title: Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism [RNA-Seq]

first: Jason

last: Moffat

summary: The de novo synthesis of fatty acids has emerged as a therapeutic target for various diseases including cancer. Since cancer cells are intrinsically buffered to combat metabolic stress, it is important to understand how cells may adapt to loss of de novo fatty acid biosynthesis. Here we use pooled genome-wide CRISPR screens to systematically map genetic interactions (GIs) in human HAP1 cells carrying a loss-of-function mutation in FASN, which catalyzes the formation of long-chain fatty acids. FASN mutant cells show a strong dependence on lipid uptake that is reflected by negative GIs with genes involved in the LDL receptor pathway, vesicle trafficking, and protein glycosylation. Further support for these functional relationships is derived from additional GI screens in query cell lines deficient for other genes involved in lipid metabolism, including LDLR, SREBF1, SREBF2, ACACA. Our GI profiles also identify a potential role for the previously uncharacterized gene LUR1/C12orf49 in exogenous lipid uptake regulation through modulation of SREBF2 signalling in response to lipid starvation. Overall, our data highlight the genetic determinants underlying the cellular adaptation associated with loss of de novo fatty acid synthesis and demonstrate the power of systematic GI mapping for uncovering metabolic buffering mechanisms in human cells.

overall_design: RNA-sequencing was performed in human HAP1 WT, C12orf49 knockout and SREBF2 knockout cells that were either control-treated or subjected to 4h of serum deprivation (using three biologically independent examples).

first: Michael

last: Aregger

first: Keith

last: Lawson

first: Maximillian

last: Billmann

last: Costanzo

first: Amy

last: Tong

first: Katherine

last: Chan

first: Mahfuzur

last: Rahman

first: Kevin

last: Brown

first: Catherine

last: Ross

first: Matej

last: Usaj

first: Lucy

last: Nedyalkova

first: Olga

last: Sizova

first: Andrea

last: Habsid

first: Judy

last: Pawling

first: Zhen-Yuan

last: Lin

first: Hala

last: Abdouni

first: Cassandra

last: Wong

first: Alexander

last: Weiss

first: Patricia

last: Mero

first: James

middle: W

last: Dennis

first: Anne-Claude

last: Gingras

first: Chad

last: Myers

first: Brenda

last: Andrews

first: Charles

last: Boone


title: RNA-seq of in vitro produced mouse oocytes derived from XX-, XO- and XY-ESCs

status: Public on Mar 05 2020

city: Fukuoka

first: Nobuhiko

last: Hamazaki

state: Fukuoka

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

department: Department of Developmental Stem Cell Biology

country: Japan

institute: Kyushu University

type: Expression profiling by high throughput sequencing

summary: We analyzed the transcriptome of in vitro oocytes induced from Embryonic Stem cells (ESCs) via Epiblast-like cells(EpiLCs) and PGC-like cells (PGCLCs).

overall_design: Non-Directional RNA-seq for ESCs, d2EpiLCs, d6PGCLCs, agg-3, agg-5 and agg-7. Directional (strand-specific)  RNA-seq for agg-9, agg-11 and agg-13

first: Katsuhiko

last: Hayashi

first: Norio

last: Hamada


title: Mis-expression of Igf2 and H19 work independently on distinct cell types to cause cardiomyopathy in a Beckwtih Wiedemann mouse model

status: Public on Mar 01 2020

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

country: USA

institute: NICHD

summary: Igf2 and H19 are linked, reciprocally imprinted genes that play critical roles in mammalian development.  Igf2 encodes a peptide hormone, Insulin-like Growth Factor 2, that binds to the InsR and Igf1R receptor kinases to regulate cell growth and metabolism through well-established pathways.  H19 encodes a 2.3 kb lncRNA whose biochemical actions are only now being identified.  Here we use a mouse model to investigate cardiomyopathies associated with maternal loss of imprinting at the locus.  Increased circulating levels of IGF2 during fetal development result in activation of pAKT/mTOR signaling in cardiomyocytes to cause cellular hypertrophy and hyperplasia in neonatal hearts. This neonatal hypertrophy is unaffected by H19 RNA levels.  However, loss of H19 does cause fibrosis and progressive cardiac pathology in adult mice.  In hearts, H19 expression is concentrated in endothelial cells associated with blood vessels and capillaries and loss of H19 results in high incidence of trans differentiation of these cells to smooth muscle.  H19 encoded miRNAs 675-3p and -5p are not sufficient to promote normal development. Thus these experiments define a novel role for the H19 lncRNA in regulating cell fate.

overall_design: Total of 4 samples: RNA-Seq from 2 genotypes: wild-type and dICR/dICR. Tissue analyzed is heart from 6 month-old mice.

first: Ki-Sun

last: Park

first: Zu-Xi

last: Yu

first: Danielle

last: Springer

first: Beenish

last: Rahat

first: Karl

last: Pfeifer


title: Chromatin profiling reveals the relationship between EWS/FLI, LSD1, and the enhancer landscape in Ewing sarcoma

status: Public on May 12 2020

city: Columbus

first: Emily

middle: Rose

last: Theisen

state: OH

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Functional characterization of thousands of type 2 diabetes-associated and chromatin-modulating variants under steady state and endoplasmic reticulum stress

status: Public on Feb 21 2020

city: Boston

first: Shubham

last: Khetan

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

summary: We tested >13,000 sequences containing each allele of 6,628 SNPs associated with altered in vivo chromatin accessibility in human islets and/or type 2 diabetes risk (T2D GWAS SNPs) for transcriptional activity in ß cell under steady state and endoplasmic reticulum (ER) stress conditions using the massively parallel reporter assay (MPRA).

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: MPRA in MIN6 treated with Thapsigargin or a solvent DMSO control

first: Michael

middle: L

last: Stitzel


title: Stop codon readthrough of a POU transcription factor regulates steroidogenesis and developmental transitions

status: Public on Aug 01 2020

city: Stockholm

first: Bo

middle: G

last: Lindberg

address: Svante Arrhenius väg 20 C

department: MBW

country: Sweden

institute: Stockholm University

summary: Translational stop codon readthrough generates C-terminally extended protein isoforms. While evidence mounts of readthrough as a global phenomenon, proofs of its functional consequences are scarce. We show that readthrough of the Drosophila POU/Oct transcription factor gene drifter (dfr) occurs at a high rate and in a spatiotemporal manner in vivo, reaching more than 50% in the larval prothoracic gland. Phylogenetic analyses suggested that readthrough of dfr is conserved among Dipterans, with C-terminal extensions harboring intrinsically disordered regions and amino acids streches implied in transcriptional activation. The extended Dfr isoform is required for maintaining normal levels of the growth hormone ecdysone through regulation of its biosynthetic genes, acting in synergy with the transcription factor Molting defective (Mld). A 14-bp deletion that abolished readthrough, caused prolonged larval development and delayed metamorphosis. This study provides a striking example of alternative genetic decoding that feeds into the progression from one life cycle stage to another.

overall_design: Two biological replicates were analyzed for each of 6 conditions (three genotypes; two treatments per genotype)

first: Yunpo

last: Zhao

first: Ylva

last: Engström


title: Contrasting Effects of Western vs. Mediterranean Diets on Monocyte Inflammatory Gene Expression and Social Behavior in a Primate Model

status: Public on Jan 28 2020

city: Seattle

first: Corbin

middle: Scott Clarke

last: Johnson

state: WA

address: 330 Guthrie Hall

department: Department of Psychology

institute: University of Washington

summary: Dietary changes associated with industrialization substantially increase the prevalence of chronic diseases, such as obesity, type II diabetes, and cardiovascular disease, which are major contributors to the public health burden. The high prevalence of these chronic diseases is often attributed to an “evolutionary mismatch,” between human physiology and modern nutritional environments. In support of this idea, Western diets enriched with foods that were scarce throughout human evolutionary history (e.g., simple sugars and saturated fats) promote inflammation and disease relative to diets more akin to hunter-gatherer diets, such as a Mediterranean diet; however, the mechanisms linking dietary mismatch to inflammation and chronic disease are poorly understood. We used a macaque model and whole diet manipulations to evaluate one possible mechanism – inflammatory polarization of monocytes – that potentially leads to this evolutionary mismatch. After consuming a Western- or Mediterranean-like diet for 15 months, monocytes from Western diet consumers exhibited a more proinflammatory phenotype, with 40% of their genes differentially expressed (FDR<0.05). Compared to the Mediterranean diet, the Western diet shifted the co-expression of 445 gene pairs, including small RNAs and transcription factors associated with metabolism and adiposity in humans, and dramatically altered animal behavior. For example, Western-fed individuals were more anxious and less socially integrated compared to the Mediterranean-fed subjects. These behavioral changes mediated some of the effects of diet on gene expression, suggesting an interaction between diet, central nervous system activity, and monocyte gene expression. The results of this study provide new insights into evolutionary mismatch at the molecular level and uncover new pathways through which Western diets generate inflammation and disease.

overall_design: 35 cynomolgus macaques (Macaca fascicularis) were fed experimental diets modeled after human dietary patterns: n = 20 Western diet, n = 15 Mediterranean diet. Experimental diets were formulated to be isocaloric with respect to protein, fat, and carbohydrate macronutrients, and identical in cholesterol content (~ 320mg / 2000 kilocalories (Cals)/day) as described previously by Shively et al. (2019, Obes. Silver Spring Md.). The Western diet was formulated to be similar to that consumed by American women age 40-49 as reported by the US Dept. Agriculture, with protein and fat derived mainly from animal sources. The Western diet was relatively high in saturated fat and sodium, and low in monounsaturated fat and n-3 fatty acids. The Mediterranean diet was formulated to mimic key aspects of the traditional Mediterranean diet, with an n-6:n-3 fatty acid ratio similar to a traditional hunter-gatherer type diet. Protein and fats were derived mainly from plant sources, fish and dairy, and monounsaturated fatty acids were relatively high. Mediterranean diet contained more complex carbohydrates and fiber, and less sodium and refined sugars than Western diet. Key ingredients included English walnut powder and extra-virgin olive oil which were the primary components provided to participants in the PREDIMED study, a landmark dietary intervention study that illustrated the role of the Mediterranean diet on cardiovascular disease prevention (Estruch et al., 2018, N. Engl. J. Med.). A more detailed breakdown of nutritional content can be found in the accompanying publication and in Shively et al. (2019, Obes. Silver Spring Md.). Peripheral blood monocytes were isolated after 15 months on experimental diet and RNA was sequenced using single-end 76-bp reads on an Illumina NextSeq 500 to an average read depth of 34.5 million reads per sample (range 25.9 – 41.6 million reads).

middle: S

first: Carol

middle: A

last: Shively

first: Kristofer

middle: T

last: Michalson

first: Amanda

middle: J

last: Lea

first: Ryne

last: DeBo

first: Timothy

middle: D

last: Howard

first: Gregory

last: Hawkins

first: Susan

middle: E

last: Appt

first: Yongmei

last: Liu

last: McCall

first: David

middle: M

last: Herrington

first: Edward

middle: H

last: Ip

first: Thomas

middle: C

last: Register

first: Noah

last: Snyder-Mackler


title: RNA-seq analysis of  active anthraquinones as anti-biofilm agents of methicillin-resistant Staphylococcus aureus

status: Public on Mar 19 2020

city: shenzhen

first: song

last: zhiman

address: Shenzhen Guangdong

department: college of life sciences and oceanography

country: China

institute: shenzhen university

summary: RNA-seq analysis was used to elucidate the mechanism of 2-Carboxyanthraquinone  and Rhein as anti-biofilm agents

overall_design: Mature MRSA biofilms were treated by 2-Carboxyanthraquinone  and Rhein at the concentration of 100ug/ml, and washed by 1×PBS three times after 8h. Then the biofilm was suspended again to collect the bacteria and the total RNA was extracted using Trizol reagent. There were 9 samples in total with 3 samples in each group. The library construction and sequencing with Illumina nova-seq6000 and data analysis were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China).

first: Zhiman

last: Song


title: NHR-8 regulated P-glycoproteins uncouple xenobiotic stress resistance from longevity in chemosensory C. elegans mutants

status: Public on Feb 04 2020

city: Cologne

first: Martin

last: Denzel

address: Joseph-Stelzmann-Str. 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary: Transcriptomics  analysis of wild type and osm-3(dh441)IV under vehicle and tunicamycin treatment for 6 hours

overall_design: Day 1 wild type and osm-3(dh441)IV C. elegans were treated with either control or 10 ug/ml tunicamycin for 6 hours with 4 biological replicates

first: Bérénice

last: Benayoun

first: Gabriel

last: Guerrero


title: Characterizing cellular heterogeneity and homeostatic gene regulatory networks in the adult mammalian stria vascularis using single cell and single nucleus transcriptional profiling

status: Public on Dec 10 2019

first: Michael

last: Hoa

address: 35 Convent Dr, Rm 1F-226

institute: National Institutes on Deafness and Other Communication Disorders, NIH

summary: Characterzing adult mouse stria vascularis heterogeneity and gene regulatory networks

overall_design:
Examination of mouse P30 Stria Vascularis

Grant information: ZIA DC000088-05


title: Sex differences in behavioral and brainstem transcriptomic neuroadaptations following neonatal opioid exposure in outbred mice

status: Public on Nov 27 2019

first: Camron

last: Bryant

address: 72 East Concord St

department: Pharmacology

institute: Boston University School of Medicine

summary: The Opioid Use Disorder epidemic led to an increase in cases of Nenonatal Opioid Withdrawal Syndrome (NOWS) in infants born to opioid-dependent mothers. Hallmark features include weight loss, irritability, inconsolability, insomnia, and increased pain sensitivity. The neurobiological basis of NOWS is largely unknown. Improved mouse models will facilitate mechanistic and treatment discovery. We treated neonatal outbred Cartworth Farms White (CFW) mice (Swiss Webster) with morphine sulfate (15 mg/kg, s.c.) twice daily on postnatal day (P)1 through P14, the  approximate third trimester-equivalent of human gestation. Weight loss was monitored and behavioral symptoms were measured on P7 and P14 at 16 h post-morphine. Brainstem containing pons and medulla was collected on P14 and processed for transcriptome analysis via mRNA sequencing (RNA-seq). Morphine induced weight loss from P2 to P14 that remained at P21 and P50. Repeated morphine also induced a delayed self-righting latency at P4 and a persistent, female-specific delay at P14. Morphine-treated females also showed an earlier increase in ultrasonic vocalizations (USVs) on P7. Both morphine-treated sexes showed a large increase in USVs on P14. Furthermore, thermal nociception via hot plate and tail withdrawal assays indicated that mice exhibited thermal hyperalgesia on P7 and P14, with females showing greater hyperalgesia (tail withdrawal) on P7. Morphine-treated mice also exhibited anxiety-like behavior at P21 (open field).  Finally, brainstem transcriptome analysis identified a canonical gene set relevant to opioid signaling in males and a distinct gene set in females that was enriched for ribosomal proteins, mitochondrial function and neurodegenerative disorders. Sex-specific transcriptomic neuroadaptations implicate sex-specific treatments.

overall_design: RNA isolation and RNA-seq. RNA was isolated using previously described methods involving Trizol (Qiagen), ethanol precipitation, filtering columns for clean-up (Qiagen), and elution with sterile, double deionized water(Yazdani et al. 2015). Samples were diluted to 50 ng/ul. RNA library preparation (poly-A selection) and RNA-seq was conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. The 12 multiplexed, pooled samples [from six saline (SAL)-treated and six morphine (MOR)-treated mice] were sequenced (100 bp single-end) on a single lane of the two-lane flowcell.  Reads were trimmed for quality using Trimmomatic (Bolger et al. 2014). Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al. 2013). The featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl. Differential gene expression analysis of normalized read counts from Rsubread (Liao et al. 2019) was performed in R using edgeR (Robinson et al. 2010). In the sex-combined analysis, we included both “Sex” and “Dam” as covariates account for variance between sexes and across families. In the female-only and male-only analyses, we included “Dam” as a covariate to account for variance across families.

first: Kristyn

last: Borrelli

first: Qiu

last: Ruan


title: Transcriptome of Drosophila S2 cells stressed upon amino-acid starvation in KRB (Krebs Ringer Bicarbonate)

status: Public on Jan 17 2020

city: Utrecht

first: Wessel

middle: van

last: Leeuwen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The phase separation of the non-membrane bound Sec bodies occurs in Drosophila S2 cells by coalescence of components of the ER exit sites under the stress of amino-acid starvation. Here we provide the comparison of the gene expression profiles of S2 cells grown in full medium (Schneider's) and S2 cells upon of amino-acid starvation in KRB

overall_design: 4 samples are analyzed, which include 2 controls (Schneider's/FED) and 2 upon amino-acid starvation (KRB/STARVATION)

first: W

last: van Leeuwen

first: A

last: Aguilera-Gomez

first: C

last: Rabouille


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods

status: Public on Dec 19 2019

city: Clayton

first: Shanika

last: Amarasinghe

state: VIC

address: 15 Innovation Walk

department: Monash Biomedicine Discovery Institute

country: Australia

institute: Monash Unviersity

summary:
Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods.
We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings.

overall_design: our experiment utilized the 5 human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827. For the single cell designs, the five cell lines were mixed equally and processed by 10X chromium, referred to as sc_10X_5cl in analysis that follows.

first: Luyi

last: Tian

first: Jafar

last: Jabbari

first: Matt

last: Ritchie


title: RNA-seq of Glioblastoma Tumors and GBOs

status: Public on Dec 26 2019

city: Philadelphia

first: Daniel

last: Zhang

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Analysis of glioblastoma tissue and corresponding glioblastoma organoids by RNA sequencing.

overall_design: RNA-sequencing of glioblastoma tumor samples and corresponding glioblastoma organoids

middle: Y

first: Hongjun


title: Smarcad1 mediates microbiota-induced inflammation by coordinationg gene expression in the intestinal epithelium [H3K9me3 ChIP-seq]

status: Public on Feb 05 2020

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: How intestinal epithelial cells interact with the host immune system and the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Specific deletion of Smarcad1 in the intestinal epithelium led to colitis resistance in the dextran sodium sulphate colitis model. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine and colon. Absence of Smarcad1 led to changes in chromatin accessibility and significant changes in histone H3K9me3 but not H3K9me2 over many sites, including many genes that are differentially regulated upon Smarcad1 deletion. Our study demonstrates that an innate immunity response can be coordinated by a chromatin remodelling factor.

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the intestinal epithelium. C57BL/6 background. H3K9me3 ChIP-seq performed in triplicates on whole crypt colon epithelium.

first: Mia

last: Mosavie

first: Juri

last: Kazakevych

first: Marco

last: Vinolo

first: Patrick

last: Varga-Weisz


title: Photoreceptor Otx2 cKO

status: Public on Sep 28 2019

city: NICE

first: PASQUALE

last: PENSIERI

address: PARC VALROSE

department: SCIENCES NATURELLES

country: France

institute: INSTITUT BIOLOGIE VALROSE

summary: Homeobox transcription factor Otx2 is a key actor in retinal development, but in adult stage its function is not yet elucidated. In order to elucidate it we induced Otx2 KO specifically in MATURE PHOTORECEPTORS. Here, we report RNA seq data, that were produced in order to investigate on the effect of Otx2 ablation on its regulatoy network. Post natal day 30 (P30) is the time of KO induction. KO mice were collected 2, 4 and 8 days after  Otx2 ablation.

overall_design: KO was induced with single tamoxifen injection at P30 and mice collected 2, 4 and 8 days after KO. Single eye from each mouse was collected, retina dissected and quickly RNA was extracted, validated for the quality and sent to the RNAseq platform. 3 mice for each condition were used. The other eye was used in parallel to validate Otx2 KO by immunostaining.

first: Thomas

last: Lamonerie

first: Pasquale

last: Pensieri

first: Annabelle

last: Mantilleri


title: Expression data from E14.5 mouse brain regions of Ts1Cje and wild-type mice

status: Public on Oct 18 2019

city: Kyoto

first: Keiichi

last: Ishihara

state: Kyoto

address: 5 Misasagi Nakauchi-cho, Yamashina-ku

department: Department of Pathological Biochemistry

institute: Kyoto Pharmaceutical University

summary: The Ts1Cje mouse model of Down syndrome (DS) has partial triplication of mouse chromosome 16, of which a large portion is homologous to human chromosome 21. The mouse model shows an impaired neurogenesis at E14.5. We analyzed the effect of Ts1Cje trisomic region on global gene expression in the embryonic brain of Ts1Cje mice at E14.5.

overall_design: RNA was extracted from the whole brain for hybridization to arrays from 3 pairs of Ts1Cje and disomic wild-type littermate control.


title: Tet1-mediated Epigenetic Programming Regulates Calcium Homeostasis and Stage-specific CNS Myelination and Regeneration

status: Public on Nov 20 2019

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

type: Methylation profiling by high throughput sequencing

summary: DNA hydroxymethylation by epigenetic modifiers TET dioxygenases is critical for gene transcription in various biological processes, however, its role in oligodendrocyte maturation and functions remain elusive. Here, we found that mice lacking Tet1 in the oligodendrocyte lineage exhibited hypomyelination in the CNS in the juvenile stage, leading to defects in action potential propagation, motor coordination, anxiety-like behavior and spatial memory capacities. Although the myelin deficiency recovered in adulthood, remyelination after cuprizone-induced demyelination was compromised in Tet1cKO mice. By integrating transcriptome and DNA methylation profiles, we identified a cohort of genes that were differentially regulated by Tet1 and hyperhydroxymethylation, including the genes associated with Ca2+ transportation. Tet1-deficient OPCs exhibited a reduction in [Ca2+] oscillations, while the agonists of calcium internal stores rescued the differentiation defect of Tet1-deficient OPCs. Thus, our results suggest that stage-specific Tet1-mediated epigenetic programming in oligodendrocytes maintain Ca2+ homeostasis for differentiation and regulate neuronal activities and myelin repair.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Control and Tet1 mutant samples.

first: Ming

first: Jian

last: Wang

first: Kaixiang

first: Guozhen

first: Xianghui

last: Zhao


title: Alcohol-abuse drug disulfiram targets pediatric glioma via MLL degradation

status: Public on Dec 20 2019

city: London

first: David

last: Michod

address: Gower St, Bloomsbury

institute: UCL

summary: RNA-seq analysis was performed to compare gene expression of glioma cells with MLL1 and MLL2 knockdown, and control glioma cells.

overall_design:
SF188 and GPC16 cells were transfected with MLL1 and MLL2 or the same amount of control siRNA. After 72 h mRNA was isolated and analyzed.
MLL1 refers to KMT2A, MLL2 to KMT2B

first: Stefanie

last: Meier


title: Single cell RNAseq gut ILCs

status: Public on Nov 22 2019

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

institute: WEHI

summary: We have generated 10x scRNA-seq of ILCs purified from small intestine and colon of WT mice

overall_design: Sorted IL7ra+ ILC from 8 week-old mice were analysed in RNA-seq. Each replicate is a pool of 8 mice.

first: Cyril

last: Seillet

middle: F


title: Widespread Long-range Cis-Regulatory Elements in the Maize Genome

status: Public on Sep 19 2019

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Genetic mapping studies on crops suggest that agronomic traits can be controlled by loci within the gene-distal intergenic space. Despite the biological importance and the potential agronomic utility of these intergenic loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic, and functional molecular evidence supporting the widespread existence of gene-distal (hereafter, distal) loci which act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic chromatin features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate eQTL-gene interactions. Additionally, putative CREs display elevated transcriptional enhancer activities, as measured by STARR-seq. These results provide functional support for the widespread existence of CREs which act over large genomic distances to modulate gene expression.

overall_design: One MethylC-seq, six RNA-seq, 30 ChIP-seq, 37 DAP-seq, six ATAC-seq, one Hi-C, two HiChIP, and three STARR-seq samples of maize

first: Zhang

last: Xiaoyu


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium

first: Felix

last: Krueger

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

overall_design: Refer to individual Series


title: Peripheral blood whole transcriptome in patients with acute myocardial infarction and at follow-up

status: Public on Nov 24 2019

city: Leuven

first: Maarten

last: Vanhaverbeke

address: Herestraat 49 box 911

department: Cardiovascular Sciences

country: Belgium

institute: KU Leuven

summary: There is an unmet need to develop new strategies to improve risk stratification in patients with myocardial infarction and to identify new targets for intervention. The aim of this study was to establish the unbiased peripheral blood whole transcriptome response in myocardial infarction, and to correlate it with clinical characteristics and outcome. RNA expression was determined in the acute phase of MI and at follow-up, and related to clinical phenotype and outcome.

overall_design: We performed peripheral blood (PAXgene) RNA profiling in 192 samples: acute MI (n=65), 30 days post-MI (n=64), 1 year post-MI (n=37), patients with stable CAD (n=22) and technical replicates (n=4). The unbiased RNA profile was determined in acute MI, and we determined to potential of selected transcript to improve prediction of clinical outcome (eg. left ventricular dysfunction).

middle: R

last: Sinnaeve


title: A gene expression-based model to predict metabolic response after two courses of ABVD in patients with classical Hodgkin Lymphoma

status: Public on Sep 26 2019

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from diagnostic tumor samples of 106 patients affected by Hodgkin Lymphoma was analyzed on the nCounter system using the PanCancer Immune Profiling Panel.

overall_design: Gene expression profile were linked to interim PET response in Hodgkin Lymphoma.

first: Alessia

last: Ciarrocchi

first: Stefano

last: Luminari


title: The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis

status: Public on Oct 21 2019

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

summary: we present an atlas of global gene expression as well as the evolutionary divergence covering embryo, endosperm and seed coat development in wheats and their diploid ancestors, providing insights into the evolution of gene expression in embryogenesis and grain development of wheat species.

sample_organism:
Triticum aestivum
Triticum monococcum
Triticum turgidum
Aegilops speltoides
Aegilops tauschii

overall_design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryo development (including the two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo), two stages of endosperm (transition stage endosperm and leaf late stage endosperm), and one pericarp stage (leaf early stage pericarp) across five wheat and ancestral grass species (AC -hexaploid, SF-tetraploid, DV-A genome diploid, SP-B genome diploid and TA-D genome diploid), two replicates for each stage.

first: Daoquan

last: Xiang

first: Raju

last: Datla

first: Youlian

last: Pan


title: Spen regulates X chromosome inactivation

status: Public on Dec 08 2019

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure


title: Genome-wide maps of chromatin state in HeLa cells.

status: Public on Aug 22 2019

city: Beijing

first: Jie

last: Gao

address: No. 10, Xitoutiao, You An Men, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: School of Basic Medical Sciences, Capital Medical University

summary: We report a series of ChIP-Seq results in HeLa cells. Briefly, we performed ChIP-Seq experiments with antibodies specific for Snail, MTA1,  and PRMT5 in HeLa cells. We found that Snail, MTA1,  and PRMT5 had similar binding motifs. This study gave us a new understanding of the role of Snail in chromatin status and gene transcription.

overall_design: Examination of Snail, MTA1,  and PRMT5  target genes in HeLa cell line.

first: Ruiqiong

first: Yan

last: Wang


title: Gene expression of human corneal epithelial cells grown with irradiated human fibroblasts or irradiated mouse 3T3 feeder layer .

status: Public on Dec 12 2019

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

institute: CUO-Recherche

summary: human corneal epithelial cells were isolated from healthy human donor eyes. Cells were cultured with irradiated 3T3 (i3T3) murine fibroblast feeder cells, irradiated human corneal fibroblasts (iHFL) or without feeder layer

overall_design: Three human corneal epithelial cells populations (primary cells) were cultured in three conditions (without feeder layer, +iHFL or +i3T3) and analyzed by gene profiling.

first: Sylvain

last: Guérin

first: Lucie

last: Germain

first: Solange

last: Landreville

first: Francis

last: Bisson

first: Louis-Philippe

first: Sergio

last: Ghio


title: TooManyCells identifies and visualizes relationships of single-cell clades

status: Public on Jan 15 2020

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

summary:
Purpose: To characterize heterogeneity of GSI-responsive and -resistant T-ALL cells
Method: We generated GSI-resistant T-ALL DND41 cells and profiled their transcriptome using single-cell RNA sequencing.
Result: We report here the presence of resistant-like subpopulation in drug naïve DND41 T-ALL cells.
Conclusion: While other popular scRNA-seq clustering algorithms failed, TooManyCells, a suite of clustering and visualization algorithm developed in our lab, could identify rare resistant-like  DND41 T-ALL cells.

overall_design: Single-cell RNA sequencing was performed on cells acquiring resistance to a gamma secretase inhibitor (GSI) after long-term ascending-dose or sustained high-dose treatments of Notch-mutated T-cell acute lymphoblastic leukemia (T-ALL) DND41 cells.

first: Yeqiao

last: Zhou

first: Jelena

last: Petrovic

first: Gregory

middle: W

last: Schwartz

middle: B


title: Analysis of transcriptomic responses of genotoxic stress in human HepaRG hepatocarcinoma cells

status: Public on Apr 16 2020

city: Berlin

first: Katrin

last: Kreuzer

address: Max-Dohrn-Str. 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Purpose: Toxicogenomics analyses may provide information about DNA-damaging properties of test compounds but are not routinely used for identification of a genotoxic potential. In this study, metabolically active human HepaRG hepatocarcinoma cells were exposed to six food-relevant genotoxic carcinogens.
Method: Transcriptomic responses were analyzed using RNA sequencing technology

overall_design: Examination with a total of 21 samples, thereof 6 control samples and 15 samples in 5 treatment groups in triplicates

first: Linda

last: Böhmert

first: Albert

last: Braeuning


title: Comparative analysis of gene expression in tomato roots during mild and severe potato spindle tuber viroid infection. [roots RNA-seq]

status: Public on Dec 31 2019

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

overall_design:
Mild (PSTVd-M) and severe (PSTVd-S23) strains were used to inoculate Solanum lycopersicum cv Rutgers plants. Root samples were collected  at 17 days post inoculation (dpi), i.e. at early stage of symptoms. Three independent biological replicates of PSTVd-M, PSTVd-S23 and pUC9 were analised. Totally 18 samples of RNA were analysed.

Please note that the *Gene_counts* file was updated on Sep 22, 2021.

first: Anna

last: Góra-Sochacka

first: Maciej

last: Lirski


title: Perturbations of PI3K/AKT, RAS/ERK, WNT/B-catenin networks in leukocytes are linked to ASD genetics and fetal origins of autism

status: Public on Jul 25 2019

city: La Jolla

first: Vahid

last: Gazestani

state: California

address: 8110 La Jolla Shores Drive, Suite 201

institute: UCSD

summary: Hundreds of genes are implicated in autism spectrum disorder (ASD) but the mechanisms through which they contribute to ASD pathophysiology remain elusive. Here, we analyzed leukocyte transcriptomics from 1-4 year-old male toddlers with ASD or typical development from the general population. We discovered a perturbed gene network that includes genes highly expressed during fetal brain development and which is dysregulated in hiPSC-derived neuron models of ASD. High-confidence ASD risk genes emerge as upstream regulators of the network, and many risk genes may impact the network by modulating RAS/ERK, PI3K/AKT, and WNT/-catenin signaling pathways. We found that the degree of dysregulation in this network correlated with the severity of ASD symptoms in the toddlers. These results demonstrate how the heterogeneous genetics of ASD may dysregulate a core network to influence brain development at prenatal and very early postnatal ages and, thereby, the severity of later ASD symptoms.

overall_design:
Leukocyte gene expression levels were analysed in autistic and typically developing infants and toddlers

Diagnosis key:
ASD: autism spectrum disorder
TD: typically developing (control)
PDDNOS: pervasive developmental disorder not otherwise specified
PreemieNoDelay: Preemie No Delay (the individual was a preemie but didn't show any mental delay)
LD: language delay
AutFeat: Autism features (individual shows some signs of autism, but doesn't meet full criteria)

ADOS_CoSo: the score of each individual for ADOS communication and social deficit, a metric used for the diagnosis of individuals with autism.  The higher the score, the more severe the case.

These data have been included in a SuperSeries with GSE42133 because the data were normalized together and are linked to that data set.

first: Tiziano

last: Pramparo

first: Eric

last: Courchesne

first: Nathan

last: Lewis


title: HPV8 mediated alterations of cellular gene expression

status: Public on Jul 04 2019

city: Cologne

first: Matthias

last: Kirschberg

state: NRW

address: Fürst-Pückler-Str. 56

department: Institute of Virology

institute: University of Cologne

summary:
We expressed either only the E7 oncoprotein or the complete early genome region (CER) of the human papillomavirus type 8 in primary human adult skin keratinocytes.
Cells were retrovirally transduced, selected, and cellular mRNA was extracted after expansion of the transgene positive keratinocytes.

overall_design: Changes in gene expression were measured using the Human Genome cDNA U133A Affymetrix Arrays in biological triplicates in cells containing either the empty vector control (pLXSN), pLXSN-HPV8-E7 or pLXSN-HPV8-CER.

first: Sandra

last: Heuser

first: Adnan

last: Syed

first: Gertrud

last: Steger

first: Martin

last: Hufbauer

first: Baki

last: Akgül


title: Analysis of gene expression in human adipose tissue-derived multipotent mesenchymal stromal cells lacking GARP/LRRC32

status: Public on Jun 05 2019

city: Granada

first: Per

last: Anderson

state: Granada

address: Avenida de las Fuerzas Armadas, Nº 2

department: Servicio de Análisis Clínicos e Inmunología

country: Spain

institute: Hospital Universitario Virgen de las Nieves

summary: Multipotent mesenchymal stromal cells (MSCs) have been shown to promote tissue repair and inhibit inflammatory/autoimmune responses in preclinical and human clinical trials A major problem for MSC-based therapies is the need to expand MSCs in vitro due to the low frequency of MSCs in tissues and the large numbers of cells needed/patient (1-10 x 10^6 cells/kg). The expansion of MSCs is associated with several problems including loss of homing capacity, onset of cellular senescence, decrease in differentiation capacityand susceptibility to genomic instability and malignant transformation, limiting the utility of MSCs as a cell-based therapy.   We have recently reported that murine adipose tissue-derived MSCs (mASCs) and human ASCs (hASCs) express glycoprotein A repetitions predominant (GARP)/leucine-rich repeat-containing 32 (LRRC32). GARP binds LAP/TGF-β1 to the surface of mASCs and hASCs, regulating their secretion and activation of TGF-β1 and promoting their immunomodulatory capacity. Interestingly, silencing of GARP in ASCs significantly decreased their proliferative capacity but the mechanisms remain unknown. As the proliferative capacity of MSCs is fundamental for their success in therapy, we have aimed at understanding how GARP modulates the expansion of MSC.

overall_design: Human adipose-tissue derived multipotent mesenchymal stromal cells (hASCs) obtained from three unrelated healthy donors were transduced with two distinct LVs, each encoding for a distinct human GARP-specific shRNA (MISSION® shRNA plasmid DNAs, RefSeq: SHCLND-NM_005512; Sigma-Aldrich), referred to as LV#18 (TRCN0000005218) and LV#19 (TRCN0000005219). A MISSION® pLKO.1-puro non-mammalian shRNA control plasmid (Sigma-Aldrich, MO, USA) was used as control (LV-CTRL). Non-transduced (NT) hASCs were also used as control.

first: Pedro

last: Carmona-Saez


title: Transcriptomic Profiling of Primary Osteoblast from a panel of Collaborative Cross mice

status: Public on Jul 11 2019

city: Charlottesville

first: Charles

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Genome-wide association studies (GWASs) for bone mineral density (BMD), one of the most significant predictors of osteoporotic fracture, have identified over 1100 independent associations; however, few of the causal genes have been identified. Recently, the “omnigenic” model of the genetic architecture of complex traits proposed two general categories of causal genes, core and peripheral. Core genes play a direct role in regulating traits; thus, their identification is key to revealing critical regulators and potential therapeutic targets. Here, we identified a co-expression module enriched for genes exhibiting properties consistent with core genes for BMD by analyzing GWAS data through the lens of a cell-type and timepoint-specific gene co-expression network for mineralizing osteoblasts. We identified multiple co-expression modules enriched for genes implicated by BMD GWAS and prioritized modules based on their enrichment for genes with core-like properties. Only one module, the purple module, was enriched for genes correlated with in vitro mineralization (r = 0.49; FDR = 0.012), with known roles in skeletal development (P <2.2 x 10-16), that when perturbed produce a bone phenotype in mice (OR = 4.1; P = 2.14 x 10-9), and are monogenic bone disease genes in humans (OR=21.3; P=6.94 x 10-9). Furthermore, the purple module contained genes from two distinct transcriptional profiles with regards to osteoblast differentiation, one of which, termed the late differentiation cluster (LDC), was more highly enriched for genes with core-like properties. Within the LDC, we found that the most highly connected genes were more likely to overlap a BMD GWAS association and associations that contained LDC genes overlapped enhancers and promoters in osteoblasts. Finally, we identified four LDC genes (B4GALNT3, CADM1, DOCK9, and GPR133) with colocalizing expression quantitative trait loci (eQTL) and altered BMD in mouse knockouts. Our network-based approach identified a “core” module for BMD and has provided a resource for expanding our understanding of the genetics of bone mass.

overall_design: 42 strains were sequenced with some replicates within strain, and sample 129 was sequenced twice, as a technical control.

first: Olivia

middle: L

last: Sabik


title: Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes

status: Public on Sep 30 2019

city: Montpellier

first: Dominique

last: Helmlinger

address: 1919 route de Mende

department: CRBM

institute: CNRS

summary: Transcription initiation involves the coordinated activities of large multimeric complexes that are organized into functional modules. Little is known about the mechanisms and pathways that govern their assembly from individual components. We report here several principles governing the assembly of the highly conserved SAGA and NuA4 co-activator complexes. Using fission yeast, which contain two functionally non-redundant paralogs of the shared Tra1 subunit, we demonstrate that Tra1 contributes to scaffolding the entire NuA4 complex. In contrast, within SAGA, Tra1 specifically promotes the incorporation of the de-ubiquitination module (DUB), defining an ordered assembly pathway. Biochemical and functional analyses elucidated the mechanism by which Tra1 assemble differentially into SAGA or NuA4 and identified a small, conserved region of Spt20 that is both necessary and sufficient to anchor Tra1 within SAGA. Finally, we establish that Hsp90 and its cochaperone TTT are required for Tra1 de novo incorporation into both SAGA and NuA4, indicating that Tra1, a pseudokinase of the PIKK family, shares a dedicated chaperone machinery with its cognate kinases. Overall, our work brings mechanistic insights into the de novo assembly of transcriptional complexes through ordered pathways and reveals the contribution of dedicated chaperones to this process.

overall_design: mRNA profiles from S. pombe strains of various genotypes were generated by deep sequencing, in triplicate, in one lane of an Illumina HiSeq 4000, with 1x 50bp single reads.

first: Alberto

last: Elias-Villalobos

first: Dom


title: Expression data from Microarray experiment in muscle and liver tissues

status: Public on Jun 03 2019

city: Barcelona

first: Emilio

last: Marmol

state: Barcelona

address: CSIC IRTA UAB UB Edifici CRAG., Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallès)

department: Animal Genetics

institute: Center for Research in Agrigenomics (CRAG)

summary: In the current work we have compared the transcriptomic and eQTL profiles of the porcine skeletal muscle and liver by using a data set of 103 Duroc pigs genotyped with the Illumina SNP60 BeadChip and with available microarray measurements of gene expression for both tissues.

overall_design: Gluteus medius and liver samples were collected from 103 Duroc pigs (Lipgen population) after slaughtering and immediately frozen at -80ºC in liquid nitrogen. Total RNA was extracted from both GM and liver samples  and mRNA expression profiles were characterized by hybridization to the GeneChip Porcine arrays

last: Mármol-Sánchez

first: Rayner

last: Gonzalez-Prendes


title: Transcriptional characterization of the myocardial infarct border zone

status: Public on Jul 22 2019

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

summary: Expression analysis of cardiomyocytes in the border and remote myocarium

overall_design: RNA-seq on infarcted mouse tissue

first: Marie

last: Günthel

first: Karel

last: van Duijvenboden


title: Transcriptional analysis of nitrite oxidizing Nitrospira growing in a continuous stirred tank reactor

status: Public on Jul 03 2019

city: Nijmegen

first: Aniela

last: Mundinger

address: Heyendaalseweg 135

institute: Radboud University

summary: Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.

overall_design: N. moscoviensis cells were grown in a bioreactor on nitrite. To analyse the stability of culturing conditions biomass samples were taken at three time points (day 112, 120, 127) and analysed by RNA Seq.

first: Christopher

last: Lawson

first: Hanna

last: Koch

first: Mike

middle: S

last: Jetten

first: Sebastian

last: Lücker


title: Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species

status: Public on Apr 09 2019

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Tumor-infiltrating myeloid cells (TIMs) comprise monocytes, macrophages, dendritic cells and neutrophils, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which may promote or limit tumor outgrowth, but remain poorly understood. Here, we used single-cell RNA sequencing to map TIMs in non-small cell lung cancer patients. We uncovered 25 TIM states, most of which were reproducibly found across patients. To facilitate translational research of these populations, we also profiled TIMs in mice. In comparing TIMs across species, we identified a near-complete congruence of population structures among dendritic cells and monocytes; conserved neutrophil subsets; and species differences among macrophages. By contrast, myeloid cell population structures in patients’ blood showed limited overlap with those of TIMs. This study determines the lung TIM landscape and sets the stage for future investigations into the potential of TIMs as immunotherapy targets.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Single cell RNA sequencing (scRNAseq) of RBC-depleted cells from non-small cell lung tumor and from blood of 7 patients. ScRNAseq of CD45-positive cells from lungs of 2 healthy mice and 2 lung tumor-bearing mice.

Human raw data are not available for this Series due to patient privacy concerns.

first: Camilla

last: Engblom

first: Christina

last: Pfirschke

first: Virginia

last: Savova

first: David

last: Zemmour

first: Hatice

last: Saatcioglu

first: Indira

last: Krishnan

first: Giorgia

last: Maroni

first: Claire

middle: V

last: Meyerovitz

first: Clara

last: Kerwin

first: Sun

last: Choi

first: William

middle: G

last: Richards

first: Assunta

last: De Rienzo

first: Daniel

last: Tenen

first: Raphael

last: Bueno

first: Elena

last: Levantini

first: Mikael

last: Pittet

first: Allon

last: Klein


title: Renal ischemia reperfusion in conditional HDAC2 knockout mice

status: Public on May 16 2019

city: Philadelphia

first: Wayne

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Data set contains 12 samples, 2 genetypes (floxed-HDAC2/ERT2cre) and (WT/ERT2cre), and 2 treatment conditions (no ischemia, 4 hours after 28 min warm ischemia), with three samples each.

overall_design: Six floxed-HDAC2/ERT2cre (HDAC2-KO) and six ERT2cre (8-12 weeks old, all female) were tamoxifen administration (100 mg/kg IP daily for 5 days, Sigma-Aldrich) with a 7-day recovery period after last administration before experimentation to achieve conditional HDAC2 deletion in the HDAC2-KO mice. For warm ischemia reperfusion injury (IRI),  HDAC2-KO and WT were anesthetized with pre-warmed pentobarbital sodium (65 mg/kg IP). Immediately after loss of a righting reflex, they were placed on a heated surgical pad (37 °C) in a temperature-controlled operative apparatus.  Core body temperature was continuously measured and maintained at 37.0 +/- 0.5 °C. Using an operating microscope, an abdominal midline incision was made, and the left renal pedicle exposed and clamped for 28 min with a microvascular clip (Roboz Surgical Instrument Company). After the clamp was released, the right kidney was removed and the abdomen closed. Animals were injected subcutaneously with 100 ml/kg of warm saline after the operation to assist in maintenance of hydration, and kept in an incubator (37 °C) from the time of anesthesia until completely awake.RNA was isolated using RNeasy kits (QIAGEN). Total RNA was assessed by UV absorbance and all had 260/280 nm ratios above 1.7.  Additionally, samples were run on the Agilent RNA 6000 Nano chip and all had RINs in the 8.0 range. Microarray experiments were performed using whole-mouse-genome oligoarrays (GeneChip™ Mouse Gene 2.0 ST Array), and array data were analyzed using Transcriptome Analysis Console 4.0 software (ThermoFisher Scientific). Array data were subjected to robust multiarray average normalization. To assess differential gene expression, fold changes of up- and downregulated genes were calculated, and significance assessed via one-way ANOVA. Data with a false discovery rate <0.1 and >1.5-fold differential expression were included in the analysis.

first: Mattew

last: Levine

first: Ulf

last: Beier


title: Single-cell RNA sequencing of zebrafish pancreatic cells

status: Public on Apr 05 2019

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: The pancreatic beta-cells regulate blood glucose levels by secreting the hormone insulin in response to increasing glucose levels. Recent work has identified molecular and functional heterogeneity among the beta-cell community. To ontain an unbiased picture into the molecular heterogeneity present in zebrafish pancreatic cells, we performed droplet based next-generation sequencing of individual pancreatic cells. Using unsupervised clustering, we could identify all the major cell types present in the pancreas. Moreover, we could define sub-populations within the major cell-types, demonstrating the presence of molecular heterogeneity within nominally homogenous cell-populations.

overall_design: We used 10x Genomics to profile pancreatic cells from zebrafish. Pancreatic islets from six animals were dissociated and single-cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired-end mode (R1: 26 cycles; I1: 8 cycles; R2: 57 cycles), thus generating ~45 mio fragments. The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software (v2.1.0) provided by 10X Genomics with the option ‘--expect-cells’ set to 5000 (all other options were used as per default). To build the reference for Cell Ranger, zebrafish genome (GRCz10) as well as gene annotation (Ensembl 87) were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger (options: ‘--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lincRNA –attribute=gene_biotype:antisense’). Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference.

middle: P

first: Nikolay

last: Ninov


title: 3'GAmES: Systematic refinement of gene termini by mRNA 3' end sequencing

status: Public on Mar 11 2020

city: Vienna

first: Stefan

middle: Ludwig

last: Ameres

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary: Motivation: Alternative cleavage and polyadenylation generates mRNA 3´ isoforms in a cell type- and tissue-specific manner. Due to finite available RNA sequencing data of organisms with vast cell type complexity, currently available gene annotation resources are incomplete, which poses significant challenges to the comprehensive interpretation and quantification of transcriptomes.  Results: We developed 3'GAmES, a stand-alone analysis pipeline to identify and annotate novel (cell-type-specific) mRNA 3´ isoforms from 3' mRNA sequencing datasets. When applied to mouse embryonic stem cells or Zebrafish embryos, 3'GAmES expands currently available mRNA 3' annotations by 47% and 57%, respectively; and the resulting annotations significantly improve comprehensive gene-tag counting by cost-effective 3' mRNA sequencing to more accurately mirror whole-transcriptome RNAseq measurements. As a stand-alone analysis tool, 3'GAmES systematically augments cell type-specific transcript annotations and increases the robustness of quantitative gene expression profiling by 3' mRNA sequencing.

overall_design: 3' end sequencing data from zebrafish 1dpf embryo

first: Pooja

last: Bhat


title: RNA-seq profiling of the human neutrophil genome during PMA- and E. coli encounter-induced activation

status: Public on Mar 14 2019

first: Matthew

last: Denholtz

address: 9500 Gilman Drive, NSB 5108

summary: Human neutrophil genome during PMA- and E. coli encounter-induced activation

overall_design: RNA-Seq

first: M

first: C

last: Murre


title: Echinacea purpurea elicits anti-viral response in THP-1 monocytes through activation of interferon, MAPK and NF-κB signaling pathways and DNA hypermethylation of repeat elements

status: Public on Mar 31 2019

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

institute: University of Antwerp

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Andy

last: Suter

first: Guy

last: Van Camp

first: Claudina

last: Perez Novo

first: Wim

last: Vanden Berghe


title: Gene expression profiles of THP1 monocyte cells following Echinaforce treatment

summary: Until today, natural Echinacea purpurea extracts are widely used to prevent and treat respiratory trac infections. Although its immunomodulatory effects have already been demonstrated by several studies, the molecular mechanisms involved are not yet completely understood. In this study, we applied a systems biology approach by integrating transcriptome, kinome and methylome profiles of THP-1 monocyte cells treated with Echinaforce®, a commercial standardized ethanolic tincture of Echinacea purpurea. The latter induced the expression of various genes linked to the anti-viral interferon pathway, NF-κB signaling and chemotaxis. In addition, kinase activity profiling showed that Echinaforce® increased  JAK1 kinase activity, which is crucial in the activation of the JAK-STAT pathway to induce interferon-stimulated genes and MAPK kinase activity. Furthermore, gene expression changes following Echinaforce® treatment occurred largely independent from DNA methylation changes. Of special note, Echinaforce® induced global DNA hypermethylation in gene bodies, intergenic, and CpG-poor repeat regions, which could be part of an evolutionary conserved anti-viral response to suppress viral integration and/or replication. Altogether, we demonstrate that Echinaforce® treatment promotes an anti-viral response in THP-1 cells through activation of interferon, MAPK and NF-κB signaling pathways and DNA hypermethylation of repeat elements.

overall_design: Gene expression profiles from THP1 cell lines treated with Echinaforce or ethanol (control) were measured using the Illumina HumanHT-12 v4.0 expression beadchip. Six biological replicates of each treatment condition were measured.


title: Next Generation Sequencing of control (Untreated), PAN injured and Adriamycin injured human podocytes

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President St.

department: Medicine/Nephrology

institute: Medical University of South Carolina

summary:
Purpose: Next-generation sequencing (NGS) was used to identify cellular pathways and genes through systems-based analysis. The goals of this study are to identify NGS-derived transcriptome profiling (RNA-seq) in control (untreated) and Injured (PAN and Adriamycin) podocyte. These high throughput data were further validated through qRT–PCR methods to confirm the cellular pathways and genes affected due to the podocyte injury.

Methods: Human podocytes were differentiated for 14 days by thermoswitching from 33⁰C to 37⁰C and removal of growth factors, insulin-transferrin-selenium from the medium.  These podocytes were incubated 4hour in serum free RPMI medium and injury was induced by using PAN (100μg/ml) and Adriamycin (0.25μg/ml) treatment for 48 hours.Further, podocytes were processed for RNA isolation and submitted to Medical University of South Carolina Sequencing Core facility for RNA-Seq. All the experiments were performed in triplicates.

Conclusions: Our study is first to describe the detailed analysis of PAN and Adriamycin induced podocyte transcriptomes using the RNA-seq technology. A comparative analysis of the differential expression profile was obtained between control vs PAN injured podocytes, and control vs Adriamycin injured podocytes. Complex genetic network and genes effected due to the injury will provide a platform to define biological pathways participate during podocytes injury process.

overall_design:
Human podocytes mRNA profiles in control (untreated) and PAN/Adriamycin injured podocytes were generated by deep sequencing, in triplicate, using Illumina.

contributor: MUSC Sequencing Core Facility

first: Ehtesham

last: Arif


title: Expression profiling of Human Muscle-Derived RNAs within the study Lifelong Football Training: effects on autophagy and healthy longevity promotion

status: Public on Mar 12 2019

city: Naples

first: Annamaria

last: mancini

address: Via Medina, 40

department: DISMEB

institute: Università Parthenope

summary:
Aging is a physiological process characterized by a progressive decline of biological functions and an increase in destructive processes in cells and organs.   Physical activity and exercise positively affects the expression of skeletal muscle markers involved in longevity pathways. Recently, a new mechanism, autophagy, was introduced to the adaptations induced by acute and chronic exercise as responsible of positive metabolic modification and health-longevity promotion. However, the molecular mechanisms regulating autophagy in response to physical activity and exercise are sparsely described. We investigated the long-term adaptations resulting from lifelong recreational football training on the expression of skeletal muscle markers involved in autophagy signaling. We demonstrated that lifelong football training increased the expression of messengers: RAD23A, HSPB6, RAB1B, TRAP1, SIRT2 and HSBPB1, involved in the auto-lysosomal and proteasome-mediated protein degradation machinery; of RPL1, RPL4, RPL36, MRLP37, involved in cellular growth and differentiation processes; of the Bcl-2, HSP70, HSP90, PSMD13 and of the ATG5-ATG12 protein complex, involved in proteasome promotion and autophagy processes in muscle samples from lifelong trained subjects compared to age-matched untrained controls.  In conclusion, our results indicated that lifelong football training positively influence exercise-induced autophagy processes and protein quality control in skeletal muscle, thus promoting healthy aging.
The aim of the present research was to investigate, through a differential transcriptomic approach, the effects of lifelong recreational football training on the expression of key markers involved in the autophagy response for the maintenance of protein quality control, related to healthy longevity promotion, in skeletal muscle from VPG compared to elderly untrained control subjects.

overall_design: Total RNA was extracted from the muscle biopsies of veteran football players (VPG) and of healthy age-matched untrained controls (CG). For strong, unbiased results, pooled RNA libraries were produced by evenly pooling six RNA samples, which resulted in three pooled CGs (named CG1, CG2 and CG3) and three pooled VPG libraries (named VPG1, VPG2 and VPG3). The pooled RNA samples underwent microarray assay to determine gene expression profile. In this study, we carried out profiling with GeneChip® Human Transcriptome Array 2.0 (HTA 2.0, Affymetrix, Santa Clara).

last: Mancini

first: Daniela

last: Vitucci

first: Morten

last: Bredsgaard Randers

first: Jakob

last: Schmidte

first: Marie

last: Hagman

first: Thomas

last: Rostgaard Andersend

first: Esther

last: Imperlini

first: Annalisa

last: Mandola

first: Stefania

last: Orrù

first: Peter

last: Krustrup

first: Pasqualina

last: Buono


title: HiC profiling of the human neutrophil genome during PMA- and E. coli encounter-induced activation

first: Matthew

last: Denholtz

overall_design: Hi-C

first: M

first: C

last: Murre


title: Human neutrophil genome during PMA- and E. coli encounter-induced activation


title: ChIP-seq profiling of the human neutrophil genome during PMA- and E. coli encounter-induced activation

overall_design: ChiP-Seq


title: Genome wide map of DMC1 in testis of Stag3-/-, Rec8-/- and Stag3-/-Rec8-/- mice.

status: Public on Mar 07 2019

city: Bar Harbor

first: Mary Ann

last: Handel

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: During mouse meiosis, DNA double-strand breaks (DSBs) are initiated by SPO11 at recombination hotspots (HSs), activated by PRDM9. Although activated HSs are marked by H3K4me3 and H3K36me3 histone modifications at open chromatin, most of the DSB-initiating and repair proteins are associated with the chromosome axis. This study addresses the mechanistic importance of the axis-associated cohesin proteins in DSB formation. We demonstrate that interactions between PRDM9 and the meiotic axis proteins STAG3 and REC8 are essential for efficient DSB formation. The absence of STAG3 or REC8 leads to inefficient meiotic DSB formation at HSs. STAG3 is critical for DSB formation, even at PRDM9-independent DSB-sites. Also, STAG3 and REC8 facilitate recruitment of the DSB-promoting proteins HORMAD1, IHO1 and MEI4 required for SPO11 activity. Together, these results support an evolutionarily conserved model in which axis-associated cohesin complexes recruit recombination-initiating proteins to DSB sites to promote meiotic recombination initiation.

overall_design:
Detection of meiotic double strand breaks sites in spermatocytes of Stag3-/-, Rec8-/- and Stag3-/-Rec8-/- mice and comparison with wild-type control

This series includes the re-analysis of GSM1273023 from GSE52628. The methods and processed data files for this re-analyzed sample are available at the foot of this record.

first: T

last: Bhattacharyya

first: A

last: Fine

last: Walker

first: Natalie

last: Power

middle: A


title: Genome-wide expression profiling of Uhrf1hepKO mouse livers at baseline and following PHx

status: Public on May 31 2019

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to investigate the mechanism behind the enhanced liver regenerative response observed in Uhrf1hepKO mice. Livers was collected at baseline and at 24hrs, 30hrs, 40hrs, 48hrs, 96hrs, 7days and 4 weeks following 2/3 partial hepatectomy surgery (PHx). These timepoints correspond to key cell cycle events that occur following PHx as established in literature.

overall_design: RNA was extracted using column based methods (Zymo DNA/RNA Duet Kit). Libraries were prepared according to Illumina Truseq RNA sample prep kit (PolyA)

first: Shuang

last: Wang


title: DNA methylation profiles of THP1 monocyte cells following Echinaforce treatment

first: Ken

last: Declerck

overall_design: DNA methylation profiles from THP1 cell lines treated with Echinaforce or ethanol (control) were measured using the Illumina Infinium MethylationEPIC Beadchip. Six biological replicates of each treatment condition were measured.

first: Andy

last: Suter

first: Guy

last: Van Camp

first: Claudina

last: Perez Novo

first: Wim

last: Vanden Berghe


title: Epigenetic compensation promotes liver regeneration


title: Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons

status: Public on Dec 04 2018

city: Cambridge

middle: C

last: Hill

state: MA

address: 75 Aimes Street

country: USA

institute: Broad Institute of MIT and Harvard

summary: Cellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions.  Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis.  To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and non-neuronal cell types. We also analyzed molecular changes during adult-born interneuron maturation, and uncovered developmental programs within their gene expression profiles. Finally, we discovered that distinct neuronal subtypes are differentially affected by sensory experience. Together, these data provide a transcriptome-based foundation for investigating subtype-specific neuronal function in the OB, charting the molecular profiles that arise during the maturation and integration of adult-born neurons, and documenting activity-dependent changes in the cellular composition of the olfactory system.

overall_design: To develop a comprehensive profile of cellular heterogeneity within the OB, here we employed high-throughput single-cell RNA sequencing (scRNA-seq) (Zheng et al. 2017) of activity manipulated and wildtype mouse olfactory bulbs. This technique allows an in-depth categorization of single cell molecular signatures, and provides an analysis of potential developmental and activity-dependent changes that occur in adult-born neuron populations. Together, our data inform the heterogeneity of interneurons within the OB, provide a molecular blueprint of stereotyped developmental programs for OB interneurons, and reveal the transcriptional changes that govern activity-dependent circuit integration of adult-born neurons. Furthermore, our results suggest that distinct molecular mechanisms act on different subsets of adult-born neurons, driving diversity and survival of adult-born interneuron subsets in an activity-dependent manner.

first: James

last: Martin

first: Benjamin

last: Arenkiel


title: Rh-30 micro array data, knockdown of  PAX3-FOXO1 and B7-H3

status: Public on Mar 02 2019

city: Kyoto

first: Takuyo

last: Kanayama

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Pediatrics

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: To investigate the effect of PAX3-FOXO1 and B7-H3 in rhabdomyosarcoma, Rh-30 (PAX3-FOXO1 positive rhabdomyosarcoma cell line) was transfected by siPAX3-FOXO1 or siB7-H3. After knockdown, total RNA was extracted and analyzed. As a result, some genes and pathways, such as chemotaxis, differentiation, and INF-gamma production were comonnly effected by PAX3-FOXO1 and B7-H3.

overall_design: Rh-30 was transfected by siControl or siPAX3-FOXO1 or siB7-H3. After 24 hours, total RNA was extracted and analyzed. There are 3 samples. Rh-30 siControl was compered by Rh-30 siPAX3-FOXO1 and/or Rh-30 siB7-H3

first: Mitsuru

last: Miyachi

first: Shigeki

last: Yagyu

last: Kikuchi

first: Kunihiko

last: Tsuchiya

first: Tomoko

last: Iehara

first: Hajime

last: Hosoi


title: BRCA2 abrogation triggers innate immune responses potentiated by treatment with PARP inhibitors

status: Public on Dec 11 2018

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

institute: Institut Imagine

summary: Heterozygous germline mutations in BRCA2 predispose to breast and ovarian cancer. Contrary to non-cancerous cells, where BRCA2 deletion causes cell cycle arrest or cell death, BRCA2 inactivation in tumors is associated with uncontrolled cell proliferation. We set out to investigate this conundrum by exploring modalities of cell adaptation to loss of BRCA2 and focused on genome-wide transcriptome alterations. Human cells in which BRCA2 expression was inhibited using a doxycycline (DOX)-inducible shRNA for 4 or 28 days were subjected to RNA-seq analyses. Gene sets differentially expressed in BRCA2-deficient versus -proficient cells revealed a biphasic response to BRCA2 abrogation. The early, acute response consisted of downregulation of genes involved in cell cycle progression, DNA replication and repair and was associated with cell cycle arrest in G1. Surprisingly, the late, chronic response consisted exclusively of upregulation of innate immune response genes controlled by interferon. Activation of the cGAS-STING pathway detected in these cells further substantiated the concept that long-term BRCA2 abrogation triggers cell-intrinsic immune signaling. Importantly, we found that treatment with PARP inhibitors stimulated the interferon response in cells and tumors lacking BRCA2. We propose that PARP inhibitors suppress growth of BRCA2-deficient cells and tumors, in part, by activating interferon signaling.

overall_design: RNA-seq data in BRCA2-/- and BRCA2+/+ human non-small cell lung carcinoma H1299 and invasive ductal breast cancer MDA-MB-231 cells.

first: Timo

last: Reisländer

first: Florian

last: Groelly

first: Ana

last: Miar Cuervo

first: Manuela

last: Porru

last: Wright

first: Helen

last: Lockstone

first: Annamaria

last: Biroccio

first: Adrian

last: Harris

first: Arturo

last: Londono-Vallejo

first: Madalena

last: Tarsounas


title: Development and Characterisation of Acquired Radioresistant Breast Cancer Cell Lines.

status: Public on Oct 04 2018

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

institute: The University of Edinburgh

summary:
Background: Radiotherapy plays an important role in the multimodal treatment of breast cancer. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Development of effective cancer treatments will require further molecular dissection of the processes that contribute to resistance.

Methods: Radioresistant cell lines were established by exposing MDA-MB-231, MCF-7 and ZR-751 parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Intrinsic differences and changes in response to radiation between parental and radioresistant cells were investigated by whole-transcriptome gene expression analysis. Gene enrichment and pathway-focused analyses identified signalling networks differentially activated in radioresistant cells, which were confirmed by western blotting.

Results: Proliferation and colony formation assays confirmed radioresistance. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition, and limited activation of DNA damage and apoptotic pathways in response to 2 Gy ionising radiation. Significantly, acquisition of radioresistance in MCF-7 and ZR-751 cell lines resulted in a loss of expression of both ERα and PgR and an increase in EGFR expression; based on gene analysis they changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. Whole-transcriptome gene expression analysis identified down-regulation of ER signalling genes and up-regulation of genes associated with PI3K, MAPK and WNT pathway activity in radioresistant cell lines derived from ER+ cells; this was confirmed by western blot, which showed increased p-AKT and p-ERK expression following radiation.

Conclusions: This is the first study to date that extensively describes the development and characterisation of three novel radioresistant breast cancer cell lines through both genetic and phenotypic analysis. More changes were identified between parental cells and their radioresistant derivatives in the ER+ (MCF-7 and ZR-751) compared with the ER- cell line (MDA-MB-231) model; however, multiple and likely interrelated mechanisms were identified that may contribute to the development of acquired resistance to radiotherapy.

overall_design:
Whole-genome transcriptomic analysis of 3 breast cancer cell lines (MCF-7, ZR-751 and MDA-MB-231) and 3 radio-resistant models derived from these (MCF-7 RR, ZR-751 RR, MDA-MB-231 RR), using Lexogen QuantSeq technology).

Please note that the 0G and 2G labels (in the sample title) refer to the treatment received: 0 Gray (untreated) or 2 Gray (radiation treatment).

first: Mark

last: Gray

first: Arran

middle: K

last: Turnbull


title: Maternal-biased H3K27me3 correlates with paternal-specific gene expression in the human morula

status: Public on Mar 01 2019

city: Boston

first: Wenhao

last: Zhang

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

summary: Genomic imprinting is an epigenetic mechanism by which genes are expressed in a parental-origin-dependent manner. We recently discovered that, like DNA methylation, oocyte-inherited H3K27me3 can also serve as an imprinting mark in mouse pre-implantation embryos. In this study, we found H3K27me3 is strongly biased toward the maternal allele with some associated with DNA methylation-independent paternally expressed genes (PEGs) in human morulae. The H3K27me3 domains largely overlap with DNA partially methylated domains (PMDs), and occupy developmental gene promoters. Thus, our study not only reveals the H3K27me3 landscape but also establishes a correlation between maternal-biased H3K27me3 and PEGs in human morulae.

overall_design: We conducted RNA-seq and H3K27me3 ChIP-seq in human morula embryos. To trace parental origin of reads, we performed exome sequencing and/or whole genome sequencing in maternal cumulus cells.

first: Zhiyuan

last: Chen

first: Qiangzong

last: Yin

first: Dan

first: Catherine

last: Racowsky

first: Yi


title: Gene expression profiles of isogenic single-cell derived clones of BRAF-mutated SK-MEL-5 melanoma cell lines

status: Public on Nov 01 2018

city: Nashville

first: B Bishal

last: Paudel

state: TN

address: 2220 Pierce Ave PRB447

department: Biochemistry

institute: Vanderbilt University

summary: We recently reported that single-cell derived isogenic subclones of SKMEL5 cells have differential initial sensitivity to BRAF-inhibitors. In order to probe differences among these subclones, we selected three subclones with unique drug responses: progressing (SK-MEL-5 SC10), stationary (SK-MEL-5 SC07), and regressing (SK-MEL-5 SC01) and performed RNASeq. This study examines differentially expressed genes (DEGs) among the subclones to identify the molecular basis for initial differences in drug sensitivity.

overall_design: Transcriptomics analysis between single-cell derived isogenic subclones of BRAF-mutated melanoma cell line, SK-MEL-5

first: Bishal

first: Vito

last: Quaranta


title: Bisulfite-seq profiling of the human neutrophil genome during PMA- and E. coli encounter-induced activation

city: La Jolla

first: Matthew

last: Denholtz

institute: UCSD

overall_design: Bisulfite-Seq

first: M

first: C

last: Murre


title: ARv7 represses tumor suppressors genes in castration-resistant prostate cancer [ChIP-Seq]

status: Public on Nov 02 2018

first: Myles

last: Brown

address: 450 Brookline Ave., D730

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Endocrine therapies in prostate cancer (PCa) treatment block androgen receptor (AR) function, but are palliative as tumors progress to a lethal, castration-resistant state (CRPC). CRPC remains dependent on AR signaling, which can act through the full-length AR (ARfl) or constitutively active splice variants, e.g. ARv7. We show here that both ARfl and ARv7 bind to the same genomic region and heterodimerize in a CRPC cell line model, but regulate distinct transcriptomes. ARv7, unlike ARfl, preferentially represses transcription and demonstrates an increased affinity for co-repressors, decreased chromatin residence time and lower dependence on FOXA1 binding. We identified a group of ARv7-repressed genes, including the UDP-galactosyltransferase B4GALT1 that are down-regulated during PCa progression and important for CRPC growth. In conclusion, we propose that ARv7 acts as a transcriptional repressor of genes that limit proliferation, a function that should be targeted in CRPC patients.

overall_design: ChIP-seq from shRNA-mediated knock-down experiments in prostate cancer cell lines

first: Anna

last: Groner

first: Laura

last: Cato

first: Jaice

last: Rottenberg

first: Jonas

last: de Tribolet-Hardy


title: Simultaneous Measurement of Transcriptional and Post-transcriptional Parameters by 3' end RNA-seq

status: Public on Aug 28 2018

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Cellular RNA levels are determined by transcription and decay rates, which are fundamental in understanding gene expression regulation. Measurement of these two parameters is usually performed independently, complicating analysis and introducing methodological biases that hamper direct comparison. Here, we present a simple approach of concurrent sequencing of S. cerevisiae polyA+ and polyA- RNA 3' ends to simultaneously estimate total RNA levels, transcription and decay rates from the same RNA sample. The transcription data generated correlate well with reported estimates and also reveal local RNA polymerase stalling and termination sites with high precision. Although the method by design uses brief metabolic labeling of newly synthesized RNA with 4-thiouridine, the results demonstrate that transcription estimates can also be gained from unlabeled RNA samples. These findings underscore the potential of the approach, which should be generally applicable to study a range of biological questions in diverse organisms.

overall_design: RNA 3' end seq of total and 2min 4-thiouracil (4tU) labelled RNA from S. cerevisiae cells. Aliquots of RNA were directly subjected to pA+ RNA 3' end sequencing (noPap samples). A second aliquot was in vitro polyadenylated using E. coli poly(A) polymerase and ribodepleted before library preparation (xPap samples).

first: Agnieszka

last: Tudek

first: Torben

middle: H

last: Jensen


title: R430: A potent inbibitor of DNA and RNA viruses

status: Public on Nov 19 2018

city: pittsburgh

first: Leonardo

last: D'aiuto

state: pa

address: 3811 O'Hare st

department: psychiatry

institute: UPMC

summary:
PURPOSE: Acyclovir (ACV) is an effective antiviral agent for treating lytic Herpes Simplex virus, type 1 (HSV-1) infections, and it has dramatically reduced the mortality rate of herpes simplex encephalitis. However, HSV-1 resistance to ACV and its derivatives is being increasingly documented, particularly among immunocompromised individuals.  The burgeoning drug resistance compels the search for a new generation of more efficacious anti-herpetic drugs. We have previously shown that 3-epi-trans-dihydrolycoricidine (R430), a lycorane-type alkaloid derivative, effectively inhibits HSV-1 infections in cultured cells.

METHODS: We employed human induced pluripotent stem cells-derived neurons (hiPSC-neurons) and neural progenitor cells (hiPSC-NPCs) to investigate the antiviral activity of R430 on HSV-1 and Zika (Strain XX), respectively. hiPSC line 73-56010-02 employed in this study established at the National Institute of Mental Health (NIMH) Center for Collaborative Studies of Mental Disorders-funded Rutgers University Cell and DNA Repository (http://www.rucdr.org/mental-health) (RUCDR). hiPSC- neurons and hiPSC-NPCs were generated as previously described (Dâ€™Aiuto et al. Organogenesis. 2014;10(4):365-77).  hiPSC based assays for HSV-1 infection.  We used a genetically engineered HSV-1 KOS strain that expresses enhanced green fluorescent protein (EGFP) and red fluorescent protein (RFP) under the control of immediate early and late gene promoters, respectively (33).  To determine the optimal conditions for evaluating drug effects, hiPSC-neurons cells were infected for 2 hours (multiplicity of infection, MOI=0.3), after which the inocula were replaced with media containing R430 (10 µM) or vehicle (DMSO).  Separately, cells were incubated in media containing R430 (10 µM) or vehicle in the absence of HSV-1. All assays were conducted in triplicate.  Cells were harvested after 6 hours post infection (hpi), 12 hpi, or 24 hpi, DNA was extracted using (QIAamp DNA Mini Kit, (Qiagen) and DNA conentrations were estimated. Subsequently, the EGFP locus was amplified to estimate viral copy number using custom primers (34).  A significant increase in viral copy number was noted in vehicle treated cells after 12h and 24h, but not after 6h. Substantial reduction in viral copy number was found following incubation with R430 at 12h or 24h.  The 12h incubation period was therefore selected for subsequent studies examining gene expression (see below).

overall_design: We employed human induced pluripotent stem cells-derived neurons (hiPSC-neurons) to investigate the antiviral activity of R430 on HSV-1. hiPSC line 73-56010-02 employed in this study established at the National Institute of Mental Health (NIMH) Center for Collaborative Studies of Mental Disorders-funded Rutgers University Cell and DNA Repository (http://www.rucdr.org/mental-health) (RUCDR). hiPSC- neurons and hiPSC-NPCs were generated as previously described (D'Aiuto et al. Organogenesis. 2014;10(4):365-77).

first: Vishwajit

last: Nimgaonkar

last: D'Aiuto

first: Matt

last: Demers

first: Joel

last: Wood


title: Gene expression patterns of trisomy 12 hPSC lines

status: Public on Oct 03 2018

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

summary: Trisomy 12 disrupts the genome-wide expression patterns that are required for proper mesendodermal differentiation.

overall_design: Gene expression analysis of 2 sublines of trisomy 12 hPSC lines compared with their parental hPSC lines.

first: Miho

last: Furue


title: Gene expression profiles associated with humoral response to influenza vaccine, Vaxigrip, in young and elderly subjects of Chinese ethnicity in Singapore

status: Public on Nov 14 2018

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: While studying influenza vaccine-induced responses, the elderly are typically considered as a homogeneous population. However, chronological age alone is insufficient in defining immune responsiveness of individuals. In this study, a stratified cohort of elderly (65 year old and above) and young (below 35 year old) individuals was recruited to study the heterogeneity of influenza vaccine-induced responses and identify innate signatures including gene expression profiles defining vaccine immunogenicity. The study was conducted in Singapore, a tropical setting without well-defined influenza seasons.

overall_design: The gene expression profiles are from 143 elderly (92 females, 51 males) and 29 young (18 females, 11 males) subjects of Chinese ethnicity in Singapore who were administered trivalent inactivated 2013-14 seasonal influenza vaccine (Vaxigrip) containing B/Massachusetts, A/H1N1/California and A/H3N2/Texas strains. Gene expression was interrogated in PBMCs collected from the vaccines prior to vaccination (day 0) and on days 2, 7 and 28 post-vaccination. Non-institutionalized community dwelling subjects were recruited as part of a phase IV clinical trial of Sanofi Pasteur’s Vaxigrip influenza vaccine approved by the National University of Singapore Institutional Review Board and registered at clinicaltrials.gov under the registration number NCT03266237. Volunteers were excluded if they had received an influenza vaccine within the 6 months preceding the trial vaccination or planned influenza vaccination during the trial. Those with suspected congenital or acquired immunodeficiency; or in receipt of immunosuppressive therapy such as anti-cancer chemotherapy or radiation therapy within the preceding 6 months; or on long-term systemic corticosteroid therapy (prednisone or equivalent for more than 2 consecutive weeks within the past 3 months) were also excluded. All volunteers provided written informed consent for the administration of seasonal influenza vaccine.

first: Anis

last: Larbi

first: Michael

last: Poidinger

first: Lucian

last: Visan


title: A nuclear export block triggers the decay of newly synthesized polyadenylated RNA

summary: Genomes are promiscuously transcribed, necessitating mechanisms that facilitate the sorting of RNA for function or destruction. The polyA (pA) tail is one such distinguishing feature, which in the S. cerevisiae nucleus is bound by the Nab2p protein, yielding transcript protection. As Nab2p also contacts the main nuclear export factor Mex67p, we asked whether transport kinetics contributes to RNA sorting. Indeed, 3’end sequencing of newly transcribed pA+ RNAs demonstrates that nuclear depletion of Mex67p elicits their instant and global decay. A similar phenotype is evident upon inactivation of other export factors and proportional to the amount of nuclear pA+ RNA. Since RNA production is partially rescued by Nab2p over-expression, we propose that an export-block out-titrates Nab2p onto nuclear retained pA+ RNA, reducing the pool of Nab2p free to protect new transcripts. More generally, we suggest that nuclear RNA decay, negotiated by Nab2p availability, aids in balancing cellular transcript supply with demand.

overall_design: pA+ RNA 3' end sequencing of total and 10min 4-thiouracil (4tU) labelled RNA from S. cerevisiae cells upon nuclear depletion of Mex67p or Nab2p using the anchor-away system for 15 minutes and undepleted control cells. RNA samples were collected in triplicate for each condition. Single replicates for negative controls not labeled with 4tU were processed in parallel.

first: Marius

last: Makaras

first: J

middle: D

last: Barrass

first: Jean

last: Beggs


title: ARv7 represses tumor suppressors genes in castration-resistant prostate cancer

first: Myles

last: Brown

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

overall_design: Refer to individual Series


title: Early Notch signals induce a pathogenic molecular signature during priming of alloantigen-specific conventional CD4+ T cells in graft-versus-host disease

status: Public on Feb 14 2019

city: Philadelphia

first: Ivan

last: Maillard

state: Pennsylvania

address: 421 Curie Blvd

department: Medicine - Hematology/Oncology

institute: University of Pennsylvania

summary: Graft-versus-host disease (GVHD) is the most serious complication of allogeneic hematopoietic cell transplantation. Notch signals delivered during the first 48 hours after transplantation drive proinflammatory cytokine production in conventional T cells (Tconv) and inhibit expansion of regulatory T cells (Tregs). Short-term Notch inhibition induces long-term GVHD protection. However, it remains unknown whether Notch blockade blunts GVHD through its effects on Tconv, Tregs, or both, and what early Notch-regulated molecular events occur in alloantigen-specific T cells. To address these questions, we engineered T cell grafts to achieve selective Notch blockade in Tconv vs. Tregs and evaluated their capacity to trigger GVHD in mice. Notch blockade in Tconv was essential for GVHD protection, as GVHD severity was similar in recipients of wild-type Tconv combined with Notch-deprived vs. wild-type Tregs. To identify the impact of Notch signaling on the earliest steps of T cell activation in vivo, we established a new acute GVHD model mediated by clonal alloantigen-specific 4C CD4+ Tconv. Notch-deprived 4C T cells had preserved early steps of activation, IL-2 production, proliferation, and T helper polarization. In contrast, Notch inhibition dampened IFN-γ and IL-17 production, diminished mTORC1 and ERK1/2 activation, and impaired transcription of a subset of Myc-regulated genes. The distinct Notch-regulated signature had minimal overlap with known Notch targets in T cell leukemia and developing T cells, highlighting the specific impact of Notch signaling in mature T cells. Our findings uncover a unique molecular program associated with pathogenic effects of Notch in T cells at the earliest stages of GVHD.

overall_design: 4 samples per cohort (Notch blockade using Dll1/4 neutralizing antibodies vs isotype control antibodies - GD) were analyzed. Additional 4 samples contained 4C T cells retrieved from syngeneic recipients.

first: Jooho

last: Chung

first: Vedran

last: Radojcic

first: Eric

last: Perkey

first: Timothy

middle: J

last: Parnell

first: Yashar

last: Niknafs

first: Xi

last: Jin

first: Ann

last: Friedman

first: Nathalie

last: Labrecque

first: Bruce

middle: R

last: Blazar

first: Todd

last: Brennan

first: Christian

last: Siebel


title: An enhancer in the middle of the Igκ locus orchestrates nuclear architecture to generate a diverse antigen receptor repertoire

status: Public on Nov 15 2018

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

summary:
Purpose:The goal of this study is to assess transcriptome profile in the absence of a potent enhancer located in the V gene region of the Igκ locus in cell lines and mice
Methods: RNAseq from CD19+ cells from B6.RAG1-/-  and E88-/-.RAG1-/- mice. RNAseq from 445.3, wild-type (WT) and E88-/-, pro-B cell lines

overall_design: RNA profiles from CD19+ cells from RAG1-/- mice in C57BL/6 and E88-/- background and 445.3, WT and E88-/-, pro-B cell lines were generated and analyzed for differential transcription.

first: Edgar

middle: M

last: Barajas-Mora

last: Feeney