title: Activin A in combination with ERK1/2 MAPK pathway inhibition sustains propagation of mouse embryonic stem cells

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
The combination of Wnt pathway activation by the GSK3 inhibitor and ERK pathway inhibition by the MEK inhibitor, which is known as 2i is a well-established method to maintain mouse embryonic stem cell (mESC) self-renewal. Here we show that Activin A also has the ability to promote naive pluripotency of mESCs when combined with the MEK inhibitor PD0325901. mESCs were efficiently propagated in a medium containing both Activin A and the MEK inhibitor (PD0325901). mESCs cultured in Activin+PD retained a pluripotency state that expresses high levels of naive pluripotency-related transcription factors and is able to differentiate into three germ layers under appropriate conditions. They also showed naive pluripotency features, including the preferential usage of the Oct4 distal enhancer and the self-renewal response to Wnt pathway activation. Our finding provides another way to maintain the naive pluripotency state and reveals a role of Activin/Nodal/TGF-β signaling in stabilizing self-renewal gene regulatory networks in mESCs.
To compare the gene expression patterns of naive and primed pluripotency states and their responses to Wnt and ERK1/2 MAPK pathway, we performed genome-wide gene expression analysis of mESCs and EpiLCs, and those treated with Wnt pathway activator alone or Wnt pathway activator combined with ERK1/2 MAPK pathway inhibitior.

overall_design: EpiLCs were induced from mESCs by culturing them in N2B27 supplemented with 20 ng/ml ActivinA  and 12 ng/ml bFGF on dishes coated with serum for 2 days. We prepared three samples for both mESCs and EpiLCs : non-treated cells, cells treated with CHIR99021, and cells treated with a combination of CHIR99021 and PD0325901. Total RNA was isolated with RNeasy Mini kit (Invitrogen). During the isolation, on-column DNaseI digestion was performed. Biotinylated sense-strand DNA was synthesized with GeneChip WT PLUS Reagent kit (Affymetrix), hybridized to Mouse Gene 2.0 ST Array (Affymetrix) and analyzed by GeneChip Scanner 7G System (Affymetrix). The data were analyzed by GeneSpringGX11.5 software (Agilent).

first: Yuhei

last: Ashida

first: May

last: Nakajima-Koyama

first: Akira

last: Hirota

first: Takuya

last: Yamamoto


title: nar nodule vs root transcriptome-analysis of symbiotic root nodule development

status: Public on Nov 01 2018

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: 12plex_medicago_2014_02 - nar nodule vs root transcriptome - which are the genes differentially expressed in alfalfa spontaneous (non rhizobium-infected) nodules vs. control roots? - biological material: aeroponically grown cuttings of a Medicago sativa (alfalfa) accession that produces empty nodules when nitrogen-starved. Samples for transcriptome comparison: isolated NAR nodules (10 days post N-starvation) vs. roots of the same plants (pools of 3 roots).

overall_design: 4 dye-swap - organ comparison

first: Pascal

last: Gamas

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Medicago truncatula R108 in symbiosis with rhizobia wt or rhizobia mutant for BacA. Comparison of the transcriptomic response of Medicago truncatula plants.

summary: 12plex_medicago_2013-08 - r108 in symbiosis with rhizobia wt or rhizobia mutant for baca. - Two experiments to compare the transcriptomic response of medicago plants: Agar medium versus Phytagel medium (exp1) and rhizobium WT versus BacA (exp2). - Medicago truncatula ecotype R108 was inoculated with the symbiotic rhizobium Sinorhizobium meliloti strain Sm1021 and with its derivative mutant delta bacA. Nodules were collected 13 days after inoculation, and RNA were prepared for transcriptome analysis, there were three biological independant experiements.

overall_design: rhizobium WT versus BacA. 3 dye-swap - gene knock out

last: Ratet


title: Two experiments to compare the transcriptomic response of medicago plants: Agar medium versus Phytagel medium (exp1) and rhizobium WT versus BacA (exp2).

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

overall_design: Refer to individual Series


title: Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Previously the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, and adult pachytene spermatocytes, round spermatids, caput epididymal sperm, and caudal sperm. The DMRs between the control versus vinclozolin lineage samples were determined for each developmental stage. The top 100 statistically significant DMRs for each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.

overall_design: The experimental design involved the development of F3 generation control and vinclozolin lineage male rats to isolate various germ cell stages for epigenetic analysis. The F0 generation gestating female rats at 90 days of age were transiently exposed to vinclozolin or a vehicle control during embryonic days 8–14 when the PGCs were migrating to colonize the indifferent gonad and during the early stages of gonadal sex determination. The F1 generation offspring were obtained and at 90 days of age were bred within the control and vinclozolin lineages, respectively, to generate the F2 generation (grand offspring) which were then bred at 90 days of age to obtain the F3 generation for each control and vinclozolin lineage. No cousin or sibling breedings were used to avoid any inbreeding artifacts. Only the F0 generation gestating females were transiently exposed to vinclozolin, which also directly exposed the F1 generation fetus and the germline within the F1 generation fetus that will generate the F2 generation. Therefore, the transgenerational F3 generation is the first generation not directly exposed and was used to study the developmental origins of the sperm epimutations. The F3 generation control and vinclozolin lineage male rats were aged to the embryonic day 16 (E16) fetal stage for prospermatogonia cell isolation, to postnatal day 10 (P10) for spermatogonial cell isolation, and to adult 120 days for pachytene spermatocyte isolation, round spermatid isolation and caput and cauda epididymal sperm isolation. The isolation procedure involved a gravity sedimentation StaPut protocol and direct isolation for the epididymal sperm collections. Three pools each from different individual sets of animals were obtained from 5-6 males per pool for the E16 stage, 6-7 males per pool for the P10 stage, 3 adult males per pool for the spermatocyte or spermatid stages, and 3 adult males per pool for the caput or cauda epididymal sperm stages. Therefore, 3-7 different males were used in each of the three different pools analyzed for both the control and vinclozolin lineages. The DNA was isolated from each pool for subsequent epigenetic analysis.

first: Eric

last: Nilsson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: John

middle: R

last: McCarrey


title: Transcriptome analysis of Meg3 KD and IG-DMR maternal deletion in ESC, pMN, and MN

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

summary: Analysis of gene expression at three time-points upon Meg3 KD and IG-DMR maternal deletion during motor neuron differentiation

overall_design: Total RNA were isolated from ESC, pMN, and MN in Meg3 KD, IG-DMR maternal deletion and WT. Subsequently, ESC, pMN, and MN in Meg3 KD, IG-DMR maternal deletion and WT transcriptome were analyzed by Agilent SurePrint G3 Mouse GE 8x60K Microarray (Agilent-G4858A-028005).

first: Jun-An

last: Chen


title: Real-time quantitative PCR analysis of the effects of chronic ethanol feeding and partial hepatectomy on gene expression in single rat hepatocytes

city: Philadelphia

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1020 Locust Street

department: Pathology, Anatomy and Cell Biology

institute: Thomas Jefferson University

summary: Heaptocytes from four different rats were analyzed for gene expression. Two animals received alcohol containing liquid diet and two other littermates were pair-fed liquid carbohydrate diet for 6-8 weeks following the Lieber-De Carli feeding protocol. The rats were then anesthetized and subjected to 70% partial hepatectomy (PHx). The left lateral and medial (LLM) lobes were removed and quickly frozen in OCT. 24 hours post hepatectomy, the rats were anesthetized again and the remnant liver was harvested. Single hepatocytes were collected from LLM and PHx liver slices using laser capture microdissection. We used the 96.96 BioMark Dynamic Array (Fluidigm) to measure the expression of functionally relevant genes in each hepatocyte.

overall_design: RT-PCR gene expression profiling of 124 hepatocytes from livers of rats fed control diet (69 hepatocytes at 0 hour after resection (LLM) and 55 hepatocytes 24 hours after resection (PHx)) and ethanol diet (55 hepatocytes at 0 hour after resection (LLM) and 54 hepatocytes 24 hours after resection (PHx)). Entire cell lysate was used for gene expression analysis.

first: Achanta

last: Sirisha

first: Verma

last: Aalap


city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

summary:
Global gene expression profiling of FOP-iMSCs after chondrogenic differentiation with ERBB2 inhibitors
1 control and 5 experimental samples

first: M


title: Medicago truncatula R108: permissive medium versus non permissive medium. Comparison of the transcriptomic response of medicago truncatula plants.

summary: 12plex_medicago_2013-08 - r108 permissive medium versus non permissive medium. - Two experiments to compare the transcriptomic response of medicago plants: Agar medium versus Phytagel medium (exp1) and rhizobium WT versus BacA (exp2). - Medicago truncatula R108 seedlings were inoculated with S. medicae WSM419 and were cultivated during three days on buffered nidulation medium solidified with Phytagel or Agar.

overall_design: Agar medium versus Phytagel medium. 3 dye-swap - null


title: Multi-omics Approach Reveals Metabolic Changes in the Heart at Birth

city: Gainesville

first: Jacquelyn

middle: Mary

last: Walejko

state: FL

department: Pharmacodynamics

institute: University of Florida

summary: During late gestation, the fetal heart relies primarily on glucose and lactate to support rapid growth and development. While numerous studies describe changes in heart metabolism a few weeks after birth to preferentially utilize fatty acids, little is known about metabolic changes of the heart within the first day of life. Therefore, we used the ovine model of pregnancy to investigate metabolic differences between the near-term fetal and the newborn heart. We observed greater abundance of metabolites involved in butanoate and propanoate metabolism, and glycolysis/gluconeogenesis in the term fetal heart (FDR-corrected p<0.10) and differential expression in these pathways were confirmed with single-sample gene set enrichment analysis (ssGSEA) (FDR-corrected p<0.05). Immediately following birth, newborn hearts displayed enrichment in purine, fatty acid, and glycerophospholipid metabolic pathways, as well as oxidative phosphorylation with significant alterations in lipids and metabolites to support transcriptomic findings. While other studies suggest a switch from carbohydrate metabolism to fatty acid metabolism in the neonatal heart in as early as 2 weeks following birth, our data show that this metabolic switch in the heart begins by the first day of postnatal life. A better understanding of metabolic alterations that occur in the heart following birth may improve treatment of neonates at risk for heart failure.

overall_design: Samples were collected for metabolomics, lipidomic, and transcriptomic approaches from the left and right ventricles and intraventricular septum in 7 fetuses at gestational day 142 and 7 newborn lambs on the day of birth.

middle: M

first: Jeremy

middle: P

last: Koelmel

first: Timothy

middle: J

last: Garrett

first: Arthur

middle: S

last: Edison

first: Maureen

last: Keller-Wood


title: Peripheral gene expression in cocaine use disorders with low and high anhedonia

status: Public on Nov 02 2018

city: Houston

first: Gabriel

last: Fries

state: TX

address: 1941 East Rd

department: Psychiatry and Behavioral Sciences

institute: The University of Texas Health Science Center at Houston

summary: Treatments for Cocaine Use Disorder (CUD) are variably effective, and there are no FDA-approved medications. One approach to developing new treatments for CUD may be to investigate and target poor prognostic signs. One such sign is anhedonia (i.e. a loss of pleasure or interest in non-drug rewards), which predicts worse outcomes in existing CUD treatments. Inflammation is thought to underlie anhedonia in many other disorders, but the relationship between anhedonia and inflammation has not been investigated in CUD. Therefore, we assessed peripheral genome-wide gene expression in n = 48 individuals with CUD with high (n=24) vs. low (n = 24) levels of anhedonia, defined by a median split of self-reported anhedonia. Our hypothesis was that individuals with high anhedonia would show differential gene expression in inflammatory pathways. No individual genes were significantly different between the low and high anhedonia groups when using t-tests with a stringent false discovery rate correction. However, an exploratory analysis identified 166 loci where t-tests suggested group differences at a nominal p < 0.05. We used DAVID, a bioinformatics tool that provides functional interpretations of complex lists of genes, to examine representation of this gene list in known pathways. It confirmed that mechanisms related to immunity were the top significant associations with anhedonia in the sample. Further, the two top differentially expressed genes in our sample, IRF1 and GBP5, both have primary inflammation and immune functions, and were significantly negatively correlated with total scores on our self-report of anhedonia across all 48 subjects. These results suggest that prioritizing development of anti-inflammatory medications for CUD may pay dividends, particularly in combination with treatment-matching strategies using either phenotypic measures of anhedonia or biomarkers of inflammatory gene expression to individualize treatment.

overall_design: HumanHT-12 v4.0 Gene Expression BeadChip (Illumina) was used to assess peripheral genome-wide gene expression in n = 48 individuals with CUD with high (n=24) vs. low (n = 24) levels of anhedonia, defined by a median split of self-reported anhedonia.

first: Sarwar

last: Khan

first: Sydney

last: Stamatovich

first: Elena

last: Dyukova

first: Consuelo

last: Walss-Bass

first: Scott

middle: D

last: Lane

first: Joy

last: Schmitz

first: Margaret

middle: C

last: Wardle


title: Blood-derived stable induced neural stem cells: Preservation of age-related DNA methylation patterns and applicability to disease modeling

city: Aachen

first: Qiong

last: Lin

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

summary: Direct transcription factor-mediated cell fate conversion provides an attractive route for the derivation of patient-specific somatic cells. Here we report on the generation of bona fide induced neural stem cells (iNSCs) from adult peripheral blood and their suitability for modeling late-onset disease. Employing restricted and integration-free expression of the transcription factors SOX2 and c-MYC we generated clonally expandable iNSCs that can proliferate across at least 20 passages, remain highly responsive to regional patterning cues and give rise to functional neurons, astrocytes and oligodendrocytes. Interestingly, and in contrast to pluripotent stem cell-derived neural cells, iNSCs exhibit partial preservation of age-related DNA methylation signatures. Employing the polyglutamine disorder Machado-Joseph disease (MJD) as an exemplar, we demonstrate that MJD iNSC-derived neurons show a striking and specific pathological protein aggregation phenotype. Our findings suggest that iNSCs may provide a particularly attractive resource for modeling late-onset neurological disorders.

overall_design: To study the relationship between blood-derived iNSCs with their parental blood cells and human pluripotent stem cell (hPSC)-derived conterparts, we selected 2 adult peripheral blood cell-derived iNSC (PB-iNSC) lines, 3 neonatal cord blood cell-derived iNSC (CB-iNSC) lines, 2 hPSC-derived small molecule-induced neural progenitor cell (smNPC) lines, 2 hPSC-derived long-term neuroepithelium stem cell (lt-NES) lines, 1 adult peripheral blood cell sample, 1 neonatal cord blood cell sample. We analyzed their global gene expression profiles via HumanHT-12 v4 Expression BeadChip Kit.

first: Chao

last: Sheng

first: Johannes

last: Jungverdorben

first: Hendrik

last: Wiethoff

first: Daniela

last: Eckert

first: Matthias

last: Hebisch

first: Jaideep

last: Kesavan

first: Julia

last: Fischer

first: Ullrich

last: Wüllner

first: Wolfgang

last: Wagner

first: Michael

last: Peitz

first: Oliver

last: Brüstle


title: The antibiotics potentiator bicarbonate causes upregulation of tryptophanase and iron acquisition proteins in Escherichia coli

city: Cuernavaca

first: Joaquin

last: Sanchez

state: Morelos

address: Calle Ixtaccihuatl Esq Leñeros

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma del Estado de Morelos

type: Expression profiling by high throughput sequencing

summary: We have reported that bicarbonate (NaHCO3) potentiates the activity of aminoglycosides in Escherichia coli, but the action mechanism was not identified. To eventually understand how NaHCO3 can potentiate antibiotics, we thought that a rational first step was to examine the effect of NaHCO3 separately and to inspect initial gene expression changes triggered by it. In this work we started by confirming that NaHCO3 can reduce the number of viable E. coli bacteria. We then investigated, via RNAseq, gene expression changes induced by NaHCO3. There were upregulated and downregulated genes, among the top upregulated genes (~10-fold increase in expression) was tnaA, the gene encoding tryptophanase (TnaA), the enzyme that degrades tryptophan to indole. Considering that higher expression of tnaA likely led to increases in indole, we tested the effect of indole and found both growth inhibition and synergy with NaHCO3. We suggest that indole may participate in growth inhibition of E. coli. The RNAseq analysis also revealed upregulation (≥4-fold) of genes encoding proteins for the acquisition of iron and downregulation (≥16-fold) of genes encoding iron-sulfur-holding proteins, hence NaHCO3 apparently triggered also an iron deficit response. We suggest that iron deficiency may also be involved in growth inhibition by NaHCO3.

overall_design: Liquid LB cultures of E. coli were followed throughout the growth curve by periodic optical density readings, usually every 20 min. When cultures were in the logarithmic phase of growth, they were exposed to 40 mM NaHCO3 and the incubation was continued for 40 minutes. The control cultures were treated exactly as the experimental cultures but they were exposed to 40 mM NaCl in lieu of NaHCO3. The treatment with NaCl was intended to standardize the ion molarity in the control cultures and in the NaHCO3-treated cultures. It should be noted however, that the LB medium already contained 1% NaCl, or a 170 mM concentration of NaCl, thus after addition of 40 mM NaCl to the control cultures the extra NaCl contributed approximately 20% to the final molarity. The extra NaCl had no apparent effect on E. coli responses, including sensitivity to antibiotics (unpublished data). At the end of the incubation period, cultures were transferred to ice and bacterial cells were collected at 4°C by centrifugation at 10,000 x g for a 10 min period. The collected cells were then subjected to RNA extraction. Sequencing was performed by the specialist company Otogenetics (Norcross, GA). According to the contracted services, the RNA-seq protocol included initial sample quality control (QC), rRNA depletion, random primed cDNA synthesis/QC; Illumina sequencing library preparation/QC; PE100 and HiSeq2000/2500 sequencing, designated 10 million reads; paired-end 2 x 100nt.

first: Marisela

last: Gutiérrez-Huante

first: Martha

middle: E

last: Martínez-Duncker

first: Elizabeth

last: Sauceda

first: Joaquín

last: Sánchez


title: Gene expression study in skin fibroblasts

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: To investigate the in vivo developmental potential, we generated dedifferentiated-skin fibroblast from adult skin fibroblasts with a FVB background, a different genetic strain from the protein-donor embryonic stem (ES) cell. Primary cardiac fibroblast (cFB) was cultered from an adult C57/BL mouse to compare with ES cells(E14-mES, C57-mES). We also introduced C57 background ES cell-derived extract proteins into cFB by reversible permeabilisation. The ES-like cells (colonies) were expanded with subculture every 3 to 5 days using the standard ES cell culture protocol.

overall_design: Total RNA was extracted from each sample. Five-hundred nanograms of total RNA were used for labeling and hybridization, according to the manufacturer’s protocols (Illumina). After the bead chips were scanned with an Illumina BeadArray Reader (Illumina), the expression level of each gene was transformed into a log 2 base before further analysis.

first: S

middle: H

last: Leem

first: I

last: Chu


title: Gene expression analysis of hyper active mutant SPORTS rat [muscle]

city: Tokushima

first: Taigo

last: Horiguchi

address: 3-18-15, Kuramoto-Cho

institute: Tokushima University

summary: To get insight into the genetic characteristics of hyper active mutant line of rat, SPORTS, and the effect of exercise on gene expression, we  compared gene expression profiles of exercised SPORTS rat, sedentary SPORTS rat, and sedentary wild type rat. Using RNA extracted from the muscle of these rats, we performed microarray analysis. Subsequent GO analyses revealed that genes belonging to muscle development and glycolysis were upregulated in exercised SPORTS rat compared to sedentary SPORTS rat, and genes related to coagulation were upreguated in  sedentary SPORTS rat compared to wild type rat. These results were consistent with phenotypes, such as hyper activity and thrombotic tendency, which were reported for SPORTS rat.

overall_design: Gene expression was measured using RNA prepared from the skeletal muscle of exercised SPORTS rat, sedentary SPORTS rat, and sedentary wild type rat. The background strain of SPORTS rat is Wistar, and the wild type rat, we used in this experimet, is also Wistar strain.

first: Keiko

last: Miyoshi

first: Ayako

last: Tanimura

first: Hiroko

last: Hagita

first: Yumiko

last: Miyatake

first: Hiroshi

last: Sakaue

first: Takafumi

last: Noma


title: Tamoxifen transcriptional regulation in human endometrial stromal cells (HESC)

city: Bethesda

first: Miriam

middle: Christine

last: Poirier

state: MD

address: 37 Convent Dr, MSC 4255, Bldg 37 Rm 4032 NIH

institute: National Cancer Institute, NIH

summary: Tamoxifen (TAM), used for adjuvant therapy of breast cancer, also increases the risk of endometrial cancer. To compare TAM-induced transcriptional changes we examined human and monkey uterus, as well as cultured normal human mammary epithelial cells (NHMECs) and human endometrial stromal cells (HESCs). Uterine DNA from TAM-exposed women (n=15) and monkeys (Erythrocebus patas n=5, and Macaca fascicularis n=12) showed no difference in 5-methyl-cytosine (5-meC) levels compared to unexposed controls. Studies comparing NHMECs and HESCs exposed to 10 µM TAM for 48 hr showed cell-specific differences by microarray, with confirmation by RT-PCR. In TAM-exposed NHMECs there was significant up-regulation of interferon signaling and immune response pathways, while the TAM-exposed HESCs showed significant up-regulation of steroid and fatty acid biosynthesis pathways. Promoter region CpG islands of several genes highly up-regulated by TAM in each cell type (NHMECs: MX1 and STAT1; HESCs: PPARG, SREBF2, HMCGS and Prune2), were examined for 5-meC, but the levels (≤ 7%), were too low to measure accurately. We also examined several histone H3 lysine dimethylases by Western blot, and showed a significant depletion of total H3 histone, H3K4, H3K27 and H3K36 in TAM-exposed HESCs, with similar but non-significant changes in TAM-exposed NHMECs. Whereas TAM exposure had no discernible effect on 5-meC levels in primate uterus, TAM exposure induced up-regulation of different transcriptional pathways in NHMECs and HESCs, and concomitantly depleted H3 histone lysine dimethylase levels. Therefore, transcriptional dysregulation by TAM, including reduction of histone H3 dimethylase levels, may be related to TAM-induced endometrial carcinogenesis.

overall_design: Human endometrial stromal cells (HESCs) were exposed to 10 uM Tamoxifen (TAM) (n=4) or vehicle (n=4) for 48 hours.


title: Tamoxifen transcriptional regulation in human mammary epithelial and endometrial stromal cells


title: Gene expression analysis of hyper active mutant SPORTS rat [brain]

summary: To get insight into the genetic characteristics of hyper active mutant line of rat, SPORTS, we  compared gene expression profiles of the sedentary SPORTS rat and the sedentary wild type rat. Using RNA extracted from the brain of these rats, we performed microarray analysis. Subsequent GO analyses revealed that genes belonging to norepinephrine synthetic pathway and coagulation were upreguated. These results were consistent with phenotypes, such as hyper activity and thrombotic tendency, which were reported for SPORTS rat.

overall_design: Gene expression was measured using RNA, prepared from the brain of three sedentary SPORTS rats and that of three sedentary wild type rats.


title: Gene expression analysis of hyper active mutant SPORTS rat


title: Transcriptional difference between wild-type and zip-3(gk3164)

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
ATFS-1 has been shown to regulate transcription of mitochondrial chaperone genes such as mtHsp70/hsp-6 and hsp-60 in response to mitocondrial stress. To identify the entire ATFS-1-mediated response, we compared the transcript profiles from wild-type and atfs-1(tm4525) worms raised in the absence and presence of mitochondrial stress.
We used microarrays to identify genes regulated by ZIP-3

overall_design: RNA samples were prepared from wild-type(wt) and zip-3(gk3164)(mutant) worms fed either control(RNAi). Worms were synchronized by bleaching, raised in liquid culture and harvested at the L4 stage. Each experiment was performed in triplicate indicated as 1,2 and 3.

first: Amrita

last: Nargund

first: Cole

last: Haynes


title: Tamoxifen transcriptional regulation in normal human mammary epithelial cells (NHMEC)

overall_design: Normal human mammary epithelial cells (NHMEC) were exposed to 10 µM Tamoxifen (TAM) (n=4) or vehicle (n=4) for 48 hours.


title: Gene expression analysis of in vivo originated bovine embryos fllushed out at 2- or 8-cell stages and cultured in vitro till blastocyst stage

status: Public on Oct 31 2018

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: There is an inevitable need for combining in vitro and in vivo culture systems during specific developmental time points to facilitate a comprehensive understanding of early embryo development which would yield insights into the molecular pathways controlling early development and to improve our knowledge in regulation of embryonic development. In current study, we aimed to understand the influences of in vitro culture conditions on bovine blastocyst originated in vivo at 2- or 8-cell stagre. The effect of this altrnative cuture conditions on developmental rate, gene expression pattern and subsequent influences on pathways and biological functions controlling bovine embryo development has been analyzed.

overall_design: Two different blastocyst groups were produced under alternative in vivo and in vitro culture conditions. Vivo_2-cell and Vivo_8-cell groups were matured, fertilized and cultured in vivo until 2- and 8-cell stage, respectively then flushed out and cultured in vitro until day 7 blastocyst stage. Complete in vivo (control group) blastocysts were also produced. Samples from the three pools (biological replicates) of each blastocyst group and in vivo control blastocyst were hybridized on EmbryoGENE’s bovine microarray using a dye-swap design (technical replicates) for a total of six arrays per each group.


title: Protein phosphorylation profiling of rat sciatic nerve stumps

city: Nantong

first: Sheng

last: Yi

state: Jiangsu, China

address: 19 Qixiu Road

country: China

institute: Nantong University

summary: Examine protein phosphorylation status during peripheral nerve regeneration when using autologous nerve graft or tissue engineered nerve graft to bridge nerve gap.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Rat sciatic nerve stump was transected for a 0.6 cm gap, bridged with autologous nerve graft or tissue engineered nerve graft, and subjected to protein phosphorylation profiling.


title: IL-18 mediates sickle cell cardiomyopathy and inducible ventricular arrhythmias

city: Tucson

first: Haiquan

last: Li

state: AZ

address: 1657 E Helen Street

department: Medicine

institute: University of Arizona

summary:
Rationale. Sickle cell cardiomyopathy is characterized by prolonged QTc, myocardial fibrosis, diastolic dysfunction, and vulnerability to ventricular tachycardia (VT). Based on previous reports, IL-18 mediates cardiac fibrosis and its promoter SNPs are associated with sudden cardiac death in a non-sickle population. We, therefore, hypothesized that IL-18 may mediate cardiomyopathy and VT in sickle cell disease.
Findings. Sickle cell patients with evidence of myocardial fibrosis demonstrated greater IL18 expression. Patients with higher IL18 gene expression levels also exhibited increased QTc intervals and overall mortality. A novel SNP within IL-18, rs5744285, was associated with both QTc and IL-18 expression levels. Similar to sickle cell patients, sickle mice demonstrated increased cardiac fibrosis and prolonged action potential duration (APD) associated with higher VT inducibility. Administration of exogenous IL-18 acutely ex vivo to hearts resulted in increased triggered activity and VTs while inhibition of IL-18 resulted in reduced cardiac NFkB expression, fibrosis, and dysfunction in sickle mice.
Conclusions. IL-18 is associated with prolonged QTc, myocardial fibrosis, and mortality in sickle cell patients, and prolonged APD associated with heightened VT susceptibility in sickle mice. Inhibition of IL-18 improves cardiac function, in part, via NFκB. Inflammatory cytokines contribute to the development of sickle cardiomyopathy and inducible VT.

overall_design: Gene expressions of left ventricular tissues of three sickle mice was compared to those of three control mice with Affymetrix GeneChip Mouse Gene 2.0 ST microarrays, to investigate the expression perturbation of genetic variations in IL18 genes.

first: Ankit

last: Desai

first: Joanne

last: Berghout

first: Yves

middle: A

last: Lussier


title: Endothelin-1 expression and Akt activation are involved in acquired resistance to dabrafenib/trametinib combination therapy of melanoma

first: Yi-Shuan

last: Sheen

address: 7 Chun-Shan South Road

department: Dermatology

institute: Natioanl Taiwan University Hospital

summary: Two-condition experiment, A375DTR#1 v.s. A375. Biological replicates: 2 control replicates, 2 transfected replicates.

first: Chia-Yu

last: Chu


title: Widespread enhancer dememorization and promoter priming during parental-to-zygotic transition

status: Public on Oct 25 2018

city: Beijing

first: Bingjie

last: Zhang

state: Beijing

address: 30 Shuangqing Rd

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The epigenome plays critical roles in controlling gene expression and development. However, how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here, we show parental-to-zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly, this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4-cell stage, and zygotic enhancers are not activated until around zygotic genome activation (ZGA). By contrast, many promoters remain hypomethylated and, unexpectedly, acquire de novo histone acetylation as early as at the 4-cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally, such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus, these data revealed widespread enhancer dememorization and promoter priming during parental-to-zygotic transition.

overall_design: By employing STAR ChIP-seq and RNA-seq, we systematically examined the genome wide presence of H3K4me3, H3K27ac, H3K27me3 and H3K36me3 in sperm, oocyte, 4-cell, 256-cell and dome stage embryos.

first: Xiaotong

last: Wu

first: Wenhao

first: Wei

last: Xie


title: Transcript profiling in peritoneal macrophages from wildtype or c-JunΔLysM mice

city: Erlangen

first: Aline

last: Bozec

address: Ulmenweg 18

institute: Universitätsklinikum Erlangen, Department of Internal Medicine 3 – Rheumatology and Immunology

summary: The polarization and activation of macrophages are controlled synergistically by transcription factors such as NF-κB and AP-1 transcription factor members. Surprisingly, little is known about the role of the AP-1 transcription factor c-Jun in macrophage activity. To determine the full profile of c-Jun network, microarray RNA expression analysis using Agilent Technologies platform was performed in wild-type and c-JunΔLysM macrophages.

overall_design: For microarray analyses, peritoneal macrophages were collected by peritoneal lavage of 8 week old wild-type (n=3) or c-JunΔLysM mice (n=2). Peritoneal cells were plated over night. The next day, suspension cells were removed and only adherent cells were used for RNA isolation.

first: Nicole

last: Hannemann

first: Stephen

last: Reid

first: Sophia

last: Sonnewald


title: Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome [NEU]

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

summary: We present and propose the application of 5-Ethynyl uridine for metabolic labeling of RNAs in plants, which allows the isolation of neo-synthesized RNAs from intact plants. This system provides the possibility to investigate neo-synthesized RNAs from living plant cells. Neu-RNAseq can be applied for the detection of splicing variants, especially RNAs containing retained introns and alternative 5’ and 3’ splice sites. A subset of unspliced RNAs identified by Neu-Seq is subjected for elimination by the NMD pathway, but the majority of the RNA splicing variants detected in Neu-Seq libraries will be further processed into mature mRNAs.

overall_design: RNA synthesized within 1 hour was analyzed in comparison to a steady-state transcriptome from the same source material. Samples were analysed in triplicates.

first: Philipp

last: Reichert

first: Emese

middle: X

last: Szabò


title: EMca: serous, endometrioid, normal (miRNA)

city: Sendai

first: ERI

last: HIROKI

address: 1-1 Seiryo-Machi, Aoba-ku

department: Obstetrics and Gynecology

institute: Tohoku University

summary: To determine the expression profiles of microRNAs (miRNAs) and to examine specific miRNA expression in endometrial serous adenocarcinoma in comparison with normal endometrial tissue and endometrial endometrioid adenocarcinoma.　Twenty-one serous adenocarcinoma tissues, 20 endometrioid adenocarcinoma tissues, and 7 normal endometrial tissues were enrolled.　miRNA expression profiles were examined using miRNA microarray.

overall_design: After obtaining informed consent, 21 serous adenocarcinoma tissues, 20 endometrioid adenocarcinoma tissues, and 7 normal endometrial tissue　were retrieved from the surgical pathology files at Tohoku University Hospital (Sendai, Japan). The research protocol was approved by the Ethics Committee at Tohoku University Graduate School of Medicine (Sendai, Japan). All specimens were obtained from surgery that was performed between January 2001 and December 2006 at Tohoku University Hospital (Sendai, Japan). We also obtained nonpathologic endometrial tissues as normal controls from hysterectomy specimens performed due to non-endometrial carcinomas. No patient had received preoperative irradiation or chemotherapy. The lesions were classified according to the Histological Typing of Female Genital Tract Tumors by the WHO and staged according to the International Federation of Gynecology and Obstetrics system. Only those patients whose endometrial carcinomas were comprised of pure adenocarcinoma and did not have any other histological components were enrolled. These specimens were processed in 10% formalin, fixed for 24-48 hours, paraffin embedded, and thin-sectioned (3 μm). All of these archival specimens were embedded immediately in OCT compound (Sakura Finetechnical, Tokyo, Japan) and stored at -80℃ for further use. Only sections containing a minimum of 90% carcinoma by examination with hematoxylin-eosin staining were used for total RNA preparation. Total RNA, including miRNA, was extracted using a QIAzol Lysis reagent (Qiagen, Valencia, CA, USA) and a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.


title: Competitive repopulation of an empty microglial yields functionally distinct subsets of microglia-like cells

status: Public on Oct 19 2018

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Although most tissue macrophages are embryonically derived it is evident that circulating monocytes can compete for virtually any macrophage niche. Monocytes can thus become long-lived replacements of tissue macrophages that are indistinguishable from their embryonic counterparts, but the factors regulating this process are incompletely understood. To study niche competition in the CNS we depleted microglia with >95% efficiency using CX3CR1CreER/+R26DTA/+ mice and monitored long-term repopulation. The microglial niche was repopulated within weeks by a combination of local microglia proliferation giving rise to CX3CR1+F4/80lowClec12a– microglia, as well as infiltration of CX3CR1+F4/80hiClec12a+ macrophages. Adoptive transfer experiments demonstrated that peripherally-derived macrophages arose directly from Ly6Chi monocytes without contribution from hematopoietic progenitors and was independent of BBB breakdown. After repopulation we sorted microglia and monocyte-derived macrophages and performed transcriptional, epigenetic (DNA methylation) and ex vivo functional profiling. This revealed that Ly6Chi monocytes upregulated microglia gene expression and adopted microglia DNA methylation signatures. However, in contrast to proliferating microglia, which rapidly regained their homeostatic gene signature, monocyte-derived macrophages retained a distinct gene signature associated with antigen presentation, interferon signaling and chemotaxis. This translated into functional changes in monocyte-derived macrophages, as demonstrated by differences in surface marker expression, phagocytosis and cytokine production. Our results demonstrate that monocytes are imprinted by the CNS microenvironment but remain transcriptionally, epigenetically and functionally distinct. This may have implications for neuroinflammatory disease states and direct design of novel therapies.

overall_design: 31 sorted samples from mice on C57BL/6 background

first: Harald

last: Lund


title: A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma

status: Public on Oct 23 2018

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

summary: Persistent or recurrent retinoblastoma (RB) is associated with the presence of vitreous or/and subretinal seeds in advanced RB and represents a major cause of therapeutic failure. This necessitates the development of novel therapies and thus requires a model of advanced RB for testing candidate therapeutics. To this aim, we established and characterized a three-dimensional, self-organizing organoid model derived from chemotherapy-naïve tumors. The responses of organoids to drugs were determined and compared to relate organoid model to advanced RB, in terms of drug sensitivities. We found that organoids had histological features resembling retinal tumors and seeds and retained DNA copy-number alterations as well as gene expression profile and protein expression of the parental tissue. Cone signal circuitry (M/L+ cells) and glial tumor microenvironment (GFAP+ cells) were primarily present in organoids. Topotecan alone or the combined drug regimen of topotecan and melphalan effectively targeted proliferative tumor cones (RXRg+ Ki67+) in organoids after 24-h drug exposure, blocking mitotic entry. In contrast, methotrexate showed the least efficacy against tumor cells. The drug responses of organoids were consistent with those of tumor cells in advanced disease. Patient-derived organoids enable the creation of a faithful model to use in examining novel therapeutics for RB.

overall_design:
Samples from human retinoblastoma organoids [2 samples from passages 1 (6-week culture) and 3 (13-week culture)] and retinoblastoma tissue [the tumor tissue used for culture (1 sample)] were used to generate RNA-seq libraries.  Gene expression profiles were generated by sequencing using NovaSeq6000.
Published gene expression profiles of fetal retina (2 samples, days 132 and 136 from Hoshino et al., 2017; Dev Cell; 43(6):763-779.e4) and retinoblastoma (1 sample from Aldiri et al., 2017; Neuron; 94(3):550-568.e10) were included for analysis.  The three reanalyzed samples are included in supplementary file kaewkhaw.tumor.organoids.668.Hsap38.Ens82.gene.CPM.tsv linked at the foot of this record.


title: Transcriptome analysis of wild type and RAR deficient frog faces during development

status: Public on Oct 15 2018

city: Richmond

first: Amanda

last: Dickinson

state: VA

address: 1000 W. Cary St. Rm 339

department: Biology

institute: Virginia Commonwealth University

summary: We utilized RNASeq to investigate the changes in mRNA expression when retinoic acid signaling is inhibited by treatment with an RAR inhibitor, BMS453.

overall_design: Embryos were treated with RAR inhibtior during the latter stage of facial development, 35-66 hours post fertilzation, facial region was dissection and global changes in gene expression were assessed. Further analyses to determine funcitonal networks that were affected was performed.

first: Stacey

last: Wahl

last: Turner


title: Evaluating the effect of CovR phosphorylation on group A streptococcus global gene expression

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary: We sought to determine how CovRS mutations varying CovR phosphorylation levels affect the gene expression profile of group A streptococcus

overall_design: There were 8 strains analyzed, each in quadruplicate replicates: 1) wild-type GAS serotype M1; 2) covS-E281A GAS serotype M1; 3) covS-T284A GAS serotype M1 4) covR-D53A GAS serotypep M1; 5)  wild-type GAS serotype M3; 6) covS-E281A GAS serotype M3; 7.) covS-T284A GAS serotype M1; 8.) covR-D53A GAS serotypep M3

first: Nicola

last: Horstmann

first: Hui

last: Yao


title: Muscle satellite cell specific proteasome deficient mice

status: Public on Oct 10 2018

city: Hiroshima-shi

first: Yasuo

last: Kitajima

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Graduate School of Biomedical and Health Sciences

institute: Hiroshima University

summary: Adult muscle stem cells (satellite cells) are required for adult skeletal muscle regeneration. A proper balance between quiescence, proliferation, and differentiation is essential for the maintenance of the satellite cell pool and their regenerative function. Although the ubiquitin-proteasome is required for most protein degradation in mammalian cells, how its dysfunction affects tissue stem cells remains unclear. Here, we investigated the function of the proteasome in satellite cells using mice lacking the crucial proteasomal component, Rpt3. Ablation of Rpt3 in satellite cells decreased proteasome activity. Proteasome dysfunction in Rpt3-deficient satellite cells impaired their ability to proliferate, survive and differentiate, resulting in defective muscle regeneration. We found that inactivation of proteasomal activity induced proliferation defects and apoptosis in satellite cells. Mechanistically, insufficient proteasomal activity upregulated the p53 pathway, which caused cell-cycle arrest. Our findings delineate a critical function of the proteasome system in maintaining satellite cells in adult muscle.

overall_design: Satellite cells were sorted from satellite cells-specific Rpt3 knockout and control mice. each 3 mice.


title: ATAC-Seq of chicken embryonic metatarsal skin treated with RCAS-CTNNB1, RCAS-GFP, and retinoic acid

city: Taichung

first: Yung-Chih

last: Lai

address: 7F., No. 6, Xueshi Road, North District

department: Integrative Stem Cell Center

institute: China Medical University Hospital

summary: The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major more modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze the transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered chromatin opening sites, and they are distributed around. When a key gene is perturbed, many other co-expressed genes in the same module also will be influenced. These findings suggest that these feather / scale fate specification genes form an interconnected network, and rewiring of the gene network can lead to changes of appendage phenotypes. This work shows the key hub positions of Beta catenin and retinoic acid signaling in the hierarchy of the scale / feather fate specification gene networks, opening up new possibilities to understand the control switches of multi-component organ phenotypes.

overall_design: Chicken E12 metatarsal skin treated with RCAS-CTNNB1, RCAS-GFP, and retinoic acid

first: Cheng-Ming

last: Chuong


title: Single-cell RNA sequencing in Trypanosoma brucei

status: Public on Oct 09 2018

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: Trypanosomes were sorted (0 cells, 1 cell, 50 cells) using a FACSaria III (BD Biosciences; precision: single-cell; nozzle: 100 µm). Forward-scatter area (FCS-A) versus side-scatter area (SSC-A) was used to gate the cells. Trypanosomes were sorted in 48-wells plate (Brand) filled with 2.6 µL of lysis buffer (0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water). Immediately after sorting cells were placed on ice for 5 minutes and stored at -80 °C. 50 and single trypanosomes were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using one fourth of reagents volumes compared to the supplier instructions. PCR amplification was performed using 26 cycles using supplier recommendations. cDNA was purified using XP beads (Beckman Coulter) and recovered in 15 µL of elution buffer (Takara). Libraries were quantified using the Qubit Hs Assay (Life Technologies) and the qualities of the libraries were further monitored using a Bioanalyzer (Agilent). Similar to what has been published previously 19, 1 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended volumes, 10 minuntes for tagmentation at 55 °C and 1 minute extension time during PCR amplification. Libraries were pooled (96 libraries for NextSeq) and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina's NextSeq 500.

sample_organism:
Trypanosoma brucei brucei
other sequences

overall_design: 47 wild-type samples, 1 wild-type negative-control, 47 H3.V-/- H4.V-/- samples, 1 H3.V-/- H4.V-/- negative control

first: Antoine-Emmanuel

last: Saliba

first: Laura

last: Müller

first: Raúl

middle: O

last: Cosentino

first: T

middle: N

last: Siegel


title: RNA Polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling

city: Philadelphia

first: Diep

last: Ganguly

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: Abstract: In plants, the molecular function(s) of the nuclear localised 5’-3’ EXORIBONUCLEASES (XRNs) are unclear, however their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using Parallel Analysis of RNA Ends (PARE) we document a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We find that a major consequence of reducing SAL1 or XRN activity is RNA Polymerase II (Pol II) 3’ read-through. This occurs at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis. Read-through is speculated to have a negative effect on transcript abundance, however we do not observe this. Rather, we identify a strong association between read-though and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (<1,000bp) and expression of the upstream gene. We observe read-though in the proximity of 903 genes upregulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may directly account for up to 23% of genes upregulated in sal1-8. Using APX2 and AT5G43770 as exemplars, we genetically uncouple read-through loci from downstream genes to validate the principle of read-through mediated mRNA regulation, potentially providing one mechanism by which an obstensibly post-transcriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.

overall_design: mRNA sequencing of pharmacologically treated Arabidopsis leaf tissue

first: Peter

last: Crisp

first: Aaron

middle: B

last: Smith

first: Kevin

last: Murray

first: Steven

last: Eichten

first: Anthony

last: Millar

first: Barry

last: Pogson


title: RNA-Seq of chicken embryonic feather/scale recombination skin explants

overall_design: Chicken embryonic epidermis and dermis recombination explants from E7 dorsal and E9 metatarsal skins cultured 3 days


title: Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells

status: Public on Sep 30 2018

city: Chiba

first: Yuki

last: Sawai

address: 1-8-1 Inohana,  Chuo-ku

department: Department of Oral Science

institute: Graduate School of Medicine, Chiba University

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

overall_design: Refer to individual Series


title: Transcriptome analyses of reprogrammed feather / scale chimeric explants revealed co-expressed epithelial gene networks during organ specification


title: Single-cell RNA sequencing in Trypanosoma brucei II

summary: Trypanosomes were sorted (1 cell, 10 cells, 50 cells) using a FACSaria III (BD Biosciences; precision: single-cell; nozzle: 100 µm). Forward-scatter area (FCS-A) versus side-scatter area (SSC-A) was used to gate the cells. Trypanosomes were sorted in 48-wells plate (Brand) filled with 2.6 µL of lysis buffer (0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water). Immediately after sorting cells were placed on ice for 5 minutes and stored at -80 °C. 50 and single trypanosomes were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using one fourth of reagents volumes compared to the supplier instructions. PCR amplification was performed using 26 cycles using supplier recommendations. cDNA was purified using XP beads (Beckman Coulter) and recovered in 15 µL of elution buffer (Takara). Libraries were quantified using the Qubit Hs Assay (Life Technologies) and the qualities of the libraries were further monitored using a Bioanalyzer (Agilent). Similar to what has been published previously 19, 1 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended volumes, 10 minuntes for tagmentation at 55 °C and 1 minute extension time during PCR amplification. Libraries were pooled (96 libraries for NextSeq) and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina's NextSeq 500.

first: Panagiota

last: Arampatzi


title: MeDIP-seq of two phytophthora species at mycelium stage

status: Public on Sep 29 2018

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

summary:
We report the 6mA methylation profiling in two Phytophthora species and one psdamt3 mutant. Genomic DNA of Phytophthora sojae P6497 mycelium (3-days old), Phytophthora infestans T30-4 mycelium and psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was extracted and sonicated to 200-400bp using Biorupter UCD-600. The antibody sysy 202003 was used to immunoprecipitation.
We find that 6mA is associated with lowly expressed genes in two Phytophthora species. 6mA methylome is preferentially associated with TEs, the genes and intergenic regions that form the gene-sparse compartments of Phytophthora genomes. In the psdamt3 mutant, 6mA level reduced in TEs and illustrates the uneven reduction pattern around the TSS.

sample_organism:
Phytophthora infestans
Phytophthora sojae

overall_design: Examination of N6-methyladenine in two phytophthora species

first: Suomeng

last: Dong

first: Han

last: Chen


title: Role of Hac1 in unfolded protein response in Candida parapsilosis

status: Public on Oct 08 2018

city: Dublin

first: Geraldine

last: Butler

address: Belfield, Dublin 4

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute

summary:
Investigation of the role of HAC1 using transcriptional profiling of Candida parapsilosis treated with 5 mM dithiothreitol
Gene expression of wild type and hac1 deletion strains were compared during growth in YPD only and growth in YPD with 5 mM DTT

overall_design: 4 independent conditions with three replicates of each, generating 12 samples.

first: Mihaela

last: Ola

first: Elise

last: Iracane

first: Paul

last: Donovan

first: Linda

last: Holland


title: Differential effects of a glucagon-like peptide 1 receptor agonist in NAFLD and in response to hepatectomy

status: Public on Sep 11 2018

city: MADRID

last: VALDECANTOS

state: MADRID

address: C/ARTURO DUPERIER, 4

country: Spain

institute: IIB ALBERTO SOLS

summary: The genomic analysis of liver from mice fed with standard or MCD diet and treated with FC-GLP-1 during two weeks before 70%partial hepatectomy (PH) and after 2 weeks PH resulted in a set of genes regulated by diet and other set regulated differentially by treatment in MCD treated animals. These genes are apparently responsible for the reversion and prevention of NAS and improvement in hepatic regeneration induced by drug treatment

overall_design: All microarray analyses were performed with RNA samples obtained from four independent liver from animals with different diet and drug treatmens.

first: M

last: Valdecantos

first: Laura

last: Ruiz

first: Angela


title: Cyclic diguanylate regulates virulence factor genes via multiple riboswitches in Clostridium difficile

status: Public on Sep 20 2018

city: Chapel Hill

first: Rita

last: Tamayo

state: NC

address: 125 Mason Farm Rd, CB# 7290

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary: The c-di-GMP regulon in C. difficile

overall_design: Transcriptional analyses of C. difficile with basal and elevated intracellular c-di-GMP

first: Robert

last: McKee

first: Carissa

last: Harvest


title: Chromatin immunoprecipitation sequencing of VgrR–DNA-binding landscapes

status: Public on Sep 22 2018

city: BeiJing

first: ChaoYing

last: Deng

state: BeiJing

address: No. 1 Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: ChIP-seq database identifies genes with promoter regions bound by VgrR in X. campestris pv. campestris grown under osmostress conditions

sample_organism: Xanthomonas campestris pv. campestris str. 8004

overall_design: Examination of VgrR–DNA-binding landscapes in the genome of X. campestris pv. campestris 8004 between the WT strain and prc mutant both grown under osmostress conditions.

first: Chaoying

first: Huan

last: Zhang

first: Wei

last: Qian


title: THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY

status: Public on Sep 14 2018

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University


title: Identification of Specific MicroRNA Biomarkers in Early Stage of Hepatocellular injury, Cholestasis, and Steatosis in Rat

status: Public on Sep 26 2018

city: Nagoya

first: Takumi

last: Kagawa

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Drug Safety Sciences

institute: Nagoya university

type: Non-coding RNA profiling by high throughput sequencing

summary: Recently, study on circulating microRNAs (miRNAs) as potential biomarkers of drug-induced liver injury (DILI), has received increasing attention. It has been demonstrated that miR-122 and miR-192, which are liver enriched, could be potential biomarkers of DILI, however, these miRNAs cannot discern types of injuries. In the present study, we comprehensively analyzed time-dependent plasma miRNA profiles in rats with drug- or chemical-induced hepatocellular injury, cholestasis, and steatosis with high-throughput miRNA sequencing. To enable comparison of miRNA expression levels between DILI models with different severity and peaks of injuries, stages of injury were defined as early, middle and late, according to cluster patterns of miRNA expression profiles. Through differential analysis, we characterized miRNAs that were specifically up- or down-regulated in each DILI model. Interestingly, several miRNAs were dramatically changed earlier than traditional biomarkers such as ALT and AST. For example, in APAP-induced hepatocellular injury model, let-7b-5p was up-regulated as early as 3 h after dosing, while significant change in ALT level was observed at 24 h. Thereafter, we focused on the DILI type-specific miRNAs which were up-regulated at early stage of injury. RT-qPCR study validated that let-7b-5p and miR-1-3p for hepatocellular injury, miR-143-3p and miR-218a-5p for cholestasis, and miR-320-3p for steatosis models have shown significant increase in the early stage of the injuries. The present study suggests the utility of miRNAs as specific biomarkers for early detection of DILI.

overall_design: Time-dependent plasma miRNA profiles in rats with hepatocellular injury, cholestasis, and steatosis were comprehensively analyzed with MiSeq system (Illumina).

first: Yuji

last: Shirai

first: Shingo

last: Oda

first: Tsuyoshi

last: Yokoi


title: Transcriptomes of two phytophthora species at mycelium stage

first: Haidong

last: Shu

summary:
Purpose and methods:Transcriptome profiling of Phytophthora sojae P6497 mycelium (3-days old) and Phytophthora infestans T30-4 mycelium (6-days old) were generated to find out the relationship between 6mA methylation and gene expression. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiling of P. sojae psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was generated to check the differential expressed genes (DEGs) between the mutant and wild-type P. sojae P6497. Read counts was calculated using featureCounts, and DEGs was calculated using DEseq2 with |log2FC|≥1, y-axis is FDR<0.05.
Conclusions: 6mA is associated with lowly expressed genes. Examination of differentially expressed genes (DEGs) in psdamt3 uncovers a total of 3156 genes, with 1544 genes up-regulated and 1622 genes down-regulated.

platform_organism:
Phytophthora infestans
Phytophthora sojae

overall_design: mRNA profiles of Phytophthora sojae P6497 mycelium (WT,3-days old),PsDAMT3 mycelium(mu,3-days old)and Phytophthora infestans T30-4 mycelium (6-days old) were generated by deep sequencing, in two or three replicates.

first: Suomeng

last: Dong

first: Han

last: Chen


title: Identification of a prognostic hypoxia- associated gene set in IDH1 mutant glioma

status: Public on Sep 25 2018

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg

summary: Glioma growth is often accompanied by a hypoxic microenvironment favorable for the induction and maintenance of the glioma stem cell (GSC) phenotype. Due to the paucity of cell models of Isocitrate Dehydrogenase 1 mutant (IDH1mut) GSCs, biology under hypoxic conditions has not been sufficiently studied as compared to IDH1 wildtype (IDH1wt) GSCs. We therefore grew well-characterized IDH1mut (n = 4) and IDH1wt (n = 4) GSC lines under normoxic (20%) and hypoxic (1.5%) culture conditions and harvested mRNA after 72 h. Transcriptome analyses were performed and hypoxia regulated genes were further analyzed using the expression and clinical data of the lower grade glioma cohort of The Cancer Genome Atlas (LGG TCGA) in a confirmatory approach and to test for possible survival associations. Results show that global expression changes were more pronounced in IDH1wt than in IDH1mut GSCs. However, when focusing on known hypoxia-regulated gene sets, enrichment analyses showed a comparable regulation in both IDH1mut and IDH1wt GSCs. Of 272 significantly up-regulated genes under hypoxic conditions in IDH1mut GSCs a hypoxia-related survival score (HRS-score) of five genes (LYVE1, FAM162A, WNT6, OTP, PLOD1) was identified by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm which was able to predict survival independent of age, 1p19q co-deletion status and WHO grade (II vs. III) in the LGG TCGA cohort and in the Rembrandt dataset. Altogether, we were able to identify and validate a novel hypoxia-related survival score in IDH1mut GSCs consisting of five hypoxia-regulated genes which was significantly associated with patient survival independent of known prognostic confounders.

overall_design: Comparative transcriptomic analysis of n=4 IDHmut and n=4 IDHwt glioma stem cell lines grown under hypoxic or normoxic conditions.

first: Rolf

last: Warta

first: Philip

last: Dao Trong


title: Global Gene Expression of H9 hESC with different passage numbers

status: Public on Sep 04 2018

city: Seoul

first: Hyuk-Jin

last: Cha

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmacy

institute: Seoul National University

summary: Transcriptome profile was obtained from a set of human embryonic stem cell (hESCs) line (WA09: H9) with different passage numbers (P1: 40s, P2: 100s, P3: 200s, P4: 300s passage). Culture adaptation occurs in hESCs during repeated in vitro culture to acquire ‘survival advantage’ to be highly resistant to various stresses. In special, difference in gene expression profile of cell death or apoptotic gene signature was evident between P1/P2 and P3/P4 hESCs.

overall_design:
Microarray analysis of human embryonic stem cells (hESCs) with different passage numbers
P1: H9 hESCs (40s passage), P2: H9 hESCs (100s passage), P3: H9 hESCs (200s passage), P4: H9 hESCs (300s passage)


title: Adenosinergic signaling alters natural killer cell functional responses

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Purpose: The goal of this study was to globally characterize the transcript levels of genes NK cells in the presence or absence of adenosine

overall_design: Method: polyA selection of mRNA from adenosine treated and untreated cells (n=3 biological replicates) and sequenced on a NovaSeq6000

last: Chambers

last: Lanman

first: Jiao

last: Wang

first: Hao

last: Yu

first: Sandro

last: Matosevic

first: Kyle

last: Lupo


title: Comprehensive transcriptome profiling and identification of potential genes responsible for salt tolerance in tall fescue leaves under salinity stress

status: Public on Sep 15 2018

city: Wuhan

first: Erick

last: Amombo

state: China

address: Wuhan Botanical Garden

institute: Wuhan Botanical Garden Chinese Academy of Science

summary: illumina RNA sequencing of tall fescue leaves generated a total of raw 144,339 reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to functional databases. Further analysis revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. Totally, 1,862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs 24 h salt treatment. Protein interaction analysis revealed the high interaction of chaperonins and Rubisco proteins in 48h vs 24h salt treatment

overall_design: one control one 24h one 48h

first: Jinmin

last: Fu

first: Guangyang

first: Xiaoning

last: Li


title: Transcriptomic study of Arabidopsis quadruple mutant (quad) for bassinosteroid receptors (BRI1, BRL1 & BRL3) and correceptor (BAK1), in control conditions and under severe drought

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Abstract: Drought is the primary cause of global agricultural losses and represents a major threat to worldwide food security. Currently, plant biotechnology stands out as the most promising strategy to increase crop growth in rain-fed conditions. The main mechanisms underlying drought resistance have been uncovered by studies of plant physiology and by engineering crops with drought-resistant genes. However, plants with enhanced drought resistance usually display lower levels of growth, highlighting the need to search for novel strategies capable of uncoupling drought resistance from growth. Here, we show that the brassinosteroid family of receptors, in addition to promoting growth, guides phenotypic adaptation to a great variety of drought stress traits analyzed herein. Whilst mutations in the ubiquitously localized BRI1 receptor pathway show an enhanced drought resistance at the expense of plant growth, we found that vascular-enriched BRL3 receptors confer drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress the BRL3 receptor pathway triggers the synthesis and mobilization of osmoprotectant metabolites, mainly proline and sugars. This preferentially occurs in the vascular tissues of the roots and favors overall plant growth. Altogether, our results uncover a new role for the spatial control of BR signaling in drought tolerance, and offer a novel strategy to address food security issues in an increasingly water-limited climate.

overall_design: 28 days-old whole plants (WT and quad) were collected from soil an flash-frozen. Experiment with a time-course design. Time 0: control condition, Time2: 2 days either in watered conditions or drought (water-holding). Time4: 4 days either in watered conditions or drought. Time 6: 6 days under watered conditions or drought. 2 Biological replicates were collected per each genotype and condition. Arrays were designed by hybridating together quad and WT for each condition in the same microarray (Agilent two-color microarrays). For the second biological replicate a dye-swap was performed in order to avoid any dye bias.

first: Norma

last: Fàbregas

first: Ana

middle: I

last: Caño-Delgado


title: scRNAseq reveals mechanisms of Merkel cell carcinoma acquired immunotherapy resistance [2]

status: Public on Sep 01 2018

city: Seattle

first: Kelly

middle: Garneski

last: Paulson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: PBMC and tumor specimen from a Merkel cell carcinoma tumor at time of immunotherapy resistance

overall_design: PBMC and tumor specimen from a human patient with MCPyV associated Merkel cell carcinoma treated with T cell therapy and avelumab (anti-PD-L1), from a time point of late immunotherapy resistance; validation patient

first: Aude

last: Chapuis


title: Transcript Profiling in the Testes and Prostates of Postnatal Day 30 Sprague-Dawley Rats Exposed Prenatally and Lactationally to 2-Hydroxy-4-methoxybenzophenone

status: Public on Aug 31 2018

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research


title: human pituitary and prolactinoma

status: Public on Sep 03 2018

city: Shanghai

first: Ni

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: Analysis the different gene expression of prolactinomas and normal pituitary tissues. Prolactinoma is a benign pituitary tumor that produces excessive prolactin  resulting in hyperprolactinemia and another disease.Tissues were microdissected and removed using the surgical microscope, rinsed in sterile saline, snap-frozen in liquid nitrogen, and stored (-80 ℃) until analysis. Results  provide insight into understanding the difference of gene expression in prolacinomas.

overall_design: 5 prolactinoma and 4 normal pituitaries

first: Zhebao

last: Wu

first: Zerui


title: Transcriptome analysis of wild-type and maternal ybx1 mutant zebrafish embryos during early development

city: Beijing

first: Jiawei

last: Sun

address: Medical Science Building, Tsinghua University

institute: School of Life Sciences, Tsinghua University

summary: To study the function of zebrafish Ybx1 during early embryogenesis, we generated maternal ybx1 (Mybx1) mutant using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic loss of maternal mRNA decay and zygotic genome activation in Mybx1 embryos during maternal-to-zygotic transition.

overall_design: Total RNA samples were prepared using WT and Mybx1 embryos at 0 hpf and 6 hpf. Ribosomal RNA depletion was performed before RNA-seq.

first: Anming

last: Meng


title: Transcriptome analysis of a spray drying-resistant subpopulation reveals a zinc-dependent mechanism for robustness in L. lactis SK11

status: Public on Sep 08 2018

city: Ede

first: Annereinou

last: Dijkstra

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary: The viability of starter cultures is essential for an adequate contribution to the fermentation process and end-product. Therefore, robustness during processing and storage is an important characteristic of starter culture strains. For instance, during spray drying cells are exposed to heat and oxidative stress, generally resulting in loss of viability. In this study, we exposed the industrially relevant but stress-sensitive Lactococcus lactis strain SK11 to two cycles of heat stress, with intermediate recovery and cultivation at moderate temperatures. After these two cycles of heat exposure, the abundance of robust derivatives was increased as compared with the original culture, which enabled isolation of heat-resistant subpopulations displaying up to 1000-fold enhanced heat stress survival. Moreover, this heat-resistant subpopulation demonstrated an increased survival during spray drying. Derivatives from two independent lineages displayed different transcriptome changes as compared with the wild type strain, indicating that the increased robustness within these lineages was established by different adaptive strategies. Nevertheless, an overlap in differential gene expression in all five derivatives tested in both lineages included three genes in an operon involved in zinc transport. The link between zinc homeostasis and heat stress survival in L. lactis was experimentally established by culturing of the wild type strain SK11 in medium with various levels of zinc ions, which resulted in alterations in heat stress survival phenotypes.   This study demonstrates that robust derivatives of a relatively sensitive L. lactis strain can be isolated by repeated exposure to heat stress. Moreover, this work demonstrates that transcriptome analysis of these robust derivatives can provide clues for improvement of the robustness of the original strain. This could boost the industrial application of strains with specific desirable traits but inadequate robustness characteristics.

overall_design: Five robust derivatives were tested against the original strain SK11, duplicate samples.

middle: R

first: Marjo

last: Starrenburg

first: Tilman

last: Todt

first: Sacha

last: van Hijum

first: Jeroen

last: Hugenholtz

first: Peter

last: Bron


title: Gene expression data of testis of PND 30 Sprague-Dawley rats (SD:Hsd) dosed prenatally and lactationally with HMB

summary: 2-hydroxy-4-methoxybenzophenone (HMB) has been reported to have weak estrogenic activity by in vivo and in vitro studies, making it a chemical with potential reproductive concern. To explore if perinatal HMB exposure altered the gene expression profiling in the rat testis, we analyzed whole genome and mitochondria-related gene expression profiling on the testis ontained from Sprague-Dawley rat offspring exposed prenatally and lactationally to varying dose of HMB.

overall_design: Time-mated Sprague-Dawley female rats (11-13 weeks old) were provided ad libitum low-phytoestrogen chow containing 0 (control), 3000, or 30000 ppm HMB from GD 6-PND 21. Testis from PND 30 male Sprague-Dawley rats exposed prenatally and lactationally to HMB were collected (n=5 per group). RNA were extracted and used for whole genome expression array (Agilent Technologies; 8 x 60K format).

first: Tao

last: Han

first: Noriko

last: Nakamura


title: Gene expression data of prostate of PND 30 Sprague-Dawley rats (SD:Hsd) dosed prenatally and lactationally with HMB

summary: 2-hydroxy-4-methoxybenzophenone (HMB) has been reported to have weak estrogenic activity by in vivo and in vitro studies, making it a chemical with potential reproductive concern. To explore if perinatal HMB exposure altered the gene expression profiling in the rat prostate, we analyzed whole genome and mitochondria-related gene expression profiling on the Prostate ontained from Sprague-Dawley rat offspring exposed prenatally and lactationally to varying dose of HMB.

overall_design: Time-mated Sprague-Dawley female rats (11-13 weeks old) were provided ad libitum low-phytoestrogen chow containing 0 (control), 3000, or 30000 ppm HMB from GD 6-PND 21. Prostate from PND 30 male Sprague-Dawley rats exposed prenatally and lactationally to HMB were collected (n=5 per group). RNA were extracted and used for whole genome expression array (Agilent Technologies; 8 x 60K format).


title: Genome-wide characterization of the Fur regulatory network reveals a link between catechol degradation and bacillibactin metabolism in Bacillus subtilis

status: Public on Aug 29 2018

city: Ithaca

first: Hualiang

last: Pi

state: NY

address: 125 Wing Dr.

department: Microbiology

institute: Cornell University

summary: The goal of this study is to obtain a genomic view of the Fur regulatory network under both iron replete and iron deficient conditions in Bacillus subtilis using ChIP-seq. Besides the known Fur target sites, 70 putative DNA binding sites were identified, and the vast majority had higher occupancy under iron sufficient conditions. In addition,we discovered a role for catechol degradation in bacillibactin metabolism, and provided evidence that catechol 2,3-dioxygenase can detoxify endogenously produced catechol substrates in addition to its more widely studied role in biodegradation of environmental aromatic compounds and pollutants.

overall_design: To modulate intracellular iron levels, we employed a high-affinity Fe2+ exporter FrvA from L. monocytogenes to impose iron starvation. Bacillus wild-type cells (with C-terminal FLAG-tagged Fur at its native locus and an IPTG-inducible ectopic copy of frvA integrated at amyE locus) were harvested at 0 and 30 min after IPTG induction to study Fur-dependent regulation under iron sufficient and deficient conditions, respectively.

first: John

last: Helmann


title: RARγ is required for mesodermal gene expression prior to gastrulation

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

institute: MGH Cancer Center

summary: The developing vertebrate embryo is exquisitely sensitive to retinoic acid (RA) concentration, particularly during anteroposterior patterning. In contrast to Nodal and Wnt signaling, RA was not previously considered to be an instructive signal in mesoderm formation during gastrulation. Here we show that RARγ is indispensable for the expression of early mesoderm markers and is, therefore, an obligatory factor in mesodermal competence and/or maintenance. We identified several novel targets up-regulated by RAR signaling in the early gastrula that are expressed in the circumblastoporal ring and linked to mesodermal development. Despite overlapping expression patterns of the RA synthetic enzyme, Aldh1a2 and the RA- degrading enzyme, Cyp26a1, RARγ1 functions as a transcriptional activator in early mesoderm development, suggesting that RA ligand is available to the embryo earlier than previously appreciated. RARγ1 is required for cellular adhesion, as revealed by spontaneous dissociation and depletion of N-CAM mRNA in animal caps harvested from RARγ1 knockdown embryos. RARγ1 knockdown obliterates somite boundaries, and causes loss of MYOD protein in the presomitic mesoderm, but ectopic, persistent expression of MYOD protein in the trunk. Thus, RARγ1 is required for stabilizing the mesodermal fate, myogenic commitment, somite boundary formation, and terminal, skeletal muscle differentiation.

overall_design: RNA-sequencing of gastrula stage embryos treated with RAR agonist TTNPB or RAR antagonist AGN193109

first: Amanda

last: Jenesick

first: Weiyi

last: Tang

first: Toshi

first: Bruce

last: Blumberg


title: MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells

status: Public on Aug 28 2018

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Proper mitochondrial function plays a central role in cellular metabolism. Various diseases as well as aging are associated with diminished mitochondrial function. Previously, we identified 19 miRNAs putatively involved in the regulation of mitochondrial metabolism in skeletal muscle, a highly metabolically active tissue. In the present study, these 19 miRNAs were individually silenced in C2C12 myotubes using antisense oligonucleotides, followed by measurement of the expression of 27 genes known to play a major role in regulating mitochondrial metabolism. Based on the outcomes, we then focused on miR-382-5p and identified pathways affected by its silencing using microarrays, investigated protein expression and studied cellular respiration. Silencing of miRNA-382-5p significantly increased the expression of several genes involved in mitochondrial dynamics and -biogenesis. Microarray analysis of C2C12 myotubes silenced for miRNA-382-5p revealed a collective downregulation of mitochondrial ribosomal proteins and respiratory chain proteins. This effect was accompanied by an imbalance between mitochondrial proteins encoded by the nuclear and mitochondrial DNA (1.35-fold, p<0.01) and an induction of HSP60 protein (1.31-fold, p<0.05), indicating activation of the mitochondrial unfolded protein response (mtUPR). Furthermore, silencing of miR-382-5p reduced basal oxygen consumption rate by 14% (p<0.05) without affecting mitochondrial content, pointing towards a more efficient mitochondrial function as a result of improved mitochondrial quality control. Taken together, silencing of miR-382-5p induces a mitonuclear protein imbalance and activates the mtUPR in skeletal muscle, a phenomenon that was previously associated with improved longevity.

overall_design: The expression of miR-382 was silenced in C2C12 immortalized mouse myoblast cells, whereafter gene expression profiling was performed by microarray and compared to control.

first: Joris

last: Hoeks

first: Patrick

last: Schrauwen

first: Alexandre

last: Houzelle

first: Dennis

last: Dahlmans

first: Pénélope

last: Andreux

first: Xu

last: Wang

first: Johanna

last: Jörgensen

first: Norman

last: Moullan

first: Sabine

last: Daemen

first: Sander

last: Kersten

first: Johan

last: Auwerx


title: High-throughput single cell transcriptome profiling of plant tissue

city: Walnut Creek

first: Christine

last: Shulse

state: CA

address: 2800 Mitchell Drive

institute: DOE Joint Genome Institute

summary: Plant tissues are composed of diverse cell populations, but their individual transcriptional profiles are not well characterized. High-throughput single cell RNA sequencing technologies can deconvolute heterogeneous tissues but have not been adopted for plants.  Exploiting Arabidopsis root protoplasts as a model, we used Drop-seq to profile >4,000 individual plant cells, capturing a diversity of cell types, identifying novel marker genes, and illuminating developmental trajectories of endodermis and hair cells.

overall_design: Two technical replicates of scRNA-seq data as well as whole tissue RNAseq from 5-day-old Arabidopsis roots were generated using Illumina HiSeq4000

first: Benjamin

middle: J

last: Cole

first: Gina

middle: M

last: Turco

first: Yiwen

last: Zhu

first: Siobhan

last: Brady

first: Diane

last: Dickel


title: ATACseq in T. brucei wild-type and histone variant deletion cell lines.

status: Public on Aug 24 2018

city: Cologne

first: Konrad

last: Förstner

address: Gleueler Str. 60

institute: ZB MED - Information Centre for Life Sciences

summary: 3x107 cells were harvested and washed in 30 ml cold 1x TDB. The pellet was resuspended in 300 µl permeabilization buffer with protease inhibitors, 3 µl of 4 mM digitonin was added and incubated for 5 minutes at RT. The cells were pelleted, resuspended in 600 µl isotonic buffer with protease inhibitors and split in two samples, containing 1x107 and 2x107 cells, respectively. The transposition reaction was performed by adding 50 µl of transposition mix to the pellet (25 µl TD (2x reaction buffer from Nextera kit), 25 µl TDE1 (Tn5 transposase from Nextera kit), 22.5 µl nuclease-free water) and incubation for 30 minutes at 37 °C. For the gDNA control, 200 ng of gDNA was treated in the same manner. The DNA samples were purified using Qiagen MinElute PCR Purification Kit and eluted in 10 µl EB (10 mM Tris-HCl, pH 8). The transposed DNA fragments were amplified using the NEBNext® High-Fidelity 2X PCR Master Mix (M0541) supplied with 2.5 µl of 25 µM barcoded primers and amplification for 13 cycles. The libraries were purified using AMPure XP beads (Beckman Coulter) following the manufacturer’s instructions. The library fragment sizes between 150 and 1000 bp were purified from a 6% polyacrylamide gel. Paired-end 76 bp sequencing was carried out using the Illumina NextSeq system with a mid-output NextSeq 500/550 kit according to the manufacturer’s instructions.

overall_design: ATACseq in T. brucei wild-type, H3.V-/-, H4.V-/- and H3.V-/- H4V-/- cells. Each performed in duplicates with 10 and 20 million cells, respectively. A gDNA control was included to check for biases in accessiblity.

first: Carolin

last: Wedel

first: T

last: Siegel

first: Laura

middle: S

last: Müller


title: Ehrlichia chaffeensis TRP47 binding sites in human genome

status: Public on Aug 14 2018

city: Galveston

first: Clayton

middle: Eugene

last: Kibler

state: TX

address: 301 University Blvd

department: Pathology

institute: UTMB

summary: Ehrlichia chaffeensis is an obligately intracellular bacterium that establishes infection in mononuclear phagocytes through largely undefined reprogramming strategies. Recently, E. chaffeensis effectors Ank200, TRP120, and TRP32 have been shown to function as nucleomodulins that enter the host nucleus and directly modulate transcription of genes implicated in cellular processes such as transcription regulation, apoptosis, phosphorylation, and immune cell activation. In this study, we found that E. chaffeensis TRP47 enters the host cell nucleus and binds regulatory regions of multiple host genes relevant to infection.

overall_design: ChIP-seq was performed using E. chaffensis-infected THP-1 cells at 48 hpi.

first: Jere

middle: W

last: McBride


title: Gene expression analysis of Huh7 cells treated with human or mouse erythroferrone (ERFE)

status: Public on Aug 10 2018

city: Oxford

first: Joao

last: Arezes

state: Oxfordshire

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Analysis of overall gene expression changes  in Huh7 cells after treatment with mouse or human erythroferrone (ERFE)

overall_design: Total RNA was obtained from Huh7 in 24-well plates and treated with human or mouse erythroferrone at 10µg/ml for 24h. Four replicates per condition

first: Niall

last: Foy

first: Kirsty

last: McHugh

first: May

last: Tam

first: Stephen

last: Taylor

first: Hal

last: Drakesmith


title: Gene expression in chicken wing flight feather regeneration

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Avian feather has robust regeneration capability. Long noncoding RNAs (lncRNAs) are non-protein coding transcripts that are involved in various biological processes. We infected the regenerating feather follicles with lentivirus to over express Wnt5a or knock down two lncRNAs (lnc3501&lnc7831) separately. The regenerated follicles were dissected at 4 days after infection. We compared gene expression of infected follicles with normal T4 control follicles. Our results revealed that lncRNAs may modulate Wnt signaling.

overall_design: Feather follicles were plucked to induce regeneration. Lentiviral vectors were used to overexpress (pLVX-Zsgreen) or knockdown (pLL3.7) gene expression in the feather follicle. The regenerated feather follicles from the wing flight feather were dissected under a stereo dissection microscope. Total RNAs of five pooled follicles were extracted by using Trizol reagent and standard protocols were followed.

first: Zhicao

last: Yue

first: Xiang

last: Lin


title: Microarray transcriptomic data from LNCaP cells treated with vehicle, 10 nM bufalin or 20 nM bufalin for 24 h

status: Public on Aug 13 2018

city: Hershey

first: Junxuan

last: Lu

state: Pennsylvania

address: R130 Pharmacology, PO BOX 850

department: Pharmacology

institute: Penn State College of Medicine

summary: Bufalin is a major cardiotonic compound in the traditional Chinese medicine Chanshu preparations of toad skin secretions. Cell culture studies have suggested anti-cancer potential involving multiple cellular processes including differentiation, apoptosis, senescence and angiogenesis. In prostate cancer (PCa) cell models, P53-dependent and independent caspase-mediated apoptosis and androgen receptor (AR) antagonism have been described for bufalin at micromolar concentrations. Since pharmacokinetic study in humans indicated single nanomolar bufalin was safely achievable in the peripheral circulation, we evaluated its cellular activity within range with the AR-positive, P53-wild type and PTEN-negative human LNCaP PCa cells in vitro. Our data show that bufalin induced caspase-mediated apoptosis at 10 nanomolar or higher exposure concentration with concomitant suppression of AR protein and its best known target prostate specific antigen (PSA) and steroid receptor co-activator 1 and 3 (SRC-1, SRC-3). Bufalin exposure induced protein abundance of P53 (not mRNA) and P21Cip1, G2 arrest and increased senescence-like phenotype (SA-galactosidase). Small interference RNA knocking down of P53 attenuated bufalin-induced senescence, whereas knocking down of P21Cip1 exacerbated bufalin-induced caspase-mediated apoptosis. In vivo, daily i.p. injection of bufalin (1.5 mg/kg body weight) for 9 weeks delayed LNCaP subcutaneous xenograft tumor growth in NSG SCID mice with a 67% decrease of final weight without affecting body weight. Tumors from bufalin-treated mice exhibited increased phospho-P53 and SA-galactosidase without detectable caspase-mediated apoptosis or suppression of AR and PSA. Our data suggest potential applications of bufalin in adjuvant therapy of PCa recurrence in patients or chemoprevention of prostate carcinogenesis, engaging a selective activation of P53-senescence.

overall_design: Microarray-based transcriptome analysis was performed by using LNCaP cells treated with vehicle, 10 nM bufalin or 20 nM bufalin for 24h

first: Yong

last: Zhang

first: Michael

last: Melkus

first: Peixin

last: Jiang

first: Sangyub

last: Kim


title: Genome-wide chromatin reconstitution with Drosophila embryo extract and nucleosome positioning by CG7372 and su(Hw)

city: Planegg-Martinsried

first: Sandro

last: Baldi

address: Großhaderner Strasse 9

department: BMC Molecular Biology

institute: LMU Munich

summary: We have reconstituted chromatin in vitro on a genome-wide level by incubating total genomic Drosophila melanogaster DNA in D. melanogaster preblastoderm embryo extract. We analyzed chromatin reconstituted with 1) extract from wildtype embryos, 2) extract from embryos lacking the chromatin remodeling enzyme subunit Acf , and 3) extract from Acf-mutant embryos supplemented with recombinant ACF (Acf + Iswi). As a comparison, we also reconstituted chromatin on genomic DNA by salt gradient dialysis. We determined nucleosome positions in reconstituted chromatin by MNase-digestion followed by paired-end sequencing of mononucleosomal fragments. We also determined nucleosome positions in D. melanogaster BG3-c2 cells depleted for the proteins su(Hw) and CG7372 by RNA interference.

overall_design: Chromatin was assembled in vitro on Drosophila genomic DNA either by incubating the DNA in Drosophila preblastoderm embryo extract or by salt gradient dialysis of purified histones onto the DNA. The assembled chromatin was digested with MNase to predominantly mononucleosomal fragments. DNA was purified and sequenced paired-end on an Illumina 1500 HiSeq machine. For mapping nucleosomes in Drosophila BG3-c2 cells, nuclei were isolated and chromatin digested with MNase. DNA was purified, run on an agarose gel, the mononucleosomal band cut out and sequenced paired-end on an Illumina 1500 HiSeq machine.

first: Peter

last: Becker


title: Axial progenitors generate trunk neural crest cells in vitro

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary: The in vitro generation of neural crest (NC) cells from human pluripotent stem cells (hPSCs) is a valuable approach to study human NC biology and isolate NC derivatives for disease modelling/regenerative medicine applications. However, conventional differentiation protocols induce only a modest yield of NC cells corresponding to the trunk level. Here we show that trunk NC cells and, their downstream derivatives, sympathoadrenal progenitors, can be produced at a high efficiency from hPSC-derived axial progenitors, the in vitro counterparts of the posteriorly-located drivers of embryonic axis elongation. Moreover, using transcriptome analysis, we define the molecular signatures associated with the emergence of human NC cells of distinct axial identities. Collectively, our findings indicate that a post-cranial NC state is achieved through two different routes: the birth of cardiac and vagal NC is facilitated by retinoic acid-induced posteriorisation of an anterior precursor whereas a trunk fate relies on a posterior axial progenitor intermediate.

overall_design: Gene expression profiling utilised total RNA extracted from ES cells (N=3); hPSC derived Cranial neural crest precursors (N=3); hPSC derived Cranial neural crest cells (N=3);  hPSC derived Cranial neural crest cells after RA treatment to posteriorise (N=3); hPSC derived Neuromesodermal progenitors (N=3); hPSC derived Trunk neural crest progenitors (N=3); hPSC derived trunk neural crest cells (N=3)

first: Thomas

last: Frith

first: Illaria

last: Granata

first: Erin

last: Stout

first: Matthew

last: Wind

first: Oliver

last: Thompson

first: Dylan

last: Stavish

first: James

last: Hackland

first: Konstantinos

last: Anastassiadis

first: Mina

last: Gouti

last: Briscoe

first: Val

last: Wilson

first: Mario

last: Guarracino

last: Andrews

first: Anestis

last: Tsakridis