgenerational Inheritance of Disease

status: Public on Apr 27 2018

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate DDT induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to DDT during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.

overall_design: The experimental design involved a transient exposure of gestating female F0 generation rats during post-conception day 8-14 to 25 mg/kg body weight of DDT in DMSO daily using an intraperitoneal injection. A control generation lineage involved the exposure during day 8-14 of gestation to vehicle DMSO (dimethylsulfoxide) alone. Six different gestating females from different litters for each control and DDT lineage were used. The F1 generation offspring were obtained and aged to 90 day postnatal age and selected males and females bred within the control or DDT lineage. The F2 generation offspring were obtained and aged to 90 days and selected males and females from different litters bred to generate the F3 generation. No sibling or cousin breeding were used to avoid any inbreeding artifacts. All the males were sacrificed at 120 days of age for epididymal sperm collection. The differential DNA methylation regions (DMRs) between the control versus DDT lineages were determined using methylated DNA immunoprecipitation (MeDIP) followed by DNA sequencing (MeDIP-Seq) and bioinformatics analysis. The differential histone retention regions (DHRs) for the F1, F2 and F3 generation for the control versus DDT lineage sperm were analyzed. The procedure involved assessment of differential histone retention sites (DHRs) through a comparison of the control versus DDT lineage sperm using the edgeR analysis similar to that used for the DNA methylation analysis.

first: Millissia

middle: B

last: Maamar

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: Eric

last: Nilsson

first: Margaux

last: McBirney

first: Chong

last: Tang

first: Wei

last: Yan


title: Altered Expression Profiles of Transfer-RNA-Derived Small RNAs Reveal the Regulating Functions in Rat Brain After Intracerebral Hemorrhage (ICH) and the Potential Therapeutic Targets of Buyang Huanwu Decoction in ICH

status: Public on Apr 26 2018

city: Changsha

first: Yang

last: Wang

address: 87 Xiangya Road

department: Xiangya Hospital

institute: Central South University

summary: Transfer-RNA-Derived Small RNA (tsRNA) is s a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the brain of intracerebral hemorrhage (ICH) and sham rats at days 21. Meanwhile, tsRNA levels in ICH treated with the Traditional Chinese Medicine named Buyang Huanwu Decoction (BYHWD) were detected. Bioinformatics analyses indicated that tsRNAs were the important regulators in ICH and potential new therapeutic targets of BYHWD.

overall_design: tiRNA and tRF profiles in the right globus pallidus of ICH, sham, and BYHWD rats at days 21, in triplicate, using Illumina NextSeq 500 system.

first: Wang

last: Yang

first: Tang

last: Tao

first: Li

last: Pengfei


title: iMEF SDHC-loss stable line RNA-seq

status: Public on May 10 2018

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We have developed a tet-inducible SV-40 lentivirus-immortalized mouse embryonic fibroblast (iMEF) cell culture model of SDH-loss paraganglioma/pheochromocytoma in which silencing gene rearrangement of the Sdhc floxed allele is driven by doxycycline-dependent expression of cre-recombinase from a tet-inducible promoter (R26M2rtTA/+;TetOcre;Sdhcfl/fl).  For comparison, we include an isogenic Sdhc wt control line (R26M2rtTA/+;TetOcre;Sdhcfl/wt) that retains one intact copy of Sdhc upon doxycycline exposure.  Following doxycycline induction of both cell lines, dilutional subcloning was employed to obtain stable Sdhc -/- (experimental) and Sdhc +/- (control) cell lines.  Sdhc gene rearrangement status for each clonally-derived cell line was confirmed by PCR.  Cell lines were grown in standard DMEM containing penicillin/streptomycin antibiotics (0.5 mg/mL), non-essential amino acids (100 micromolar each of glycine, alanine, asparagine, aspartic acid, glutamic acid, proline, and serine), sodium pyruvate (1 mM), and HEPES buffer (10 mM) at 21% O2 and 5% CO2.  Following cell line derivation and verification of Sdhc genetic status, transcriptomic profiling for each cell line was performed by RNA-seq.

overall_design: Included in this dataset are single replicate RNA-seq data for six experimental (R26M2rtTA/+;TetOcre;Sdhc-/-) and  two control (R26M2rtTA/+;TetOcre;Sdhc+/-) cell lines derived by dilutional subcloning following induction of Sdhc gene rearrangement with doxycycline.

first: Louis

middle: J

last: Maher


title: Epigenetic findings in periodontitis in UK twins: a cross sectional study

status: Public on Nov 25 2018

city: London

first: Juan

last: Castillo-Fernandez

address: St Thomas Hospital

department: Department of Twin Research

country: United Kingdom

institute: King's College London

type: Methylation profiling by genome tiling array

summary: Genetic and environmental risk factors contribute to periodontal disease, but the underlying susceptibility pathways are not fully understood. Epigenetic mechanisms are malleable regulators of gene function that can change in response to genetic and environmental stimuli, thereby providing a potential mechanism mediating risk effects in periodontitis. The aim of this study is to identify epigenetic changes across tissues that are associated with periodontal disease.

overall_design: Self-reported gum bleeding and tooth mobility were used as indicators of periodontal disease. DNA methylation profiles were generated using the Infinium HumanMethylation450 BeadChip in whole blood, buccal, and adipose samples from predominantly older female twins (mean age 58) from the TwinsUK cohort. Epigenome-wide association scans (EWAS) of gum bleeding and tooth mobility were conducted in whole blood in 528 and 492 twins, respectively. Subsequently, 28 genomic signals were explored for phenotype- methylation associations in 41 (Tooth mobility) and 43 (Gum bleeding) buccal samples, and 501 (Tooth mobility) and 556 (Gum bleeding) adipose DNA samples.

first: Yuko

last: Kurushima

first: Pei-Chien

last: Tsai

first: Alexessander

last: Cuoto Alves

first: Julia

middle: S

last: El-Sayed Moustafa

first: Caroline

last: Le Roy

first: Mark

last: Ide

first: Francis

last: Hughes

first: Kerrin

last: Small

first: Claire

last: Steves

first: Jordana

middle: T

last: Bell


title: Long-term correction of diabetes in mice by in vivo reprogramming of pancreatic ducts

status: Public on May 01 2018

city: Ashburn

first: Yuhan

last: Wang

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Here, we report in vivo reprogramming of pancreatic ductal cells through intra-ductal delivery of an adenoviral vector expressing the transcription factors Pdx1, Neurog3 and Mafa (adPNM). To better understand the extent of reprogramming in induced pancreatic ductal cells, comparative single cell RNA sequencing was performed on insulin+ pancreatic ductal cells and pancreatic β-cells. Compared with pancreatic β cells, we show that insulin+ pancreatic ductal cells had established a β-cell gene expression program, albeit with immature features.

overall_design: single cell RNAseq in insulin+ pancreatic ductal cells and pancreatic β-cells from the same animal through FACS

first: Michael

last: Heskett

first: Markus

last: Grompe

first: Paul

last: Spellman


title: Next gen. sequencing of RNAs isolated from freshly isolated, proliferating and differentiating skeletal muscle stem cells

status: Public on Apr 14 2018

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: The study addresses the transcriptional changes occuring during activation, proliferation and differentiation of satellite cells isolated form muscle of Mus musculus

overall_design: RNA was isolated at different stages of satellite cell differentiation, three independent samples originating form different animals were used for each developmental stage

first: Stas

last: Wüst


title: Genome-wide maps of H3K27me3 in endpoint Ezh2+/+ or Ezh2-/- Tet ON PyVmT mouse mammary gland tumours

status: Public on Mar 01 2018

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

country: Canada

institute: McGill University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in endpoint tumours from Ezh2+/+ or Ezh2-/- Tet ON PyVmT mammary gland tumours. In order to understand the H3K27me3 targets in the context of mouse mamamry gland tumorigenesis, data  were generated by deep sequencing a pool of 5 tumours per genoype, in duplicate using Illumina HiSeq2500. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10). Raw reads were trimmed for length (n>=32), quality (phred score >= 30) and adaptor sequence using fastx v0.0.13.1.Trimmed reads were (pools of 5 different tumors per genotype) then aligned to the mouse reference genome mm10 using BWA v0.5.9 Broad peaks were called using MACS v1.4.1 software (mfold=10,30; bandwith=300; pvalue cutoff=1E-5) using sequenced libraries of input DNA as control. Peak list intersections were done using BEDTools v2.12.0. Binding peaks were considered overlapping if at least 1 base of the peaks overlapped. Our study demonstrated the first mapping of H3K27me3 in the endpint tumours of tetracycline ducible PyVmT mouse mamary tumours.

overall_design: Examination of a histone modification in two different genotypes of mouse mammary gland tumours

first: A

last: Hirukawa

first: W


title: Expression data from endpoint mammary gland tumours from Ezh2 +/+ or Ezh2 -/- Tet ON PyVmT mice

status: Public on Feb 26 2018

summary: In this dataset we include expression profiles of whole endpoint tumours snap frozen in liquid nitrogen that have been crushed and processed with the Qiagen RNeAsy mRNA extraction kit

overall_design: 5 WT samples (Ezh2 +/+) and 5 KO samples (Ezh2-/-) were analyzed. We generated the pairwise comparisons between gentoypes using the Affymetrix Transcriptome Analysis Console software. Genes with an ANOVA p-value of 0.05 were considered for further analyses.


title: Whole-organism clone-tracing using single-cell sequencing

status: Public on Mar 30 2018

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institue

summary: We present ScarTrace, a single-cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast, we find that cells in the eyes, brain, and caudal tail fin arise from many embryonic progenitors, which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types.

overall_design: Single cell sequencing data from cells isolated from zebrafish organs (whole kidney marrow, forebrain, hindbrain, left eye, right eye, left midbrain, right midbrain, and regenerated fin). For each cell, we provide libraries with transcritpome and with clonal information, respectively.

first: Maria

last: Florescu

first: Chloé

last: Baron

first: Josi

last: Peterson-Maduro

first: Alexander

last: van Oudenaarden


title: A Macrophage Colony-Stimulating Factor-Producing gamma-delta T Cell Subset Prevents Malarial Parasitemic Recurrence

status: Public on Jan 22 2018

city: Stanford

first: Mark

middle: M.

last: Davis

address: 279 Campus Drive

department: Department of Microbiology and Immunology

institute: Stanford University

summary: Despite evidence that gd T cells play an important role during malaria, their precise role remains unclear. During murine malaria induced by Plasmodium chabaudi infection and in human P. falciparum infection, we found that gd T cells expanded rapidly after resolution of acute parasitemia, in contrast to ab T cells that expanded at the acute stage and then declined. Single-cell sequencing showed that TRAV15N-1 gd T cells were clonally expanded in mice and had convergent complementarity-determining region 3 sequences. These gd T cells expressed specific cytokines, M-CSF, CCL5, CCL3, which are known to act on the myeloid compartment, indicating that this gd T cell subset may have distinct functions. Both gd T cells and M-CSF were necessary for preventing parasitemic recurrence. These findings point to an M-CSF-producing gd T cell subset that fulfills a specialized protective role in the later stage of malaria infection when ab T cells have declined.

overall_design: Total gamma-delta T cells from C57BL/6J mice infected with Plasmodium chabaudi chabaudi AJ strain were collected at 19 days post-infection. RNA was extracted and a library was prepared for sequencing.

first: Murad

middle: R

last: Mamedov

first: Yue

last: Zhang


title: Global transcriptome of Arabidopsis thaliana and Solanum lycopersicum infected by S. sclerotiorum

status: Public on Dec 12 2017

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

summary: Plant pathogens with a broad host range are able to infect plant lineages that diverged over 100 million years ago. They exert similar and recurring constraints on the evolution of unrelated plant populations. Plants generally respond with quantitative disease resistance (QDR), a form of immunity relying on complex genetic determinants. In most cases, the molecular determinants of QDR and how they evolve is unknown. Here we identify in Arabidopsis thaliana a gene mediating QDR against Sclerotinia sclerotiorum, agent of the white mold disease, and provide evidence of its convergent evolution in multiple plant species. Using genome wide association mapping in A. thaliana, we associated the gene encoding the POQR prolyl-oligopeptidase with QDR against S. sclerotiorum. Loss of this gene compromised QDR against S. sclerotiorum but not against a bacterial pathogen. Natural diversity analysis associated POQR sequence with QDR. Remarkably, the same amino acid changes occurred after independent duplications of POQR in ancestors of multiple plant species, including A. thaliana and tomato. Genome-scale expression analyses revealed that parallel divergence in gene expression upon S. sclerotiorum infection is a frequent pattern in genes, such as POQR, that duplicated both in A. thaliana and tomato. Our study identifies a previously uncharacterized gene mediating QDR against S. sclerotiorum. It shows that some QDR determinants are conserved in distantly related plants and have emerged through the repeated use of similar genetic polymorphisms at different evolutionary time scales.

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum

overall_design: mature leaves inoculated or not by the fungus, three independent replicates

first: Malick

last: Mbengue


title: microRNA-triggered transposon small RNAs mediate genome dosage response (sRNA-Seq)

status: Public on Dec 31 2017

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

institute: Institut Jean-Pierre Bourgin - INRAE

summary: Chromosome dosage plays a significant role in reproductive isolation and speciation in both plants and animals, but underlying mechanisms are largely obscure. Transposable elements can promote hybridity through maternal small RNA, and have been postulated to regulate dosage response via neighboring imprinted genes. Here, we show that a highly conserved microRNA in plants, miR845, targets the tRNAMet primer-binding site (PBS) of LTR-retrotransposons in Arabidopsis pollen, and triggers the accumulation of 21 to 22-nucleotide small RNA in a dose dependent fashion via RNA polymerase IV. We show that these epigenetically activated small-interfering RNAs (easiRNAs) mediate hybridization barriers between diploid seed parents and tetraploid pollen parents  (“the triploid block”), and that natural variation for miR845 may account for “endosperm balance” allowing formation of triploid seeds. Targeting the PBS with small RNA is a common mechanism for transposon control in mammals and plants, and provides a uniquely sensitive means to monitor chromosome dosage and imprinting in the developing seed.

overall_design: Small RNA sequencing of Arabidopsis pollen

first: Robert

last: Martienssen


title: Gene expression profiles of mouse glioblastoma tissues following anti-PD-1 and/or temozolomide treatment

status: Public on Feb 21 2018

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

country: South Korea

institute: The Catholic University of Korea

summary: Microarrays were used to examine the ability of anti-PD-1 and/or temozolomide to reprogram transcriptional profiles. Samples were obtained from tumor mass formed by orthotopic implantation of GL261 cells.

overall_design: GL261 cells (mouse glioblastoma cell line) were orthotopically implanted to male 8 wk old C57BL/6 mice, and anti-PD-1 antibody and/or temozlomide were administered. 16 days after injection, mice were sacrificed and their brains were removed.

first: Seok-Gu

last: Kang


title: microRNA-triggered transposon small RNAs mediate genome dosage response

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

overall_design: Refer to individual Series


title: Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites

status: Public on Jan 12 2018

first: Michael

last: Skinner

summary: Female and male rats of an outbred female Sprague Dawley rats were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection. Sperm from multiple individual rats was pooled into single samples. For the control samples, 2 pools were made using 6 animals and 1 pool with 5 animals. For the DDT samples, 3 pools were mady using 4 animals. For the Vinclozolin samples, 3 pools were made using 4 animals. Genomic DNA was isolated and histone chromatin immunoprecipitation with genomic DNA was performed. Each pooled sample received a separate index primer. NGS was performed at the WSU Spokane Genomics Core using Ilumina HiSeq 2500 with a PE50 application, with a read size of approximately 50 bp and approximately 35 million reads per pool.

overall_design: Female rats were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day), or DDT (25 mg/kg BW/day) or dimethyl sulfoxide (DMSO) in oil (1 µl/kg BW/day vehicle). Vinclozolin and DDT (dichlorodiphenyltrichloroethane) were obtained from Chem Service Inc. (West Chester, PA). Vinclozolin and DDT were injected in DMSO vehicle. Treatment lineages are designated “control” or “vinclozolin” or “DDT” lineages. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1. Non-littermate females and males aged 70-90 days from F1 generation of control, vinclozolin or DDT were bred to obtain F2 generation offspring. The F2 generation rats were similarly bred to obtain the F3 generation offspring. Individuals were maintained for 120 days and euthanized for sperm collection and sample processing. Both DDT and vinclozolin samples were seperately compared to the DMSO control samples.

first: Millissia

last: Ben Maamar

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck


title: The effects of doxorubicin and blocking activin receptor 2B ligands in mice [heart]

status: Public on Dec 04 2017

city: Jyväskylä

first: Juha

last: Hulmi

address: Rautpohjankatu 8a Viv

department: Biology of Physical Activity

institute: University of Jyväskylä

summary:
Doxorubicin is a widely used and effective anthracycline chemotherapy drug. However, it causes cardiotoxicity and also a few negative effects on skeletal muscle as well. As a result, cancer treatment might actually worsen cancer-induced cachexia and consequently the prognosis of the disease. Inhibiting myostatin/activin signaling is known to increase muscle size. This pathway blockade by soluble activin receptor IIB (sAcvR2B-Fc) has also prolonged survival in cancer, even of animals in which tumor growth is not inhibited. It is not known, however, whether blocking this pathway affects chemotherapy-induced muscle wasting.
We found that doxorubicin induces muscle atrophy which is prevented by a blocker for activin receptor 2B ligands (sAcvR2B-Fc)

overall_design: Total RNA obtained from heart of mice divided into 3 groups: 1) control (injected with PBS, n= 5), 2) doxorubicin injected alone (Dox, n=5 ), 3) sAcvR2B-Fc administration 48 hours before doxorubicin injection (n=3 ).  sActRIIB-Fc, doxorubicin and PBS were injected intraperitoneally. Mice were euthanized 20 hours after doxorubicin or PBS injection.

first: Riikka

last: Kivelä

first: Tuuli

last: Nissinen


title: Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids

status: Public on Jan 09 2018

city: Parkville

first: Luke

last: Zappia

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

summary: These files represent single cell RNA-Seq data generated on a 10x Chromium genomics platform from three biological replicates from the embryonic day (E)18.5 developing mouse kidney and three biological replicates of iPSC-derived human kidney organoids differentiated according to our published protocol (Takasato et al., Nature Protocols 2016). When aggregated, the mouse data represents >6000 cells that passed our QC, containing most major cell types known to exist in the developing mouse kidney. The aggregated human organoid data contains of >7000 cells that passed our QC and contains populations representing endothelial cells, podocytes, stroma, nephron, and off-target populations with similarity to neurons.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of the celular composition of human kidney organoids by comparison to mouse embryonic kidney

first: L

first: A

middle: N

last: Combes


title: Selected tissues of two Polish goat breeds do not differ on genomic level

status: Public on Jun 10 2017

city: Warszawa

first: Joanna

last: Pławińska-Czarnak

address: Nowoursynowska 159

country: Poland

institute: WULS-SGGW

summary:
The aim of the study was to investigate differences in the gene expression profiles of selected tissues in two most popular goat’s breeds in Poland: Polish White Improved (PWI) and Polish Fawn Improved (PFI). Three different types of tissue samples were selected: somatic cells isolated from goats’ milk (MSC), milk fat globules (MFG) and peripheral nuclear blood cells (PBNC)
Since there were no earlier genetic studies focused on genetic differences between these two goat breeds we decided to evaluate hypothetical genomic differences assuming that such a differences should be the consequence of genetic differences. We created the hypothesis that if genomic differences exist they should be revealed in hierarchical clustering of transcriptomic profiles of selected tissues. Should the genomic differences exist the clusters obtained are grouping goat breeds and not goat’s tissues. The results of hierarchical clustering however show something completely different. The clusters are grouping goat tissues (milk fat globules, milk somatic cells, peripheral blood nuclear cells) without any relation with goat breed. So the analytical tool does not recognize the goat breed as a driver of transcriptomic difference. Moreover, we were not able to find significantly regulated genes between two breeds

overall_design: The experiment was performed on 24 transcriptomic microarrays using a common reference design. The common reference comprised a pool of equal amounts of RNA from 7 healthy goats in 4th lactation from both Polish breeds (PWI n=4 and PFI n=3). Samples were taken after finishing of lactation period. Experimental samples were collected from healthy goats in 3rd lactation (PWI n=4, PFI n=4) and RNA was isolated from 3 different sources:  MSC, MFG and nucleated blood cells

last: Zarzyńska

first: Alicja

last: Majewska

first: Michał

last: Jank

first: Emilia

last: Bagnicka

first: Jarosław

last: Kaba


title: Novel contribution of acetylated histone variant H2A.Z in activation of neo-enhancers in prostate cancer [NOMe-seq]

status: Public on Sep 05 2017

city: Darlinghurst

first: Fatima

last: Valdes Mora

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active promoters and is associated with oncogene activation in prostate cancer, but its role in enhancer function is still poorly understood. Here we show that H2A.Zac containing nucleosomes are commonly redistributed to neo-enhancers in cancer resulting in a concomitant gain of chromatin accessibility and ectopic gene expression. Notably incorporation of acetylated H2A.Z nucleosomes is a pre-requisite for activation of Androgen receptor (AR) associated enhancers. H2A.Zac nucleosome occupancy is rapidly remodelled to flank the AR sites to initiate the formation of nucleosome-free regions and the production of AR-enhancer RNAs upon androgen treatment. Remarkably higher levels of global H2A.Zac correlate with poorer prognosis. Together these data demonstrate the novel contribution of H2A.Zac in activation of newly formed enhancers in prostate cancer.

overall_design: Genome-wide binding analyses of H2A.Z and H2A.Zac in PrEC, LNCaP full media and LNCaP with or without DHT (5alpha-dihydrotestosterone) stimulation (0, 2h, 4h, 16h) using ChIP-Seq, as well as ChIP-seq for 6 histone marks to partition the genome in LNCaP/PrEC cells into different states.

last: Valdes-Mora

first: Cathryn

last: Gould

first: Yolanda

last: Colino-Sanguino

first: Fabian

last: Buske

first: Aaron

middle: L

last: Statham

first: Shalima

last: Nair

first: Susan

last: Clark


title: Identification of GLYMA.08G357600 binding sites in soybean mid-maturation embryos.

status: Public on Jul 20 2017

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.08G357600 in mid-maturation embryos using ChIP-seq.

overall_design:
Identification of Glyma.08G357600 binding sites in soybean embryos at the mid-maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates, with two technical replicates (sequencing lanes) for each sample.  A total of 4 samples were sequenced using the Illumina HiSeq2500 platform.

**Please note that the processed data *narrowPeak files have been updated on Jan 19, 2021**

first: Julie

last: Pelletier

first: Russell

last: Baden

first: Leonardo

last: Jo

first: Min

last: Chen

first: Robert

last: Golberg


title: Genome-wide effect of constitutive interferon on gene-expression

status: Public on Jun 29 2017

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

summary: Using mice deficient for several genes that contribute to constitutive levels of type I interferon, we compared genome-wide expressionof RNA in rested macrophages of these mice.

overall_design: To look for the role of constitutive interferon, we matured bone marrow derived macrophages from different mouse strains including strains with deficiency for IFNAR (interferon receptor) and STING (Stimulator if Interferon Genes) and compared levels of expression of Interferon-stimulated genes (ISGs). One replica of each sample is provided

first: Joe

last: Sarhan


title: The expression of genes encoding palmitoylated proteins in axonal and synaptic compartments is affected in CLN1/PPT1 transfected neuronal cells

status: Public on Sep 20 2017

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

country: Italy

institute: Universita' degli Studi di Verona

summary: CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 is also related to specific functions in the synaptic compartment. The aim of this study was to recognize molecular signatures and functional modules connected with CLN1. We utilized differentiated SH-SY5Y neuroblastoma cells to overexpress wild type CLN1 (SH-p.wtCLN1) and introduced selected mutations previously detected in CLN1 patients. wtCLN1 and two mutant CLN1- harbouring cell lines were characterized by whole transcriptomic profiling using RNA-seq, to subsequently identify differentially expressed genes (DEGs) and alterations in related neuronal functions.

overall_design: Examination of transciptomic profiles of three transfected SH-SY5Y neuroblastoma cell lines, which over-expressed either wtCLN1 or two mutated CLN1 constructs

first: Francesco

last: Pezzini

first: Marzia

last: Bianchi

first: Salvatore

last: Benfatto

first: Francesca

last: Griggio

first: Stefano

last: Doccini

first: Rosalba

last: Carrozzo

first: Filippo

last: Santorelli

first: Maciej

last: Lalowski

first: Alessandro

last: Simonati


title: The effects of doxorubicin and blocking activin receptor 2B ligands in mice

status: Public on Apr 11 2017

first: Juha

last: Hulmi


title: RNA-seq analysis of RNA from DBA/2J retinal ganglion cells

status: Public on Mar 07 2017

city: Bar Harbor

first: Pete

last: Williams

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells

overall_design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls

first: Simon

middle: W

last: John


title: MicroRNA-24-3p is overexpressed in Hodgkin lymphoma and protects Hodgkin and Reed-Sternberg cells from apoptosis

status: Public on Feb 26 2017

city: Groningen

first: Ye

last: Yuan

state: Groningen

address: Hanzeplein 1

department: pathology

institute: UMCG


title: Rbm10 promotes heterochromatin assembly by interacting with Clr6 and chromatin remodeling complexes

status: Public on Jan 23 2017

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses confirmed that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodeling complexes known to be essential for heterochromatin silencing. We propose that Rbm10 serves as a platform to recruit Clr6 and chromatin remodelers to mediate heterochromatin formation. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.

overall_design: Poly (A) RNA was prepared from total RNA by two rounds of oligo (dT)25 Dynabeads (Invitrogen) purification. Following fragmentation at 94°C for 3.5 min, the RNA was converted to first strand cDNA using random hexmer primer and Supescript II (Invitrogen), followed by second strand cDNA synthesis with Eschericcia coli DNA pol I (Invitrogen) and RNAse H (Invitrogen). The barcoded sequencing library was prepared and sequenced on Illumina HiSeq for 1 × 100 cycles following the standard protocol.

first: Martina

last: Weigt

first: Qingsong

last: Gao

first: Hyoju

last: Ban

first: Haijin

last: He

first: Guido

last: Mastrobuoni

first: Stefan

last: Kempa

first: Wei

last: Chen

first: Fei

last: Li


title: Novel contribution of acetylated histone variant H2A.Z in activation of neo-enhancers in prostate cancer [Microarray expression]

first: Fatima

last: Valdes Mora

last: Valdes-Mora

first: Cathryn

last: Gould

first: Yolanda

last: Colino-Sanguino

first: Fabian

last: Buske

first: Aaron

last: Statham

first: Nicola

last: Armstrong

first: Susan

last: Clark


title: RNA-Seq analysis of dietary restriction and loss of SEK-1 in C. elegans

status: Public on Dec 27 2016

city: Shanghai

first: Ziyun

last: Wu

state: Shanghai

address: 800 Dongchuan RD

department: Food Science and Engineering

institute: Shanghai Jiao Tong University

summary: mRNA expression profiling of genes regulated by dietary restriction and SEK-1.

overall_design: Three days liquid DR worms (Day 6 adult) N2 AL, N2 DR, sek-1(km4) AL and sek-1(km4) DR at 20°C were evaluated.

first: T

last: Blackwell


title: The effects of doxorubicin and blocking activin receptor 2B ligands in mice [muscle]

status: Public on Sep 25 2016

first: Juha

last: Hulmi

summary:
Doxorubicin is a widely used and effective anthracycline chemotherapy drug. However, it causes cardiotoxicity and also a few negative effects on skeletal muscle as well. As a result, cancer treatment might actually worsen cancer-induced cachexia and consequently the prognosis of the disease. Inhibiting myostatin/activin signaling is known to increase muscle size. This pathway blockade by soluble activin receptor IIB (sAcvR2B-Fc) has also prolonged survival in cancer, even of animals in which tumor growth is not inhibited. It is not known, however, whether blocking this pathway affects chemotherapy-induced muscle wasting.

We found that doxorubicin induces muscle atrophy which is prevented by a blocker for activin receptor 2B ligands (sAcvR2B-Fc).

overall_design: Total RNA obtained from tibialis anterior muscle of mice divided into 3 groups: 1) control (injected with PBS, n= 5), 2) doxorubicin injected alone (Dox, n=5 ), 3) sAcvR2B-Fc administration 48 hours before doxorubicin injection (n=5 ).  sActRIIB-Fc, doxorubicin and PBS were injected intraperitoneally. Mice were euthanized 20 hours after doxorubicin or PBS injection.

first: Riikka

last: Kivelä

first: Tuuli

last: Nissinen


title: MicroRNA-24-3p is overexpressed in Hodgkin lymphoma and protects Hodgkin and Reed-Sternberg cells from apoptosis [small RNA-Seq]

first: Ye

last: Yuan

summary: Micro (mi)RNAs not only play important roles in biological processes such as proliferation, metabolism, differentiation and apoptosis, but also in diseases such as cancers. We identified miRNAs with deregulated expression in Hodgkin lymphoma (HL) and investigated their role in the pathogenesis of HL. Small RNA sequencing revealed 84 significantly differentially expressed miRNAs in HL cell lines as compared to GC-B cells. Three upregulated miRNAs, miR-23a-3p, miR-24-3p and miR-27a-3p, were derived from one primary-miRNA transcript. Loss-of-function analysis for these miRNAs and their seed family members resulted in decreased growth upon miR-24-3p inhibition in three and of miR-27a/b-3p inhibition in one HL cell line. Apoptosis analysis indicated that the effect of miR-24-3p on cell growth is at least in part caused by an increase of apoptotic cells. Argonaute 2 (Ago2)-IP revealed 1,142 genes consistently targeted by miRNAs in at least three out of four HL cell lines. Furthermore, 52 out of the 1,142 genes were predicated targets of miR-24-3p. Functional annotation analysis revealed a function related to cell growth, cell death and/or apoptosis for 15 out of the 52 genes. Western blotting of the top-5 genes showed increased protein levels upon miR-24-3p inhibition for CDKN1B and MYC. In summary, we showed that miR-24-3p is upregulated in HL and its inhibition impaired cell growth possibly via targeting CDKN1B and MYC.

overall_design: Expression of all known and novel miRNAs was assessed in  HL cell lines, BL cell lines and GC-B cells

first: Joost

last: Kluiver

first: Jasper

last: Koerts

first: Debora

last: de Jong

first: Bea

last: Rutgers

first: Fazlyn

last: Reeny Abdul Razak

first: Martijn

last: Terpstra

first: Boudewijn

last: Plaat

first: Ilja

last: Nolte

first: Arjan

last: Diepstra

first: Lydia

last: Visser

first: Klaas

last: Kok

first: Anke

last: van den Berg


title: Genome-wide binding data for TRIM24 in androgen-dependent and castration-resistant prostate cancer cells

status: Public on May 27 2016

first: Anna

middle: C

last: Groner

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We report a novel and important role for the TRIM24-dependent transcriptional program in promoting prostate cancer progression to a castration-resistant state.

overall_design: Examination of TRIM24 binding in androgen-dependent and castration-resistant prostate cancer cells. More specifically, we determine binding in androgen-dependent LNCaP cells stimulated for 4h with vehicle (ETOH) or 10nM DHT, and in castration-resistant LNCaP-abl cells grown under vehicle conditions.

first: Jonas

last: de Tribolet-Hardy

first: Patrick

last: Tschopp

first: Lei

last: Gu

first: Jean-Philippe

last: Theurillat

first: Myles

last: Brown


title: An Investigation of Circulating microRNA Profile in Clinical Cases of Subarachnoid Hemorrhages of Hong Kong

status: Public on Aug 31 2016

city: Shatin

first: Kwok Chu

last: Wong

address: Prince of Wales Hospital

department: Surgery

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
circulating microRNA analysis in Subarachnoid hemorrhages (SAH) patients and Heathy controls
circulating microRNA profiling has been shown for  biomarker discovery for early disease detection in serum, which is stable and accessible. we describe our progress and propose a workflow to investigate and directly compare the circulating microRNA profiles of SAH patients and healthy individuals, in order to characterize potential biomarkers for SAH. Then we verified the top microRNA by quantitative PCR. Informatics analysis of KEGG provided important mechanistic insight to their potential involved pathways. Finally we demonstrated a possible workflow and initial results which indicated that circulating miRNAs can be potential biomarkers of SAH.

overall_design: We analyzed circulating miRNA from healthy controls (n=20) and SAH patients (n=20) using the Affymetrix miRNA 3.0 platform. Array data was processed by Affymetrix ConsoleTool. No techinical replicates were performed.

first: George


title: Revisiting the microRNA expression profiling of human intervertebral disc degeneration (IDD)

status: Public on Jun 30 2016

city: Xi'an

first: Hai-Qiang

last: Wang

email: hqwang@sntcm.edu.cn, drwanghq@163.com

address: Xixian Avenue, Xixian District

department: Insititute of Integrative Medicine

institute: Shaanxi University of Chinese Medicine

summary: MicroRNA expression profiling of human nucleus pulposus derived from patients with IDD in comparison with those derived from cadaveric disc as normal control. We have identified the expression profiles of miRNAs in IDD using scoliotic nucleus pulposus as controls (GSE19943). It is noteworthy that scoliotic discs are not strictly normal discs. Therefore, the microRNA expression profiles were revisited using normal discs as control.

overall_design:
Two-condition experiment: control nucleus pulposus vs. degenerative nucleus pulposus. Biological replicates: 5 control, 5 degenerated, independently harvested (the same samples as in GSE56081). Four replicates per array.

Previous affiliation: Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University)

first: Hai

middle: Q

first: Chi

last: Ma


title: The expression profiling of circular RNAs (circRNA) in human intervertebral disc degeneration (IDD)

status: Public on Aug 04 2016

summary: Circular RNA expression profiling of human nucleus pulposus derived from patients with IDD in comparison with those derived from cadaveric disc as normal control. We have identified the expression profiles of miRNAs (GSE63492), lncRNAs, mRNAs (GSE56081) in IDD using 5 normal discs as control and 5 IDD discs. Accumulating evidence indicates that circRNAs are key regulators of gene expression by interacting with miRNAs.  circRNA is a novel type of RNA that, unlike linear RNA, forms a covalently closed continuous loop, and is highly represented in the eukaryotic transcriptome.

overall_design:
Two-condition experiment: control nucleus pulposus vs. degenerative nucleus pulposus. Biological replicates: 5 control, 5 degenerated, independently harvested (the same samples as GSE56081 and GSE63492). Four replicates per array.

Previous affiliation: Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University)

first: Chi-Jiao

first: Xu

last: Liu


title: miRNA-mediated expression switch of cell adhesion genes driven by microcirculation in chip

status: Public on May 26 2016

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

summary:
Changes in cell adhesion molecule (CAM) expression and miRNAs regulating them are known to be involved in malignant progression in colon cancer. We investigated expression profiles of CAM genes and non-coding RNAs in CaCo2 colon cancer cells in static culture and under dynamic flow conditions perfused in microfluidic chip emulating physiological microenvironment.
We incubated monolayers of CaCo2 cells in Transwell® units either under static conditions or under flow in a microfluidic chip. We identified 7 up-regulated CAM genes (CD44, CDH7, CEACAM5, CEACAM6, CYR61, L1CAM and VCAN), 7 down-regulated genes (COL12A1, FGA, FGB, FGG, GJA1, ITGA5 and LAMA1) and 69 miRNAs targeting them under the influence of microcirculation. The revealed network comprised CAM genes known to interact with each other and 13 miRNAs simultaneously regulating more than one of them.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Undifferentiated Caco2 cells were seeded on individual polyether membrane inserts with 0.143 cm2 surface area and 1.0 μm pore diameter, cut out from HTS Transwell®-96 well permeable support (Corning Inc., USA), with cell density approximately 60,000 cells/well. The cells were incubated under conditions for differentiation for 7 days in MEM with 10% FBS, 0.1 mM non-essential aminoacids, 0.1% penicillin-streptomycin in 5% CO2, 37° C, changed three times. Transwell® inserts with CaCo2 monolayers were either kept on the microplate or put into microfluidic chip. The culture medium microcirculation parameters were ±20 kPa and 2 Hz resulting in the pulsatile (0 - 0.85 µl/s) medium flow with mean flow rate of 4.13 μl/min. After 24-h incubation the cells were lysed in 700 μl of Qiazol lysis reagent (Qiagen, Germany) and subjected to microarray expression analysis. The experiments were performed in triplicates.

first: Timur

last: Samatov

first: Vladimir

middle: V

last: Galatenko

first: Nadezhda

last: Senyavina

first: Alexey

middle: Y

first: Evgeniy

last: Knyazev

first: Alexander

middle: G

last: Tonevitsky


title: Gene expression in the pancreas of healthy control, auto-antibody positive, and type 1 diabetic subjects

status: Public on Nov 01 2015

city: Stanford

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

summary:
These experiments were performed to identify differentially expressed genes in the pancreas of healthy humans, auto-antibody positive and type 1 diabetic patients.
All samples were obtained from the network of pancreatic organ donors with diabetes (nPOD).  ID numbers are specified.  Patient information can be obtained at http://www.jdrfnpod.org/

overall_design: Pancreas tissues were homogenized in Trizol reagent (Invitrogen).  Total RNA was extracted from the aqueous phase using the RNeasy mini kit (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Reagent Kit (Agilent). One color microarrays were performed at the Stanford Human Immune Monitoring Center using the SurePrint G3 Human GE 8x60K microarray kit (Agilent Technologies). All samples were processed and run at the same time.


title: Targeted Pten deletion plus p53-R270H mutation in mouse mammary epithelium induces aggressive claudin-low and basal-like breast cancer

status: Public on Dec 15 2015

city: Toronto

first: Jeff

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary:
WAP-Cre:Ptenf/f:p53lox.stop.lox_R270H composite mice were generated by genetic crossing. In these mice, Pten is deleted and a R270H p53 mutation in the DNA binding domain is induced upon expression of Cre recombinase in pregnancy-identified alveolar progenitors. Tumors were characterized by histology, marker analysis, various bioinformatics methods, high-throughput (HTP) FDA-drug screen as well as orthotopic injection to quantify tumor initiating cells (TICs) and tail-vein injection to identify lung-metastasis.
Expression data comparing 2 types of Pten-deficient tumors (spindle and poorly differentiated) with other modles of mouse mammary tumors

overall_design: 2 types of  Pten deletion plus p53-R270H mutation tumors (spindle and poorly differentiated) was compared with MMTV-Neu, Spindle Pten-p53-deficient tumors, and wild-type mammary gland cells.

first: Sharon

first: Eldad

last: Zacksenhaus


title: Prognostic significance of overexpression of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer  [copy number analysis]

status: Public on Nov 21 2015

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Introduction: The potential of expression profiling using microarray analysis as a tool to predict the prognosis for different types of cancer has been realized. This study aimed to identify a novel biomarker for colorectal cancer (CRC).  Experimental design: The expression profiles of cancer cells in 153 patients with CRC were examined using laser microdissection and oligonucleotide microarray analysis. Overexpression in CRC cells, especially in patients with distant metastases, was a prerequisite to select candidate genes. We analyzed the protein expression and localization of the candidate gene by immunohistochemical study and investigated the relationship between protein expression and clinicopathologic features in 271 CRC patients.  Results: Using microarray analysis, we identified 11 candidate genes related to distant metastases in CRC patients. Among these genes, Traf2- and Nck- interacting kinase (TNIK) was known to be associated with aggressiveness in CRC through Wnt signaling.  Absence of overexpression of TNIK protein was associated with significantly better overall survival (p < 0.001) and relapse-free survival (p < 0.001). Moreover, overexpression of TNIK protein was an independent risk factor for CRC recurrence (p = 0.009).  Conclusion: Overexpression of TNIK might be a predictive biomarker of CRC recurrence.

overall_design: Copy number analysis was performed using LCM samples of 125 colorectal cancer patients by GeneChip Human Mapping 250k Sty arrays. Non-tumor tissues obtained from 47 patients were used as unpaired reference samples.

first: Hidenori

last: Takahashi

first: Toshiaki

last: Ishikawa

first: Noriko

last: Iwata

first: Yasunori

last: Someno

first: Akifumi

last: Kikuchi

first: Shinichi

last: Yamauchi

first: Megumi

last: Ishiguro

first: Hirotoshi

last: Kobayashi

first: Satoru

last: Iida

first: Hiroyuki

last: Uetake


title: Prognostic significance of overexpression of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer [gene expression]

overall_design: Gene expression profiles for 125 cancer tissues from colorectal cancer patients were measured by Affymetrix HG-U133 Plus 2.0 arrays. Normalization was performed by robust multi-array average (RMA) method under R 2.12.1 statistical software with affy package from BioConductor. The normalized gene expression levels were presented as log2-transformed values by RMA.


title: SOX9 Regulates Multiple Genes in Chondrocytes, Including Genes Encoding ECM Proteins, ECM Modification Enzymes, Receptors, and Transporters

status: Public on Oct 15 2015

city: Seoul

first: Hideyo

last: Yasuda

address: 1 Hwayang-dong, Kwangjin-gu

department: Animal Biotechnology

institute: Konkuk University

summary: We investigated mRNA that is regulated by SOX9 in mouse chondrocytes

overall_design: The primary culture of rib chondrocytes from floxed Sox9 mice is infected with Adeno-CMV-Cre or Adeno-CMV-Null. The expression levels of mRNA  was compared between SOX9 depleted and not-depleted chondrocytes by RNA-Seq.

first: Chundo

last: Oh


title: Effect of LSD1 depletion on gene expression in oocytes

status: Public on Oct 07 2015

city: Smithville

first: Jeesun

last: Kim

state: Texas

address: 1808 Park Road 1C

department: Department of Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

summary: The objective of the experiment is to compare the transcriptomes of LSD1 knockout (KO) and control oocytes

overall_design: RNA-seq analysis of GV oocytes, with three biological replicates for each genotype

first: Taiping

last: Chen


title: RNAseq of xylem tissue of transgenic and wildtype Populus trichocarpa (NSF Plant Genome Research Program Project 0922391)

status: Public on Mar 07 2016

city: Raleigh

first: Vincent

last: Chiang

state: NC

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

summary: We transformed Populus trichocarpa and generated transgenics with knockdown or overexpression of monolignol genes and transcription factors

overall_design: RNAseq of xylem tissue of transgenic and wildtype Populus trichocarpa. 378 samples.

first: V


title: Expresion data from yeast (wild type and gcn5 mutants) exposed to Congo Red (CR)

status: Public on Oct 01 2015

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramón y Cajal, S/N

department: Facultad de Farmacia, Departamento de Microbiologia II

institute: Universidad Complutense de Madrid

summary: We analyzed the genome-wide expression profile of the wild type strain and the gcn5 mutant (component of the SAGA complex) under basal and cell wall stress (CR during 3 hours) conditions.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Three biological samples were analyzed for each strain (wild type and gcn5 mutant) and condition (with and without CR). A microarray experiment were carried out for each sample.


title: RNA-sequencing and ChIP-exo of wildtype and RTR1 and RRP6 deletion mutants in Saccharomyces cerevisiae reveal a role for RTR1 and RRP6 in noncoding transcript termination by Nrd1

status: Public on Oct 05 2016

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

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

overall_design: Refer to individual Series


title: The RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma

status: Public on Jun 29 2015

city: Los Angeles

first: Philip

middle: James

last: Uren

state: CA

address: 1050 Childs Way, RRI201

institute: University of Southern California

summary: The conserved RNA-binding protein Musashi1 (MSI1) has emerged as a key oncogenic factor in numerous solid tumors, including glioblastoma. However, its mechanism of action has not yet been established comprehensively. We set out to map its impact on the transcriptome in U251 cells using RNA-seq and iCLIP.

overall_design: Examination of gene expression and splicing changes upon KD of Musashi1 in U251 cells and link to iCLIP-identified Musashi1 RNA binding sites

first: Luiz

middle: O

last: Penalva


title: lncRNA and mRNA expression profiles during osteoclastogenesis

status: Public on Aug 28 2015

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

institute: Third Military Medical University

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

summary: Total RNA were extracted from osteoclasts differentiated from RAW264.7 cells at different stages: Monocytes (0h), Pre-osteoclasts (24h), Mature osteoclasts (72h) and activated osteoclasts (96h). LncRNA and mRNA expression profiles were decided by microarray.

overall_design: RAW264.7 cells were cultured with RANKL (100ng/ml) and M-CSF (50ng/ml) for 0h, 24h, 72h and 96h. TRAP stain, FAK stain, pit formation assay,  fusion assay and q-PCR were performed to validate the in vitro model.

first: Jianzhong

last: Xu

first: Shiwu

last: Dong


title: MicroRNA Profiling in Ovarian Cancer

status: Public on Jul 30 2015

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

summary: Deregulated expression of miRNAs contributes to ovarian cancer. This study is aimed to identify which miRNAs are differentially expressed in Ovarian cancer compared to endometriosis

overall_design:
Paired ovarian cancer and endometriosis tissues from FFPE were used to isolate total RNA. miRNA expression were analyzed by miRNA microarray assay

Please note that each sample represents 19 paired cases tissue samples of endometriosis and ovarian cancer pooled together and ran in quadruplicate with their group mean values, and the raw data for pooled tissue sample is provided in the 'Raw data.xls'.

first: F

middle: H

first: S

last: Ali


title: Tat controls RNA Polymerase II and the epigenetic landscape to precisely rewire cellular transcriptional programs (ChIP-Seq)

status: Public on Jun 15 2015

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: Transcription factors mediate precise regulation of gene expression programs to modulate key biological processes.  In addition to controlling HIV transcription, Tat appears to modulate cellular transcription to alter the biology of target immune cells and generate a permissive state for HIV infection.  However, the molecular mechanisms of transcriptional control have remained elusive.  Here, we identified the direct target genes of Tat using genomics and defined mechanisms by which Tat selectively rewires cellular transcriptional programs.  Interestingly, Tat functions as both transcriptional activator and repressor of a defined set of genes sharing functional annotations and regulated by master transcriptional regulators such as T-cell identity factors.  Tat is recruited to precise genomic domains (promoters and intragenic enhancers) through interaction with master transcriptional regulators to control both the transcription initiation and elongation steps.  Tat mediates transcription initiation by modulating Pol II recruitment to promoters and intragenic enhancers and fine-tuning chromatin looping.  Tat stimulates or blocks RNA Polymerase (Pol) II recruitment or promoter-proximal pause release thereby promoting gene activation or repression, respectively.  Global analysis of chromatin signatures revealed correlation of transcription activity marks with Pol II recruitment or pause release status at gene promoters and enhancers, and transcription elongation at coding units.  We propose that Tat has evolved these unique properties to hijack precise genomic domains to control cellular transcription using unexpected regulatory mechanisms, which showed marked differences to the regulation of the HIV genome.  Our studies also reveal that Tat can be used as a molecular probe to decode general principles of transcriptional regulation.

overall_design: ChIP of various DNA binding proteins

first: Jonathan

middle: E

last: Reeder

first: Iván


title: Alternative splicing in genes encoding adhesion- and motility-related proteins in breast cancer

status: Public on Jun 01 2015

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

summary: In this study, combining 1) RNA-Sequencing on MCF-7 cell line, 2) a new computational approach to identify splice isoforms and 3) an extensive experimental validation (in vitro - on MCF-10, MCF-7 and MDA-MB-231 – and ex vivo – on human breast cancer tissues) we investigated simultaneously gene expression and alternative splicing in genes encoding for adhesion and motility-related molecules-, including Semaphorins and their receptors and co-receptors.

overall_design: Transcriptome profiles of MCF7 cell line were generated by deep sequencing, in duplicate, using Hi-Seq Illumina

first: R

last: Aversa

first: A

last: Sorrentino

first: M

last: Ambrosio

last: Esposito

last: Ciccodicola

first: L

last: D'Apice


title: Genome-wide microRNA transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

status: Public on May 01 2015

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

summary: We report the genome-wide microRNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. microRNA-seq was performed to identify all microRNAs expressed in both ESCs and neuronal cells. In total, 534 expressed microRNAs we identified, of which 18 were up-regulated and 6 were down-regulated (fold change (FC) > -/+2.0 and p-value < 0.05) during Retinoic Acid-induced neuronal differentiation. The top up-regulated microRNAs identified were Mir10a, Mir615, Mir217 and Mir219a-2. The top down-regulated microRNAs identifed were Mir211, Mir292, Mir302a and Mir302c.

overall_design: Examination, identification and comparision of microRNA expression profliles in two cellular states.


title: Characterization of extended transcripts by RNA-Seq suggests that Rrp6 influences Nrd1-dependent termination

status: Public on Apr 14 2015

first: Yunlong

last: Liu

summary: RNAPII is responsible for transcription of protein-coding genes and short, regulatory RNAs. In Saccharomyces cerevisiae, termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex (comprised of Nrd1, Nab3, and Sen1) processing by the exosome, and the nuclear specific catalytic subunit, Rrp6. It has been shown that Rrp6 interacts directly with Nrd1, but whether or not Rrp6 is required for NNS-dependent termination is unclear. Loss of Rrp6 function may result in extension (or inhibition of termination) of NNS-dependent transcripts, or Rrp6 may only function after the fact to carry out RNA 3’ end processing. Here, we performed in-depth differential expression analyses and compare RNA-sequencing data of transcript length and abundance in cells lacking RRP6 to previously published sequencing data measuring the length of RNAs in Nrd1-depleted cells. We find many transcripts that were defined as unterminated upon loss of Nrd1 activity are of similar length in rrp6Δ, and expression levels of downstream genes are significantly decreased. This suggests a similar transcription interference mechanism occurs in cells lacking either Nrd1 or Rrp6, supporting the hypothesis that Rrp6 activity is required for proper NNS termination in vivo.

overall_design: Four biological replicates each for deletion mutant (RRP6) and reference cells (WT)

first: Melanie

middle: J

last: Fox

first: Hongyu

last: Gao

first: Amber

last: Mosley


title: Pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation


title: Genome-wide transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

summary: We report the genome-wide RNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. RNA-seq was performed to identify all RNAs expressed in both ESCs and neuronal cells. In total, In total, 14,443 expressed genes were detected, of which 1,834 were up-regulated and 1,477 down-regulated (fold change (FC) > -/+2.0 and p-value < 0.035) during RA-induced neuronal differentiation. The top down-regulated genes included members of the pluripotency core transcriptional network, including Klf4, Sox2, Oct4, Nanog, Suz12, Esrrb, Stat3 and Tcfcp2l1. The top up-regulated genes are important for neuronal differentiation (e.g. Pax3, Irx3, Rest and Foxd3) and reside in the RA-pathway (e.g. various homeobox genes), the retinoic acid receptors and the RA-degradation enzyme Cyp26a1.

overall_design: Examination, identification and comparision of mRNA expression profliles in two cellular states.


title: Genome-wide binding profiles of nuclear FGFR1, RXRα and Nur77 in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

summary: We report the genome-wide binding patterns of nuclear FGFR1, RXRα and Nur77 in pluripotenet mESC and as mESC differentiate towared a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. We also report the genome-wide incorporation of histone varant H3.3 into chromatin specifically during Retinoic Acid-induced differentiation. This study presents nuclear FGFR1 as a global factor that controls genomic function by binding within the promoters of thousands of genes, both alone and in cooperation with RXR, Nur77 and histone H3.3, by targeting consensus DNA sequences of diverse transcription factor families. As such, it identifies a previously unknown, multifaceted form of control of major ontogenic pathways and gene networks targeted by the nuclear form of FGFR1.

overall_design: Examination of nuclear FGFR1, RXRα, and Nur77 binding sites in 2 celluar states. Examination of H3.3 incorporation in 1 cellular state.


title: Prognostic significance of overexpression of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer

first: Kaoru

last: Mogushi

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


title: Identification of genes are regulated by AURKA at transcription level

status: Public on Oct 28 2015

city: guangzhou

first: fei meng

last: zheng

state: guangdong

address: dongfeng East Road No. 651,yuexiu District

institute: Sun Yat-sen university cancer center

summary: Purpose: AURKA plays an important role in breast cancer development. Exploring the gene expression profiles regulated by AURKA will facilitate to understand the mechanism which is responsible for AURKA induced breast cancer development.  Results: We found that 350 genes were significantly up-regulated during AURKA overexpression in MCF-10A cells, 346 genes were significantly down-regulated during AURKA overexpression in MCF-10A cells.   Conclusions: Our study indicated that 696 differentially expressed genes might contribute to AURKA induced breast cancer development.

overall_design: MCF-10A cells overexpressed AURKA or the empty vector were subjected to RNA extraction. The resulted RNA samples were performed RNA-sequencing analyses of gene expression profiles.

first: Quentin


title: UM-UC cell: ALDH(+) vs ALDH(-)

status: Public on Mar 12 2015

city: Sapporo

first: Ryuta

last: Inoue

state: Hokkaido

address: South1 West16

department: pathology

institute: Sapporo medical university

summary: Transcriptional profinng of human urothelial carcinoma cell line UM-UC3 ALDH1 high activity cells comparing ALDH1 low activity cells.

overall_design: Two-condition experiment, ALDEFLUOR positive vs. negative cells. Biological replicates: 1 ALDEFLUOR positive replicates, 1 negative replicates.

first: Akari

last: takahashi

first: Yoshihiko

last: Hirohashi


title: Identification of Cottontail rabbit papillomavirus E2 protein regulated genes

status: Public on Mar 28 2015

city: Tuebingen

first: Frank

last: Stubenrauch

address: Elfriede-Aulhorn-Str. 6

department: Institute for Medical Virology

institute: University Hospital Tuebingen

summary: Transcriptome analyses of RNA from C33a cells after induction of CRPV E2 expression by doxycycline

overall_design: C33a cells were established that carry the doxycycline-inducible pRTS-CRPV E2 vector. We analyzed 3 biological replicates (induced/uninduced) using the Affymetrix Human Exon 1.0 ST platform.

first: Maria

last: Delcuratolo

first: Jasmin

last: Fertey

first: Natalie

last: Leiprecht

first: Johanna

last: Schütz

first: Ben

last: Hudjez

first: Stephan

last: Brodbeck

first: Silke

last: Wagenhäuser

first: Marcel

last: Dreer

first: Markus

last: Schneider

first: Roxana

middle: M

last: Schwab

first: Shwu-Yuan

last: Wu

first: Cheng-Ming

last: Chiang

first: Thomas

last: Iftner


title: Tat controls RNA Polymerase II and the epigenetic landscape to precisely rewire cellular transcriptional programs

first: Ivan

last: D'Orso


title: aCGH profiling for Frozen tumour samples of 50 Hepatocellular Carcinoma patients and 14 Adjacent normal samples

status: Public on Mar 30 2015

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

institute: astrazeneca

type: Genome variation profiling by genome tiling array

summary:
Purpose: To gain molecular insights of HBV integration that may contribute to HCC tumorigenesis, we performed whole transcriptome sequencing and whole genome copy number profiling of hepatocellular carcinoma (HCC) samples from 50 Chinese patients.
Conclusions: This is the first report on the molecular basis of the MLL4 integration driving MLL4 over-expression. HBV-MLL4 integration occurred frequently in Chinese HCC patients, representing a unique molecular segment for HCC with HBV infection.

overall_design: We profiled 50 Chinese Hepatocellular Carcinoma patients and 14 adjacent tissues  using Agilent 244K array CGH technology.  50 Tumor samples also did RNASeq profiling.

first: Lan

last: Zhang

first: Ziliang

last: Qian

first: Zhenggang

last: Ren

first: Qunsheng

last: Ji


title: Gene expression profiling of Puf knockouts in N. crassa

status: Public on Mar 16 2015

city: Stanford

first: Greg

last: Hogan

address: 259 Campus Drive

institute: Stanford University / HHMI

summary: Gene expression profiling was performed to compare RNA abundances in mycelium of Puf knockout strains compared to that in mycelium of wild-type N. crassa

sample_organism:
Neurospora crassa
Neurospora crassa OR74A

overall_design: Two-condition experiment, total RNA from knockout vs total RNA from wild-type. Biological replicates: 5 x Puf3KO, 5 x Puf8KO, 4 x Puf4NtermKO, and 5 x Puf4pumKO. One replicate per array.

first: Hogan

last: Greg


title: Transcriptional response in mouse thyroid tissue after 211At administration: effects of absorbed dose, initial dose-rate and time after administration

status: Public on Feb 20 2015

city: Göteborg

first: Nils

last: Rudqvist

state: VG

address: Gula stråket 2b

country: Sweden

institute: Gothenburg university

summary:
Transcriptomic profiling of normal mouse thyroid tissue following 211At irradiation
Introduction   The cellular response to stimuli can be studied on different molecular levels, including gene expression regulation. RNA microarray is a high-throughput technique that enables comparison of genome-wide transcriptional status between samples. 211At-labeled radiopharmaceuticals are potentially useful for tumor therapy. Metabolically released 211At accumulates in the thyroid gland, which is one of the main critical organs for such therapy. The aim of this study was to determine the effect of absorbed dose, dose-rate, and time after 211At exposure on transcriptional expression in mouse thyroid gland.    Method  BALB/c mice were i.v. injected with 1.7, 7.5 or 100 kBq 211At. Animals injected with 1.7 kBq were killed after 1, 6, or 168 h with mean absorbed doses to thyroid of 0.023, 0.32, and 1.4 Gy, respectively. Animals injected with 7.5 and 100 kBq were killed after 6 and 1 h, respectively, resulting in mean absorbed doses to thyroid of 1.4 Gy. Animals were killed through cardiac puncture under anesthesia, and thyroids were removed and snap-frozen. Total RNA was extracted from pooled thyroid tissue samples and mRNA levels were determined with the Illumina RNA microarray platform. Nexus Expression 3.0 was used to identify differentially expressed transcripts (adjusted p-value <0.01, fold change >1.5) and enriched GO terms (p-value <0.05) between irradiated groups and controls.     Results  In total, 1232 differentially expressed transcripts were detected after 211At administration, demonstrating a profound effect on gene regulation. The number of regulated transcripts increased with higher initial dose-rate/absorbed dose when the exposure time was 1 or 6 h. However, the number of regulated transcripts decreased with mean absorbed dose/time after 1.7 kBq 211At administration. This suggests that initial dose-rate (thus injected activity) is an important parameter in radiation-induced responses. Furthermore, the regulation profiles of groups administered 1.7 kBq were similar. Few previously proposed radiation responsive genes were identified in the present study, but, e.g. Gadd45g and Cdkn1a were among the regulated genes identified in the present study. A response involving immunological processes was identified especially at 1, 6, and 168 h after 1.7 kBq administration (0.023, 0.32, 1.8 Gy).     Conclusion  The present study allowed a comprehensive assessment of how variations in exposure parameters affect transcriptional regulation. The regulation profiles were dependent on both absorbed dose and time after exposure, but, initial dose-rate was the most influential parameter. Functional annotation of regulated genes revealed exposure-specific effects on biological processes. Additionally, we have identified several recurrently regulated genes after 211At exposure that may play a role in how mouse thyroid tissue responds to 211At exposure.   Introduction   The cellular response to stimuli can be studied on different molecular levels, including gene expression regulation. RNA microarray is a high-throughput technique that enables comparison of genome-wide transcriptional status between samples. 211At-labeled radiopharmaceuticals are potentially useful for tumor therapy. Metabolically released 211At accumulates in the thyroid gland, which is one of the main critical organs for such therapy. The aim of this study was to determine the effect of absorbed dose, dose-rate, and time after 211At exposure on transcriptional expression in mouse thyroid gland.    Method  BALB/c mice were i.v. injected with 1.7, 7.5 or 100 kBq 211At. Animals injected with 1.7 kBq were killed after 1, 6, or 168 h with mean absorbed doses to thyroid of 0.023, 0.32, and 1.4 Gy, respectively. Animals injected with 7.5 and 100 kBq were killed after 6 and 1 h, respectively, resulting in mean absorbed doses to thyroid of 1.4 Gy. Animals were killed through cardiac puncture under anesthesia, and thyroids were removed and snap-frozen. Total RNA was extracted from pooled thyroid tissue samples and mRNA levels were determined with the Illumina RNA microarray platform. Nexus Expression 3.0 was used to identify differentially expressed transcripts (adjusted p-value <0.01, fold change >1.5) and enriched GO terms (p-value <0.05) between irradiated groups and controls.     Results  In total, 1232 differentially expressed transcripts were detected after 211At administration, demonstrating a profound effect on gene regulation. The number of regulated transcripts increased with higher initial dose-rate/absorbed dose when the exposure time was 1 or 6 h. However, the number of regulated transcripts decreased with mean absorbed dose/time after 1.7 kBq 211At administration. This suggests that initial dose-rate (thus injected activity) is an important parameter in radiation-induced responses. Furthermore, the regulation profiles of groups administered 1.7 kBq were similar. Few previously proposed radiation responsive genes were identified in the present study, but, e.g. Gadd45g and Cdkn1a were among the regulated genes identified in the present study. A response involving immunological processes was identified especially at 1, 6, and 168 h after 1.7 kBq administration (0.023, 0.32, 1.8 Gy).     Conclusion  The present study allowed a comprehensive assessment of how variations in exposure parameters affect transcriptional regulation. The regulation profiles were dependent on both absorbed dose and time after exposure, but, initial dose-rate was the most influential parameter. Functional annotation of regulated genes revealed exposure-specific effects on biological processes. Additionally, we have identified several recurrently regulated genes after 211At exposure that may play a role in how mouse thyroid tissue responds to 211At exposure.

overall_design: Total RNA was isolated from fresh-frozen tissue samples (Normal balb/c mouse thyroids)

first: Johan

last: Spetz

first: Emil

last: Schüler

first: Toshima

middle: Z

last: Parris

first: Britta

last: Langen

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: aCGH and RNA-Seq expression profiling of Chinese hepatocellular carcinoma patients

country: China


title: Transcriptome profile analysis of cell proliferation molecular processes during multicellular trichome formation induced by tomato Wov gene in tobacco

status: Public on Aug 25 2015

city: wuhan

first: Yanna

last: Gao

address: hongshan area, shizishan street

institute: Huazhong agricultural university

summary:
Purpose: Trichomes, developing from the epidermis of nearly all terrestrial plants, provide good structural resistance against insect herbivores and an excellent model for studying the molecular mechanisms underlying cell fate determination. Regulation of trichomes in Rosids has been well characterized. However, little is known about the cell proliferation molecular processes during multicellular trichome formation in Asterids.
Methods: The transcriptomes of  between Wov transgenic and wild-type tobacco by RNA-seq analysis were evaluated using the Illumina HiSeq™ 2000 sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by Tophat and DEGseq software.  qRT–PCR validation was performed using  SYBR Green assays.
Results: In this study, we identified two point mutations in a novel allele (Wov) at Wo locus. Ectopic expression of Wov in tobacco and potato induces much more trichome formation than wild type. To gain new insights into the underlying mechanisms during the processes of these trichomes formation, we compared the gene expression profiles between Wov transgenic and wild-type tobacco by RNA-seq analysis. A total of 544 co-DEGs were detected between transgenic and wild-type tobacco. Functional assignments of the co-DEGs indicated that 33 reliable pathways are altered in transgenic tobacco plants. The most noticeable pathways are fatty acid metabolism, amino acid biosynthesis and metabolism, and plant hormone signal transduction. Results suggest that these enhanced processes are critical for the cell proliferation during multicellular trichome formation in transgenic plants. In addition, the transcriptional levels of homologues of trichome regulators in Rosids were not significantly changed, whereas homologues of genes (Wo and SlCycB2) in Asterids were significantly upregulated in Wov transgenic tobacco plants.
Conclusions: This study presents a global picture of the gene expression changes induced by Wov- gene in tobacco. And the results provided us new insight into the molecular processes controlling multicellular formation in tobacco. Furthermore, we inferred that trichomes in solanaceous species might share a common network.

overall_design: The transcriptomes of  between Wov transgenic and wild-type tobacco by RNA-seq analysis were evaluated, in duplicate, using the Illumina sequencing platform.

first: Zhibiao

last: Ye

first: Changxian

last: Yang


title: Tat controls RNA Polymerase II and the epigenetic landscape to precisely rewire cellular transcriptional programs (RNA-Seq)

first: Ivan

last: D'Orso

country: USA

overall_design: Tat vs. GFP

first: Jonathan

last: Reeder

first: Iván


title: Molecular and Structural Bases of Hypothalamic  Puberty

status: Public on Dec 20 2014

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

summary: To compare the global profile of hypothalamic gene expression in agonadal male Rhesus Monkeys before and after reactivation of the pulsatile GnRH release during the pubertal phase of development.

overall_design: 20 Samples looking at Cortex and Mediobasal hypothalamus in 3 stages of Rhesus Monkeys (early pubertal, late juvenile, and late pubertal).

first: Sergio

middle: R

last: Ojeda

first: Tony

last: Plant

first: R

last: Ramaswamy

first: Valerie

last: Matagne


title: Dose-specific transcriptional responses in thyroid tissue in mice after 131I administration

status: Public on Jan 31 2015

first: Nils

last: Rudqvist

summary:
Transcriptomic profiling of normal mouse thyroid tissue following 131At irradiation
In the present investigation, microarray analysis was used to monitor transcriptional activity in thyroids in mice 24 h after 131I exposure. The aims of this study were to 1) assess the transcriptional patterns associated with 131I exposure in normal mouse thyroid tissue and 2) identify novel biomarkers for 131I exposure.
Methods:
Adult BALB/c nude mice were i.v. injected with 13, 130 or 260 kBq of 131I and killed 24h after injection. The corresponding absorbed doses delivered to the thyroid gland were 0.85, 8.5, or 17 Gy. Mock-treated mice were used as controls. Total RNA was extracted from thyroids and processed using MouseRef-8 Whole-Genome Expression BeadChips (Illumina). Nexus Expression 2.0 software were used for analysis.
Results:
In total, 497, 546, and 90 transcripts were regulated in the thyroid after 0.85, 8.5, and 17 Gy, respectively. These were involved in several biological functions, e.g. oxygen access, inflammation and immune response, and apoptosis/anti-apoptosis. Approximately 50% of the involved transcripts at each absorbed dose level were dose-specific and 18 transcripts were commonly detected at all absorbed dose levels. The Agpat9, Plau, Prf1, and S100a8 gene expression displayed a monotone decrease in regulation with absorbed dose, and may function as dose-related biomarkers for 131I exposure.
Conclusion:
Distinct and substantial differences in gene expression and affected biological functions were detected at the different absorbed dose levels. The transcriptional profiles were specific for the different absorbed dose levels. We propose that the Agpat9, Plau, Prf1, and S100a8 genes are novel potential absorbed dose-related biomarkers for 131I exposure.

overall_design: Total RNA was isolated from fresh-frozen tissue samples (Normal Balb/c mouse thyroids)


title: The evolutionary interplay between Puf RNA binding proteins and their RNA targets

first: Greg

last: Hogan

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

sample_organism:
Saccharomyces cerevisiae
Neurospora crassa
Neurospora crassa OR74A

overall_design: Refer to individual Series