title: Use single cell RNA sequencing to study the molecular siganature of primary human Megakaryocytic-erythroid progenitor

city: New Haven

first: Yi-Chien

last: Lu

address: 10 Amistad Street

department: Laboratory Medicine

institute: Yale Medical School

summary: Megakaryocytic-Erythroid Progenitors (MEP) produce circulating red blood cells and platelets. Although much is known regarding megakaryocytic (Mk) and erythroid (E) maturation, detailed molecular mechanisms underlying the MEP fate decision have not been determined. Single cell RNA sequencing of highly enriched populations of primary human common myeloid progenitors (CMP), MEP, megakaryocyte progenitors (MKP) and erythroid progenitors (ERP), revealed that MEP have a distinct molecular signature with co-expression of genes otherwise expressed exclusively in CMP, MKP or ERP. Cell cycle genes are significantly differentially expressed between MEP, MKP, and ERP. We therefore tested the effects on MEP fate of genetic and pharmacologic modulation of cell cycle progression, and found that cell cycle activity mechanistically controls MEP fate decisions; cell cycle activation promotes E whereas cell cycle inhibition promotes Mk specification. The data obtained from healthy cells can now be applied to the mechanisms underlying benign and malignant disease states of Mk and E production.

overall_design: To address the heterogeneity of the MEP enriched population, we performed single-cell mRNA sequencing (scRNA-seq) of FACS-enriched MEP, MKP and ERP, and CMP. Specifically, we tested whether MEP have an expression signature that is distinct from CMP, MKP and ERP. Single cells were captured and lysed using the Fluidigm C1 platform and sequenced to more accurately identify and profile the transcriptome of multi-lineage cells. On average, there were 504,984 aligned reads per cell, with an average of 5,028 genes expressed (FPKM>0.1) per cell. We first performed an analysis of the scRNA-seq data from sorted CMP, MEP, MKP and ERP populations from a single PBSC donor (donor-1, n=246 cells). Unsupervised analysis with the recently described ICGS software identified separate major gene expression clusters for each of the sorted populations along with subdivisions of the CMP, MEP, MKP and ERP. To confirm the major gene expression clusters associated with the four sorted populations, we performed scRNA-Seq analysis of cells from a different donor (donor-2, n=294 cells) sorted using a complementary gating strategy, but running 1 plate of MEPs and 1 plate of a mix of 55% MKP and 45% ERP.

first: Nathan

last: Salomonis

first: Juliana

last: Xavier-Ferrucio

first: Lin

last: Wang

first: Ping-Xia

last: Zhang

first: Meenakshi

last: Venkatasubramanian

first: Kashish

last: Chetal

first: Bruce

last: Aronow

first: Diane

last: Krause


title: Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression

status: Public on Nov 01 2018

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

country: USA

institute: Emory University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [RNA-seq]

city: Dublin

first: Gerard

middle: L

last: Brien

address: Lincoln Place Gate

department: Genetics

country: Ireland

institute: Trinity College Dublin

summary: We used a CRISPR-based screening approach to identify functional vulnerabilities in pediatric sarcoma cell types, identifying BRD9 as an important dependency in synovial sarcoma cells.

overall_design: RNA-seq in synovial cells treated with dBRD9A or DMSO for 6hrs, or the same cells expressing control (Renilla) or SS18-SSX1 specific shRNAs.

first: Scott

middle: A

last: Armstrong


title: Nuclear-mitochondrial genetic mismatch elicits an interferon-mediated cellular immune response

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

summary: In this study, we used mRNA-Seq and functional assays to investigate the transcriptomic and cellular responses to nuclear-mitochondrial genetic mismatches using the xenomitochondrial cybrid panel. RNA-Seq revealed a remarkable reprogramming of nuclear gene expression in response to variation in the mitochondrial genome that involved adaptive changes in cellular metabolism and cell cycle regulation. Unexpectedly, we found that nuclear-mitochondrial mismatch elicits a strong interferon-mediated cellular response

overall_design: We have previously generated a panel of rodent xenomitochondrial cybrid cell lines that contain identical nuclear DNA (from the common laboratory strain Mus musculus domesticus) and mtDNA from progressively more divergent species relative to Mus musculus domesticus, including Mus spretus, Mus terricolor (formerly known as Mus dunni), Mus caroli, Mus pahari, Rattus norvegicus or Otomys irroratus, which represent mitochondrial genetic variance spanning 2-12 million years (McKenzie 2003; PMID: 12777531).  In this work, we performed RNA-seq on these lines in triplicate.

first: Isabel

middle: G

last: Lopez Sanchez

first: Matthew

last: McKenzie

first: Annabell

last: Bachem

first: Rahul

last: Makam

first: Sheridan

last: Keene

first: Jonathan

last: Crowston

first: Justin

last: St. John

first: Assam

last: El-Osta

first: Sammy

last: Bedoui

first: Ian

last: Trounce


title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of BRD9, SS18-SSX1 in cells treated with BRD9 targeting degraders. ChIP-seq of steady state profiles of H3K27Ac and RNAPII. ChIP-seq of WT and mutant BRD9 proteins at steady state.


title: Molecular, Spatial and Functional Single-Cell Profiling of the Hypothalamic Preoptic Region

city: Boston

first: Jeffrey

last: Moffitt

state: MA

address: 200 Longwood Ave

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: Single-cell RNA sequencing of ~31,000 cells dissociated and captured from the preoptic region of the hypothalamus from multiple male and female mice

overall_design: Three replicates each of male and female mice

first: Xiaowei

last: Zhuang

first: Catherine

last: Dulac


title: Mice Harboring the Human SLC30A8 R138X Loss-of-Function Mutation Have Increased Insulin Secretory Capacity

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: SLC30A8 encodes a zinc transporter that is primarily expressed in the pancreatic islets of Langerhans. In beta-cells it transports zinc into insulin-containing secretory granules. Loss-of-function (LOF) mutations in SLC30A8 protect against type 2 diabetes in humans. In this study, we generated a mouse model carrying one of the most common human LOF mutations for SLC30A8, R138X. The R138X mice had normal body weight, glucose tolerance and pancreatic beta-cell mass. Interestingly, in hyperglycemic conditions induced by the insulin receptor antagonist S961, the R138X mice showed a 50% increase in insulin secretion. This effect was not associated with enhanced beta-cell proliferation or beta-cell mass. Our data suggest that the SLC30A8 R138X LOF mutation in humans may protect from type 2 diabetes in part by increasing the capacity of beta-cells to secrete insulin.

overall_design: Gene expression profiling of SLC30A8 R138X mutation and wild type mice in pancreatic islets

first: Sandra

last: Kleiner

first: Jesper

last: Gromada


title: Replication maps of RPE-1 cells grown under various conditions

city: New York

first: Duncan

last: Smith

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

summary: Okazaki fragments were purified and sequenced from RPE-1 cells. The sequencing data were used to infer sites and efficiencies of replication initiation and termination.

overall_design: To map sites of replication initiation and termination in RPE-1 cells grown under various conditions

first: Sarah

last: Keegan

first: Tony

last: Huang


title: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma

first: Gerard

last: Brien


title: Gene expression profile of imMKCLs cultured with thrombopoietin (TPO) or TA-316.

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

country: Japan

institute: Nissan Chemical Industries

summary:
We have recently established a self-renewing immortalized megakaryocyte progenitor cell lines (imMKCLs) from hiPSCs, displaying long-term expansion capability with yields of functional platelets (Nakamura et al. Cell Stem Cell, 2014). However, the platelets production using imMKCLs have not been fully sufficient or cost-effective for clinical application, and further improved culture conditions are needed to accomplish the industrialization of hiPSCs-derived platelets. We screened c-MPL agonists and identified TA-316 as the most potent compound that increases platelet productivity using imMKCLs more efficiently and cost effectively as compared to TPO.
Gene microarrays were used to observe the global gene expression in imMKCLs cultured with TPO or TA-316 and identified distinct classes of up or down-regulated genes.

overall_design: imMKCLs were cultured for 11 days with TPO or TA-316.

last: Aihara


title: RNA sequencing data for diffuse gastric cancer

city: Goyang

first: Hark

middle: K

last: Kim

state: Gyeonggi

address: 323 Ilsanro, Ilsan

country: South Korea

institute: National Cancer Center

summary: To identify altered transcriptomic profiles in early-onset diffuse gastric cancer (DGC), we performed RNA sequencing on DGCs collected from 80 young (≤ 45 years) Korean patients who had not been treated with chemotherapy or radiation

overall_design: RNA sequencing analysis of diffuse gastric cancer (DGC)


title: Expression data from miR-142 WT and KO spleen and bone marrow

city: St. Louis

first: Todd

middle: A.

last: Fehniger

state: MO

address: Department of Medicine, Oncology Division

department: Internal Medicine, Oncology Division

institute: Washington University

summary:
miR-142 is critical for the presence of NK cells in the periphery.
Global gene expression analysis of bone marrow and splenic NK cells

overall_design: WT and KO spleen and bone marrow NK cells were subjected to RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the genes differentially expressed that might contribute to our phenotype.

first: Pavin

last: Reddy


title: Septin 9 over expression in MCF7

city: Bronx

first: Cristina

last: Montagna

address: 1301 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: Septin 9 (SEPT9), a member of the septin gene family, is strongly linked to cancer, particularly breast cancer, where genomic amplification occurs in ~11% of cases. SEPT9 is a putative oncogene as it is amplified in the form of double minute chromosomes in murine models of breast cancer, is a fusion partner of mixed lineage leukemia (MLL) gene in leukemia, and it is a known hot spot of retroviral tagging insertion. SEPT9 contributes to cytoskeleton dynamics, thus oncogenic functions have been proposed based on the broad range of cellular functions it partakes. Yet, a clear mechanism by which SEPT9 elicits tumor-promoting functions is lacking. To obtain unbiased insights on molecular signatures of SEPT9 upregulation in breast tumors, we overexpressed several of its isoforms in breast cancer cell lines. Global transcriptomic profiling supports a role of SEPT9 in invasion. Functional studies indicate that SEPT9 upregulation is sufficient to increase degradation of the extracellular matrix, while its downregulation inhibits this process. The degradation pattern is associated with focal adhesions (FA) at the cell periphery. Increased extracellular matrix digestion during epithelial–mesenchymal transition digestion is significantly associated with increased expression of matrix metalloproteinases. In SEPT9 over expressing cells, MMP3 is secreted to the media at FAs. Downregulation of SEPT9 or chemical inhibition of septin filaments assembly impairs recruitment of MMP3 to FAs. Our results indicate that SEPT9 promotes both trafficking and secretion of MMPs near FAs, thus enhancing migration and invasion of breast cancer cells.

overall_design: MCF7_SEPT9_v1, MCF7_SEPT9_v2, and MCF7_SEPT9_v3-overexpressing cell lines and the MCF7 control cells (MCF7_C) were used. A total of 12 samples were used for RNA-Seq analysis (three biological replicates from each of the MCF-7 isoforms and control cells).

first: Michal

last: Bejerano-Sagie

first: Jenna

last: Zechmeister-Marcus


title: Gene expression profiling of the olfactory tissues from sex-separated and sex-combined female and male mice

city: Aurora

first: Stephen

middle: William

last: Santoro

state: Colorado

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

summary: We sought to investigate the scope of cellular and molecular changes within a mouse’s olfactory system as a function of its exposure to odors emitted from members of the opposite sex. To this end, we housed mice either separated from members of the opposite sex (sex-separated) or together with members of the opposite sex (sex-combined) until six months of age and then profiled transcript levels within the main olfactory epithelium (MOE), vomeronasal organ (VNO), and olfactory bulb (OB) of the mice via RNA-seq. For each tissue type, we then analyzed gene expression differences between sex-separated males and sex-separated females (SM v SF), sex-combined males and sex-combined females (CM v CF), sex-separated females and sex-combined females (SF v CF), and sex-separated males and sex-combined males (SM v CM). Within both the MOE and VNO, we observed significantly more numerous gene expression differences between males and females when mice were sex-separated as compared to sex-combined. Chemoreceptors were highly enriched among the genes differentially expressed between males and females in sex-separated conditions, and these expression differences were found to reflect differences in the abundance of the corresponding sensory neurons.

overall_design: For each combination of tissue (MOE, VNO, OB), sex (F, M), and condition (sex-separated [S], sex-combined [C]), we generated three biological replicate samples of RNA, each of which contained equal quantities of RNA from two different mice. This resulted in a total of 36 samples.

middle: W

first: Susanne

last: Jakob


title: Dioxin and AHR impairs mesoderm gene expression and cardiac differentiation in human embryonic stem cells

status: Public on Oct 31 2018

city: Research Triangle Park

first: Guang

last: Hu

state: NC

address: 111 TW Alexander DR

department: ESCBL

institute: National Institute of Environmental Health Sciences

first: Hualing

last: Fu


title: Dioxin and AHR impairs mesoderm gene expression and cardiac differentiation in human embryonic stem cells (RNA-Seq)

summary: Dioxin and dioxin-related polychlorinated biphenyls are potent toxicants with association with developmental heart defects and congenital heart diseases. However, the underlying mechanism of their developmental toxicity is not fully understood. Further, different animals show distinct susceptibility and phenotypes after exposure, suggesting possible species-specific effects. Using a human embryonic stem cell (ESC) cardiomyocyte differentiation model, we examined the impact, susceptible window, and dosage of 2,3,7,8‑tetrachlorodibenzo‑p‑dioxin (TCDD) on human cardiac development. We showed that treatment of human ESCs with TCDD at the ESC stage inhibits cardiomyocyte differentiation, and the effect is largely mediated by the aryl hydrocarbon receptor (AHR). We further identified genes that are differentially expressed after TCDD treatment by RNA-sequencing, and genomic regions that are occupied by AHR by chromatin immunoprecipitation and high-throughput sequencing. Our results support the model that TCDD impairs human ESC cardiac differentiation by promoting AHR binding and repression of key mesoderm genes. More importantly, our study demonstrates the toxicity of dioxin in human embryonic development and uncovered a novel mechanism by which dioxin and AHR regulates lineage commitment. It also illustrates the power of ESC-based models in the systematic study of developmental toxicology.

overall_design: RNA-Seq profiling to identify genes that are differentially expressed in ESC and mesoderm after ESC stage TCDD exposure


title: Identification of regulatory elements from nascent transcription using dREG

city: Ithaca

first: Charles

last: Danko

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

summary: Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified by their distinctive patterns of transcription initiation. We previously introduced dREG to identify TIRs using PRO-seq data. Here we introduce an efficient new implementation of dREG that uses PRO-seq data to identify both uni- and bidirectionally transcribed TIRs with 70% improvements in accuracy, 3-4-fold higher resolution, and >100-fold increases in computational efficiency. Using a novel strategy to identify TIRs based on their statistical confidence reveals extensive overlap with orthogonal assays, yet also reveals thousands of additional weakly-transcribed TIRs that were not identified by H3K27ac ChIP-seq or DNase-I-hypersensitivity. Novel TIRs discovered by dREG were often associated with RNA polymerase III initiation or bound by transcription factors that recognize DNA concurrently with a nucleosome. We provide a web interface to dREG that can be used by the scientific community (http://dREG.DNASequence.org).

overall_design: We report the development of dREG, a sensitive machine learning tool to identify transcriptional regulatory elements in a sample of interest.

first: Lauren

last: Choate

first: Edward

middle: J

last: Rice


title: Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells

city: Nashville

first: James

last: Patton

state: Tennessee

address: Biological Sciences, Vanderbilt University

department: Department of Biological Sciences

institute: Vanderbilt University

summary: Long RNA-seq analysis on cellular and extracellular samples from a KRAS mutant colorectal cancer cell model, in association with Hinger et al 2018

overall_design: Biological triplicates of 3 exosome RNA samples with biological triplicates of 6 cellular RNA samples. Cellular samples are submitted as biological triplicates of 3 RNA samples, with either no treatment or treatment with ionomycin. All samples are derived from 3 distinct colorectal cancer cell lines dependent of KRAS status of the cells. These include WT/- (DKs8), WT/MUT (DLD1), and -/MUT (DKO1).

first: Scott

last: Hinger

first: Diana

last: Cha

first: Jeffrey

last: Franklin

middle: N

last: Higginbotham

first: Yongchao

last: Dou

first: Jie

last: Ping

first: Lihua

last: Shu

first: Nripesh

last: Prasad

first: Bing

last: Zhang

first: Qi

last: Liu

first: Alissa

middle: M

last: Weaver

first: Robert

last: Coffey


title: Single-cell RNA sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: We use single-cell RNA sequencing (scRNA-seq) to explore the transcriptional changes associated with estrogen-induced dysplasia in mouse ovarian surface epithelial cells

overall_design: scRNA-seq of control and estrogen-treated (100nM) mOSE cultured for 15 days. scRNA-seq was performed using the Fluidigm HT 3' RNA-seq protocol on the Fluidigm C1

middle: P

first: Barbara

middle: C

last: Vanderhyden


title: Sensory Food Perception Rapidly Primes Postprandial ER-Homeostasis through Melanorcortin-Dependent Control of Liver mTOR Activation

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Adaptation of liver to the postprandial state requires coordinate regulation of protein synthesis and folding aligned with changes in lipid metabolism. Here we demonstrate that sensory food perception is sufficient to elicit early activation of hepatic mTOR-signaling, Xbp1-splicing, increased expression of ER-stress genes and phosphatidylcholine synthesis, which translate into a rapid morphological ER-remodeling. These responses overlap with those activated during refeeding, where they are maintained and constantly increase upon nutrient supply. Sensory food perception activates POMC-neurons in the hypothalamus, optogenetic activation of POMC-neurons activates hepatic mTOR-signaling and Xbp1-splicing and lack of MC4R-expression attenuates these responses to sensory food perception. Chemogenetic POMC-neuron activation promotes sympathetic nerve activity (SNA) subserving the liver, and norepinephrine evokes the same responses in hepatocytes in vitro and liver in vivo as observed upon sensory food perception. Collectively, our experiments unravel that sensory food perception coordinatly primes postprandrial liver ER adaption through a melanocortin-SNA-mTOR-Xbp1s-axis

overall_design: In total 60 independent samples were analyzed. Three biological replicates were measured. Three conditions: fasted, refed, caged. For refed and caged 4 times (30,60,120,240 min) were analyzed.

first: Claus

last: Brandt

first: Hendrik

last: Nolte

first: Sinika

last: Henschke

first: Linda

middle: E

last: Ruud

first: Motoharu

last: Awazawa

first: Donald

last: Morgan

first: Paula

last: Gabel

first: Hans-Georg

last: Sprenger

first: Martin

last: Hess

first: Thomas

last: Langer

first: Kamal

last: Rahmouni

first: Henning

last: Fenselau

first: Marcus

last: Krüger

first: Jens

last: Brüning


title: CHD7 is Suppressed in the Perinecrotic/Ischemic Microenvironment and is a Novel Regulator of Angiogenesis

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

summary: In a study focused on the role for CHD7 in angiogenesis we completed RNA-sequencing of D456, a glioblastoma xenograft line and neural precursor cells after CHD7 knockdown

overall_design: RNA-sequencing after shRNA KD of CHD7 in two cell lines

first: S

first: A

middle: B

last: Hjelmeland


title: Transcriptome analyses of somatotropes and lactotropes reveal novel regulators of cell identity in the pituitary

city: Philadelphia

first: Michael

middle: Thomas

last: Peel

state: PA

address: 415 Curie Blvd.

institute: University of Pennsylvania

summary: The differentiation of the hormone-producing cell lineages of the anterior pituitary represents an informative model of mammalian cell fate determination. The generation and maintenance of two of these lineages, the growth hormone (GH) producing somatotropes and prolactin (PRL) producing lactotropes, is dependent on the pituitary-specific POU-homeo domain transcription factor, POU1F1. While POU1F1 is expressed in both cell types, and plays a direct and essential role in the activation of both the Gh and Prl genes, GH expression is restricted to somatotropes and PRL expression is restricted to lactotropes. These observations imply the existence of additional, cell type-enriched factors, that contribute to the somatotrope and lactotrope cell identities. Here, we use a set of transgenic mouse models to facilitate sorting of somatotrope and lactotrope populations based on the expression of distinct fluorescent markers expressed under Gh and Prl gene transcriptional controls, respectively. The transcriptomic analyses reveal a concordance of gene expression profiles in the two populations. The limited number of divergent mRNAs between the two populations includes a set of transcription factors that may have roles in pituitary lineage divergence or in regulating the expression of key lineage-specific genes after lineage divergence. Four of these factors were validated for lineage enrichment at the level of protein expression, two somatotrope-enriched and two lactotrope-enriched, and three of these four factors were shown to have corresponding activities in appropriate enhancement or repression of landmark genes. These studies establish a useful database for further study of the somatotrope and lactotrope cells as well as identify novel regulators of lineage marker expression in the anterior pituitary.

overall_design: 6 total samples, 3 biological replicates of the somatotrope cell type and 3 biological replicates of the lactotrope cell type

middle: T

first: Stephen

last: Liebhaber


title: Long non-coding RNA FAM83H-AS1 is regulated by human papillomavirus 16 E6 independently of p53 in cervical cancer cells

city: Morgantown

first: Ivan

last: Martinez

state: WV

address: 1838 MBRCC PO Box 9300

department: Microbiology / Cancer Center

institute: West Virginia University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Global long non-coding RNA (lncRNA) expression profile in primary human keratinocytes post-expression of high-risk HPV-16 E6 oncoprotein
Purpose: The goal of this study is to utlize high-throughput RNA sequencing (RNA-seq) to identify differentially expressed host lncRNAs with the presence of the high-risk HPV-16 E6 oncoprotein in primary human foreskin keratinocytes.
Methods: Primary human foreskin keratinocytes (HEKa) stably expressing HPV-16 E6 compared to GFP control were analyzed, in triplicates, by RNA-seq (Illumina). qRT-PCR validation was performed using SYBR Green assays.
Results: 151 up- and 100 down-regulated host lncRNAs were altered greater than 1.5-fold change in HEKa expressing HPV-16 E6 compared to GFP control cells. Altered expression of 16 genes (8 up- and 8 down-regulated) were confirmed by qRT-PCR, demonstrating the high-degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first global screening of host lncRNAs altered specifically by HPV-16 E6 oncoprotein expression.

overall_design: Host lncRNA profiles of HEKa stably expressing HPV-16 E6 compared to control cells were generated, in triplicate, and analyzed by RNA-seq (Illumina).

first: Jamie

last: Barr

first: Karen

last: Hayes


title: Profiling of vascular organoid endothelial cells and pericytes from iPS cells

city: Vienna

first: Reiner

last: Wimmer

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: Diabetes is prevalent worldwide and associated with severe health complications, including blood vessel damage that leads to cardiovascular disease and death. Here we report the development of a 3D blood vessel organoid culture system from human pluripotent stem cells. These human blood vessel organoids contain endothelial cells and pericytes that self-assemble into interconnected capillary networks enveloped by a basement membrane. Human blood vessel organoids transplanted into mice form a stable, perfused human vascular tree, including human arteries, arterioles and venules. Exposure of blood vessel organoids to hyperglycemia and inflammatory cytokines in vitro induced thickening of the basal membrane, a hallmark of human diabetic microangiopathy. Human blood vessel, exposed in vivo to a diabetic milieu in mice, also mimick the microvascular changes in diabetic patients. We finally performed a drug screen and uncovered γ-secretase and DLL4-Notch3 as key drivers of “diabetic” vasculopathy in human blood vessels in vitro and in vivo. Thus, organoids derived from human stem cells faithfully recapitulate the structure and function of human blood vessels and are amenable to model and identify drug targets for diabetic vasculopathy, which affects hundreds of millions of patients.

overall_design: Vascular organoids were differentiated from iPSC cells and cultured in control, diabetic or diabetic media supplemented with the gamma-secretase inhibitor DAPT. Endothelial cells (CD31 positive) and pericytes (PDGFRbeta positive) were isolated by FACS and subjected to RNA Seq. Accordingly, CD31 positive endothelial cells and PDGFRbeta positive pericytes differentiated from iPS cells in 2D as a well as primary endothelial (HUVECS) and pericytes (Placenta) were FACS sorted and subjected to RNA Seq.

first: Josef

last: Penninger


title: Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification

first: dario

last: nicetto

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

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

overall_design: Refer to individual Series


title: Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification (srHC-seq)

summary: Domains of transcriptionally repressed heterochromatin, decorated by histone 3 lysine 9 trimethylation (H3K9me3), are reduced in embryonic stem cells compared to fully differentiated cells. However, the establishment and dynamics of closed regions of chromatin at protein coding genes, in natural embryologic development, has not been described. We developed a novel, antibody-independent method to isolate and map compacted heterochromatin from low cell number samples. Unexpectedly, we uncovered extensive high levels of H3K9me3-decorated, compacted heterochromatin at protein coding genes in early, uncommitted cells in the three germ layers, undergoing profound rearrangements and reduction upon differentiation, concomitant with cell type-specific gene expression. Perturbation of the three H3K9me3-related methyltransferases revealed that H3K9me3 heterochromatin is required to maintain cell lineage fidelity. We propose a key role for chromatin-based restriction of gene activity via H3K9me3 during embryologic development

overall_design: Study is an analysis by sonication resistant heterochromatin seq (srHC-Seq) of pancreatic and hepatic development, with a trajectory including definitive endoderm (e8.25 ENDM1+), adult hepatocytes as well as mature beta cells (8 week INS-RFP+); Ctrl and TKO 1 month old livers; each stage has two replicates; ENDM1+ is treated for some analyses as a baseline condition

first: Dario

last: Nicetto

first: Greg

last: Donahue

first: Tanya

last: Jain

first: Tao

last: Peng

first: Simone

last: Sidoli

first: Lihong

last: Sheng

last: Montavon

first: Justin

middle: S

last: Becker

first: Jessica

last: Grindheim

first: Kimberly

last: Blahnik

first: Benjamin

last: Garcia

first: Kai

last: Tan

first: Roberto

last: Bonasio

last: Jenuwein

first: Kenneth

last: Zaret


title: Transcriptome-wide mapping of RNA:protein interactions of three SR proteins in HeLa cells

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

institute: Goethe University Frankfurt


title: Dioxin and AHR impairs mesoderm gene expression and cardiac differentiation in human embryonic stem cells (ChIP-Seq)

first: Guang

last: Hu

overall_design: Chromatin immunoprecipitation and sequencing was performed to discover the genomic regions that are occupied by AHR after TCDD exposure

first: Hualing

last: Fu


title: Transcriptome-wide mapping of RNA:protein interactions of three SR proteins in HeLa cells by iCLIP

summary: We used GFP-tagged SR proteins expressed at endogenous levels and iCLIP to compare the extent and pattern of SR protein binding to expression-matched lincRNAs and protein-coding RNAs

overall_design: For each GFP-tagged SR protein,  3-4 biological replicates were subjected to the iCLIP procedure with UV-crosslinking at 254 nm. An anti-GFP antibody as used for IPs.


title: WT HeLa total RNA-seq (RiboMinus)

summary: We sequenced total RNA from HeLa WT cells to quantify the expression of protein-coding mRNAs and lincRNAs. RPKM values were used to normalize iCLIP binding to RNA abundance.

overall_design: total RNA after rRNA removal (RiboMinus), 2 biological replicates


title: Loss of H3K9me3 heterochromatin at protein coding genes enables developmental lineage specification  (RNA-Seq)

first: dario

last: nicetto

overall_design: Study is an analysis by RNA-seq of pancreatic and hepatic development, with a trajectory including definitive endoderm (e8.25 ENDM1+), hepatic precursor (e10.5 Liv2+), and adult hepatocytes as well as pancreatic precursor (e10.5 PDX1+), immature beta cells (e18.5 INS-RFP+) and mature beta cells (8 week INS-RFP+); Ctrl and TKO 1 month old livers; each stage has two replicates; ENDM1+ is treated for some analyses as a baseline condition

last: Nicetto

last: Donahue

first: Thomas

middle: A


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild-type (WT) and Uba3fl/fl-Lck Cre+ (KO) splenic CD44hiCD4+ T cell transcriptomes

city: Beijing

first: Qianqian

last: Cheng

address: 27 Taiping Road

department: Department of Molecular Immunology

country: China

institute: Institute of Basic Medical Sciences

summary: We analyze the impact of T cell-specific deletion of Uba3 gene on CD4+ T cell responses during Plasmodium infection using the RNA-seq techonology. We isolated CD44hiCD4+ T cells in spleens from wild-type (WT) and Uba3fl/fl-LckCre+ (KO)mice at day 5 of Plasmodium yoelii 17XNL infection. RNA samples were prepared for deep-sequencing on an Illumina Hiseq platform and 150 bp paired-end reads were generated.Quanlity control was performed to generate high quality data for further analysis.By comparing gene expression levels of different CD4+ T cell lineages, we observed defects in the expression of several signature genes that related to Th1 and Tfh responses in KO mice.

overall_design: Splenic CD44hiCD4+ T cell mRNA profiles of day 5 Plasmodium yoelii 17XNL-infected wild-type (WT) and Uba3fl/fl-Lck Cre+ (KO) mice were generated by deep sequencing using Illumina Hiseq platform.

first: Jiyan

last: Zhang


title: Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. [RNA-seq]

city: Montréal

first: Gregor

middle: Ulrich

last: Andelfinger

state: QC

address: 3175, Chemin de la Côte-Sainte-Catherine

department: Cardiology

institute: CHU Sainte-Justine

summary: RNA sequencing of human dermal fibroblasts from CAID patients passage 8 and passage 14

overall_design: RNA sequencing was perfomed on 3 wild type controls and 3 CAID patients fibroblast cell lines at cell passages 8 and 14. Sequencing was performed on Illumina Hiseq4000, 8 samples/lanes, paired-end.

first: J

last: Piché

first: G


title: Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. [BiSulfite-seq]

type: Methylation profiling by high throughput sequencing

summary: RRBS of human dermal fibroblasts from CAID patients passage 8 and passage 14

overall_design: RRBS was perfomed on 3 wild type controls and 3 CAID patients fibroblast cell lines at cell passages 8 and 14. Sequencing was performed on Illumina Hiseq2500, 6 samples/lanes, paired-end.


title: Identification of Sin3B regulated genes during quiescence

city: New York

first: Gregory

last: David

address: 550 1st Avenue, 411

department: Biochemistry and Molecular Pharmacology

institute: New York University School of Medicine

summary: We report differences in gene expression between WT and Sin3B KO T98G cells throughout the cell cycle

overall_design: T98G WT and Sin3B KO cells were serum starved for 72 hours and then released into serum and at designated time points cells were harvested in duplicate for RNA-sequencing.

first: Anthony

last: Bainor


title: Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. [ATAC-seq]

summary: ATAC_seq of human dermal fibroblasts from CAID patients passage 8 and passage 14

overall_design: ATAC_seq was perfomed on 3 wild type controls and 3 CAID patients fibroblast cell lines at cell passages 8 and 14. Sequencing was performed on Illumina Hiseq2500, 6 samples/lanes, paired-end.


title: Differential gene expression between wild type and Wnt11 mutant embryonic kidneys

city: Chapel Hill

first: Lori

last: O'Brien

state: North Carolina

address: 111 Mason Farm Road

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

summary: The goal of this study was to identify changes in gene expression within nephron progenitors and the whole embryonic kidney between Wnt11 mutants and wild type animals. Wnt11 mutant kidneys have disorganized nephron progenitor niches. Ultimately, nephron endowment is reduced by 50% in Wnt11 mutants. Gene expression changes are minimal between mutant and wild type samples, suggesting Wnt11 may act through non-canonical, non-transcritional mechanisms to regulate kidney development.

overall_design: Total RNA was isolated from either E15.5 whole kidneys or Six2+GFP+ FACS-isolated kidney nephron progenitors. Wnt11 homozygous mutant kidneys were compared to wild type controls. Wnt11tm1a animals were crossed to the Six2TGC transgenic line in order to label and isolate GFP+ nephron progenitors. For the FACS isolated cells, three biological replicates for each group (Wild type vs. Mutant) were collected. For whole kidneys, six biological replicates from each group were collected. Samples represent a mix of female and male animals. Isolated RNA was subjected to high throughput sequencing analyses to identify differentially expressed transcripts.

middle: L

first: Peter

middle: H

last: Whitney

first: Andrew

last: McMahon


title: Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics.


title: Affymetrix analysis for host cells transcriptome

status: Public on Oct 30 2018

first: Dirk

last: Dittmer

address: 450 West Dr

department: Microbiology and Immunology

summary: Analyze possible changes in the transcriptome of host cell line infected with a recombinant EBV virus.  The recombinant virus is an Akata cell-derived NeoR EBV strain, previously used in PMID: 12969959

overall_design: 6 samples analyzed. Parental KSHV-infected Primary effusion lymphoma (PEL) cell lines or KSHV and EBV-infected PEL cells.

first: Rachele

last: Bigi

first: Justin

last: Landis

first: Hyowon

last: An

first: Carolina

last: Caro-Vegas

first: Nancy

last: Raab-Traub


title: Genome-wide chromatin accessibility and transcriptome profiling shows that minimal epigenome changes lead to coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

institute: University of Michigan


title: Genome-wide chromatin accessibility and transcriptome profiling shows that minimal epigenome changes lead to coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice (RNA-seq)

summary: Danforth’s short tail (Sd) mice provide an excellent model for investigating the underlying etiology of human caudal birth defects, which affect 1 in 10,000 live births. Sd animals exhibit aberrant axial skeleton, urogenital, and gastrointestinal development similar to human caudal syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. Previous studies have shown that the Sd mutation results from an endogenous retroviral (ERV) insertion upstream of the Ptf1a gene causing its ectopic expression at E9. Though the genetic lesion has been determined, the resulting epigenomic and transcriptomic changes driving the phenotype have not been investigated. Here, we performed ATAC-seq experiments on isolated E9.5 tailbud tissue revealing localized changes in chromatin accessibility in Sd/Sd mutant embryos. Interestingly, chromatin changes were localized to a small genomic sequence overlapping a Ptf1a enhancer region, which is conserved in both mouse and humans. Furthermore, mRNA-Seq experiments revealed increased transcription of Ptf1a target genes and, importantly, the downregulation of the hedgehog pathway genes. Reduced Sonic hedgehog signaling (Shh) was confirmed by both in-situ hybridization and immunofluorescence experiments indicating that the Sd mutation may result, in part, from downregulated Shh signaling. Taken together these data indicate that human caudal dysgenesis disorders may result from dysregulation of hedgehog signaling pathways. Thus it will be important to investigate how epigenome and transcriptome alterations result in hedgehog pathway disruption.

overall_design: RNA-seq was performed on DNA isolated from the tailbuds of E9.5 WT and homozygous Danforth mutant mice (n = 3 per group). Tailbuds from 2 mice were pooled when necessary to ensure sufficient input material.

last: Orchard

first: James

last: White

first: Peedikayil

last: Thomas

first: Anna

last: Mychalowych

first: Anya

last: Kiseleva

first: John

last: Hensley

first: Benjamin

last: Allen

first: Catherine

last: Keegan


title: Genome-wide chromatin accessibility and transcriptome profiling shows that minimal epigenome changes lead to coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s short tail mice (ATAC-seq)

overall_design: ATAC-seq was performed on DNA isolated from the tailbuds of E9.5 WT and homozygous Danforth mutant mice (n = 4 per group). Tailbuds from 2 mice were pooled when necessary to ensure sufficient input material.


title: miRTrace quality control of small RNA-Seq data prepared from low-input, degraded and contamianted HEK-293T RNA samples

city: Solna

first: Wenjing

last: Kang

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

summary: miRTrace is a tool for quality control and tracing taxonomic origins of microRNA sequencing data. It operates in two modes: Trace mode, in which the software reports the composition of clade-specific miRNAs; and QC mode, in which it performed an all-round quality control. To validate the QC mode of the software, we subjected the in-house control samples from HEK-293T cells to various treatments, such as cross-species contamiantion with Drosophila S2 RNAs, sample dilution and RNase A digestion. These samples were processed using QC mode of miRTrace. We demonstrate that miRTrace accurately identities poor-quality samples and to some extent even the causes of the compromised quality.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: miRTrace quality control profiles of standard HEK-293T and Drosophila S2 samples (with 1000 ng total RNA as input) and compromised HEK-293T samples that are contaminated with S2 RNAs in ratio 10:1, 100:1 and 1000:1, diluted to 50 ng and degraded with RNase A enzyme.

first: Yrin

last: Eldfjell

first: Bastian

last: Fromm

first: Xavier

last: Estivill

first: Inna

last: Biryukova

first: Marc

middle: R

last: Friedländer


title: Increased Hematopoietic Extracellular RNAs and Vesicles in the Lung during Allergic Airway Responses

city: San Francisco

first: Heather

last: Pua

state: CA

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

summary: Extracellular RNAs (exRNAs) can be released by numerous cell types in vitro, are often protected within vesicles, and can modify recipient cell function. To determine how the composition and cellular sources of exRNAs and the extracellular vesicles (EVs) that carry them change in vivo during tissue inflammation, we analyzed bronchoalveolar lavage fluid (BALF) from mice before and after lung allergen challenge. In the lung, extracellular microRNAs (ex-miRNAs) had a composition highly correlated with airway lining epithelium. Using cell-type specific membrane tagging and single vesicle flow, we also found that 80% of detected vesicles were of epithelial origin. After the induction of allergic airway inflammation, miRNAs selectively expressed by immune cells, including miR-223 and miR-142a, increased and hematopoietic cell derived EVs also increased >2-fold. Together these data demonstrate that infiltrating immune cells release ex-miRNAs and EVs in inflamed tissues to alter the local extracellular environment.

overall_design: Expression analysis of extracellular miRNAs from biofluids (airway lining fluid and serum) and miRNAs from cells in the lung (airway immune cells and pulmonary epithelium) during airway allergic responses in a mouse model of asthma.

first: Karl

last: Ansel


title: Exploring the Genetic Basis of Human Population Differences in DNA Methylation and their Causal Impact on Immune Gene Regulation

city: Paris

first: Lucas

middle: Theo

last: Husquin

state: --- Select a state ---

address: 28 rue du docteur Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

summary: Background: DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA methylation, its genetic determinants, and their respective causal impact on immune gene regulation remain elusive.  Results: We report extensive population differences in DNA methylation between 156 individuals of African and Europeandescent —detected in primary monocytes that were used as a model of a major innate immunity cell type. Most of these differences (~70%) were driven by DNA sequence variants nearby CpG sites (meQTLs), which account for ~60% of the variance in DNA methylation. We also identify several master regulators of DNA methylation variation in trans, including a regulatory hub nearby the transcription factor-encoding CTCF gene, which contributes markedly to ancestry-related differences in DNA methylation. Furthermore, we establish that variationin DNA methylation isassociated with varying gene expression levelsfollowing mostly, but not exclusively, a canonical model of negative associations, particularly in enhancer regions. Specifically, we find that DNA methylation highly correlates with transcriptional activity of 811 and 230 genes, at the basal state and upon immune stimulation, respectively. Finally, using a Bayesian approach, we estimate causal mediation effects of DNA methylation on gene expression in ~20% of the studied cases, indicating that DNA methylation can play an active role in immune gene regulation.  Conclusion: Using a system-level approach, our study reveals substantial ancestry-related differences in DNA methylation and provides evidence for their causal impact on immune gene regulation.

overall_design: 156 Samples analyzed, 78 of African descent and 78 of European descent. Replicates are not included

first: Maxime

last: Rotival

first: Maud

last: Fagny

first: Hélène

last: Quach

first: Nora

last: Zidane

first: Lisa

last: McEwen

first: Julia

last: MacIsaac

first: Michael

last: Kobor

first: Hugues

last: Aschard

first: Etienne

last: Patin

first: Lluis

last: Quintana-Murci


title: Gene regulation of PHF6 in mouse developing cortex

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: we performed RNAseq between WT/KO and WT/C99F to understand the function of PHF6 in gene regulation

overall_design: RNAseq for WT, KO and C99F cortex at p0

first: Cheng

last: Cheng


title: Reciprocal Reprogramming of Cancer Cells and Associated Mesenchymal Stem Cells in Gastric Cancer.

city: Haifa

first: Maty

last: Tzukerman

address: Efron, 1

department: Faculty of Medicine

country: Israel

institute: Technion

summary: We utilized gastric cancer cells (GSC1) to demonstrate subversion of naïve Mesenchymal Stem Cells (MSC) from adjacent tissue, which are reprogrammed to express a tumor-promoting phenotype, whose cardinal manifestation is to sustain cancer stem cells. Paracrine effects of such primed MSC are sufficient to enable 2D growth of GSC1, while cell-cell interactions are necessary for 3D growth or in vivo tumor formation. Increased expression of R-spondin in primed MSC mediated elevation of Lgr5 expression in GSC1, activation of the WNT/β-catenin signaling pathway and translocation of β-catenin into the nucleus of most Lgr5 positive cells. Subversion of MSC in the tumor microenvironment (TME) by cancer cells, appears to be a prominent means to sustain the cancer stem cell underpinning of tumor progression.

overall_design: Examination of the alteration in gene expression in naïve MSC recruited into the tumor site by the cancer cells and reprogramming them into a tumor promoting stroma. Alterations were identified in the original tumor-derived MSC to identify the mechanism of sustaining tumor grow and maintenance of stemness properties in the cancer cells by the tumor stromal MSC.

first: Yeela

last: Shamai

first: Dalia

last: Cohen Alperovich

first: Zohar

last: Yakhini

last: Skorecki


title: Characterization of H3K4me3 histone modifications in intestinal epithelial cells among healthy controls and newly-diagnosed pediatric Crohn's disease patients.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: We report profiling of H3Kme3 histone modifications in intestinal epithelial cells from ileal endoscopic biopsies obtained from healthy controls and newly-diagnosed Crohn's disease (CD).  We identified 1066 shared sites, corresponding to 1038 genes with increased H3K4me3 in CD, and 539 sites corresponding to 548 genes with reduced H3K4me3 in CD.

overall_design: We examine chromatin H3Kme3 modifications through ChIP-seq of intestinal epithelial cells harvested from ileal endoscopic biopsies obtained from healthy controls and newly-diagnosed Crohn's patients.

first: Karns

last: Rebekah

first: Alenghat

last: Theresa

first: Kelly

last: Daniel


title: Transcriptomic profile of intestinal epithelial cells obtained from ileal endoscopic biopsies from newly-diagnosed, pediatric Crohn's disease patients and healthy controls.

summary:
Purpose: To uncover differentially-regulated transcripts and pathways/biological processes in newly-diagnosed, pediatric Crohn's disease in comparison to healthy controls.
Methods: Intestinal epithelial cells were dissociated from ileal endoscopic biopsies, and stored at -80C in RNAlater.  The polyA RNA fraction was purified, and single-end, 50 bp reads were sequenced and aligned to the Hg19 genome using the TopHat2 aligner.  Differential analysis was performed using Bioconductor packages including edgeR, where significance was defined as p<0.05 and fold change>2.
Results: We obtained 15788 reasonably-expressed transcripts that were included in differential analyses.
Conclusions: Our study characterizes the dysregulation of intestinal epithelial cells in treatment-naïve Crohn's disease using RNA sequencing for transcriptomic profile of cells obtained through ileal endoscopic biopsies.

overall_design: mRNA profiles of intestinal epithelial cells obtained from newly-diagnosed ileal biopsies in healthy controls and newly-diagnosed Crohn's disease.


title: Determination of branch point (BP) usage by wild-type and mutant SF3B1 using a minigene library

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

summary: We address define differential usage of branchpoint (BP) in by wild-type SF3B1  SF3B1-K700E using a synthetic mini-gene synthetic library with variable 3' spice sites (3'SS).  Minigene-specific libraries were prepared and sequenced on the illumina platform to determine differnces in splice-site usage.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: Minigene-based analysis of differential splicing

first: Manoj

last: Pillai

first: Kiran

last: Paul

first: Abhishek

middle: K

last: Gupta


title: Transcriptome analysis of Group 3 and 4 medulloblastoma orthotopic xenograft mice with digoxin treatment

city: Houston

first: LEI

last: HUANG

state: TX

department: Systems medicine and Bioengineering

institute: Houston Methodist Research Institute

summary: RNA-seq data of Group 3 and 4 medulloblastoma with digoxin treatment.

overall_design: Investigate the differential expressed genes in Group 3 and 4 Medulloblastoma under digoxin treatment

first: Lei

last: Huang


title: RNA-Seq analysis of bone marrow and splenic erythroid cells

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

summary: The gene expression profiles of steady-state bone marrow erythroid cells and UVB/tumor-induced splenic erythroid cells are compared by RNA-Seq analysis.

overall_design: Erythroid cells were purified from the steady-state bone marrow and from the spleens of UVB-irradiated or tumor-bearing mice by using anti-CD71 magnetic beads and subjected to RNA-Seq analysis.

first: Yasuyo

last: Sano

first: Jin-Mo


title: COX2 Induction in the Ovarian Epithelium Promotes Cell Survival During Ovulatory Wound Repair

city: Ottawa

first: David

last: Cook

address: 501 Smyth Rd

institute: Ottawa Hospital Research Institute

summary: We leverage RNA sequencing to identify the transcriptional changes assocaited with a TGFB1-induced epithelial-mesenchymal transition in the mouse ovarian surface epithelium

overall_design: RNA sequencing of mOSE cells treated with 10ng/mL TGFB1 or an untreated control (n=3)

first: Lauren

last: Carter

first: Barbara

last: Vanderhyden


title: Small RNA non-coding landscape of extracellular vesicles from human stem cells

city: Helsinki

first: Sippy

last: Kaur

address: PO Box 63

department: Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

summary: In this study, we used RNA sequencing to provide a comprehensive overview of the expression profiles of small non-coding transcripts carried by the extracellular vesicles (EVs) derived from human adipose tissue stromal/stem cells (AT-MSCs) and human pluripotent stem cells (hPSCs), both human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSC). Small non-coding RNA sequencing from EVs showed that the profile of miRNA expression in PSC follow the profile reported for cell derived miRNA; further, most abundant miRNAs were found to originate from specific miRNA families which are regulating pluripotency, reprograming and differentiation (miR-17–92, mir-200, miR-302/367, miR-371/373, CM19 microRNA cluster). For the AT-MSCs, the highly expressed miRNAs were found to be regulating osteogenesis (mir-let-7/98, miR-10/100, miR-125, miR-196, miR-199, miR-615-3p, mir-22-3p, mir-24-3p, mir-27a-3p, mir-193b-5p, mir-195-3p). Additionally, abundant small nuclear and nucleolar RNA were detected in PSCs, whereas Y- and tRNA were found in AT-MSCs. Identification of EV-miRNA and non-coding RNA signatures released by these stem cells will provide clues towards understanding their role in intracellular communications, and well as their roles in maintaining the stem cell niche.

sample_organism:
Homo sapiens
other sequences

platform_organism:
Homo sapiens
other sequences

overall_design: Small non-coding RNA profiles of extracellular vesicles derived from adipose tissue stromal/stem cells (AT-MSCs) and human pluripotent stem cells (hPSCs) generated by next-generation sequencing.

first: Ahmed

middle: G

last: Abu-Shahba

first: Riku

middle: O

last: Paananen

first: Hanna

last: Hiidenmaa

first: Heidi

last: Hongisto

first: Heli

last: Skottman

first: Riitta

last: Seppänen-Kaijansinkko

first: Bettina

last: Mannerström


title: Genome-wide maps of nucleosome positioning in asynchronously growing yeast cells

city: Seattle

first: Sam

last: Cutler

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch Cancer Research Center

summary:
MNase-seq was performed in WT, isw2∆, nhp10∆, and isw2∆ nhp10∆ cells.
Sample naming convention: MNase_<growth condition>_<genotype-replicate>_<strain name>_<units MNase>

overall_design: For each experiment, DNA was digested with micrococcal nuclease (MNase) and exonuclease I


title: Genome-wide maps of RNA Polymerase I and III in asynchronously growing yeast cells

summary:
ChIP-seq of FLAG-tagged RPA190 (subunit of RNA Polymerase I) or FLAG-tagged RPO31 (subunit of RNA Polymerase III) was performed on WT and isw2∆ nhp10∆ cells.
Sample naming convention: <ChIP target>_<growth condition>_<genotype>_<strain name>

overall_design: For each experiment, IP samples were normalized to matched input DNA from the same preparation of chromatin.


title: Genome-wide maps of histone H3 in asynchronously growing yeast cells

summary:
ChIP-seq of histone H3 was performed on two biological replicates of the same W303 strain of wild-type cells and two independent isolates of each of isw2∆, nhp10∆, and isw2∆ nhp10∆ cells.
Sample naming convention: <ChIP target>_<growth condition>_<genotype-replicate>_<strain name>


title: Genome-wide binding of Nkx2-5

city: London

first: Timothy

middle: J

last: Mohun

address: The Ridgeway, Mill Hill,

department: Developmental Biology Division

country: United Kingdom

institute: MRC National Institute for Medical Research

type: Genome binding/occupancy profiling by genome tiling array

summary: Genome-wide binding of Nkx2-5

overall_design: Genome-wide binding of Nkx2-5

first: Catherine

last: Shang


title: Isw2 and Ino80 chromatin remodeling factors regulate chromatin, replication, and copy number at the yeast ribosomal DNA locus

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin remodeling factors Isw2 and Ino80 in asynchronously growing yeast cells

summary:
ChIP-seq of Isw2 (subunit of Isw2 complex) and Nhp10 (subunit of Ino80 complex) was performed on two independent isolates of FLAG-tagged Isw2 or Nhp10
Sample naming convention: <ChIP target>_<growth condition>_<genotype-replicate>_<strain name>


title: Excised linear introns regulate growth in yeast

status: Public on Oct 29 2018

city: Cambridge

first: Jeffrey

last: Morgan

address: 455 Main Street

institute: Whitehead Institute

summary: Spliceosomal introns are ubiquitous non-coding RNAs typically destined for rapid debranching and degradation. Here, we describe 34 excised Saccharomyces cerevisiae introns that, although rapidly degraded in log-phase growth, accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, a key integrator of growth signaling. Introns that become stabilized remain associated with components of the spliceosome and differ from other spliceosomal introns in having a short distance between their lariat branch point and 3´ splice site, which is necessary and sufficient for their stabilization. Deletion of these unusual introns is disadvantageous in saturated conditions and causes aberrantly high growth rates of yeast chronically challenged with the TORC1 inhibitor rapamycin. Reintroduction of native or engineered stable introns suppresses this aberrant rapamycin response. Thus, excised introns function within the TOR growth-signaling network of S. cerevisiae, and more generally, excised spliceosomal introns can have biological functions.

overall_design: 10 total S. cerevisiae samples from a variety of growth conditions, including 3 samples with depleted stable introns.

first: Gerald

last: Fink

middle: P

last: Bartel


title: Transcriptome profile Carnegie Stage 22 gut of different RET haplotypes

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: Total mRNA seq was perfomed on human fetal gut tissue at CS22 on 3 samples having different RET haplotype which progressively reduce expression of RET. R haplotypes are resistant and S haplotypes are susceptible to Hirschsprung disease

overall_design: Total RNA from 2 replicates each of wildtype (RR), heterozygous (RS) and homozygous (SS)  embryonic gut was converted to cDNA  and run on HiSeq 2000 (100 bp paired end). R haplotypes are resistant and S haplotypes are susceptible to Hirschsprung disease.

first: Aravinda

last: Chakravarti


title: Genome-wide maps of DNA Polymerase pausing in asynchronously growing yeast cells

summary:
ChIP-seq of FLAG-tagged Pol2 (subunit of DNA Polymerase epsilon)  was performed on two independent isolates of each of WT, isw2∆, nhp10∆, and isw2∆ nhp10∆ cells.
Sample naming convention: <ChIP target>_<growth condition>_<genotype-replicate>_<strain name>


title: Effect of soluble Siglec-14 on macrophage polarization

city: Taipei

first: Takashi

last: Angata

address: 128, Section 2, Academia Road, Nangang District

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Influence of soluble Siglec-14 on macrophage poloarization was examined by analyzing the transcripts from human macrophages cultured in the presence or absence of recombinant soluble Siglec-14 protein

overall_design: Two samples (i.e., in vitro differentiated human macrophages, incubated with or without recombinant soluble Siglec-14) were analyzed (replicate = 1)

first: Po-Chun

last: Huang


title: Expression data from human induced pluripotent stem cells II

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

summary:
We used microarrays to detail the global gene expression of human induced pluripotent stem cells
We investigated reference gene expression in human iduced pluripotent stem cells.

overall_design: 10 human induced pluripotent stem cell lines (201B7, 253G1, 409B2, HiPS-RIKEN-1A, HiPS-RIKEN-2A, HiPS-RIKEN-12A, 454E2, mc-iPS, ATCC-DYR0100hiPSc, ATCC-DYR0103hiPSc)

first: Satoshi

last: Yasuda

first: Yoji

last: Sato


title: Perturbation of the OGT-TET1 interaction in mouse embryonic stem cells (WGBS)

first: Joel

last: Hrit

address: 600 16th Street

department: Biochemistry and Biophysics

institute: University of California San Francisco

summary: Whole genome bisulfite sequencing of wild type embryonic stem cells and cells bearing a mutation that perturbs the OGT-TET1 interaction

overall_design: Whole genome bisulfite sequencing in wild type and Tet1 D2018A mutant mESCs

first: Bang-An

last: Wang

first: Rosa

last: Castanon

first: Joseph

last: Nery


title: PAR-CLIP in Smchd1-GFP and Smchd1WT neural stem cells.

city: Parkville

first: Marnie

last: Blewitt

state: Victoria

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

summary: We sought to examine whether the non-canonical SMC protein Smchd1 interacts with enodgenous RNA in cells and whether these interactions may be important for Smchd1's localisation to the chromatin.

overall_design: n=4 Smchd1GFP/GFP vs n=4 Smchd1+/+ and n=4 Smchd1GFP/GFP - UV365nm female neural stem cell lines analysed by PAR-CLIP

first: Natasha

last: Jansz


title: transcriptional response to endothelial cell-specific inactivation of Tspan12 in the mature retina

city: Boulder

first: Harald

last: Junge

state: Colorado

address: 347 UCB

institute: University of Colorado at Boulder

summary: Blood-retina barrier (BRB) formation and retinal angiogenesis depend on beta-catenin signaling induced by the ligand norrin (NDP), the receptor frizzled4 (FZD4), co-receptor LRP5, and the tetraspanin TSPAN12. Impaired NDP/FZD4 signaling causes familial exudative vitreoretinopathy (FEVR), which may lead to blindness. Endothelial-cell specific inactivation of the Tspan12 gene at P28 using a Cdh5-CreERT2 driver shows that TSPAN12 functions in ECs to promote vascular morphogenesis and BRB formation in developing mice, and BRB maintenance in adult mice. 12 month after Tspan12 inactivation and loss of BRB maintenance with massive IgG and albumin extravasation we observe complement activation, cystoid edema, and impaired beta-wave in electroretinograms. RNA-Seq 6 month after Tspan12 inactivation provides a detailed view on the transcriptional response, including activation of antibody effector systems (complement and Fc receptors), inflammation and microglia responses, extracellular matrix organization and remodeling, and other responses.

overall_design: Endothelial cell-specific inactivation of floxed Tspan12 was induced at P28 using a Cdh5-CreERT2 driver and total retina RNA (ribodepleted) from 4 control or ECKO retinas (8 samples) was subjected to RNA-Seq 6 months later

first: Chi

last: Zhang


title: The subiculum is a patchwork of discrete subregions

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

summary: Subiculum pyramidal cells constitute a prominent output neuron class of the hippocampus. Here, we examined diversity in this cell type using single-cell RNA-seq.

overall_design:
Examination of subiculum pyramidal cell transcriptomes.

Please note that there are total 28 samples from scRNA-seq, representing Read 1 and Read 2 of 14 datasets. The metadata.txt (with 1344 rows) contains the information on each well (96 well plate) for the 14 datasets (1344 = 96 X 14).
For the combinedTables.txt, the analysis only retained wells that were not control wells (e.g., not empty, not spike-in as annotated in metadata.txt as such), resulted in 1190 cells (included in the further analysis after removing these wells). The column headers/names represent the original dataset they emerged from.

first: Nelson

last: Spruston


title: Perturbation of the OGT-TET1 interaction in mouse embryonic stem cells

city: San Francisco


title: MKL1 augments megakaryocyte maturation by enhancing the SRF regulatory axis

city: New Haven

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University


title: Genome wide DNA methylation of Psoriasis patients from disease and adjacent Normal skin skin tissue samples

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

summary: Genome wide DNA methylation profiling of psoriatic disease skin tissue and adjacent Normal skin samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tissue samples. Total 48 samples were taken including 24 paired tissues.

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2


title: MKL1 augments megakaryocyte maturation by enhancing the SRF regulatory axis [ChIP-seq]

summary: SRF is a ubiquitous transcription factor that binds DNA in association with myocardin-family proteins (e.g. MKL1), or the ternary complex factor (TCF) family of ETS proteins. In primary hematopoietic cells, knockout of either SRF or MKL1 decreases megakaryocyte maturation caused thrombocytopenia, and MKL1 over-expression (MKL1OE) in the Human Erythroleukemia (HEL) cell line enhances megakaryopoiesis, but the mechanisms underlying these effects are unknown. To elucidate the role of SRF and MKL1 in megakaryopoiesis, integrated analysis was performed of anti-SRF ChIP-seq and RNA-seq data in undifferentiated and differentiated HEL cells, both with and without induction of MKL1OE. MKL1OE enhances TPA-induced megakaryopoiesis with 25% of genes upregulated, as opposed to 11% with TPA alone. MKL1OE increases SRF binding to genomic sites, and enhances expression of specific target cytoskeletal genes in response to TPA.  Genes upregulated in response to TPA are predicted to be regulated by SRF and ETS factors, whereas those upregulated in TPA plus MKL1OE lack ETS binding motifs. Using ChIP-PCR, we validated that both SRF and MKL1 have increased binding at target upregulated genes, e.g. CORO1A, with MKL1OE. We show for the first time that MKL1 increases both the genomic association and activity of SRF, and upregulates genes that enhance megakaryopoiesis.

overall_design: 4 treatment groups of HEL-iMKL1 cells were studied for anti-SRF ChIP-seq: untreated, Dox-treated (MKL1^OE), TPA-treated (TPA+), and Dox+TPA-treated (TPA+MKL1^OE).  Two replicates of each type were used.

first: Nur-Taz

last: Rahman

first: Vincent

first: Lin

first: Patrick

last: Gallagher

first: Oleg

last: Denisenko

first: Francesco

last: Gualdrini

first: Cyril

last: Esnault

first: Diane

last: Krause


title: MKL1 augments megakaryocyte maturation by enhancing the SRF regulatory axis [RNA-seq]

overall_design: 4 treatment groups of HEL-iMKL1 cells were studied for RNA-seq: untreated, Dox-treated (MKL1^OE), TPA-treated (TPA+), and Dox+TPA-treated (TPA+MKL1^OE).  Two replicates of each type were used.

last: Wang


title: MIR sequences recruit zinc finger protein ZNF768 to expressed genes

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: U2OS osteosarcoma cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) and Raji B-cells in RPMI 1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS, Bio&Sell), 2 mM L-glutamine (Gibco), 100 U/mL penicillin (Gibco), and 100 µg/mL streptomycin (Gibco) at 37°C at 8% or 5% CO2, respectively. Chromatin immunoprecipitation for ChIP-seq:  Cells were crosslinked using a formaldehyde containing solution (10mM NaCl, 0,1mM EDTA pH 8, 0,05mM EGTA pH 8, 5mM HEPES pH 7.8 and 1% formaldehyde) for 10 minutes at 20°C, the reaction was quenched by the addition of glycin to a final concentration of 250uM for 5 minutes. Crosslinked cells were collected and washed twice with PBS before snap freezing in liquid nitrogen and storage at -80°C until subsequent use.   Prior to sonication, the crosslinked cells were resuspended in lysis buffer (50mM Hepes pH 7.5, 140mM NaCl, 1mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100, 1X protease inhibitor cocktail) at 4°C for 20 minutes. Nuclei were collected by centrifugation and washed in a second buffer (200mM NaCl, 1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 1X protease inhibitor cocktail) for 10 minutes at 4°C then collected by centrifugation and resuspended in the shearing buffer (1mM EDTA pH 8, 0.5mM EGTA pH 8, 10mM Tris pH 8, 100mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1X protease inhibitor cocktail). Sonication was carried out in a Bioruptor Pico ultrasounds water bath (Diagenode B01060001) for 30 cycles of 30 sec ON and 30 sec OFF pulses in 4°C water. Sonicated extracts were centrifuged at high speed in the presence of 0,1% of Triton X-100 and snap frozen in liquid nitrogen then stored at -80°C until subsequent use.   Prior to ChIP, the ZNF768 mAb was coupled to protein-G coated magnetic beads (Dynabeads, life technologies) by incubation in 0,5% BSA PBS overnight at 4°C. Pre-coated beads were then washed and incubated with the sonicated chromatin extracts, the ChIP was carried out overnight at 4°C on a rotating wheel. The equivalent of 10 × 107 cells sonicated extract was used for each ZNF ChIP experiment for both cell lines. After incubation, the beads were washed 7 times with Wash buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate, 1X protease inhibitor cocktail) followed by one wash with TE-NaCl buffer (10mM Tris pH 8 and 1mM EDTA pH 8, 50mM NaCl). Immunoprecipitated chromatine was eluted by two sequential incubations with 100µl Elution buffer (50mM Tris pH 8, 10mM EDTA pH 8, 1% SDS) at 65°C for 15 minutes. The two eluates were pooled and incubated at 65°C for 12 hours to reverse-crosslink the chromatin followed by treatment with RNase A (0.2µg/mL) at 37°C for two hours and Proteinase K (0.2µg/mL) at 55°C for two hours. The DNA was isolated by phenol:chloroform: isoamylalcohol (25:24:1 pH 8) extranction followed by Qiaquick PCR Purification (Qiagen, Germany) and quantified with Qubit DS DNA HS Assay (ThermoFisher Scientific, USA).  At least 1ng of ChIP DNA was used to prepare sequencing library with Illumina ChIP Sample Library Prep Kit (Illumina, USA) with a few optimizations to the protocol. The ChIP DNA was size selected using Ampure beads (Life technologies) to enrich for fragments < 400Bp prior to end-repair, 3’end adenylation and adapter ligation. Library fragments were then directly amplified by 10 cycles of PCR.

overall_design: ZNF768 ChIP-seq

first: Michaela

last: Rohrmoser

first: Michael

last: Kluge

first: Yousra

last: Yahia

first: Anita

last: Eber-Gruber

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Ann

last: Greifenberg

first: Matthias

last: Geyer

first: Nicolas

last: Descostes

first: Ahmad

last: Maqbool

first: Jean-Christophe

last: Andrau

middle: C

first: Dirk

last: Eick


title: Single-cell RNA sequencing unveils a unique IL-10-producing T follicular helper subset that sustains humoral immunity during chronic viral infection

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University


title: RNA-seq of Tfh IL21+ single producers and Tfh IL21+ IL10+ double producers

summary: During chronic viral infection, the inflammatory function of CD4 T cells becomes gradually attenuated. Concurrently, Th1 cells progressively acquire the capacity to secrete the cytokine IL-10, a potent suppressor of antiviral T cell responses. To determine the transcriptional changes that underlie this T cell adaption process, we applied a single-cell RNA-sequencing approach and assessed the heterogeneity of IL-10-expressing CD4 T cells during chronic infection. Unexpectedly, our analyses revealed an IL-10-producing population with a robust Tfh-signature. Using IL-10 and IL-21 double-reporter mice, we further demonstrate that IL-10+IL-21+co-producing Tfh cells arise predominantly during chronic but not acute LCMV infection. Importantly, depletion of IL-10+IL-21+co-producing CD4 T cells or deletion of Il10 specifically in Tfh cells resulted in impaired humoral immunity and viral control. Mechanistically, B cell-intrinsic IL-10 signaling was required for sustaining germinal center reactions. Lastly, we demonstrate that IL-27 and type I IFNs differentially regulate the formation of this protective IL-10-producing Tfh subset. Thus, our findings elucidate a critical role for Tfh-derived IL-10 in promoting humoral immunity during persistent viral infection.

overall_design: 3 samples (Naive, Tfh IL21+ IL10-, Tfh IL21+ IL10+), 2-3 biological replicates per sample

first: David

middle: M

last: Schauder


title: Characterization of host responses during Pseudomonas aeruginosa acute lung infection in the lungs and blood and after treatment with the synthetic immunomodulatory peptide IDR-1002

city: Burnaby

first: Amy

middle: H.

last: Lee

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

summary: Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial pneumonia and infects patients with cystic fibrosis. P. aeruginosa lung infections are difficult to treat due to bacterial resistance to antibiotics, and strains with multi-drug resistance are becoming more prevalent. Here we examined the use of a small host defense peptide, innate defense regulator 1002 (IDR-1002), in an acute P. aeruginosa lung infection in vivo. IDR-1002 significantly reduced the bacterial burden in the bronchoalveolar lavage fluid (BALF) as well as MCP-1 in the BALF and serum, KC in the serum, and IL-6 in the BALF. RNA-Seq was conducted on lungs and whole blood and the effects of P. aeruginosa, IDR-1002, or the combination of P. aeruginosa and IDR-1002 were evaluated. Differential gene expression analysis showed that P. aeruginosa increased multiple inflammatory and innate immune pathways as well as affected hemostasis, matrix metalloproteinases, collagen biosynthesis, and various metabolism pathways in the lungs and/or blood. Infected mice treated with IDR-1002 had significant changes in gene expression compared to untreated infected mice, with fewer differentially expressed genes associated with the inflammatory and innate immune responses to microbial infection, and treatment also affected morphogenesis, certain metabolic pathways, and lymphocyte activation. Overall, these results show that IDR-1002 was effective in treating P. aeruginosa acute lung infections and associated inflammation.

overall_design: RNA-Seq profiling of mouse lung tissue or whole blood, with 4 conditions (negative control, IDR-1002 control, PA103 infected, and IDR-1002 treated PA103 infected), with 3-5 replicates per condition.

first: Kelli

last: Wuerth

first: Reza

last: Falsafi

first: Erin

middle: E

last: Gill

first: Robert

middle: W

last: Hancock


title: Single cell RNA-seq of IL-10-producing CD4 T cells during chronic LCMV infection

overall_design: One sample prepared using 10x Genomics Chromium platform


title: Perturbation of the OGT-TET1 interaction in mouse embryonic stem cells (RNA-Seq)

first: Joel

last: Hrit

summary: RNA-seq of wild type embryonic stem cells and cells bearing a mutation that perturbs the OGT-TET1 interaction

overall_design: RNA-seq of biological and technical replicates of wild type and mutant cells

first: Barbara

last: Panning


title: Role of Humoral Immunity against Hepatitis B Virus Core Antigen in the Pathogenesis of Acute Liver Failure

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

summary: To investigate the role of viral and host factors in acute liver failure, we analyzed serum and multiple liver specimens obtained at the time of liver transplantation from four well-characterized patients. We carried out an integrated clinicopathological analysis, gene and microRNA expression profiling, next-generation sequencing, antibody-displaying phage libraries, and in vitro functional analysis of HBV variants.

overall_design: Liver samples were obtained from 4 patients with HBV-associated acute liver failure (ALF), 10 liver donors and 7 subjects who underwent hepatic resection for liver angioma. As this is the continuation of a previous study (Title: Integrated ordination of miRNA and mRNA expression profiles; Authors: Diaz et al.) miRNA (microRNA) data are already available at the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under the accession number GSE62037. The present submission concerns only mRNA data.

first: Zhaochun

last: Chen

first: Teresa

last: Pollicino

first: Huaying

last: Zhao

first: Ronald

last: Engle

first: Peter

last: Schuck

first: Chen

last: Shen

first: Fausto

last: Zamboni

first: Zhifeng

last: Long

first: Juraj

last: Kabat

first: Davide

last: De Battista

first: Kevin

last: Bock

first: Ian

middle: N

last: Moore

first: Kurt

last: Wollenberg

first: Cinque

last: Soto

first: Sugantha

last: Govindarajan

middle: D

last: Kwong

last: Kleiner

last: Purcell

first: Patrizia

last: Farci


title: LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state

status: Public on Oct 28 2018

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state [mouse]

summary: Deregulated activity of the LATS tumor suppressors has broad implications on cellular and tissue homeostasis. We examined the consequences of downregulation of either LATS1 or LATS2 in breast cancer. Consistent with their proposed tumor suppressive roles, expression of both paralogs is significantly downregulated in human breast cancer, and loss of either paralog accelerated mammary tumorigenesis in mice. However, each paralog had a distinct impact on breast cancer. Thus, LATS2 depletion in luminal B tumors resulted in metabolic rewiring, with increased glycolysis and reduced PPARg signaling. Furthermore, pharmacological activation of PPARg elicited LATS2-dependent death in luminal B-derived cells. In contrast, LATS1 depletion augmented cancer cell plasticity, skewing luminal B tumors towards increased expression of basal-like features, in association with increased resistance to hormone therapy. Hence, these two closely related paralogs play distinct roles in protection against breast cancer; tumors with reduced expression of either LATS1 or LATS2 may rewire signaling networks differently and thus respond differently to anti-cancer treatments.

overall_design: RNA was isolated from Lats1-CKO and Lats2-CKO PyMT tumors (4 samples from each). For each genotype, the corresponding wt littermate controls were used (3 samples in each batch).

first: Noa

last: Furth

first: Yael

last: Aylon

first: Devora

last: Bakaev

first: Gil

last: Stelzer

first: Moshe

last: Oren


title: LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state [human]

overall_design: RNA from ZR75-1 and MCF7 transfected with siControl, siLATS1 or siLATS2 oligonucleotides was isolated and subjected to RNA-seq as above. For ZR75-1, three independent biological replicates were used. For MCF7, two independent biological replicates were used. ZR75-1 were transfected with either GFP only, GFP-LATS1 or GFP-LATS2. GFP-positive cells were sorted by FACS 24h following transfection (~80000 cells per sample). Two independent replicates were used.


title: High-Density Lipoproteins - small RNA Signatures in Systemic Erythematosus Lupus.

status: Public on Oct 27 2018

city: Nashville

first: Kasey

last: Vickers

state: TN

address: 312B Preston Research Building

country: USA

institute: Vanderbilt University

summary: Study of high-density lipoproteins using 6 human plasma samples. The study sought to find small RNA signatures in systemic erythematosus lupus.

overall_design: 6 different human plasma samples - 3 healthy controls and 3 systemic lupus erythematosus. RNA source for all samples is HDL-containing protein-lipid-RNA complex and RNA isolation kit used is miRNeasy (Qiagen). Starting material was total RNA.


title: Single cell sequencing of mouse syngeneic tumor models

city: South San Francisco

first: Manu

last: Kumar

state: California

address: 650 Gateway Blvd Suite 100

institute: Asher Biotherapeutics

summary: Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor interactions. Targeting ligand-receptor interactions, for instance with immune check-point inhibitors, can provide significant benefit for patients. However, our knowledge of which interactions occur in a tumor and how these interactions affect outcome is still limited. We present an approach to characterize communication by ligand-receptor interactions across all cell types in a microenvironment using single-cell RNA sequencing. We apply this approach to identify and compare ligand-receptor interactions present in six syngeneic mouse tumor models.  To identify interactions potentially associated with outcome, we regress interactions against phenotypic measurements of tumor growth rate. In addition, we quantify ligand-receptor interactions between T-cell subsets and their relation to immune infiltration using a publicly available human melanoma data-set.  Overall, this approach provides a tool for studying cell-cell interactions, their variability across tumors, and their relationship to outcome.

overall_design: We used three different types of immuno-competent inbred mouse strains: BALB/c, and A/J z. All animals enrolled in our study were 6-8 weeks old female mice that were housed in vivarium under specific pathogen free conditions in cages of up to 5 animals and receiving special rodent diet (Teklad). We implanted two mice for each syngeneic model resulting in a total of 12 samples. Each mouse tumor was harvested when the tumor size reached 100 – 200 mm3. Each sample was minced and digested with reagents from Mouse Tumor Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. Cells were resuspended at 2x105 cells/mL in PBS-0.04% BSA. Each sample was processed individually and run in technical duplicates. For each sample (except CT26 and MC-38) one replicate was enriched for CD45 positive cells. Live CD45 positive cells were sorted with BD Aria after staining with FITC-CD45 (Biolegend) and 7-AAD. Single cell suspensions of all samples were resuspended in PBS-0.04% BSA at 5x105 cells/mL and barcoded with a 10x Chromium Controller (10x Genomics). In total, this procedure resulted in 24 samples.

first: Jinyan

last: Du

first: Andreas

last: Raue

first: Douglas

middle: A

last: Lauffenburger


title: Endothelial-specific mitochondiral complex III KO leads to lung endothelial cell gene deregulation.

status: Public on Oct 26 2018

first: Navdeep

middle: S

last: Chandel

address: 240 E Huron

summary: Endothelial cells (ECs) require glycolysis for proliferation and migration during angiogenesis; however, the necessity for the mitochondrial respiratory chain during angiogenesis is not known. Here we report that inhibition of respiratory chain complex III impairs proliferation, but not migration of ECs in vitro by decreasing the NAD+/NADH ratio. To determine whether mitochondrial respiration is necessary for angiogenesis in vivo, we conditionally ablate a subunit of the respiratory chain complex III (QPC) in ECs.  Loss of QPC decreases respiration, resulting in diminished EC proliferation, and impairment in retinal and tumor angiogenesis.  Loss of QPC does not decrease genes associated with anabolism or nucleotides levels in ECs, but diminishes amino acid levels. Our findings indicate that mitochondrial respiration is necessary for angiogenesis, and that the primary role of mitochondria in ECs is to serve as biosynthetic organelles for cell proliferation.

overall_design: We conditionally knocked out a subunit of mitochondrial complex III (QPC) in Endothelial cells. KO was initiated via tamoxifen treatment on P0. Lungs were collected from WT and KO P15 mice and endothelial cells were isolated by positively sorting for CD31+ cells via FACS.

first: Lauren

last: Diebold


title: Blimp1 maintains regulatory T cell identity at sites of inflammation through epigenetic imprinting

city: Munich

first: Thomas

last: Korn

state: Bavaria

address: Ismaninger Str. 22

department: Neurology

institute: Technical University of Munich

summary: Foxp3+ regulatory T (Treg) cells restrict immune pathology in inflamed tissues; however, an inflammatory environment presents a threat to Treg cell identity and function. We here establish a transcriptional signature of central nervous system (CNS) Treg cells that accumulate during experimental autoimmune encephalitis (EAE) and identify a pathway that maintains Treg cell function and identity during severe inflammation. This pathway was dependent on the transcriptional regulator Blimp1, which prevented dismantling of Foxp3 expression and "toxic" gain-of-function of Treg cells in the inflamed CNS. Blimp1 negatively regulated IL-6- and STAT3-mediated methylation of Treg cell-specific conserved non-coding sequence 2 (CNS2) in the Foxp3 locus. Consequently, CNS2 was heavily methylated when Blimp1 was ablated, leading to loss of Foxp3 expression and severe disease. These findings identify a Blimp1-dependent epigenetic pathway that preserves Treg cell stability in inflamed non-lymphoid tissues.

overall_design: Comparison of DNA accessibility by Omni-ATAC-seq in conventional T cells (Tconv) and regulatory T cells (Treg) of wild-type vs Treg conditional Blimp1 deficient mice isolated from the CNS and spleen at the peak of experimental autoimmune encephalitis (EAE). All samples were FACS sorted ex vivo according to CD4+Foxp3(GFP)- = Tconv and CD4+Foxp3(GFP)+ = Treg from mixed bone morrow chimeras with congenically marked wild-type (CD45.1) and Treg conditional Blimp1 KO compartments (CD45.2).

first: Garima

last: Garg

first: Gildas

last: Lepennetier

first: Gunnar

last: Schotta

first: Helena

last: Domínguez Moreno


title: Transcription factors activate genes through the phase separation capacity of their activation domains [RNA-seq]

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding domains (DBDs) and activation domains (ADs). The DBDs have been well- characterized, but little is known about the mechanisms by which ADs effect gene activation. Here we report that diverse ADs form phase-separated condensates with the Mediator coactivator. For the OCT4 and GCN4 TFs, we show that the ability to form phase-separated droplets with Mediator in vitro and the ability to activate genes in vivo are dependent on the same amino acid residues. For the estrogen receptor (ER), a ligand-dependent activator, we show that estrogen enhances phase separation with Mediator, again linking phase separation with gene activation. These results suggest that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensates with Mediator is involved in gene activation.

overall_design: RNA-seq in mouse embryonic stem cells after OCT4 degradation or LIF withdrawal

first: Ann

last: Boija

first: Isaac

last: Klein

first: Benjamin

middle: R

last: Sabari

first: Alessandra

last: Dall'Agnese

first: Eliot

middle: L

last: Coffey

first: Alicia

middle: V

last: Zamudio

first: Charles

middle: H

last: Li

first: Krishna

last: Shrinivas

first: John

last: Manteiga

first: Nancy

last: Hannett

first: Brian

last: Abraham

first: Lena

last: Afeyan

first: Yang

last: Gouo

first: Jenna

last: Rimel

first: Charli

middle: B

last: Fant

first: Jurian

last: Schuijers

first: Tong

middle: I

last: Lee

first: Dylan

last: Taatjes


title: Transcription factors activate genes through the phase separation capacity of their activation domains [ChIP-seq]

first: Richard

last: Young

overall_design: ChIP-Seq against OCT4 and MED1 in mouse embryonic stem cells after OCT4 degradation

first: Ann

last: Boija

first: Isaac

last: Klein

middle: J

middle: K

last: Guo


title: Transcription factors activate genes through the phase separation capacity of their activation domains


title: Type 3 inflammation drives liver fibrosis by enhancing TGF-beta signaling through activation of MAPKS

city: Montreal

first: Naglaa

last: Shoukry

state: QC

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

institute: CRCHUM

summary: Type 3 inflammation characterized by increased production of IL-22 is a common driver of liver fibrosis during chronic liver injury through enhancement of TGF-β signaling in a p38 MAPK dependent manner.

overall_design: Three lots of human primary hepatitic stellate cells. Each lot was stimulated for 48h with either PBS, TGFlo (0.1ng/mL), TGFhi (2,5ng/mL), IL-17A (40ng/mL), IL-17A + TGFlo, IL-22 (40ng/mL) or IL-22 + TGFlo. Each lot comes from a single donor.

first: Thomas

last: Fabre

first: Manuel

middle: F

last: Molina

first: Geneviève

last: Soucy

first: Jean-Philippe

middle: P

last: Goulet

first: Bernard

last: Willems

first: Jean-Pierre

last: Villeneuve

first: Marc

last: Bilodeau


title: CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome  positioning

first: Marlies

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: Using 5C, ATAC-seq and CUT&RUN we find loss of CTCF binding, CTCF loops and TADs in mitosis

overall_design: 5C, ATAC-seq and CUT&RUN

first: Anders

last: Hansen

first: Yu

last: Liu

first: Xavier

last: Darzacq

first: Job

last: Dekker


title: A transcription factor addiction imposed by an oncogene promoter sequence

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory


title: A transcription factor addiction imposed by an oncogene promoter sequence [RNA-seq]

summary: Transcriptome analysis by high throughput sequencing

overall_design: Gene expression profiles in AML with gene knockout

first: Bin

last: Lu

first: Yusuke

last: Tarumoto

first: Christopher

last: Vakoc


title: Quantitative Analysis of p53 and/or TGFBR2 Knockdown Endothelial Transcriptomes after Irradiation

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon Gu

institute: Korea Institute of Radiological & Medical Sciences

summary: Transcriptional profiling p53 or TGFBR2 knockdown HUVECs with or without irradiation.

overall_design: mRNA profiles of control, p53 knockdown, TGFBR2 knockdown, and p53+TGFBR2 knockdown endothelial cells with or without irradiation were generated by deep sequencing using Illumina HiSeq 2500. HUVEC cells were collected 48 hrs post-irradiation. Two biological replicates for each condition were pooled together and sequenced.

first: Seo-Hyun

last: Choi


title: A transcription factor addiction imposed by an oncogene promoter sequence [ChIP-seq]

summary: Genome-wide binding/occupancy profiling by high throughput sequencing

overall_design: Genome-wide analysis of ZFP64 binding and H3K27ac modification in AML


title: Chromatin and tissue plasticity precede commitment to intestinal differentiation during endoderm development

city: Boston

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
Intestinal differentiation during endoderm development
We used RNA-sequencing to profile gene expression changes during the embryonic development of the gastrointestinal tract.

overall_design: ATAC-seq, RNA-seq and CDX2 ChIP-Seq analysis of purified mouse embryonic epithelial cells from the developing mouse gastrointestinal tract.

first: Kushal

last: Banerjee

first: Madhurima

last: Saxena

first: Namit

last: Kumar

first: Lei

last: Chen

first: Alessia

last: Cavazza

first: Natalie

last: Toke

first: Nicholas

last: O'Neill

first: Shariq

last: Madha

first: Unmesh

last: Jadhav

first: Michael

last: Verzi


title: Linking single-cell measurements of mass, growth rate, and gene expression

first: Sanjay

last: Prakadan

address: 77 Massachusetts Ave, E25-356

institute: Massachusetts Institute of Technology

summary: We introduce a microfluidic platform that enables single-cell mass and growth rate measurements upstream of single-cell RNA-sequencing (scRNA-seq) to generate paired single-cell biophysical and transcriptional data sets. Biophysical measurements are collected with a serial suspended microchannel resonator platform (sSMR) that utilizes automated fluidic state switching to load individual cells at fixed intervals, achieving a throughput of 120 cells per hour. Each single-cell is subsequently captured downstream for linked molecular analysis using an automated collection system. From linked measurements of a murine leukemia (L1210) and pro-B cell line (FL5.12), we identify gene expression signatures that correlate significantly with cell mass and growth rate. In particular, we find that both cell lines display a cell-cycle signature that correlates with cell mass, with early and late cell-cycle signatures significantly enriched amongst genes with negative and positive correlations with mass, respectively. FL5.12 cells also show a significant correlation between single-cell growth efficiency and a G1-S transition signature, providing additional transcriptional evidence for a phenomenon previously observed through biophysical measurements alone. Importantly, the throughput and speed of our platform allows for the characterization of phenotypes in dynamic cellular systems. As a proof-of principle, we apply our system to characterize activated murine CD8+ T cells and uncover two unique features of CD8+ T cells as they become proliferative in response to activation: i) the level of coordination between cell cycle gene expression and cell mass increases, and ii) translation-related gene expression increases and shows a correlation with single-cell growth efficiency. Overall, our approach provides a new means of characterizing the transcriptional mechanisms of normal and dysfunctional cellular mass and growth rate regulation across a range of biological contexts.

overall_design: Single-cell RNA-Sequencing of L1210 cells, FL5.12 cells, activated T cells, and cells from a patient derived glioblastoma cell line.

middle: M

first: Alex

last: Shalek