title: Dietary lipids modulate Notch signaling and influence adult intestinal development and metabolism in Drosophila

city: Baltimore

first: Allan

last: Spradling

state: MD

address: 3520 San Martin Dr.

department: Embryology

institute: Carnegie Institution/HHMI

summary: We mapped about 25 million reads per sample to the Drosophila melanogaster genome (dm6). We confirmed that sterol processing genes are selectively expressed in the posterior midgut. Modifying sterol metabolism in the diet or with Hr96 mutants resulted in significant changes in metabolism transcripts, hormones expressed in enteroendocrine cells, and Notch pathway related genes.

overall_design: Anterior and posterior midgut mRNA profiles of wild type (y[1]w[1) flies fed a control, lipid-depleted, and high cholesterol (4x control levels) diet, and Hr96[1] and Hr96[2x] mutants. Each sample was sequenced in triplicate using Illuman NextGen sequencing.

first: Rebecca

last: Obniski

first: Matthew

last: Sieber


title: Molecular Changes of Lung Malignancy in HIV Infection

status: Public on Sep 04 2018

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

country: USA

institute: NIDDK/NIH

summary: To evaluate the molecular changes of lung malignancy in HIV infection, we analyzed the differential gene expression profiles and screened the early detection biomarkers of HIV-associated lung cancer using Affymetrix arrays. RNA was for transcriptomic profiles analysis in the HIV lung cancer tumor tissue samples from 3 patients with AC and 1 patient with squamous cell carcinoma (SCC) including 3 pairs of tumor/adjacent normal tissue paraffin specimens and 1 pair of tumor/adjacent normal fresh tissue samples.

overall_design: Identification of genes expressed in HIV associated lung cancer in two groups (tumor/adjacent normal tissue) with four replications per group.

first: Jin

last: Wang


title: Expression profiling of NRAS knockout in embryonal rhabdomyosarcoma (ERMS) cells

status: Public on Sep 03 2018

city: Seattle

first: Eleanor

state: WA

address: 1959 NE Pacific Street

department: Pathology

institute: University of Washington

type: Expression profiling by high throughput sequencing

summary: Targeted disruption of NRAS was performed in a stable 381T ERMS cell line harboring tamoxifen inducible CRISPR/Cas9 gRNA against NRAS

overall_design: RNA sequencing was performed using RNA extracted from uninduced control 381T ERMS cells as well as tamoxifen (TAM)-induced ERMS cells with NRAS CRISPR/Cas9-mediated knockout. Each in 3 biological replicates.

first: Michael

last: Phelps


title: Bone protection by inhibition of microRNA-182

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

summary: We performed RNA-seq experiments, one with the WT control and Mir182ΔM/ΔM osteoclast precursors at baseline and after RANKL stimulation, the other with miR-182 gain of function approach using the control and Mir182mTg BMMs, to identify genes regulated by miR-182 in osteoclast precursors.

overall_design: Bone marrow macrophages mRNA profiles of WT, myeloid specific deletion of miR-182(Mir182ΔM/ΔM), control(LysMcre(+)) and myeloid specific overexpression of miR-182(Mir182mTg) mice were generated by deep sequencing using Illumina Hiseq4000.

first: Baohong

last: Zhao


title: Fresh-Frozen samples profiled on HG-U219 array with Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module  [dataset 3]

status: Public on Sep 05 2018

city: Brussels

first: Vinu

last: Jose

address: Rue Meylemeersch 90

country: Belgium

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

summary: The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method.  The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.

overall_design: RNAs were extracted from eight Fresh-Frozen preserved breast cancers. RNAs were amplified and labeled using Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module, and profiled on Affymetrix® HG-U219 Array Plate according to Affymetrix's standard procedure.

first: Debora

last: Fumagalli

first: Françoise

last: Rothé

first: Samira

last: Majjaj

first: Sherene

last: Loi

first: Stefan

last: Michiels

first: Christos

last: Sotiriou


title: The accessible chromatin landscape of the murine hippocampus at single-cell resolution

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

summary: We report a high depth single-cell combinatorial indexing (sci-)ATAC-seq map of the murine hippocampus from fresh and frozen tissue as well as cultured neurons

overall_design: sci-ATAC-seq on fresh, frozen, and cultured neurons from the mouse hippocampus

middle: C

first: Kristof

middle: A

last: Torkenczy


title: HNF1A is a Novel Oncogene and Central Regulator of Pancreatic Cancer Stem Cells [ChIP-seq]

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The biological properties of pancreatic cancer stem cells (PCSCs) remain incompletely defined and the central regulators are unknown. By bioinformatic analysis of a PCSC-enriched gene signature, we identified the transcription factor HNF1A as a putative central regulator of PCSC function. Levels of HNF1A and its target genes were found to be elevated in PCSCs and tumorspheres, and depletion of HNF1A resulted in growth inhibition, apoptosis, impaired tumorsphere formation, PCSC depletion, and downregulation of OCT4 expression. Conversely, HNF1A overexpression increased PCSC numbers and tumorsphere formation in pancreatic cancer cells and drove PDA cell growth. Importantly, depletion of HNF1A in primary tumor xenografts impaired tumor growth and depleted PCSCs in vivo. Finally, we established an HNF1A-dependent gene signature in PDA cells that significantly correlated with reduced survivability in patients. These findings identify HNF1A as a central transcriptional regulator of the PCSC state and novel oncogene in pancreatic ductal adenocarcinoma.

overall_design: Chromatin binding of HNF1A in the primary human pancreatic cancer cell lines NY8 and NY15.  This study consists of 8 ChIP-seq samples.  2 sets of libraries (biological replicates) were generated from HNF1A ChIP and input DNA from each cell line.

first: Ethan

middle: V

last: Abel

first: Masashi

last: Goto

first: Brian

last: Magnuson

first: Saji

last: Abraham

first: Nikita

last: Ramanathan

first: Emily

last: Hotaling

first: Anthony

last: Alaniz

first: Chandan

last: Kumar-Sinha

first: Michele

middle: L

last: Dziubinski

first: Sumithra

last: Urs

first: Lidong

first: Jiaqi

last: Shi

first: Meghna

last: Waghray

first: Howard

last: Crawford

first: Diane

middle: M

last: Simeone


title: RNA seq in human gastroparesis

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Both diabetic and idiopathic gastroparesis have unique and overlapping changes in the transcriptome.  Immune signaling predominately plays a role in the pathogenesis of gastroparesis.

overall_design: RNA sequencing was completed on full thickness gastric body samples from diabetic gastroparetics, diabetic non-gastroparetics controls, idiopathic gastroparetics and non-diabetic non-gastroparetic patients.

first: Madhusudan

last: Grover

first: Gianrico

last: Farrugia


title: HNF1A is a Novel Oncogene and Central Regulator of Pancreatic Cancer Stem Cells [Bru-seq]

first: Mats

last: Ljungman

overall_design: Nascent RNA expression following HNF1A RNAi in the human pancreatic cancer cell lines NY8 and NY15.  This study consists of 12 Bru-seq samples. 2 sets of libraries (biological replicates) were generated from shRNA-treated cells from each cell line, including a control shRNA (LacZ sh) and two different HNF1A-targeting shRNAs (HNF1A sh1 and sh2).

first: Ethan

last: Abel

first: Masashi

last: Wang


title: The single cell RNA seq of PDGFRa-GFP+ cells in mouse lung

city: San Diego

first: Rongbo

last: Li

address: 9500 Gilman Dr. MC0766

department: Pediatrics

institute: UC San Diego

summary: Pdgfra-expressing (Pdgfra+) cells have been implicated as progenitors in many mesenchymal tissues. To further characterize Pdgfra+ cells during alveologensis, we performed single-cell RNA sequencing (scRNA-Seq) analysis using fluorescence-activated cell sorting (FACS) sorted GFP+ cells from Pdgfra-GFP lungs at P7 and P15.

overall_design: We perfomed 10X genomics single-cell RNA-seq of Pdgfra-GFP+ cells at P7 and P15

first: Xin

last: Sun


title: Differencial gene expression between cortex and striatum of WT and ASCT1 (Slc1a4)-knockout mice

city: haifa

first: Herman

last: Wolosker

address: 1 Efron St

department: Biochemistry

country: Israel

institute: Technion-Israel Institute of Technology

summary: In order to explore possible consequence of ASCT1 (Slc1a4) deletion in neurodevelopment, we carried out RNA sequencing of the striatum, which was altered in MRI analysis, and compared with the neocortex, which was unaffected. We found significant changes in 375 transcripts in the striatum of adult mice at adjusted p values lower than 0.05. No changes in gene expression were observed in the neocortex. Enrichment analysis using non-redundant reciprocal linkage of genes identified 11 metagroups, with overrepresentation of genes linked to axonal guidance and neurodevelopmental processes in the striatum. The most significant changes were seen in axon guidance genes, suggesting changes in neurodevelopmental-related gene transcripts in ASCT1-KO mice, compatible with the findings in human familial ASCT1 mutations.

overall_design: We generated RNAseq data from the cerebral cortex and striatum of Wild Type and ASCT1-KO mice on Illumina NextSeq500, 75 bp single-end reads, high-output mode (Illumina, FC-404-2005).

first: Eitan

last: Kaplan

first: Liat

last: Linde

first: Ronit

last: Modai-Hod

first: Elizabeta

last: Ginzburg

first: Doron

last: Foguel


title: YAP-TEAD signaling promotes Basal Cell Carcinoma development via c-JUN/AP1 axis [RNA-seq]

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: The mammalian Hippo signaling pathway, through its effectors YAP and TAZ, coerces epithelial progenitor cell expansion for appropriate tissue development or regeneration upon damage.  Its ability to drive rapid tissue growth explains why many oncogenic events frequently exploit this pathway to promote cancer phenotypes.  Indeed, several tumor types including basal cell carcinoma (BCC) show genetic aberrations in the Hippo (or YAP/TAZ) regulators.  Here, we uncover that while YAP is dispensable for homeostatic epidermal regeneration, it is required for BCC development.  Our clonal analyses further demonstrate that few emerging Yap-null dysplasia have lower fitness and thus are diminished as they progress to invasive BCC.  Mechanistically, YAP depletion in BCC tumors leads to effective impairment of the JNK-JUN signaling, a well-established tumor driving cascade.  Importantly, in this context, YAP does not influence canonical Wnt or Hedgehog signaling.   Overall, we reveal the Hippo signaling as an independent promoter of BCC pathogenesis and thereby a viable target for drug-resistant BCC.

overall_design: YAP transcriptional function in BCC

first: Dejan

last: Maglic

first: Karin

last: Schlegelmilch

first: Antonella

middle: F

last: Dost

first: Riccardo

last: Panero

first: Michael

last: Dill

first: Fernando

middle: D

last: Camargo


title: Integration of genome-wide DNA methylation and transcription uncovered aberrant methylation-regulated genes and pathways in the peripheral blood mononuclear cells of systemic sclerosis [methylation]

status: Public on Sep 01 2018

city: Dallas

first: Quan

state: TX

address: 6001 Forest Park Rd

department: Immunology

institute: UTSW

summary: The identified MeDEGs may represent novel candidate factors which lead to the abnormal activation of immune regulatory pathways in the pathogenesis of SSc. They may also be used as diagnostic biomarkers for SSC and clinical complications

overall_design: Genome-wide mRNA transcription and global DNA methylation analysis were performed on PBMC from 18 SSc patients and 19 matched normal controls (NC) using Illumina BeadChips

first: Honglin

last: Zhu

first: Chengsong

first: Wentao

last: Mi

first: Tao

last: Chen

first: Hongjun

last: Zhao

first: Xiaoxia

last: Zuo

first: Hui

last: Luo

first: Quan-Zhen


title: scRNAseq reveals mechanisms of Merkel cell carcinoma acquired immunotherapy resistance [1]

first: Kelly

middle: Garneski

last: Paulson

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Serial blood draws from a single patient and serial tumor biopsies from the same patient  with metastatic Merkel cell polyomavirus Merkel cell carcinoma, who was treated with cellular immunotherapy targeting MCPyV (autologous endogenous T cell therapy) followed by checkpoint inhibitors (anti-PD1 and anti-CTLA4).  The patient had a 22 month clinical response followed by late/acquired resistance.  We performed scRNAseq using the 10x genomics 3' Chromium expression assay to determine potential mechanisms contributing to immunotherapy response and late resistance

overall_design: Serial blood draws from four time points, serial tumor biopsies from two time points - single cell digests were viably preserved, comparisons were performed on a within tissue basis, discovery patient for associated manuscript

middle: G

first: Aude

last: Chapuis


title: Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer

status: Public on Sep 12 2018

city: Shenzhen

first: Yan

last: Zhang

state: Guangdong

address: No.3688，Nanhai Avenue

department: College of Life Sciences and Oceanography

country: China

institute: Shenzhen University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we used RNA-seq to investigate the transcriptomic (mRNA and miRNA) profiles of pancreatic cancer in 10 paired tumor and normal pancreatic samples from patients


title: Identification of EGR1 binding sites in melanoma cells

city: Boston

first: Carl

last: Novina

state: MA

address: 450 Brookline Ave

department: Cancer Immunology

institute: Dana-Farber Cancer Institute

summary: We report the genome wide identification of EGR1 binding sites in the A375 melanoma cell line.

overall_design: ChIP-seq to identify EGR1 binding sites in the A375 melanoma cell line.

first: Karyn

last: Schmidt


title: Identification of Androgen Receptor binding sites in hormone-depleted melanoma cells

summary: We report the genome wide identification of AR binding sites in hormone-deprived A375 melanoma cell line, with either endogenous levels of the lncRNA SLNCR, or a vector expressing SLNCR1.

overall_design: Comparison of AR binding sites in hormone-deprived A375 melanoma cells transfected with either an empty- or SLNCR1 lncRNA expressing vector.


title: Global identification of Androgen Receptor and EGR1 binding sites in melanoma reveals enriched co-binding at genes regulated by the lncRNA SLNCR

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

overall_design: Refer to individual Series


title: The BCL-2 Inhibitor Venetoclax in Combination with Azacitidine Disrupts Energy Metabolism and Targets Leukemia Stem Cells in Acute Myeloid Leukemia Patients

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

summary: The manuscript summarizes clinical and laboratory-based evaluation of 33 AML patients treated with a novel drug combination, venetoclax and azacytidine. Our findings indicate that this regimen is exceptionally promising for the treatment of de novo AML patients. The improvement in outcomes in comparison to conventional therapy is quite remarkable. The manuscript explores the mechanistic basis for the clinical outcomes, testing the hypothesis that venetoclax and azacytidine effectively target leukemia stem cells (LSCs) in vivo. Our findings indicate the regimen is highly active towards the LSC population. Specifically, we describe a mechanism that suppresses the activity of electron transport complex II, resulting in inhibition of oxidative phosphorylation.

overall_design: Respective populations were sorted from human bone marrow mononuclear cells after patients received venetoclax and azacitidine for 6 hours (pre drug time 0 collected and post drug 6 hr labelled accordingly), after staining with CellRox dye and sorting the lowest 20% of the blasts staining for CellROX.

first: Craig

middle: T

last: Jordan


title: Communication of prostate cancer cells with bone cells via extracellular vesicle RNA; a potential mechanism of metastasis

city: Leicestershire

first: Victoria

last: James

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

summary: Analysis of miRNA and mRNA within extracellular vesicles obtained from prostate cancer PC3 cells. Kaighn ME, et al. Establishment and characterization of a human prostatic carcinoma cell line (PC-3). Invest. Urol. 17: 16-23, 1979. PubMed: 447482

overall_design: miRNAs and mRNA from PC3 extracellular vesicles tested by RNAseq in duplicate using an Illumina Nextseq 500 mid Output run

first: V

first: T

last: Dottorini


title: Microglial gene expression after conditional deletion of Tgfbr2 in vivo

city: Rostock

first: Björn

last: Spittau

address: Gertrudenstraße 9

department: Institute of Anaomy

country: Germany

institute: University of Rostock

overall_design: Microglia derived from adult Tgfbr2-KO and control mice


title: Prolonging culture of primary human keratinocytes isolated from suction blisters with the Rho kinase inhibitor Y-27632

first: Timothy

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Keratinocytes are the most abundant cell type in the epidermis. They prevent desiccation and provide immunological and barrier defense against potential pathogens such as Staphylococcus aureus and Candida albicans. The study of this first line of immune defense may be hindered by invasive isolation methods and/or improper culture conditions to support stem cell maintenance and other potential mechanisms contributing to long-term subcultivation in vitro. Primary keratinocytes have been successfully isolated from blister roofs induced by negative pressure, which separates the epidermis from the dermis in vivo in human subjects. This method allows collection of pure epidermal cells without dermal contamination in a minimally invasive manner. However, the isolated keratinocytes differentiate and senesce when cultured in vitro beyond five passages. Here, we present evidence that the Rho kinase (ROCK) inhibitor Y-27632 can be used to effectively increase the proliferative capabilities of keratinocytes isolated using the suction blister method, similar to what has been previously reported for primary keratinocytes isolated using alternative methods. We show that the increase in passage number is directly correlated to delayed differentiation, and that cells passaged long term with the inhibitor retain their ability to stratify in organotypic raft cultures and respond to cytokine treatment; additionally, the late passage cells have a heterogeneous mix of differentiated and non-differentiated cells which may be predicted by a ratio of select differentiation markers. The described method presents a minimally invasive procedure for keratinocyte isolation and prolonged culture that allows analysis of keratinocyte function in both healthy volunteers and patients with dermatologic diseases.

overall_design: Keratinocytes isolated using the suction blister method were grown in the absence (passages 4, 5, and 6) and presence (passages 5 and 6) of ROCK inhibitor Y-27632 or cytokines (IL17 + IFN-g)

first: Erik

last: Anderson

first: Inka

last: Sastalla

first: Noah

last: Earland

first: Minai

last: Mahnaz

first: Ian

middle: N

last: Moore

first: Francisco

last: Otaizo-Carrasquero

first: Christopher

last: Myles

first: Sandip

middle: K

last: Datta


title: Total RNA-Seq of Germ-free (GF) male mice liver injected with ghrelin.

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

summary: Gut microbiota and the circadian clock are both key regulators of the metabolic processes. Although recent evidence points to the impact of the circadian clock on microbiota, gut microbiota effect on diurnal host gene expression remains elusive. A transcriptome analysis of germ-free mice reveals subtle changes in circadian clock gene expression. However, a lack of microbiome leads to liver feminization and alters the expression of male-specific genes involved in lipid metabolism and xenobiotic detoxification associated with sustained activation of the Growth Hormone pathway. These results emphasize the mutual interaction of gut microbiota and its host even on unexpected functions.

first: Benjamin

last: Weger

first: Eva

last: Martin

first: Aline

last: Charpagne

first: Chieh-Jason

last: Chou

first: Frederic


title: Total RNA-Seq of primary hepatocytes treated with serum of conventionally raised (convR) and Germ-free (GF) male and female mice.


title: Total RNA-Seq of testis and ovaries of conventional raised (convR) and Germ-free (GF) female mice under ad libitum feeding regimen.

overall_design: Total RNA-Seq of testis and ovaries of conventional raised (convR) and Germ-free (GF) female mice under ad libitum feeding regime.


title: Methylomic Profiling of BDE-47 Effects on Human Placental Cytotrophoblasts

city: SAN FRANCISCO

first: Joshua

last: Robinson

state: CA

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

type: Methylation profiling by genome tiling array

summary: CpG methylomic characterization of BDE-47 exposed cultured primary human cytrophoblasts (2nd trimester) undergoing differentiation in vitro.

overall_design:
CpG methylome of human villous cytotrophoblasts exposed to BDE-47 or DMSO (vehicle control) for 24h; either exposed after attachment (~3h in culture) or following cell-cell aggregation (~15h).
Sample processing and hybridization was performed by the UCSF Gladstone Institute

first: J

first: M

last: Kapidzic

first: S

middle: J

last: Fisher


title: Total RNA-Seq of Germ-free (GF) male mice liver injected with growth hormone.


title: IL-27 in vaccine elicited cellular immunity

first: Ross

middle: M.

last: Kedl

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: 5000 congenically marked (CD45.1) WT or IL-27R-/- OT1 T cells were transferred into WT B6 hosts (CD45.2). One day later, the mice were immunized with ovalbumin (100 µg), PolyIC (40 µg) and anti-CD40 antibody (FGK4.5, 40 µg).  3 days after immunizayion, spleens were harvested and the OT1 T cells isolated by flow sorting based on CD45.1 expression. Each sample is the result of pooling T cells from 3 individual mice.  RNA was isolated from the sorted cells and RNAseq performed.

overall_design: RNAseq of transferred WT and IL-27R-/- OT1 T cells isolated 3 days  after combined polyIC/aCD40 immunization

first: Trevor

last: Blain

first: Thomas

last: Danhorn

first: Walton

last: Kendra


title: Gene expression analysis in lungs of Mtb infected Fth+/+ and Fth-/- mice by employing RNA-Seq

city: Birmingham

first: Adrie

middle: JC

last: Steyn

state: AL

address: 308, BBRB

department: Microbiology

institute: University of Alabama at Birmingham

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study is to compare gene expression (RNA-seq) profile between Mtb infected Fth+/+ and Fth-/- mice at 9 weeks post Mtb infection. Gene expression analysis demonstrated an essential role for FtH in mitochondrial function and maintenance of central intermediary metabolism in vivo

overall_design: Total RNA was isolated from lungs of Mtb infected Fth+/+ and Fth-/- mice at 9 weeks post infection

first: Vineel

middle: P

last: Reddy


title: Transcriptional profiling of WM1976 cells with siRNA knockdown of the long non-coding RNA SLNCR

first: Carl

last: Novina

summary: RNA-Seq was used to profile transcriptional changes induced by siRNA knockdown of the long non-coding RNA SLNCR (all isoforms).

overall_design: The WM1976 melanoma short-term culture transfected with either scrambled or SLNCR-targeting siRNAs

first: Karyn

last: Schmidt


title: LKB1 deficiency in T cells promotes the development of gastrointestinal polyposis

city: Grand Rapids

first: Russell

last: Jones

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: mRNA expression in CD8+ T cells expressing or lacking LKB1

overall_design: RNA-seq analysis of in vitro activated control and LKB1-deficient CD8+ T cells. CD8+ T cells of each genotype were activated with anti-CD3 and anti-CD28 antibodies for 48 hours, after which total mRNA was isolated for analysis.

first: Maya

last: Poffenberger

first: Radia

last: Johnson

first: Ekaterina

last: Loginicheva

first: Maxim

last: Artyomov


title: Affinity-seq of mouse and human ZFY proteins and mouse CTCF

city: Bar Harbor

first: Petko

last: Petkov

state: Maine

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: This experiment determines all possible genome-wide binding sites of the proteins of interest

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The proteins of interest were expressed in E. coli as fused proteins with an N-terminal 6HisHALO tag and partially purified on SP-sepharose. Mouse spleen genomic DNA was sheard to an average of 200 bp fragments and used as binding target. The partially purified protein and the sheared genom DNA were allowed to bind in solution and the complexes were then isolated on Ni2+ beads preincubated with expressed 6HihHALO tag only to reduce the background. The eluted DNA was used to prepare NextGen libraries which were sequenced on Illumina HiSeq 2000.

first: Michael

last: Walker

first: Timothy

last: Billings


title: Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements

city: Darlinghurst

middle: John

last: Peters

state: NSW

address: 384 Victoria St

institute: Garvan Institute of Medical Research


title: Tip60 complex promotes expression of a differentiation factor to regulate germline differentiation in female Drosophila

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

summary: Germline stem cells (GSCs) self-renew and differentiate to sustain a continuous production of gametes. In the female Drosophila germ line, two differentiation factors, bag of marbles (bam) and benign gonial cell neoplasm (bgcn), work in concert in the stem cell daughter to promote the generation of eggs. In GSCs, bam transcription is repressed by signaling from the niche and is activated in stem cell daughters. In contrast, bgcn is transcribed in both the GSCs and stem cell daughters, but little is known about how bgcn is transcriptionally modulated. Here, we find that the conserved protein Nipped_A acts through the Tat interactive protein 60kDa (Tip60) Histone acetyl transferase (HAT) complex in the germ line to promote GSC differentiation. We find that Nipped_A is required for efficient exit from the gap phase 2 (G2) of cell cycle of the GSC daughter and for expression of differentiation factor bgcn. Loss of Nipped_A results in accumulation of GSC daughters. Forced expression of bgcn, in Nipped_A germline-depleted ovaries rescues this differentiation defect. Together, our results indicate that Tip60 complex coordinates cell cycle progression and expression of bgcn to help drive GSC daughters toward a differentiation program.

overall_design: Two genotypes, 2 replicates each

first: Alicia

last: McCarthy

first: Aron

last: Deiulio

first: Elliot

last: Martin

first: Maitreyi

last: Upadhyay


title: Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements [Whole RNA-Seq]

summary: We empirically assess the measurement precision and sensitivity of a suite of gene expression technologies via a consensus modelling method called the row-linear model.

overall_design: 2 Ribo-Zero libraries (1 LNCaP cell line, 1 PrEC cell line) were prepared using Epicentre (Illumina) ScriptSeq v2 RNA-Seq Library Preparation Kit. The resultant cDNA libraries were sequenced at the University of Western Sydney Next Generation Sequencing Facility

first: T

first: C

last: Stirzaker

first: J

last: Song

first: H

last: French

last: Janitz


title: Transcriptome profiling of Normal and Cancerous Prostate Cells [expression array]

summary: To identify aberrant non coding gene expression in prostate cancer, we performed expression profiling of normal prostate epithelial cells (PrEC) and the prostate cancer cell line LNCaP using Affymetrix HuGene 2.0 ST expression arrays. These expression arrays were validated by expression qPCR of selected genes.

overall_design: Total Input RNA was extracted from prostate cancer (LNCaP) and normal (PrEC) cells and hybridised to Affymetrix HuGene 2.0ST arrays (3 replicates of each cell type).

first: Hugh

first: Amita

last: Limaye

first: Aaron

last: Statham

first: Fabian

last: Buske

first: Clare

first: Susan

last: Clark


title: Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements [HuGene2.0st]

overall_design: Purified NDMC1 (n=3) and NDMC2 (n=3) were obtained during surgery for RNA extraction and hybridization on Affymetrix HuGene2.0st microarrays.

first: S

last: Bradford


title: Perivascular signals alter global genomic profile of glioblastoma and response to temozolomide in a gelatin hydrogel

city: Urbana

first: Brendan

last: Harley

state: Illinois

address: 110 Roger Adams Laboratory MC 712

department: Chemical and Biomolecular Engineering

institute: University of Illinois Urbana Champaign

summary: Glioblastoma (GBM) is the most common primary malignant brain tumor, with patients exhibiting poor survival (median survival time: 15 months). Difficulties in treating GBM include not only the inability to resect the diffusively-invading tumor cells but also therapeutic resistance. The perivascular niche within the GBM tumor microenvironment contributes significantly to tumor cell invasion, cancer stem cell maintenance, and has been shown to protect tumor cells from radiation and chemotherapy. In this study, we describe the development of an in vitro artificial perivascular niche (PVN), culturing endothelial and stromal cells along with GBM cells within a methacrylamide-functionalized gelatin hydrogel, in order to examine how the presence of the PVN alters global genomic expression profiles. Using RNA-seq, we demonstrate that the inclusion of perivascular niche cells with GBM cells upregulates genes related to angiogenesis and remodeling, while downregulated genes are related to cell cycle and DNA damage repair. Signaling pathways and genes commonly implicated in GBM malignancy, such as MGMT, EGFR, PI3K-Akt signaling, and Ras/MAPK signaling are also upregulated in the presence of perivascular niche cells. We describe the kinetics of gene expression within the PVN hydrogels over a course of 14 days, observing the patterns associated with previously-observed GBM-mediated endothelial network co-option and regression that are altered in the presence of covalently-bound hyaluronic acid. We finally examine the effect of PVN culture on GBM cell responsiveness to temozolomide, a frontline chemotherapy used clinically against GBM. Notably, the presence of a PVN leads to significantly increased TMZ resistance compared to hydrogels containing only GBM cells. Overall, these results demonstrate that inclusion of cellular and matrix-associated elements of the PVN within in vitro models of GBM provide critical signals to regulate the phenotype and therapeutic responsiveness of GBM cells.

overall_design: Tri-Culture RNA samples were compared to Mixed Culture RNA samples. RNA for Tri-Culture groups was extracted from methacrylamide-functionalized gelatin (GelMA) hydrogels containing human umbilical vein endothelial cells (HUVECs), normal human lung fibroblasts (NHLFs), and U87-MG cells cultured together. For Mixed samples, RNA from GelMA hydrogels containing only U87-MG cells was mixed with RNA from GelMA hydrogels containing HUVECs and NHLFs cultured together, such that the fraction of RNA belonging to NHLFs was equivalent between Tri-Culture and Mixed samples. Three replicates were tested for both groups (Tri-Culture and Mixed).

first: Mai

last: Ngo


title: PatchSeq analysis of Pthlh expressing cells of the mouse dorsolateral striatum

status: Public on Aug 31 2018

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: In order to investigate how electrophysiological properties vary within the Pthlh population in the dorsolateral striatum we performed PatchSeq analysis of neurons labeled in 5HT3a(EGFP) and Pvalb(cre)::RCE/tdTomato mouse lines, which included Th, Npy/Mia, Cck, and Cck/Vip expressing cells.

overall_design: 98 FACS-sorted single cells isolated from the dorso-lateral striatum from either a 5ht3a-EGFP mouse line or a Lhx6-cre mouse crossed onto a R26R-tdTomato reporter mouse line

first: Ana

middle: B

last: Muñoz-Manchado

first: Amit

last: Zeisel

first: Jens

last: Hjerling-Leffler


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq 2]

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.

overall_design: RNA from mouse embryonic stem cells and embryoid bodies differentiated for three days was analysed by next generation sequencing upon depletion of RBM7 with shRNAs, using a scrambled shRNA as control. Total RNA was collected for each condition in triplicates. Control samples are included in GSE115714.

first: Marta

last: Lloret-Llinares

first: Yun

last: Chen

first: Luke

last: Wojenski

first: Geno

last: Villafano

first: Jette

last: Bornholdt

first: Robin

last: Andersson

first: Leighton

last: Core

first: Albin

last: Sandelin

first: Torben

middle: H

last: Jensen


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation [PRO-Seq 2]

overall_design: PROseq experiments were carried out in mouse embryonic stem cells and embryoid bodies differentiated for three days upon depletion of RBM7 with shRNAs, using a scrambled shRNA as control. The experiments were performed in duplicates. Control samples are included in GSE115713.


title: Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

summary: A methionine substitution at lysine 27 on histone H3 variants (H3K27M) characterizes ~80% of diffuse intrinsic pontine gliomas (DIPG) and inhibits PRC2 in a dominant negative fashion. Yet, the mechanisms for this inhibition and abnormal epigenomic landscape have not been resolved. Using quantitative proteomics, we discovered that robust PRC2 inhibition requires levels of H3K27M greatly exceeding those of PRC2, seen in DIPG. While PRC2 inhibition requires interaction with H3K27M, we found this interaction on chromatin is transient with PRC2 largely being released from H3K27M.  Unexpectedly, inhibition persisted even after PRC2 dissociated from H3K27M-chromatin suggesting a lasting impact on PRC2. Furthermore, allosterically activated PRC2 is particularly sensitive to K27M leading to a failure to spread H3K27me3 at distinct foci. In turn, levels of Polycomb antagonists such as H3K36me2 are elevated suggesting a more global, downstream effect on the epigenome. Together, these findings reveal the conditions required for H3K27M-mediated PRC2 inhibition and reconcile seemingly paradoxical effects of H3K27M on PRC2 recruitment and activity.

overall_design: Role of PRC2 in H3K27M pediatric glioma

first: James

last: Stafford

first: Chul-Hwan

last: Lee

first: Philipp

last: Voigt

first: Nicolas

last: Descostes

first: Ricardo

last: Saldaña-Meyer

first: Jia-Ray

last: Yu

first: Gary

last: Leroy

first: Ozgur

last: Oksuz

first: Jessica

middle: R

last: Chapman

first: Fernando

last: Suarez

first: Aram

middle: S

last: Modrek

first: N

last: Bayin

first: Dimitris

last: Placantonakis

first: Matthias

middle: A

last: Karajannis

first: Matija

last: Snuderl

first: Beatrix

last: Ueberheide

first: Danny

last: Reinberg


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE 2]

first: Evdoxia

last: Karadoulama

overall_design: CAGE experiments were carried out in mouse embryonic stem cells and embryoid bodies differentiated for three days upon depletion of RBM7 with shRNAs, using a scrambled shRNA as control. The experiments were performed in duplicates. Control samples are included in GSE115710.

first: Marta

last: Lloret-Llinares

first: Yun

last: Chen

first: Luke

last: Wojenski

first: Geno

last: Villafano

first: Jette

last: Bornholdt

first: Robin

last: Andersson

first: Leighton

last: Core

first: Albin

last: Sandelin

first: Torben

last: Jensen


title: Integration of genome-wide DNA methylation and transcription uncovered aberrant methylation-regulated genes and pathways in the peripheral blood mononuclear cells of systemic sclerosis

city: Dallas

first: Quan

last: Li

address: 6001 Forest Park Rd

institute: UTSW

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Generation of esophageal basal progeitor cells from human pluripotent stem cells

city: NEW YORK

first: Jianwen

last: Que

state: NJ

address: 650 W 168TH ST BLACK BLDG 8-810

department: Department of Medicine

institute: Columbia University

summary: We established an efficient protocol to generate esophageal epithelial progenitors (EPCs) from human pluripotent stem cells (hPSCs). Inhibition of TGFß and BMP signaling is required for the differentiation of hPSCs into EPCs which can be further purified with EPCAM and Integrin ß4. These purified EPCs express human fetal esophageal genes and recapitulate the normal development of the stratified squamous epithelium. We performed global transcriptomic profiling of E12.5 mouse embryonic esophageal epithelia, human fetal esophageal epithelia and human embryonic stem cell RUES2-derived esophageal progenitor cells through RNA sequencing. We found that these cells shared similar expression of NOTCH components including Jag1 and 2, Dll1, 3 and 4, and Notct1, 3, 4. The gene expression profile allows to understand transcriptional program in mouse and human developing esophagus.

overall_design: Analysis of global transcriptomes of E12.5 mouse embryonic esophageal epithelia, human fetal esophageal epthelia and human embryonic stem cell RUES2-derived esophageal progenitor cells.

first: Yongchun

last: Zhang


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE]

summary: Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.

overall_design: CAGE experiments were carried out in mouse embryonic stem cells and embryoid bodies differentiated for three days upon depletion of RRP40 with shRNAs, using a scrambled shRNA as control. The experiments were performed in duplicates


title: Developmentally regulated isoform of HNF4α reprograms the adult liver

city: Riverside

first: Jonathan

middle: Robert

last: Deans

address: 3111 BSB, University of California Riverside

department: Molecular, Cell and Systems Biology

institute: University of California Riverside

summary: Hepatocyte Nuclear Factor 4α (HNF4α), master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2). P1-HNF4α but not P2-HNF4α is expressed in normal adult liver while both P1- and P2-HNF4α are expressed in fetal liver and liver cancer. To determine the physiological function of the HNF4α isoforms, we compared P2-HNF4α-expressing exon swap mice to wildtype (WT) using RNA-seq, ChIP-seq, proteomics, protein binding microarrays (PBMs) and metabolomics. P2-HNF4α orchestrates a distinct transcriptomic and metabolomic profile.

overall_design:
Liver RNA-seq samples from both genotypes (WT and a7HMZ, P1- and P2-HNF4α respectively) were taken at three time-points as well as a 12-hr fast with both genotypes at the earliest time-point.

Please note that three different time points are indicated in the sample titles as the time of the day, in 24hr notation (i.e. 1030 = 10:30am, 1330 = 1:30pm, and 2030 = 8:30pm).

first: Linh

middle: M

last: Vuong

first: Frances

last: Sladek


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq]

overall_design: RNA from mouse embryonic stem cells and embryoid bodies differentiated for three days was analysed by next generation sequencing upon depletion of RRP40 with shRNAs, using a scrambled shRNA as control. Total RNA was collected for each condition in triplicates.


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation


city: New York

first: Chae Ho

last: Lim

address: 550 First Ave.

department: Dermatology

institute: New York University School of Medicine

summary: We found dermal Hh activation is sufficient to induce hair follicle neogenesis in wounded skin. We analyzed gene expression profile at single cell level in the dermis of SM22-Tomato (control) and SM22-SmoM2/Tomato (Hh activation in dermis).

overall_design: Single-cell RNA-sequencing libraries of Single cell RNA-seq analysis in dermis of SM22rtTA; tetO-Cre; R26-Tomato (SM22-Tomato, control) and SM22rtTA; tetO-Cre; R26-SmoM2/Tomato (SM22-SmoM2/Tomato, forced Hh activation in wound dermis) at 3 days after complete reepithelialization

first: Mayumi

last: Ito

first: Chae


title: Development of a novel cell-based assay to diagnose recurrent Focal and Segmental Glomerulosclerosis

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President street

department: Medicine

institute: Medical University of South Carolina

summary: In this study we plan to compare the profiles of control sample (C) with the disease (FSGS) samples to identify differentially expressed genes. We hope to identify genes that are specifically activated in response to treatment with FSGS plasma.

overall_design: Upregulated genes on incubating with plasma from recurrent FSGS plamsa sample in cultured human podocytes cells were probed


title: Determination of the Forkhead box A2 (FOXA2) Cistrome in the Human Endometrium

status: Public on Aug 30 2018

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Uterine glands are central to endometrial function and fertility, however the mechanisms regulating their development and function are not well understood. The pioneer forkhead box A2 (FOXA2) transcription factor is distinctively expressed in the glands of the endometrium in both the human and mouse uterus. Studies in mice established that FOXA2 is a critical regulator of gland development in the neonatal uterus as well as differentiated gland function in the adult uterus. An integrative approach was used here to define the FOXA2 cistrome in the human endometrium. Genome-wide mapping of FOXA2 binding sites by chromatin immunoprecipitation sequencing (ChIP-Seq) was performed on proliferative (P) and mid-secretory (MS) phase endometrium and combined with the transcriptome determined by RNA sequencing (RNA-Seq). Distinctive binding of FOXA2 was observed between the P and MS endometrium, and FOXA2 binding intervals were enriched for different transcription factor binding motifs between the phases of endometrium. Pathway analysis revealed different biological processes regulated by FOXA2 bound genes in the P and MS endometrium. Thus, FOXA2 is proposed to regulate gene expression in concert with other transcription factors to influence gland function in a cycle phase-dependent manner. Further analysis identified potential FOXA2 regulated genes that influence endometrial growth, uterine receptivity, and stromal cell decidualization. This analysis of the FOXA2 cistrome provides a foundation essential to understanding fundamental aspects of uterine gland development, differentiation, function, and disease.

overall_design: (6) proliferative phase and (5) mid-secretory phase human endometrium biopsies

first: Andrew

last: Kelleher

first: Susanta

last: Behura

first: Gregory

middle: W

last: Burns

first: Steven

middle: L

last: Young

first: Franco

last: DeMayo

middle: E


title: Human Treg NaCl stimulation

city: New Haven

first: Tomokazu

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine

summary: Human Tregs isolated from PBMCs were cultured in the absence or presence of additional NaCl (40mM) for four days and were performed mRNA-seq.

overall_design: mRNA profiles of human Treg stimulated with additional NaCl

first: David

last: Hafler


title: Human Treg


title: The RNA exosome contributes to gene expression regulation during stem cell differentiation [PRO-Seq]

first: Evdoxia

last: Karadoulama

overall_design: PROseq experiments were carried out in mouse embryonic stem cells and embryoid bodies differentiated for three days upon depletion of RRP40 with shRNAs, using a scrambled shRNA as control. The experiments were performed in duplicates

first: Marta

last: Lloret-Llinares

first: Yun

last: Chen

first: Luke

last: Wojenski

first: Geno

last: Villafano

first: Jette

last: Bornholdt

first: Robin

last: Andersson

first: Leighton

last: Core

first: Albin

last: Sandelin

first: Torben

last: Jensen


title: Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria

city: Los Angeles

first: Samuel

middle: Jackson

last: Balin

address: 10833 Le Conte Ave, Div of Dermatology, 52-121 CHS

institute: UCLA

summary: Human cytotoxic T cell subsets were sorted based on cytotoxic molecule expression and RNA sequencing was performed on these subsets

overall_design: Human T cells from two donors were sorted by Flow based on expresssion of Granzyme B, Perforin and Granulysin in to subsets of cells experssing non of these markers, expressing ony granzyme B (monocytotoxic - MCTL) expressing granzyme B and perforin (dicytotoxic -DCTL), expressing all three (Tri-cytotoxic, TCTL - also called Polycytotoxic PCTL).  RNA sequencing was performed on these sorted subsets and gene expression was compared to generate specific signatures of these subsets allowing for surface marker identification that permitted isolation for functional study.

first: Robert

last: Modlin


title: Human Treg IL-12 stimulation

summary: Human Tregs isolated from PBMCs were cultured in the absence or presence of IL-12 (20ng/ml) for four days and were performed mRNA-seq.

overall_design: mRNA profiles of human Treg stimulated with IL-12 (Th1 condition)


title: Targeted reactivation of FMR1 transcription in FXS embryonic stem cells

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: The aim of this work is to selectively increase transcription from the FMR1 locus in FXS hESC lines using CRISPR-Cas9 fused to transcriptional activators.

overall_design:
Endonuclease deficient Cas9 (dCas9) was fused to VP192 transcriptional activation domain and transfected in WT and FXS hESCs along with a guide RNA targeted to the CGG repeat.
Total RNA was isolated from untransfected WT(UM 4-6), FXS( UM 139-2) hESCs treated with CGG guide RNA and dCas9-VP192 as well as a scramble guide RNA control and dCas9-VP192.
RNA seq analysis was carried out on all these samples.

first: Peter

last: Todd

first: Geena

last: Skariah


title: The relative contributions of cell-dependent cortical microcircuit aging to cognition and anxiety

city: Toronto

first: Etienne

last: Sibille

state: Ontario

address: RM,133, 250 college street

department: Neuroscience of Aging and Depression

country: Canada

institute: Center for Addiction and Mental Health

summary:
Background: Aging is accompanied by altered thinking (cognition) and feeling (mood) functions that depend to some extent on information processing by brain cortical cell microcircuits. We hypothesized that age-associated long-term functional and biological changes are mediated by gene transcriptomic changes within neuronal cell-types forming cortical microcircuits, namely excitatory pyramidal cells (PYC) and inhibitory GABAergic neurons expressing vasoactive intestinal peptide (Vip), somatostatin (Sst) and parvalbumin (Pvalb).
Methods: To test this hypothesis, we assessed locomotor, anxiety-like and cognitive behavioral changes between young (2 months, n=9) and old (22 months, n=12) male C57BL/6 mice, and performed frontal cortex cell-type specific molecular profiling, using laser-capture microscopy and RNA sequencing.
Results: Old-mice displayed increased anxiety and reduced working memory. The four cell-types displayed distinct age-related transcriptomes and biological pathway profiles, affecting metabolic and cell signaling pathways, and selective markers of neuronal vulnerability (Ryr3), resilience (Oxr1), and mitochondrial dynamics (Opa1), suggesting high age-related vulnerability of PYCs, and variable degree of adaptation in GABAergic neurons. Correlations between gene expression and behaviors suggest that changes in cognition and anxiety associated with age are partly mediated by normal age-related cell changes, and that additional age-independent decreases in synaptic and signaling pathways, notably in PYC and SST-neurons further contribute to behavioral changes.
Conclusions: Our study demonstrates cell-dependent differential vulnerability and coordinated cell-specific cortical microcircuit molecular changes with age. Collectively, the results suggest intrinsic molecular links between aging, cognition and mood-related behaviors with SST-neurons contributing evenly to both behavioral conditions.

overall_design: Male C57BL/6 mice, Young (2 months, n=9) and old (22 months, n=12), performed frontal cortex cell-type specific molecular profiling, using laser-capture microscopy and RNA sequencing using illumina HiSeq

first: Rammohan

last: Shukla

first: Thomas

middle: D

last: Prevot

first: Leon

last: French

first: Ruth

last: Isserlin

first: Brad

last: Rocco

first: Mounira

last: Banasr

first: Gary

last: Bader


title: Short-term effect of Boost versus Radical doses of Intraoperative electron Radiotherapy in breast cancer tumor bed using high-throughput approaches

city: Tehran

first: Mohammad Esmael

last: Akbari

address: Shahrdari

country: Iran

institute: Cancer Research Center

summary:
Importance: Intra-operative electron Radiation Therapy as a partial-breast single high dose radiotherapy, leads to decrease the local recurrence through tumor bed modification.
Objective: This study designed to investigate short-term effect of the dose- dependent and -independent molecular mechanisms and biological pathway of tumor bed modification induced by Intra-operative electron Radiation
Methods: Six random selected breast cancer patients entered into our study and all patients by referee to their pathological report were treated by doses of 12Gy as a Boost dose and 21Gy as a Radical dose and the samples were categorized into three groups which included: Margin Before irradiation, Margin After immediately irradiation and Margin 24 hours After irradiation.
Resluts: Using mRNA-sequencing, ~6 Giga base clean data (20 Million Reads, 150 base pair) per individual sample and totally 125.3 million reads of transcriptome sequence were generated from the patient samples.
Discussion: Appropriate Intra-operative electron Radiation Therapy short-term effects of molecular mechanisms in tumor bed seems to be dose-independent.

overall_design: A single high dose 12Gy of Intra-operative electron Radiation Therapy as a Boost dose and 21Gy as a Radical dose after breast-conserving surgery (BCS) immediately and 24 hours after irradiation on tumor bed compared with tumor bed before irradiation.

first: Minoo

last: Shahani

first: Jafar

last: Shakeri

first: Babak

last: Arefnezhad


title: PRSS1 gene mutated mouse ES cells

city: Suita

first: Ayumu

last: Asai

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

summary: To confirme the influenece of introduction of T29I mutation in PRSS1 to the gene expression profile of ES cells, we isolated mRNA from wild-type ES cells or  mutation-introduced ES cells.  This data showed that the introduction of T29I mutation didn't affect the gene expression profile of ES cells.

overall_design: RNA-seq for wild-type ES cells or mutation-introduced ES cells.

first: Masamitsu

last: Konno

first: Jun

last: Koseki

first: Hideshi

last: Ishii


title: Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency

city: NEW HAVEN

first: Zheng

last: Wang

state: Connecticut

address: 10 amistad street, yale stem cell center, yale stem cell center

department: genetics

institute: YALE UNIVERSITY


title: Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency (RNA-seq)

summary: As somatic cells are converted to iPSCs, their chromatin undergoes wide-ranging rearrangements that affect the ratio of euchromatin-to-heterochromatin, DNA methylation patterns and the regulation of enhancers and promoters. The molecular machinery underlying this process remains largely unknown. Here, we show that Dppa2 and Dppa4, two thus far poorly characterized mES-specific factors, play a key role in resetting the epigenome to a pluripotent configuration. They function as a heterodimer, are induced in late reprogramming intermediates, and are required for reprogramming. When overexpressed with OSKM factors, Dppa2/4 yield reprogramming efficiencies exceeding 75% of the starting culture and accelerate reprogramming kinetics, generating iPSCs in as little as 4 days. When chromatinbound, Dppa2/4 initiate global chromatin decompaction via the DNA damage response pathway, which subsequently activates mES promoters and enhancers and enables an efficient progression to pluripotency. Our work provides critical insights into how the epigenome is remodeled during cell fate transitions.

overall_design: Transcriptional regulation by the Dppa2 and Dppa4 investigated by ChIP-Seq and RNA-Seq

first: Natalia

last: Ivanova

first: Sameet

last: Mehta


title: Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency (ChIP-seq)


title: Human Treg IFNg/IL-10 subpopulations

first: Tomokazu

last: Sumida

summary: Human Tregs isolated from PBMCs were sorted into 4 different subpopulations based on IFNg and IL-10 production and were performed mRNA-seq.

overall_design: mRNA profiles of human Treg subpopulations

first: David

last: Hafler


title: Bulk RNA-sequencing of cell populations in mouse Anterior Lateral Motor (ALM) cortex based on four projection targets

first: Vilas

last: Menon

institute: Columbia University Medical Center

summary: We profiled populations of mouse neurons in the Anterior Lateral Motor (ALM) cortex, as defined by retrograde projection labeling. For each sample, we injected one of four regions (thalamus, IRN in medulla, superior colliculus, or pons) using the retrograde virus rAAV2-retro with a fluorescent repoter, and collected cells in the ALM whose projections to the target area were labelled. 50-120 cells were collected from each injection experiment and then profiled using standard bulk RNA-seq protocols

overall_design: We originally collected 7 biological replicates (from different mice) each of thalamus-projecting and medulla-projecting cells, and 3 biological replicates each of super colliculus-projecting and pons-projecting cells. After alignment and quantification of the RNA-seq data, principal component analysis identified one thalamus-projecting and one medulla-projecting sample as outlier samples, and these have been labeled as such in the sample titles

first: Michael

last: Economo

first: Sarada

last: Viswanathan


title: Transcriptome analysis reveals non-foamy rather than foamy plaque macrophages are pro-inflammatory in atherosclerotic murine models

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

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

overall_design: Refer to individual Series


title: Single cell RNA sequencing of aortic CD45+ cells and foam cells from atherosclerotic aorta

summary: In atherosclerosis, several immune cells are involved in plaque formation. Foam cell formation is a major cellular process in atherosclerotic lesion. It is important to understand which cells participate in foam cell formation. To characterize the immune cells and foam cells in atherosclerotic aorta, we performed single cell RNA sequencing of aortic CD45+ leukocytes from Ldlr-/- mice and foamy cells from ApoE-/- mice. The single cell RNA-seq analyses revealed the heterogeneity of aortic macrophages and foam cells in atherosclerotic aorta.

overall_design:
Single cell RNA sequencing of aortic CD45+ cells from atherosclerotic Ldlr-/- mice (n=6, WD for 12 wks). 3781 cells identified, Using Illumina HiSeq4000.
Single cell RNA sequencing of aortic foam cells from atherosclerotic ApoE-/- mice (n=6, WD for 27 wks), 809 cells identified, Using Illumina HiSeq4000.

first: Kyeongdae

last: Kim

first: Dahee

last: Shim

last: Lee

first: Konstantin

last: Zaitsev

first: Jesse

last: Williams

first: Gwendalyn

middle: J

last: Randolph

middle: N

first: Cheolho

last: Cheong

first: Jae-Hoon

last: Choi


title: RS07910/07915 TCS multipath regulates clavulanic acid metabolic pathways in Streptomyces clavuligerus F613-1

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

institute: Shandong Academy of Medical Sciences

summary: Streptomyces clavuligerus F613-1 produces a clinically important β-lactamase inhibitor, clavulanic acid (CA). The biosynthesis pathway of CA has been basically elucidated, however, the global regulation of CA biosynthesis remains unclear. In order to further elucidate the regulatory mechanism of clavulanic acid synthesis, TCS RS07910/07915 which is next to the CA biosynthetic gene cluster was deleted in Streptomyces clavuligerus. F613-1. Deletion of RS07910/07915 results in decreased the production of CA, but the phenotype was not affected. Both the transcriptome and ChIP-seq data revealed that the TCS RS07910/07915 mainly regulate genes involved in primary metabolism (such as fatty acid degradation, glyceraldehyde 3-phosphate (G3P) metabolism, arginine biosynthesis) and CA biosynthesis. EMSA assays revealed  that RS07915 could bind to the promoter fragments of argG, argC, oat1, oat2, ceaS1 and claR in vitro, indicating that RS07915 could direct regulate the biosynthesis genes of arginine and CA. This study indicated that RS07910/07915 is a pleiotropy regulatory TCS, RS07910/07915 could directly affect the biosynthesis of CA, and indirectly affect CA production through affecting primary metabolism of arginine and G3P (precursors of CA).

overall_design: mRNA profiles of Streptomyces wild-type and ΔRS07910/07915 mutant strains were generated by deep sequencing

first: Jiafang

last: Fu

first: Ronghuo

last: Qin


title: RNA sequencing reveals transcriptional changes after Hippo signaling activation in podocytes

city: Münster

first: Jakob

last: Bonse

state: NRW

address: Albert-Schweitzer-Campus 1

department: Internal Medicine D

institute: Molecular Nephrology

summary: Podocytes are crucial for the establishment and maintenance of the blood-urine filtration barrier in the glomeruli of the kidney. Activation of the Hippo signaling pathway in podocytes leads to the induction of apoptosis and could be linked to the pathogenesis of proteinuric diseases like focal segmental glomerulosclerosis (FSGS). To investigate the Hippo signaling controlled gene transcription, podocytes overexpressing LATS2, a core kinase of the Hippo pathway, were analyzed via RNA sequencing.

overall_design: The gene expression of 4 samples from a 8 h doxycyclin induced LATS2 overexpressing podocyte cell line was compared to 4 untreated samples by RNA sequencing.

first: Beate

last: Vollenbröker

first: Dirk

middle: O

last: Wennmann


title: Expression regulation by Yaf2 in mouse embryonic stem cells

city: Nanjing

first: Wukui

last: Zhao

state: Jiangsu

address: 12 Xuefu Road

department: Model Animal Research Center

institute: Nanjing University

summary: The Polycomb group (PcG) proteins are the key epigenetic regulators with well-established roles in stem cell maintenance. To date, biochemical analyses have identified noncanonical PRC1(nc-PRC1) complexes characterized by the presence of Rybp/Yaf2 and the lack of CBX proteins. The biological significance of these nc-PRC1s and the potential mechanisms by which they mediate gene repression are largely unknown. Here we show that disruption of Yaf2 results in compromised proliferation and abnormal differentiation in mouse embryonic stem cells (mESCs). Deletion analysis identifies the region encompassing amino acid residues 102–150 required for the assembly of Yaf2 into nc-PRC1 complexes. Furthermore, we found that substitution of serine 166 by alanine (S166A) caused a loss of Yaf2-phosphorylation signal in mESCs. Loss of such Yaf2-phosphorylation compromises Ring1B-mediated H2A monoubiquitination and in turn lose its ability to repress target gene expression. We therefore propose that Yaf2 phosphorylation enhances its ability to maintain the pluripotent state in mESCs.

overall_design: Yaf2-KO and wildtype mESCs

first: Mengjie

last: Liu

first: Jinzhong


title: Mechanism sharing between genetic and gestational hypoxia-induced cardiac anomalies

city: Gainesville

first: Hideko

last: Kasahara

state: Florida

address: 1345 Center Drive, Room M-557

department: Physiology and Functional Genomics

institute: University of Florida

summary:
Purpose: Mutations in several genetic loci lead to cardiac anomalies, with mutations in transcription factor NKX2-5 gene being one of the largest mutations known. Gestational hypoxia, such as seen in high-altitude pregnancy, has been known to affect cardiac development, and this paper aims to uncover information about the underlying mechanisms of this phenomena.
Methods: Wild-type female mice were mated with Nkx2-5 mutant males, to produce offsprings. The pregnant females were then separated into two groups, one left in normal air and one breathing hypoxic, 14% oxygen, air from gestation day 10.5 to 12.5. Hearts were dissected from E12.5 embryos, subjected to RNA purification followed by RNA-seq. Wild-hypoxia and mutant-normoxia were compared to control wild-normoxia.
Conclusions: The results of our study provide insights into a common molecular mechanism underlying non-genetic/epigenetic and genetic cardiac anomalies.

overall_design: Embryonic mice were produced with either wild-type or mutant genomes, and some from each group were exposed to hypoxia during gestation, then physical analysis and RNA sequencing was done on the embryos.

first: Olivia

last: Moumne

first: Rajib

last: Chowdhurry

first: Cassandra

last: Doll

first: Natalia

last: Pereira

first: Mustafa

last: Hashimi

first: Tabor

last: Grindrod

first: James

last: Dollar

first: Alberto

last: Riva


title: Quantitative Analysis of Neurog2 Heterozygote, Mutant and and Mash1KI Retinal Transcriptomes by RNA Sequencing

city: Davis

first: Nadean

last: Brown

state: CA

address: 4407 Tupper Hall

department: Dept of Cell Biology and Human Anatomy

institute: University of California, Davis

summary: To generate an unbiased view of changes to the retinal gene network in Neurog2 retinal mutants as well as understanding the effects of Mash1 ectopic expression in a Neurog2 retinal mutant, we generated and compared the E12.5 transcriptomes from Neurog2 heterozygote, Neurog2 mutant and Neurog2 mutant;Mash1 knock-in mice.  A pair of E12.5 retinas from each biologic replicate underwent FACS sorting to isolate GFP+ cells. GFP+ cells were used to produce libraries for high throughput sequencing (n = 3 biologic replicates/genotype).  Reads were aligned with BWA and Bowtie programs to the mm10 genome.  Aligned reads were then analyzed for differentially expressed transcripts using the CuffDiff program in the Galaxy online bioinformatics package (www.usegalaxy.org).

overall_design: Total RNA from Neurog2GFP/+(heterozygote; n = 3), Neurog2GFP/GFP(mutant; n = 3), and Neurog2GFP/Mash1KI(Mash1 knock-in; n = 3) E12.5 retinas.

first: Angelica

last: Kowalchuk

first: Kate

last: Maurer


title: Neurons under T cell attack orchestrate phagocyte-mediated synaptic stripping

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: RNA-seq libraries purified from rLCMV-Cre infected neurons using the Ribotag allele. Seq libraries are provided from STAT1 competent (Stat1+/+ x Rpl22HA/+) or STAT1-deficient (Stat1fl/fl x Rpl22HA/+) rLCMV-Cre carrier mice which have been challenged intravenously with LCMVwt at 5 weeks of age and then sacrificed after 9 days. These seq libraries represent the response of rLCMV-Cre infected neurons to CD8+ T cell attack following challenge with LCMVwt.

overall_design: To investigate how neuronal JAK/STAT1 signaling results in synaptic alterations, we profiled the neuronal translatome by exploiting RiboTag mice (Rpl22HA/+). Upon Cre-mediated recombination of their gene-targeted locus, Rpl22HA/+ mice express an HA-tagged ribosomal protein L22, enabling the immunoprecipitation of ribosome-bound RNA. We inoculated neonatal Rpl22HA/+ mice with rLCMV-Cre, inducing HA-tagged ribosomal expression in infected neurons. Mice were sacrificed 9 days after challenge with LCMVwt in order to extract ribosome-bound mRNA from the brains and perform next generation RNA sequencing. We compared the neuronal translatome of intravenously (i.v) LCMVwt. challenged STAT1-competent (Rpl22HA/+xStat1+/+), conditionally STAT1-deficient (Rpl22HA/+xStat1fl/fl) and non-challenged (Rpl22HA/+ xStat1+/+) rLCMV-Cre carrier mice, respectively. Independent biological replicates (n= 4-7) were analyzed for each group.

first: G

last: Di Liberto

first: S

last: Pantelyushin

first: D

last: Merkler


title: Regulation of follicular T-helper cell positioning and function by PD-1

city: Beijing

first: Hai

last: Qi

state: Beijing

address: Tsinghuayuan Street

department: School of Medicine

institute: Tsinghua University

summary: Follicular T-helper (TFH) cells highly express the programmed cell death-1 (PD-1) molecule. Whereas inhibition of T cell receptor (TCR) signaling and CD28 co-stimulation is thought to be the primary mode of PD-1 functions, how PD-1 regulates TFH development and function remains unclear. Here we show that, when engaged by the ensemble of bystander B cells constitutively expressing PD-1 ligand 1 (PD-L1), PD-1 inhibits T-cell recruitment into follicles. This inhibition involves suppression of PI3K activities downstream of follicle-guidance receptor CXCR5, is independent from co-signaling with the TCR, and necessitates ICOS signaling to overcome. PD-1 further restricts CXCR3 upregulation on TFH cells, serving to concentrate these cells toward the GC territory, where PD-L1-PD-1 interactions between individual TFH and B cells optimize B-cell competition and affinity maturation. Therefore, operating in both costimulation-independent and -dependent manners, PD-1 plays an integral role in orchestrating tissue positioning and function of TFH cells.

overall_design: Differential expression analysis between WT and Pdcd1KI/KI CXCR5hi Tfh cells

first: Jingwen

last: Shi

first: Shiyue

last: Hou

first: Qian

last: Fang

first: Xin

last: Liu

first: Xiaolong


title: Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) recycle post-termination 40S subunits in vivo

city: Bethesda

first: Nicholas

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: The recycling of ribosomal subunits after translation termination is critical for efficient gene expression. Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) function as 40S recycling factors in vitro, but it is unknown whether they perform this function in vivo or serve as alternative initiation factors. Ribosome profiling of strains missing these factors revealed 80S ribosomes queued behind the stop codon, consistent with a block in 40S recycling. We found that unrecycled ribosomes could reinitiate translation at AUG codons in the 3’UTR, as evidenced by peaks in the footprint data and 3’UTR reporter analysis. In vitro translation experiments using reporter mRNAs containing upstream ORFs (uORFs) further established that reinitiation increased in the absence of these proteins. In some cases, 40S ribosomes appeared to rejoin with 60S subunits and undergo an alternative 80S reinitiation process in 3’UTRs. These results support a crucial role for Tma64, Tma20, and Tma22 in the recycling of 40S ribosomal subunits at stop codons and translation reinitiation.

overall_design: 14 biological samples are included in the study for ribosome footprinting. These include wild-type and combination knockouts of TMA64, TMA20, and TMA22, and mutation of SUI1.

first: David

last: Young

first: Desislava

last: Makeeva

first: Fan

last: Zhang

first: Aleksandra

last: Anisimova

first: Elena

last: Stolboushkina

first: Abdollah-Fardin

last: Ghobakhlou

first: Ivan

last: Shatsky

first: Sergey

last: Dmitriev

first: Alan

middle: G

last: Hinnebusch


title: Exploring the transcriptome of resident spinal microglia after collagen antibody-induced arthritis

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

summary: Microglia have emerged as crucial players in the maintenance of mechanical hypersensitivity in models of chronic pain, including rheumatoid arthritis. Recent studies have suggested that there is a sexually dimorphic microglial involvement in chronic pain, but the debate is still ongoing.     Here, we have used the collagen antibody-induced arthritis (CAIA) mouse model to ascertain possible differences between male and female microglia in the context of arthritis-induced pain. We have focused on the late phase of this arthritis model, when joint inflammation has resolved but mechanical hypersensitivity and microglial activation persist. We found that intrathecal administration of minocycline reversed mechanical thresholds to control levels in male, but not female mice. Moreover, we isolated resident microglia from the lumbar dorsal horns of male and female mice and observed a significantly lower number of microglial cells in females by flow cytometry analysis. Furthermore, genome-wide RNA sequencing results pointed to several transcriptional differences between male and female microglia, but no convincing differences were identified between control and CAIA groups.     Taken together, these findings suggest that there are significant but subtle sex differences in microglial expression profiles independent of treatment. To what extent they help bring about the behavioural sexual dimorphism observed after minocycline administration remains to be explored. Finally, our experiments failed to identify the underlying biological correlates of the microglial activation that is present in the late phase of the CAIA model. It is likely that transcriptional changes are either subtle and highly localised and therefore difficult to identify with bulk isolation techniques or that other factors, such as changes in protein expression or epigenetic modifications are at play.

overall_design: RNA-seq of male and female saline or CAIA treated mice

first: Teresa

last: Fernandez-Zafra

first: Camilla

middle: I

last: Svensson


title: Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model

status: Public on Aug 29 2018

city: Madison

first: Federico

last: Rey

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin-Madison

summary:
Background: Humans with metabolic and inflammatory diseases frequently harbor lower levels of butyrate-producing bacteria in their gut. However, it is not known whether variation in the levels of these organisms is causally linked with disease development and whether diet modifies the impact of these bacteria on health.
Results: We use germ-free apolipoprotein E-deficient mice colonized with synthetic microbial communities that differ in their capacity to generate butyrate to demonstrate that Roseburia intestinalis interacts with dietary components to (i) impact gene expression in the intestine, directing metabolism away from glycolysis and toward fatty acid utilization, (ii) improve intestinal barrier function, (iii) lower systemic inflammation and (iv) ameliorate atherosclerosis. Furthermore, intestinal administration of butyrate improves gut barrier function and reduces atherosclerosis development.
Conclusions: Altogether, our results illustrate how modifiable diet-by-microbiota interactions impact cardiovascular disease, and suggest that interventions aimed at increasing the representation of butyrate-producing bacteria may provide protection against atherosclerosis.

overall_design: Intestinal mRNA profiles of gnotobiotic ApoE KO mice colonized with "core" community or "core plus Roseburia intestinalis" were generated by deep sequencing using Illumina HiSeq.

first: Kazuyuki

last: Kasahara


title: Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

institute: CRCHUM

summary: Most individuals exposed to hepatitis C virus (HCV) become persistently infected while a minority spontaneously eliminate the virus. Although early immune events influence infection outcome, the cellular composition, molecular effectors, and timeframe of the host response active shortly after viral exposure remain incompletely understood. Employing specimens collected from people who inject drugs (PWID) with high risk of HCV exposure, we utilized RNA-Seq to characterize immune function in peripheral blood before, during, and after acute HCV infection resulting in spontaneous resolution. Our results provide a detailed description of innate immune programs active in peripheral blood during acute HCV infection, which include prominent type I interferon and inflammatory signatures. Innate immune gene expression rapidly returns to pre-infection levels upon viral clearance. This innate response coincides with a decrease in B cell transcriptional signatures. These results represent the first longitudinal transcriptomic characterization of human immune function in acute HCV infection and identify several dynamically regulated features of the complex response to natural HCV exposure.

overall_design: mRNA-Seq of peripheral blood mononuclear cells (PBMC) collected from individuals before, during, and after acute HCV infection. Acute HCV infection resulted in spotaneous viral resolution (n=6) or chronic infection (n=8). Four time points were examined per subject: i) Pre-infection baseline (Variable); ii) Early acute (2-9 weeks, mean 6 weeks); iii) Late acute (15 – 20 weeks, mean 17 weeks); and iv) Follow up (25 – 71 weeks, mean 52 weeks)

middle: H


title: RNA-sequencing of tamoxifen-resistant and -sensitive breast cancer cell lines.

city: Helsinki

first: Susanne

last: Hultsch

address: Tukholmankatu 8

department: FIMM, HiLife

country: Finland

institute: University of Helsinki

summary: We performed RNA-sequencing on 7 tamoxifen-resistant (MCF-7 Tam1, T-47D Tam1, T-47D Tam2, ZR-75-1 Tam1, ZR-75-1 Tam2, BT474 Tam1 and BT-474 Tam2) and their isogenic parental (MCF-7, T-47D, ZR-75-1 and BT-474) breast cancer cell lines. The tamoxifen-resistant cell lines were generated from the parentel cell lines by continuous administration of 1 µM 4-OH-tamoxifen for eight to twelve months. RNA- sequencing was performed to determine the changes in the expression of genes in the resistant clones as well as pathways. In addition, we compared the expression changes of the cell lines with those of the GSE58708 data set which we reanalyzied in our pipeline.

overall_design: Paired-end RNA-sequencing of 7 tamoxifen-resistant (MCF-7 Tam1, T-47D Tam1, T-47D Tam2, ZR-75-1 Tam1, ZR-75-1 Tam2, BT474 Tam1 and BT-474 Tam2) and their isogenic parental (MCF-7, T-47D, ZR-75-1 and BT-474) breast cancer cell lines and re-analysis of GSE58708.

first: Matti

last: Kankainen

first: Sara

last: Kangaspeska


title: Transcriptomic Reprogramming of Prostate Cancer Cells Driven by Stroma-Derived SPINK1

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Recent advances in next generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways and responses. We performed this study to investigate the transcriptome profiling (RNA-seq) of prostate cancer cells upon in vitro treatment with the conditioned media from prostate stromal cells exogenously expressing human SPINK1.

overall_design: Overall transcript profiles of prostate cancer cell lines including PC3 and DU145 were generated by deep sequencing, in triplicate, using Illumina HiSeq X10. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Fei

last: Chen


title: Joint profiling of chromatin accessibility and gene expression in thousands of single cells

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: Here we describe sci-CAR, a combinatorial indexing strategy to jointly profile chromatin accessibility and mRNA in each of thousands of single cells. As a proof-of-concept, we apply sci-CAR to 4,825 cells comprising a time-series of dexamethasone treatment, as well as to 11,233 cells from the mouse kidney.

overall_design: single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment), and wild type mouse kidney.

first: Darren

last: Cusanovich

first: Vijay

last: Ramani

first: Hannah

last: Pliner

first: Andrew

last: Hill

first: Delasa

last: Aghamirzaie

first: Riza

last: Daza

first: Jose

last: McFaline

first: Jonathan

last: Packer

first: Lena

last: Christiansen

first: Frank

last: Steemers

last: Adey

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: RNA-Seq analysis of long-term estrogen-deprived (LTED) MDA-MB-134VI (MM134) and SUM44PE (SUM44) ILC cell lines

city: Pittsburgh

first: Kevin

last: Levine

state: Pennsylvania

address: 204 Craft Ave

institute: University of Pittsburgh

summary:
Background: Invasive lobular breast carcinoma (ILC) is a histological subtype of breast cancer that is characterized by loss of E-cadherin, and high expression of estrogen receptor alpha (ER). Many patients with ILC are effectively treated with adjuvant aromatase inhibitors (AIs), however, acquired AI resistance remains a significant problem.
Methods: To identify underlying mechanisms of acquired antiestrogen resistance in ILC, we developed a total of 6 long-term estrogen-deprived (LTED) variant cell lines of the human ILC cell lines SUM44PE (SUM44; 2 lines) and MDA-MB-134VI (MM134; 4 lines). To better understand mechanisms of AI resistance in these models, we performed transcriptional profiling analysis by RNA-sequencing.
Results: MM134 LTED cells expressed ER at decreased level and lost growth response to estradiol, while SUM44 LTED cells retained partial ER activity. Our transcriptional profiling analysis identified shared activation of lipid metabolism across all 6 independent models. However, the underlying basis of this signature was distinct between models. Oxysterols were able to promote the proliferation of SUM44 LTED cells, but not MM134 LTED. In contrast, MM134 LTED cells displayed high expression of the Sterol regulatory element-binding protein 1 (SREBP1), a regulator of fatty acid and cholesterol synthesis, and were hypersensitive to genetic or pharmacological inhibition of SREBPs. Several SREBP1 downstream targets involved in fatty acid synthesis, including FASN, were induced, and MM134 LTED cells were more sensitive to etomoxir, an inhibitor of the rate-limiting enzyme in β-oxidation, than their respective parental control cells.
Conclusions: Our characterization of a unique series of AI-resistant ILC models identifies a lipogenic phenotype, including overexpression of SREBP1. This novel metabolic target deserves further study for the prevention and treatment of AI-resistance for patients with ILC.

overall_design: Parental and LTED MM134 and SUM44 cells were seeded in triplicates in 6-well plates. Parental cells were hormone deprived for three days before cell collection. RNA-Seq was carried out by Illumina HiSeq 2000. Raw sequence data were mapped to hg38 genome (ensembl release version 82) and gene counts were quantified with Salmon (version 0.6.0)

first: Tian

last: Du

first: Matthew

last: Sikora

first: Nilgun

last: Tasdemir

first: Rebecca

middle: B

last: Riggins

first: Stacy

last: Wendell

first: Bennet

last: Van Houten

first: Steffi

last: Oesterreich


title: Effect of norepinephrine and focal adhesion kinase (FAK) knockdown in prostate cancer

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

summary: Chronic stress is associated with hormonal alterations that are known to promote cancer progression. The stress hormone norepinephrine promotes migration and metastasis of prostate cancer cells. Focal adhesion kinase (FAK) is a non-receptor protein tyrosine kinase which is phosphorylated during chronic stress or norepinephrine treatment. Here, we investigated how norepinephrine modulates the gene expression in Myc-CaP prostate cancer cell line. We also focused on the effect of FAK knockdown in norepinephrine-induced changes of the gene expression profile.

overall_design: Myc-CaP cells stably transfected with shRNAs targeting FAK or negative control were treated with 10μM norepinephrine or vehicle for 24 hours. The effect on gene expression was assessed by RNA-Seq.

first: Yong

last: Yang


title: Oligodendrocyte precursor differentiation and survival requires chromatin remodeling by Chd7 and Chd8

city: Paris

first: Carlos

last: Parras

address: 47 bd de l'hopital batiment ICM

country: France

institute: ICM

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

overall_design: Refer to individual Series


title: Oligodendrocyte precursor differentiation and survival requires chromatin remodeling by Chd7 and Chd8 [ATAC-seq]

summary: Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming implicating chromatin remodeling. Here, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin-binding profile combined with transcriptome and open-chromatin analysis of Chd7-deleted OPCs, demonstrates that Chd7 controls OPC differentiation through chromatin-opening and transcriptional activation of key regulators such as Sox10, Nkx2.2 and Gpr17. Chd7 is however dispensable for oligodendrocyte stage progression, consistent with Chd8 compensatory function, as suggested by its chromatin binding profile. Furthermore, Chd7 protects non-proliferative OPCs from apoptosis by chromatin-closing and transcriptional repression of p53. Mutations in CHD7 and CHD8 are associated with developmental disorders, such as CHARGE syndrome and autism respectively, and our results offer new avenues to understand and modulate their functions in disease.

overall_design: ATAC-seq from Chd7iKO and Control O4+ sorted cells

first: Corentine

last: Marie


title: RNA-seq of the lacrimal gland epithelial tissue in control vs Pea3-depleted tissue in mouse embyro

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

summary: The goal of the study is to find the transcriptional targets downstream of Pea3-mediated signaling in the lacrimal gland epithelium. In order to look for the potential targets, we performed laser capture microdissection of the lacrimal gland epithelial tissue at embryonic day E14.5 from control embryos as well as mutant embryos containing epithelium-specific deletion of Pea3. After tissue harvest, RNA was extracted. Conversion to cDNA as well as amplification was performed by Clontech SMART-seq v4 Ultra low input RNA kit, as well as cDNA library construction was performed using Nextera XT DNA library preparation kit by core facility at Columbia university prior to RNA sequencing.  After preparation of cDNA library, each sample was sequenced using  Illumina platform.

overall_design: For this experiment, 3 control samples and 3 mutant samples were analysed.

first: Ankur

last: Garg


title: Oligodendrocyte precursor differentiation and survival requires chromatin remodeling by Chd7 and Chd8 [RNA-seq]

summary: Oligodendrocyte precursor cells (OPCs) constitute the main proliferative cells in the adult brain, and deregulation of OPC proliferation-differentiation balance results in either glioma formation or defective adaptive (re)myelination. OPC differentiation requires significant genetic reprogramming implicating chromatin remodeling. Mounting evidence indicates that chromatin remodelers play important roles during normal development and their mutations are associated with neurodevelopmental defects, with CHD7 haploinsuficiency being the cause of CHARGE syndrome and CHD8 being one of the strongest Autism Spectrum Disorder (ASD) high-risk associated genes. Here, we report on uncharacterized functions of the chromatin remodelers Chd7 and Chd8 in OPCs. Their OPC-chromatin-binding profile combined with transcriptome and chromatin accessibility analyses of Chd7-deleted OPCs, demonstrates that Chd7 protects non-proliferative OPCs from apoptosis by chromatin-closing and transcriptional repression of p53. Furthermore, Chd7 controls OPC differentiation through chromatin-opening and transcriptional activation of key regulators, including Sox10, Nkx2.2 and Gpr17. Chd7 is however dispensable for oligodendrocyte stage progression, consistent with Chd8 compensatory function, as suggested by their common chromatin binding profiles and genetic interaction. Finally, CHD7 and CHD8 bind in OPCs to a majority of ASD-risk associated genes, suggesting an implication of oligodendrocyte lineage cells in ASD neurological defects.  Our results thus offer new avenues to understand and modulate the CHD7 and CHD8 functions in normal development and disease.

overall_design: RNA-seq from Chd7iKO and Control O4+ soted cells


title: Aberrant expression of CITED2 promotes prostate cancer metastasis by activating the nuceolin-AKT pathway.

status: Public on Aug 28 2018

city: Seoul

first: Seung-Hyun

last: Shin

address: 103, Daehak-ro, Jongno-gu

department: Pharmacology

country: South Korea

institute: Seoul National University

summary: We found that CITED2 is highly expressed in metastatic prostate cancer, and its expression is correlated with poor survival in pateints. In this study, we used an siRNA to decrease CITED2 expression in PC3 cells. A RNA-seq approach was utilized in order to determine global gene expression changes  in CITED2 knockdown cells compared to control cells.

overall_design: PC3 cells transfected with control siRNAs were used as controls. Cells transfected with siRNAs targeting CITED2 were used as experimental group. Cells were transfected for 72 hr and the analyses were done.

first: Ga Young

last: Lee

first: Mingyu

first: Jengmin

last: Kang

first: Hyun-Woo

first: Yang-Sook

last: Chun

first: Jong-Wan

last: Park


title: CXXC1 is not essential for normal DNA double-strand break formation and meiotic recombination in mouse

city: Bar Harbor

first: Hui

last: Tian

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: In most mammals, including mice and humans, meiotic recombination is determined by the meiosis specific histone methytransferase PRDM9, which binds to specific DNA sequences and trimethylates histone 3 at lysine-4 and lysine-36 at the adjacent nucleosomes. These actions ensure successful DNA double strand break formation and repair that occur on the proteinaceous structure forming the chromosome axis. The process of hotspot association with the axis after their activation by PRDM9 is poorly understood. Previously, we and others have identified CXXC1, an ortholog of S. cerevisiae Spp1 in mammals, as a PRDM9 interactor. In yeast, Spp1 is a histone methyl reader that links H3K4me3 sites with the recombination machinery, promoting DSB formation. Here, we investigated whether CXXC1 has a similar function in mouse meiosis. We created two Cxxc1 conditional knockout mouse to deplete CXXC1 generally in germ cells, and before the onset of meiosis. Surprisingly, male knockout mice were fertile, and the loss of CXXC1 in spermatocytes had no effect on hotspot trimethylation, double-strand break formation or repair. Our results demonstrate that CXXC1 is not an essential link between PRDM9-activated recombination hotspot sites and DSB machinery and that the hotspot recognition pathway in mouse is independent of CXXC1.

overall_design: We performed ChIP-seq with antibodies against single strand DNA binding protein DMC1 in spermatocytes isolated from Cxxc1 heterozygous and Cxxc1 conditional knockout mouse to analyze meiotic DNA double strand formation level.

first: Petko

last: Petkov


title: Oligodendrocyte precursor differentiation and survival requires chromatin remodeling by Chd7 and Chd8 [ChIP-seq]

overall_design: Chd7 & Chd8 ChIP-seq from in vivo mouse O4+ cells

first: Romain

last: Daveau


title: Genome-wide Estrogen Receptor-alpha activation time-course

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

summary: Estrogen Receptor-alpha (ER) is the key driver of 75% of all breast cancers. Upon stimulation by its ligand estra-2-diol, ER forms a transcriptionally active complex binding chromatin. Previous studies have reported that ER binding follows a cyclical binding pattern with a periodicity of 90 minutes. However, these studies have been limited to individual ER target genes and most were done without replicates. Thus, the robustness and generality of ER cycling are not well understood. Here we present a comprehensive genome-wide analysis of the time dependence of ER binding affinity up to 90 minutes after activation, based on 6 replicates at 10 time points using our previously reported method for precise quantification of binding, Parallel-Factor ChIP-seq (pfChIP-seq). In contrast to previously described cyclical binding, our approach identifies a unidirectional sustained increase in ER binding affinity, as well as a class of estra-2-diol independent binding sites. Our results are corroborated by a quantitative re-analysis of data from multiple independent studies. Our new model reconciles the results of multiple conflicting studies into the activation of ER at the TFF1 promoter. We provide a detailed understanding of ER's response to estra-2-diol in the context of the receptor's fundamental role as both the main driver and therapeutic target of breast cancer

overall_design: 6 indepednant pfChip-seq replicates measuring ER binding at 10 timepoints between 0 to 90 minutes.

first: Amy

last: Cullen

first: Florian

last: Markowetz