title: Host transcriptional responses during chronic Toxoplasma gondii infection reveals sex specific differences that lead to altered protection against secondary infection

status: Public on Jul 24 2018

first: Laura

last: Knoll

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

country: USA

institute: UW-Madison

summary: We sequenced the cerebral cortex transcriptome of both male and female mice either infected with T. gondii or age-matched uninfected controls. These transcriptomes were determined along the infection timeline with early (21 and 28 days) and late (3 and 6 months) chronic represented. We obtained 5.7 billion paired-end sequences and aligned them to the Mus musculus genome. We found that a majority of the host genes with greater abundance at day 21 post-infection are still more abundant 6 months post-infection in male and female mice, although, females have far fewer genes that are significantly less abundant. Genes that were significantly less abundant in males are involved with the immune response, and may lead to the slight increase in cyst numbers in males during chronic infection.

overall_design: The RNA from the cerebral cortex of CBA/J mice infected with the T. gondii strain ME49 strain after 21, 28, 90, and 180 days of infection was processed for Illumina sequencing.

first: Andrew

middle: L

last: Garfoot

first: Patrick

middle: W

last: Cervantes


title: Effect of amphetamine on the transcriptome of overactive and control mouse lines

status: Public on Dec 19 2018

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

type: Expression profiling by high throughput sequencing

summary: The goals of this study were to advance the understanding of the distinct impact of amphetamine across mouse lines with different genetic predisposition for neurological disorders treatable by this psychostimulant

overall_design: 10 male mice were treated with d-amphetamine (25mg/kg) and 10 male mice were treated with saline at approximately 6 month of age. Half of the mice in each group were from a line selected for cage overactivity and the rest served as control. The striatum from was obtained 2 hours after treatment with the psychostimulant. Samples were profiled using paired-end RNA sequencing


title: Chronic Gene Expression after Traumatic Brain Injury

status: Public on Sep 01 2018

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: This project continues our acute TBI studies and initiates chronic studies -- characterizing the temporal genomic profile of the injured brain up to 12 months post-TBI. Thus, the primary objective of this proposal is to determine the long-term effects of traumatic brain injury on gene expression in the hippocampus and cortex, two brain regions known to be particularly vulnerable to TBI.

overall_design: Rats were prepared for fluid percussion traumatic brain injury or sham injury (Naive rats had no anesthesia and were not handled in any way and gene expression in their brains serve as baseline data) and sacrificed 24 hr, 2 week, 3 month, 6 month and 1 year post-injury, hippocampi and cortex were obtained, and stored in RNA later. Total RNA was isolated, quantitified and used for Agilent microarray analysis at GenUs Biosystems. Each group of naive, sham control, TBI has four biological replicates.

first: Debbie

last: Boone

first: Harris

last: Weisz

first: Mike

first: Karen

last: Torres

first: Helen

last: Hellmich


title: Exon Level Machine Learning Analyses Elucidate Novel Candidate miRNA Targets in an Avian Model of Fetal Alcohol Spectrum Disorder

status: Public on Aug 01 2018

city: Chapel Hill

first: Abrar

middle: E

last: Al-Shaer

state: NC

address: 135 Dauer Dr

department: Nutrition

institute: University of North Carolina Chapel Hill

summary: An RNA-seq dataset obtained from neural fold-stage chicken (Gallus gallus, strain Special Black) embryos that were exposed to a pharmacologically-relevant alcohol concentration (52 mM for 90 min) or isotonic saline. The cranial headfolds were isolated 6 hours following the initial alcohol exposure. Following RNA isolation, cDNA synthesis, and quality assurance (20), paired-end reads (75 bp) were generated on an Illumina Genome Analyzer IIx (University of Wisconsin Biotechnology Center).

overall_design: Paired end runs with 2 replicate ethanol exposed samples (pool of 23 individual neural folds) and 2 saline control samples (pool of 23 individual neural folds).

first: Susan

middle: M

last: Smith


title: Alternative splicing analysis of pediatric B-cell acute lymphoblastic leukemia compared to normal bone marrow derived pro-B cells

status: Public on Oct 02 2018

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. hnRNPA1. hnRNPA1 3’UTR was most pervasively misspliced, yielding the transcript  subject to nonsense-mediated decay. Thus, we knocked it down in B-lymphoblastoid cells, identified 213 hnRNPA1-dependent splicing events, and defined the hnRNPA1 splicing signature in pediatric leukemias. One of its elements was DICER1, a known tumor suppressor gene; its LSVs involved the 5’ UTR, suggestive of splicing as a mechanism of translational deregulation. Additionally, we searched for LSVs in other leukemia and lymphoma drivers and discovered 81 LSVs in 41 genes. 77 LSVs were confirmed using two large independent B-ALL RNA-seq datasets. In fact, the twenty most common B-ALL drivers showed higher prevalence of aberrant splicing than of somatic mutations. Thus, post-transcriptional deregulation of SF can drive widespread changes in B-ALL splicing and likely contribute to disease pathogenesis.

overall_design: Refer to individual Series


title: Effect of Menin cKO on MLL-AF9 transformed cells

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: We determined the effect of conditional deletion of Menin in MLL-AF9 transformed leukemia cells

overall_design: Sorted LSK cells were transformed by MLL-AF9 and serially-passaged cells were then treated with 100 nM 4-OHT for 24 hours. After removing the drug, cells were cultured for 2 additional days then collected for RNA extraction and RNA-seq.

first: Yufei

last: Chen

first: Patricia

last: Ernst


title: Genome-wide chromatin accessibility and gene expression profiling of renal cell carcinoma and matched normal kidney tubules [DNase-seq]

status: Public on Jul 19 2018

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We generated primary cultures from renal cell carcinoma and matched normal primary kidney cortex tubule cell cultures from 3 patients. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-seq) and gene expression profiling (RNA-seq). Studying these paired and patient-matched controlled data sets will shed light on the epigenomic changes that underlie transformation of kidney tubules into malignant cancers.

overall_design:
Paired DNase-seq and RNA-seq data sets from 2 different primary human kidney cell types (normal and cancer)
Note from submitter: The HIM23 samples have a more narrow consent and their raw data will be submitted to dbGaP.

first: Shreeram

last: Akilesh

first: Richard

last: Sandstrom


title: Gene activation precedes DNA demethylation in response to infection in human dendritic cells

status: Public on Jul 03 2018

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: DNA methylation is considered to be a relatively stable epigenetic mark. Yet, a growing body of evidence indicates that DNA methylation levels can change rapidly, for example, in innate immune cells facing an infectious agent. Nevertheless, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we generated time-course data on DNA methylation, gene expression, and chromatin accessibility patterns during infection of human dendritic cells with Mycobacterium tuberculosis. We found that the immune response to infection is accompanied by active demethylation of thousands of CpG sites overlapping distal enhancer elements. However, virtually all changes in gene expression in response to infection occur prior to detectable changes in DNA methylation, indicating that the observed losses in methylation are a downstream consequence of transcriptional activation. Footprinting analysis revealed that immune-related transcription factors (TF), such as NF-κB/Rel, are recruited to enhancer elements prior to the observed losses in methylation, suggesting that DNA demethylation is mediated by TF binding to cis-acting elements. Collectively, our results show that DNA demethylation is not necessarily required for the establishment of the core regulatory program engaged upon infection.

overall_design: H3K27ac profiles of non-infected (NI) and Salmonella (S)-infected macrophages.

first: Florence

last: Mailhot-Léonard

first: Ludovic

last: Tailleux

first: Haley

last: Randolph

first: Vania

last: Yotova

first: Anne

last: Dumaine

first: Jean

middle: C

last: Grenier

first: Luis

middle: B

last: Barreiro


overall_design: Gene expression profiles of non-infected (NI) and Mycobacterium tuberculosis (MTB)-infected dendritic cells, at multiple time points (in hours (h)). MTB was used either live or after heat inactivation (HI).


title: Augmented Pla2g4c/Ptgs2/Hpgds Axis in Bronchial Tissues of Experimental Asthma

city: Tokyo

first: Yoshihiko

last: Chiba

address: 2-4-41 Ebara, Shinagawa-ku

department: Department of Physiology and Molecular Sciences

country: Japan

institute: Hoshi University School of Pharmacy

summary: Rationale: Augmented smooth muscle contractility of the airways is one of the causes of airway hyperresponsiveness in asthmatics. However, the mechanism of the altered properties of airway smooth muscle cells is not well understood. Objectives: To identify differentially expressed genes (DEGs) related to the bronchial smooth muscle (BSM) hyper-contractility in a murine asthma model. Methods: The ovalbumin (OA)-sensitized mice were repeatedly challenged with aerosolized OA to induce asthmatic reaction. Transcriptomic profiles were generated by microarray analysis of BSMs from the OA-challenged and control animals, and KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway Analysis was applied. Measurements and Main Results: Tension study showed a BSM hyperresponsiveness to acetylcholine (ACh) in the OA-challenged mice. A total of 770 genes were differentially expressed between the OA-challenged and control animals. Pathway analysis showed a significant change in arachidonic acid (AA) metabolism pathway in BSMs of the OA-challenged mice. Validation of DEGs by quantitative RT-PCR showed a significant increase in PLA2 group 4c (Pla2g4c)/COX-2 (Ptgs2)/PGD2 synthase 2 (Hpgds) axis. PGD2 level in bronchoalveolar fluids of the OA-challenged mice was significantly increased. A 24-h incubation of BSMs with PGD2 caused a hyperresponsiveness to ACh in naive control mice. Conclusions: AA metabolism is shifted towards PGD2 production in BSMs of asthma. Increased PGD2 level in the airways might be a cause of the BSM hyperresponsiveness in asthma.

overall_design: A murine model of allergic bronchial asthma was prepared. In brief, male BALB/c mice (8 weeks of age) were actively sensitized by intraperitoneal injections of 8 µg ovalbumin (OA) with 2 mg Imject Alum on Day 0 and Day 5. The sensitized mice were challenged with aerosolized OA-saline solution (5 mg/mL) for 30 min on Days 12, 16 and 20. A control group of mice received the same immunization procedure but inhaled saline aerosol instead of OA challenge. Twenty-four hours after the last OA challenge, mice were sacrificed by exsanguination from abdominal aorta under urethane anesthesia (1.6 g/kg, i.p.) and both the left and right main bronchi were immediately isolated, and then total RNA was extracted using Trizol reagent according to the manufacturer’s protocol. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). To identify differentially expressed genes related to the disease, total RNAs of the OA-challenged (N=4) and control animals (N=4) were subjected to microarray analysis (Agilent One-Color Microarray-Based Gene Expression Analysis protocol (v6.5, Agilent Technologies)) and compared.

first: Wataru

last: Suto

first: Hiroyasu

last: Sakai


overall_design: Chromatin accessibility profiles of non-infected (NI) and Mycobacterium tuberculosis (MTB)-infected dendritic cells, at multiple time points (in hours (h)). MTB was used after heat inactivation (HI).


title: Global transcriptome analysis of HAP1 cells

status: Public on Aug 05 2018

city: Oslo

first: Roza Berhanu

last: Lemma

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: We analyzed the global change in transcription upon CHD3-KO and SENP1-KO compared to control HAP1 cells.

overall_design: CRISPR-Cas9-generated knockout HAP1 cells for CHD3 and SENP1 compared to HAP1 control cell line were profiled for changes in transcriptome-wide expression using RNA-seq. Three biological replicates were used for RNA sequencing, where 150 bp PE-reads were obtained using Illumina Hiseq 4000 sequencer

first: Odd

middle: S

last: Gabrielsen

first: Roza


title: RNA Expression data for early diabetic nephropathy (EDN)

city: Boston

first: Towia

last: Libermann

state: MA

address: 99 Brookline Ave.

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary:
There is a temporal window from the time diabetes is diagnosed to the appearance of overt kidney disease during which time the disease progresses quietly without detection.  Currently, there is no way to detect early diabetic nephropathy (EDN).
Here we performed an unbiased assessment of gene-expression analysis of postmortem human kidneys using microarrays to identify candidate genes that may contribute to EDN.

overall_design: Postmortem biological samples (blood and kidney tissue) from non-diabetic and individuals with EDN were obtained from the National Disease Research Interchange (Philadelphia, PA).  Except for obesity, there was no significant difference in any of the parameters between study groups.  There were more obese individuals in the EDN group than among non-diabetic controls. All diabetic donors had type 2 diabetes.  Diabetes status was defined as hemoglobin A1c (HgbA1c) >6.5%.  Proteinuria was identified by urine dipstick performed during the terminal hospital admission. These diagnoses were confirmed by careful review of pre– and postmortem clinical health records.  There were stringent inclusion and exclusion criteria. Inclusion criteria included: 1) donors be between 17 to 80 years of age, 2) diabetic status confirmed as noted above, and 3) postmortem time within 24h from cross-clamping in the operating room (OR); the only exception with respect to HgbA1c testing was if a donor had been prescribed and/or using glycemic agent(s) including but not limited to metformin and insulin, in which case repeat A1c testing was not mandatory. Exclusion criteria included active infection, malignancy, severe glomerulosclerosis as determined in frozen OR biopsy material, history of renal replacement therapy (hemodialysis or peritoneal dialysis at any time), and any known genetic renal condition such as polycystic kidney disease, etc.  Pathologic staging of diabetic tissues was performed using the 2010 Renal Pathology Society classification system for diabetic kidney disease.9  From each postmortem nephrectomy sample more than 100 glomeruli were reviewed in tissue sections.  Pathologic stages I-III diabetic kidney disease were considered as EDN and used in the study.  Stage III kidneys were included since the renal function in these donors are preserved. mRNA was extracted exclusively from kidney cortical tissue.  Total RNA from flash-frozen kidney tissue was subjected to Trizol® (Invitrogen, USA) extraction and purified using RNeasy mini kit. mRNA preparations were processed by the BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, per the standard Affymetrix® protocol using the Affymetrix® Human Transcriptome 2.0 GeneChip (Affymetrix®, Inc., USA).

first: S

last: Karumanchi

first: Ravi

middle: I

last: Thadhani

first: Monica

last: Sircar


title: Topo-Seq application for topoisomerases binding sites identification with a single-nucleotide resolution

status: Public on Jul 17 2018

city: Seattle

first: Dmitry

last: Sutormin

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Topo-Seq is a ChIP-Seq-based methodology that allows high-throughput identification of topoisomerases binding (cleavage) sites with a single-base precision. On a first stage of the project DNA-gyrase binding sites on a Escherichia coli DY330 genome are investigated.

overall_design: Escherichia coli DY330 cultures were treated with a range of DNA-gyrase poisons (ciprofloxacin, microcin B17, oxolinic acid) during exponential phase (OD600=0.6), than cells were harvested and lysed with sonication. Complexes of gyrase with DNA were immunoprecipitated using ANTI-FLAG M2 affinnity resin, proteins were degraded with proteinase K and DNA extracted by phenol-chlorophorm followed by precipitation in alcohol. Lybraries from the DNA recovered were prepared using NGS Accel 1S Plus DNA kit (Swift Bioscience). Reads were mapped to E. coli w3110 MuSGS genome (with BWA MEM), signals (Gyrase Cleavage Sites - GCSs) were identified using Audic-Claveiry statistic (custom scripts  with detailed descriptions could be found at https://github.com/sutormin94/Gyrase_Topo-seq).

last: Ghilarov


first: Alain

last: Pacis

type: Methylation profiling by high throughput sequencing

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


title: Cryptic promoter activation drives POU5F1 (OCT4) expression in renal cell carcinoma

first: John

last: Stamatoyannopoulos


title: Global Gene Networks in Porcine Alveolar Macrophage Cells, 3D4/31, Stimulated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA and IVA

status: Public on Jun 27 2018

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

summary:
Purpose: The goals of this study are to examine the host response with porcine alveolar macrophages (PAMs) cells, 3D4/31 by stimulation of four antigenic epitopes of App exotoxins, ApxIA, IIA and IVA.
Methods: total RNA profiles of porcine alveolar macrophage cells stimulated with ApxIA Ct, ApxIIA Nt, ApxIVA C1, ApxIVA C2 and DPBS were generated by transcriptome sequencing, in duplicate, using  HiSeq4000 platform.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays
Results: RNA sequencing yielded 617 million 101 bp paired-end clean reads, varying from 28 to 32 million for each sample. Among the clean reads, approximately 95.24% clean reads were uniquely mapped onto the version 11.1 of the sus scrofa. Gene expression was quantified through FPKM conversion of raw reads. The 15,269 genes (mean FPKM of the 10 samples > 0) were considered as expressed in PAMs over the 30,511 gene annotations. RNA-seq data confirmed stable expression of 1 known housekeeping genes, and 5 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.906.
Conclusions: Transcriptional responses of the porcine alveolar macrophages (PAMs) stimulated with the antigenic epitopes of ApxIA, ApxIIA, and ApxIVA were analyzed to identify the precious mechanism of Apx toxins in the host. This study will be foundational to understanding the host response by Apx toxins.

overall_design: Transcriptomic analysis of porcine alveolar macrophage cells, 3D4/31, stimulated with antigenic epitopes of actinobacillus pleuropneumoniae ApxIA, IIA and IVA by transcriptome sequencing, in duplicate, using HiSeq4000.

first: Han

last: Yoo


overall_design: DNA methylation profiles of non-infected (NI), Mycobacterium tuberculosis (MTB)-infected and Salmonella-infected (S) dendritic cells or macrophages, at multiple time points (in hours (h)). MTB was used either live or after heat inactivation (HI).

first: Florence

last: Mailhot-Léonard

first: Ludovic

last: Tailleux

first: Haley

last: Randolph

first: Vania

last: Yotova

first: Anne

last: Dumaine

first: Jean

last: Grenier


title: Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures (Dnase-Seq)

status: Public on Jun 19 2018

summary: We generated primary cultures from mechanically isolated kidney glomeruli (filtration unit of the nephron) which are composed of podocytes and mesangial cells. In parallel, we generated primary kidney cortex tubule cell cultures, which are composed primarily of proximal tubule cells. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-seq) and gene expression profiling (RNA-seq). We found thousands of dynamically regulated enhancers in both cell types that potentially regulate nearby and distal target genes that are differentially expressed. These data will be useful for understanding the epigenomic regulation of gene transcription in key kidney cell types.

overall_design:
Paired DNase-seq and RNA-seq data sets from 2 different primary human kidney cell types
-------------------------------------
For HIM23 and HIM26, authors state "we will be submitting the raw data to dbGaP".

first: Shreeram

last: Akilesh

first: Richard

last: Sandstrom


title: Genome-wide chromatin accessibility and gene expression profiling of renal cell carcinoma and matched normal kidney tubules [RNA-Seq]


title: An essential role for dNTP homeostasis following CDKinduced [Pu-seq]

status: Public on May 26 2018

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

summary: Replication stress is a common feature of cancer cells, and thus a potentially  important therapeutic target. Here we show that CDK-induced replication  stress is synthetic lethal with mutations disrupting dNTP homeostasis in  fission yeast. Wee1 inactivation leads to increased dNTP demand and  replication stress through CDK-induced firing of dormant replication origins.  Subsequent dNTP depletion leads to inefficient DNA replication, Mus81-  dependent DNA damage, and to genome instability. Cells respond to this  replication stress by increasing dNTP supply through Set2-dependent MBFinduced  expression of Cdc22, the catalytic subunit of ribonucleotide reductase  (RNR). Disrupting dNTP synthesis following Wee1 inactivation, through loss  of Set2-dependent H3K36 tri-methylation, results in further dNTP depletion  due to reduced RNR expression, leading to replication catastrophe and cell  death. This lethality can be rescued by increasing dNTP levels. Similarly, we  find loss of the DNA integrity checkpoint results in synthetic lethality with  Wee1 inactivation, which is also associated with replication collapse through  critically low dNTP levels. Together, these findings support a ‘dNTP supply  and demand’ model in which maintaining dNTP homeostasis is essential in  preventing replication catastrophe in response to CDK-induced replication  stress.

overall_design:
We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and used the data for finding location and efficiency of replication origins by subsequent informatics analysis.

Please note that processed data was generated from both delta and epsilon mutant together and is linked to the corresponding delta mutant sample records.

first: Chen-Chun

last: Pai

first: Samuel

last: Durley

first: Kuo-Feng

last: Hsu

first: Stephen

last: Kearsey

first: Charalampos

last: Rallis

first: Lisa

middle: K

last: Folkes

first: Rachel

last: Deegan

first: Sarah

last: Wilkins

first: Sophia

middle: X

last: Pfister

first: Christopher

middle: J

last: Schofield

first: Jürg

last: Bähler

first: Antony

last: Carr

first: Timothy

last: Humphrey


title: Integrated Chromatin Accessibility Mapping and Expression Profiling Enables Functional Annotation of Kidney GWAS Loci

first: John

last: Stamatoyannopoulos


title: Endogenous glucocorticoids control host resistance to viral infection through the tissue-specific regulation of PD1 expression on NK cells

status: Public on May 24 2018

city: Marseille

first: Bertrand

last: Escaliere

address: 163 avenue de Luminy

country: France

institute: CIML

summary:
Purpose: Controlling the balance between immunity and immunopathology is crucial for host resistance to pathogens. Upon infection, activation of the hypothalamic-pituitary-adrenal (HPA) axis leads to the production of glucocorticoids (GCs). However, the pleiotropic effects of these steroid hormones make it difficult to decipher their precise role in vivo. Our purpose was to study how GCs regulate the function of group 1 ILCs in spleen and liver upon Murine Cytomegalovirus (MCMV) infection.
Methods: We studied the in vivo effect of endogenous GCs released upon MCMV infection on NK cells in spleen and liver and ILC1s in the liver. We compared WT mice with GRNcr1-iCre mice, in which the gene encoding for GC receptor (GR) is selectively deleted in Ncr1+ cells.
Results: We found that the regulation of NK function by the GR is required for host protection against MCMV. Mechanistically, endogenous GCs produced shortly after infection induce the selective and tissue-specific expression of the immune checkpoint PD1 on NK cells. This GC-PD1 pathway mediates its immunoregulatory functions by limiting interferon (IFN)-g production by splenic NK cells, preventing lethal immunopathology. Importantly, this regulation does not compromise viral clearance.
Conclusions:The fine-tuning of a selective subset of ILCs by the HPA axis preserves tissue integrity without impairing pathogen elimination, revealing a novel aspect of neuro-immune regulation.

overall_design: Splenocytes (after NK cell enrichment with the mouse NK Cell Isolation Kit II, Miltenyi Biotec) and liver lymphocytes were pooled from three mice for each genotype. A FACS Aria III (BD Biosciences) was used to sort approximately 5 x 10^5 NK cells from the spleen and liver and 5 x 10^4 liver-resident ILC1s 44h post MCMV infection. We compared gene expression between glucocorticoid receptor (GR)-sufficient and deficient ILCs to identify the genes whose expression is regulated by GCs. Three biological replicates were generated for all samples except for the GRNcr1-iCre liver ILC1s sample (two biological replicates).

first: Linda

last: Quatrini

first: Sophie

last: Ugolini


title: Genome wide gene expression profiling demonstrated that mouse ESC and iPSC differentiated osteoblast progenitors resemble osteoblasts

status: Public on May 01 2018

city: stanford

first: Hui

last: Zhu

address: 1651 Page Mill Road

institute: Stanford Universtiy

summary: We differentiated mouse Col2.3 GFP ESCs and iPSCs to osteoblast progenitors and confirmed the osteoblast identity of ESC- and iPSC-derived osteoblasts using RNA-sequencing and hierarchical clustering, and demonstrate that Col2.3GFP+ sorted cells are more similar to freshly isolated Col2.3GFP+ osteoblasts from mouse bone than to unsorted cells based on whole genome expression profiling.

overall_design: ESC- and iPSC-derived osteoblasts, and Col2.3GFP+ sorted cells and  freshly isolated Col2.3GFP+ osteoblasts

first: Joy

last: Wu


title: Bloodstream infection in leukemia

status: Public on Jun 26 2018

city: Peoria

first: Peter

last: Gyarmati

address: 1 Illini Drive

institute: University of Illinois

summary: We examine the role of the gastrointestinal lymphatic tissue (GALT) in the formation of bloodstream infections in leukemia

overall_design: Leukemia was induced in mice using xenograft. Five weeks later the small intestine was removed and the GALT cells were extracted (intraepithelial lymphocytes (IEL) and lamina propria (LP) cells). RNA was extracted from the cells and sequenced on a HiSeq 4000 machine.

first: Yajing

last: Song


title: PIXUL-ChIP-seq analysis of genome-wide epigenetic marks binding in human HCT116 cells

status: Public on Jun 15 2018

first: Karol

last: Bomsztyk

address: 850 Republican Street

institute: University of Washington

summary: High throughput PIXUL-ChIP-seq genome-wide study allows the mapping of epigenetic marks in human HCT116 cells.

overall_design: Human HCT116 cells were grown and sheared  in a 96-well plate using  PIXUL, high throughput chromatin sonication instrument. HCT116 cells were grown to a density of 200,000 cells per well, crosslinked, quenched, and sonicated for 6 minutes per well in 100µL on the PIXUL 96-well sonicator. ChIP and library prep was performed for each factor from a single well using Active Motif’s Low Cell ChIP-Seq Kit (Catalog number 53084). Libraries were sequenced on a NextSeq 500 as SE75 with dual 8bp indexing, allowing for PCR de-duplication with molecular identifiers at the i5 position (see product manual).

first: Adam

last: Blattler

first: Daniel

last: Mar

first: Thomas

last: Matula

first: Yuliang

last: Wang


title: Enzyme promiscuity shapes evolutionary innovation and optimization

status: Public on May 14 2018

city: La Jolla

last: Feist

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California, San Diego

summary: A computational model of underground metabolism and laboratory evolution experiments were employed to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non-native substrates in E. coli K-12 MG1655. After as few as 20 generations, the evolving populations repeatedly acquired the capacity to grow on five predicted novel substrates--D-lyxose, D-2-deoxyribose, D-arabinose, m-tartrate, and monomethyl succinate--none of which could support growth in wild-type cells. Promiscuous enzyme activities played key roles in multiple phases of adaptation. Potential mechanisms for optimizing growth on the non-native carbon sources were explored by analyzing the transcriptomes of initial and endpoint populations.

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

overall_design: RNAseq was performed on various evolved populations grown on four different carbon sources: D-lyxose, D-2-deoxyribose, D-arabinose, and m-tartrate. Differentially expressed genes were examined comparing endpoint (optimized) samples to initial (innovation) samples.

first: Gabriela

last: Guzman


title: Expression analysis of human stage Ta bladder tumours

city: Leeds

first: Margaret

last: Knowles

state: West Yorkshire

address: Becket Street

department: LICAP

institute: University of Leeds

summary:
Expression data derived from this analysis was used to compare expression signatures between genomic subgroups identified from DNA copy number analysis.
In this dataset, we include the expression data obtained from 79 stage Ta primary bladder tumours

overall_design: 79 tumour samples were analysed in parallel on the Affymetrix HTA 2.0 platform


title: The role of DOCK10 in the regulation of the transcriptome and aging

status: Public on May 10 2018

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional response to long-term soybean aphid infestation in susceptible and resistant soybean plants

city: Ames

first: Gustavo

middle: Carlos

last: MacIntosh

state: Iowa

address: 4108 Molecular Biology Bldg., 2437 Pammel  Dr.

department: Biochemistry

institute: Iowa State University

summary:
Soybean aphids are phloem-feeding pests that can cause significant yield losses in soybean plants. Soybean aphids thrive on susceptible soybean lines but not on resistant lines. Aphids do not normally kill their host and colonize plants for long periods of time, up to several months in soybean. However, our knowledge of plant responses to long-term aphid colonization is very limited.
We used microarrays to characterize the soybean plant's transcriptional response against aphids in two related cultivars, a susceptible line and a resistant line with the Rag1 aphid-resistance gene. We measured transcript levels in leaves after 21 days of aphid infestation.

overall_design: This was a full-factorial experiment with two factors: soybean variety (susceptible SD01-76R,resistant LD05-16060), and aphid treatment (control, aphids). There were three replicates per treatment, for a total of 12 samples. The experiment was carried out in a growth chamber. At the V3 growth stage, thirty aphids were added to the third trifoliate leaves of the aphid-treated plants. Each plant was covered with a net to prevent aphid movement among different plants. The aphids were removed prior to sampling.

first: Matthew

last: Studham


title: The lncRNA and mRNA sequencing result from mouse E12.5 cerebral cortex

status: Public on Jun 21 2018

city: Xiamen

last: Miao

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

country: China

institute: Huaqiao University

summary: To obtain the highly expressed lncRNA and mRNA at E12.5 cortice of mouse

overall_design: The RNAs for RNA-seq from three E12.5 mouse cerebral cortices,and have 3 replicates

first: Tao

last: Sun


title: Cell type transcriptome atlas for the planarian Schmidtea mediterranea

status: Public on Apr 17 2018

city: Cambridge

first: Christopher

last: Fincher

address: 455 Main St

institute: Whitehead Institute

summary: The transcriptome of a cell dictates its unique cell-type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and is a powerful new approach to metazoan biology.

sample_organism:
Homo sapiens
Mus musculus
Schmidtea mediterranea

overall_design:
Single cell transcriptomes for the planarian Schmidtea mediterranea were generated using Drop-seq.
Please note that each processed data file was generated from multiple samples, as indicated in the corresposponding sample description field.

middle: T

first: Omri

last: Wurtzel

first: Thom

last: de Hoog

first: Kellie

last: Kravarik

last: Reddien


title: Next Generation Sequencing Facilitates Quantitative of Transcriptomes in Various Cells Treated with or without LD100 and siRNA of SOD1

status: Public on Mar 23 2018

city: Wuhan

first: Xiang

last: Li

state: Hubei

address: No.152 Luoyu Road

department: School of Chemistry

institute: Central China Normal University

summary:
Purpose: mRNA-sequencing has revolutionized systems-based analysis of cellular pathways. The goals of this study are to systemically research the biological functions of SOD1 in ROS signaling pathway using specific SOD1 inhibitor-LD100 and its validated siRNA.

Methods: We reported the mRNA-sequencing data of HeLa cells (designated as C), LD100-treated HeLa cells (L), SOD1 knockdown HeLa cells (S), DU145 cells (DC), LD100-treated DU145 cells (DL), RWPE-1 cells (RC) and LD100-treated RWPE-1 cells (RL). All the samples were sequenced in triplicate, using Illumina HiSeq PE150. Remaining paired-end clean reads were aligned to the reference genome (GRCh38) using HISAT aligner. After calculating the reads numbers mapped to each gene by HTSeq, we estimated gene expression levels via FPKM. Differential expression analysis of two different groups was performed using the DESeq R package, which was based on a model of negative binomial distribution.

Results: A total of 133,070,980 reads in the control group, 128,097,025 reads in the SOD1 knockdown group, and 129,315,055 in the LD100-treated group were mapped to the reference genome. The total of 4513 differentially expressed genes (DEGs) was identified in the knockdown group, and the total of 2650 DEGs was identified in the SOD1 inhibition group compared to the control group. A total of 170,657,327 and 175,502,302 reads in the control group of DU145 and RWPE-1, 181,591,462 and 179,503,168 reads in the LD100-treated group of DU145 and RWPE-1 were respectively mapped to the reference genome. Among them, 8806 DEGs were identified in the LD100-treated DU145 cells compared to the control, but only 1503 DEGs were identified in the LD100-treated RWPE-1 cells compared to the control.

Conclusions: The global transcriptomic data on HeLa, DU145 and RWPE-1 after SOD1 inhibition using its specific inhibitor-LD100 indicated that the most changed expression upon this interruption of ROS homeostasis is the key genes in plenty of signaling pathways inside cancer cells, not inside normal cells, although mRNA levels of numerous genes are altered in three lines of cells. The modulation of gene expression leads to repression of multiple signaling pathways including ERK, PI3K and NF-KB and their crosstalk to promote cell growth and activation of the signaling pathways to cause both cell cycle arrest and apoptosis. These modulated signaling pathways constitute a ROS signaling network, and SOD1 is a master hub in modulation of the network to selectively kill cancer cells.

overall_design: Examination of transcriptomes in HeLa cells (designated as C), LD100-treated HeLa cells (L), SOD1 knockdown HeLa cells (S), DU145 cells (DC), LD100-treated DU145 cells (DL), RWPE-1 cells (RC) and LD100-treated RWPE-1 cells (RL).

first: Changlin

last: Liu


title: Identification of a myofibroblast-specific expression signature in skin wounds

status: Public on Dec 30 2017

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

summary: After skin injury fibroblasts migrate into the wound and transform into contractile extracellular matrix-producing myofibroblasts to promote skin repair. Persistent activation of myofibroblasts can cause excessive fibrotic reactions, but the underlying mechanisms are not fully understood. We used SMA-GFP transgenic mice to study myofibroblast recruitment and activation in skin wounds. Myofibroblasts were initially recruited to wounds three days post injury reached a maximum after seven days and subsequently declined. Expression profiling showed that 1749 genes were differentially expressed in sorted myofibroblasts from wounds seven days post injury. GO-Term analysis associated most of these genes with the extracellular region and cell periphery including upregulated genes encoding for ECM proteins, integrins and focal adhesion proteins and a specific set of growth factors, cytokines and chemokines promoting the healing response. In contrast, cell adhesion molecules involved in cell-cell interaction were downregulated. Novel genes not yet known to be expressed in myofibroblast were found. Hence, this first characterization of a myofibroblast specific expression network at the peak of granulation tissue formation in situ provides important insights into myofibroblast activation in skin wounds and identifies novel target genes to control excessive ECM deposition during fibrotic reactions.

overall_design: Non-hematopoietic (CD45-)/non-endothelial (CD31-) cell populations with low expression of SMA-GFP from dermis (SMA-GFP+) and with high expression from wounds 7 days post injury  (SMA-GFP+++) were isolated by cell sorting from transgenic SMA-GFP mice. Total RNA of was isolated with TRIZOL (Life Technologies) and RNA quality was confirmed using micro capillary electrophoresis (2100 Bioanalyzer, Agilent).   ~50ng of RNA was amplified, labeled and hybridized to Sureprint G3 human GE 8x60K or whole genome mRNA microarray according to the manufacturer’s specifications (Low input Quick Amp Labeling kit, Agilent). The arrays were scanned (Agilent G2595C scanner), data extracted and processed to create a generic gene level experiments from two technologies using the Genespring 14.5 software (Agilent).


title: Astrocyte-derived Interleukin-33 promotes microglial synapse engulfment and neural circuit development I

status: Public on Feb 05 2018

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

summary: Neuronal synapse formation and remodeling is essential to central nervous system (CNS) development and is dysfunctional in neurodevelopmental diseases. Innate immune signals regulate tissue remodeling in the periphery, but how this impacts CNS synapses is largely unknown. Here we show that the IL-1 family cytokine Interleukin-33 (IL-33) is produced by developing astrocytes and is developmentally required for normal synapse numbers and neural circuit function in the spinal cord and thalamus. We find that IL-33 signals primarily to microglia under physiologic conditions, that it promotes microglial synapse engulfment, and that it can drive microglial-dependent synapse depletion in vivo. These data reveal a cytokine-mediated mechanism required to maintain synapse homeostasis during CNS development.

overall_design: 16 samples total consisting of 4 biological replicates per group of flow sorted IL-33pos and neg astrocytes from thalamus or spinal cord at P15 (IL-33mCherry reporter from M. Colonna lab)

first: Anna

middle: V

last: Molofsky

middle: D

first: Kevin

last: Kelley


title: mRNA-sequencing of U87 glioblastoma and DAOY medulloblastoma spheroidal aggregates undergoing electrotaxis

status: Public on Jun 09 2018

city: Durham

first: Johnathan

middle: G

last: Lyon

address: 1427 FCIEMAS BOX 90281

department: Biomedical Engineering

institute: Duke University

summary: Treatment of neuroepithelial cancers remains a daunting clinical challenge, particularly due to an inability to address rampant invasion deep into eloquent regions of the brain. Given the lack of access, and the dispersed nature of brain tumor cells, we explore the possibility of electric fields inducing directed tumor cell migration. In this study we investigate the properties of populations of brain cancer undergoing electrotaxis, a phenomenon whereby cells are directed to migrate under control of an electrical field. We investigate two cell lines for glioblastoma and medulloblastoma (U87mg & DAOY, respectively), plated as spheroidal aggregates in matrigel-filled electrotaxis channels, and report opposing electrotactic responses. To further understand electrotactic migration of tumor cells, we performed RNA-sequencing for pathway discovery to identify signaling that is differentially affected by the exposure of direct-current electrical fields.

overall_design: U87 glioblastoma and DAOY medulloblastoma cells were plated as spheroidal aggregates and exposed to continuous direct-current electrical fields (250 V/m for 0, 2, or 8h, n=3) to measure their propensity to electrotax. Cell lysates from these experiments were collected for performing RNA-SEQ and differential transcript expression.

first: Sheridan

middle: L

last: Carroll

first: Nassir

last: Mokarram

first: Ravi

last: Bellamkonda


title: Astrocyte-derived Interleukin-33 promotes microglial synapse engulfment and neural circuit development

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


title: Genome-wide gene expression profiling of primary human glomerular and kidney cortex tubular outgrowth cultures (RNA-seq)

city: SEATTLE

first: John

last: Stamatoyannopoulos

address: 2211 Elliott Avenue, 6th Floor

institute: Altius Institute / University of Washington

first: Shreeram

last: Akilesh

first: Richard

last: Sandstrom


title: Exposure to ALS-inhibiting gametocide tribenuron-methyl affects pollen wall formation, lipid metabolism, chloroplast structure, and cell cycle in the flower buds of rapeseed

status: Public on Apr 26 2018

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

summary: To reveal the possible molecular mechanism underpinning the male sterility induced by a sulfonyflurea herbicide tribenuron-methyl (TBM), a comparative transcriptome analysis between rapeseed plants exposed to a TBM solution of 0.2 mg/L concentration and the control (spray with water) was conducted  by using Illumina digital gene expression tag profiling technology (DGE). A transcriptomic analysis of the flower buds of TBM treatment identified 208 up-regulated and 164 down-regulated differential expression genes in comparison with the control. It was showed by the genetic network that the main groups of GO terms including response to chemical and hormone stimulus (response to stress), developmental process (pollen wall and pollen exine formation), lipid metabolism, and cellular amino acid derivative biosynthesis process were significantly influenced by the TBM treatment. The cytological and transcriptomic alterations in the treated plants were in accordance with reduction of chlorophyll, photosynthetic rate, and elevation of ethylene release.

overall_design: The young flower buds (microsporocyte cell (MMC) to uni-nucleate microspore stage, length ≤ 3 mm) corresponding to the key stage sensitive to gametocide, were dissected from the plants 5 days after treatment and the control plants. The two biological replicates were designed as HS1, HS2 for the treatment and CK1 and CK2 for the control.Two groups of Illumina DGE (digital gene-expression tag profiling) libraries (HS1 and HS2) and the control (CK1 and CK2) were constructed using the cDNAs of young floral buds of TBM-treated plants and the control with Illumina’s DGE Tag Profiling Kit according to the manufacturer’s protocol. We performed a single end sequencing on an Illumina Hiseq2500 platform following the vendor's recommended protocol. The raw data containing adaptor sequences, tags with low quality sequences and unknown nucleotides N were filtered to obtain clean reads with 36 nt in length. Clean reads were then conducted for quality assessment. All clean tags were aligned to the Brassica genome in JGI (http://genome.jgi.doe.gov/) by Bowtie2 ver 2.1.0 (http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/), only 1 bp mismatch is allowed.  The number of perfect reads matching to each unigene was normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM). The significant DETs among the two groups of samples were selected, with false discovery rate (FDR) ≤ 0.05 and fold-change ≥ 2. The sequence of each DET was further searched by BLAST to get more information in NCBI nucleotide collection database and the functional annotation was searched in Uniprot databse (http://www.uniprot.org/). The genetic networks of GO (Gene Ontology) terms for the DETs were drew by BiNGO software in Cytoscape (www.cytoscape.org/).


title: Estrogen responsive transcriptome of estrogen receptor positive normal human breast cells in 3D cultures

city: Berkeley

first: Paul

last: Yaswen

address: One Cyclotron Road, Building 977

institute: LBNL

summary: Understanding how differentiation, microenvironment, and hormonal milieu influence human breast cell susceptibility to malignant transformation will require the use of physiologically relevant in vitro systems. We developed a 3D culture model that enables the propagation of normal estrogen receptor alpha (ER)+ cells. The purpose of this experiment was to assess ER functionality and compare estrogen-induced transcripts among samples and systems.

overall_design: RNA-seq was performed on RNA prepared from replicate 3D cultures from 3 normal 3D breast culture specimens exposed to 10nM estradiol or vehicle alone for 6 or 24 hours.

first: Alex

last: Loguinov


title: RUNX2 promotes the development of Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

status: Public on Feb 06 2018

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

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

department: IRCMS

institute: Kumamoto University

summary: To understand how RUNX2 promoted the development of BPDCN, we transduced RUNX2-directed shRNA vectors in a BPDCN cell line, CAL-1 and performed microarray analysis of RUNX2-knocked down CAL-1 cells

overall_design: CAL-1 cells were transduced with two distinct RUNX2-directed shRNA vectors containing IRES-GFP. As RUNX2-directed shRNA-transduced cells significantly reduced levels of RUNX2 expression, compared to the control Luciferase-directed shRNA-transduced cells, we perfomed gene expression analysis of RUNX2-knocked down CAL-1 cells.

first: Sho

last: Kubota


title: Gene expression profiles in systemic sclerosis tenosynovial biopsies

status: Public on Jun 30 2017

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary:
Systemic sclerosis is a connective tissue disease affecting skin and internal organs, characterized by a triad of inflammation, vasculopathy and progressive fibrosis, due to deposition of mainly type I collagen. Out of the intricate mechanisms involved in the pathogenesis of the disease, evidence indicates that TGFbeta signaling plays a central role in mediating the effects of several pro-fibrotic effectors. In addition, TGFbeta is induced by hypoxia in cultured fibroblasts, an observation suggesting a role for this cytokine in linking vasculopathy and fibrosis in the disease. Not surprisingly, TGFbeta and Wnt signaling are among the most prevalent pathways found in global gene expression studies performed on systemic sclerosis skin biopsies. In this perspective, modulation of TGFbeta activity remains a top therapeutic target in systemic sclerosis drug development.
We recently performed whole-body magnetic resonance imaging (MRI) studies in systemic sclerosis patients, and evidenced deep connective tissue infiltrates surrounding tendons in patients with active disease, and tendon friction rubs. Tenosynovitis and arthritis were also found by MRI in one third of the patients. We performed tenosynovial biopsies in patients with clinically active tenosynovitis, in order to evaluate whether such samples would provide additional information on disease mechanisms. Here, we report that these samples are characterized by the over-expression of genes involved in fibrosis, TGFbeta/Wnt signaling, chemokines and cytokines, but also by the concurrent over-expression of several ubiquitin-specific peptidases (USPs).
Among the USPs overexpressed in systemic sclerosis tenosynovial biopsies, USP15 is known to specifically deubiquitinate SMAD3, and the TGFbeta Receptor 1. These results triggered us to perform additional experiments in order to test whether USP15 overexpression plays a role in the pathogenesis of systemic sclerosis via decreased ubiquitin-mediated degradation of proteins involved in TGFbeta signaling.

overall_design:
Five tenosynovial biopsies were obtained from diffuse systemic sclerosis patients undergoing surgical procedures due to refractory pain and/or loss of function caused by tenosynovitis. These samples were used in high-density transcriptomic and immunohistochemistry experiments.
Samples SSc1 to SSc5 are related to this submission.  25 synovial biopsy samples harvested previously by our group in patients with several rheumatic conditions (GSE36700) were used in the normalization procedure.
For samples SSc1 to SSc5 , race, age and sex are blinded to preserve patients' confidentiality.

middle: R

first: Christine

last: Galant

first: Julie

last: Ducreux

first: Frédéric

last: Houssiau


title: MicroRNA expression in preoperative chemoradiotherapy for rectal cancer (LARC)

status: Public on May 17 2017

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

institute: University of Granada

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

summary:
The incorporation of chemoradiation prior to resection of the tumour has revolutionized the management of locally advanced rectal cancer. However, a large proportion of these patients are resistant to preoperative treatment schedule. We recently reported that c-Myc gene expression correlates negatively with this resistance in patients with rectal cancer. In this study, we carried out integrated analysis of miRNA and mRNA expression profiling in 45 pre-treatment rectal tumour. Further, expression of miRNAs and c-Myc, and their relationship with clinicopathological factors and patient survival was analysed. As a result, we found that 12 miRNAs were differentially expressed between responder and non-responder rectal cancer patients. Functional classification revealed an association between differentially expressed miRNAs and c-Myc. Subsequent quantitative real-time PCR results showed that both, miRNA-148 and miRNA-375 levels were significantly lower in responder compared to non-responder patients. Notably, the higher level of miRNA-375 was significantly negatively correlated with c-Myc. These results suggest that miRNA-375 and its targeted c-Myc play an important role as predictive biomarker of response to neoadjuvant treatment in patients with locally advanced rectal cancer, but still not suitable for prognosis.
Pre-treatment biopsies of 22 patients with LARC were prospectively collected and freshly frozen according to an institutional board-approved protocol. Tumour response was assessed in surgical specimens by pathological examination based on the semi-quantitative tumour regression grading (TRG) system described by Mandard in 1994[36]: TRG1 and TRG2 scores were considered responders, whereas TRG3, TRG4, and TRG5 were classified as non-responders. The inclusion criteria were: histologically proven rectal tumour at a clinical stage UICC II-III (cT3-4/and or N positive), following endorectal ultrasound and/or MRI scan. Patients were excluded if they had the tumour located above 13 cm from the anal verge by rigid rectoscopy, synchronic colonic cancer assessed by colonoscopy, distant metastases by 18FDG PET-CT scan, and suspicion of hereditary colorectal cancer. All patients subsequently received a total dose of 50.4Gy of radiation (28 fractions of 1.8Gy) associated with capecitabine (oral form of 5-FU) with or without oxaliplatine, according to our Hospital Clinical Practice Guidelines. Standardized Surgery was performed, including total mesorectal excision, following an interval of 8-10 weeks after completion of CT/RT.

overall_design: 22 samples of preoperative chemoradiotherapy LARC samples (10 from responders and 12 from non-responders) were profiled on a total of 35 TaqMan® OpenArray® MicroRNA Plates (Life Technologies), consisting of DNA probes synthesized in situ that represent 754 human miRNAs from the Sanger miRBase (Version 14), using the one-color technique in accordance with the manufacturer's instructions. Replicates of the 22 samples were profiled in different plates.

first: M

last: Cuadros


title: IGBMC-human-HeLa-TAF10 and TBP-HeLa-polysome RNA Ips

status: Public on Oct 28 2017

city: Illkirch Graffenstaden

first: Ivanka

last: Kamenova

state: Alsace

address: 1 Rue Laurent Fries

institute: IGBMC

summary:
RNA immunoprecipitation using mouse monoclonal antibody against human TAF10 protein from HeLa polysome extracts
Cells dedicate significant energy to building proteins1, which are often organized in multiprotein assemblies with tightly regulated stoichiometries2. Cotranslational assembly, a process of synchronous translation and protein heterodimerization, is a potential mechanism for efficient matching of partner subunits and avoiding the negative effects of protein aggregation3. Recent studies in bacteria demonstrate that cotranslational assembly of the LuxA-LuxB dimer follows the order established by operon structure and is more efficient than post-translational assembly4. As genes encoding protein complex subunits are dispersed among chromosomes in eukaryotes, it is unclear how cotranslational assembly is accomplished mechanistically, but studies in yeast have nevertheless suggested it as a potential assembly pathway5,6,7. Here we show that mammalian transcription complexes, such as the RNA polymerase II general transcription factor TFIID and the TRanscription and EXport complex-2 (TREX-2) assemble co-translationally. Moreover, we show that the position of heterodimerization domains determines the order of cotranslational assembly in mammalian TFIID. In polysomes, the TATA binding protein associated factor 10 (TAF10), which contains a C-terminal histone-fold dimerization domain (HFD) is recruited cotranslationally to its HFD-containing binding partner TAF8. This interaction is established unidirectionally and determined by the position rather than the sequence of the dimerization domain. We further show that similar mechanisms guide the assembly of other TFIID subunits. Our results thus predict that cotranslational assembly of eukaryotic multisubunit complexes is a general principle in building multiprotein machines.
We used microarrays to assess globally the mRNAs associated with TAF10 and TBP immunoprecipitations from HeLa polysomes.

overall_design: We prepared polysome-containing cytoplasmic extracts from HeLa cells treated with cycloheximide (100 ug/ml for 15min at 37deg) and performed immunoprecipitations (IP) with a mouse monoclonal antibody against the N-terminus of human TAF10 and against GST as a control. We isolated input and IP RNA and hybridized the corresponding cDNA to microarrays in order to analyze the enrichment of specific transcripts in the IPs. 3 biological replicates per condition (input, mock IP, IP) were analyzed.

first: Pooja

last: Mukherjee

first: Doulaye

last: Dembele

first: Laszlo

last: Tora


title: RNAseq comparison of fadR deletion mutant and the wild type strain

status: Public on Dec 14 2017

city: Stockholm

first: kun

last: wang

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholms Universitet

summary: To unravel the regulon of FadR (Saci_1107), comparative transcriptomic analysis was performed for the fadR deletion mutant versus the isogenic WT strain using RNA-seq approach.

overall_design: Examination of gene expression between knock out mutant and wild type strain

first: Kun

last: Wang


title: Regulation of gene expression in GOT1 midgut carcinoid in nude mice following injection with 177Lu-octreotate

status: Public on Dec 31 2017

city: Boston

first: Johan

last: Spetz

address: HSPH2, Room 229, 655 Huntington Ave.

department: JBL Center for Radiation Sciences

institute: Harvard School of Public Health

summary: The radiolabelled somatostatin analogue 177Lu-octreotate is a promising treatment option for malignant neuroendocrine tumors that overexpress somatostatin receptors. The human small intestine neuroendocrine tumor cell line GOT1 and Medullary thyroid carcinoma model GOT2 have shown promising treatment response to 177Lu-octreotate in xenografted mice. In clinical studies, however, only low cure rates have been achieved to date. In xenografted tumors, the human stromal components have been replaced with mouse stroma, which may have an impact in the treatment response of the xenografts.

overall_design: GOT2-tumor-bearing  BALB/c nude mice were i.v. injected with 10 MBq 177Lu-octreotate and killed after 0.5 h, 23 h, or 70 h. GOT1-tumor-bearing BALB/c nude mice were i.v. injected with 7 MBq 177Lu-octreotateand killed 24 h after injection. Control animals were injected with NaCl. Tumor samples were excised and snap frozen in liquid nitrogen, followed by total RNA extraction.

first: Britta

last: Langen

first: Toshima

middle: Z

last: Parris

first: Nils

last: Rudqvist

first: Khalil

last: Helou

first: Ola

last: Nilsson

first: Håkan

last: Ahlman

first: Eva

last: Forssell-Aronsson


title: Mesenchymal (MES)- and Adrenergic (ADN) neuroblastoma cell line pairs of isogenic origin

status: Public on May 19 2017

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: Cell line pairs with different phenotypes were isolated from individual patients to study intra-tumor heterogeneity in neuroblastoma

overall_design: Expression analysis of cell line pairs with different phenotypes was used to study intra-tumor heterogeneity

first: Rogier

last: Versteeg

last: van Nes


title: Astrocyte-derived Interleukin-33 promotes microglial synapse engulfment and neural circuit development II

first: Ilia

last: Vainchtein

overall_design: 13 samples consisting of 3-4 biological replicates each of flow sorted astrocytes (Aldh1l1-GFP+) and microglia (CD11b+) from spinal cord P9-P12 Il33 KO and littermates control mice (Pichery et al., 2012; J Immunology)

first: Anna

last: Molofsky

first: Kevin

middle: W

last: Kelley


title: Optimization of 177Lu-octreotate treatment of neuroendocrine tumours

status: Public on Mar 11 2017

overall_design: Refer to individual Series


title: Expression data from ancestrally diverse group of prostate cancer patients

status: Public on Dec 09 2016

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

summary:
African American men are disproportionately affected by both vitamin D deficiency and increased risk of prostate cancer.
We used microarrays to quantify gene expression of vitamin D-related genes in the benign epithelium in a diverse group of radical prostatectomy patients

overall_design:
The benign epithelium from a cross-sectional group of African American and Caucasian prostate cancer patients was collected by laser capture microdissection. Vitamin D-related genes were quantified by microarray
Grant: Department of Defense Prostate Cancer Research Program Idea Award for Disparities Research PC121923 (W81XWH-13-1-0252) PI Nonn

first: Richards

last: Zachary

first: Nonn

last: Larisa


title: A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response

status: Public on Dec 15 2016

first: Thomas

last: Norman

summary: Functional genomics efforts face tradeoffs between number of perturbations examined and complexity of phenotypes measured.  We bridge this gap with Perturb-seq, which combines droplet-based single-cell RNA-seq with a strategy for barcoding CRISPR-mediated perturbations, allowing many perturbations to be profiled in pooled format. We applied Perturb-seq to dissect the mammalian unfolded protein response (UPR) using single and combinatorial CRISPR perturbations. A genome-scale CRISPR interference (CRISPRi) screen identified genes whose depletion perturbs ER homeostasis. Subjecting ~100 hits to Perturb-seq enabled high-precision functional clustering of genes. Single-cell analyses revealed epistasis among the three UPR branches, bifurcated UPR branch activation between cells subject to the same perturbation, and differential activation of the branches across hits, including a feedback loop between the translocon and the IRE1α branch. These studies provide insight into how the three sensors of ER homeostasis monitor distinct types of stress and highlight the ability of Perturb-seq to dissect complex cellular responses.

overall_design: 3 different pooled CRISPR screening experiments were conducted via Perturb-seq

middle: M

first: Britt

last: Adamson

first: Jonathan

last: Weissman


title: Functional Evaluation of Mesenchymal Stem Cells Derived from Canine Induced Pluripotent Stem Cells

status: Public on Jan 26 2017

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary:
Comparison of gene expression profiles of canine induced pluripotent stem cells (iPSC) and iPS derived mesenchymal stem cells (iMSC) by microarray
Mesenchymal stem cells (MSCs) exhibit broad immune modulatory activity in vivo and can suppress T cell and dendritic cell activation in vitro.  Currently, most MSC for clinical usage are derived from adipose or bone marrow tissues from younger donors, in part due to ease of procurement and to the superior immune modulatory activity of young MSC.  However, use of MSC from multiple unrelated donors makes it difficult to standardize MSC cellular products with uniform immune modulatory properties.  One solution to this problem is the use of MSC derived from induced pluripotent stem cells (iPSC), as iPSC-derived MSC have nearly unlimited proliferative potential and exhibit in vitro phenotypic stability.  Given the value of dogs as a spontaneous disease model for pre-clinical evaluation of stem cell therapeutics, we investigated the functional properties of canine iPSC-derived MSC (iMSC), including their immune modulatory properties and their potential for teratoma formation.  We found that canine iMSC downregulated expression of pluripotency genes and appeared morphologically similar to conventional MSC.  Importantly, iMSC retained a stable phenotype even after multiple passages, did not form teratomas when inoculated in immune deficient mice, and did not induce tumor formation in purpose-bred dogs following systemic injection.  The immune potency of iMSC was similar to that of adipose and bone-marrow derived MSC with respect to suppression of T cell and DC activation. We concluded therefore that iMSC were phenotypically stable, immunologically potent, and safe with respect to tumor formation, and represented an important new source of cells for therapeutic modulation of inflammatory disorders.

overall_design: Mesenchymal stem cells were derived from canine iPS cell by TGFb inhibition, cells were passaged in vitro and RNA extracted for analysis on Affymetrix microarray

first: Lyndah

last: Chow


title: Gene expression profile of spleen B cells from Dock10 knockout mice and its regulation by IL-4

status: Public on Sep 21 2016

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: The goals of this study were to identify alterations in the gene expression profile (GEP) of spleen B cells purified from Dock10 knockout (ko) mice [C57BL/6 Dock10tm1a(EUCOMM)Hmgu/Ieg, European Mouse Mutant Archive] by comparison with the GEP of spleen B cells purified from C57BL/6 wild-type (wt) mice, and to identify alterations in the GEP of spleen B cells of the Dock10 ko mice in response to culture with IL-4 during 18 hours, by comparison with the response of the wt mice.

overall_design: Spleen B cells from 10 C57BL/6 wt mice and 10 C57BL/6 Dock10 ko mice of 12 weeks of age were purified by negative selection using the Miltenyi Pan B Cell Isolation Kit, mouse. Five of the wt samples and 5 of the ko samples, those numbered from 6 to 10 were cultured with nothing (Ctrl) or with mouse recombinant interleukin 4 (IL-4) during 18 hours. Equimolar RNA amounts from 5 of the same ko samples before culture (Pre), those numbered 6 to 10, were pooled, labelled with cy3, and used as reference sample. Each of the wt samples and the ko samples, including Pre, Ctrl, and IL-4, was labelled with cy5 and used as a test sample. The reference sample and the test samples were hybridized together onto Agilent Mouse GE 4x44K v2 Microarrays (technology 26655), scanned in an Agilent G2565CA DNA Microarray Scanner using the Agilent Scan Control software, processed with the Agilent Feature Extraction software, and analyzed using the GeneSpring GX software.


title: Mesenchymal (MES)- and Adrenergic (ADRN) neuroblastoma cell line pairs of isogenic origin

first: Johan


title: Wnt/β-catenin signaling mediates resistance of colorectal cancer cells to chemoradiotherapy

status: Public on May 01 2017

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

summary:
Activation of Wnt/β-catenin signaling plays a central role in the development and progression of colorectal cancer (CRC). Previously, we demonstrated that the Wnt transcription factor, TCF7L2, was overexpressed in primary rectal cancers that were resistant to chemoradiotherapy (CRT), and that TCF7L2 functionally mediates resistance of CRC cells to CRT. However, it remained unclear whether the resistance was mediated by a TCF7L2 inherent mechanism or Wnt/β-catenin signaling in general. We now show that silencing of β-catenin resulted in sensitization of the CRC cell lines LS1034, SW480, and SW837 to CRT, demonstrating a relationship between Wnt/β-catenin signaling and CRT resistance. To investigate the potential role of Wnt/β-catenin signaling in controlling therapeutic responsiveness, non-tumorigenic RPE-1 cells were stimulated with Wnt-3a, a physiological ligand at the Frizzled receptor, which significantly increased resistance to CRT.
This effect could be recapitulated by overexpression of mutated, undegradable β-catenin (S33Y). Again, this resulted in a significantly boosted resistance of RPE-1 cells to CRT, which was abrogated by siRNA-mediated silencing of β-catenin. Consistent with these findings, we observed higher expression levels of active (unphosphorylated) β-catenin as well as increased TCF/LEF reporter activity in SW1463 cells that evolved radiation-resistance due to repeated radiation-treatment. Global gene expression profiling identified several altered pathways associated with treatment response as a consequence of Wnt/β-catenin pathway activation, sheading new light on PPARD signaling as a possible mechanism of Wnt mediated resistance. Hence, synergistic pathway inhibition of either Wnt and/or one of the downstream-pathways may represent a promising strategy to increase therapeutic responsiveness to CRT.

overall_design: 12 samples are compared in total. There are 3 replicates for each condition. Conditions are: 1. SW1463 2. SW1463 radiation resistant. 3 and 4 the same conditions, but this time RNA isolation was performed 6h after irradiation with 4Gy

first: Georg

last: Emons

first: Melanie

last: Spitzner

first: Sebastian

last: Reineke

first: Janneke

last: Möller

first: Noam

last: Auslander

first: Frank

last: Kramer

first: Tim

last: Beissbarth

first: Hendrik

middle: A

last: Wolff

first: Margret

last: Rave-Fränk

first: Elisabeth

last: Heßmann

first: Jochen

last: Gaedcke

first: B

last: Ghadimi

last: Johnsen

last: Ried

first: Marian

last: Grade


title: Transcriptomic profiling of human GOT1 and GOT2 tumor xenografts in Balb/c nude mice following 177Lu irradiation and/or Sonidegib treatment

status: Public on Mar 08 2017

last: Spetz

summary: The radiolabelled somatostatin analogue 177Lu-octreotate is a promising treatment option for malignant neuroendocrine tumors that overexpress somatostatin receptors. The human small intestine neuroendocrine tumor cell line GOT1 and Medullary thyroid carcinoma model GOT2 have shown promising treatment response to 177Lu-octreotate in xenografted mice. In clinical studies, however, only low cure rates have been achieved to date. In vitro and preclinical in vivo studies have shown that irradiation can up-regulate the expression of somatostatin receptors and thereby give an increased uptake of 177Lu-octreotate. The cellular processes that underlie positive treatment response to 177Lu-octreotate are otherwise largely unknown. Genome-wide analysis of tumor cell responses in this successful mouse model offers a venue to identify critical treatment parameters and to optimize clinical effectiveness of 177Lu-octreotate therapy. Combining 177Lu-octreotate with other anti-tumor agents has also been proposed as a strategy for optimization. Some studies have shown synergistic effects in tumor cell killing and volume reduction The hedgehog signaling pathway is involved in embryonic development and tissue regeneration and can be/is abnormally activated in various cancers. Inhibition of the hedgehog signaling pathway has yielded promising therapeutic effects on NE tumors and may potentially enhance the effects of 177Lu-octreotate treatment in patients.

overall_design: Tumor-bearing BALB/c nude mice were i.v. injected with 5, 7, 10, 15 or 30 MBq 177Lu-octreotate. The groups receiving 5 and 10 MBq 177Lu-octreotate were given an additional 10 or 5 MBq 177Lu-octreotate 24 h after the first injection, respectively. One group was given Sonidegib (80 mg/kg twice a week via oral gavage), and one group was given Sonidegib together with 30 MBq 177Lu-octreotate. Control animals were injected with NaCl. Animals were killed after 1, 3, 7 or 41 days for the 5+10, 10+5 and 15 MBq treatments, after 24 hours for the 7 MBq treatment, and after 41 days for the 30 MBq treatment. Tumor samples were excised and snap frozen in liquid nitrogen, followed by total RNA extraction.

first: Britta

last: Langen

first: Toshima

last: Parris

first: Nils

last: Rudqvist

first: Johanna

last: Dalmo

first: Emil

last: Schüler

first: Bo

last: Wängberg

first: Khalil

last: Helou

first: Ola

last: Nilsson

first: Eva

last: Forssell-Aronsson


title: Mechanisms of Immune Suppression Utilized by Canine Adipose and Bone Marrow Stem Cells

status: Public on Nov 23 2016

first: Steven

last: Dow

summary:
Comparison of gene expression profiles of canine adipose and bone marrow derived mesenchymal stem cells by microarray
Mesenchymal stem cells (MSC) from rodents and humans have been shown to suppress T cells by distinct primary pathways, with NO-dependent pathways dominating in rodents and IDO-dependent pathways dominating in humans.  However, the immune suppressive pathways utilized by canine MSC have not been as thoroughly studied, nor have BM-MSC and Ad-MSC been directly compared for their immune modulatory potency or pathway utilization. Therefore, canine BM-MSC and Ad-MSC were generated in vitro and their potency in suppressing T cell proliferation and cytokine production was compared, as well as differential gene expression. Mechanisms of T cells suppression were also investigated for both MSC types.  We found that BM-MSC and Ad-MSC were roughly equivalent in terms of their ability to suppress T cell activation. However, the two MSC types used both shared and distinct biochemical pathways to suppress T cell activation.  Adipose-derived MSC utilized, TGF-β signaling pathways and adenosine signaling to suppress T cell activation, whereas BM-MSC used cyclooxygenase TGF-β, and adenosine signaling pathways to suppress T cell activation.  These results indicate that canine MSC are distinct from human and rodent MSC terms of their immune suppressive pathways, relying primarily on cyclooxygenase and TGF-β pathways for T cell suppression, rather than on NO or IDO-mediated pathways.

overall_design: Mesenchymal stem cells were derived from extracted canine adipose and bone marrow, cells were passaged in vitro and RNA extracted at low passages for analysis on Affymetrix microarray

first: Lyndah

last: Chow


title: PRRX1 over-expression in SK-N-BE(2C)

first: Richard

last: Volckmann

summary: PRRX1 is expressed in mesenchymal-type neuroblastoma cells. Over-expression of PRRX1 in adrenergic-type cell line was used to study reprogramming towards a mesenchymal lineage.

overall_design: SK-N-BE(2C) cells were transduced with lentiviral vector pInducer containing a doxycycline-inducible promoter driving PRRX1A. Time-course mRNA was analyzed after PRRX1-induction.

first: Rogier

last: Versteeg

first: Johan

last: van Nes


title: Study of the molecular stability of patient-derived tumor xenograft (PDX) for human renal cell carcinoma (RCC) in nude mice during subsequent passages in mice

status: Public on Jun 29 2016

city: Strasbourg

first: Thierry

last: Massfelder

address: 11 rue Humann

institute: INSERM

summary: We established a large panel of preclinical models of human RCC directly from patients, faithfully reproducing the biological features of the original tumor. RCC tissues were collected for 8 years from 336 patients undergoing surgery, xenografted subcutaneously in nude mice, and serially passaged into new mice up to 13 passages. Tissue samples from the primary tumor and tumors grown in mice through passages were analyzed at the histology, genetic and for of them at the molecular levels for biological tissue stability.  We established a large panel of 30 RCC models and 5 them of the clear cell type (clear cell renal cell carcinoma, CCC) were characterized at the mRNA expression level.

overall_design: We used Affymetrix whole genome microarrays to analyze the stability of the PDX models comparing the primary tumor (P0) with the subsequent passages in mice (P1 …).

first: Hervé

last: Lang

first: Claire

last: Beraud

first: Audrey

last: Bethry

first: Sabrina

last: Danilin

first: Véronique

last: Lindner

first: Catherine

last: Coquard

first: Sylvie

last: Rothhut


title: Expression profiles of circular RNAs in bladder cancer

status: Public on Dec 22 2016

city: Chongqing

first: Zhenyu

last: Zhong

address: No. 1 Yixueyuan Road

institute: Chongqing Medical University

summary: To explore circular RNA (circRNA) expression profiling and their biological functions in bladder cancer, we surveyed the circRNA expression signature of 4 pairs of matched bladder cancer and para-cancer tissues from clinical patients using microarray. Hundreds of significantly changed circRNAs were identified. Our findings provide a novel perspective on transcriptional group and lay the foundation for future research of potential roles of circRNAs in bladder carcinoma.

overall_design: Total RNA from four pairs of human bladder carcinomas and matched para-carcinomas were used for microarray analysis.

first: Junxia

last: Chen


title: miRNA expression between CD4+PD1+ and CD4+PD1- T cells

status: Public on Aug 01 2015

city: London

first: Nathan

last: Johnston

state: Ontario

address: 339 Windermere Road

institute: Western University

summary:
Recent success in cancer immunotherapy has come from the blockade of inhibitory receptors on T cells, such as programmed cell death-1, which can induce a state of T cell exhaustion upon constant antigen stimulation. Understanding miRNA regulation of PD1 can be useful to discover miRNAs for use in therapy or as prognostic markers in various diseases including cancer, autoimmunity and transplantation.
We used microarrays to discover global miRNA expression changes upon PD1 upregulation and identified miRNAs that are both up- and down-regulated.

overall_design: B16F10 cells were injected subcutaneously into C57BL/6 mice and 16 days later CD4+PD1+ and CD4+PD1- were sorted from the lymph nodes and spleen for RNA extraction and hybridization on Affymetrix miRNA array.


title: Gene expression profiles of the M1/M2 polarized Kupffer cells

status: Public on Sep 03 2016

city: Seoul

first: Yong-Hyun

last: Han

state: Seoul

address: Daehak-ro

department: College of Pharmacy

institute: Seoul National University

summary: To reveal the transcriptomes associated with M1 or M2-polarized Kupffer cells, the primary Kupffer cells isolated from mouse liver were treated with lipopolysaccharides or IL-4 and the gene expression patterns were analyzed by microarray. To study the role of RORα in Kupffer cell polarization, Kupffer cells were treated with RORα ligands and transcriptions were compared with those of the M1/M2 polarized Kupffer cells.

overall_design: Gene expression profiles were obtained from lipopolysaccharide-treated (M1), IL-4-treated (M2), SR3335 (RORα inverse agonist), and SR1078 (ROR agonist) and compared.

first: Mi-Ock

last: Lee


title: Gene expression analysis of breast cancer cell lines treated with PI3K and PDK1 inhibitors

status: Public on May 22 2016

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Here we demonstrate the differential gene expression of two breast cancer cell lines treated with PI3K and PDK1 inhibitors.

overall_design: Total RNA was isolated after 4h of treatment from breast cancer cell lines JIMT1 and HCC1954 from three biological replicates. Treatments were DMSO (0.1%), BYL719 (PI3K alpha inhibitor) 1 uM, GSK2334470 (PDK1 inhibitor) 1uM, and the combination of both agents. Samples for each group in triplicate were processed for Illumina BeadArrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.

first: Pau

last: Castel

first: José

last: Baselga


title: Gene expression profiles of LS180 cells in which MYU, CTNNB1, or MYC expression was suppressed.

status: Public on Sep 10 2016

city: Tokyo

first: Testu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: Tokyo University

summary: Aberrant activation of Wnt beta-catenin signalling is a major driving force in colon cancer. Wnt beta-catenin signalling induces the expression of the transcription factor c-Myc, leading to cell proliferation and tumourigenesis. c-Myc regulates multiple biological processes through its ability to directly modulate gene expression. However, the mechanisms underlying c-Myc-induced oncogenesis remain to be established. Here we identify a novel direct target of c-Myc, MYU (c-Myc-upregulated long non-coding RNA) and show that MYU is upregulated in most colon cancers and is required for the tumourigenicity of colon cancer cells. We further demonstrate that MYU associates with the RNA-binding protein hnRNP-K to stabilize CDK6 expression, and thereby promotes the G1-S transition of the cell cycle. These results suggest that the MYU/hnRNP-K/CDK6 pathway functions downstream of Wnt/c-Myc signalling and plays a critical role in the proliferation and tumourigenicity of colon cancer cells. MYU might be a promising molecular target for the therapeutic treatment of c-Myc-driven cancers.

overall_design: LS180 cells were transfected with a siRNA targeting MYU, CTNNB1, or MYC.

first: K

last: Matsumura

first: Y

last: Kawasaki


title: cold stress -Impact of cold stress on grapevine inflorescence

status: Public on Oct 01 2016

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: 12plex_vitis_2012_04 - cold stress  - In temperate species, low temperatures adversely affect plant growth and development, constraining spatial expansion and productivity. Cold can trigger adaptive process or lead to alterations in physiological traits when stress intensity exceeds a certain threshold. Grapevine flower development and fruit set are influenced by cold nights in the vineyard. The correct formation of sexual organs and the success of reproduction are dependent upon sugar supply which can be affected by low temperatures. Many pathways of carbon metabolism may be affected by low temperatures however limited information is available about fluctuations in carbon metabolism in inflorescences. - Experiments were performed on inflorescence of Vitis vinifera L. cv. Pinot noir fruiting cuttings. First, inflorescences at female meiosis were collected the day of the experiment, then cuttings with the inflorescence were placed at 0°C for a 8 h night. Control plants were maintained in a growth chamber for 8 h at 19°C. Inflorescences were collected after 1 h and 8 h of cold. Additional time point was performed 2 h after the end of the cold night by placing the inflorescence at 25°C after the end of the cold night. Control plants were also collected.

overall_design: 12 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Nathalie

last: Vaillant-gaveau

first: Marie-Laure

last: Martin-Magniette


title: Gene expression profiles from PBMCs collected from chronic smokers and moist snuff consumers

status: Public on Feb 20 2017

city: Winston-Salem

first: Gaddamanugu

last: Prasad

state: NC

institute: RAI Services Company

summary:
Data  reveal that smokers exhibit distinct gene expression profiles relative to non-smokers and moist snuff consumers. Moist snuff consumer gene expression largely resembles that of non-tobacco consumers.
Gene expression profiles were used to identify the effects of combustible (smoking) and non-combustible tobacco (moist snuff) products use.

overall_design: In a cross sectional study, smokers, moist-snuff consumers and non-tobacco consumers (aged 35-60 years, generally healthy all male study subjects) were enrolled. Following a overnight clinical confinement and fasting from tobacco and food, blood was collected and PBMCs were isolated.  Transcript levels were measured using Affymetrix U133 microarrays.

first: G


title: Distinct classes of genes behave as either drivers or dependents of replication timing switches (Replication-Timing).

status: Public on May 28 2015

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

summary: Duplication of the genome in mammalian cells occurs in a defined temporal order referred as its replication-timing program (RT). RT is regulated in units of 400-800 Kb referred as replication domains (RDs) and changes dynamically during development. Changes in RT are generally coordinated with transcriptional competence and changes in sub-nuclear position. We generated genome-wide RT profiles for 29 distinct human cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development. We identified clusters of RDs that replicate at unique times in each stage (RT signatures). Surprisingly, transcriptome data revealed that, despite an overall correlation between early replication and transcriptional activity, most genes that switched RT during differentiation can be expressed when late replicating. Intriguingly, this class of genes was nonetheless induced to high expression levels prior to a late to early RT switch and down-regulated after the switch back to late replication. These results clarify the complex relationship between transcription and RT and identify classes of genes that behave as potential drivers of the RT switch vs. those that may depend upon an RT switch for transcriptional induction.

overall_design: Genome-wide replication timing profiles were constructed from 60 human samples covering 29 distinct cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development.

first: JuanCarlos

last: Rivera-Mulia

first: Quinton

last: Buckley

first: Takayo

last: Sasaki

first: Jared

last: Zimmerman

first: Ruth

last: Didier

first: Kristopher

last: Nazor

first: Jeanne

middle: F

last: Loring

first: Zheng

last: Lian

first: Sherman

last: Weissman

first: Allan

last: Robins

first: Thomas

middle: C

last: Schulz

first: Laura

last: Menendez

first: Michael

last: Kulik

first: Stephen

last: Dalton

first: Haitham

last: Gabr

first: Tamer

last: Kahveci


title: CD34+DNAMbrightCXCR4+ CLP mobilized in chronic inflammation

status: Public on Jul 01 2015

city: Baltimore

first: Maria

middle: Libera

last: Ascierto

address: 5500 Orleans Street

department: Oncology

institute: Johns Hopkins

summary: During the course of many chronic inflammatory disorders, a persistent Natural Killer (NK) cell derangement and activation is observed. While increased cell turnover is expected in these cases, little is known about whether and how NK cell homeostatic balance and numbers are maintained by CD34+ progenitor cells. Accordingly, we studied peripheral blood progenitor cells in patients with chronic inflammatory disorders including HIV-1, HCV, TB, COPD and PAPA. Cytometric analysis revealed the presence of a so far unidentified CD34+CD226(DNAM-1)brightCXCR4+ cell population in all these conditions. Further, microarray and PCR analysis showed transcriptional signatures typical of common lymphocyte precursors. Culture of CD34+CD226brightCXCR4+ cells gave rise to NK cell progenies characterized by high expression of activating receptors and mature function. Importantly, in healthy donors CD34+CD226brightCXCR4+ cells reside in bone marrow but do not circulate in peripheral blood and are absent in umbilical cord blood. The proportion of CD34+CD226brightCXCR4+ PBMC were found to correlate with the degree of inflammation, and represent an indicator of lymphoid cell turnover/reconstitution during chronic inflammation. Identification of CD34+CD226brightCXCR4+ circulation offers a novel view of emergency recruitment of cell-precursors upgrade our understanding and monitoring of chronic inflammatory conditions, and provide new insight of intermediate stages of NK cell development.

overall_design: Four samples from CD34+ hematopoietic stem cells of healthy individuals (n=2) and HIV-infected patients (n=2) were analyzed using GeneChip Human Gene 1.0 ST Arrays.


title: DICKKOPF-1 locates in the nucleus of human differentiated epithelial intestinal and mammary cells and regulates gene expression

status: Public on Mar 30 2015

city: Madrid

first: beatriz

last: Morte

address: C/arturo Duperier 4

institute: CIBERER

summary: Wnt/b-catenin pathway is a key modulator of intestinal homeostasis by regulating stem cell biology during gut organogenesis and in adult life. DICKKOPF (DKK)-1 is a secreted inhibitor of Wnt/b-catenin signaling from plasma membrane receptors. We found that in human intestine, DKK-1 locates within the nucleus of differentiated enterocytes and enteroendocrine cells but not of proliferating and stem cells at the bottom of the crypts. DKK-1 is also nuclear in colon cancer cells locating at sites of active gene transcription. ChIP-seq and transcriptomic analysis both confirmed that DKK-1 binds chromatin and regulates gene expression. Thus, we demonstrate that DKK-1 is a multifunctional protein that inhibits Wnt/b-catenin signaling at plasma membrane and controls specific genes in the nucleus, suggesting that these functions are relevant for intestinal homeostasis.

overall_design: Analysis of DKK-1 location and associated roles in human colon cancer cells and  crypts of small and large bowel.

first: O

last: Aguilera

first: J

last: González-Sancho

first: A

last: Fernandez

first: S

last: Zazo

last: Tapia

first: F

last: Canals

last: Aguilar

first: B

first: C

last: Huidobro

last: Orgaz

first: M

middle: P

last: Freije

last: Jiméne

last: Graña

first: D

last: Pisano

last: Lafarga

last: Fraga

last: Rojo

last: López-Otin

last: Muñoz


title: Regulation of Tlx3 by Pax6 is required for the restricted expression of Chrnα3 in Cerebellar Granule Neuron progenitors during development

status: Public on Jun 30 2016

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Homeobox gene Tlx3 is known to promote glutamatergic differentiation and is expressed in post-mitotic neurons of CNS.  Contrary to this here, we discovered that Tlx3 is expressed in the proliferating progenitors of the external granule layer in the cerebellum, and examined factors that regulate this expression. Using Pax6-/-Sey mouse model and molecular interaction studies we demonstrate Pax6 is a key activator of Tlx3 specifically in cerebellum, and induces its expression starting at embryonic day (E)15. By Postnatal day (PN)7, Tlx3 is expressed in a highly restricted manner in the cerebellar granule neurons of the posterior cerebellar lobes, where it is required for the restricted expression of nicotinic cholinergic receptor-α3 subunit (Chrnα3) and other genes involved in formation of synaptic connections and neuronal migration. These results demonstrate a novel role for Tlx3 and indicate that Pax6-Tlx3 expression and interaction is part of a region specific regulatory network in cerebellum and its deregulation during development could possibly lead to Autistic spectral disorders (ASD)

overall_design: Anterior and posterior lobes of PN7 mouse cerebellum were isolated separately and differentially expressed genes were identified.

first: Thulasi

middle: S

last: Divya

first: Chandramohan

last: Subashini

first: Rajendran

last: Sanalkumar

first: Sivadasan

middle: B

last: Dhanesh

first: Soundararajan

last: Lalitha

first: Surendran

last: Parvathy

first: Vazhanthodi

last: Rasheed

first: Mundackal

first: Jackson

last: James


title: Plasma microRNA array analysis following cardiac ischemia-reperfusion (I/R) injury

status: Public on Nov 13 2015

city: Charlestown

first: Yan

last: Feng

state: MA

address: 149 13th Street, Rm4423

department: Anesthesia, Critical Care and Pain Medicine

institute: MGH

summary: In this study, total 68 cardiac diseases-related miRNAs were detected

overall_design: Two groups: Sham and I/R

first: Wei

last: Chao


title: Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis

status: Public on Oct 21 2014

city: Chung-Li

first: Julia

middle: Tzu-Ya

last: Weng

address: 135 Yuan-Tung Road

department: Department of Computer Science and Engineering

country: Taiwan

institute: Yuan Ze University

summary:
Tuberculosis (TB) is a serious infectious disease, but current methods of detection require improvement in sensitivity, efficiency or specificity.
We conducted a microarray experiment, comparing the gene expression profiles in peripheral blood mononuclear cells among individuals with active TB, latent infection, and healthy conditions in a Taiwanese population. These differentially expressed genes may be potential biomarkers that can differentiate between active TB and latent infection.

overall_design: We isolated total RNA from the PBMC from 7 active TB, 7 latent infection, and 7 healthy individuals and profiled their transcriptional profiles to identify signficantly differentially expressed geens that differ among these three groups

middle: T

first: Shih-Wei

last: Lee

first: Guan-Mau

last: Huang

first: Lawrence

last: Wu


title: Transcriptome profiling reveals a genomewide role of G-proteins

status: Public on Feb 25 2015

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

institute: Guru Gobind Singh Indraprastha University

summary:
Knock out mutants of GPA1 (gpa1-5), GCR1 (gcr1-5) as well as their double mutant (gpa1-5 gcr1-5) were used to obtain genomewide transcriptome profile to deduce genomewide effect of both the subunits alone or in combination.
Heterotrimeric G-protein signaling pathways have been implicated in a variety of biological processes in plants. While an impressive range of important plant responses are known to be mediated by G-protein signaling pathways, the genes that respond through these pathways are not yet known completely. More importantly, the role of G-proteins in mediating plant metabolic regulation, which is well established in animal systems, has not received adequate attention. The availability of loss-of-function G_alpha (GPA1) and G-protein coupled receptor (GCR1) mutant(s) as well as their double mutant in Arabidopsis provided an opportunity for a genome-wide microarray analysis in the current study for the first time.

overall_design: transcriptome profile of mutants gpa1-5, gcr1-5 and double mutant gpa1-5 gcr1-5 were compared to that of the corresponding wild type, ws2. biological duplicates of each sample wa used and hybridized using single color array

first: Navjyoti

last: Chakraborty