title: Expression data from mouse brain in response to intracerebral LPS challenge

city: Edinburgh

first: Barry

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary:
A model of self-limiting acute brain inflammation induced by intracerebral injection of LPS was validated in the mouse tailored to enable study of inflammation resolution.
Transcriptome-wide changes in gene expression were assessed by microarray at induction and resolution phases of the inflammatory response

overall_design: C57Bl/6J mice received intrastriatal injection of LPS or PBS and brain samples were dissected from the injected hemisphere after transcardiac saline perfusion  for mRNA and miRNA extraction. Samples were collected 1 d after LPS (induction phase, n=9), 4 d after LPS (resolution phase, n=9) or 4 d after PBS (n=9) treatments. For each treatment group, samples were pooled to form three biological replicates for microarray i.e. each replicate comprised a pooled RNA sample derived from 3 different mice (with equivalent quantity of RNA from each constituent sample).

first: Claire

last: Davies


title: Dietary Effects on T Cell Methylomes and Functional Inhibition of DNA Methyltransferase Attenuates Salt-Sensitive Hypertension and Renal Damage in Dahl SS Rat

status: Public on Jun 10 2019

city: Wauwatosa

first: John

middle: Henry

last: Dasinger

state: Wisconsin

address: 8701 W. Watertown Plank Road

country: USA

institute: Medical College of Wisconsin

type: Methylation profiling by high throughput sequencing

summary: The Dahl salt-sensitive (SS) rat is an established model of hypertension and renal damage that is accompanied with an activation of the immune system in the response to a high salt diet. Investigations into the effects of sodium-independent and –dependent components of the diet were shown to affect the disease phenotype with Dahl SS/JrHsdMcwi (SS/MCW) rats maintained on a purified diet (AIN-76A) presenting with a more severe phenotype relative to the grain-fed Dahl SS/JrHsdMcwiCrl rat (SS/CRL). Recently, T cells isolated from the kidneys of the two strains unveiled that transcriptomic and functional differences may contribute to the susceptibility of hypertension and renal damage. Since contributions of the immune system, environment and diet are documented to alter this phenotype, this present study examined the epigenetic profile of T cells isolated from the periphery and the kidney from these strains. In response to high salt challenge, the methylome of T cells isolated from the kidney of SS/MCW exhibit significantly more differentially methylated regions with a preference for hypermethylation compared to the SS/CRL kidney T cells. Circulating T cells exhibited similar methylation profiles between the strains. Utilizing transcriptomic data from T cells isolated from the same animals upon which the DNA methylation analysis was performed, a predominant negative correlation was observed between gene expression and DNA methylation in all groups. Lastly, inhibition of DNA methyltransferases blunted salt-induced hypertension and renal damage in the SS/MCW rats providing a functional role for methylation. The study demonstrated the influence of epigenetic modifications to immune cell function, highlighting the need for further investigations.

overall_design: 5 experimental groups; 4 pools/experimental group; 3 rats/pool

middle: H

first: Ammar

middle: J

last: Alsheikh

first: Justine

middle: M

last: Abais-Battad

first: Xiaoqing

last: Pan

first: Daniel

last: Fehrenbach

first: Hayley

last: Lund

first: Michelle

last: Roberts

first: Allen

middle: W

last: Cowley Jr

first: Srividya

last: Kidambi

first: Theodore

middle: A

last: Kotchen

first: Pengyuan

last: Liu

first: Mingyu

last: Liang

first: David

middle: L

last: Mattson


title: CRKL regulates alternative splicing of genes that function in tumorigenesis and cancer progression

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

type: Expression profiling by high throughput sequencing

summary: CRKL adaptor protein was demonstrated to have important effects in various types of human cancer and contributes to malignant cell growth and chemoresistance as an overexpressed oncoprotein in cervical carcinoma. But the special molecular mechanisms of CRKL in cervical cancer remain unknown. Here we reported that CRKL regulates genes in cervical cancer related pathways via targeting alternative splicing. We analyzed the expression level of CRKL in 300 cervical cancer tissue samples available in TCGA database, showing a significant increase expression in Stage I cancer samples. From these tumor samples, we selected 40 cancer samples with 20 showing high CRKL expression and 20 showing low, which were analyzed for the potential impact of CRKL on alternative splicing regulation of cancer transcriptome. We further explored the potential function of CRKL in promoting cell proliferation and regulating alternative splicing in HeLa cells using shRNA to knock-down CRKL expression. More importantly, we showed that 34 (94%) of CRKL-regulated alternative splicing events detected in HeLa cells could be validated by qPCR approach and more than a half of these validated events detected in HeLa cells were also correlated with the CRKL expression level in cervical cancers. These results together support a conclusion that CRKL adaptor protein extensively regulates alternative splicing of many genes which are important in tumorigenesis and cancer progression, which expands the functional importance of signaling adaptors in coordinating the dynamic activation of signaling pathways with cellular responses at the alternative splicing level.

overall_design: transcrptional analysis of CRKL knockdown and control in Hela cells

first: Qingling

last: Song


title: MenSCs inhibit HCC growth through oncogenic pathway suppression via regulating 5-hmC in enhancer elements [RNA-seq]

city: Hangzhou

first: Yichen

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

department: College of Medicine

institute: Zhejiang University

summary: We utilize MeDIP-seq, hMeDIP-seq and RNA-seq technologies to explore the epigenetic alterations in HCC after MenSC therapy. We provide distinct epigenetic landscapes of HCC cells mediated by MenSCs and demonstrate that MenSCs exert anticancer functions by regulating 5-hmC and 5-mC abundance in enhancer and promoter regions of oncogenic pathways. Deactivation of PI3K/AKT and RAF/ERK signaling attenuated the inhibition of FOXO3 and promoted downstream apoptosis. Moreover, an increase in PTEN further strengthened the suppressive effect on PI3K/AKT. Additionally, inactivation of phosphorylated ERK repressed c-myc-mediated EMT. Taken together, our results provided important epigenetic evidence for clarifying the mechanism of crosstalk between cancer and MSCs in the microenvironment and screening effective epigenetic targets for future therapy strategies based on modified MSCs.

overall_design: 5-hmC, 5-mC profiles of HCC cells after MenSC therapy

first: Charlie

last: Xiang


title: MenSCs inhibit HCC growth through oncogenic pathway suppression via regulating 5-hmC in enhancer elements [MeDIP-seq]


title: MenSCs inhibit HCC growth through oncogenic pathway suppression via regulating 5-hmC in enhancer elements [hMeDIP-seq]


title: 2-hydroxyglutarate inhibits transcription factor mediated differentiation by preventing H3K9 demethylation

city: New York

first: Richard

last: Koche

state: NY

address: 430 East 67th Street

institute: Sloan Kettering Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
ATAC-seq associates impairment of myogenic differentiation in cells with an IDH2 mutation with differences in chromatin accessibility. Differences are especially apparent in regions flanking binding sites for myogenic regulatory factors and key myogenesis noncoding RNA linc-MD1.

Oncogenic IDH1/2 mutations produce 2-hydroxyglutarate (2HG), resulting in competitive inhibition of DNA and protein demethylation. IDH-mutant cancer cells show an inability to differentiate but whether 2HG accumulation is sufficient to perturb differentiation directed by lineage-specifying transcription factors is unknown. A MyoD-driven model was used to study the role of IDH mutations in the differentiation of mesenchymal cells. The presence of 2HG produced by oncogenic IDH2 blocks the ability of MyoD to drive differentiation into myotubes. DNA 5mC hypermethylation is dispensable while H3K9 hypermethylation is required for this differentiation block. IDH2-R172K mutation results in H3K9 hypermethylation and impaired accessibility at myogenic chromatin regions but does not result in genome-wide decrease in accessibility. The results demonstrate the ability of the oncometabolite to 2HG block transcription factor-mediated differentiation in a molecularly defined system.

overall_design:
ATAC-seq of mouse 10T1/2 cells, WT for IDH2 vs. R172K mutation of IDH2, with tamoxifen-inducible differentiation via activation of MyoD-ER.
ChIP-seq of mouse 10T1/2 cells, WT for IDH2 vs. R172K mutation of IDH2, with tamoxifen-inducible differentiation via activation of MyoD-ER, with and without UNC0638, a G9a/GLP inhibitor.

first: Juan

last: Schvartzman

first: Vincent

last: Reuter

middle: P

first: Craig

last: Thompson


title: Differential RNA-seq analysis of chemosensory sensilla of the wing

city: New Haven

first: Zhe

last: He

state: CT

address: Carlson Lab / KBT 1142 Dept. of Molecular, Cellular, and Developmental Biology Yale University P.O. Box 208103

department: Molecular, Cellular and Developmental Biology

institute: Yale University

summary: We carry out a differential RNAseq analysis of a row of sensilla on the anterior wing margin and find expression of many genes associated with pheromone and chemical perception.

overall_design: We collected wings from wild type and from Poxn mutants that lack chemosensory sensilla on the wing.  We performed RNAseq on three biological replicates from each genotype.

last: Luo

first: Xueying

last: Shang

first: Jennifer

middle: S

last: Sun

first: John

middle: R

last: Carlson


title: Alpha-1 Antitrypsin Deficiency Liver Disease, Mutational Homogeneity Modulated by Epigenetic Heterogeneity With Links to Obesity

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Alpha-1 antitrypsin deficiency (AATD) liver disease is characterized by marked heterogeneity in presentation and progression, despite a common underlying gene mutation, strongly suggesting the involvement of other genetic and/or epigenetic modifiers. Variation in clinical phenotype has added to the challenge of detection, diagnosis, and testing of new therapies in patients with AATD. We examined the contribution of DNA methylation (5-methylcytosine [5mC]) to AATD liver disease heterogeneity because 5mC responds to environmental and genetic cues and its deregulation is a major driver of liver disease. Using liver biopsies from adults with early-stage AATD and the ZZ genotype, genome-wide 5mC patterns were interrogated. We compared DNA methylation among patients with early AATD, and among patients with normal liver, cirrhosis, and hepatocellular carcinoma derived from multiple etiologic exposures, and linked patient clinical/demographic features. Global analysis revealed significant genomic hypomethylation in AATD liver-impacting genes related to liver cancer, cell cycle, and fibrosis, as well as key regulatory molecules influencing growth, migration, and immune function. Further analysis indicated that 5mC changes are localized, with hypermethylation occurring within a background of genome-wide 5mC loss and with patients with AATD manifesting distinct epigenetic landscapes despite their mutational homogeneity. By integrating clinical data with 5mC landscapes, we observed that CpGs differentially methylated among patients with AATD disease are linked to hallmark clinical features of AATD (e.g., hepatocyte degeneration and polymer accumulation) and further reveal links to well-known sex-specific effects of liver disease progression. Conclusion: Our data reveal molecular epigenetic signatures within this mutationally homogeneous group that point to ways to stratify patients for liver disease risk.

overall_design: Bisulphite converted DNA from the 94 Alpha-1 Antitrypsin Deficiency (AATD) patients  and 14 cirrhotic AATD patients were hybridised to the Illumina Infinium 850K Infinium® MethylationEPIC BeadChip

first: Keith

middle: D

last: Robertson

first: Mark

last: Brantly

first: George

last: Marek

first: Ryan

last: Hlady

first: Liguo

last: Wang


title: IRF1 regulates IFN dependent and independent gene expression

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary: We report the RNA sequencig results for the constitutive and IFN inducible gene expression in respiratory epithelial cell line (BEAS-2B). We generated IRF1 KO BEAS-2B cells using CRISPR method.  Parent and IRF1 KO cells were treated with IFNβ or IFNλ1 for 24h and subjected for RNA isolation and sequencing in Illumina platform. Three independent biological experiments were used for RNA sequenccing.

overall_design: Examination of constitutive and interferon inducible transcriptome by Illumina NGS. Tripliate biological experiments were used to compare the differential gene expression between parental cells to that of IRF1 KO cells.

first: Ronald

last: Rabin


title: Single cell transcriptome of peritoneal cells

status: Public on Jun 09 2019

city: Guangzhou

first: Meijun

last: Si

state: Guangdong

address: 600 Tianhe Ave.

department: Nephrology

institute: The 3rd Affiliated Hospital of Sun Yat-sen University

summary: To define the transcriptomic landscape of human mesothelial cells in response to PD, we analyzed single cell transcriptomes including cells dissociated from normal peritoneum (hernia surgery, n = 3), and peritoneal cells from effluent of short-term PD patients (PD less than 2 weeks, n = 6) and from long-term PD patients (PD more than 6 years, n = 4) ,we demonstrate that mesothelial cells develop hyperglycolysis, a metabolic alteration that is correlated with the development of peritoneal fibrosis.

overall_design: We studied cells dissociated from normal peritoneum (hernia surgery, n = 3  ), and peritoneal cells from effluent of short-term PD patients (PD less than 2 weeks, n = 6) and from long-term PD patients (PD more than 6 years, n = 4)

first: Hui

last: Peng

first: Zhaoyong

last: Hu


title: Whole lung transcriptomics of a house dust mite/cyclic di-GMP model of severe asthma

status: Public on Jun 08 2019

city: Reno

first: William

middle: T

last: Gerthoffer

state: Nevada

address: 1440 N Virginia St

department: Pharmacology

institute: University of Nevada, Reno

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:  Identify whole lung gene expression patterns in a house dust mite model of severe asthma
Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by ribosome-depleted, 100 nt, paired-end, stranded RNA-seq with Illumina HiSeq v4.  Sequence reads were analyzed  with Sailfish-cir to identify linear RNA transcripts and circular RNAs. Differential expression of linear RNAs was assessed with Deseq2 . QRT–PCR validation was performed using TaqMan and SYBR Green methods.
Results: 100 million sequence reads per sample were mapped to the mouse genome (build mm10) using Sailfish-cir to identify linear and circular RNA transcripts. Pathway analysis of differentially expressed genes identified upregulation of gene sets for human Th17 high, Th2 low asthma. An LNA/DNA miR-155 antagonist upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung. Dexamethasone did not consistently reduce expression of Th2 or Th17 biomarker genes.
Conclusions: Cyclic di-GMP plus house dust mite allergens elicited a Th2 low, Th17 high gene expression profile that was not consistently modified by treatment with dexamethasone.

overall_design: Linear and circular RNA transcript expression was compared in whole lung tissue from unsensitized, house dust mite sensitzed, antimiR-155 treated and dexamethasone-treated mice

first: Sabrina

middle: C

last: Ramelli

first: Tong

last: Zhou


title: RNA-seq data for skin tissues from 3-days-old wildtype and RNF31fl/fl-K14-cre mice.

city: Beijing

first: Yong

last: Tang

address: Tsinghua University

department: Medical School

institute: Tsinghua Universtity

summary: mRNA expression profile for skin tissues from 3-days-old wildtype and RNF31fl/fl-K14-cre mice.

overall_design: isolated skin tissues from 3-days-old wildtype and RNF31fl/fl-K14-cre mice, and mRNA of the tissues were isolated with TRIZOL and subject to RNA-seq

first: Xin

last: Lin

first: Lin

last: Li


title: Nonsense suppression as a mechanism of genetic complemtation in the opportunistic pathogen Mycobacterium marinum

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Here, we report the discovery of a novel mechanism of genetic complementation in M. marinum. We found that nonsense suppression was causing genetic complementation. Nonsense suppression was linked to alterations in cell permeability and exposure to the aminoglycoside antibiotic, hygromycin.

overall_design: Examination of differences between wild-type, mutant and complemented strains of M. marinum.

first: Felix

last: Medie

first: Emily

last: Williams

first: Rachel

middle: E

last: Bosserman

first: Benjamin

middle: K

last: Johnson

first: Cristal

last: Reyna

first: Matthew

last: Champion

middle: B

first: Patricia


title: HDAC5AA but not HDAC5DAD regulate the expression of genes associated with axon growth

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

institute: Washington University in St. Louis

summary: Expressing HDAC5 mutant whose serine 259 and 488 have been replaced by alanine (HDAC5AA) promotes optic nerve regeneration in retinal ganglion cells. However, expressing GFP, HDAC5WT and HDAC5DAD, whose serine 259 and 498 have been replaced by aspartic acid and serine 280 by alanine, do not promote optic nerve regeneration. The goal of this experiment was to determine the underlying mechanisms leading to the phenotypical differences in optic nerve regeneration between control GFP, HDAC5DAD, and HDAC5AA by analyzing the retinal transcriptome of the different treatments.

overall_design: GFP, HDAC5DAD, and HDAC5AA were overexpressed in C57B/6 mice retinal ganglion cells by intravitreally injecting adenoassociated virus (AAV2) containing the vector of expression for these genes. After two weeks, these animals received an optic nerve crush.  On the 4th day post injury, mice were  sacrificed and retinas were extracted for sequencing.

first: Wolfgang

last: Pita-Thomas

first: Marcus

last: Mahar


title: Gene expression profile of HGC27 and LMSU gastric cancer cell p53 KO and KD

status: Public on Jun 07 2019

city: Boston

first: Osamu

last: Kikuchi

state: MA

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

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

overall_design: Refer to individual Series


title: Expression data from human gastric tumor and human normal stomach tissues

city: Xuzhou

first: Li

state: Jiangsu

address: No. 99 West Huaihai Road, Xuzhou, Jiangsu 221002, P.R. China.

institute: the Affiliated Hospital of Xuzhou Medical University

summary: We identified several hub genes and key pathways associated with GAC initiation and progression by analysising the microarray data on DEGs, whcih provided a detailed molecular mechanism underlying GAC occurrence and progression.

overall_design: We analyzed the gene expression profile in GAC-associated tissues. 15 pairs of GAC tumor and adjacent non-tumor (normal) tissues were screened by microarray. Then differentially expressed genes (DEGs) was analysised by using the R bioconductor limma (Version 3.36.2). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis were used to annotate the unique biological significance and important pathways of enriched DEGs, which was identified by Fisher’s exact test (p＜0.05). To find the hub genes and key pathways, we constructed thre protein-protein interaction (PPI) network by Cytoscape and conducted KEGG enrichment analysis of the prime module extracted from the PPI network. We further applied the TCGA database to start the survival analysis of these hub genes by Kaplan-Meier estimates.

first: Sujuan

last: Fei

first: Jiang

last: Cao


title: Co-expression of CD163 and CD141 Identifies Human Circulating IL-10-Producing Dendritic Cells (DC-10) [RNA-seq]

city: Milano

first: Silvia

last: Gregori

state: Non-US/Canada

address: via olgettina , 58

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy (SR-TIGET),  IRCCS San Raffaele Scientific Institute.

summary: Tolerogenic dendritic cells (DC) are key players in maintaining immunological homeostasis, dampening immune reactions, and promoting tolerance. DC-10, a tolerogenic population of human IL-10-producing DC characterized by the expression of HLA-G and ILT4, play a pivotal role in promoting tolerance via T regulatory type 1 (Tr1) cells. Thus far, the absence of specific biomarkers that uniquely identify DC-10 limited their studies in vivo. By gene expression profiling of in vitro differentiated human DC, we identified CD141 and CD163 as specific surface markers for DC-10. The co-expression of CD141 and CD163 in combination with CD14 and CD16 enables the ex vivo isolation of blood circulating DC-10. FACS-isolated CD14+CD16+CD141+CD163+ cells (ex vivo DC-10) from peripheral blood of healthy subjects produced spontaneously and upon activation IL-10 and limited levels of IL-12. Moreover, in vitro stimulation of allogeneic naive CD4+ T cells with ex vivo isolated CD14+CD16+CD141+CD163+ cells induced the differentiation of allo-specific Tr1 cells. Finally, ex vivo isolated CD14+CD16+CD141+CD163+ cells and in vitro differentiated DC-10 exhibited a similar transcriptional profile, characterized by anti-inflammatory and pro-tolerogenic signature. These results provide new insight into the DC-10 phenotype and on the role of circulating DC-10 in modulating T cell responses and promoting Tr1 cells. These findings open the opportunity to track DC-10 in vivo and to define their role in physiological and pathological settings.

overall_design: Identification of the transcriptional prfile of ex vivo isolated DC-10

first: Michela

last: Comi

first: Daniele

last: Avancini

first: Matteo

last: Villa

first: Molly

last: Javier Uyeda

first: Francesca

last: Santoni de Sio

last: Floris

first: Daniela

last: Tomasoni

first: Alessandro

last: Bulfone

first: Maria

middle: G

last: Roncarolo


title: Gene expression profile of Huh7 cells with long and short telomeres

city: Seoul

first: Eunkyong

last: Ko

address: Gwanak ro

country: South Korea

institute: Seoul National University

summary:
We sorted H2O2–treated HCC Huh7-cells harboring telomeres in the top 20th percentile (long telomeres) and bottom 20th percentile of telomere length (short telomeres) according to fluorescence-activated cell sorting based on the fluorescence intensity associated with the telomere-binding protein, followed by whole-genome mRNA-expression microarray analysis. In detail, a stable Huh7 cell line expressing GFP-tagged telomere-binding protein adrenocortical dysplasia protein homolog (TPP1) was established using 1 mg/mL G418 as a selection antibiotic. The telomere lengths in living cells were measured by assessing the expression of TPP1 by fluorescence-activated cell sorting (FACS) under the assumption that the expression level of the telomere binding protein is proportional to telomere length. The cells were dissociated at 37°C in 0.2 % w/v trypsin-EDTA for 10 min. After gentle pipetting to induce dissociation, the cells were washed twice with cold PBS solution containing 0.6 % w/v ultra-pure bovine serum albumins (A0100-010) and filtered using a cell strainer (BD Bioscience). HCC cells displaying weak or strong GFP expression were isolated from the mock- or H2O2-treated cells using a FACS Aria II (BD Bioscience), respectively.

A whole genome mRNA expression microarray (Macrogen, Seoul, Korea) was used to compare the gene expression patterns between HCC cells possessing short or long telomeres.

overall_design:
duplicate experiment; two replicates for each telomere length

Contributor: Macrogen (South Korea, Seoul)


title: Gene expression profile of HGC27 gastric cancer cell p53 KO and KD

summary: HGC27 gastric cancer cells were manipulated to express mutant p53

overall_design: Examination of mRNA expression in HGC27 gastric cancer cells following overexpression of mutant p53

first: Nilay

last: Sethi

first: Adam

last: Bass


title: Gene expression profile of LMSU gastric cancer cell p53 KO and KD

summary: LMSU gastric cancer cells were manipulated to either knockout or knockdown mutant p53-R175H, which is endogenously mutated and expressed in this cell line.

overall_design: Examination of mRNA expression in LMSU gastric cancer cells following knockout or knockdown of mutant p53-R175H


title: Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: Universtiy of Washington

summary: Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns of NHEJ are strongly biased by sequence context, but these studies were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ~1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB repair of 6,872 synthetic target sequences, introduced into a human cell line via lentiviral infection. We find that: 1) insertions are dominated by 1 bp events templated by sequence immediately upstream of the cleavage site, 2) deletions are predominantly associated with microhomology, and 3) targets exhibit variable but reproducible diversity with respect to the number and relative frequency of the mutational outcomes to which they give rise. From these data, we trained a model (Lindel) that uses local sequence context to predict the distribution of mutational outcomes. Exploiting the bias of NHEJ outcomes towards microhomology mediated events, we demonstrate the programming of deletion patterns by introducing microhomology to specific locations in the vicinity of the DSB site. We anticipate that our results will inform investigations of DSB repair mechanisms as well as the design of CRISPR/Cas9 experiments for diverse applications including genome-wide screens, gene therapy, lineage tracing and molecular recording.

overall_design: 6,872 target sequence were profiled with 3 replicates

first: Wei

last: Chen


title: Butyrate alters  gene expression profiles in gBT-I cells

city: Clayton

first: Moshe

last: Olshansky

state: Vic

address: 19 Innovation Walk (Bldg 76)

department: Microbiology

country: Australia

institute: Monash University

summary:
Purpose: The aim of this study is to dissect if the microbiota-derived metabolite butyrate alters the transcriptome of antigen-activated CD8+ T cells.
Methods: mRNA profiles from Ctrl and Butyrate-treated gBT-I were generated by deep sequencing, in triplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: The analysis of RNAseq data of Ctrl and Butyrate-treated gBT-I lead to ~2,000 differentially expressed genes (FDR < 0.05; fold change>2). GSEA enrichment analysis revealed enrichment of memory T cells signatures in gBT-I following butyrate-treatment  (Sarkar et al., 2008).
Conclusions: Our data shows that butyrate alters the transcriptome of effector CD8+ T cells, in particular their memory signature.

overall_design: in vitro activated gBT-I mRNA profiles on d6 were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Sammy

last: Bedoui

first: Annabell

last: Bachem


title: Genome-wide analysis of ferroptosis related genes in liver cancer cells.

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

summary: To seek ferroptosis related genes in liver cancer cells, we treated HepG2 cells using ferroptosis inducer Erastin and inhibitor Ferrostatin, respectively. We found that a subset of genes were up-regulated in Erastin treatment groups and down-regulated in Ferrostatin treatment groups, suggesting that these genes might be correlated with ferroptosis.

overall_design: Examination of ferroptosis related genes in HepG2 cells.

first: Xiao

first: Jiayi

last: Wang


title: Co-expression of CD163 and CD141 Identifies Human Circulating IL-10-Producing Dendritic Cells (DC-10)

first: Silvia

last: Gregori


title: Gene expressions of TCRαβ+ CD8αα+ intraepithelial lymphocyte (IELs) in the small intestine with or without Rbpj gene

city: Tokushima

first: Chieko

last: Ishifune

address: 3-18-15 Kuramoto

department: Department of Immunology and Parasitology

country: Japan

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

summary: cDNA microarray data of TCRαβ+ CD8αα+ IELs in the small intestine with or without Rbpj gene

overall_design: Small intestinal TCRαβ+ CD8αα+ IELs were sorted form Rbpjf/f (Control) and CD4-Cre Rbpjf/f (RFF4) mice, total RNA was purified and cDNA microarray was performed.

first: Koji

last: Yasutomo


title: Transcriptomic evaluation of CD4+CD62L-CD44+FoxP3-CD45RbLo (RbLo TEM) versus CD4+CD62L+CD44-FoxP-CD45RbHi (RbHi TN) cells following activation

city: Cleveland

first: Brian

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

department: Pathology

institute: Case Western Reserve University School of Medicine

summary: Deep sequencing of splenic RbLo TEM and RbHi TN cells 72 hours following anti-CD3 stimulation.

overall_design: mRNA was collected from snap-frozen cells at 72 hours post stimulation.

first: Mark

last: Jones

first: Jenny

last: Johnson

first: Carlos

last: Alvarez

first: Nathan

last: Morris


title: H3.3 phosphorylation promotes enhancer acetylation and lineage specification [ChIP-seq]

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

summary: H3.3 phosphorylation promotes high levels of histone acetylation in mouse embryonic stem cells, which are central to the initiation of new transcription during lineage specification.

overall_design: Native ChIP analysis of H3K27ac in several mouse embryonic stem cell lines (Control and H3.3KO, HIRAKO, ATRXKO, DAXXKO). Native ChIP analysis of H3K64ac, H3K122ac, H3K4me1 in two embryonic stem cell lines (Control and H3.3KO). Crosslinking ChIP analysis of H3.3 (Control, ATRXKO and DAXXKO) and p300 (Control and H3.3KO). Native ChIP analysis of H3K27ac in embryoid bodies at Day 4 of differentiation (WT and H3.3KO and addback cells). All inputs sequenced.

first: Sara

last: Martire

first: Aishwarya

last: Gogate

first: Amanda

last: Whitmill

first: Amanuel

last: Tafessu

first: Jennifer

last: Nguyen

first: Yu

last: Teng

first: Melodi

last: Tastemel


title: GFI1 promotes gastric cancer cell HS746T proliferation

city: Shanghai,China

first: long

last: li

address: 320 Yueyang Road

institute: State Key Laboratory of Cell Biology

summary: To investigate the function of GFI1 in GC, we ectopically expressed GFI1 in HS746T cells and analysised the transciptional data from HS746T GFI1 over-expression cells and wild type cells by human microarray

overall_design: Examination of 2 different transcriptional data in HS746T GFI1 over-expression cells and wild type cells.

first: Long

last: Li

first: Daming

last: Gao


title: RNAseq identifies distinct gene expression profiles in gBT-I isolated from SPF and GF animals.

first: Moshe

last: Olshansky

summary:
Purpose: The aim of this study is to disentangle if microbiota influences the transcriptome of antigen-activated CD8+ T cells.
Methods: gBT-I mRNA profiles from SPF and GF mice  were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: The analysis of RNAseq data of gBT-I from SPF and GF mice lead to 371 differentially expressed genes (FDR < 0.05; fold change >2). GSEA enrichment analysis revealed depletion of memory T cells signatures in gBT-I from GF mice  (Sarkar et al., 2008), and underrepresentation of OXPHOS-related genes.
Conclusions: Our data shows that microbiota has an impact on the transcriptome of effector CD8+ T cells, in particular their memory and metabolism signature.

overall_design: in vitro activated and transferred gBT-I mRNA profiles of SPF and GF mice on d7 were generated by deep sequencing, in duplicate, using Illumina GAIIx.

first: Sammy

last: Bedoui

first: Annabell

last: Bachem


title: Gene expression profile of hepatocellular carcinoma with marked immune cell infiltration II

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

institute: Asan Medical Center

summary: Tumor microenvironmental characteristics using gene expression profiles in hepatocellular carcinoma  with marked immune stroma (HCC-IS) compared to conventional hepatocellular carcinoma (C-HCC).

overall_design:
Total 19 HCCs-IS including 8 newly sequenced cases and 195 C-HCCs were compared using gene expression profile.
---------------------------------
submitter states "We will submit the raw data to dbGap because of patient privacy concerns"

first: Chang-Ohk

first: Hyo-Jeong

last: Kang

first: Eunsil

last: Yu

first: Sung-Min

last: Chun


title: Mouse livers lacking NF-kappaB RelA (p65) during bacteremia

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Using a mouse model with hepatocyte-specific deletion of transcription factor NF-κB RelA (p65), our group has previously revealed the important role of RelA in inducing the acute phase response, maintaining host defense, and preventing liver injury during sepsis. To goal of this study was determine the influence of RelA on hepatic gene changes that provide liver protection during infection.
Mice were generated with functional deletion of NF-kappaB RelA (p56) in hepatocytes using a Cre-LoxP system. Mutant mice expressed Cre-recombinase under the transcriptional control of an albumin promotor and homozygous floxed RelA alleles. Wild type control mice lack the Cre-recombinase. Microarray analysis was performed on liver RNA collected from both genotypes of mice in the absence and presence of pneumococcal bacteremia.

overall_design: RNA samples from liver tissue of control or mutant mice infected intravenously with 10^6 CFU of Streptococcus pneumoniae (serotype 3) at three time points (0, 6, and 24 hours) were analyzed. (n = 3 to 5 biological replicates per group)

first: Yuri

last: Kim

first: Lee

last: Quinton


title: Gene expression profile of hepatocellular carcinoma with marked immune cell infiltration I

last: Ahn

first: Ju-Hyun

last: Shim

first: Deokhoon


title: H3.3 phosphorylation promotes enhancer acetylation and lineage specification [ATAC-seq]

first: Laura

last: Banaszynski

overall_design: ATAC-seq analysis in mouse embryonic stem cell lines (WT and H3.3KO, and WT and HIRAKO). ATAC-seq analysis in embryoid bodies at D4 of differentiation (Control and H3.3KO).

first: Sara

last: Martire

first: Aishwarya

last: Gogate

first: Amanda

last: Whitmill

first: Amanuel

last: Tafessu

first: Jennifer

last: Nguyen

first: Yu

last: Teng

first: Melodi


title: Co-expression of CD163 and CD141 Identifies Human Circulating IL-10-Producing Dendritic Cells (DC-10) [expression array]

first: Silvia

last: Gregori

overall_design: Comparison of the transcriptional profile of in vitro differentiated DC-10 and mature DC (mDC)

first: Michela

last: Comi

first: Daniele

last: Avancini

first: Matteo

last: Villa

first: Molly

last: Javier Uyeda

first: Francesca

last: Santoni de Sio

last: Floris

first: Daniela

last: Tomasoni

first: Alessandro

last: Bulfone

first: Maria

last: Roncarolo


title: The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and converts them into tumorigenic cells

status: Public on Jun 06 2019

city: Munich

first: Julia

last: Philippou-Massier

state: Bavaria

address: Feodor-Lynen-Strasse 25

department: Gene Center

country: Germany

institute: LMU

summary: Cutaneous squamous cell carcinoma (cSCC) is the most aggressive tumor among non-melanoma skin cancers (NMSC), showing a high potential for local invasion and metastasis. In recent years, the incidence of cSCC has increased tremendously due to increased UV exposure. The secretome of cancer cells is currently the focus of many studies in order to identify new marker proteins for different types of cancer and to investigate its influence on the tumor microenvironment. In our study we evaluated whether the secretome of cSCC cells has an impact on keratinocytes, the surrounding tissue cells of cSCC. Therefore, we analyzed and compared the secretome of human A431 cancer cells and of HaCaT keratinocytes by mass spectrometry. In a second experiment, keratinocytes were exposed to the secretome of A431 cells and the transcriptome was analyzed by next-generation sequencing. Several proto-oncogenes including MYC and EGFR were up-regulated and tumor suppressor genes such as CDKN2A and TP53 were down-regulated in keratinocytes treated with A431 conditioned medium (CM). HaCaT cells incubated with A431-CM revealed a significantly activated mTOR pathway with a concomitant increase in proliferation and migration. In contrast, the inhibition of mTOR by rapamycin led to a decreased proliferation- and migration-rate of A431-CM treated keratinocytes, which demonstrated the relevance of the mTOR complex in these processes. In conclusion, our data demonstrate the impact of the secretome of cancer cells on the transcription machinery of the cells surrounding the tumor, leading to a tumorigenic cell fate. These observations underline the influence of mTOR on cSCC and might bear significance for novel strategies in cancer therapy.

overall_design: Overall 12 samples were analyzed: two cell lines (A431, HACAT) with 1 treatment and 1 control and 3 replicates per condition.

first: Christine

last: Hoesl

first: Enrica

last: Zanuttigh

first: Thomas

last: Fröhlich

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Maik

last: Dahlhoff


title: H3.3 phosphorylation promotes enhancer acetylation and lineage specification

first: Laura

last: Banaszynski

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

overall_design: Refer to individual Series


title: Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors [ChIP-seq]

city: Birmingham

first: Christopher

last: Middleton

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

summary: Development requires the cooperation of tissue-specific and ubiquitously expressed transcription factors, such as Sp-family members. However, the molecular details of how ubiquitous factors participate in developmental processes are still unclear. We previously showed that during the differentiation of embryonic stem cells lacking Sp1 DNA binding activity (Sp1deltaDBD/deltaDBD cells), early blood progenitors are formed. However, gene expression during differentiation becomes progressively deregulated and terminal differentiation is severely compromised. Here we studied the cooperation of Sp1 and its closest paralogue Sp3 in hematopoietic development and demonstrate that Sp1 and Sp3 binding sites largely overlap. Sp3 cooperates with Sp1deltaDBD/deltaDBD but is unable to support hematopoiesis in the complete absence of Sp1. Using single cell gene expression analysis, we show that the lack of Sp1 DNA binding leads to a distortion of cell fate decision timing, indicating that stable chromatin bi  nding of Sp1 is required to maintain robust differentiation trajectories.

overall_design: ChIP-seq in ESC and Flk+

first: Jane

last: Gilmour

first: Leigh

last: O'connor

first: Nynke

last: Gillemans

first: Peter

last: Keane

first: Jean

last: Baptiste-Cazier

first: Sjaak

last: Phillipsen

first: Constanze

last: Bonifer


title: Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors


title: RNA-Seq analysis of prostate cancer cell line LNCaP treated with vehicle, androgen, androgen and IMTPPE, androgen and JJ-(+)-450, androgen and JJ-(-)450, androgen and enzalutamide

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary:
RNA-Seq analysis of prostate cancer cell line LNCaP treated with vehicle (C), androgen (R), androgen and IMTPPE (R + IMTPPE), androgen and JJ-(+)-450 (androgen + (-)450), androgen and JJ-(-)450 (androgen + (-)450), androgen and enzalutamide (androgen +Enz).
To evaluate if our compounds can inhibit AR function specifically and completely, LNCaP mRNA profiles of cells treated with IMTPPE, (+)-JJ-450 and (-)-JJ-450, comparing to enzalutamide. RNA isolation was performed using RNeasy Mini kit (Qiagen), RNA Sequencing was carried out by Genomics Research Core of University of Pittsburgh using Illumina NextSeq 500 system. The sequence reads that passed FASTQC were analyzed at the transcript level. Each sample was mapped to the Human Ensembl reference genome GRCh38. We definied different expression genes with a fold change ≥2.0 and FDR <0.05. Both (-)-JJ-450 and enzalutamide are very specific to AR, with 56 and 186 DE genes comparing to control samples respectively. IMTPPE and (+)-JJ-450 can inhibit most of the androgen responsive genes, but also some other genes were affected. (-)-JJ-450 is a novel compound inhibts AR function specifically and completely, and it is a potential lead compound for the treatment of CRPC, including those resistant to enzalutamide.

overall_design: LNCaP prostate cancer cells treated with androgen and vehicle/IMTPPE/JJ-(+)-450/JJ-(-)-450/enzalutamide mRNA profiles were generated by deep sequencing, using Illumina NextSeq 500 system.

first: Wang

last: Zhou

first: Yang

last: Zhenyu

first: Avula

last: Raghunandan

first: Chakka

last: Anish Bhaswanth

first: Chandran

last: Uma

first: Lamb

last: Janette

first: Hollingshead

last: Deborah


title: Next Generation Sequencing Facilitates Quantitative Analysis of TICs with or without H19 knockdown.

city: New Orleans

first: Jinqiang

last: Zhang

address: 1430 Tulane Ave

institute: Tulane University

summary:
The goals of this study are to compare mRNA and miRNA profiling between Tumor Initiating hepatoCytes (TICs) with or without H19 knockdown by shRNA.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study showed that knockdown of H19 in TICs led to increased expression of TP53 and CDKN1A/p21 target genes, increased expression of genes which are normally suppressed by Akt, and decreased expression of Src target genes

overall_design: Methods: mRNA and miRNA profiles of TICs with or without H19 knockdown were generated by deep sequencing using Illumina HiSeq. For mRNA, reads were trimmed and mapped to the mouse GRCm38 reference genome using the STAR aligner v.2.5.2b. Totally, 40M unique mapped reads for each samples were used for differential gene expression analysis using DESeq2 package.  For miRNA, 6-8 M reads (with length of 15 to 31 nucleotides) per sample were retained for subsequent analysis. To annotate the small RNAs, trimmed reads were searched against miRBase 21.

first: Chang

last: Han

first: Tong

last: Wu


title: Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation [MeDIP-seq]

city: Macau

first: Gang

last: Li

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

summary: TET-mediated oxidation of 5-mC participates in both passive and active DNA demethylation, which exerts a significant influence on diverse biological processes. Mass spectrometry has identified multiple phosphorylation sites of TET2. However, the functions of these phosphosites and their corresponding kinases are mostly unknown. Here we showed that AMP-activated protein kinase (AMPK) phosphorylates murine TET2 at the serine residue 97 (S97), enhances TET2 stability through promoting its binding to 14-3-3β. AMPK ablation resulted in decreased global 5-hmC levels at the myotube stages, severe differentiation defects of C2C12 cells and, significantly, total loss of expression of Pax7. Genome-wide analyses revealed increased DNA methylation at genic and enhancer regions of AMPK-null myoblasts and myotubes. Using CRISPR/Cas9 technology, we showed that a novel enhancer, which is hypermethylated in AMPK-null cells, regulates Pax7 expression. The phospho-mimicking mutant, TET2-S97E, could partly rescue the differentiation defect in AMPK ablated C2C12 cells. Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2.

overall_design: MeDIP sequencing of WT and AMPK-/- C2C12 cells at day 0 and day 8 of differentiation. Two clones of AMPK-/- cells were used and input DNA controls were included for all samples.

first: Ting

first: Xiaowen

last: Guan

first: Un-Lam

last: Choi

first: Jianming

last: Zeng


title: H3.3 phosphorylation promotes enhancer acetylation and lineage specification [RNA-seq]

first: Laura

last: Banaszynski

overall_design: RNA-Seq analysis in mouse embryonic stem cells (Control, H3.3KO, HIRAKO, ATRXKO, DAXXKO) and embryoid bodies at Day 4 of differentiation (Control and H3.3KO).

first: Sara

last: Martire

first: Aishwarya

last: Gogate

first: Amanda

last: Whitmill

first: Amanuel

last: Tafessu

first: Jennifer

last: Nguyen

first: Yu

last: Teng

first: Melodi

last: Tastemel


title: Comprehensive integration of single-cell data

first: Andrew

last: Butler

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

summary: Single-cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate cell types and states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, and spatial positioning, a key analytical challenge is to integrate these datasets into a harmonized atlas that can be used to better understand cellular identity and function. Here, we developed a computational strategy to "anchor" diverse datasets together, enabling us to integrate and compare single-cell measurements not only across scRNA-seq technologies, but different modalities as well. As one demonstration of the method, we anchor single-cell protein measurements with a human bone marrow atlas to annotate and characterize lymphocyte populations. The multimodal data, generated using CITE-seq, is provided here alongside a corresponding bulk validation experiment.

overall_design: Human PBMCs were profiled using CITE-seq and bulk RNA-seq.

first: Tim

last: Stuart


title: mTORC1 to AMPK Switching Underlies β-Cell Metabolic Plasticity During Maturation and Diabetes

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

summary: Pancreatic beta cells (β-cells) differentiate during fetal life, but only postnatally acquire the capacity for glucose-stimulated insulin secretion (GSIS). The molecular mechanisms driving this maturation of β-cell function remain incompletely understood. Here, we show that the control of cellular signaling in β-cells fundamentally switches from the nutrient sensor target of rapamycin (mTORC1) to the energy sensor 5'-adenosine monophosphate-activated protein kinase (AMPK), and that this is critical for functional maturation. Moreover, AMPK is activated by the dietary transition taking place during weaning, and this in turn inhibits mTORC1 activity to drive the adult β-cell phenotype. While forcing constitutive mTORC1 signaling in adult β-cells relegates them to a functionally immature phenotype with characteristic transcriptional and metabolic profiles, engineering the switch from mTORC1 to AMPK signaling is sufficient to promote β-cell mitochondrial biogenesis, a shift to oxidative metabolism, and functional maturation. We also show that type 2 diabetes, a condition marked by both mitochondrial degeneration and dysregulated GSIS, is associated with a remarkable reversion of the normal AMPK-dependent adult β-cell signature to a more neonatal one characterized by mTORC1 activation. Manipulating the way in which cellular nutrient signaling pathways regulate β-cell metabolism may thus offer new targets to improve β-cell function in diabetes.

overall_design: 1- pancreatic β-cells mRNA profile of P6 (WT) and P45 (WT) were generated by deep sequencing in triplicate.  2- whole islets from βTSC1 KO and controls (CTRL) were genrated by deep sequencing in duplicate.  3- whole islets from db and control (Control) were genrated by deep sequencing in duplicate.

first: Rami

last: Jaafar

first: Stella

last: Tran

first: Ajit

last: Shah

first: Gao

last: Sun

first: Martin

last: Valdearcos

first: Piero

last: Marchetti

first: Matilde

last: Masini

first: Avital

last: Swisa

first: Ernesto

last: Bernal-Mizrachi

first: Aleksey

last: Matveyenko

first: Matthias

last: Hebrok

first: Yuval

last: Dor

first: Guy

last: Rutter

first: Suneil

last: Koliwad

first: Anil

last: Bhushan


title: During development, the Sku6 mutant roots engage different genes than wild type Col-0 roots, either on the ground or in spaceflight.

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: The wild type Col-0 plants and the Sku-6 mutant plants of the Col-0 background were germinated on ISS or on the ground and the gene expression profiles in roots at 4 days or 8 days were established. The Sku6 gene (At2g03680) codes for a protein that localizes to microtubule within the cortical array and putatively acting as an intramolecular linker. The development of Col-0 and Sku-6 plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. However the development of Sku-6 mutant plants also differs from Col-0 at either age and in either environment, suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku-6 roots in orbit engaged more genes than the 4 days old Col-0 roots in orbit but also more than the 4 days old Sku-6 roots on the ground. Overall the 4 days old roots differentially expressed more genes in spaceflight relative to ground than the 8 days old roots of either genotype.

overall_design: APEX03-2 (Advanced Plant Experiment 03-2) also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System—Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with the overhead LED lighting of the VPS. At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth, the harvested material was used to compare the transcriptomes of each genotype and each age using RNAseq technology. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment. For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.

first: Anna-Lisa

last: Paul

first: Agata

last: Zupanska


title: Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors [RNA-seq]

first: Christopher

last: Middleton

overall_design: RNA-Seq in ESC, Flk, HE1, HE2 and progenitor cells with WT, Sp1deltaDBD or Sp3KO

first: Jane

last: Gilmour

first: Leigh

last: O'connor

first: Nynke

last: Gillemans

first: Peter

last: Keane

first: Jean

last: Baptiste-Cazier

first: Sjaak

last: Phillipsen

first: Constanze

last: Bonifer


title: Expression data from WT, p110α-/-, p110δ-/-, and p110αδ double knockout HSC and LMPP hematopoietic populations

city: Bronx

first: Shayda

last: Hemmati

address: 1300 Morris Park

institute: Albert Einstein College of Medicine

summary:
Many cytokines and chemokines that are important in hematopoiesis activate the phosphatidylinositol 3-kinase kinase(PI3K) signaling pathway. Because this pathway is frequently mutated and activated in cancer, PI3K inhibitors have been developed for the treatment of several malignancies, and are now being tested in the clinic in combination with chemotherapy. However, the role of PI3K in adult hematopoietic stem cells (HSCs), particularly during hematopoietic stress, is still unclear.
To understand the molecular mechanisms of how p110α and p110δ regulate the HSC and progenitor stress response, we examined the effects of p110α and p110δ  deletion on gene expression in hematopoietic stem cells (HSCs) and  lymphoid-primed multipotential progenitors (LMPPs).

overall_design: We sorted HSCs (Lin-ckit+Flk2-CD150+CD48-) and LMPPs (Lin-ckit+Flk2+ CD150-CD48+) from pooled bone marrow transplant recipients and performed DNA microarray analysis in triplicate using the Affymetrix Mouse Transcriptome Assay 1.0 kit.

first: Taneisha

last: Sinclair

first: Meng

last: Tong

first: Boris

last: Bartholdy

first: Rachel

middle: O

last: Okabe

first: Kristina

last: Ames

first: Leanne

last: Ostrodka

first: Tammana

last: Haque

first: Imit

last: Kaur

first: Taylor

last: Mills

first: Anupriya

last: Agarwal

first: Eric

last: Pietras

middle: J

last: Zhao

first: Thomas

last: Roberts

first: Kira

last: Gritsman


title: RNA-Seq analysis of Aspergillus oryzae admA and admB gene deletion strains

city: Fuchu-shi

first: Takuji

last: Kobayashi

state: Tokyo

address: 3-5-8 Saiwai-cho

institute: Tokyo Univ. of Agriculture and Technology

summary: We aimed to elucidate biological function of A Disintegrin and Metalloprotease (Adm) A and AdmB in Aspergillus oryzae. To observe influences of admA and admB deletions, each gene deletion strain was analyzed by RNA-Seq. mRNA of Deletion-control, ∆admA∆admB, ∆admA and ∆admB cultivated in wheat bran solid culture were sequenced, in quintuplicate, using Illumina GAIIx.

overall_design: mRNA of Deletion-control, ∆admA∆admB, ∆admA and ∆admB cultivated in wheat bran solid culture was sequenced, in quintuplicate, using Illumina GAIIx.

first: Toshinori

last: Kozaki

first: Kazuo

last: Ishii

first: Tsutomu

last: Arie

first: Youhei

last: Yamagata


title: Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells

status: Public on Jun 05 2019

city: Memphis

first: Doug

last: Green

state: Tn

address: 262 Danny Thomas Pl

department: Immunology

institute: St. Jude Children's Research Hospital

summary: Intra-tumor genetic heterogeneity comes from whole chromosome and/or focal copy number variations (CNVs).  We investigated the impact of whole chromosome CNVs on gene expression by performing single-cell RNA sequencing on a chromosomally unstable glioblastoma cancer stem cell (CSC) line and a control normal, diploid neural stem cell (NSC) line.  From the gene expression data, we computationally inferred large-scale CNVs in single cells.  We find that gene expression across large genomic regions scales proportionally to whole chromosome copy number in chromosomally unstable CSCs.  Also, we find that the differential expression of most genes between normal NSCs and glioblastoma CSCs is largely accounted for by copy number alterations.  However, we identify 269 genes whose differential expression in glioblastoma CSCs relative to normal NSCs is independent of copy number.  Moreover, a gene signature derived from the subset of genes that are differential expressed independent of copy number in glioblastoma CSCs correlates with tumor grade and is prognostic for patient survival.  In conclusion, this study demonstrates the utility of single-cell RNA sequencing when analyzing chromosomally unstable cells.

overall_design: Single-cell RNA sequencing of normal neural stem cells and glioblastoma cancer stem cells using C1 Single Cell Auto Prep system from Fluidigm and Illumina Nextera XT library sequencing as C1- protocol.

first: Yanding

first: Robert

last: Carter

first: Sivaraman

last: Natarajan

first: Frederick

last: Varn

first: Duane

last: Compton

first: Charles

last: Gawad

first: Chao

last: Cheng

middle: M

last: Godek


title: Characterization of a Candida albicans Isolated from a recurrent Cervical Lymphadenitis Patient and it’s Clinic Indication

city: Nanjing

first: Chengzhen

last: Zhang

address: 22 Han-kou road

institute: Nanjing University

summary: Purpose: To reveal the global regulatory genes of clinical strain, we performed comparative transcriptomic analyses of the SC5314 and JL01.Methods: We isolated a clinical Candida albicans strain JL01 (Jinling Hospital in Nanjing, China) from a 21-year-old man who presented to our hospital with recurrent cervical lymphadenitis. Cells of the JL01 and SC5314 were inoculated from overnight cultures by 1% into liquid YPD plus 10% serum medium at 37°C for 3 h. Cells were collected and total RNA was extracted as described. RNA-Seq analysis was performed by the company Majorbio (Shanghai, China). mRNA was purified, fragmented and used to synthesize cDNA. The library products were sequenced on the HiSeq 4000 platform using the HisSeq 4000 PE Cluster Kit and HisSeq 4000 SBS Kit.Results: 421 genes were significantly differentially regulated (P≤0.05, |log2FC|≥1) in JL01 compared with SC5314. Of these 421 DEGs (differentially expressed genes), 216 were up-regulated, and 205 were down-regulated.  Conclusions: Together the clinical, morphological and biological analyses, we suggest that azole drug resistance, invasive defect and hypo-virulence of the JL01 strain may correlate with its contribution in chronic fungal infection.


title: RNA-seq of HCT116 and HCT116-DKO colon cancer cell lines

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: RNA-seq was performed on parental HCT116 colon cancer cell line and on HCT116 DKO (double knock-out) cell line, which contains genetic knockouts of both DNA methyltransferases DNMT1 (-/-) and DNMT3b (-/-).

overall_design: Total RNA was isolated from HCT116 and HCT116-DKO cell lines using Rneasy Mini Kit (Qiagen) from HCT116 and HCT116-DKO cell lines. Duplicate strand-specific RNA libraries were generated from 1 μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina). Sequencing was performed at Fox Chase Cancer Center Genomic Facility using paired end reads on the HiSeq2500 platform (Illumina). Sequenced reads were aligned to the hg19 genome assembly using TopHat2. RPKM were calculated using RSeQC package. In particular, RPKM_count.py script was used. For comparing RPKM values between cell lines count values were first normalized using quantile normalization.

first: Yan

first: Matteo

last: Cesaroni

first: Biao

last: Luo

first: Priyanka

last: Miadireddi

first: Jean-Pierre

last: Issa


title: Neuronal Small RNAs Control Behavior Transgenerationally

city: Tel Aviv

first: Itai

middle: Antoine

last: Toker

address: Haim levanon St.

department: Neurobiology

country: Israel

institute: Tel Aviv University

summary: It is unknown whether the activity of the nervous system can be inherited. In Caenorhabditis elegans nematodes, parental responses can transmit heritable small RNAs that regulate gene expression transgenerationally. In this study we show that a neuronal process can impact the next generations. Neurons-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations. Further, the production of small RNAs in neurons controls the chemotaxis behavior of the progeny for at least three generations via the germline Argonaute HRDE-1. Among the targets of these small RNAs we identified the conserved gene saeg-2, which is transgenerationally downregulated in the germline. Silencing of saeg-2 following neuronal small RNA biogenesis is required for chemotaxis under stress. Thus, we propose a small RNA-based mechanism for communication of neuronal processes transgenerationally.

overall_design: C. elegans worms expressing pan-neuronal rde-4 (generation P0) in a rde-4 mutant background, under the promoters Psng-1 and Prgef-1, and their rde-4 mutant progeny (generations F1-F3) were grown at 20 degrees on standard OP-50 bacteria. RNA was extracted from one day adult worms. We collected samples from whole animals, isolated neurons or gonads.

first: Rachel

last: Posner

middle: A

first: Olga

last: Antonova

first: Ekaterina

last: Star

first: Eran

last: Azmon

first: Michael

last: Hendricks

first: Shahar

last: Bracha

first: Sarit

last: Anava

first: Hila

last: Gingold

first: Oded

last: Rechavi


title: Noncoding deletions reveal a gene that is critical for intestinal function

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Large-scale genome sequencing is poised to provide a substantial increase in the rate of discovery of disease-associated mutations, but the functional interpretation of such mutations remains challenging. Here we show that deletions of a sequence on human chromosome 16 that we term the intestine-critical region (ICR) cause intractable congenital diarrhoea in infants. Reporter assays in transgenic mice show that the ICR contains a regulatory sequence that activates transcription during the development of the gastrointestinal system. Targeted deletion of the ICR in mice caused symptoms that recapitulated the human condition. Transcriptome analysis revealed that an unannotated open reading frame (Percc1) flanks the regulatory sequence, and the expression of this gene was lost in the developing gut of mice that lacked the ICR. Percc1 knockout mice displayed phenotypes similar to those observed on ICR deletion in mice and patients, whereas an ICR-driven Percc1 transgene was sufficient to rescue the phenotypes found in mice that lacked the ICR. Together, our results identify a gene that is critical for intestinal function and underscore the need for targeted in vivo studies to interpret the growing number of clinical genetic findings that do not affect known protein-coding genes.

overall_design: Total RNA-seq from dissected regions of the digestive tract, from wild-type and percc1-/- mice.

first: I

first: Y

last: Zhu

first: M

last: Osterwalder

first: D

last: Dickel

first: A

last: Nord

first: H

last: Wu

last: Visel

first: L

last: Pennacchio


title: Lincomycin treatment of Col-0 and gun1-101

city: Potsdam

first: Guo-Zhang

state: Brandenburg

address: Am Muehlenberg 1

institute: Max-Planck Institute of Molecular Plant Physiology

summary:
Retrograde signals emanate from the DNA-containing cell organelles (plastids and mitochondria) and control the expression of a large number of nuclear genes in response to environmental and developmental cues. GENOMES UNCOUPLED1 (GUN1) participating in multiple retrograde signaling pathways that collectively regulate the nuclear transcriptome.
We used microarrays to further investigate the regulation of nuclear gene expression by PGE retrograde signals mediated by GUN1.

overall_design: Since the PGE pathway of retrograde signaling is mainly active during the first few days after germination when massive chloroplast biogenesis is occurring, we grew germinated seedling in the dark for 5 days followed by 2 days in continuous light to mimic the chloroplast biogenesis events occurring during the first days after germination.

first: Etienne

middle: H

last: Meyer

first: Si

first: Ralph

last: Bock


title: m6A safeguards transcriptome integrity by restricting RNA chimera formation at rearranged loci in plants

city: Perpignan

first: Thierry

last: Lagrange

address: 58 Avenue Paul Alduy

country: France

institute: CNRS

overall_design: Refer to individual Series


title: HITS-CLIP in Metarhizium robertsii

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: High-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation in Metarhizium robertsii

overall_design: we isolated and identified small RNAs including miRNAs and their targets associated with the Metarhizium robertsii Argonaute protein, by the HITS-CLIP method combined with bioinformatics and biologic experimental analysis. These data reveal a genome-wide miRNA-mRNA interaction map in Metarhizium robertsii in vivo, which will help us understand the complex gene regulatory network in this fungi.

first: Hui-min

last: Meng

first: Bo

last: Huang


title: Integrative analysis of competing endogenous RNA networks reveals the functional lncRNAs in Alzheimer’s diseased

status: Public on Jun 27 2019

city: Hangzhou

first: jun

middle: Xian

last: Ding

address: Qingchun Rd. East

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University

type:
Expression profiling by array
Third-party reanalysis

summary: There is increasing evidence that long non-coding RNAs (lncRNAs) play an important role in the pathogenesis of Alzheimer's disease (AD). In addition, lncRNA can act as a ceRNA by affecting mRNA expression levels by sponges miRNAs. The role of many biologi

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overall_design:
We systematically analyzed the microarray data of large samples of AD to construct a dysregulated ceRNA network to find candidate diagnostic biomarkers or potential therapeutic targets.
Normalized using the RMA of the R package affy, and next the batch effect was removed by the combat of the R package SVA

first: Xianjun


title: Brassica biased gene retention during diploidization linked to 3D genome organization

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

summary: By combining Hi-C and histone modification, we provided the insights into the chromatin architecture and its implications for function and evolution

sample_organism:
Brassica rapa
Brassica oleracea

platform_organism:
Brassica rapa
Brassica oleracea

overall_design: Two grams of harvested leaves per accessions was sampled and then cross-linked with 1% formaldehyde in a vacuum for 15 min. After crosslinking was stopped with 0.125 M glycine under a vacuum for12 min, the extracted chromatin of these crosslinked tissue sles was sonicated to 100-300 bp. With protein G beads, the proteins of interest were pulled down by adding a specific antibody to H3K4me3 (Abcam; ab8580), H3K27me3 (CST; 9733S), and H3K9ac (CST; 9649). The DNA binding to the protein of interest was harvested by digesting the protein with proteinase K. The input DNA was also purified as a control20, 59. The ChIP libraries were constructed following the protocol of the NEXTflex® Rapid DNA-Seq Kit and sequenced on Illumina HiSeq X-Ten with the PE 150 method.

first: Ting

last: Xie


title: Illumina Sequencing of Wild Type, nerd-1 and complemented nerd-1+T transcriptomes

summary: The goals of this study are to compare plant transcriptome profiling (RNA-seq) obtained from various plant lines, including a Wild Type control, the nerd-1 mutant , and the complemented nerd-1 mutant expressing a Wild Type version of the NERD protein.

overall_design: Plant mRNA profiles of 14-day old wild typeType, nerd-1, and nerd-1+T plants were generated by deep sequencing, in duplicate using Illumina with  single reads, 1x 125bp and 21-52x106 reads per library

last: LAGRANGE


title: ASBT

status: Public on Jun 04 2019

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

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


title: Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors [ATAC-Seq]

city: Birmingham

first: Christopher

last: Middleton

address: Vincent Drive

institute: University of Birmingham

summary: Development requires the cooperation of tissue-specific and ubiquitously expressed transcription factors, such as Sp-family members. However, the molecular details of how ubiquitous factors participate in developmental processes are still unclear. We previously showed that during the differentiation of embryonic stem cells lacking Sp1 DNA binding activity (Sp1deltaDBD/deltaDBD cells), early blood progenitors are formed. However, gene expression during differentiation becomes progressively deregulated and terminal differentiation is severely compromised. Here we studied the cooperation of Sp1 and its closest paralogue Sp3 in hematopoietic development and demonstrate that Sp1 and Sp3 binding sites largely overlap. Sp3 cooperates with Sp1deltaDBD/deltaDBD but is unable to support hematopoiesis in the complete absence of Sp1. Using single cell gene expression analysis, we show that the lack of Sp1 DNA binding leads to a distortion of cell fate decision timing, indicating that stable chromatin bi  nding of Sp1 is required to maintain robust differentiation trajectories.

overall_design: ATAC-Seq in A17 or E14 cells in ESC, Flk+Cells, with either  WT, Sp1deltaDBD, Sp1hetrozygous, Sp1KO

first: Jane

last: Gilmour

first: Leigh

last: O'connor

middle: P

first: Nynke

last: Gillemans

first: Peter

last: Keane

first: Jean

last: Baptiste-Cazier

first: Sjaak

last: Phillipsen

first: Constanze

last: Bonifer


title: IVD transcriptome with age

city: London

first: Matthew

last: Veras

state: ON

address: 1151 Richmond St.

country: Canada

institute: Western University

summary: This study sought to elucidate the transcriptomic changes in the murine nucleus pulposus (NP) with age. These findings will contribute to the understanding of murine intervertebral disc (IVD) aging and degeneration.

overall_design: There are 3 timepoints in this data set and therefore 3 groups total: 2.5 month NP, 6 month NP, and 21 month NP

middle: R

last: McCann

first: Cheryle

last: Séguin


title: Exploring ILF2 regulatory genes by next-generation sequencing

city: Tianjin

first: Meng

last: Zhao

address: Huan-hu-xi Road He-xi District

institute: Tianjin Medical University Cancer Institute and Hospital

summary: We knocked down the expression of ILF2 in the A549 cell line and sequenced the RNA genes with the untreated A549 cells to find the regulatory gene of ILF2.

overall_design: Examination of ILF2 regulatory genes in A549 cell line.

first: Yahui

last: Liu


title: Transcriptomic and alternative splicing analyses reveal mechanisms of the difference in salt tolerance between barley and rice

first: Liangbo

last: Fu

state: Zhejiang

address: Yuhangtang Road 866

department: college of agriculture and biotechnology

institute: Zhejiang University

summary: Both barley (Hordeum vulgare) and rice (Oryza sativa) belong to Poaceae family, but differ greatly in salt tolerance. In order to understand molecular mechanisms in the difference of salt tolerance between the two species, the responses of transcriptomic profiles to salt stress were compared between rice (cultivar Nipponbare) and barley (accession XZ26) to reveal how alternative splicing (AS) coordinates with transcriptional regulation in adaptation to salt stress. Physiological study showed that XZ26 had higher salt tolerance than Nipponbare, as reflected by less growth inhibition, lower shoot Na+ concentration and higher K+/Na+ ratio when exposed to salt stress. Transcriptomic analysis showed that XZ26 had higher ROS scavenging ability, less degradation of protein kinases and enhanced anti-oxidation. Moreover, AS genes related to ion transporter genes and transcription factors could enhance and amplify K+/Na+ homeostasis and signal transduction cascades. We proposed that higher salt tolerance of barley accession XZ26 is attributed to its superior K+/Na+ homeostasis, tissue detoxication and less energy consumption. The present results provide insights at transcriptomic levels into reasons why barley has higher salt tolerance than rice.

sample_organism:
Hordeum vulgare
Oryza sativa

platform_organism:
Hordeum vulgare
Oryza sativa

overall_design: After 7 d of salt treatments, fresh roots and the latest completely expanded leaves of barley (XZ26) and rice (Nipponbare) were sampled from both salt treatment and control, and immediately stored in liquid nitrogen for further transcriptomic analysis. Three biological replicates were done

first: Qiufang

last: Shen

first: Liuhui

last: Kuang

first: Dezhi

last: Wu

first: Guoping

last: Zhang


title: DNA methylation profiling in acute myeloid leukemia

first: Jaroslav

last: Jelinek

summary: We analyzed levels of 5-methyl cytosine CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

overall_design:
Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of human genomic DNA from the bne marrow of patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the human genome.

Raw data are unavailable for GSM2188184-GSM2188189 and GSM2188193-GSM2188214 due to data loss.

first: Priyanka

last: Madireddi

first: Justin

middle: T

last: Lee

first: Rong

last: He

first: Matteo

last: Cesaroni

first: Jozef

last: Madzo

first: Frank

last: Neumann

first: Yue

last: Lu

first: Andrew

middle: D

last: Kelly

first: Jean-Pierre

last: Issa


title: Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation

city: Macau

first: Gang

last: Li

address: Avenida da Universidade, Taipa

institute: University of Macau


title: Toxoplasma gondii infection of human retinal pigment epithelial cells

city: Adelaide

first: Justine

last: Smith

address: Bedford Park

institute: Flinders University

summary: We performed RNA-Sequencing (RNA-Seq) of primary human retinal pigment epithelial cells and the ARPE-19 cell line 24 hours following infection with GT-1 strain T. gondii tachyzoites. Gene ontology and pathway enrichment analyses of differentially expressed total RNA identified a strong immunologic transcriptomic signature. There were limited changes in the small RNA transcriptome. We used RT-qPCR for 26 immune response-related protein-coding and long non-coding transcripts in different primary epithelial cell isolates to confirm immunological activity of infected cells.

overall_design: Transcriptomic profiles of human retinal pigment epithelial cells 24 hours following infection with T. gondii or mock infection


title: Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors

first: Peter

last: Keane

department: Institute for Cancer and Genomic Sciences

summary: Development requires the cooperation of tissue-specifically and ubiquitously expressed transcription factors, such as Sp-family members. However, the molecular details of how ubiquitous factors participate in developmental processes are still unclear. We previously showed that during the differentiation of embryonic stem cells lacking Sp1 DNA binding activity (Sp1DDBD/DDBD cells), early blood progenitors are formed. However, gene expression during differentiation becomes progressively deregulated and terminal differentiation is blocked. Here we studied the cooperation of Sp1 and its homologue Sp3 in hematopoietic development and demonstrate that Sp1 and Sp3 binding sites largely overlap. Sp3 cooperates with Sp1DDBD/DDBD cells but is unable to support hematopoiesis in the complete absence of Sp1. Using single cell gene expression analysis, we show that the lack of Sp1 DNA binding leads to a distortion of cell fate decision timing, indicating that stable chromatin binding of Sp1 is required to maintain robust differentiation trajectories.

overall_design: Chromium 10X - Single-cell RNA-seq of Sp1 wild-type and Sp1 DNA binding domain mutant cells

first: Jane

last: Gilmour

first: Leigh

last: O'Connor

first: Christopher

last: Middleton

first: Nynke

last: Gillemans

first: Jean-Baptiste

last: Cazier

first: Sjaak

last: Philipsen

first: Constanze

last: Bonifer


title: Ca-K mediated Cd-Zn interactions in Polish wheat seedlings(Triticum polonicum L.)are reflected in the differentially exprressed genes

city: Wenjiang Chendu

first: Wendi

last: Shuai

state: Sichuan

address: Huimin Road

institute: Sichuan Agricultural University

summary: The sample was obtained from the treatment and the control,we analyzed gene expression by using RNA-Seq and caclude differentially expressed genes.

overall_design: we uesd the dwarf Polish wheat as the main material . Seeds were germinated for 1 week, and the seedling was breed in the growth chamber at 25 °C, 16 h light/8 h dark for 2 weeks.Then all seedlings were divided into two groups, lack and supply of Ca/K,which were treated with 0 μM CdCl2 + 5 μM ZnSO4 (CK; 5 μM ZnSO4 is a basal dosage of nutrient solution), 80 μM CdCl2 (Cd), 500 μM ZnCl2ZnSO4 (Zn), 80 μM CdCl2 + 500 μM ZnCl2ZnSO4 (Cd+Zn). For supply of Ca/K, 5 mM KNO3 and 4 mM Ca(NO3)2·4H2O were supplied additionally.  roots mRNA profiles of the development were generated by deep sequencing, in  triplicate, using SMRT-seq.

first: Ying

last: Wang


title: Ocular disease mechanisms elucidated by genetics of human fetal retinal pigment epithelium gene expression

city: Stanford

first: Douglas

last: Vollrath

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary: The eye is an intricate organ with limited representation in large-scale functional genomics datasets. The retinal pigment epithelium (RPE) serves vital roles in ocular development and retinal homeostasis. We interrogated the genetics of gene expression of cultured human fetal RPE (fRPE) cells under two metabolic conditions. Genes with disproportionately high fRPE expression are enriched for genes related to inherited ocular diseases. Variants near these fRPE-selective genes explain a larger fraction of risk for both age-related macular degeneration (AMD) and myopia than variants near genes enriched in 53 non-ocular human tissues. Increased mitochondrial oxidation of glutamine by fRPE promoted expression of lipid synthesis genes implicated in AMD. Expression and splice quantitative trait loci (e/sQTLs) analyses revealed shared and metabolic condition-specific loci of each type and several eQTLs not previously described in any tissue. Fine mapping of fRPE e/sQTLs across AMD and myopia genome-wide association data suggests new candidate genes, and mechanisms by which the same common variant of RDH5 contributes to both increased AMD risk and decreased myopia risk. Our study highlights the unique transcriptomic characteristics of fRPE and provides a resource to connect e/sQTLs in a critical ocular cell type to monogenic and complex eye disorders.

overall_design: Examination of 24 fRPE cell lines under glucose and galactose metabolic conditions

first: Boxiang

last: Liu

first: Melissa

last: Calton

first: Nathan

middle: S

last: Abell

first: Gillie

last: Benchorin

first: Michael

last: Gloudemans

first: Ming

last: Chen

last: Hu

first: Xin

first: Brunilda

last: Balliu

first: Dean

last: Bok

first: Stephen

last: Montgomery