title: Transcriptional response to PORCN inhibition using an HPAF-II orthotopic model upon MYC perturbation

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

institute: Cardiff University

summary: SRP137043 - PRJNA448654 - Timecourse RNA-seq response to PORCN inhibition using an HPAF-II orthotopic model with different MYC states

overall_design: Timecourse to investigate drug response in an orthotopic model of RNF43 mutant PDAC in different cell lines with different MYC states (WT, MYC OE, MYC T58A). RNA-seq performed at multiple timepoints (0 hrs, 8 hrs, 56 hrs)

first: Nathan

last: Harmston

first: Babita

last: Madam

first: Enrico

last: Petretto

first: David

last: Virshup


title: RNA-Seq in two Ewing sarcoma cell lines: A673 and SKNMC

status: Public on Dec 04 2018

city: Guangzhou

first: Lehang

last: Lin

address: 107, West Yanjiang Road

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

type: Expression profiling by high throughput sequencing

summary: As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, and plays a key pro-survival role in Ewing sarcoma. Moreover, APCDD1, another super-enhancer-associated gene, acting as a downstream target of both MEIS1 and EWS-FLI1, is also characterized as a novel tumor-promoting factor in this malignancy. These data delineate super-enhancer-mediated transcriptional deregulation in Ewing sarcoma, and uncover numerous candidate oncogenes which can be exploited for further understanding of the molecular pathogenesis for this disease.

overall_design: Ewing sarcoma cell lines were treated with DMSO or THZ1, and RNA-seq was performed.

first: Dechen


title: RNA Sequencing Analysis of Nestin-creERT2, NG2-creERTM, and Synapsin-cre Tumors

city: New York

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: RNA sequencing analysis was performed on glioma primary tissue harvested from different mouse models

overall_design: GBM tissue was collected from multiple mouse models representing the different cell of origin

first: Sheila

middle: R

last: Alcantara Llaguno

first: Zilai

last: Wang

first: Luis

middle: F

last: Parada


title: Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1

city: New Haven

first: Janghoo

last: Lim

state: CT

address: 295 Congress Ave, BCMM

institute: Yale University

summary:
Purpose: The goals of this study were to identify the molecular alterations in the SCA1 inferior olive, and determine whether these changes are found in other affected tissues.
Methods: mRNA profiling was conducted in two different SCA1 mouse models (Atxn1 154Q/2Q KI and ATXN1-82Q Tg), in two different affected tisues (inferior olive and cerebellum) during early disease initiation and progression (5 week and 12 week time-points). All analyses were conducted relative to appropriate wild-type controls. TopHat2 v2.1.0 was utilized to align reads to the mouse reference genome (mm10) before quantification and differential expression analysis with Cufflinks v2.2.1. Normalized expression values were generated using Cuffnorm.
Results: Differentially regulated genes identified in the SCA1 inferior olive segregated into several enriched biological pathways, including the Defense Response at 12 weeks of age. Our study demonstrates that vulnerable tissues in SCA1 are not uniform in their gene expression changes, and express discrete and commonly enriched biological pathways. In addition, we found that brain region-specific differences occur early in disease initiation and progression at 5 weeks of age.
Conclusions: The findings from this study suggest that different mechanisms of neurodegeneration are at work in the SCA1 inferior olive and cerebellum.

overall_design: mRNA profiling was conducted on an Illumina HiSeq 2500. Three biological replicates were sequenced for each genotype (Atxn1 154Q/2Q KI mice and wild-type controls; ATXN1-82Q Tg mice and wild-type controls) in each brain region (inferior olive and cerebellum) at each time-point (5 weeks old and 12 weeks old), yielding a total of 48 biological samples.

first: Terri

middle: M

last: Driessen

first: Paul

middle: J

last: Lee


title: Aging alters the epigenetic asymmetry of HSC division

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin

city: Los Angeles

first: James

last: Joly

state: California

address: 923 Bloom Walk

department: Chemical Engineering

institute: University of Southern California

summary: We sought to determine whether Ldh activity in SCC tumors is a marker of the cell type from which these cells arise, or a key metabolic activity important for tumor initiation or progression.  Here we show that genetic abrogation of Ldh enzyme activity in HFSC-mediated tumorigenesis had no effect on tumor number, time to tumor formation, tumor proliferation, epithelial to mesenchymal transition in tumors, gene expression in tumors, tumor pathology, or the immune response to tumors.

overall_design: Examination of mRNA profile of five LDHA knockout mice vs five wild type (WT) mice using Illumina HiSeq2500.

first: Aimee

last: Flores

first: Bill

last: Lowry


title: Human iPSC-derived glomeruli provide an advanced model to interrogate podocyte biology and accurately recapitulate podocytopathy

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

summary: Podocytes are highly specialised cells within the glomeruli of the kidney that maintain the filtration barrier by forming interdigitating foot processes and slit-diaphragms. Disruption to these features result in proteinuria and glomerulosclerosis. Studies into podocyte biology and disease have previously relied on conditionally immortalised cell lines due to the non- proliferative nature of this cell type. Here we describe an advanced model to study both podocyte and glomerular biology using isolated glomeruli from kidney organoids derived from human pluripotent stem cells.

overall_design: Gene expression profiling of day three 17, 21 and 26 day kidney organoid derived glomeruli respectively with heterzygous genotype for BFP tagged MAFB; gene expression profiling of  three day 25 kidney organoid derived glomeruli; gene expression profiling of three organoid-derived podocytes grown out for 3 days from day 25 kidney organoid derived glomeruli.

first: Lorna

last: Hale


title: Aging alters the epigenetic asymmetry of HSC division [scRNA-Seq]

summary: Hematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain homeostasis. With aging, the  frequency of polar HSCs decreases. Cell polarity in HSCs is controlled by the activity of the small RhoGTPase Cdc42. Here  we demonstrate, using a comprehensive set of paired daughter cell analyses that include single cell 3D-confocal imaging,  single cell transplants, single cell RNA-seq as well as single cell ATAC-seq, that the outcome of HSC divisions is strongly  linked to the polarity status before mitosis, which is in turn determined by the level of the activity Cdc42 in stem cells.  Aged apolar HSCs undergo preferentially self-renewing symmetric divisions, resulting in daughter stem cells with  reduced regenerative capacity and lymphoid potential, while young polar HSCs undergo preferentially asymmetric  divisions. Mathematical modeling in combination with experimental data implies a mechanistic role of the asymmetric  sorting of Cdc42 in determining the potential of daughter cells via epigenetic mechanisms. Therefore, molecules that  control HSC polarity might serve as modulators of the mode of stem cell division regulating the potential of daughter  cells.

overall_design: Sorted single cells were cultured with and without treatment in the presence of cytokines until first cell division (40-44hrs). The daughter cells were manually separated, washed with PBS and collected for RNA sequencing.


title: ChIP-seq from GM12878 (ENCSR933EYC)

status: Public on Dec 03 2018

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Sensory neuron lineage mapping and manipulation in the Drosophila olfactory system

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: We assessed the differential expression of genes in the adult antennae of pnt RNAi and control flies to understand how the expressions of olfactory receptors could change in response to cell fate alteration in the antennae.

overall_design: Two groups of flies (pnt RNAi and controls) with four biological replicates per group, paired design

first: Phing

middle: C

last: Chai

first: Steeve

last: Cruchet

first: Richard

last: Benton


title: ChIP-seq from omental fat pad (ENCSR968GYD)


title: ChIP-seq from H1-hESC (ENCSR814KIO)


title: ChIP-seq from H1-hESC (ENCSR850KIP)


title: ChIP-seq from cardiac muscle cell (ENCSR713SXF)


title: ChIP-seq from MM.1S (ENCSR894QWM)


title: ChIP-seq from H1-hESC (ENCSR771SNW)


title: Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease

city: Toronto

first: Art

last: Petronis

state: Ontario

address: 250 College St

department: Campbell Family Mental Health Research Institute

country: Canada

institute: Centre for Addiction and Mental Health

type: Methylation profiling by genome tiling array

summary:
Background: Maintenance of physiological circadian rhythm plays a crucial role in human health. Numerous studies have shown that disruption of circadian rhythm may increase risk for malignant, psychiatric, metabolic, and other diseases.

Results: Extending our recent findings of oscillating cytosine modifications (osc-modCs) in mice, in this study, we show that osc-modCs are also prevalent in human neutrophils. Osc-modCs may play a role in both gene regulation, can explain parts of intra- and inter-individual epigenetic variation, and are signatures of aging. Finally, we show that osc-modCs are linked to three complex diseases and provide a new interpretation of cross-sectional epigenome-wide association studies.

Conclusions: Our findings suggest that loss of balance between cytosine methylation and demethylation during the circadian cycle can be a potential mechanism for complex disease. Additional experiments, however, are required to investigate the possible involvement of confounding effects, such as hidden cellular heterogeneity. Circadian rhythmicity, one of the key adaptations of life forms on Earth, may contribute to frailty later in life.

overall_design: Venous peripheral blood samples were collected continuously every 3 hours for 72 hours (24 samples in total) from a 52 yr old caucasian male. Neutrophils were isolated from whole blood by immunomagnetic negative selection with EasySep Direct Human Neutrophil Isolation Kit (STEMCELL) according to the manufacturer's protocol. The negative selection for neutrophils was repeated three times and the cells resuspended in phosphate buffered saline. The neutrophils were stored in -80 °C before DNA extractions.  The microarray experiment was performed in technical duplicates.

first: Gabriel

last: Oh

first: Karolis

last: Koncevičius

first: Sasha

last: Ebrahimi

first: Matthew

last: Carlucci

first: Daniel

middle: E

last: Groot

first: Akhil

last: Nair

first: Aiping

last: Zhang

first: Algimantas

last: Kriščiūnas

first: Edward

middle: S

first: Viviane

last: Labrie

first: Albert

middle: H

last: Wong

first: Juozas

last: Gordevičius

first: Peixin

last: Jia

first: Miki

last: Susic


title: ChIP-seq from OCI-LY1 (ENCSR768JED)

first: ENCODE

last: DCC


title: ChIP-seq from OCI-LY3 (ENCSR756ZKG)


title: ChIP-seq from PC-9 (ENCSR793USK)


title: ChIP-seq from PC-9 (ENCSR702GMW)


title: ChIP-seq from ovary (ENCSR509SEX)


title: ChIP-seq from MM.1S (ENCSR542YRH)


title: ChIP-seq from MCF-7 (ENCSR560BUE)


title: ChIP-seq from A673 (ENCSR611JJS)


title: ChIP-seq from PC-3 (ENCSR617RSQ)


title: ChIP-seq from SK-N-SH (ENCSR541AMF)


title: ChIP-seq from OCI-LY3 (ENCSR584ATA)


title: ChIP-seq from Loucy (ENCSR464DKE)


title: ChIP-seq from HCT116 (ENCSR429CLV)


title: ChIP-seq from HepG2 (ENCSR508LMH)


title: ChIP-seq from KMS-11 (ENCSR430YRJ)


title: ChIP-seq from ovary (ENCSR149EOW)


title: ChIP-seq from GM12878 (ENCSR091BOQ)


title: ChIP-seq from PC-3 (ENCSR359LOD)


title: ChIP-seq from PC-3 (ENCSR218QFN)


title: ChIP-seq from HCT116 (ENCSR240PRQ)


title: ChIP-seq from neural progenitor cell (ENCSR125NBL)


title: ChIP-seq from OCI-LY1 (ENCSR072EUE)


title: Hypothalamus transcriptome analysis of Shank3-overexpressing mice

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

summary: Shank3 is a core excitatory postsynaptic protein expressed in multiple brain regions including the medial prefrontal cortex, striatum, and hippocampus. We have previously generated and characterized Shank3-overexpressing transgenic mice, and found that these mice exhibited manic-like behavioral phenotypes and increased food intake. To understand molecular mechanisms underlying the behavioral changes, we performed transcriptome (RNA-sequencing) analysis of the hypothalamic tissues from 10 to 12-week-old wild-type and Shank3 transgenic mice.

overall_design: Hypothalamus transcriptome of 10 to 12-week-old wild-type and Shank3 transgenic (TG) mice.

first: Chunmei

last: Jin

first: Hyojin

last: Kang


title: ChIP-seq from neural progenitor cell (ENCSR069DPL)


title: c-Maf is an essential commitment factor for IL-17-producing gd T cells

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine


title: Transcriptome expression study for miRNA-mRNA target discovery

first: Stanley

middle: K

last: Liu

address: 2075 Bayview Avenue

department: Radiation Oncology

institute: Sunnybrook Research Institute

summary: Total RNA was collected from DU145-control(scr) and DU145-miR-106a transfected cells. Gene expression analysis was performed by The Centre for Applied Genomics (The Hospital for Sick Children, Toronto, Canada) using Affymetrix GeneChip Human Gene 2.0 ST array. Data were normalized using the default parameters in Affymetrix Expression Console Software 1.4. Genes downregulated 0.8-fold in miR-106a compared to control(scr) were identified as possible mRNA targets.

overall_design: Two samples: DU145 cells transfected with control(scr) or miR-106a mimic

first: Christianne

last: Hoey


title: ChIP-seq from HCT116 (ENCSR046HGP)


title: Differential RNA-seq analysis of control vs. dnFGFR2b-expressing mouse otocysts reveals targets of FGFR2b signaling at the beginning of inner ear morphogenesis

city: Salt Lake City

first: Suzanne

middle: L.

last: Mansour

state: UT

address: 15 North 2030 East

department: Human Genetics

institute: University of Utah

summary: Induction of dnFGFR2bfor 3 partially overlapping intervals at the early stages of otocyst morphogenesis revealed expected and novel up and downregulated genes that were validated by in situ hybridization analysis. Cell cyle genes were enriched in the downregulated datasets and human hearingloss genes were enriched in the upregulated datasets.

overall_design: Differential mRNA expression analysis of pooled Rosa26rtTA/+ (control) and pooled Rosa26rtTA/+;Tg(tetO-s(dn)Fgfr2b)/+ (experimental) embryos induced with doxycycline for the indicated intervals. N=4 biological replicates per treatment (i.e. 4 pregnant females)

middle: L


title: c-Maf is an essential commitment factor for IL-17-producing gd T cells [ATAC-seq]

summary: IL-17-producing gd T (Tgd17) cells are early mediators of immunity and autoimmunity that undergo effector programming in the thymus. While Vg subset-restricted regulators of Tgd17 specialization are known, a universal type 17 commitment factor for all gd T cells remains undefined. In this study, we identify the transcription factor c-Maf as an essential and uniform regulator of Tgd17 differentiation and maintenance. The absolute lineage block caused by Maf deficiency reveals a critical effector acquisition checkpoint at the immature CD24+ CD45RBlo gd thymocyte stage. Here, c-Maf enforces Tgd17 identity by promoting chromatin accessibility and activating expression of lineage-defining RORgt and key type 17 program genes, while coordinately antagonizing the negative regulator TCF1, which promotes the alternative IFNg+ Tgd1 fate. During specialization, c-Maf expression is tuned by gdTCR signal strength, implicating c-Maf as a rheostat controlling effector gd T cell generation and connecting gdTCR signals to a core node in the Tgd17 network.

overall_design: Evaluation of differential ATAC-seq accessibilty in Maf-deficient E17-E18 immature fetal Tgd17 thymocytes. The Omni ATAC protocol was performed on replicate samples of immature CD4- CD8- CD3e+ TCRgd+ CD24+ CD45RBlo/- gd thymocytes isolated from Maf+/+ Il7r-Cre and Maf fl/fl Il7r-Cre fetal thymi.

first: Morgan

last: Parker

first: Joshua

middle: D

last: Wheaton


title: c-Maf is an essential commitment factor for IL-17-producing gd T cells [RNA-seq]

overall_design: Evaluation of differential expression in Maf- or Rorc(t)-deficient E17-18 fetal Tgd17 thymocytes. RNA was extracted from two replicate samples of CD27- CD25- CD3+ TCRgd+ gd thymocytes from Maf+/+ Il7r-Cre and Maf fl/fl Il7r-Cre fetal thymi, and four replicate samples from Rorc(t)+/+ and Rorc GFP/GFP null fetal thymi.

first: Matthew

last: Zuberbuehler


title: Leo1 occupancy in presence of dengue virus NS5

city: San Francisco

first: Nevan

last: Krogan

state: CA California

address: 1700 4th Street, 308 Byers Hall, Box 2530

institute: University of California, San Francisco

summary: We use ChIP-seq on PAF1C member Leo1 to determine how PAF1C occupancy at interferon stimulated genes is impacted by dengue virus NS5 protein.

overall_design: Leo1 complex member of PAF1C was subjected to ChIP-seq following interferon beta treatment in cells expressing GFP or dengue virus NS5 protein.

first: Priya

last: Shah


title: Bulk RNA-Seq profiling of progenitor exhausted (Slamf6+Tim-3-) and terminally exhausted (Slamf6-Tim-3+) CD8+ T-cells from tumors and chronic viral infection

status: Public on Dec 02 2018

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Transcriptionally similar subpopulations of exhausted CD8+ T-cells are found in chronic viral infection and tumors

overall_design: RNA-seq analysis of progenitor exhausted and terminally exhausted CD8+ T-cells isolated from spleens of mice chronically infected with LCMV Clone 13 (day 30 post-infection) or isolated from B16-ova tumors (day 22 post tumor implantation), with or without anti-PD-1 treatment

first: Bi

last: Kevin

first: Miller

last: Brian

first: Al

middle: A

last: Rose


title: Blue light exposure and nutrient conditions influence the expression of genes involved in simultaneous hyphal knot formation in Coprinopsis cinerea.

city: Kitakami

first: Yuichi

last: Sakamoto

state: Iwate

department: Department of Bioresource

country: Japan

institute: Iwate Biotechnology Research Center

summary:
To identify genes express in earliest stage of fruiting body initiation in Coprinopsis cinerea, strain #326 (AmutBmut haploid fruiting strain), genes expressed at 0, 0.5, 1, 3h after light exposure were compared by Super-SAGE
Approximately, 1 million tags were sequenced from each mycelial sample to obtain 65,535 unique tags. First, we made matches between the tags and predicted genes of the WT strain, and 24.4% tags matched to predicted genes. Tags of 11.4% genes that did not match with predicted genes matched with the genome sequence of strain #326, and 64.1% of unique tags (2.5~4.5% of total tag counts) were not identified in the #326 genome sequence. In tags that matched to #326 strain genome, we obtained reads 1,000 bp upstream of the genome sequence from the tags, and found that 81% of 1000 bp upstream genome sequences contain predicted genes. The tag counts that matched the same predicted genes were incremented, and fisher’s exact test was carried out using IDEG6

overall_design: After cultivation for 6days in dark on MY1/2G (0.2% glucose), mycelia were exposed by light for 0.5, 1 and 3h. Mycelia were harvested by excising the mycelial colony edge with a knife and scraping it gently off the cellophane sheet 0h (no light exposure), 0.5h, 1h, and 3h after light stimulation, then immediately freezing them in liquid nitrogen, and total RNA was extracted.

first: Y

last: Ando

first: T

last: Kamada


title: Assessement of transcriptional consequences of CD27 signaling on Tregs during Th17 polarization

first: Kelly

last: Remedios

address: 513 Parnassus Ave, HSW1201B

institute: UCSF

summary: The goal of this study was to identify transcripts that were differentially expressed in untreated vs FcCD70 treated Tregs cultured in Th17 promoting conditions.

overall_design: Tregs were sort purified from FOXP3-GFP reporter mice and cultured with anti-CD3/anti-CD28 coated Dynalbeads in Th17-polarizing conditions in the presence or absence of FcCD70. On day 6 we performed whole transcriptome RNAseq on purified cells.

first: Michael

last: Rosenblum


title: Characterization of gene expression in antibody secreting cells

city: Gaithersburg

first: Christopher

last: Groves

state: MD

address: One MedImmune Way

institute: MedImmune

summary: The CD19 positive antibody secreting cells (ASC) in both bone marrow (BM) have the capacity to provide immune memory in addition to cells traditionally considered long-lived, the CD19-negative BM ASC.  We performed flow cytometry (FCM) immunophenotyping, fluorescence-activated cell sorting (FACS) for cell subset isolation, ELISpot assays detecting the isotype of antibody secretion as well as antibodies against vaccine derived antigens, and comparative gene expression analyses of CD19- ASC, CD19+ ASC, CD20- B cells, and CD20+ B cells from BM. The findings may aid in the understanding of the differential cell subsets created through vaccination and lead to improved vaccine strategies and production. FACS sorted tissue B cells and antibody secreting cell subset gene expression.

overall_design: We sought to compare gene expression in antibody secreting cells (ASC) subsets purified from bone marrow, as defined by the presence or absence of their cell-surface markers based on fluorescence-activated cell sorting (FACS).  The subsets of interest are CD19+ ASC (n=9), CD19- ASC (n=5), and CD20+ B cells (n=6), and CD20- B cells (n=7).

first: Chris

first: Bhargavi

last: Rajan

last: Morehouse


title: Hi-C detects novel rearrangements in HL60 and HL60/S4 cell lines

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

overall_design: Hi-C sequencing of HL60/S4 cells differentiated into the granulocytic form with retinoic acid

first: Elsie

last: Jacobson


title: Characterization of the genes that were regulated by feeding with CBM 588

status: Public on Dec 01 2018

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

summary: In the present study, we investigated the effect of CBM 588 on lifespan and multiple-stress resistance using Caenorhabditis elegans as a model animal. When adult C. elegans were fed a standard diet of Escherichia coli OP50 or CBM 588, the lifespan of the animals fed CBM 588 was significantly longer than that of animals fed OP50. Moreover, the worms fed CBM 588 were more resistant to certain stressors, including infections with pathogenic bacteria, UV irradiation, and the metal stressor Cu2+. CBM 588 failed to extend the lifespan of the daf-2/IR, daf-16/FOXO and skn-1/Nrf2 mutants. Transcriptional profiling comparing CBM 588-fed and control-fed animals suggested that DAF-16-dependent class II genes were regulated by CBM 588. In conclusion, CBM 588 extends the lifespan of C. elegans probably through regulation of the insulin/IGF-1 signaling (IIS) pathway and the Nrf2 transcription factor, and CBM 588 improves resistance to several stressors in C. elegans.

overall_design: Transcriptional profiling of eight-day-old worms that were fed OP50 or CBM 588 for five days, by deep sequencing, using Illumina HiSeq.


title: ChIP-chip in Hrr25 mutant strains

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcrption. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific readers. While phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we investigate the genome-wide occupancy of Pol II, phospho-Thr4, Hrr25, and key reader Rtt103 in WT and irreversibly sensitive Hrr25 (hrr25is) mutant strains of S. cerevisiae.

overall_design: ChIP of Rpb3, phospho-Thr4, Hrr25, and Rtt103 in WT or hrr25is cells, with or without CMK inhibitor.

first: C

last: Nemec

first: A

middle: Z


title: ATAC-Seq profiling of progenitor exhausted and terminally exhausted CD8+ T-cells from tumors and chronic viral infection

first: Kevin

last: Bi

summary: Epigenetically similar subpopulations of exhausted CD8+ T-cells are found in chronic viral infection and tumors

overall_design:
ATAC-Seq analysis of progenitor exhausted and terminally exhausted CD8+ T-cells isolated from spleens of mice chronically infected with LCMV Clone 13 (day 30 post-infection) or isolated from B16-ova tumors (day 22 post tumor implantation), with or without anti-PD-1 treatment
Peak-calling was performed on merged bams and the data is linked to the first replicate records.

first: Bi

first: Sen

last: Debattama


title: Targets of JAK STAT signaling in Drosophila cells

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary:
Purpose: analyze ligand and receptor genes regulated at early time points following JAK STAT pathway stimulation
During development and homeostasis, cells integrate multiple signals originating either from neighboring cells or systemically. In turn, responding cells can produce signals that act in an autocrine, paracrine, or endocrine manner. Although the nature of the signals and pathways used in cell-cell communication are well characterized, we lack, in most cases, an integrative view of signaling describing the spatial and temporal interactions between pathways (e.g., whether the signals are processed sequentially or concomitantly when two pathways are required for a specific outcome). To address the extent of cross-talk between the major metazoan signaling pathways, we characterized immediate transcriptional responses to either single- or multiple pathway stimulations in homogeneous Drosophila cell lines. Our study, focusing on seven core pathways, epidermal growth factor receptor (EGFR), bone morphogenetic protein (BMP), Jun kinase (JNK), JAK/STAT, Notch, Insulin, and Wnt, revealed that many ligands and receptors are primary targets of signaling pathways, highlighting that transcriptional regulation of genes encoding pathway components is a major level of signaling cross-talk. In addition, we found that ligands and receptors can integrate multiple pathway activities and adjust their transcriptional responses accordingly.
RNA-seq data is for JAK STAT pathway only

overall_design: S2R+ or STAT92E mutant cells were treated with upd ligand or control media for 1 hour before harvesting RNA and sequencing

first: Noemia

last: Ammeux

first: Benjamin

last: Housden

first: Andrew

last: Georgiadis

first: Norbert

last: Perrimon


title: Gene expression analysis of dengue-infected cells

first: Nevan

last: Krogan

summary: We use RNA-seq on mRNA to identify genes that are differential expressed in human cells following dengue virus infection

overall_design: mRNA from mock- and dengue-infected cells was purified and subjected to RNA-seq analysis. For dengue-infected cells, a MOI of 3 was used to ensure near 100% infection rate.

first: Priya

last: Shah


title: KLF4, a gene regulating prostate stem cell homeostasis, is a barrier to malignant progression and predictor of a good prognosis in prostate cancer

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

type: Expression profiling by genome tiling array

summary: We propose that genes that control adult stem cell homeostasis in slowly turning over organs, such as prostate, control cancer fate. One such gene, KLF4, highly expressed in murine prostate stem cells, regulates their homeostasis, blocks malignant transformation and controls the self-renewal of tumor initiating cells. KLF4 loss induces molecular features of aggressive cancer and converts PIN lesions to invasive sarcomatoid carcinomas; its re-expression in vivo reverses this process. Bioinformatic analysis links these changes to human cancer. KLF4 and its signature containing downstream targets identify indolent tumors and predict recurrence-free survival in 2 prostate cancer cohorts. Thus, the link between normal stem cells and cancer control provides new approaches to improve prognosis and for identifying therapeutic targets for advanced cancer.

overall_design: The Akt transformed prostate stem cell line was infected with shKlf4 (shKlf4) or non-silencing control (shCon) lentivirus. After 48 hr cells were selected by puromycin for 2 days and passaged for 10 days to allow cells to undergo EMT. The infected shCon and shKlf4 cells were collected for RNA extraction. Another cohort of shKlf4 cells was infected with BFP tagged Doxycycline inducible human KLF4 (shKlf4+KLF4) or BFP tagged Doxycycline inducible empty vector (shKlf4+EV) lentivirus. After 3 days, 100 ng/ml of Dox was added to cultures of shKlf4+KLF4 and shKlf4+BFP cells to induce KLF4 expression while companion cultures (shKlf4+KLF4 and shKlf4+EV cells) received no Dox. Two days later, all shKlf4+KLF4 and shKlf4+EV cells with or without Dox treatment were collected for RNA extraction. Total RNA was extracted using an RNeasy mini kit (Qiagen, CA). RNA-seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA).

first: Xiaozhong

last: Xiong

first: Hua

last: Zhou

first: Aristotelis

last: Tsirigos

first: Elaine

last: Wilson


title: RNA-seq analysis of splenic follicular IgD low and IgD high, and marginal zone B cells

city: Milwaukee

first: Sridhar

last: Rao

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: RNA sequencing was performed to determine the uniqueness of splenic follicular IgD low B cells compared to splenic follicular IgD high and marginal zone B cells.

overall_design: Splenic follicular IgD low and IgD high , and MZ B cells  were sorted by FACS from naïve 8-10 weeks old mice. Total RNA was isolated from the sorted cells using RNAqueous® −4PCR kit and RNA sequencing was performed. Splenocytes from five mice were pooled for each sorting. Three independent sorting was performed for each B cell subset.


title: Recruiting Endogenous ADARs with Antisense Oligonucleotides to Reprogram the Transcriptome

city: STANFORD

first: Jin

middle: Billy

last: Li

address: 300 Pasteur Dr.

institute: Stanford University

summary: Huge efforts are made to engineer safe and efficient genome editing tools. An alternative might be the harnessing of ADAR-mediated RNA editing. We now present the engineering of chemically optimized antisense oligonucleotides that recruit endogenous human ADARs to edit endogenous transcripts in a simple and programmable way, an approach we refer to as RESTORE. Notably, RESTORE was markedly precise, and there was no evidence for perturbation of the natural editing homeostasis. We applied RESTORE to a panel of standard human cell lines, but also to several human primary cells including hepatocytes. In contrast to other RNA and DNA editing strategies, this approach requires only the administration of an oligonucleotide, circumvents the ectopic expression of proteins, and thus represents an attractive platform for drug development. In this respect we have shown the repair of the PiZZ mutation causing α1-antitrypsin deficiency and the editing of phosphotyrosine 701 in STAT1.

overall_design: Identification of off-target editing events and Interferon-a influence in HeLa cell line transfected with an ASO for RNA editing by RNA-Seq, 2 samples (ASO +/- IFN) , 2 control sample (+/-IFN),  2 biologically independent experiments for each sample, 8 samples in total

first: Tobias

last: Merkle

first: Sarah

last: Merz

first: Philipp

last: Reautschnig

first: Andreas

last: Blaha

first: Qin

first: Paul

last: Vogel

first: Jacqueline

last: Wettengel

middle: B

first: Thorsten

last: Stafforst


title: Single-cell RNA sequencing of mouse Circulating tumor cells (CTCs) and tumor cells

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd

department: Department of Radiation Oncology

institute: University of Pennsylvania Perelman School of Medicine

summary: To analyze transcriptional expression profile in CTC and tumor cells

overall_design: Single CTCs and tumor cells were harvested, followed by RNA extraction and RNA-seq.  A total of 6 single cells were profiled by RNA-Seq.

first: Tianrun

last: Liu

first: Haineng

last: Xu


title: Expression data from three Japonica varieties and their F1 progenies

city: Kunming

first: Dongsun

last: Lee

state: Yunnan

address: Fengyuan

department: Rice Research Institute

institute: Yunnan Agricultural University

summary:
Hybrid weakness is an important post zygotic reproductive barrier between natural populations. Expression of hybrid weakness can lead to significant decrease in yield and even lethality and is thus an undesirable agronomic trait. We observed that F1 hybrids produced from crossing between any two of three Japonica varieties(CH7, CH8, CH9) exhibit hybrid weakness phenotype. Exploring the molecular mechanism underlying hybrid weakness in important crops like rice is worthy.
We used microarrays to obtain a global picture of gene expression changes that occurred in the F1 hybrids with characteristic hybrid weakness phenotype.

overall_design: Whole rice plant samples were selected at tillering stage includ parental lines (CH7, CH8, CH9) and F1 hybrids (CH7/8, CH7/9, CH8/9). Three biological replicates were used for each sample. Total RNA extraction, cDNA and labelled cRNA synthesis and Affymetrix expression GeneChip hybridization were conducted by CapitalBio Technology (Beijing, China).

first: Dong-Sun

first: Li-Juan

last: Chen

first: Sadia

last: Nadir

first: Wei

first: Sehroon

last: Khan

first: Qian

last: Zhu

first: Xiao-Ling

last: Zhang

first: Hui

first: Meng-Ting

first: Li


title: Expression array of carcinoma cell Mmp14-targeted MMTV-PyMT mammary tumors

city: Ann Arbor

first: Stephen

middle: J.

last: Weiss

state: MI

address: 210 Washtenaw Avenue

department: Life Sciences Institute

institute: University of Michigan

summary:
Breast carcinoma cell invasion is thought to depend on the mobilization of the membrane-anchored matrix metalloproteinase, Mmp14/MT1-MMP, to drive the remodeling of extracellular matrix and trigger associated signaling cascades. However, the roles that this proteinase plays during breast tumor progression and invasion in vivo remain undefined. A highly penetrant syngeneic mouse model for luminal B breast cancer driven by the polyoma middle T (PyMT) antigen, in tandem with recently developed Mmp14-floxed mice and MMTV-Cre transgenics that express Cre recombinase throughout the mammary epithelial cell compartment, were used to characterize the impact of conditional Mmp14-targeting on breast carcinoma cell invasion programs in vivo.
Transcriptome profiling of intact MMTV-PyMT carcinoma tumors was used to investigate the functional roles of carcinoma cell-derived MT1-MMP in MMTV-PyMT tumor progression and invasion in an unbiased fashion

overall_design: Intact mammary tumor tissue was harvested from conditional knockout [MMTV-Cre+/Mmp14(f/f)] MMTV-PyMT mice and wild-type [Mmp14(f/f)] MMTV-PyMT littermates on a congenic FVB/NJ background at 3-4 months for RNA extraction and hybridization on Affymetrix microarrays.

first: Tamar

middle: Y

last: Feinberg


title: A versatile mouse model of epitope-tagged histone H3.3 to study epigenome dynamics

city: New York

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

summary: H3.3 knock-in mice serve as a useful experimental model to study epigenome regulation in development and in various adult cells in vivo.

overall_design: ChIP-Seq of epitope-tagged(HA) H3.3 and RNA-seq of untreated or IFNB-treated MEFs.

first: Chao


title: Expression array of mammary epithelial cells isolated from MMTV-Cre-expressing mammary glands

summary:
Mammary gland branching morphogenesis is thought to relie on the mobilization of the membrane-anchored matrix metalloproteinase, Mmp14/MT1-MMP, to drive mammary epithelial invasion by remodeling the extracellular matrix and triggering associated signaling cascades. However, the roles that this proteinase plays during postnatal mammary gland development in vivo remain undefined. A mammary gland branching program that occurs during the first 4 weeks of postnatal mouse development, in tandem with recently developed Mmp14-floxed mice and MMTV-Cre transgenics that express Cre recombinase throughout the mammary epithelial cell compartment, were used to characterize the impact of deleting epithelial cell Mmp14 on mammary gland morphogenesis.
Transcriptome profiling of mammary epithelial cells was used to investigate the effects of MMTV-Cre expression on the postnatal mammary epithelial cell compartment in an unbiased fashion

overall_design: Mammary epithelial cells were harvested from the mammary glands of Cre-expressing [MMTV-Cre+] mice and wild-type littermates on a congenic FVB/NJ background at 4 weeks after birth for RNA extraction and hybridization on Affymetrix microarrays.

middle: J


title: EZH2 Variants Differentially Regulate Polycomb Repressive Complex 2 in Histone Methylation and Cell Differentiation

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

summary: Background: Polycomb repressive complex 2 (PRC2) is responsible for establishing and maintaining histone H3K27 methylation during cell differentiation and proliferation. H3K27 can be mono-, di-, or tri-methylated, resulting in differential gene regulation. However, it remains unknown how PRC2 specifies the degree and biological effects of H3K27 methylation within a given cellular context. One way to determine PRC2 specificity may be through alternative splicing of Ezh2, PRC2’s catalytic subunit, during cell differentiation and tissue maturation. Results: We fully characterized the alternative splicing of Ezh2 in somatic cells and male germ cells and found that Ezh’s exon 14 was differentially regulated during mitosis and meiosis. The Ezh2 isoform containing exon 14 (ex14-Ezh2) is upregulated during cell cycle progression, consistent with a role in maintaining H3K27 methylation during chromatin replication. In contrast, the isoform lacking exon 14 (ex14D-Ezh2) was almost exclusively present in spermatocytes when new H3K27me2 is established during meiotic differentiation. Moreover, Ezh2’s transcript is normally controlled by E2F transcription activators, but in spermatocytes, Ezh2’s transcription is controlled by the meiotic regulator MYBL1. Compared to ex14-EZH2, ex14D-EZH2 has a diminished efficiency for catalyzing H3K27me3 and promotes embryonic stem cell differentiation. Conclusions: Ezh2’s expression is regulated at transcriptional and post-transcriptional levels in a cellular context-dependent manner. EZH2 variants determine functional specificity of PRC2 in histone methylation during cell proliferation and differentiation.

overall_design: ChIP-seq in wild-type and Ezh2 knock-out E14 Embryonic Stem Cells for H3k27me3 and Ezh2

first: Weipeng

last: Mu

first: Della

last: Yee

first: Terry

last: Magnuson


title: RNA-seq of Sall2 wild-type, heterozygous and knockout MEFs

city: Concepción

first: Carlos

last: Farkas

state: Biobío

address: Chacabuco 1140, 1808

department: Bioquímica y Biología Molecular

country: Chile

institute: Universidad de Concepción (UDEC)

summary: Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Due to historical reasons, gene targeting was at first done in embryonic stem cells (ESC) derived from the 129 family of inbred strains, leading to mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies genomic segments from 129-derived ESC can be introgressed into the C57BL/6 genome at different levels, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions of experiments using GEM models. We sequenced wild-type (WT), heterozygous (Het) and knockout (KO) mouse embryonic fibroblasts (MEFs) from a knockout model of Sall2 (Sato A. et al, Zinc finger protein sall2 is not essential for embryonic and kidney development. Mol Cell Biol 2003, 23:62-69) maintained in a mixed background between C57BL/6J and 129P2OlaHsd mice. We also treated these cells with doxorubicin, as a global perturbation of the gene expression. With this schema, we aimed to detect genetic introgression of 129 mice onto C57BL/6J, KO-ligated variants (the so-called congenic footprint) and potential modifier genes.

overall_design: Sall2 wild-type (WT), heterozygous (Het) and knockout (KO) MEFs treated or not with doxorubicin 1 µM for 16 hours

first: C

first: R

last: Pincheira


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FXRalpha-/- testicular Transcriptomes with Environmental Exposure

city: Clermont-Ferrand

first: David

last: VOLLE

address: 28 place Henri Dunant

country: France

institute: INSERM

summary: The goals of this study are to define the putatitve impacts of FXRalpha deficiency in testicular physiology following environmental exposure (bisphenol-A and stigmasterol)

overall_design: Testis  mRNA profiles of 10-day old wild type (WT) and FXralpha-/- mice were generated by deep sequencing, on 3 to 4 individual mouse for each genotype  and treatment, sequence on flowcell HS249.

first: Lauriane

last: SEDES

first: D


title: Affymetrix microarrays of mammary epithelial cells isolated from *Mmp14*-targeted mammary glands

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

overall_design: Refer to individual Series


title: Expression array of mammary epithelial cells isolated from epithelial Mmp14-targeted mammary glands

summary:
Mammary gland branching morphogenesis is thought to relie on the mobilization of the membrane-anchored matrix metalloproteinase, Mmp14/MT1-MMP, to drive mammary epithelial invasion by remodeling the extracellular matrix and triggering associated signaling cascades. However, the roles that this proteinase plays during postnatal mammary gland development in vivo remain undefined. A mammary gland branching program that occurs during the first 4 weeks of postnatal mouse development, in tandem with recently developed Mmp14-floxed mice and MMTV-Cre transgenics that express Cre recombinase throughout the mammary epithelial cell compartment, were used to characterize the impact of deleting epithelial cell Mmp14 on mammary gland morphogenesis.
Transcriptome profiling of mammary epithelial cells was used to investigate the functional roles of MT1-MMP in the postnatal mammary epithelial cell compartment in an unbiased fashion

overall_design: Mammary epithelial cells were harvested from the mammary glands of conditional knockout [MMTV-Cre+/Mmp14(f/f)] mice and wild-type [Mmp14(f/f)] littermates on a congenic FVB/NJ background at 4 weeks after birth for RNA extraction and hybridization on Affymetrix microarrays.


title: LHX9 rescues KRAS suppression through transcriptional regulation of YAP1

first: Seav Huong

last: Ly

address: 450 Brookline Avenue Dana 1511

institute: Harvard University


title: Adaptation of necrotrophic infection strategies by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a function of  tomato fruit ripening

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

summary: Worldwide, 20-25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply handling chain due to spoilage by fungal pathogens. Most impactful postharvest pathogens exhibit necrotrophic lifestyles, resulting in rotting of the host tissues and complete loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit, or remain quiescent until host and environmental conditions stimulate a successful infection. Current research on necrotrophic infections of fruit was mainly focused on the host by characterizing genetic and physicochemical factors that inhibit or promote the disease. However, the pathogenicity and virulence strategies employed by necrotrophic pathogens in ripe and unripe fruit are mostly understudied. Here, we provide a first comparative transcriptomics study of fungal postharvest pathogens: Botrytis cinerea, Rhizopus stolonifer and Fusarium acuminatum, all of which display necrotrophic behavior when infecting fruit. We de novo assembled and annotated the transcriptomes of R. stolonifer, and F. acuminatum and performed a differential gene expression analysis comparing the three fungal transcriptomes during fruit infection with that of fungal in-vitro growth. Analysis of the differentially expressed genes for enrichment of functional annotations revealed shared strategies of the three fungi during infection of compatible (ripe fruit) and incompatible (unripe fruit) hosts. We furthermore selected candidate genes that are involved in these strategies to characterize their expression during infection of unripe and ripe-like fruit of the non-ripening (nor) tomato mutant, both of which are physiologically and biochemically similar to unripe wildtype fruit. By enabling a better understanding of fungal necrotrophic infection  strategies, we move closer to generating accurate models of fruit diseases and development of early detection tools and effective management strategies.

sample_organism:
Solanum lycopersicum
Rhizopus stolonifer
Fusarium acuminatum
Botrytis cinerea

overall_design: Differential expression analysis of pathogen genes in green or red fruit compared to in vitro. Classification of differentially expressed genes by gene ontology, Pfam domains, and other functional categories.

first: Stefan

last: Petrasch

first: Christian

last: Silva

first: Saskia

last: Mesquida-Pesci

first: Victor

last: Papin

first: Karina

last: Gallegos

first: Casper

middle: v

last: den Abeele

first: Francisco

last: Fernandez-Acero

first: Steven

last: Knapp


title: RNAseq analysis of whole islets from pre-weaning wild type and Akita mice

city: Jerusalem

first: Yael

last: Riahi

address: Ein Kerem

country: Israel

institute: Hadassah Medical Center

summary: This study aims to determine the effects of proinsulin misfolding/ER stress on β-cell dynamics and function in Akita mice.  The RNAseq experiment offers the opportunity to investigate the impact of proinsulin misfolding/ ER stress on the genetic signature of islets isolated during the neonatal period in the Akita mice preceding the development of hyperglycemia.

overall_design: P19-21 Akita and age-matched control mice (n=3 in each group, each sample is pooling of islets from 3 mice) were isolated and processed for RNA exctraction. RNA sequencing libraries were then constructed from 120 ng of total RNA.

first: Gil

last: Leibowitz


title: LHX9 rescues KRAS suppression through transcriptional regulation of YAP1 [ChIP-Seq]

city: Boston

summary: Oncogenic KRAS signaling is required for tumor survival in cancers that harbor KRAS mutations. We recently performed a genome-scale expression screen to identify genes that bypass KRAS dependency. Here we demonstrate that the developmental transcription factor LHX9 rescues KRAS suppression in vitro and xenograft models. Furthermore, LHX9 decreases cell sensitivity to KRASG12C and MEK1/2 inhibitors. LHX9 promotes transcriptional changes associated with KRAS. Importantly, YAP1 upregulation by LHX9 is required for the rescue of KRAS suppression. Together we identify LHX9 as a YAP1 transcriptional regulator that permits KRAS-dependent cells to proliferate without KRAS expression.

overall_design: ChIP-seq of HCT116 cells expressing LHX9-V5 open reading frame and tet-inducible shKRAS were generated by sequencing, in duplicates, using Illumina Hiseq-2500

first: Seav

first: William

middle: C

last: Hahn


title: Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris

city: Guangzhou

first: Xihao

last: Liao

state: Guangdong

address: No.382, Outer Ring East Road, Higher Education Mega Center

department: School of Biological and Bioegineering

institute: South China University of Technology

summary: In this study, we screened 27 RP deletion strains of P. pastoris and expressed two heterologous proteins eGFP and phytase (Phy) in them.To verify the transcription level and translation initiation efficiency in RP deletion strains, the typical “enhancing” strains of rpl38∆, rpl9a∆, rps25∆ and a “non-enhancing” strain of rps7∆ expressing Phy are chosen as representative strains. While these strains accumulate heterologous proteins in a time-dependent manner, the mRNA level of the Phy remained constant over the time and across the strains, with a standard deviation of only 50ppm, determined by mRNA-seq quantified using rpkM. Meanwhile, the RNC-mRNA (mRNAs attached to the ribosomes) of Phy, representing the Phy mRNA which entered translation process, remained also constant over the time and across the strains, with a standard deviation of 153ppm, determined by RNC-seq. These results demonstrated that deletion of the non-essential RPs did not influence the transcription and translation engagement of the heterologous mRNA at all.

overall_design: mRNA and RNC-mRNA profiles of wild type and rpl38∆, rpl9a∆, rps25∆, rps7∆ at early and middle stage of fermentation by using next-generation sequencing, in duplicte.

first: Ying

last: Lin


title: Selection of the dimeric sweet taste receptor for surface expression and intersubunit interactions

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The sweet taste receptor is a heterodimer of two class C G protein-coupled receptors (GPCRs), T1R2 and T1R3. While homologous structures of individual domains have been determined, the architecture of the full length T1R2-T1R3 dimer is unknown. Using random mutagenesis and cell sorting, we identify single point mutations and a C-terminal intracellular retention motif in human T1R2 that modulate surface expression and co-trafficking with T1R3 in a HEK293-derivative cell line. A comprehensive mutational scan of T1R2 based on surface expression of both subunits revealed conserved sites for T1R3 interactions, including surfaces on lobe 1 of the ligand binding domain, cysteine rich domain, and transmembrane helix 6. Using the mutational scan to guide modeling of the T1R2-T1R3 dimer predicts a twisted architecture that can explain how outwards motion of lobes 2 in the ligand-binding domains is translated into reorganization of transmembrane regions, and further predicts that extracellular loops 2 form continuous folded structures with the cysteine-rich domains near the dimer axis. These insights into the putative structural organization of the human sweet taste receptor have general implications for the mechanism of class C GPCRs.

overall_design: FLAG-tagged three site-saturation mutagenesis libraries of human T1R2 (covering N-terminal, central, and C-terminal regions) were transfected into Expi293F cells stably expressing myc-tagged human T1R3. Twenty-four hours post-transfection, surface expression of T1R2 and T1R3 was detected by anti-FLAG-Cy3 and anti-myc-Alexa647 staining, respectively. To determine the effects of T1R2 mutations on T1R2 surface expression, 100% or 55% of Cy3-positive cells were collected by fluorescence-activated cell sorting. For determining the effects of T1R2 mutations on co-trafficking with T1R3 to the plasma membrane, the top 20% of Alexa647-positive cells were sorted after gating for 100% or 50% of Cy3-positive cells. RNA was extracted from the sorted cells, and cDNA was synthesized and deep sequenced. Enrichment ratios for all single amino acid substitutions of T1R2 were calculated by comparing mutation frequencies between the naïve and sorted libraries.

first: Jihye

last: Park


title: Expression data from mouse fetal and adult intestinal organoid cultures and intestinal tissues

city: Amsterdam

first: Vanesa

last: Muncan

address: Meibergdreef 69

department: Gastroenterology and Hepatology

country: Netherlands

institute: Tytgat institute for Liver and Intestinal research

summary: Here we profiled fetal intestinal epithlelium derived organoids at day 3 (group1) and 30 (group2) of culture, adult orgnanoids at day 3 (group3) and 30 (group4) of culture and whole intestinal tissues at P0(group5) and adult (group6).

overall_design: Each group is  presented with 4 replicates


title: Comparative transcriptomic analysis of 3T3-L1 adipocytes with modulated level of Foxk1 and Foxk2 transcription factor

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

summary: The goal of this study was to apply Next Generation Sequencing analyses to identify genes and pathways regulated by the Foxk1 and Foxk2 transcription factor in 3T3-L1 adipocytes. We found, that series of enzymes involved in metabolism of lipids and carbohydrates, as well as cell migration, proliferation and adhesion are regulated in response to this transcription factor, thereby providing important insight into biological role of Foxk1 and Foxk2 for cells survival and metabolism.

overall_design: Next Generation Sequencing analyses of 3T3-L1 adipocytes with overexpression and downregulation of Foxk1 and Foxk2

first: Sven

last: Enerback

first: Valentina

last: Sukonina

first: Chandrasekhar

last: Kanduri


title: Alarmin S100A11 initiates a chemokine response to the human pathogen Toxoplasma gondii

city: Rochester

first: Felix

last: Yarovinsky

address: 601 Elmwood Ave, Box 609

department: Department of Microbiology and Immunology

institute: University of Rochester Medical Center

summary:
Purpose: The goal of this study is to compare NGS-derived transcriptome profiling of human PBMC infected with T. gondii, PRU and RH strains, (RNA-seq) to not stimulated human PBMC transcriptome (RNA-seq).
Methods: After 24h post infection PBMC and non-infected PBMC mRNA profiles were generated by deep sequencing.  The sequence reads were analyzed within Galaxy platform: FastQC(*) program was used to generate quality control reports followed by employment of Trimmamatic (*) to trim “noisy” ends; TopHat mapped reads to hg38 human genome; Cuffdiff (*) was used to find significant changes in transcript expression between infected with T. gondii human PBMC and not infected PBMC.
Results:  RNA-seq data for genes with a fold change ≥2.5 and p value <0.05.
Conclusions: human  innate responses to T. gondii were primarily characterized by the induction of chemokine expression, including CCL2

overall_design: Human PBMC mRNA profiles of infected cell with T. gondii and non infected cells were generated by deep sequencing,in quintuplicate

first: Alexandra

last: Safronova

first: Alessandra

last: Araujo

first: Ellie

middle: T

last: Camanzo

first: Taylor

last: Moon

first: Michael

middle: R

last: Elliott

first: Daniel

middle: P

last: Beiting


title: Transcriptional respose to Wnt activation regulates the regenerative capacity of the murine postnatal cochlea

first: Rory

last: Kirchner

address: 677 Huntington Ave

department: Department of Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary:
Purpose: Wnt activation can induce regeneration in the early postnatal cochlea, but the regenerative capacity of the postnatal cochlea diminishes between P0 to P5. The goal of this study was to utilize RNA-Seq for the overall evaluation of expression patterns, comparing P1 and P4 newborn cochlea with and without Wnt activation.
Methods: Sox2-CreER; β-cateninflox(Exon3)/+ mice were used to stabilize β-catenin in Sox2+ cochlear supporting cells. Tamoxifen was injected to the mother at either P1 or P4 to induce Cre activation in the pups. mRNA libraries were generated from treated and untreated pups 3 days after injection in triplicates (overall 12 samples) using ThruPLEX DNA-seq kit (Rubicon Genomics) and then sequenced using Illumina NextSeq500 Single-End 75bp. Reads were aligned to mm10 and quality control was assessed using FastQC and Qualimap followed by FeatureCounts, Sailfish v0.10.1 and tximport. Differential expression was evaluated using DESeq2 and subsequent pathway analysis was performed using Ingenuity Pathway Analysis Software (Qiagen).
Results: 40-50 million reads were detected per sample. PCA and Pearson correlation demonstrated a clear segragation of the samples by age that was supported by the identification of 2914 differentially expressed genes between P1 and P4 samples. Additional affect of treatment resulted is 530 differentially expressed genes between treated and untreated samples at P1 and 304 genes were differentially expressed between treated and untreated samples at P4. Clear activation of the Wnt pathway was apparent at both time-points after treatment. However, activation of downstream pathways that may be involved in regeneration was detected at P1 but not at P4, mainly the involvement of cell-cycle and proliferation as well as Erbb2 associated genes.
Conclusions: Our results suggest that the Wnt pathway is still active and can be further induced at early and late postnatal stages in a similar manner. However, at early stages, exogenous Wnt activation potentially promotes an arrest of maturation progression or even partial dedifferentiation of supporting cells into a less mature state that enables regeneration, while the downstream affect is not as prominenet later on. Proliferative capacity in the early postnatal cochlea is correlated with a unique transcriptional response that diminishes in the older cochlea, including a robust increase in the expression of cell cycle genes and cellular growth and development genes. Our results suggest that the downstream transcriptional response to Wnt activation is the key factor mediating a regenerative response, or a lack-thereof, in the mammalian cochlea and that efforts to stimulate regeneration in the adult auditory organ may require recapitulating the transcriptional response of the early neonatal cochlea to exogenous Wnt activation and subsequent alterations of silenced state of Wnt target genes. .

overall_design: Samples were generated in triplicates from treated (tamoxifen injection to Sox2-CreER; β-cateninflox(Exon3)/+ mice leading to β-catenin stabilization) and untreated (tamoxifen injection to mice without CreER) pups at P4 (injected at P1) and P7 (injected at P4). During the analysis process, treated samples were compared to untreated at every time-point as well as between time-points.

first: Danielle

last: Lenz

first: Albert

middle: S

last: Edge


title: Intrahepatic MAIT cell gene expression revealed by RNA-seq

city: Shanghai

first: MENG

last: DUAN

state: Shanghai

address: 180 Fenglin Road

institute: Zhongshan Hospital

summary: RNA-seq was carried out as described by Simone Picelli et al. with minor modifications (Genome Res 2014;24:2033-40). Briefly, RNA was extracted from 5000 cells using a miRNeasy Micro Kits (Qiagen, German). RNA quality was assessed with an Agilent RNA 6000 Pico Kit (Agilent Technologies, cat#5067-1513, USA) on an Agilent 2100 Bioanalyzer. Each library was prepared from 2ng of total RNA. After reverse transcription, cDNA was amplified for 8 cycles followed by Agencourt AMPure XP purification, the quality of cDNA library was checked on an Agilent High Sensitivity DNA Kit (Agilent Technologies, cat#5067-4626). The cDNA was sheared to a 200-500 bp size range using the Covaris AFA system. The final library was carried out by using the NEB Next ULTRA II DNA Prep Kit, and their quality and size were checked using the Agilent High Sensitivity DNA Kit. The libraries were sequenced using a Hiseq 4000 system (Illumina, USA). At least million reads were obtained for each sample. For all RNA-seq reads, we cut the 5’ adaptor (AAGCAGTGGTATCAACGCAGAGTACAT GGG) using cutadapt (version 1.10) with the parameter –e 0.17, and then aligned to the hg19 genome using OSA (version 2.10.8). The aligned data were merged and count by Samtools (version 0.1.19+), and differentially expressed genes were found based on the edgeR with default parameters (Bioinformatics 2010;26:139-40). A gene was differentially expressed if (1) p < 0.05 (2) |log2(fold change)| > 1. For hierarchical clustering, the RPKM values of differentially expressed genes were log2-transformed and standardized. 1- Pearson correlation was then used as the distance for clustering. Differentially expressed genes were selected for GO analysis using R package clusterProfiler (Omics 2012;16:284-7).

overall_design: Sorted mucosal-associated invariant T (MAIT) cells for RNA-Seq from tumor and peritumor tissues in five hepatocellular carcinoma (HCC) patients and normal liver tissues in five healthy donors.

first: Meng

last: Duan

first: Zhao

last: Zhang


title: NK cell-mediated cytotoxicity contributes to tumor control by a cytostatic drug combination

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Accumulating evidence suggests that molecularly targeted therapies, which were originally developed to target  the underlying cell autonomous genetic drivers of tumorigenesis, can provoke tumor specific immune  responses. Using immunocompetent mouse models of KRAS mutant lung adenocarcinoma, we show that a  combination of MEK and CDK4/6 inhibitors can induce natural killer (NK) cell immune surveillance that is  necessary for its full anti-tumor effect. Mechanistically, we show that the drug combination – but neither agent  alone – drives RB-mediated cellular senescence induction leading to potent cell cycle arrest and activation of  the immunomodulatory senescence-associated secretory phenotype (SASP). This, in turn, leads to an increase in  tumor-specific NK cell ligand expression and secretion of TNF-α that provokes NK cell-mediated targeting of  senescent tumor cells, culminating in tumor regressions and long-term survival in genetically engineered mouse  models of lung cancer. These studies identify a means and method of invoking a unique form of NK cell  mediated immune surveillance in lung tumors through molecularly targeted therapies that induce senescence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For RNA-seq analysis of transcriptional changes after drug treatment of human KRAS mutant lung and pancreas cancer cell lines, total RNA was extracted using the RNeasy Mini Kit (Qiagen) from cell lines following 8 day treatment with vehicle (DMSO), trametinib (25 nM), palbociclib (500nM), or both in combination. For RNA-seq analysis of transcriptional changes in Natural Killer (NK) cells in vivo, total RNA was extracted as described above from CD45+CD3-NK1.1+ NK cells sorted from the lungs of tumor bearing KP transplant mice following 1 week treatment with vehicle or combined trametinib (1 mg/kg body weight) or palbociclib (100 mg/kg body weight). PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation. For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

first: Marcus

last: Ruscetti

first: Josef

last: Leibold

first: Matthew

last: Bott

first: Myles

last: Fennell

first: Amanda

last: Kulick

first: Chi-Chao

last: Chen

first: Timour

last: Baslan

first: Nelson

last: Salgado

first: Francisco

last: Sanchez-Rivera

first: Sha

last: Tian

first: Paul

last: Romesser

first: John

last: Poirier

first: Charles

middle: M

last: Rudin

first: Elisa

last: de Stanchina

first: Eusebio

last: Manchado

last: Sherr

first: Scott

last: Lowe


title: Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we have used both chromatin accessibility and enhancer activity marks to study enhancer activation and changes in transcriptional networks during the differentiation of human MSC into osteoblasts and adipocytes.  We demonstrate that adipogenesis is driven by considerable remodeling of the chromatin landscape and de novo activation of enhancers, while osteogenesis involves activation of pre-established enhancers. Using machine learning algorithms for in silico modeling of transcriptional regulation we predict the repertoire of transcription factors that drive the two differentiation pathways. We show that osteoblast differentiation depends on the activation of a large and diverse transcriptional network of pro-osteogenic and anti-adipogenic transcription factors. Intriguingly, knockdown of single members of this network is sufficient to modulate differentiation in both directions, indicating that lineage-determination is a delicate balance between activities of many different transcription factors.

overall_design:
Genome-wide profiling of chromatin accessibility and enhancer activity using H3K27ac and MED1 ChIP-seq during differentiation of human mesenchymal stem cells towards osteoblasts and adipocytes

Raw data are not available for primary stromal cell samples due to patient privacy concerns. If you are interested in accessing these data, please contact the submitter directly.

first: Alexander

last: Rauch

first: Anders

middle: K

last: Haakonsson

first: Jesper

middle: G

last: Madsen

first: Mette

last: Larsen

first: Martin

first: Elvira

middle: L

last: Van Hauwaert

first: Christian

last: Wiwie

first: Naja

last: Jespersen

first: Michaela

last: Tencerova

first: Ronni

last: Nielsen

first: Bjørk

first: Richard

last: Röttger

first: Jan

last: Baumbach

first: Camilla

last: Scheele

first: Moustapha

last: Kassem


title: Transcriptome data from Eomes-overexpressing Th17 cells

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Th17 cells were sorted ex vivo from PB of healthy donors as CD4+CD161+CCR6+CXCR3-. Following, cells were transduced with a lentiviral vector carrying the Eomes gene or with an empty vector. Infected cells were then enriched by MACS separation using the reporter gene NGFR as selection marker. Finally, cells were frozen for RNA analysis.

overall_design: Th17 cells from one donor were transduced with a lentiviral vector carrying the Eomes gene or with a control vector. Two technical replicates were performed.

first: Alessio

last: Mazzoni

first: Francesco

last: Siracusa

first: Gianni

last: Montaini

first: Laura

last: Maggi

first: Hyun-Dong

last: Chang

last: Annunziato


title: Transcriptome data from human Th17, classic Th1 and non-classic Th1 cell clones

summary: Human T cell clones were derived according to standard protocols, once assessed for their functional profile were studied for gene expression. The purpose of this study is to analyze human classic Th1, non-classic Th1 and Th17 clones with and without stimulation with anti-CD2+anti-CD3+anti-CD28 coated beads to measure differences in gene expression.

overall_design: 5 different T helper cell clones were analyzed for each phenotype. Each clone was analyzed either resting either after 6 hours stimulation with anti-CD2+anti-CD3+anti-CD28.

first: Manuela

last: Capone

first: Maria

last: Rossi

first: Lorenzo

last: Cosmi


title: Molecular characterization of PRM associated endometrial changes, PAEC, following mifepristone treatment.

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary:
The molecules significantly altered in endometrium displaying PAEC after three months of mifepristone exposure are mainly involved in the structural architecture of tissue, which may explain the morphological features of PAEC
Our study has generated new knowledge on the molecular profile of endometrium displaying PAEC after 3 months of mifepristone treatment due to symptomatic leiomyoma. This knowledge is of great importance as the application of progesterone receptor modulators (PRMs) for the medical management of benign gynecological conditions is increasing.

overall_design: A comparative analysis of gene and protein expression between endometrium displaying PAEC (n=7) and endometrium that did not develop PAEC (n=4) after three months of mifepristone treatment was performed.

first: Nageswara

first: Lalit

last: Kumar

first: Kristina

last: Danielsson

first: Cecilia

last: Berger


title: LHX9 rescues KRAS suppression through transcriptional regulation of YAP1 [RNA-Seq]

first: Seav Huong

last: Ly

state: MA

overall_design: mRNA profiles of HCT116 cells expressing different open reading frames and tet-inducible shKRAS were generated by sequencing, in duplicates, using Illumina Hiseq-2500

first: Seav

middle: H

first: William

last: Hahn


title: Targeting EphA4 abrogates intrinsic resistance to chemotherapy in well-differentiated tumors

city: nakagami-gun

first: Shinichiro

last: Kina

state: Okinawa

address: 207 Uehara, Nishihara

department: Department of Clinical Neuroscience Oral and Maxillofacial Functional Rehabilitation

institute: University of Ryukyus

summary: Purpose Alkylating reagent chemotherapy for human cancers is not curative, and relapse occurs due to the continued presence of tumor cells, referred to as minimal residual disease (MRD).   Methods The survival of MRD cells after chemotherapy, a phenomenon referred to as intrinsic resistance, depends on reactive oxygen species (ROS). Well-differentiated regions of the tumor are intrinsically resistant to chemotherapy.   Results Here, we report that ROS produced by cisplatin exposure induce the tyrosine phosphorylation of the receptor tyrosine kinase erythropoietin-producing human hepatocellular receptor A4 (EphA4). EphA4 protein is highly expressed in the well-differentiated tumor-derived cervical cancer cell line Caski, but not in poorly differentiated tumor-derived cervical cancer cell lines such as HeLa or SiHa. Pharmacological inhibition of EphA4 increased cisplatin-induced cell death in Caski cells. Moreover, we observed increased expression levels of the senescence marker cyclin-dependent kinase inhibitor 2A (p16) and IL-8 in the absence of EphA4 kinase function after stimulation of Caski cells with hydrogen peroxide or cisplatin exposure.  Conclusion Our data demonstrate that EphA4 expression levels determine the threshold of alkylating reagent chemotherapy. Therefore, ROS-induced tyrosine phosphorylation of EphA4 confers intrinsic resistance to alkylating reagent chemotherapy in a well-differentiated tumor, and may represent a unifying Achilles’ heel for chemotherapy resistance of well-differentiated tumors.

overall_design: 3 samples  Caski cells were grown with cisplatin (20μM) or cisplatin plus C1(EphA4 inhibitor) for 12h, and purified using the RNeasy kit (Qiagen, Valencia, CA). For the first experiment (experiment 1; cisplatin-induced changes in gene expression in Caski cells with the aim of determining changes in gene expression that are modulated by cisplatin), the data were normalized to the median of untreated control Caski cells. For the second experiment (experiment 2; cisplatin-induced changes in gene expression in Caski cells treated with or without C1), the data were normalized to the median of samples without C1.


title: Global Transcriptome Analysis during Mucociliary Differentiation of Human Nasal Polyp/Nasal Mucosa Basal Stem/Progenitor Cells

city: BARCELONA

first: Borja

last: Callejas-Díaz

state: CATALUÑA

address: Carrer de Casanova, 143, CELLEX Sector 2B

department: Clinical and Experimental Respiratory Immunoallergy

country: Spain

institute: IDIBAPS, HOSPITAL CLÍNIC

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

summary:
The aim of this study was to perform a genome-wide transcriptional analysis (mRNA + microRNA) during in vitro mucociliary differentiation of primary human basal stem/progenitors cells (BSCs) cultured at the air-liquid interface (ALI) system.
We used microarrays to detail the global gene expression underlying mucociliary differentiation of human upper airways basal stem/progenitor cells isolated from nasal polyps and control nasal mucosa.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Basal stem/progenitor cells were isolated from Nasal Polyps or control Nasal Mucosa by the explant technique, cultured and differentiated at the air-liquid interface (ALI) cell culture system. At the different days of ALI culture (0, 14 and 28 days), total RNA was extracted from cells and finally processed for microarrays analysis (Human Genome U219 24-Array Plate).

first: Guerau

last: Fernàndez

first: Joaquim

last: Mullol


title: Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis

city: Spring House

first: K

last: Li

address: 1400 McKean Road

country: USA

institute: Janssen R&D

summary:
To acquire a better understanding of the molecular pathogenesis of pediatric UC with different disease extent, we performed mRNA microarray studies to compare gene expression of patients with extensive UC vs. that of patients with limited UC.
No significant difference was observed in mRNA expression between extensive and limited UC in pediatric patients.

overall_design: Mucosal biopsy samples (13 extensive and 6 limited UC) were collected for RNA extraction and microarray analysis.

first: R

last: Strauss

first: D

last: Chan

first: C

last: Brodmerkel

first: J

last: Friedman


title: Brain microglia are maintained and regenerated from a specialized cellular subset

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: Microglia, macrophages of the brain parenchyma, are essential for normal brain development and function as well as local immune responses. However, they can also induce and perpetuate severe brain pathology in certain conditions. Microglia are derived from early, fetal yolk sac (YS) progenitors and they are then maintained locally behind the blood brain barrier (BBB) without any external cellular input. It is thought that all microglia cells, like many other tissue-resident macrophages, have self-renewal capacity to maintain its cellularity. Here we, however, report an identification of a minor microglial stem cell-like cells (MgSCs) that are responsible of microglia expansion and maintenance during development and during steady state. MgSCs resemble somatic, unipotent stem cells: they are self-renewing and able to differentiate to the bulk of sessile microglia which , on the need , can dedifferentiate back to MgSCs. Due to their central role in microglia turnover MgSCs can become valuable, therapeutic targets in neuropathological conditions.

overall_design: MgSCs (CD45intCD11bhiF4/80hiLy6chi), bulk microglia cells (CD45intCD11bhiF4/80hiLy6cneg) and spleen monocytes (CD115posLy6chi) were isolated by cell sorting and total RNA from biological triplicates was then isolated according established procedures. We determined the gene expression profiles of MgSCs and how they relate to those of mature microglia and spleen monocytes. This analysis showed how robustly we can identify MgSCs as a separate cell lineage when compared to its closest biological “neighbors”. Importantly, these data sets allowed us to identify signatures of signalling pathways that control the MgSC state needed for regenerating microglia. In addition, we found more surface markers among the differentially expressed genes that define MgSCs, especially we identified human MgSCs and our “proband” marker, Ly6c, does not have a human homolog.

first: Klaus

middle: E

last: Karjalainen

first: Christiane

last: Ruedl


title: Bipolar disorder and lithium-induced gene expression in two peripheral cell models

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
Bipolar disorder is a severe and heritable psychiatric disorder and affects up to 1% of the population worldwide. Lithium is recommended as first-line treatment for the maintenance treatment of bipolar-affective disorder in current guidelines, its molecular modes of action are however poorly understood.
Cell models derived from bipolar patients could prove useful to gain more insight in the molecular mechanisms of bipolar disorder and the common pharmacological treatments. As primary neuronal cell lines cannot be easily derived from patients, peripheral cell models should be evaluated in their usefulness to study pathomechanisms and the mode of action of medication as well as in regard to develop biomarkers for diagnosis and treatment response.

overall_design: Here, we examined the global transcriptional response of lympho- and fibroblast cell lines derived from 10 bipolar disorder patients and 11 unaffected controls to 1 mM LiCl2.

first: Max

last: Hilscher

first: Sarah

last: Kittel-Schneider

first: Andreas

last: Reif


title: Intermittent Drug Treatment of BRAFV600E Melanoma Cells Delays Resistance by Sensitizing Cells to Rechallenge

city: Boulder

first: Natalie

last: Ahn

state: CO

address: 596 UCB

department: Department of Biochemistry

institute: University of Colorado Boulder

summary: Melanoma patients receiving drugs targeting BRAFV600E and MKK1/2 invariably develop resistance and continue progression, limiting the efficacy of treatment.  As an alternative to continuous dosing schedules, intermittent treatment strategies involving intervening periods of drug withdrawal have been proposed to delay resistance. The efficacy of this treatment strategy has been supported by preclinical findings and several clinical case reports. The beneficial effect of intermittent treatment has been attributed to “drug addiction”, in which the cell viability of resistant cells is compromised during periods of drug removal, presumably due to MAPK pathway hyperactivation. However, the cellular and molecular responses to intermittent treatment are still incompletely understood. Here, we investigate effects of intermittent treatment with the BRAFV600E inhibitor, encorafenib, in a metastatic melanoma cell line engineered to express genes conferring resistance to BRAF inhibition. We show that intermittent treatment shows superior growth suppression compared to continuous treatment for resistant cells that substantially reactivate the MAPK pathway.  While drug addiction is clearly observable in these cells, it fails to account for the advantageous effects of intermittent treatment. Instead, growth suppression can mainly be explained by resensitization as most cell death is observed upon readdition of drug following periods of drug removal. Gene expression analysis shows that a unique and reversible transcriptional state is induced in intermittently treated cells following periods of drug removal. Thus, we conclude that the beneficial effects of intermittent treatment in our model are best explained by adaptive, non-mutational changes in transcription which confer drug resensitization.

overall_design: RNA-seq data from WM239A cells overexpressing BRAF V600E

first: Scott

middle: A

last: Stuart

first: Andrew

last: Kavran

first: Joel

last: Basken

first: Patrice

last: Lee

first: Barbara

last: Brandhuber


title: Single-cell RNA sequencing enables transcriptomic analysis of iPSC-derived beta-cells in a model of neonatal diabetes caused by insulin mutations.

city: Helsinki

first: Diego

last: Balboa

address: Biomedicum 1, Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Insulin gene mutations are a leading cause of neonatal diabetes. They can lead to proinsulin misfolding and its retention in endoplasmic reticulum (ER). This results in increased ER-stress suggested to trigger beta-cell apoptosis. In humans, the mechanisms underlying beta-cell failure remain unclear. Here we show that misfolded proinsulin impairs developing beta-cell proliferation without increasing apoptosis. We generated iPSCs from diabetics carrying insulin mutations, engineered isogenic CRISPR-Cas9 mutation-corrected lines and differentiated them to beta-like cells using a 3D-suspension differentiation protocol. Single-cell RNA-sequencing analysis showed increased ER-stress and reduced proliferation in INS-mutant beta-like cells compared with corrected controls. Upon transplantation to mice, INS-mutant grafts presented reduced insulin secretion and aggravated ER-stress. Cell size, mTORC1 signaling, and respiratory chain subunit expression were all reduced in INS-mutant beta-like cells, yet apoptosis was not increased at any stage. Our results demonstrate that neonatal diabetes-associated INS-mutations lead to defective beta-cell mass expansion, contributing to diabetes development.

overall_design: Gene expression profiling of iPSC-derived pancreatic cells. Two samples from differentiated patient-derived iPSC carrying a C96R insulin mutation (independent differentiation experiments), and two samples from differentiated isogenic CRISPR-Cas9 mutation-corrected iPSC (independent differentiation experiments).

first: Daniel

last: Borshagovski

first: Mantas

last: Survila


title: microRNA-seq reveals microRNAs under the regulation of miR-125b in NCCIT tumor cells

status: Public on Nov 30 2018

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression microRNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by microRNA-seq.

overall_design: Total RNA (1 μg for each samples) was extracted from miR-125b antagomir-, miR-125b agomir-, and control oligonucleotide (GenePharma, Shanghai, China)-transfected NCCIT (ATCC® CRL-2073) cells using miRcute miRNA Isolation Kit (Tiangen, Beijing, China). Three duplicate samples for each treatment were included. Then, equal amounts of total RNA were analysed using BGISEQ-500 platform and the sequencing procedure was performed by BGI (Shenzhen, China)

first: Aalia

last: Batool


title: RNA sequencing in healthy controls, intermittent claudicant, and CLI patient skeletal muscle

city: Greenville

first: Joseph

middle: M.

last: McClung

state: NC

address: 115 Heart Drive East Carolina Heart Institute

department: Physiology

institute: East Carolina University

summary: Gastrocnemius muscle biopsies were obtained from 15 health older adults without peripheral artery disease (PAD), 20 PAD patients with intermittent claudication, and 16 patients with critical limb ischemia undergoing limb amputation.  Gene expression analysis was performed using RNA sequencing analysis.

overall_design: Examination of gene expression differences across the clinical spectrum of PAD (healthy vs. claudicant vs. critical limb ischemia)

first: Terence

last: Ryan


title: Human NK cells under normoxic and hypoxic conditions

city: Genova

first: Davide

last: Cangelosi

address: Via Gerolamo Gaslini 5

institute: IRCCS Istituto Giannina Gaslini

summary: Hypoxia, which characterizes most tumor tissues, can alter the function of different immune cell types, favoring tumor escape mechanisms. In this study, we show that hypoxia profoundly acts on NK cells by influencing their transcriptome, affecting their immunoregulatory functions, and changing the chemiotactic responses of different NK cell subsets.

overall_design: The transcriptome of fresh isolated human NK cells cultured under normoxia and hypoxia was studied.

first: Monica

last: Parodi

first: Federica

last: Raggi

first: Claudia

last: Manzini

first: Mirna

last: Balsamo

first: Fabiola

last: Blengio

first: Alessandra

last: Eva

first: Luigi

last: Varesio

first: Gabriella

last: Pietra

first: Lorenzo

last: Moretta

first: Maria

last: Mingari

first: Massimo

last: Vitale

last: Bosco


title: Gene expression profiling of mucosal biopsies from adult patients with moderately to severely active ulcerative colitis

first: K

last: Li

state: PA

summary:
To acquire a better understanding of the molecular pathogenesis of adult UC, we performed mRNA microarray studies to compare gene expression of UC patients to that of normal subjects.
A significant difference was observed in mRNA expression between UC and normal.

overall_design: Mucosal biopsy samples (87 UC and 21 normal) were collected for RNA extraction and microarray analysis.

first: S

last: Telesco

first: C

last: Marano

first: R

last: Strauss

last: Brodmerkel


title: Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction

city: Chapel Hill

first: Austin

last: Hepperla

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: Spt6 is a histone chaperone that associates with RNA polymerase II and deposits nucleosomes in the wake of transcription. Although Spt6 has an essential function in nucleosome deposition, it is not known whether this function is regulated by post-translational modification. Here, we report that casein kinase II (CKII) phosphorylation of Spt6 directs nucleosome reassembly at the 5’ ends of a broad range of genes to prevent aberrant antisense transcription and enforce transcriptional directionality.  Mechanistically, we show that interaction of Spt6 with Spn1 – a constitutive binding partner required for chromatin reassembly and full recruitment of Spt6 to genes is positively regulated by CKII phosphorylation of Spt6. Together, our study defines a previously unknown function for CKII phosphorylation in transcription, and further, highlights the importance of post-translational modification as a mechanism to fine-tune the functions of histone chaperones.

overall_design: Understanding the role of Spt6 phosphorylation by Casein kinase 2 and the role of such phosphorylation in the regulation of biological functions of Spt6

first: Raghuvar

last: Dronamraju

first: Jenny

last: Kerschner

first: Sarah

last: Peck

first: Alexander

last: Adams

first: Katlyn

middle: D

last: Hughes

first: Sadia

last: Aslam

first: Ian

last: Davis

first: Amber

last: Mosley

first: Brian

last: Strahl


title: Rapid Response and Slow Recovery of the H3K4me3 Epigenomic Marker in the Liver After a Light-Mediated Phase Advance of the Circadian Clock

city: Portland

first: Michael

last: Rountree

state: OR

address: 3429 NE Sandy Blvd. #330

institute: Nzumbe, Inc.

summary: Mammalian tissues display circadian rhythms in which transcription levels rise and fall throughout a 24-hour day.  These rhythms include histone modifications.  Here we asked whether an advance of the light-dark cycle could alter rhythms in the liver epigenome at the H3K4me3 (trimethylation of lysine 4 on histone 3) modification, which is found at active and poised gene promoters.  H3K4me3 levels were first measured at 4-time points (Zeitgeber Time [ZT] 3, 8, 15, and 20) during a normal 12L:12D light:dark cycle.  Peak levels were observed during the early dark phase at ZT15, and dropped to low levels around lights-on (ZT0) between ZT20 and ZT3.  A six-hour phase advance at ZT18 (new lights-on after only 6 h of darkness) led to a transient extension of peak H3K4me3 levels.  Although locomotor activity re-entrained within a week after the phase advance, H3K4me3 rhythms failed to do so with peak levels remaining in the light phase at the one-week recovery time point.  Eight weekly phase advances, with one-week recovery times between each phase advance, also led to disruption of the liver circadian epigenome.  A model to explain these results is offered.

overall_design: 20 H3K4me3 ChIP-Seq samples were analyzed with 1 Input IgG ChIP-Seq control.  Each sample represents ChIP-Seq performed on four mouse livers and then the four samples pooled.

first: Dmytro

last: Grygoryev

first: Mitchell

last: Turker


title: RNA-seq profiling of trastuzumab or lapatinib sensitive and resistant SKBR3 breast cancer cells

city: Salt Lake City

first: Alana

last: Welm

address: 2000 Circle of Hope

institute: University of Utah

summary: RNAseq was done using Library protocol =Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection , HiSeq 101 Cycle Paired-End Sequencing v4

overall_design:
Paired-End Sequencing  of breast cancer cell line samples
Illumina HiSeq Sequencing

first: Theresa

last: Puig


title: Gene expression profiling of mucosal biopsies from pediatric or adult patients with moderately to severely active ulcerative colitis

first: K

last: Li

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

overall_design: Refer to individual Series


title: The role of the bHLH factor E47 in modulating hepatic glucocorticoid receptor action (metabolism) [ChIP-seq]

city: Neuherberg

first: Henriette

last: Uhlenhaut

state: Munich

address: Ingolstaedter Landstr 1

department: HDC

institute: Helmholtz

summary: We performed ChIP-Sequencing for E2A and GR in mouse livers and demonstrate that E47 co-occupies metabolic promoters and enhancers together with GR. Together with the corresponding RNA-Seq data, our results illustrate how GR and E47 synergize during the transcriptional activation of hepatic metabolism.

overall_design: ChIP-Sequencing of GR and E2A in wildtype mouse livers with 2 biological replicates each.

first: Marie

last: Hemmer

first: Franziska

last: Greulich

first: Nina


title: The role of the bHLH factor E47 in modulating hepatic glucocorticoid receptor action (metabolism) [RNA-seq]

summary: We performed RNA sequencing in different wildtype and E47ko tissues in response to treatment with glucocorticoids. We show a global deregulation of gene expression programs involved in lipid, triglyceride and cholesterol metabolism & transport for E47 mutant liver tissue.

overall_design: mRNA profiles of different wildtype and E47ko tissues in response to long-term and short-term treatment with glucocorticoids (Dex, Cort).


title: Precocious expression of Blimp1 in the B cell lineage causes autoimmunity

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: The transcription factor Blimp1 is not only an essential regulator of plasma cells, but also a risk factor for the development of autoimmune disease. Here, we demonstrate that the mouse Prdm1 (Blimp1) gene was partially activated at the chromatin and transcription level in early B cell development, although mature Prdm1 mRNA did not accumulate due to posttranscriptional regulation. By analyzing a mouse model that facilitated ectopic Blimp1 protein expression throughout B lymphopoiesis, we could demonstrate that Blimp1 impaired B cell development by interfering with the B cell gene expression program, while leading to an increased abundance of plasma cells by promoting premature plasmablast differentiation of immature and mature B cells. With progressive age, these mice developed an autoimmune phenotype characterized by the presence of autoantibodies and glomerulonephritis. Hence, these data identified ectopic Blimp1 expression as a novel mechanism that can explain how Blimp1 as a risk factor contributes to the development of autoimmune disease.

overall_design: 17 samples in total: 1 ATAC-Seq, 4 GRO-Seq (2x2 replicates), 2 ChIP-Seq, 10 RNA-Seq (Follicular B cell, Pre-B cell, Pro-B cell, 2 replicates each)

first: Peter

last: Bönelt

first: Martina

last: Minnich

first: Miriam

last: Woehner

first: Hiromi

last: Tagoh

first: Maria

last: Fischer

first: Markus

last: Jaritz

first: Mikael

last: Karlsson

first: Anja

last: Ebert

first: Meinrad

last: Busslinger


title: RNA-seq reveals RNAs under the regulation of miR-125b in NCCIT tumor cells

first: Su-Ren

last: Chen

summary: To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression RNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by RNA-seq.

first: Aalia

last: Batool


title: Pluripotency-associated miR-290/302 family of microRNAs promote the dismantling of naive pluripotency

status: Public on Nov 29 2018

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

summary: Upon RNA profiling of WT and Dgcr8-/- mESCs in 2iL and differentiation for 48 hours, miRNAs are proved to be important for the transcriptional changes during ESC exiting from pluripotency. Further miRNA sequencing of WT ESCs in different timepoints revealed that miRNAs expression changes dynamically during ESC to EpiLC transition and identified miR-290/302 as key miRNAs facilitating the dismantling of naive pluripotency.

overall_design: Total RNA was analyzed from WT and Dgcr8-/- mESCs and Dgcr8 in 2iL and differentiation for 48 hours. Small RNA was sequenced for WT mESCs in 4 timepoints during exiting from pluripotency.Two biological replicates were sequenced for each sample.

first: Kai-Li

last: Gu

first: Qiang

last: Zhang