title: High Throughput sequencing of NLRC4-T337S/T337S and WT mouse duodenal epithelium

status: Public on Jan 11 2018

first: Eric

middle: Smith

last: Weiss

address: RKMFI, 4401 Penn Ave

department: Pediatrics

summary:
Purpose: Nlrc4-T337S mice have shown phenotypic differences in their intenstinal epithelia. The goal of this experiment was to determine the differences at the level of transcription between Nlrc4-T337S mice and WT in order to identify further areas of inquiry.
Methods: Pooled cDNA libraries were sequenced on Illumina HiSeq 2000 platform, mapped to mm9 using Tophat v2.1, and quantified using Partek GSv6.6 software. Reads were converted to TPM and a 0.5 TPM offset added to all transcripts. Non-coding genes and genes with no sample > 1 TPM were removed
Results: Using tophat/2.1.0, we mapped about 50 million sequence reads per sample to the mouse genome (build mm9) and identified 22986 transcripts in the intestines of WT and Nlrc4-T337S mice. Compared to WT IECs, Nlrc4-T337S had a 17-fold increase in Ubd, as well as increases in multiple genes that were identified as part of the MHC-II antigen presentation pathway.
Conclusions: Our study found that Nlrc4-T337S IECs have a different RNA-profile than WT mice caused by their point mutation, which led to the discovery of increased proliferation of Nlrc4-T337S IECs as well as increased MHC-II expression.

overall_design: Duodenal intestinal epithelial cells (IECs) mRNA profiles of 6-week old wild type (WT) and Nlrc4-T337S mice were generated using Illumina Hiseq 2000.

first: Scott

last: Canna


title: Expression data from human adipocytes after adenylate cyclase activation

status: Public on Jan 22 2018

city: Worcester

first: Silvia

last: Corvera

state: MA

address: 373 Platantion Street

department: Molecular Medicine

country: USA

institute: UMASS Medical School

summary:
Progenitors in human vasculature expanded in-vitro were differentiated with adipogenic cocktail for 12 days, following which they were stimulated with forskolin for 7 days
Microarrays were used to detail the program of differentiation of thermogenic human adipose cells

overall_design: Adipose tissue from two individuals was cultured in hydogel under pro-angiogenic conditions. Capillary networks emerging from the explants were subcultured on plastic, grown to confluence, subjected to adipogenic differentiation and after 12 days treated with vehicle or forskolin for 7 days

first: So

middle: Y

last: Min


title: Regulatory elements governing neurogenesis and proliferation in developing human neocortex

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: Neuroscience Research Building 8109C, 115 Mason Farm Rd

department: Genetics

institute: UNC Chapel Hill

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Non-coding regions compose most of the human genome, yet their functionality is poorly defined. In the developing human neocortex, non-coding regulatory elements tightly regulate expression to direct neural progenitor proliferation and neurogenesis. Here, we define thousands of non-coding elements involved in human neurogenesis by contrasting chromatin accessibility via ATAC-seq from the germinal zone and cortical plate.

overall_design:
Tissues were obtained from three independent donors (15-17 post conception weeks) and three to four technical replicates from each tissue were processed for ATAC-seq. Coronal sections were taken from dissociated tissue that visually appeared cortical. Under a dissection microscope, the coronal sections were cut with a razor blade along the less dense intermediate zone to divide the tissue into two segments from each donor (1) GZ: the neural progenitor rich region encompassing the ventricular zone, subventricular zone, and intermediate zone and (2) CP: the neuron rich region encompassing the subplate, cortical plate, and marginal zone. ATAC-seq processing followed the original protocol (Buenrostro et al., Nat Methods, 2013).

Please note that RNA-Seq raw data will be made available through dbGaP (controlled access; phs001438) due to patient privacy concerns.

first: Daniel

middle: H

last: Geschwind

first: Luis

last: de la Torre-Ubieta


title: Reduced Abd-B Hox function during kidney development results in lineage infidelity

status: Public on Jan 20 2018

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

type: Expression profiling by high throughput sequencing

summary: In this study, in order to better understand shared core Hox functions, we examined kidney development in mice with frameshift mutations of multiple Abd-B type Hox genes. The resulting phenotypes included  dramatically reduced branching morphogenesis of the uretreric bud, premature depletion of nephron progenitors and abnormal development of the stromal compartment. Most unexpected, however, we also observed a cellular level lineage infidelity in nephron segments.

overall_design: E14.5 mouse kidney cells were analyzed using Drop-seq

first: S

middle: S

last: Potter


title: Role of SUMOylation in differential ERα transcriptional repression by SERMs and pure antiestrogens in breast cancer cells

status: Public on Jan 09 2018

city: MONTREAL

first: Sylvie

last: Mader

state: QC

address: CP 6128 Succursale centre ville

department: Biochemistry and Molecular Medicine

country: Canada

institute: Université de Montréal

summary: RNA-seq: Gene expression profiling in MCF-7 cells treated with vehicle (0), estradiol (E2), the Selective ER Modulator 4-hydroxytamoxifen (OHT), or the pure antiestrogen fulvestrant (ICI). ChIP-seq: Genome-wide DNA binding profile of ERα and SUMO2/3 in MCF-7 cells treated with vehicle, E2 or ICI.

overall_design: RNA-seq: MCF-7 cells cultured in estrogen-depleted media were treated with vehicle, 5 nM E2, 100 nM OHT or 100 nM ICI for 16 h. Fold-Change of mRNA levels compared to vehicle was determined for each treatment condition (3 biological replicates for each). ChIP-seq: MCF-7 cells cultured in estrogen-depleted media were treated with vehicle, 5 nM E2 or 100 nM ICI for 30 min or 3 h. ChIP-seq with an antibody for ERα (Santa Cruz Biotechnology sc-543) was performed, and ERα peaks were called for each condition (3 biological replicates) relative to the corresponding input samples. MCF-7 cells cultured in estrogen-depleted media were treated with vehicle or 100 nM ICI for 30 min or 3 h. ChIP-seq with an antibody for SUMO2/3 (Cedarlane M114-3) was performed, and SUMO2/3 peaks were called for each condition (2 biological replicates) relative to the corresponding input samples.

first: Tatiana

last: Traboulsi

first: Vanessa

last: Dumeaux

last: Audemard


title: Genome-wide maps of histone modification and chromatin remodeler binding in acute myeloid leukemia blast cells and normal hematopoietic cells

status: Public on Jan 10 2018

city: Kolkata

first: Amitava

last: Sengupta

state: West Bengal

address: CN 6, Sector V, Salt Lake

department: Cancer Biology & Inflammatory Disorder Division

country: India

institute: CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)

summary: We have used chromatin immunoprecipitation followed by high throughput sequencing to map regions of chromatin remodeler binding accompanied by histone modification state. We have used this data to distinguish between the transcriptional state of regulatory genes in leukemic and normal hematopoietic cells, and thus understand contribution of the chromatin remodeler towards leukemogenesis.

overall_design: Binding profiles of 2 different histone modifications, H3K27ac and H3K27me3, and the core ATP-ase subunit of the SWI/SNF chromatin remodeler, in duplicate, in blast cells derived from 3 different AML patients, and normal hematopoietic cells derived from 1 healthy individual, used as the control.


title: Comparison of methylation profile of human somatic and pluripotent stem cells

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by genome tiling array

summary: Reprogramming to induced pluripotent stem cells (iPSCs) and differentiation of pluripotent stem cells (PSCs) are primarily regulated by epigenetic machinery. Tripartite motif protein 28 (TRIM28), a universal mediator of Krüppel-associated box domain zinc fingers (KRAB-ZNFs), is known to regulate both processes, however exact mechanism and identity of participating KRAB-ZNF genes remains unknown. Here, using a novel reporter system, we first showed that TRIM28/KRAB-ZNFs alter DNA methylation patterns in addition to H3K9me3 to cause gene repression during reprogramming. Next, using several expression datasets, we identified novel KRAB-ZNFs (ZNF114, ZNF483 and ZNF589) in the human genome that regulate pluripotency. Mechanistically, we demonstrated that these KRAB-ZNFs directly alter gene expression of important developmental genes by modulation of H3K9me3 and DNA methylation on their promoters. In summary, TRIM28 employs novel KRAB-ZNFs to evoke epigenetic silencing of its target differentiation genes by H3K9me3 and DNA methylation.

overall_design: Microarray analysis of methylation profile of 2 primary human fibroblast cell lines, 4 lines of human induced pluripotent stem cells, one line of human embryonic stem cells and cells on different timepoints during reprogramming of primary human dermal fibroblasts into iPS cells - one normal line and one line with KAP1/TRIM28 knockdown.

first: Maciej

last: Wiznerowicz

first: Holger

last: Heyn

first: Marta

last: Gładych

first: Urszula

last: Oleksiewicz


title: Comparison of wild type mouse colon carcinoma cancer cell lines to transfected cell lines with Kras sh RNA

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

summary: We compared different mouse cancer cell lines to identify their unique cell signatures.

overall_design: Samples from different cancer cell lines were analyzed using Genespring 12.5 GX to obtain the data.

first: Nikolaos

middle: I

last: Kanellakis


title: Differential miRNA Expression in B Cells/T Cells Associated with Inter-individual Differences in Humoral Immune Response to Measles Vaccination

city: Rochester

first: Gregory

middle: A.

last: Poland

state: MN

address: 200 1st St SW

institute: Mayo Clinic

type: Non-coding RNA profiling by high throughput sequencing

summary: Through Next Generation Sequencing (mRNA-Seq) of intracellular miRNAs in measles virus-stimulated B and CD4+ T cells isolated from high and low antibody responders to measles vaccination, we identified a set of B cell-specific miRNAs (e.g., miR-151a-5p, miR-223, miR-29, miR-15a-5p, miR-199a-3p, miR-103a, and miR-15a/16 cluster) associated with measles-specific antibody response after vaccination. No CD4+ T cell-specific miRNA expression differences between high and low antibody responders were found. DIANA tool was used for gene/target prediction and pathway enrichment analysis and this yielded several biological processes/pathways, including regulation of adherens junction proteins, Fc-receptor signaling pathway, phosphatidylinositol-mediated signaling pathway, growth factor signaling pathway/pathways, transcriptional regulation, apoptosis and virus-related processes, that were significantly associated with neutralizing antibody titers after measles vaccination.   This study demonstrates that miRNA expression directly or indirectly influences humoral immunity to measles vaccination and suggests that B cell-specific miRNAs may potentially serve as predictive biomarkers of vaccine response.

overall_design: Examination of miRNA expression differences in/between purified B and CD4+ T cells of high and low responders to measles vaccination.

first: Iana

last: Haralambieva

first: Richard

middle: B

last: Kennedy

first: Whitney

last: Simon

first: Krista

middle: M

last: Goergen

first: Diane

middle: E

last: Grill

first: Inna

middle: G

last: Ovsyannikova

middle: A


title: An oncogenic axis of STAT-mediated BATF3 upregulation causing MYC activity in classical Hodgkin and anaplastic large cell lymphoma.

status: Public on Jan 08 2018

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: Gene expression profiles were compared between L-428 HRS cells transduced with shRNA against AP-1 transcription factor BATF3 and L-428 HRS cells transduced with a non-targeting shRNA as control.

first: L

first: M

last: Weniger

first: A

last: Lollies

first: R

last: Küppers


title: A cell-permeable stapled peptide inhibitor of the estrogen receptor/coactivator interaction

city: Chicago

first: Thomas

last: Speltz

state: IL

address: 833 S Wood St., room 539

department: Department of Medicinal Chemistry and Pharmacognosy

institute: University of Illinois at Chicago

summary: We and others have proposed that coactivator binding inhibitors, which block the interaction of estrogen receptor and steroid receptor coactivators, may represent a potential class of new breast cancer therapeutics. The development of coactivator binding inhibitors has been limited, however, because many of the current molecules which are active in in vitro and biochemical assays are not active in cell-based assays. Our goal in this work was to prepare a coactivator binding inhibitor active in cellular models of breast cancer. To accomplish this, we used molecular dynamics simulations to convert a high-affinity stapled peptide with poor cell permeability into R4K1, a cell-penetrating stapled peptide. R4K1 displays high binding affinity for estrogen receptor ɑ, inhibits the formation of estrogen receptor/coactivator complexes, and distributes throughout the cell with a high percentage of nuclear localization. R4K1 represses native gene transcription mediated by estrogen receptor ɑ and inhibits proliferation of estradiol-stimulated MCF-7 cells. Using RNA-Seq, we demonstrate that almost all of the effects of R4K1 on global gene transcription are estrogen receptor-associated. This chemical probe provides a significant proof-of-concept for preparing cell-permeable stapled peptide inhibitors of the estrogen receptor/coactivator interaction.

overall_design: mRNA profiles were generated for MCF-7 cells under six conditions. Experiments were performed in duplicate. Conditions: 1)vehicle treated (DMSO control), 2) estradiol (10 nM), 3) 4-hydroxytamoxifen (1 μM), 4) estradiol (10 nM) + 4-hydroxytamoxifen (1 μM), 5) R4K1 stapled peptide (15 μM), 6) estradiol (10 nM) + R4k1 (15 μM).

first: Jeanne

last: Danes

first: Joshua

middle: D

last: Stender

first: Jonna

last: Frasor

first: Terry

middle: W

last: Moore


title: Modulation of EMP2 in HEC1A cells

status: Public on Jan 01 2018

city: LA

first: Madhuri

last: Wadehra

state: CA

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

institute: UCLA

summary: Previous studies have suggested that overexpression of the oncogenic protein epithelial membrane protein-2 (EMP2) correlates with endometrial carcinoma progression and ultimately poor survival from disease.  To understand the role of EMP2 in the etiology of disease, gene analysis was performed to show transcripts that are reciprocally regulated by EMP2 levels.  In particular, EMP2 expression correlates with and helps regulate the expression of several cancer stem cell associated markers including aldehyde dehydrogenase 1 (ALDH1).

overall_design: Cells which overexpress EMP2 or express a shRNA knockdown (Sh KD) vector were used.


title: Expression data on CD4+ Tfh populations from Peyer's Patches of IL-21eGFP BAC transgenic

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: The production of IL-21 by T follicular helper (Tfh) cells is vital in driving the germinal centre reaction and high affinity antibody formation. However, the degree of Tfh cell heterogeneity and function is not fully understood. Using a novel IL-21eGFP reporter mouse strain, we identified a subpopulation of GFP+ highly differentiated Tfh cells in Peyer’s Patches. In vitro, GFP+ cells that did not co-express IL-17 or Foxp3 were induced by CD3 and CD28 stimulation of naïve CD4+ cells from IL-21eGFP mice in cultures containing IL-6, TGFβ and retinoic acid. In vivo, the differentiation of GFP+Tfh cells in Peyer’s Patches was induced by intestinal bacteria, and required CD4+ T cells and B cells with diverse repertoires. Analysis of the TCRβ repertoire of Peyer’s Patches CD4+ T cell subpopulations demonstrated that GFP+Tfh cells are polyclonal and closely related to GFP-Tfh cells. Importantly, ablation of GFP+ cells resulted in a reduced frequency of Peyer’s Patches germinal center B cells and small but significant shifts in gut microbiome composition. Thus, using a new IL-21-reporter mouse we have identified a subpopulation of Tfh cells induced by the gut microbiota and necessary for optimal Peyer’s Patches germinal center responses.

overall_design: The goal of this experiment was to determine gene expression differences between GFP+ Tfh cells and GFP- Tfh cells from Peyer’s Patches of IL21eGFP mice. Affymetrix mouse gene arrays were utilized to determine gene expression in purified CD4 samples from Peyer’s Patches.

first: Leigh

last: Jones

first: Francesca

last: Zolezzi

first: Maria

last: Curotto del Lafaille

first: Gerladine

last: Koh


title: AP-2α and AP-2β cooperatively orchestrate homeobox gene expression during branchial arch patterning

status: Public on Jan 03 2018

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

summary: RNA-seq of RNA isolated from E10.5 mandibular prominence of 3 control and 3 Tfap2a;Tfap2b;Wnt1CRE mutant mouse embryos.

overall_design: E10.5 mutant and litter-matched control embryos were dissected in ice-cold PBS. Subsequently, the mandibular prominences were carefully dissected from each embryo and stored in RNAlater (Ambion/Life Technologies) until later use. Following genotyping, RNA was extracted, essentially as previously described (Van Otterloo et al., 2016), from paired (i.e. left and right) mandibular prominences (3 control and 3 DCM embryos – 3 biological replicates) using the microRNA Purification Kit (Norgen Biotek Corp., Thorold, ON), following manufacturer's protocol. Following elution, mRNA was further purified using the Qiagen RNeasy Kit (Qiagen, Valencia, CA), according to manufacturer's protocol. Quality of extracted mRNA was assessed using DNA Analysis ScreenTape (Agilent Technologies, Santa Clara, CA) to ensure that it was of sufficient quality for library production. Following validation of extracted mRNA, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). Following library generation and subsequent quality control assessment, cDNA was sequenced using the Illumina HiSeq2500 platform and single-end reads (1x150).

first: Trevor

last: Williams


title: Expression data from murine skin upon RNAdjuvant treatment.

city: Tuebingen

first: Regina

last: Heidenreich

address: Paul-Ehrlich-Str 15

institute: CureVac GmbH

summary: Changes in gene expression at the injection site (site) upon application of RNAdjuvant was analyzed

overall_design: Mice were injected intradermally with 25mg RNAdjuvant, control mice were left untreated. Skin biopsies were isolated 1.5, 6 or 24h post treatment with RNAdjuvant and on Affymetrix GeneChip® Mouse Gene 1.0 Arrays.

first: Aleksandra

last: Kowalczyk


title: Structural basis for DNMT3A-mediated de novo DNA methylation (HumanMethylation450 BeadChip)

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

summary: DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) is essential for genome regulation and development. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-Å crystal structure of the DNMT3A-DNMT3L-DNA complex where two DNMT3A monomers simultaneously attack two CpG dinucleotides, with the target sites separated by fourteen base pairs within the same DNA duplex. The DNMT3A-DNA interaction involves a target recognition domain (TRD), a catalytic loop and DNMT3A homodimeric interface. A TRD residue Arg836 makes crucial contact with CpG, ensuring DNMT3A enzymatic preference towards CpG sites in cells. Hematological cancer-associated somatic mutations at the substrate-binding sites decrease DNMT3A activity, induce CpG hypomethylation and promote transformation of hematopoietic cells. Together, our study reveals the mechanistic basis for DNMT3A-mediated DNA methylation and establishes its etiologic link to human disease.

overall_design: TF-1 cells were stably expressed with either wild-type DNMT3A or its hematopoietic cancer-associated mutants. Genomic DNA was extracted and analyzed by the Illumina 450k Methylation array.

first: Greg

last: Wang

first: Zhimin

last: Zhang

first: Jikui

last: Song


title: Differential gene expression analysis of MYCN-amplified neuroblastoma cells after transfection with Control siRNA, LYAR siRNA-6 or LYAR siRNA-10

status: Public on Dec 31 2017

city: Sydney

first: Tao

last: Liu

state: NSW

address: C25 Lowy Cancer Research Center Gate 9 High St UNSW

department: Histone Modifications

country: Australia

institute: Children's Cancer Institute

summary:
N-Myc oncoprotein induces neuroblastoma and exerts its biological effects through modulation of its target genes.
We identified that MYCN modulates LYAR expression and we are interested to determine which signaling pathway LYAR regulates.

overall_design: We performed Affymetrix microarray experiments in BE(2)-C cells after transfection with control siRNA, LYAR siRNA-6 or LYAR siRNA-10 for 32 hours.

first: Bernard

last: Atmadibrata

first: Bing

last: Lee

first: Nicholas

last: Ho


title: Analysis of DNA methylation in traditional serrated adenomas

city: Sapporo

first: Eiichiro

last: Yamamoto

address: South-1, West-16, Chuo-ku

country: Japan

institute: Sapporo medical university

summary: We aimed to identify epigenetic alterations associated with the development of traditional serrated adenomas (TSAs). Through DNA methylation analysis with HumanMethylation450 BeadChip in TSAs and sessile serrated adenoma/polyp (SSA/Ps), we identified DNA methylation specifically associated with TSA development.

overall_design: We compared the methylation status between the protruding and flat components of the TSAs, and identified a series of CpG sites which were highly methylated in the protruding portions. We then compared the methylation status of the selected CpG sites between the protruding TSAs and SSA/Ps, and identified a set of CpG sites that were predominantly methylated in protruding TSAs.


title: Gene expression profile (GEP) of MAF-overexpressing CD34+ hematopoietic progenitor cells (HPCs)

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Primary Myelofibrosis (PMF) is a myeloproliferative neoplasm characterized by hyperplastic megakaryopoiesis and myelofibrosis. Through a gene expression profile (GEP) study we recently highlighted the MAF upregulation in PMF versus healthy donor (HD) CD34+ hematopoietic progenitor cells (HPCs). To shed some light into the role of MAF in PMF pathogenesis, here we unravelled the effects of the overexpression of MAF in HPCs forcing its expression in HPCs.
We showed that MAF overexpression favours the megakaryocyte and monocyte/macrophage commitment and leads to the abnormal expression of genes coding for proinflammatory and profibrotic mediators. Due to the key role of the above-mentioned processes in PMF pathogenesis, we selected a subset of genes coding for secreted molecules for further validation by quantitative enzyme-linked immunoassays. Noteworthy, our data unveiled a causal connection between the upregulation of MAF and the increased plasma levels of key proinflammatory/profibrotic  mediators (IL8, CCL2, PLAUR and MMP9) in PMF patients. Similarly, the upregulation of MAF was responsible for the deranged expression of LGALS3 and SPP1, that are profibrotic mediators increased in PMF patients compared with HDs.

overall_design: RNA from CD34+ HPCs retrovirally transduced to overexpress either the MAF splicing variant 1 (RefSeq NM_005360.3) or the MAF variant 2 (RefSeq NM_001031804.1). RNA was collected from a set of 3 independent experiments.

first: Elisa

last: Bianchi

first: Samantha

last: Ruberti

first: Tiziana

last: Fanelli

first: Sebastiano

last: Rontauroli

first: Ruggiero

last: Norfo

first: Valentina

last: Pennucci

first: Giuditta

middle: C

last: Fattori

first: Carmela

last: Mannarelli

first: Chiara

last: Rossi

first: Roberta

last: Zini

first: Simona

last: Salati

first: Zelisa

last: Prudente

first: Sergio

last: Ferrari

first: Enrico

last: Tagliafico

first: Paola

last: Guglielmelli

first: Alessandro

last: Vannucchi


title: Cell hashing enable sample multiplexing, multiplet identification and super-loading on droplet-based single cell RNA-sequencing platforms

status: Public on Jan 02 2018

city: Boston

first: Soumya

last: Badrinath

address: One Jimmy Fund Way

institute: Dana-Farber Cancer Institute

summary: We reasoned that by using a distinct set of oligo-tagged antibodies against ubiquitously expressed proteins, we could uniquely label multiple populations of cells, multiplex them together, and use the barcoded antibody signal as a fingerprint. We refer to this approach as cellular "hashing", as our set of oligos defines a "look up table" to assign each multiplexed cell to its original sample. We demonstrate application of the technique to combine eight samples and run them simultaneously in a single droplet based scRNA-seq run. We show that cell hashtags allow sample multiplexing, confident multiplet identification and super-loading in the context of a commonly used droplet-based scRNA-seq method to drive down the per-cell cost of large-scale scRNA-seq experiments

overall_design: We chose a set of monoclonal antibodies directed against ubiquitously and highly expressed immune surface markers (CD45, CD98, CD44, and CD11a) and combined these antibodies into eight identical pools (pool A-H), and subsequently conjugated each pool to a distinct hashtag oligonucleotide (henceforth referred to as HTOs). The HTOs contain a unique 10- or 12-bp barcode that could be read out and linked to the cellular transcriptome, through minor modifications to standard scRNA-seq protocols.

first: Marlon

last: Stoeckius

first: Shiwei

last: Zheng


title: Differential gene expression of neuroblastoma cells stably expressing doxycycline-inducible DOT1L small hairpin RNA

first: Tao

last: Liu

summary:
We were interested in studying the role of DOT1L-mediated H3K79 methylation on N-Myc target gene transcription in MYCN-induced neuroblastoma.
We aimed to determine whether knocking down DOT1L in MYCN-amplified neuroblastoma would affect N-Myc target gene expression.

overall_design: We generated neuroblastoma BE(2)-C cells stably expressing control (SCRAMBLE) or DOT1L shRNA and treated the cells with control vehicle (DMSO) or doxycycline to induce DOT1L expression knockdown for 96 hours.

first: Matthew

last: Wong

first: Bernard

last: Atmadibrata

first: Andrew

last: Tee


title: A survey of DNA methylation polymorphism identifies environmentally responsive co-regulated networks ofepigenetic variation in the human genome

city: New York City

first: Ricky

middle: Shantilal

last: Joshi

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Understanding the causes and consequences of genomic variation is a major goal in the field of genetics. While studies such as the Hapmap and 1000 Genomes Projects have resulted in detailed maps of genetic variation, to date there are no robust maps of epigenetic variation in humans, and as a result few insights have been made into their significance or underlying biology. Here we set out to define and characterize sites of common epigenetic variation in humans, that we term Variable Methylation Regions (VMRs). Using a robust approach we identify hundreds of VMRs in each cell type that show common variability in DNA methylation levels in the normal population.

overall_design: Human fibroblast cells from GM04503 individual were grown to various levels of growth and confluency reflecting cellular stress. Cells were harvested after 3, 5, 7, 10 and 12 days of growth (TP 1-5) where the medium was changed every two days to maintain optimal growth.  A subset of cells were grown in parallel and harvested at exactly the same time points however the media were left unchanged to promote cellular stress. From each treatment, whole DNA was extracted and global DNA methylation levels were assessed using Illumina Infinium HumanMethylation450 BeadChip.

first: Paras

last: Garg

first: Corey

last: Watson

middle: J

last: Sharp


title: Deep sequencing and methylation profiling of both treated and untreated primary and recurrent tumours confirms the heterogeneous and dynamic nature of glioblastoma

city: Clayton

first: Nicholas

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: Combined targeted amplicon sequencing and DNA methylation analysis of a defined cohort of Adult Glioma patients was performed on primary and matching recurrent tumour samples to investigate tumour evolution.

overall_design: 21 patients from which primary and matching recurrent tumour samples were analysed for DNA methylation using Illumina HumanMethylation450K bead array. Samples from 6 patients were performed in replicate.


title: Genomic Profiling of Diabetic Foot Ulcers Identifies miR-15b-5p as a Major Regulator that Leads to Suboptimal Inflammatory Response and Diminished DNA Repair Mechanisms

status: Public on Dec 28 2017

city: Miami

first: Horacio

middle: Adrian

last: Ramirez

state: Florida

address: 1600 NW10th Avenue RMSB room 2029A

department: Dermatology

institute: University of Miami

summary: Diabetic foot ulcers (DFUs) are the leading cause of lower leg amputations in diabetic population. To better understand molecular pathophysiology of DFUs we used patients’ specimens and genomic profiling. We identified 3900 genes specifically regulated in DFUs. Moreover, we compared DFU to human skin acute wound (AW) profiles and found DNA repair mechanisms and regulation of gene expression among the processes specifically suppressed in DFUs, whereas essential wound healing-related processes, inflammatory/immune response or cell migration, were not activated properly. To identify potential regulators of DFU-specific genes, we used upstream target analysis. We found miR-15/16 family enriched in DFUs, but not in AW, which was confirmed by qPCR. We found that infection with the most common DFU colonizer, Staphylococcus aureus, triggers induction of miR-15-5p, which in turn, targets multiple DFU-specific genes, including genes involved in DNA repair (WEE1, MSH2 and RAD50) and the regulator of inflammatory pathway, IKBKB. Induction of miR-15b-5p, either by miR-mimic transfection in vitro or by S. aureus infection of acute wounds ex vivo, suppressed both WEE1 and IKBKB. Consequently, we detected an increase in DNA double strand breaks in DFUs. In summary, our data indicate that S. aureus infection, via induction of miR-15b-5p, may lead to suppression of DNA repair mechanisms and a sub-optimal inflammatory response, contributing to pathophysiology of DFU patients

overall_design: Total RNA including the miRNA fraction was extracted from the samples using the QIAGEN miRNeasy mini kit and following the manufacturer’s instructions. The RNA quality was assessed using the AGILENT bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) to estimate the RNA integrity number (RIN). Samples with a RIN higher than 5 were used for mRNA profiling. All processing and analysis of microarrays utilized standard protocols at the University of Miami Microarray Core Facility. Briefly, between 100 to 300 ng of total RNA was reverse transcribed, amplified, then the sense strand cDNA synthesized, labeled, and hybridized on arrays. The amplified, fragmented and biotin-labeled cDNAs were hybridized to the Affymetrix GeneChip Human Gene 2.0 ST microarray according to the manufacturer’s recommendations. Arrays were washed and stained using Affymetrix Fluidic stations 450 and scanned using Affymetrix GeneChip scanner 3000 7G. Image analysis was performed using the Affymetrix Command Console Software (AGCC). Resulting CEL files was imported into Expression Console™ Software (Affymetrix, Santa Clara, CA, USA) and underwent gene level normalization and signal summarization. The output files from this step were imported in Transcriptome Analysis Console (TAC) 3.0 Software (Affymetrix, Santa Clara, CA, USA) to identify differentially expressed genes and carry out clustering analysis between DFUs and FS. Genes with an FDR lower than 0.05 and a fold-change greater than 2 were considered as differentially expressed

first: Irena

last: Pastar

first: Ivan

last: Jozic

first: Olivera

last: Stojadinovic

first: Rivka

last: Stone

first: Nkemcho

last: Ojeh

first: Robert

last: Kirsner

first: Marjana

last: Tomic-Canic


title: Myeloid-targeted immunotherapies act in synergy to induce inflammation and anti-tumor immunity

status: Public on Dec 27 2017

city: New Haven

first: Curtis

last: Perry

address: 1 Gilbert st.

institute: Yale University

summary:
Purpose: Eliciting effective anti-tumor immune responses in patients who fail checkpoint inhibitor therapy is a critical challenge in cancer immunotherapy, and in such patients, tumor-associated myeloid cells and macrophages (TAMs) are promising therapeutic targets. We demonstrate in an autochthonous, poorly immunogenic mouse model of melanoma that combination therapy with an agonistic anti-CD40 mAb and CSF1R inhibitor potently suppressed tumor growth. Microwell assays to measure multiplex protein secretion by single cells identified that untreated tumors have distinct TAM subpopulations secreting MMP9 or co-secreting CCL17/22, characteristic of an M2-like state. Combination therapy reduced the frequency of these subsets, while simultaneously inducing a separate polyfunctional inflammatory TAM subset co-secreting TNF, IL-6, and IL-12. Tumor suppression by this combined therapy was partially dependent on T cells, TNF and IFN. Together, this study demonstrates the potential for targeting TAMs to convert a “cold” into an “inflamed” tumor microenvironment capable of eliciting protective T cell responses.
Methods: Total RNA was purified with the use of QIAzol and RNeasy Mini kit (QIAGEN), in which an on-column DNase treatment was included. Purified RNA was submitted to the Yale Center for Genomic Analysis where it was subjected to mRNA isolation and library preparation. Non-strand specific libraries were generated from 50ng total RNA using the SMARTer Ultra Low Input RNA for Illumina Sequencing kit.  Libraries were pooled, six samples per lane, and sequenced on an Illumina HiSeq 2500 (75-bp paired end reads), and aligned using STAR to the GRCm38 (mm10) reference genome. A count-based differential expression protocol was adapted for this analysis(Anders et al., 2013); mappable data were counted using HTSeq, and imported into R for differential expression analysis using the DESeq2.To find differentially regulated sets of genes for signature generation, a 1.5-Log2 fold-change difference between samples and p-adjusted (Holm-Sidak) ≤ 0.01 was used.
Results: To begin to understand how these treatments modulated T cells to control tumor growth, and to possibly illuminate additional biomarkers of response, we examined the transcriptomes of CD11b+ Ly6G- cells treated with CD40 or CSF1Ri, alone or in combination, relative to control, using high throughput RNA-sequencing. Principal components analysis (PCA) on the genome-wide dataset demonstrated that treating with CD40 and CSF1Ri individually caused largely non-overlapping changes in transcription, as indicated by their movement along orthogonal principal components (PC) relative to the control. Importantly, combination therapy was visualized as a systems-level combination of each individual treatment in PC space.     We then examined the mRNAs most altered by either treatment alone or in combination relative to Controls (Log2FC>1.5, p<.01) by unsupervised hierarchical clustering. Five major gene patterns emerged from the clustering of genes. Cluster #1 comprises genes that are upregulated by CD40 and CSF1Ri+CD40 treatment but are mostly unaffected by CSF1Ri, suggesting that CD40 is the primary driver of this cluster in the combination treatment. Notable genes in this cluster include Tnfa, IfngIl12b and Cxcl9; interestingly, for Tnfa and Il12b, CSF1Ri+CD40 appears to have a synergistic effect on expression. In contrast to Cluster #1, Cluster #5 contains genes substantially downregulated by CSF1Ri and CSF1Ri+CD40 treatments, but are largely unaffected by CD40, suggesting that CSF1Ri is the driver of this cluster in the combination treatment. Cluster #5 genes include Cd36 and Fabp4, suggesting alterations in lipid homeostasis in the TAMs after treatment. Cluster #2 includes genes that are modestly upregulated by CD40 and CSF1Ri individually, leading to a stronger upregulation when combined. Finally, Clusters #3 and #4 include, for the most part, genes that are differentially affected by CD40 versus CSF1Ri and for which the combination treatment yields an intermediate response. In summary, these data show that CSF1Ri and CD40 agonism elicit predominantly distinct changes in gene expression in the CD11b+ cells, indicating they target different biological processes in myeloid cells. The net result of the changes in myeloid gene expression from the combination of CSF1Ri+CD40 treatment reveal additive effects by the individual treatments, but also synergy in the expression of several pro-inflammatory genes (e.g., Tnfa, Ifng, Il6 and Il12b).   We further examined our dataset with Gene Set Enrichment Analysis (GSEA). Although CSF1Ri and CD40 treatments did not closely match any immunological signatures in the immunological database of MSigDb, combined CSF1Ri+CD40 had a strikingly similar signature to myeloid cells exposed to a variety of inflammatory stimulants, most closely reflected by BMDMs treated with lipopolysaccharide (LPS). This motivated us to look specifically at categories of NF-κB target genes that are significantly affected by LPS treatment, including transcription factors, cytokines and chemokines. Indeed, most of these NF-κB target genes associated with inflammation were strongly upregulated by CSF1Ri+CD40 treatment. Finally, Ingenuity Pathway Analysis identified TNFR1 and TNFR2 signaling and Acute phase response signaling among the top genetic signatures produced by the CSF1Ri+CD40 treatment combination, matching what we observed with GSEA. Thus, gene expression analysis not only revealed several biomarkers of response that may be relevant for assessing therapeutic activity in ongoing clinical trials using these drugs, but illuminated lead biological factors that may cause tumor regression.
Conclusions: myeloid-targeted immunotherapies anti-CD40+CSF1R inhibition synergistically induce a pro-inflammatory microenviroment

overall_design: mRNA profiles of tumor infiltrating lymphocytes (TILs) in mice were generated by deep sequencing, in triplicate, using Illumina.

first: Andrés

middle: R

last: Muñoz-Rojas

first: Durga

last: Thakral


title: Next generation sequencing analysis of gene expression profiles in splenic CD4+ T cells from EAE mice treated with TRAIL

city: Taipei

first: I-Tsu

last: Chyuan

address: No.1 Jen Ai Rord Section 1

country: Taiwan

institute: National Taiwan University

summary:
Purpose: To elucidate the potential immune-regulatory mechanism of TRAIL of activated T cells in EAE, we analyzed gene expression profiles of splenic CD4+ T cells from EAE mice treated with TRAIL by RNA sequencing and transcriptome analysis.
Methods: Splenic CD4+ T cell mRNA profiles of control or EAE mice treated with vehicle or TRAIL were generated by deep sequencing using Illumina Solexa. Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit for 75SE (Single-End or Paired-End) sequencing on Solexa platform. The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit. Raw sequences were obtained from the Illumina Pipeline software bcl2fastq v2.0 and expected to generate  20M  (million reads or Gb) per sample.
Results: By comparing mRNA exression of splenic CD4+ T cells from EAE mice treated with vehicle or TRAIL, there were 244 genes significantly differentially expressed. By analyzing these 244 significant genes categorized by a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the most significantly enriched category for CD4+ T cells was “cell cycle” (multiple of enrichment: 3.13, p = 1.64 × 10−5) followed by “TCR signaling pathway” (multiple of enrichment: 2.80, p = 8.25 × 10−4). In addition, significant genes in the“TCR signaling pathway” tended to be downregulated while those in “cell cycle”tended to be upregulated in a volcano plot analysis. Consistent with the volcano plot results, by using unsupervised hierarchical clustering, the heatmap showed that significant TCR signaling pathway-associated genes were downregulated, while significant cell cycle-associated genes were upregulated in splenic CD4+ T cells from EAE mice treated with TRAIL
Conclusions: Our study demonstrated the gene transcription pattern from CD4+ T cells of TRAIL-treated EAE mice were involved in distinct TCR signaling and cell cycle pathways.

first: Chyuan

last: I-Tsu

first: Hsu

last: Ping-Ning


title: Expression data from sorted humanized TREM2 murine microglia

status: Public on Dec 29 2017

city: Saint Louis

first: Marco

last: Colonna

state: Missouri

address: 660 S Euclid Ave

institute: Washington University in St. Louis

summary:
The R47H variant of TREM2 is associated with higher risk of Alzheimer's disease. We generated mice expressing the common variant or R47H variant of human TREM2
in the absence of murine TREM2 on the 5XFAD mouse model of Alzheimer's disease.

overall_design: CD45+ CD11b+ microglia were sorted from brains of 8.5-month-old mice expressing common variant, R47H, or no human TREM2 on a background of murine TREM2 deficiency and the 5XFAD mouse model of Alzheimer's disease.

first: Wilbur

last: Song


title: Impact of regulatory variation across human iPSCs and differentiated cells [ATAC-seq LCL]

status: Public on Dec 23 2017

first: Nicholas

last: Banovich

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell type-specific chromatin accessibility.

overall_design: Chromatin accesibility profiled using the ATAC-seq protocol

first: Yang

last: Li

first: Anil

last: Raj

first: Michelle

last: Ward

first: Po

middle: Y

last: Tung

first: Jonathan

last: Burnett

first: Marsha

last: Myrthil

first: Samantha

last: Thomas

first: Diego

last: Calderon

first: Peyton

last: Greenside

first: Anshul

last: Kundaje

middle: K

last: Pritchard

first: Yoav

last: Gilad


title: Single-cell RNA sequencing of vascularized brain organoids

city: Shanghai

first: Xiang-Chun

last: Ju

address: Yueyang Road 320

country: China

institute: Institute of Neuroscience

summary: Organoids have been widely used as unique models of human brain development and disorders. However, the lack of vasculatures in brain orgnoids limits their application in the study of brain vasculature development and diseases. Here, we described to the generation of vascularized brain organoids (VBOrs) with different brain regions from human embryonic stem cells. The goals of this study are to analyze the cell populations of the new model of vasularized brain organoids cultured from human embryonic stem cells (H9). We found that VBOrs contain variant brain cells inculding neural progenitors, neuronal cells, astrocytes, sparse endothelial cells, and pericytes. The new model of VBOrs should be valuable for addressing questions between brain vasculatures and neural cells.

overall_design: VBOrs were generated by two methods distinct in the step of vascular progenitor induction: method 1 (group BMPi), EBs were treated with bFGF, VEGF and SB431542 for two days; method 2 (group BMPa), EBs were treated with bFGF, VEGF and BMP4 for two days. Single-cell suspensions from two groups of VBOrs (BMPa and BMPi) were prepared by 20-min digestion in 0.25 mg/ml trypsin. About 10,000-12,000 cells for each sample (2 independent repeats) were loaded for soating, barcoding and library construction. Sequencing was performed with HiSeq X.

first: Zhen-Ge

last: Luo


title: Impact of regulatory variation across human iPSCs and differentiated cells [ATAC-seq iPSC-CM]

city: Chicago


title: A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers (Sorted Bulk RNA-Seq)

city: Berkeley

first: Michael

last: Cole

address: 378 Stanley Hall

institute: UC Berkeley

summary: Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-Seq to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. We discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4+ T cell counts and lower HIV-1 viral loads, and that effectively primes polyfunctional T cell responses in vitro. We identify and validate select immunomodulators that increase the fractional abundance of this state in primary peripheral blood mononuclear cells (PBMCs) from healthy individuals in vitro.

overall_design: Bulk RNA-seq profiling of sorted cDC subsets associated with cell-intrinsic HIV-1 immune recognition.

first: Enrique

last: Martin-Gayo

first: Kellie

last: Kolb

first: Zhengyu

last: Ouyang

first: Jacqueline

last: Cronin

first: Samuel

last: Kazer

first: Jose

last: Ordovas-Montanes

first: Mathias

last: Lichterfeld

first: Bruce

last: Walker

first: Nir

last: Yosef

first: Alex

last: Shalek

first: Xu

last: Yu


title: Impact of regulatory variation across human iPSCs and differentiated cells [ATAC-seq iPSC]

first: Nicholas

last: Banovich

first: Yang

last: Li

first: Anil

last: Raj

first: Michelle

last: Ward

first: Po

last: Tung

first: Jonathan

last: Burnett

first: Marsha

last: Myrthil

first: Samantha

last: Thomas

first: Diego

last: Calderon

first: Peyton

last: Greenside

last: Kundaje


title: Mechanical cues control mutant p53 stability through a Mevalonate/RhoA axis

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary:
To investigate the genes differentially expressed upon plating on top of matrixes with different stiffness, we compared the expression profiles of MDA-MB-231 breast cancer cells plated on a stiff substrate (plastic) with the same cells plated on a soft substrate (hydrogels 0.7 kPa).

Keywords: expression profiling by array

overall_design: We collected RNA from MDA-MB-231 cells plated and cultured from 2 days on a stiff substrate and on a soft substrate. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Four biological replicas (A, B, C, D) were used for each condition for a total of 8 samples.

first: Luca

last: Azzolin

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo

first: Giannino

last: Del Sal


title: A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers

first: Michael

last: Cole

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

overall_design: Refer to individual Series


title: INO80 Chromatin Remodelling Coordinates Metabolic Homeostasis with Cell Division

city: Stanford

first: Graeme

last: Gowans

address: Gilbert Building, 371 Serra Mall

department: Biology

institute: Stanford University

summary: We performed RNA-seq across the yeast metabolic cycle (YMC) in wild-type and a strain lacking ARP5, a central component of the INO80 chromatin remodelling complex. We also perform ATAC-seq on the same samples to examine chromatin architecture across the YMC.

overall_design: RNA-seq and ATAC-seq in wild-type and arp5∆ yeast

first: Ashby

last: Morrison


title: Transcriptomic study of zinc-deficient Saccharomyces cerevisiae wild-type, atg1Δ, and atg41Δ strains

city: Madison

first: David

last: Eide

state: WI

address: 1415 Linden Drive

department: Nutrional Sciences

institute: University of Wisconsin-Madison

summary:
Purpose: ATG41 is involved both in autophagy and zinc-deficient growth. The goal of this study is to compare transcriptomic profiles of wild-type and atg41Δ strains to discover autophagy-independent molecular phenotypes for the mutant. The atg1Δ mutant is a control for autophagy activity.
Methods: Wild-type and mutant yeast were grown to mid-log phase in replete medium and shifted to zinc-deficient medium for 8 hours, after which, cells were harvested for RNA sequencing to detect differential gene expression.
Results: Gene expression data for virtually every gene (~6,000) was obtained with ~12,000,000 reads per sample. Differential gene expression analysis showed that several hundred genes were differentially experessed in the atg41Δ mutant (greater than 2-fold) at an FDR of 0.5.
Conclusions: Most strikingly, we found that the atg41Δ mutant transcriptome shows signs that sulfur metabolism is distrupted during zinc-deficinet growth. Expression of Met4 gene targets is increased.

overall_design: mRNA from wild-type, atg1Δ, and atg41Δ yeast strains was prepared from zinc-deficient cultures in quadruplicate and sequenced. Single-end, 100bp sequencing was performed, using v4 SBS chemistry on an Illumina HiSeq2500 sequencer.

last: Bucci


title: Screen of differential expressed genes from residual MHCC97H treated by POSTN or not

first: Rui

last: Zhang

address: Fenglin road of Xuhui district

institute: Zhongshan hospital of Fudan University

summary:
Incomplete thermal ablation may induce invasiveness of hepatocellur carcinoma, however, the mechasim is not fully understood. Here, we investigated whether activated hepatic stellate cells would accelerate the progression of residual HCC after sublethal heat treatment via the secretion of POSTN.
We used microarrays to detail the global programme of up-regulated genes of residual HCC cells induced by POSTN.

overall_design: Residual MHCC97H pre-treated by POSTN or not for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain differential expression profiles. To that end, we prepared six samples of two groups, and three replicates for each group.

first: Min

last: Ma

first: Xia-hui

last: Lin

first: Jie

last: Chen

first: Jun

first: Dong-mei

last: Gao

first: Jie-feng

last: Cui

first: Zheng-gang

last: Ren

first: Rong-xin


title: ICAMs are not obligatory for functional immune synapses between naïve CD4 T cells and lymph node DCs

status: Public on Dec 21 2017

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: The quantitative deep bulk MARS-seq analysis demonstrated that DCs from ICAM-1/2 double knockout (DKO) chimeric LNs  display similar transcriptomes to those of WT DCs in both their resting and CD40 mAb activated states.

overall_design: Transciptome analysis of activated and resting classical DCs from either WT or ICAM-1/2 DKO chimeric mice was performed. DC cells were isolated from popliteal lymph nodes and sorted according to the following markers: CD45, CD11c and MHC-II

first: Sara

last: Feigelson

first: Caterina

last: Curato

first: Steffen

last: Jung

first: Ronen

last: Alon


title: Differentially modulated transcriptomes of mouse skeletal muscle (gastrocnemius) during postnatal development

status: Public on Dec 22 2017

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Purpose: During postnatal development the fetal skeletal muscle undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS)
Methods:We performed RNA-seq for high-resolution analysis of transcriptome changes during postnatal mouse skeletal muscle development using RNA from gastrocnemius muscle from embryonic day 18.5, postnatal day 2 (PN2), PN14, PN28, adult (22 weeks).
Results: We identified a novel role for AS in several cellular functions including calcium handling and membrane organization during postnatal skeletal muscle development. Furthermore, AS transitions within calcium handling genes are responsive to Celf1 and Mbnl1, RNA-binding proteins with developmentally regulated expression.
Conclusions: We identified a novel role for AS in several functional categories during postnatal development including calcium handling, vesicular trafficking and cell junctions.

overall_design: Mouse skeletal muscle mRNA profiles of  embryonic day 18.5, postnatal day 2 (PN2), PN14, PN28, adult (22 weeks) gastrocnemius muscle were generated by deep sequencing using Illumina HiSeq 2500.

first: Amy

last: Brinegar

first: Wei

last: Li

first: Thomas

last: Cooper


title: Patient-derived organoids (PDOs) model treatment response of metastatic gastrointestinal cancers.

city: London

first: Georgios

last: Vlachogiannis

address: 15 Cotswold Road

country: United Kingdom

institute: The Institute of Cancer Research

summary: We report RNAseq data from subsequent passages of five organoid cultures.

overall_design: RNA extracted from subsequent PDO passages was subjected to RNAseq.

first: Nicola

last: Valeri


title: Expression data from PVTT control cells and PVTT hPCL3s overexpressing cells

first: yuezhen

last: deng

address: 320 Yueyang Road, Shanghai, China

institute: The Chinese Academy of Science

summary: Our previous studies have clearly demonstrated the roles of hPCL3s (PHF19) in the migration, invasion and metastasis of HCC cells. The microarray analysis was performed to screen the differentially expressed genes in the PVTT/hPCL3s

overall_design: RNA was extracted from PVTT/con and PVTT/hPCL3s cells and the gene expression microarray was performed to investigated the genes regulated by hPCL3s.

first: Yuezhen

last: Deng

first: Dong

last: Xie


title: IKZF2 is required for myeloid leukemic stem cells by driving self-renewal and inhibiting the myeloid differentiation program I

city: New York

first: Hyein

middle: Sophia

last: Cho

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We report that IKZF2 is required for maintaining chromatin accessibility in leukemic stem cells in myeloid leukemia. RNA seq and ATAC-seq were performed to investigate the changes in chromatin accessibility of differentially expressed genes in leukemic stem cells when IKZF2 was absent. We found that IKZF2 maintains open accessibility in self-renewal transcription factor motifs such as HOXA9 sites whereas motifs of differentiation transcription factors including C/EBPs are kept closed.

overall_design: 4 RNA-seq, 4 ATAC-seq; 2 Ikzf2 WT each, 2 Ikzf2 KO each

first: Sun-Mi

last: Park

first: Angela

last: Thornton

first: Hyunwoo

first: Trevor

middle: S

last: Barlowe

first: Timothy

last: Chou

first: Sagar

last: Chhangawala

first: Lauren

last: Fairchild

first: James

last: Taggart

first: Arthur

last: Chow

first: Alexandria

last: Schurer

first: Matthew

last: Witkin

first: Ethan

last: Shevach

first: Andrei

last: Kristov

first: Scott

last: Armstrong

first: Christina

last: Leslie

first: Michael

last: Kharas


title: ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells

status: Public on Dec 20 2017

city: Nashville

first: Andrea

last: Perreault

state: TN

address: 746 Robinson Research Building

institute: Vanderbilt University

summary: The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as ChIP-seq. While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA-polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo.

overall_design:
ChIP-seq was performed by isolating 50 million cells and crosslinking with 37% formaldehyde. Cells are then lysed and sonicated, to achieve fragments of 200-500 basepairs. Cells are incubated overnight at 4C with antibody to locate protein of interest genome-wide. Chromatin is eluted from antibody and beads and cross links are reversed. Several enzymatic reactions prepare the DNA fragments for sequencing, including end polishing, A-tailing, and adapter ligation. DNA is purified and amplified using PCR. DNA is run on an agarose gel and gel purified. DNA libraries are then sequenced using an Illumina NextSeq500 sequencer as single-end reads 50 or 75 nucleotides in length.

ChIP-exo was performed by isolating 50 million cells and crosslinking with 37% formaldehyde. Cells are then lysed and sonicated, to achieve fragments of 200-500 basepairs. Cells are incubated overnight at 4C with antibody to locate protein of interest genome-wide. After several on-bead enzymatic reactions (the most important of which is the lambda exonuclease), chromatin is eluted from antibody and beads. Crosslinks are reversed and DNA is extracted. Adapters are ligated, which is necessary for identification post sequencing. DNA is purified and amplified using PCR. DNA is run on an agarose gel and gel purified. DNA libraries are then sequenced using an Illumina NextSeq500 sequencer as single-end reads 50 or 75 nucleotides in length.

The main difference between the two assays is the enzymatic reactions and the most important of these is the lambda exonuclease digestion

Please note that the bigWig files are merged biological replicates (as indicated in the corresponding sample description field). For example, the ChIP_exoMerge.bw is the processed file where ChIPexo for Pol2 from rep 1 and rep2 were merged and converted to the bigWig format.

first: Zenab

middle: F

last: Mchaourab

first: Bryan

last: Venters


title: A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers (scRNA-Seq)

middle: B

last: Cole

overall_design: Single-cell RNA-seq profiling of HIV-1-exposed cDCs and media controls from 3 elite controllers used to identify reproducible gene expression programs associated with cell-intrinsic HIV-1 immune recognition.

first: Enrique

last: Martin-Gayo

first: Kellie

last: Kolb

first: Zhengyu

last: Ouyang

first: Jacqueline

last: Cronin

first: Samuel

last: Kazer

first: Jose

last: Ordovas-Montanes

first: Mathias

last: Lichterfeld

first: Bruce

last: Walker

first: Nir

last: Yosef

first: Alex

last: Shalek

first: Xu

last: Yu


title: RNA deep sequencing analysis of glioma stem cells(GSCs) and non-GSCs

city: Philadelphia

first: Yi

last: Fan

state: Pennsylvania

address: 3400 Civic Center Blvd, Smilow Center for Translational Research, Rm 8-132

department: Department of Radiation Oncology

institute: University of Pennsylvania

summary: To explore potential molecular mechanisms underlying the temporal process of DNA damage and repair in CSCs, we utilized deep RNA sequencing to analyze the expression of DNA damage and repair-associated genes at the transcriptome level. Our gene set analysis of CSCs and matched non-CSCs revealed a stemness-associated upward trend of global gene expression, particularly in NHEJ, mismatch excision repair (MMR) and HR pathways.

overall_design: The RNA profiles of IN528, T3961, and T4121 CSCs and matched non-CSCs were generated by deep sequencing.

first: Yanling

last: Wang


first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

institute: National Taiwan University, Taiwan

summary: Genomewide methylation profiles in coronary artery ectasia patients and matched healthy controls.

overall_design: A total of 11 CAE patients and 12 healthy controls were analyzed. Peripheral blood specimens were collected and DNA was extracted. A propensity score algorithm was performed to select matched individuals

first: Jyh-Ming

last: Juang


title: RNAs associated with affinity captured LINE-1 ribonucleoproteins

first: John

last: LaCava

address: 1230 York ave

institute: The Rockefeller University

summary: RNAs extracted from affinity enriched L1 RNPs were subjected to next-gen RNA-seq

overall_design:
Synthetic L1s expressed in HEK293T_LD from pLD401, pLD567, and pLD624
Synthetic L1s expressed from pLD401 were subjected to split-tandem affinity enrichement, via ORF2p-3xFLAG (1st) and direct IP of ORF1p (2nd)
Synthetic L1s expressed from pLD567 and pLD624 were subjected to affinity enrichement via ORF2p-3xFLAG only


title: RAF/MEK/extracellular signal–related kinase pathway suppresses dendritic cell migration and traps dendritic cells in Langerhans cell histiocytosis lesions

first: Brandon

last: Hogstad

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary:
Expression data from dendritic cell subsets derived or sorted from control littermate and CD11c-Cre/BRAFV600E(flox-CA) mice
Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by granulomatous lesions containing pathological CD207+ dendritic cells (DCs) with constitutively activated mitogen-activated protein kinase (MAPK) pathway signaling. Approximately 60% of LCH patients harbor somatic BRAFV600E mutations localizing to CD207+ DCs within lesions. However, the mechanisms driving BRAFV600E+ LCH cell accumulation in lesions remain unknown. Here we show that sustained extracellular signal–related kinase activity induced by BRAFV600E inhibits C-C motif chemokine receptor 7 (CCR7)–mediated DC migration, trapping DCs in tissue lesions. Additionally, BRAFV600E increases expression of BCL2-like protein 1 (BCL2L1) in DCs, resulting in resistance to apoptosis. Pharmacological MAPK inhibition restores migration and apoptosis potential in a mouse LCH model, as well as in primary human LCH cells. We also demonstrate that MEK inhibitor-loaded nanoparticles have the capacity to concentrate drug delivery to phagocytic cells, significantly reducing off-target toxicity. Collectively, our results indicate that MAPK tightly suppresses DC migration and augments DC survival, rendering DCs in LCH lesions trapped and resistant to cell death.

overall_design: 18 samples; 2-3 replicates per organ and genotype; WT are littermate control reference relative to CD11c-Cre/BRAFV600E(flox) specimens

first: Marie

middle: L

last: Berres

first: Rikhia

last: Chakraborty

first: Carl

last: Allen

first: Miriam

last: Merad


title: A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers (TLR perturbation Bulk RNA-Seq)

first: Michael

last: Cole

overall_design: Bulk RNA-seq profiling of TLR-perturbed cDCs and controls from a healthy donor for comparison with gene expression programs associated with cell-intrinsic HIV-1 immune recognition.

first: Enrique

last: Martin-Gayo

first: Kellie

middle: E

last: Kolb

first: Zhengyu

last: Ouyang

first: Jacqueline

last: Cronin

first: Samuel

last: Kazer


title: Comprehensive DNA Microarray Analysis for the Gene Sets Involved in Allergic Reaction by Allergic Effector Cells

city: Uchinada Kahoku

first: Toshiki

last: Yabe-Wada

state: Ishikawa

address: 1-1 Daigaku

department: School of Medicine

institute: Kanazawa Medical University

summary:
Mast cells, basophils, and eosinophils play an important role in allergic disorders as effector cells. These cells secrete abundant serine proteases as well as chemical mediators and cytokines. Various serine proteases including SLPI are also important for to regulate an allergic response in these effector cells, although the expression profiles and functions of these proteases still remain unclear.
We carried out DNA microarrays to clarify the role of SLPI in allergic responses.

overall_design: Total RNAs were isolated from each allergic effector cells derived from bone marrow cells of wild type or SLPI deficient mice. Hybridized Affymetrix GeneChip was scanned and the data was analyzed.

first: Tetsuya

last: Sato

first: Shintaro

last: Matsuba


title: Investigation of gene expression changes after mindfulness awareness program or health education program

status: Public on Dec 19 2017

city: Singapore

first: Ene Choo

last: Tan

address: 100 Bukit Timah Road

department: KKRC

institute: KK Women's & Children's Hospital

summary:
Research shows that mindfulness practice can alter the expression of genes associated with energy metabolism, telomere maintenance, inflammatory and stress response. The aim of this study was to determine if mindfulness awareness practice (MAP) or health education program (HEP) might reverse cognitive impairment and/or prevent further cognitive decline in 60 subjects (aged 60-90). We investigated the  gene expression changes in subject with mild cognitive impairment randomized to either group after 9 months.
We used Affymetrix GeneChip Human Genome U133 Plus 2.0 array to determine the differential gene expression between Pre- and Post-treatment samples from MAP and HEP group.

overall_design: This is an intervention study with a control group of HEP participants. Sixty subjects with mild cognitive impairment were randomised to either MAP or HEP group. MAP participants were taught mindfulness awareness practice techniques. HEP participants were taught healthy living topics related to maintaining and improving cognitive function. Total of 18 sessions were conducted for 40 minutes weekly for 12 weeks and thereafter 40 minutes monthly for 6 months. Blood sample (1-3ml) was collected in Tempus Blood RNA Tube from 51 subjects before the start of intervention (Pre-treatment) and 36 subjects after nine months (Post-treatment)

first: Hwee-Woon

last: Lim

first: Rathi

last: Mahendran

first: Woei-Yuh

last: Saw

first: Lei

last: Feng

first: Ee-Heok

last: Kua

first: Ene-Choo


title: Analysis of gene expression levels between RacGAP1 silenced and control SMMC7721 cells

first: Xiao-Mei

last: Yang

address: Room 419, Wenxuan Building of Medicine,  800 Dongchuan Road,  Shanghai

institute: Shanghai Cancer Institute

summary: To investigate the altered genes by RacGAP1 silencing

overall_design: Scrambled siRNA control cells (n = 3) and RacGAP1 silenced cells (n = 3)

first: Zhi-Gang

last: Zhang


title: mRNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

city: Houston

first: Jenny

last: Chang

state: TX

address: 6670 Bertner Ave.

department: Houston Methodist Cancer Center

institute: Houston Methodist Hospital

summary:
(HN1L) is a targetable breast cancer stem cell (BCSC) gene that is altered in 25% of whole breast cancer and significantly correlated with shorter overall or relapse-free survival in triple negative breast cancer (TNBC) patients. HN1L silencing reduced the population of BCSCs, inhibited tumor initiation, re-sensitized chemo-resistant tumors to docetaxel, and hindered cancer progression in multiple TNBC cell line derived xenografts.
We used microarray to compare mRNA expression profiles from PDX BCM2665 xenograft tumors with or without HN1L knockdown, to identify role of HN1L in regulating cancer stem cells.

overall_design: mRNA arrays were performed on 10 snap-frozen tumor samples from scrambled siRNA-treated and HN1L siRNA-treated BCM2665 xenografts (5 samples from each treatment group). Differencial expression was performed to identifiy significantly differencially expressed mRNA and corresponding pathways.

first: Stephen

last: Wong

first: Yi

last: Liu

first: Dong

last: Choi

first: Helen

first: Yang

last: Cong

first: Jianting

last: Sheng


title: Intrauterine hyperglycemia exposure per se altered metabolic functions in F2 offspring via reprogramming F1 PGCs

city: Hangzhou

first: Jun

last: Ren

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Intrauterine hyperglycemia has been linked to an elevated risk of diabetes in next and further generations. Existing reports about transmission effects of intrauterine hyperglycemia have included both intrauterine and postnatal metabolic exposure factors, the impact of intrauterine hyperglycemia per se has not been separately assessed. To investigate effect of intrauterine hyperglycemia exposure per se on further generations, we selected non-phenotypic F1-GDM and F2-GDM male mice to examin metabolic changes in next generation and performed a methylome on day 13.5 primordial germ cells (PGCs) of F1-GDM male fetus to explore its underlying mechanism. We found that intrauterine hyperglycemia exposure per se resulted in obesity, insulin resistance and/or glucose intolerance in F2 male mice, and no changes in F3 male mice. Methylome of day 13.5 PGCs of F1-GDM male fetus revealed differently methylation genes enriched in obesity and diabetic pathogenesis. Methylation validation of targeted gene Fyn showed consistent hypo-methylation status in F1 PGCs, F1 fetal testis, sperm of F1/N-GDM mice, and somatic cells of F2-GDM male mice. While fetal testis of F2-GDM mice showed no alteration in Fyn methylation. Our data indicates that intrauterine hyperglycemia exposure per se contributes to metabolic changes in F2 but not F3 generation, by altering methylation erasure in PGCs of F1 generation.

overall_design: PGCs of D13.5 male fetus from control pregnant mice (n=8) and GDM pregnant mice (F1-GDM, n=8). For each group, PGCs from every two pregnant mice were mixed to meet the required amount for sequencing. Thus we got 4 control samples and 4 GDM samples for RRBS.

first: Jian

middle: z


title: RNA differencial expression data between scrambled siRNA-treated mice and HN1L siRNA-treated mice tumor samples

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: c-Maf-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

first: Dan

last: Littman

state: New York

address: 430 East 29th Street, Alexandria West 4th Floor

department: Pathology

institute: New York University School of Medicine

summary: Both microbial and host genetic factors contribute to the pathogenesis of autoimmune disease. Accumulating evidence suggests that microbial species that potentiate chronic inflammation, as in inflammatory bowel disease (IBD), often also colonize healthy individuals. These microbes, including the Helicobacter species, have the propensity to induce pathogenic T cells and are collectively referred to as pathobionts. However, an understanding of how such T cells are constrained in healthy individuals is lacking. For this study we wanted to compare the transcriptomes of H. hepaticus-specific T effector cells from mice that were IL-10-deficient to those that were Maf-deficient in the Treg compartment to determine if they share an inflammatory signature. We also compared Maf -sufficient and -deficient polyclonal iTreg to determine molecular targets of the TF c-Maf.

overall_design: 12 samples with 2 replicates each

first: Maria

middle: V

last: Pokrovskii

first: Mo

last: Xu


title: eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: BG 49 RM 2C08, 49 Convent Dr.

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development,

institute: National Institutes of Health

summary: The translation pre-initiation complex (PIC) scans the mRNA for an AUG codon in favorable context, and AUG recognition stabilizes a closed PIC conformation. The unstructured N-terminal tail (NTT) of yeast eIF1A deploys five basic residues to contact tRNAi, mRNA, or 18S rRNA exclusively in the closed state. Interestingly, EIF1AX mutations altering the human eIF1A NTT are associated with uveal melanoma (UM). We found that substituting all five basic residues, and seven UM-associated substitutions, in yeast eIF1A suppresses initiation at near-cognate UUG codons and AUGs in poor context. Ribosome profiling of NTT substitution R13P reveals heightened discrimination against unfavorable AUG context genome-wide. Both R13P and K16D substitutions destabilize the closed complex at UUG codons in reconstituted PICs. Thus, electrostatic interactions involving the eIF1A NTT stabilize the closed conformation and promote utilization of suboptimal start codons. We predict UM-associated mutations alter human gene expression by increasing discrimination against poor initiation sites.

overall_design: We examined the effect of tif11-R13P on global translational efficiencies (TEs) by ribosome footprint profiling of isogenic WT and tif11-R13P strains. The study includes 8 samples, comprised of 4 mRNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates of tif11? mutant strains harboring plasmid-borne tif11-R13P or the WT TIF11 allele. Additional Ribosome profiling data were used for yeast uORF identification.

first: P

last: Martin-Marcos

first: F

last: Zhou

first: C

last: Karunasiri

first: J

last: Dong

last: Nanda

first: Kulkarni

middle: D

last: Shardul

first: N

last: Sen

first: M

last: Tamame

last: Zeschnigk

first: A

middle: G

last: Hinnebusch


title: Gene expression profile of tumor cells from primary tumors, ascites and metastases of high grade serous ovarian cancer patients

city: Wuhan

first: Zongyuan

last: Yang

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

summary:
HGSOC, the most aggressive form of OC, is characterized by insidious onset, rapid intraperitoneal spread and development of massive ascites. Peritoneal adhesion was considered as the first step of abdominal metastasis, underscoring that only tumor cells gain access to peritoneal adherence contribute to metastasis. Studies on ovarian cancer progression were mainly focused on the primary and metastatic tumor cells, while understanding of the ascitic tumor cells is limited. We hypothesized that uncovering the gene expression profiles of ascitic tumor cells from high grade serous ovarian cancer patients will allow us to understand more specifically their unique phenotype which mediates the peritoneal adhesion. In this study, gene expression profiling was completed for 15 magnetic sorted tumor cells samples from matched primary tumors, ascites and metastases of 5 high grade serous ovarian cancer patients. By comparing the expression data from ascitic tumor cells with primary and metastasis tumor cells, we identified a set of differential expressed genes in ovarian ascitic tumor cells advantageous for peritoneal adhesion and metastasis. Further study revealed that ascites microenvironment modulated the ascitic tumor cells phenotype and contributed to ovarian cancer dissemination through facilitating CAFs in formation of compact spheroids with ascitic tumor cells.
We used microarrays to profile the expression of 15 matched tumor cells samples in order to identify molecular alteration between primary tumor cells, ascitic tumor cells and metastatic tumor cells in high grade serous ovarian cancer.

overall_design: Transcriptome profiling analyses were performed on 15 magnetical sorted epithelial tumor samples from matched primary tumors, ascites and metastases in high grade serous ovarian cancer patients, using the Affymetrix human genome U133 Plus 2.0 microarray.

first: Qinglei

last: Gao


title: Gene expression profile of tumor cells from primary tumors, ascites and metastases of low grade serous ovarian cancer patients

summary:
Differ from the aggressive nature of HGSOC (high grade serous ovarian cancer), LGSOC (low grade serous ovarian cancer) is characterized by an early age of disease onset, slow growth pattern, and poor response to chemotherapy. To understand more specifically the underlying gene profiling discrepancy that contributes to their behavior distinction, we performed parallel gene expression profiling in 9 magnetic sorted tumor cells samples from matched primary tumors, ascites and metastases of 3 LGSOC patients as in HGSOC. By comparing the expression data among primary tumor cells, ascitic tumor cells and metastasis tumor cells, we identified a set of differential expressed genes along LGSOC progression. Further study revealed that the gene phenotype perturbance along LGSOC progression was quite different from that of HGSOC patients.
We used microarrays to profile the expression of 9 matched tumor cells samples in order to identify molecular alteration between primary tumor cells, ascitic tumor cells and metastatic tumor cells in low grade serous ovarian cancer.

overall_design: Transcriptome profiling analyses were performed on 9 magnetical sorted epithelial tumor samples from matched primary tumors, ascites and metastases in low grade serous ovarian cancer patients, using the Affymetrix human genome U133 Plus 2.0 microarray.


title: Gene expression profile of tumor cells from primary tumors, ascites and metastases of high and low grade serous ovarian cancer patients


title: Snail-dependent epithelial splicing regulatory protein 1 (ESRP1) silencing drives malignant transformation of human pulmonary epithelial cells [mRNA]

status: Public on Dec 16 2017

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

summary: The significance of epithelial-to-mesenchymal transition (EMT)-inducing transcription factors in the onset of non-small cell lung cancer has not been resolved.  Here, we report increased Snail expression in pulmonary premalignant lesions relative to histologically normal-appearing pulmonary epithelium.  Utilizing immortalized human pulmonary epithelial cells and isogenic derivatives, we document Snail-dependent anchorage-independent growth of the epithelial cells in vitro, as well as transformation, primary tumor growth, and metastatic behavior in vivo.  Epithelial splicing regulatory protein 1 (ESRP1) tumor suppressor silencing was a requirement for Snail-driven transformation in vivo, and we identified ESRP1 loss in Snail-expressing pulmonary premalignant lesions in situ.  Snail drives these and other carcinogenic signaling programs in an ALDH+CD44+CD24- pulmonary stem cell subset in which ESRP1 and stemness-repressing micro-RNAs are inhibited.

overall_design: Two distinct HBEC cell lines were transduced with a retroviral vector containing human SNAI1 (Snail) cDNA or the empty vector.  They were gene expression profiled to determine the impact of ectopic Snail expression on the isogenic epithelial background of the HBECs.

first: Tonya

middle: C

last: Walser

first: Zhe

last: Jing

middle: M

first: Ying

last: Lin

first: Natalie

last: Yakobian

first: Gerald

last: Wang

first: Kostyantyn

last: Krysan

first: Li

middle: X

last: Zhu

first: Sherven

last: Sharma

first: Mi-Heon

last: Lee

first: John

middle: A

last: Belperio

first: Aik

last: Ooi

first: Brigitte

middle: N

last: Gomperts

first: Jerry

middle: W

last: Shay

first: Jill

last: Larsen

last: Minna

first: Long-Sheng

last: Hong

first: Michael

last: Fishbein

first: Steven

last: Dubinett


title: Snail-dependent epithelial splicing regulatory protein 1 (ESRP1) silencing drives malignant transformation of human pulmonary epithelial cells

first: Linh

last: Tran

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae


title: Somatic cell contamination in sperm human DNA methylatoin studies

city: Salt Lake City

first: Douglas

last: Carrell

state: UT

address: 675 Arapeen Dr. Suite 201

institute: University of Utah

summary: We assessed a novel benchtop approach to detecting somatic cell contamination in human sperm epigenetic studies.

overall_design: We identified samples that were knonw to be contaminated based on array data and samples that we knew were pure based on methylatoin array data.

first: Tim

last: Jenkins

first: Ki

last: Aston

first: Lihua

last: Lui


title: Enzyme-free digital counting of endogenous circular RNA molecules in Formalin-Fixed Paraffin-Embedded tissues from patients with B-cell malignancies

status: Public on Dec 15 2017

city: Aarhus

first: Lasse

middle: Sommer

last: Kristensen

address: CF Møllers Allé 3

country: Denmark

institute: Aarhus University

summary: Circular RNAs (circRNAs) are covalently closed endogenous RNA molecules with tissue- and disease specific expression patterns, which have potential as diagnostic and prognostic biomarkers in cancer. The landscape of circRNA expression has not been characterized in B-cell malignancies. We quantified circular RNA expression by total RNA sequencing of four different Mantle Cell Lymphoma cell lines, REC-1, Granta-519, Z138 and UPN2 and the Multiple Myeloma cell line, H929.

overall_design: High quality RNA samples were depleted for ribosomal RNA and sequenced on a HiSeq 4000 from Illumina, no replicates were done. CircRNA quantification was done using the bioinformatics algorithms known as Find_circ and CIRI2. The data was used for designing a panel of NanoString assays for specific circRNAs

middle: S

first: Jørgen

last: Kjems


title: Single-cell RNA-sequencing reveals distinct populations of glucagon-like peptide-1 producing cells in the mouse upper small intestine

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: Enteroendocrine L-cells release hormones that control metabolism and appetite and are targets under investigation for the treatment of diabetes and obesity. Understanding L-cell diversity and expression profiles is critical for identifying target receptors that will translate into altered hormone secretion. We performed single cell RNA sequencing of mouse L-cells from the upper small intestine to distinguish cellular populations, revealing that L-cells form 3 major clusters: a group with typical characteristics of classical L-cells, including high expression of Gcg and Pyy; a cell type overlapping with Gip-expressing K-cells; and a unique cluster expressing Tph1 and Pzp that was predominantly located in duodenal villi and co-produced 5HT. Expression of G-protein coupled receptors differed between clusters, suggesting the cell types are differentially regulated, and would be differentially targetable. Our findings support the emerging concept that many enteroendocrine cell populations are highly overlapping, with individual cells producing a range of peptides previously assigned to distinct cell types.

overall_design: Single cell RNA sequencing of mouse duodenal L-cells  cells

first: Leslie

last: Glass

first: Fernando

middle: J

last: Calero-Nieto

first: Wajid

last: Jawaid

first: Pierre

last: Larraufie

first: Berthold

last: Göttgens

first: Frank

last: Reimann

first: Fiona

last: Gribble


title: Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

city: Amsterdam

first: Remond

middle: JA

last: Fijneman

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions. Proof of concept was obtained by applying Splicify to RNA sequencing and mass spectrometry data obtained from colorectal cancer cell line SW480, before and after siRNA-mediated down-modulation of the splicing factors SF3B1 and SRSF1. These analyses revealed 2172 and 149 differentially expressed isoforms, respectively, with peptide confirmation upon knock-down of SF3B1 and SRSF1 compared to their controls. Splice variants identified included RAC1, OSBPL3, MKI67 and SYK. One additional sample was analyzed by PacBio Iso-Seq full-length transcript sequencing after SF3B1 down-modulation. This analysis verified the alternative splicing identified by Splicify and in addition identified novel splicing events that were not represented in the human reference genome annotation. Therefore, Splicify offers a validated proteogenomic data analysis pipeline for identification of disease specific protein biomarkers resulting from mRNA alternative splicing. Splicify is publicly available on GitHub (https://github.com/NKI-TGO/SPLICIFY) and suitable to address basic research questions using pre-clinical model systems as well as translational research questions using patient-derived samples, e.g. allowing to identify clinically relevant biomarkers. This dataset corresponds to a publication in Molecular & Cellular Proteomics 16: 10.1074/mcp.TIR117.000056, 1850–1863, 2017, PMID: 28747380. Mass spectrometry data corresponding to this entry is available at ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD006486.

overall_design: Down-modulation of splicing factors SF3B1 (48h) and SRSF1 (72h) was performed in CRC cell line SW480 three times. The knock-downs and the paired non-targeting (NT) controls were subjected to RNA-sequencing and LC-MS/MS tandem mass spectrometry. Down-modulation of SF3B1 was repeated in a separate experiment, including PacBio Iso-Seq sequencing of full length transcripts. Differential mRNA splice variants were identified for down-modulation vs the non-targeting control.

first: Malgorzata

last: Komor

first: Annemieke

last: Hiemstra

first: Anne

last: Bolijn

first: Pien

last: Delis-van Diemen

first: Marianne

last: Tijssen

first: Robert

middle: P

last: Sebra

first: Meredith

last: Ashby

first: Gerrit

last: Meijer

first: Connie

middle: R

last: Jimenez


title: Whole genome RNA-seq analysis of wild type or HIPK2-/- immortalized bone marrow-derived macrophages (iBMDM), with or without vesicular stomatitis virus (VSV) infection

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

summary:
Wild type or HIPK2-/- immortalized bone marrow-derived macrophages (iBMDM) were infected with VSV for 6h, followed by whole genome RNA-seq analysis.
Conclusions: HIPK2 deficiency aggravates viral infection and inhibited the production of IFNβ.

overall_design: Wild type or HIPK2-/- immortalized bone marrow-derived macrophages (iBMDM) were infected with VSV for 6h. Cells were harvested, followed by whole genome RNA-seq analysis.

first: Lili

first: Fuping

last: You


title: Global transcriptomic analysis of human pancreatic islets [RNAseq]

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

summary: RNA sequencing in 88 human pancreatic islet donors

overall_design: mRNA profiles of human pancreatic islets from 88 donors. The data were generated by deep sequencing using Illumina HiSeq 2000.


title: ATAC-Seq of CD8+ T cell terminal effector and memory precursor subsets during LCMV infection

city: La Jolla

first: John

middle: Justin

last: Milner

state: CA

address: 9500 Gilman Dr. MC0377

institute: UCSD

summary: Tissue-resident memory CD8+ T cells (Trm) are positioned at common sites of pathogen exposure where they elicit rapid and robust protective immune responses. However, the molecular signals controlling Trm differentiation and homeostasis are not fully understood. Here we show that mouse Trm precursor cells represent a unique CD8+ T cell subset that is distinct from the precursors of circulating memory populations at the levels of gene expression and chromatin accessibility. Exploiting computational and functional RNAi in vivo screens, we identified the transcription factor (TF) Runx3 as a key regulator of Trm differentiation and homeostasis. Runx3 was required to establish Trm populations in diverse tissue environments and supported expression of critical tissue-residency genes while suppressing genes associated with tissue egress and recirculation. Analysis of the accessibility of Runx3 target genes in Trm-precursor cells revealed a distinct regulatory role for Runx3 in controlling Trm differentiation despite relatively widespread and uniform expression among all CD8+ T cell subsets. Further, we show that human and murine tumor-infiltrating lymphocytes (TIL) share a core tissue-residency gene-expression signature with Trm. In a mouse model of adoptive T cell therapy for melanoma, Runx3-deficient CD8+ TIL failed to accumulate in tumors, resulting in greater rates of tumor growth and mortality. Conversely, overexpression of Runx3 enhanced TIL abundance, delayed tumor growth, and prolonged survival. In addition to establishing Runx3 as a central regulator of Trm differentiation, these results provide novel insight into the signals that promote T cell residency in tissues, which could be leveraged to enhance vaccine efficacy or adoptive cell therapy treatments that target cancer.

overall_design: 4 samples, 2 replicates each, Day 7 LCMV infection CD8+ T cell subsets

first: J

first: A

last: Goldrath


title: RNA sequence on the fed and fasted state of kidneys in mice

city: New York

first: Diego

last: Scerbo

state: NY

institute: Columbia University Medical Center

summary:
We studied whether the accumulation of lipids in the fasted kidney are derived from lipoproteins or (non-esterified fatty acids) NEFAs.
With overnight fasting, kidneys accumulated triglyceride, but had reduced levels of ceramide and glycosphingolipid species. Fasting led to a nearly 5-fold increase in kidney uptake of plasma [14C]oleic acid. Increasing circulating NEFAs using a β adrenergic receptor agonist caused a 15-fold greater accumulation of lipid in the kidney, while mice with reduced NEFAs due to adipose tissue deficiency of adipose triglyceride lipase had reduced triglycerides. Cluster of differentiation (Cd)36 mRNA increased 2-fold, and angiopoietin-like 4 (Angptl4), an LPL inhibitor, increased 10-fold. Fasting-induced kidney lipid accumulation was not affected by inhibition of LPL with poloxamer 407 or by use of mice with induced genetic LPL deletion. Despite the increase in CD36 expression with fasting, genetic loss of CD36 did not alter fatty acid uptake or triglyceride accumulation.
Our data demonstrate that fasting-induced triglyceride accumulation in the kidney correlates with the plasma concentrations of NEFAs, but is not due to uptake of lipoprotein lipids and does not involve the fatty acid transporter, CD36.

overall_design: Mice (n=4-5/group) were either fasted for 16 hours or fed ad libitum. Kidneys were removed and snap frozen. RNA was extracted for sequencing.

first: Ira

last: Goldberg


title: RNA sequencing of a Spinocerebellar ataxia type 3 (SCA3) mouse model containing the full human ATXN3 gene with a repeat expansion of 75-80 CAGs II

city: Leiden

first: Lodewijk

last: Toonen

address: einthovenweg 20

department: human genetics

institute: LUMC

summary: We have performed RNA sequencing analysis of brain tissue and blood from the MJD84.2 mouse model for SCA3 (described by Cemal et al, Human molecular genetics 2002, 11:1075-1094). Blood samples were taken by tailcut at 40 and 75 weeks of age (9.2 and 17.2 months). RNA was isolated from blood, globin reduction and RNA sequencing on polyA enriched RNA were performed.

overall_design: 8 wildtype vs 6 transgenic SCA3 mice. Brainstem, cerebellum, cortex and striatum at 17.5 months of age.

first: Willeke

last: van Roon-Mom


title: Gene expression data from embryonic stem cells

status: Public on Dec 14 2017

city: Bronx

first: Sanjeev

last: Gupta

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

summary:
Understanding the identity of lineage-specific cells arising during manipulations of stem cells is necessary for developing their potential applications. For instance, replacement of crucial functions in organ failure by transplantation of suitable stem-cell-derived cells will be applicable to numerous disorders, but requires insights into the origin, function and fate of specific cell populations. We studied mechanisms by which the identity of differentiated cells arising from stem cells could be verified in the context of natural liver-specific stem cells and whether such differentiated cells could be effective for supporting the liver following cell therapy in a mouse model of drug-induced acute liver failure. By comparing the identity of naturally occurring fetal human liver stem cells, we found that cells arising in cultures of human embryonic stem cells (hESCs) recapitulated an early fetal stage of liver cells, which was characterized by conjoint meso-endoderm properties. Despite this fetal stage, hESC-derived cells could provide liver support with appropriate metabolic and ammonia-fixation functions, as well as cytoprotection, such that mice were rescued from acute liver failure. Therefore, spontaneous or induced differentiation of human embryonic stem cells along the hepatic endoderm will require transition through fetal-like stages. This offers opportunities to prospectively identify whether suitable cells have been generated through manipulation of stem cells for cell therapy and other applications.
Gene expression was analyzed

overall_design: We studied Wicell H-1 embryonic stem cells without differentiation (hESC) or after spontaneous differentiation into cells expressing meso-endoderm phenotype (hESC-MEC).