title: Characterization of an Immortalized Human Small Airway Basal Stem/Progenitor Cell Line with Airway Region-specific Differentiation Capacity [array]

first: Yael

last: Strulovici-Barel

summary:
The pathology of chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis and the majority of lung cancers involve the small airway epithelium (SAE), the single continuous layer of cells lining the airways ?6th generations. The basal cells (BC) are the stem/progenitor cells of the SAE, responsible for the differentiation into intermediate cells and ciliated, club and mucous differentiated cells. To facilitate the study of the biology of the human SAE in health and disease, we immortalized and characterized a normal human SAE basal cell line.
The immortalized hSABC-NS1.1 cell line has diverse differentiation capacities and retains SAE features, which will be useful for understanding the biology of SAE, the pathogenesis of SAE-related diseases, and testing new pharmacologic agents.

overall_design: Small airway basal cells were purified from brushed SAE of a healthy nonsmoker donor with a characteristic normal SAE transcriptome. The BC were immortalized by retrovirus-mediated telomerase reverse transcriptase transduction and single cell drug selection. The resulting cell line (hSABC-NS1.1) was characterized by RNAseq, TaqMan PCR, protein immunofluorescence, differentiation capacity on air-liquid interface culture, transepithelial electrical resistance, airway region-associated features and response to genetic modification with SAM Pointed Domain Containing ETS Transcription Factor (SPDEF).

first: Guoqing

last: Wang

first: Howard

last: Lou

first: Jacqueline

last: Salit

first: Philip

last: Leopold

first: Sharon

last: Discoll

first: Matt

last: Thomas

first: Juergen

last: Schymeinsky

first: Karsten

last: Quast

first: Suda

last: Visvanathan

first: Jay

middle: S

last: Fine

first: Ronald

middle: G

last: Crystal


title: Characterization of an Immortalized Human Small Airway Basal Stem/Progenitor Cell Line with Airway Region-specific Differentiation Capacity [RNA-Seq]

status: Public on Sep 03 2019

city: New York

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

type: Expression profiling by high throughput sequencing

summary:
The pathology of chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis and the majority of lung cancers involve the small airway epithelium (SAE), the single continuous layer of cells lining the airways ≥6th generations. The basal cells (BC) are the stem/progenitor cells of the SAE, responsible for the differentiation into intermediate cells and ciliated, club and mucous differentiated cells. To facilitate the study of the biology of the human SAE in health and disease, we immortalized and characterized a normal human SAE basal cell line.
The immortalized hSABC-NS1.1 cell line has diverse differentiation capacities and retains SAE features, which will be useful for understanding the biology of SAE, the pathogenesis of SAE-related diseases, and testing new pharmacologic agents.

middle: L


title: Williams RNA-Seq Samples from Various Organ and Developmental Stages

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: 11 RNA-Seq samples from Williams (PI548631), with a variety of tissues especially immature seeds represented; 1 sample is from Williams 55, i mutation with black seed coat (PI547881)

overall_design: 12 samples total, no replicates

middle: O

first: Young

middle: B

last: Cho

first: Sarah

middle: I

last: Jones


title: Expression profile of RCC4 cells with TAZ (WWTR1) silencing

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive

institute: Duke University

summary: TAZ, also known as WWTR1, is the one of the effectors of Hippo pathway. With its paralog, YAP, TAZ promotes organ size growth as well as tumor metastasis. In human renal carcinoma cells, we found that TAZ-silencing induces resisntance toward erastin-induced ferroptosis. In this study, TAZ is silencing in clear cell carcinoma cell line RCC4 to elucidate the downstream targets that promotes the resistance toward erastin-induced ferroptosis.

overall_design: Human clear cell renal carcinoma cell line RCC4 were transfected with siRNA targeting TAZ (siTAZ) and compared with non-targeting siRNA control (siNT). All samples were prepared as biological triplicates. Total RNA was collected after 2 days of reverse transfection for cDNA synthesis. The influence of silencing TAZ on gene expression was derived by zero transformation process, in which we compared the gene expression level with siTAZ to the average of gene expression level in control (siNT) samples.

first: Wen-Hsuan

last: Yang

first: Chien-Kuang

middle: C

last: Ding


title: Gene Expression data for melanocyte stem cells and melanoblasts isolated from the skin of wild-type mice and B-raf and C-raf double knock-out mice

status: Public on Sep 02 2019

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary:
Melanocyte are melanin-producing cells located in the bottom layer of the skin's epidermis and in the hair follicle. Melanin is the pigment primarily responsible notably for skin and hair color. Our team had previously shown a role for B-raf and C-raf genes in the maintenance of melanocyte stem cells located in mice hair follicle (Valluet et al, 2012).
The aim of the present project was to understand the role of B-RAF and C-RAF kinases in melanocyte stem cell self-renewal. To reach this goal, we have generated a new mouse model in which cells of the melanocyte lineage can be followed by GFP expression. We performed gene array on melanocyte stem cell B-raf+/+; C-raf+/+ and B-raf-/-; C-raf-/-in order to identify the RAF kinases target genes which are involved in melanocyte stem cell self-renewal. Moreover, to better characterize the melanocyte stem cell population, we compared its gene expression profile to the melanoblast one (melanocyte stem cell's progenitors).

overall_design: gene expression of melanoblats from the skin of 4-day old mice (2 replicates fom 2 different animals) were compared to the gene signature of melanocyte stem cells from the skin of 21-day old mice (2 replicates from 2 mice). In parallel, gene expression of melanocyte stem cell B-raf-/-;C-raf-/- and B-raf +/+;C-raf +/+ were compared to identify genes involved in melanocyte stem cell maintenance.

first: Celine

last: Barbotin

first: Alain

last: Eychene


title: ChIP-seq data for zfp148 and zfp281 chromatin occupancy in hemin-induced human K562 cells

city: Boston

first: Gabriela

last: Pregernig

state: Massachusetts

address: 1325 Boylston Street, Suite 500

institute: Decibel Therapeutics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq was carried for zfp148 and zfp281 in human K562 cells to test the hypothesis that these two transcription factor family members play overlapping roles in erythropoiesis.

overall_design: Because of concern for possible cross-reactivity of antibodies against zfp148 and zfp281, K562 cells stably expressing the bacterial biotin ligase Bir A were stably transfected with recombinant forms or either zfp148 and zfp281 containing a 23 amino acid amino terminal BirA recognition/biotin accepter motif ("bio-zfp148" and "bio-zfp281").  Clones were selected that expressed the recombinant proteins at close to the same levels as the endogenous proteins.  The parental K562 cells expressing BirA alone were included as controls.  The cells were treated with 50 mM hemin (final conc) for 48 hrs to induce erythroid maturation, and then streptavidin-based ChIP-seq was performed.

first: Alan

last: Cantor

first: Andrew

middle: J

last: Woo

first: Alireza

last: Ghamari

first: Ernest

last: Fraenkel


title: Expression data from human femur marrow adipose tissue (fMAT) and subcutaneous white adipose tissue of the thigh (tsWAT)

city: Innsbruck

first: Carina

middle: Michelle

last: Miggitsch

address: Rennweg 10

department: Immunology

country: Austria

institute: Institute for Biomedical Aging Research

summary:
The bone marrow (BM) is a major reservoir of resting memory T cells and long-lived plasma cells, capable of providing protection against recurrent infections. Whether the age-related accumulation of adipose tissue in the BM affects the functionality and maintenance of memory cells is not well understood. For the first time, we compare human femur marrow adipose tissue (fMAT) and subcutaneous white adipose tissue of the thigh (tsWAT) obtained from the same donors. Using microarrays, we show that fMAT significantly differs from tsWAT regarding specific gene expression profiles including inflammatory responses and adipogenesis. fMAT adipocytes express increased levels of pro-inflammatory molecules concomitant with an elevated generation of reactive oxygen species (ROS) and impaired function of plasma cells in the BM. The reduced expression of adipocyte-specific genes and a less mature adipocyte phenotype in fMAT, relative to tsWAT, suggests that fMAT has more immune regulatory functions. Our findings indicate that fMAT is a unique type of adipose tissue contributing to inflammation and impairment of plasma cell function.
We used microarrays to detail the gene expression profil of fMat in comparison to tsWAT in regard to the inflammatory response, adipogenesis/fatty acid metabolism, and redox regulation, and identified distinct classes of up-regulated genes.

overall_design: Eight human female individuals were used. From each donor we received femur marrow adipose tissue and subcutaneous white adipose tissue. Bone marrow biopsies and subcutaneous fat were fragmented, treated with collagenase to digest the tissues, and afterwards single adipocytes were isolated. To ensure high purity of adipocyte samples for microarray analysis a customized EasySep® protocol using the EasySep® purple magnet (Stemcell Technology, Cat#18000) was applied to remove residual leukocytes, erythrocytes, endothelia, and mesenchymal cells. RNA was isolated from purified bone marrow and subcutaneous adipocytes using the RNeasy Lipid Tissue Mini Kit (Qiagen) including the reagent Qiazol according to the manufactures’ protocol. Furthermore, isolated total mRNA with a RIN value >7 was used for microarray analysis which was done by Eurofins Genomics AROS from Denmark using Affymetrix® Human Gene ST Array Plate (chip type: HuGene 2.1).

middle: M


title: Interaction between oncogenic FREM2 with IL-1β signaling contributes to esophageal squamous cell carcinoma progression

city: Shanghai

first: Lin

last: Wang

address: 180 Fenglin Rd.

department: Department of thoracic surgery

country: China

institute: Zhongshan Hospital, Fudan University

summary: Inflammatory signals can promote tumorigenesis. The pro-inflammatory cytokine interleukin (IL)-1β is overexpressed in many types of tumor; however, it is unclear whether it directly interacted with oncogenes in esophageal squamous cell carcinoma. In this study, we performed RNA sequencing to identify tumorgenesis and recurrence-related factors in ESCC and identified FRAS1-related extracellular matrix protein (FREM)2 as a candidate oncogene. IL-1β and IL-1R1 were upregulated in ESCC tissue, which was accompanied by elevated Frem2 expression. FREM2 formed complex with IL-1R1 at the cell surface and promoted ESCC cell proliferation and migration via activation of nuclear factor-κB–p65/mitogen-activated protein kinase–c-Jun N-terminal kinase signaling. IL-1β stimulation resulted in the upregulation of FREM2 in ESCC cells through inhibition of Forkhead box P1. Increased FREM2 and IL-1R1 levels were correlated with shorter survival time in ESCC patients.

overall_design: RNA profiles of tumor tissues and  paired normal tissues from 4 ESCC patients were generated by sequencing

first: Zongwu

last: Lin


title: Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1 [ChIP-seq]

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast cancer (TNBC) and plays crucial roles in tumor progression. However, a systematic analysis of the composition of the Fra-1 protein network specifically on chromatin is still missing. Here we performed endogenous purification of Fra-1 transcriptional complex under ChIP conditions, followed by mass spectrometry, to identify chromatin-bound partners of Fra-1 in TNBC cells. This study allowed the identification of 118 interactors, highlighting DDX5 as the high ranking of Fra-1 interacting proteins. DDX5, a previously unrecognized protein in the network, is recruited globally to Fra-1 binding sites and shares a substantial set of Fra-1 target genes required for the TNBC cell growth. We provide evidence that DDX5 expression enhances Fra-1 transcriptional activity, thereby enhancing Fra-1-driven tumorigenesis. By integrating ChIP-seq and RNA-seq, we show that DDX5 target gene signature predicts poor clinical outcome in breast cancer patients. DDX5 protein level was higher in triple-negative basal like tumors than in non-basal like tumors, including luminal A, luminal B and HER2-enriched subtypes. Collectively, this comprehensive Fra-1 interaction profiling provides a broad and deep view of Fra-1 chromatin interaction landscape, which will help in deciphering mechanisms of AP-1 regulation of gene expression.

overall_design: Identifiation of Fra-1 and DDX5 specific and common binding events in BT549 cells.

first: Huan

last: He

first: Dandan

last: Song

first: Indranil

last: Sinha

first: Bernd

last: Hessling

first: Xidan

last: Li

first: Lars-Arne

last: Haldosén

first: Chunyan

last: Zao


title: Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1 [RNA-seq]

overall_design: Examination of genes regulated by knockdown of Fra-1 or DDX5 in BT549 cells


title: Characterization of the transcriptional changes during soybean root hair cell development.

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Root hair cells growth under contolled conditions harvested at 3 different time points (276, 288 and 312 hours after sowing). For each time point, 3 biological replicates have been produced

overall_design: Nine RNA-seq samples of soybean

first: Marc

last: Libault


title: Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1

summary: Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast cancer (TNBC) and plays crucial roles in tumor growth. Here we report the identification of 118 proteins interacting with endogenous chromatin-bound Fra-1 in TNBC cells, highlighting DDX5 as the most enriched Fra-1-interacting protein. DDX5, a previously unrecognized protein in the Fra-1 transcriptional network, shows extensive overlap with Fra-1 cistrome and transcriptome that are highly associated with the TNBC cell growth. We provide evidence that DDX5 expression enhances Fra-1 transcriptional activity and potentiates Fra-1-driven cell proliferation. Furthermore, we show that the DDX5 target gene signature predicts poor clinical outcome in breast cancer patients. DDX5 protein level was higher in triple-negative basal-like tumors than in non-basal-like tumors, including luminal A, luminal B, and HER2-enriched subtypes. Collectively, by combining proteomic and genomic approaches we reveal a role for DDX5 as a regulatory protein of Fra-1 signaling and suggest DDX5 as a potential therapeutic target for TNBC.

overall_design: Refer to individual Series


title: Transcriptome analysis of sciatic nerve in mutant krox20 mice at 14 day post natal compared to wild-type mice

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: RNAseq was performed on sciatic nerves from controls and Krox20 mutants to elucidate the role of Krox20 inthe myelinisation process.

overall_design: Sciatic nerve mRNA profiles of 14-day old wild type (WT) and Krox20 mutant mice were generated by deep sequencing, in triplicate, using an Illumina Nextseq500.

first: Fanny

last: Coulpier

first: Sophie

last: Lemoine


title: Dynamic incorporation of histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization

first: Dylan

last: McNally

institute: Weill Cornell Medicine

summary: Carcinomas can acquire metastatic potential by undergoing a cellular program referred to as epithelial-to-mesenchymal transition (EMT). During EMT, the genome undergoes major epigenetic changes required for the expression of genes that promote cell motility, invasiveness, and survival under stress. While recent data point to a crucial role of chromatin remodeling in this process, little is known about the nature of this remodeling and the signals that trigger it. Here we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin. This triggers deposition of H3.3 to the promoters of EMT-inducing transcription factors and poor prognosis genes, a phenomenon that is sufficient and necessary for the induction of EMT and metastasis. Together, we have discovered histone H3.3 variant as a major regulator of cell fate during tumorigenesis and histone chaperones as valuable therapeutic targets for metastatic disease.

overall_design: Global analysis of RNA levels to determine transcriptional reprogramming in MCF-10A cells upon CAF-1 suppression, in triplicate

first: John

last: Blenis

first: Ana

middle: P

last: Gomes

first: Didem

last: Ilter

first: Martin

middle: A

last: Rivas

middle: R

first: Ari

last: Melnick


title: Loss of the mitochondrial pyruvate carrier promotes stem cell gene expression in colon adenomas.

city: Salt Lake City

first: Jordan

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

summary: Loss of the mitochondrial pyruvate carrier promotes stem cell gene expression in AOMDSS colon adenomas, though loss of Apc promotes a more unified pehnotype.

overall_design: In this study, we generated tissue samples of normal colon crypts, adjacent normal colon crypts, and colon adenomas using two mouse models of colon cancer initiation to distinguish if loss of the mitochondrial pyruvate carrier promoted a more stem cell like gene expression pattern using a custom probeset consisting of intestinal stem and differntiation markers

first: Claire

last: Bensard

first: Jared

last: Rutter


title: Alpha-kinase 1 functions upstream of IKKs to regulate NF-κB activation in Helicobacter infection

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Gastric mucosa responds to the pathogen Helicobacter pylori (H. pylori) by producing and release of pro-inflammatory cytokines that activate the innate immune system mainly through activation of the transcription factor NF-κB. Although NF-κB signaling is well studied for many possible inducers, induction by H. pylori remains poorly understood.  Here, we performed a high-throughput genome-wide RNAi screen for genes influencing H. pylori-induced NF-κB activation. In comparison to TNFα or IL‐1β NF‐κB signaling, we identified 21 proteins unique necessary for H. pylori NF-κB pathway and 24 factors that inhibited the activation. Furthermore, we present here the R/Bioconductor package Nested Effect Model for systematic use in high-throughput screens to classify newly identified factors. We identified alpha kinase 1 (ALPK1) as particular important for the H. pylori NF‐κB pathway without affecting TNFα or IL‐1β signaling. ALPK1 silencing inhibits activity of TAK1 and the IκB kinases (IKKs), degradation of the NF‐κB inhibitor IκBα, nuclear translocation of the NF‐κB subunit p65, and transcription of the NF‐κB target genes, e.g. IL‐8. Thus, we identify ALPK1 as a novel inflammatory regulator functioning particularly in the NF‐κB signaling network activated by H. pylori.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent whole mouse catalog 4x44K (Agilent-014850) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Sina

last: Bartfeld

first: Cindy

last: Rechner

first: André

last: Mäurer

first: Jianping

last: Liu

first: Frithjof

last: Glowinski

first: Olga

last: Sokolova

first: Bianca

last: Bauer

first: Nikolaus

last: Machuy

first: Klaus-Peter

last: Pleissner

first: Roland

last: Schwarz

first: Florian

last: Markowetz

first: Michael

last: Naumann

first: Thomas

middle: F

last: Meyer


title: AML1-ETO induced leukemia stem cell self-renewal depends on Plcg1

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

summary: Leukemia stem cells are characterized by aberrant self-renewal capacity. Targeting oncogenic fusions that mediate this aberrant self-renewal capacity remains a therapeutic challenge. The t(8;21) translocation, resulting in the oncogenic fusion AML1-ETO (AE, RUNX1-RUNXT1) is among the most common chromosomal rearrangements found in acute myeloid leukemia (AML). By conducting high-resolution proteomic analysis on myeloid leukemia stem cells we identified Phospholipase C- and Ca++-signaling pathways to be differentially regulated in AE/t(8;21) AML. Phospholipase C gamma 1 (Plcg1) was specifically, and highly expressed in t(8;21) AML and could be identified as a direct target of the AML1(RUNX1)-ETO fusion. Genetic inactivation of Plcg1 resulted in abrogation of disease initiation by AE, reduction of intracellular Ca++ release and loss of AE-driven self-renewal programs. Plcg1 deletion after onset of AE-induced leukemia significantly reduced disease penetrance, number of leukemia stem cells and resulted in abrogation of leukemia development in secondary recipients. Inactivation of Plcg1 in human AE-positive AML cells by RNAi reduced colony formation and AML development in vivo. In contrast, Plcg1 was dispensable for steady state hematopoiesis and maintenance of murine and human hematopoietic stem cells (HSC). Translationally, we used pharmacologic inhibition of Ca++ signaling downstream of Plcg1 in AE-driven AML and this resulted in impaired proliferation and self-renewal capacity. The Plcg1 pathway represents a novel, specific vulnerability of AE-driven leukemia and represents an important new therapeutic target.

overall_design: Kasumi-1 cells were transduced with validated lentiviral shRNAs against human PLCG1 or non-targeting control and subjected to GeneExpression and lncRNA profiling on Agilent-079487 Arraystar Human LncRNA microarray V4

first: Tina

last: Schnoeder


title: Whole exome sequencing analysis of bone marrow c-Kit+ leukemia cells in Nras-G12D with Ezh2 KO (E2-KO) mice

status: Public on Sep 01 2019

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

type: Genome variation profiling by high throughput sequencing

summary: Epigenetic gene regulation and metabolism are highly intertwined, yet little is known whether and how altered epigenetics influences cellular metabolism in cancer progression. Here we show that EZH2 and NRasG12D mutations cooperatively induce progression of myeloproliferative neoplasms to fully penetrant, transplantable and lethal myeloid leukemias in mouse. EZH1, an EZH2 homolog, is indispensable for EZH2-deficient leukemia-initiating cells (LICs) and constitutes an epigenetic vulnerability. BCAT1, the first enzyme catalyzing transamination of branched-chain amino acids (BCAAs), is repressed by EZH2 in normal hematopoiesis and aberrantly activated in EZH2-deficient myeloid neoplasms in mouse and human. Enhanced BCAT1 promotes BCAA production in LICs ex vivo and in vivo, resulting in activated mTOR signaling. Genetic and pharmacological inhibition of BCAT1 selectively impairs EZH2-deficient LICs and constitutes a metabolic vulnerability. These findings establish an example how epigenetic alterations modify metabolic adaptation in myeloid transformation and provide a rationale for targeting the epigenetic and metabolic liabilities of cancer-initiating cells.

overall_design: Genome DNA were isolated from c-Kit+ leukemia cells from E2-KO moribund mice and processed for whole exome sequencing (WES) analysis using Agilent SureSelect XT Mouse All Exon Kit (cat# 1000001746) following manufacturer’s protocols. WES libraries were sequenced on BGISEQ500 platform by pair-end 100bp.

first: Zhimin

last: Gu

first: Yuxuan

first: Yuannyu

last: Zhang


title: The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
Lung cancer is the leading cause of cancer death worldwide, with poor prognosis and a high rate of recurrence despite early surgical removal. Hypoxic regions within tumors represent sources of aggressiveness and resistance to therapy. While long non-coding RNAs (lncRNAs) are increasingly recognized as major gene expression regulators, their regulation and function following hypoxic stress are still largely unexplored. Combining profiling studies on early stage lung adenocarcinomas (LUAD) biopsies and on A549 LUAD cell lines cultured in normoxic or hypoxic conditions, we identified a subset of lncRNAs that are both correlated with the hypoxic status of tumors and regulated by hypoxia in vitro.
We focused on a new transcript, NLUCAT1 that is strongly upregulated by hypoxia in vitro and correlated with hypoxic markers and poor prognosis in LUADs. Full molecular characterization showed that NLUCAT1 is a large nuclear transcript composed of 6 exons and mainly regulated by NF-ĸB and NRF2 transcription factors. CRISPR-Cas9-mediated invalidation of NLUCAT1 revealed a decrease in proliferative and invasive properties, an increase in oxidative stress and a higher sensitivity to cisplatin-induced apoptosis. Transcriptome analysis of NLUCAT1-deficient cells showed repressed genes within the anti-oxidant and/or cisplatin-response networks. We demonstrated that the concomitant knockdown of 4 of these genes, GPX2, GLRX, ALDH3A1 and PDK4, significantly increased ROS-dependent caspase activation, thus partially mimicking the consequences of NLUCAT1 inactivation in LUAD cells.
Overall, we demonstrate that NLUCAT1 contributes to an aggressive phenotype in early-stage hypoxic tumors suggesting it may represent a new potential therapeutic target in LUADs.

This SuperSeries is composed of the SubSeries listed below.

first: R

last: Rezzonico

first: N

last: Nottet

first: B

last: Mari

first: P

last: Barbry

first: K


title: Transcriptomics analysis of wild type and Wdr26 knockout MEL cells

city: Hangzhou

first: Caiyong

last: Chen

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Wdr26 is a gene induced during red cell development. In order to understand the function of wdr26 during erythropoiesis, we analyzed the transcriptomes of wild type and Wdr26-knockout mouse eythroleukemia (MEL) cells. We found that loss of Wdr26 did not cause a global increase in the expression of genes that encode nuclear proteins.

overall_design: The mRNA profiles of wild type and Wdr26 knockout MEL cells were generated by deep sequencing, in duplicate, using Illumina HiSeq platform.


title: FOXO1 knockdown is toxic for BL cell lines.

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

institute: Ulm University

summary: We found that FOXO1 knock-down  inhibits cell cycle progression in BL cell lines BL41, Namalwa and Jiyoye.

overall_design: BL cell lines BL41, Namalwa and Jiyoye were transduced with sh_hFOXO1.H-10381 in pRSI12-U6-sh-UbiC-TagRFP-2A-Puro lentiviral vector (DECIPHER shRNA Library, Human Module I (Cellecta, https://www.cellecta.com/) obtained from BioCat, Heidelberg, Germany). On Day 4 after transduction total RNA was isolated with RNeasy mini kit (QIAGEN). RNA-sequencing as well as data processing were done by BGI (Hong-Kong). RNA libraries were prepared for sequencing using standard BGI protocols. SOAPnuke software was used for data filtering and Bowtie2 was used to map clean reads to reference. RSEM was used to calculate gene expression level and DEseq2 was used to detect DEGs. The human reference genome hg38 was used.

first: Franziska

last: Gehringer

last: Wirth


title: Macrophage Ad5f35 M2 Challenge

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

summary: Control untransduced or anti-HER2 CAR (Ad5f35 transduced) human macrophages were exposed to control media, human IL-4, or human IL-13, and the response to these cytokines was measured at a transcriptome-wide level. RNA was harvested 24 hours post cytokine exposure with Ambion RiboPure RNA Purification Kit (Thermo Fisher) and RNA-Seq libraries were generated using TruSeq RNA Library Prep Kit (Illumina). Libraries were sequenced on 75bp single-end reads using a NextSeq (Illumina).

overall_design: RNA-Seq evaluation of the impact of IL4 or IL13 on control vs. Ad5f35 transduced human CAR macrophages. Data is shown from two distinct normal human donors.

first: Michael

last: Klichinsky

first: Xueqing

last: Lu

first: Saar

last: Gill


title: Transcriptome analysis of reticulated platelets reveals a prothrombotic profile [mRNA-Seq]

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

summary:
To compare immature and mature platelet transcriptome
Methods: reticulated or immature platelets(RPs) were defined as the platelets with the highest thiazole orange staining intensity (15% highest, RNAhigh) according to previous experiences and mature platelets were defined as the platelet with the 30% lowest thiazole orange staining intensity (RNAlow) and sorted (supplemental Figure S1D).
We detected more than 1700 differentially expressed gene, incluning activation receptors
RPs have a prothrombotic transcriptomic profile

overall_design: Platelets RNA was acquired frome healthy donors. And analyzed using using NextSeq-500

first: Dario

last: Bongiovanni


title: Antifungal Activity of Mammalian Serum amyloid A1 against Candida albicans

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

summary: Human serum amyloid A (SAA) is a major acute phase protein and shows a massive increase of concentration in plasma during inflammation. In the current study, we report that recombinant human and mouse SAA1 (rhSAA1 and rmSAA1) have a potent antifungal activity against the major fungal pathogen Candida albicans. rhSAA1 binds to the cell surface of C. albicans and promotes cell aggregation. At high concentrations, rhSAA1 disrupts the membrane integrity and induces rapid cell death of C. albicans. Further investigation demonstrates that rhSAA1 targets on the cell wall adhesin Als3 of C. albicans. Inactivation of ALS3 in C. albicans leads to remarkably decreased cell aggregation and death upon rhSAA1 treatment, implying that Als3 plays a critical role in SAA1 sensing. Moreover, deletion of the ALS3 transcriptional regulators such as AHR1, BCR1, and EFG1 in C. albicans results in a similar effect on cell responses to that of the als3/als3 mutant upon rhSAA1 treatment. Global gene expression profiling analysis indicates that rhSAA1 has a remarkable impact on the expression of cell wall- and metabolism-related genes in C. albicans. Our finding of the antifungal activity of rhSAA1 against C. albicans expands the function of this protein and would provide new insights into the understanding of the host-Candida interaction during infections.

overall_design: total RNA profiles of Candida albicans treated with SAA1 and PBS

first: Jiao

last: Gong

first: Jun

last: Wu

first: Guanghua

last: Huang

first: Gong

last: Jiao


title: Shoot regeneration process of callus derived from the wild type (Col-0), lba1-1/upf1-1, and upf3-1 hypocotyls of Arabidopsis thaliana

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: NAIST

summary: Plants generally possess a strong ability to regenerate organs; for example, in tissue culture, shoots can regenerate from callus, a clump of actively proliferating, undifferentiated cells. Processing of pre-mRNA and ribosomal RNAs is important for callus formation and shoot regeneration. However, our knowledge of the roles of RNA quality control via the nonsense-mediated mRNA decay (NMD) pathway in shoot regeneration is limited. Here, we examined the shoot regeneration phenotypes of the low-beta-amylase1 (lba1)/upstream frame shift1-1 (upf1-1) and upf3-1 mutants, in which the core NMD components UPF1 and UPF3 are defective. These mutants formed callus from hypocotyl explants normally, but this callus behaved abnormally during shoot regeneration: the mutant callus generated numerous adventitious root structures instead of adventitious shoots in an auxin-dependent manner. Quantitative RT-PCR and microarray analyses showed that the upf mutations had widespread effects during culture on shoot-induction medium. In particular, the expression patterns of early auxin response genes, including those encoding AUXIN/INDOLE ACETIC ACID (AUX/IAA) family members, were significantly affected in the upf mutants. Also, the upregulation of shoot apical meristem-related transcription factor genes, such as CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, was inhibited in the mutants. Taken together, these results indicate that NMD-mediated transcriptomic regulation modulates the auxin response in plants and thus plays crucial roles in the early stages of shoot regeneration.

overall_design: Total RNAs of callus derived from the wild type (Col-0), lba1-1/upf1-1, and upf3-1 hypocotyls were obtained after 0, 3, and 3 d of the culture on shoot-inducing medium. The total RNAs were used for microarray analysis to reveal genes affected by the upf mutations.

first: Ryosuke

last: Sano

first: Taku

last: Demura


title: Morphological and transcriptomic analysis reveal robust nonhost resistance response during chickpea interaction with Alternaria brassicae

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Plant Genome Research

summary: Alternaria brassicae is a necrotrophic fungal pathogen which infects brassica crops and lead to huge loss in crop production. There is a need to exploit the novel resistance mechanism against A. brassicae. Under field condition, chickpea is the potential nonhost plant for A. brassicae. At molecular level, it is not known how the NHR in chickpea operates against A. brassicae. In present study, we did the transcriptomic analysis in chickpea plants exposed to nonhost pathogen, A. brassicae by using microarray. Chickpea plants were spray inoculated with the spore suspension of A. brassicae. The leaf samples were harvested after 24 hpi and 48 hpi from pathogen treated plants and from the mock-treated control plants. The Transcriptome analysis were done from the leaf samples obtained at both the time-points by microarray using Agilent ChickpeaGXP_8X60K chip. Our result suggested the robust transcriptional reprogramming leading to defense response against A. brassicae.

overall_design: Organism : Chickpea, Agilent custom Chickpea Gene Expression  8x60k Array (AMADID: 037094) designed by Genotypic Technology Private Limited

first: Urooj

last: Fatima

first: Priyadarshini

last: Bhorali

first: Muthappa

last: Senthil-Kumar


title: Altered expression of genes in DANCR knockdown bladder cancer cells

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

summary: The prognosis for bladder cancer (BCa) patients with lymph node (LN) metastasis is forlorn and restrainedly improved by current treatment. DANCR is reported to play a role in prostate cancer and liver cancer. However, its function and underlying mechanism in BCa remains unknown. The goal of this study is to identify the target genes of DANCR in bladder cancer. Our results indicate that the genes regulated by DANCR are involved in a variety of biological functions, such as proliferation and metastasis.

overall_design: Bladder cancer cell line UM-UC-3 was transfected with the control siRNA or two different DANCR siRNA for 48h. The RNA of the transfected cells was extracted and hybridized on Affymetrix microarrays. We identified the putative target genes of DANCR in both DANCR siRNAs by comparing the different expressed genes among control, DANCR siRNA1 and DANCR siRNA2. We further validated the data of microarray in UM-UC-3 and T24 by RT-qPCR and Western blotting.

first: Ziyue

first: Ruihui

last: Xie

first: Tianxin

last: Lin


title: Transcriptome analysis of different brain areas in Hcrt gene and Hcrt cell ablated mice

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: Hypocretin (HCRT) and melanin concentrating hormone (MCH) are brain neuropeptides regulating a wide range of functions including sleep and metabolism. Loss of function of HCRT causes the sleep disorder narcolepsy. We found that loss of HCRT neurons in Hcrt-ataxin-3 mice results in a specific 50% decrease in another orexigenic neuropeptide QRFP that might explain the metabolic syndrome in narcolepsy.

overall_design: To identify cell type-specific regulators of HCRT cells, we used two commonly used mouse models of narcolepsy with cataplexy: Hcrt gene knockout (Hcrtko/ko) mice and Hcrt-ataxin-3 mice in which HCRT cells are ablated by the expression of ataxin-3 gene. We hypothesized that comparing the brain transcriptome of these mice and their controls might identify transcriptional changes due both to a lack of Hcrt gene and HCRT neurons altogether (as in narcolepsy).

first: Ali

last: Seifinejad

first: Sha

last: Li

first: Cyril

last: Mikhail

first: Anne

last: Vassalli

first: Yoan

last: Arribat

first: Hassan

last: Modarres

first: Bridget

last: Allen

first: Rosalind

last: John

first: Francesca

last: Amati

first: Mehdi

last: Tafti


title: Transcriptional profile of Mycobacterium tuberculosis mycP1-eccE1 deletion mutant

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

institute: University of Bern

summary: Mycobacterium tuberculosis is a slow-growing intracellular bacterium with the ability to induce host cell death and persist indefinitely in the human body. This pathogen uses the specialised ESX-1 secretion system to secrete virulence factors and potent immunogenic effectors required for disease progression. ESX-1 is a multi-subunit apparatus with a membrane complex that is predicted to form a pore in the cytoplasmic membrane. In M. tuberculosis this complex is made of five membrane proteins: EccB1, EccCa1, EccCb1, EccD1, EccE1. In this study, we have characterised the membrane component EccE1, and we found that deletion of eccE1 leads to disruption of ESX-1 secretion and attenuation of M. tuberculosis ex vivo.

overall_design: In this study, we have characterized the membrane component EccE1, and we found that deletion of eccE1 leads to disruption of ESX-1 secretion and attenuation of M. tuberculosis ex vivo.

first: Paloma

last: Soler

first: Stewart

middle: T

last: Cole


title: Transcriptome analysis of Y79 retinoblastoma cells upon Lysyl oxidase propeptide (LOX-PP) overexpression

city: Chennai

first: Karunakaran

last: Coral

state: Tamilnadu

address: 41, College road

department: R S Mehta Jain Department of Biochemistry and Cell Biology,

institute: Vision Research Foundation, Chennai

summary: Lysyl oxidase (LOX) is an copper dependent amine oxidase enzyme involved in cross linking of collagens and elastins. Lysyl oxidase propeptide (LOX-PP) is 18 kDa region cleaved during maturation of LOX and its anti-tumorigenic role were studied in various cancers. The effect of LOX-PP overexpression in retinoblastoma cancer cells (Y79) using transient transfection of LOX-PP gene accessed for global gene deregulations. The analysis resulted in RB cancer cell death through deregulation of retinoblastoma in cancer, cell cycle, apoptosis, focal adhesion-PI3K-AKT signaling and DNA repair mechanism pathway. Further validations were done using RT-PCR and western blot analysis. Our results provide evidence that inducing apoptosis through AKT-NFκB signaling.

overall_design: We analyzed Y79 cell from 2 Empty vector and 2 LOX-PP overexpressed cells using the Affymetrix Human Transcriptome array 2.0 platform. Array data was processed by Affymetrix Transcriptome Analysis Console (TAC) 4.0 - Exon level Array Computational Tool. No techinical replicates were performed.

first: Nareshkumar

last: Ragavachetty Nagaraj

first: Sulochana

last: Konerirajapuram Natarajan

first: Coral

last: Karunakaran


title: RNA-Seq Data

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: We report here the RNA-Seq data for Control_Untreated_BMDMS, Control_LPS Treated_BMDMs and SRF-KO-LPS Treated_BMDMs

overall_design: Examination of effect of LPS on gene expression and role of SRF

first: NIKHIL

last: JAIN


title: Time-dependent transcriptomic responses of Daphnia magna exposed to metabolic disruptors that enhanced storage lipid accumulation.

city: Barcelona

first: Inmaculada

last: Fuertes

state: Barcelona

address: Calle Jordi Girona, 18-26

department: Department of Environmental Chemistry

country: Spain

institute: CSIC

summary:
Transcriptomic profiling of Daphnia magna samples exposed to tributyltin (TBT), pyriproxyfen (PP) and bisphenol A (BPA) at 8 and 24 hours.
The analysis of lipid disruptive effects in invertebrates is limited by our poor knowledge of their lipidomes and of the associated metabolic pathways. Here we analyzed the subsequent transcriptome changes, using tributyltin (TBT), pyriproxyfen (PP) and bisphenol A (BPA). Changes in the whole transcriptome were assessed after 8 and 24 h of exposure, the period showing the greatest variation in storage lipid accumulation. The three compounds affected similarly to a total of 1388 genes (965 overexpressed  and 423 underexpressed transcripts), but only after 24h of exposure. In addition,225 transcripts became up-regulated only in samples exposed to tributyltin for both 8h and 24 h. Using functional annotation from  D. melanogaster, we determined that upregulated genes were enriched in members of KEGG modules implicated in fatty acid, phosphoinositol, glycerophospholipid,  and glycerolipid metabolic pathways, as well as in  genes related to  membrane constituents , and to chitin and cuticle metabolic pathways. Conversely, down-regulated genes appeared mainly related with to visual perception, and to oocyte development signalling pathways. Many tributyltin specifically upregulated genes were related to neuro-active ligand receptor interaction signalling pathway. These changes are consistent with the previous observation that exposure of  D. magna to the  tested compounds increases lipid accumulation and reduces egg quality.

overall_design: In total, 24 samples were analysed. 12 samples corresponding to juveniles of Daphnia 8h after the exposure just after the third molt, including 3 control-solvent samples, 3 exposed to 1 mg/L of tributyltin,  3 exposed to 1 mg/L of pyriproxyfen and 3 exposed to 10 mg/L for bisphenol A;  and 12 samples corresponding to juveniles of daphnia 24h after the exposure, including the same treatments mentioned before.

first: Rita

last: Jordão

first: Benjamín

last: Piña

first: Carlos

last: Barata


title: Molecular codes defining lateral hypothalamic sleep regulating neurons

first: Sylvain

last: Pradervand

summary: Hypothalamic hypocretin (HCRT) and melanin concentrating hormone (MCH) have multiple functions including sleep and metabolism. How these neuropeptides are produced and involved in divers functions remain unknown. We developed methods to sort and purify HCRT and MCH neurons from mouse hypothalamus. RNA-sequencing revealed key factors of fate determination for HCRT (Peg3, Ahr1, Six6, Nr2f2 and Prrx1) and MCH (Lmx1, Gbx2 and Peg3) neurons. Amongst these, loss of Peg3 in mice significantly reduces HCRT and MCH cell numbers while knock-down of Peg3 ortholog in zebrafish completely abolishes their expression resulting in a two fold increase in sleep. The transcriptome results were used to produce HCRT and MCH neurons from induced pluripotent stem cells (iPSCs) and ascorbic acid was found necessary for HCRT and BMP7 for MCH cell differentiation. Our results provide a platform to understand the development and expression of HCRT and MCH and their multiple functions in health and disease.

overall_design: Sorted cells mCherry positive (reporter in HCRT cells) versus mCherry negative; and sorted cells EGFP positive (reporter in MCH cells) versus EGFP negative.

first: Ali

last: Seifinejad

first: Sha

last: Li

first: Cyril

last: Mikhail

first: Anne

last: Vassalli

first: Yoan

last: Arribat

first: Hassan

last: Modarres

first: Bridget

last: Allen


title: Analysis of Fusarium verticillioides gene expression in response to nitric oxide (NO)

city: Athens

first: Anthony

middle: E.

last: Glenn

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

summary: Investigation of whole transcriptional changes in F. verticillioides wild-type (WT) strain FRC M-3125 and gene deletion strain ΔFVEG_10494-6.4 when treated with and without 1.5 mM diethylenetriamine (DETA) NONOate for 30 min, with three biological replicates each.  DETA NONOate is a NO-donor molecule.

overall_design: Strains were grown for three days in potato dextrose broth (PDB) buffered with 0.1 M sodium phosphate.  Prior to harvesting samples, the NO treatments received a 30 min exposure to 1.5 mM DETA NONOate dissolved in 0.01 M NaOH.

first: Shan

last: Gao

middle: E

first: Scott

last: Gold


title: Real-time quantitative PCR analysis of lungs from Litomosoides sigmodonis-infected mice

city: Paris

first: Frédéric

last: Fercoq

address: 61 Rue Buffon

department: AVIV

institute: MNHN

summary:
A pool of cDNA from naive BALB/c mice lungs (n=8) was compared with one from D70 p.i. Litomosoides sigmodontis-infected mice (n=8) by profiling 84 cytokine-related genes simultaneously.
Screening of inflammatory lung environment was performed with a qRT-PCR array (Mouse Cytokines & Chemokines RT2 Profiler PCR Array, Qiagen, Germany) according to manufacturer’s instructions.

overall_design: qPCR gene expression profiling. Equal amounts of total RNA per mice were used in the assay.

first: Coralie

last: Martin

first: Marc

last: Hübner


title: Cancer-educated mesenchymal stem cells promote pre-metastatic niche formation for disseminated cancer cells via the induction of PMN-MDSC expansion

city: Changsha

first: Buqing

last: Sai

state: Hunan

address: 110 Xiangya Road

institute: Buqing Sai

summary: We subcutaneously injected the RFP-LLC cells and GFP-BMSCs into C57BL/6 mice and then collected GFP-BMSCs from the primary inoculation cancer site and from the bone marrow by flow cytometric sorting technology.

overall_design: Examination of 4 different group of BMSCs. Gene expression profiling was performed on BMSCs collected from 3 samples for each group.

first: Juanjuan

last: Xiang


title: Macrophage Ad5f35 PhenoMap

first: Paul

last: Wang

summary: Human monocyte derived macrophages (GM-CSF differentiated) were stimulated with control media, IFNy/LPS (M1), IL4 (M2), empty vector Ad5f35 (MOI 1000), or anti-HER2 CAR Ad5f35 (MOI 1000). RNA was harvested 48 hours post transduction with Ambion RiboPure RNA Purification Kit (Thermo Fisher) and RNA-Seq libraries were generated using TruSeq RNA Library Prep Kit (Illumina). Libraries were sequenced on 75bp single-end reads using a NextSeq (Illumina).

overall_design: Examination of the transcriptome of control (n=4), M1 (n=3), M2 (n=4), empty vector adenovirally transduced (n=4), or anti-HER2 CAR adenovirally transduced human macrophages (n=4). Each n represents a unique normal human donor.

first: Michael

last: Klichinsky

first: Xueqing

last: Lu

first: Saar

last: Gill


title: Global gene expression profiling in A549 cells exposed to TCDD and BaP for 2 weeks

city: Brno

first: Jirina

last: Prochazkova

address: Kralovopolska 135

department: Cytokinetics

country: Czech Republic

institute: Institute of Biophysics CAS

summary:
Comparison of expression profiles detected in A549 cells exposed to DMSO, TCDD, and BaP for 2w
Exposure to persistent ligands of aryl hydrocarbon receptor (AhR) has been found to cause lung cancer in experimental animals and lung adenocarcinomas are often associated with enhanced AhR expression and aberrant AhR activation. In order to better understand the action of toxic AhR ligands in lung epithelial cells, we performed global gene expression profiling in order to analyse TCDD- induced changes in A549 transcriptome, and compare them with changes in transcriptome of A549 cells exposed to BaP for 2w.

overall_design: Control DMSO-treated A549 cells compared with A549 cells exposed to TCDD or BaP for 2 weeks, respectively.

first: Jiri

last: Klema

first: Miroslav

last: Machala


title: Protein arginine methyltransferase PRMT1 is essential for palatogenesis

city: Los Angeles

first: Jian

last: Xu

state: CA

address: 2250 Alcazar Street, CSA 106

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

summary: We report that neural crest-specific deletion of Prmt1 caused craniofacial malformations including cleft palate.

overall_design: It is expected that genes involved in proliferation and cell cycle control are altered by Prmt1 deficiency.

first: Yongchao

last: Gou

first: Jingyuan

last: Li

first: Olan

last: Jackson-Weaver

last: Wu

first: Tingwei

last: Zhang

first: Yusuke

last: Higuchi

first: Ihnbae

last: Cho

first: Thach-Vu

last: Ho

first: Yibu

last: Chen

first: Meng

first: Stéphane

last: Richard

first: Jun

first: Yang

last: Chai


title: Next Generation Sequencing Facilitates Quantitative Analysis of testis Transcriptomes in Xenopus laevis

city: Ji Nan

first: Sai

last: Linlin

state: Shan Dong

address: 18877 Jingshi Road, Lixia District

institute: Shandong Academy of Occupational Health and Occupational Medicine, Jinan, Shandong, China

summary:
Purpose: Circular RNAs (circRNAs) are implicated in multiple developmental anomalies. The goals of this study are to research whether circRNAs involve in the effects in atrazine (AZ)-exposed X. laevis
Methods: At Nieuwkoop-Faber (NF) stage 47 (13 d post-hatch), mixed sex X. laevis tadpoles exposed to 100 µg/L AZ for 180 days. Then total RNAs from individual testis was isolated. RNA library construction and circRNA sequencing was analysis
Results: CircRNAs were detected and identified with Find_circ software. We found that treatment of AZ led to 405 circRNAs differentially expressed including 44 upregulated and 361 downregulated compared with froglets in the control groups. Two hundreds and eighty two differentially expressed circRNAs played miRNA sponges roles. Kyoto Encyclopedia of Genes and Genomes pathway analysis of miRNA targets showed that AZ-affected circRNAs are mainly involved in 19 pathways
Conclusions: This study for the fisrt time provides evidence that AZ can alter circRNAs which play a role in AZ-induced testicular degeneration of developing male X. laevis through regulation of expressions of functional genes in the testes of X. laevis.

overall_design: Examing circRNAs of testes of  X. laevis from 2 conditions including AZ-treated and control, each with 3 replicates, using Illumina HiSeq 4000

first: sai

last: linlin


title: Detoxifying doxorubicin

city: Leiden

first: Daniel

middle: M.

last: Borras

address: Einthovenweg 20

department: CI

country: Netherlands

institute: LUMC

summary: The anthracycline doxorubicin is a highly effective anti-cancer drug associated with severe side effects, including secondary tumors and cardiotoxicity. Doxorubicin induces DNA damage through double-strand breaks (DSBs) and epigenetic or chromatin damage through histone eviction. We examined whether separation of these activities can help to detoxify doxorubicin, while maintaining its chemotherapeutic efficacy. We show that anthracycline variants harboring the histone eviction activity alone remain potent anti-cancer drugs, while greatly alleviating cardiotoxicity and secondary tumor formation. We thus demonstrate that treatment-limited side effects of doxorubicin can be synthesized away, yielding effective chemotherapeutics towards improved and prolonged treatment responses and higher patient quality of life.

overall_design: Comparison of FAIRE-seq and yH2AX ChIP-seq signal for several anticancer drugs

first: Xiaohang

last: Qiao

first: Sabina

last: van de Zanden

first: Dennis

last: Wander

first: Olaf

last: van Tellingen

first: Jeroen

last: Bakker

first: Ji-Ying

last: Song

first: Arjo

last: Rutten

first: Noortje

last: van Gils

first: Charlotte

last: Zuur

first: Baoxu

last: Pang

first: Linda

last: Smit

first: Hermen

last: Overkleeft

first: Jacques

last: Neefjes


title: Cell-intrinsic Depletion of Aml1-ETO-positive Pre-leukemic HSCs by K-Ras Activating Mutation

city: Oxford

first: Cristina

last: Di Genua

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Somatic mutations in acute myeloid leukemia (AML) are acquired sequentially and hierarchically. First, pre-leukemic mutations, such as t(8;21) that encodes AML1-ETO, are acquired within the hematopoietic stem cell (HSC) compartment, while signaling pathway mutations, including K-RAS activating mutations, are late events acquired during transformation of leukemic progenitor cells and rarely detectable in HSCs. This raises the possibility that signaling pathway mutations are detrimental to clonal expansion of pre-leukemic HSCs. To address this hypothesis we here used conditional genetics to introduce Aml1-ETO and K-RasG12D into murine HSCs, either individually or in combination.  In the absence of activated Ras, Aml1-ETO expression conferred a competitive advantage to HSCs. However, activated K-Ras had a marked detrimental effect on Aml1-ETO expressing HSCs, leading to loss of both phenotypic and functional HSCs. Cell cycle analysis revealed a loss of quiescence in HSCs co-expressing Aml1-ETO and K-RasG12D, accompanied by an enrichment in E2F and Myc target gene expression and depletion of HSC self-renewal-associated gene expression. These findings provide a mechanistic basis for the observed absence of KRAS, and potentially other, signaling mutations in the pre-malignant HSC compartment.

overall_design: RNA-sequencing of bulk LSKCD150+Flt3-CD45.2+ cells from five different competitively transplanted recipients of WT, Aml1ETO/+, KrasG12D/+ and Aml1ETO/+;KrasG12D/+  fetal liver cells eight weeks post-poly(I:C)

first: Adam

last: Mead

first: Claus

last: Nerlov


title: Transcriptional profiling of neurons in the thalamus of a Cbln1-TRAP (NIDA030) mouse line

status: Public on Aug 31 2019

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the thalamus of adult Cbln1-EGFP/Rpl10a (NIDA030) mice.  This work was supported by a grant from the National Institute on Drug Abuse P30DA035756 to N.H.

overall_design: TRAP-Seq of neurons in the thalamus of adult Cbln1-EGFP/Rpl10a (NIDA030) control mice.

first: Jim

last: Li

first: Nathaniel

last: Heintz


title: Transcriptional profiling of neurons in the rostral pons of a Cbln2-TRAP (NIDA172) mouse line

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the rostral pons of adult Cbln2-EGFP/Rpl10a (NIDA172) mice.  This brain area includes the locus coeruleus and parabrachial nuclei.  This work was supported by a grant from the National Institute on Drug Abuse P30DA035756 to N.H.

overall_design: TRAP-Seq of neurons in the rostral pons of adult Cbln2-EGFP/Rpl10a (NIDA172) control mice.

first: Cuidong

last: Wang


title: Impairment of cardiac natriuretic peptide signaling develops the excessive cardiac hypertrophy during lactation period

city: Suita

first: Kentaro

last: Otani

address: 5-7-1 Fujishiro-dai

department: Department of Regenerative Medicine and Tissue Engineering

institute: National Cerebral and Cardiovascular Center Research Institute

summary:
Two natriuretic peptides, atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) act through the common receptor, guanylyl cyclase-A (GC-A) to lower blood pressure, induce diuresis/natriuresis and dilate blood vessels. Recently, we discovered that the excessive cardiac hypertrophy accompanied with cardiac dysfunction was induced in the lactating natriuretic peptide receptor 1 (Npr1, which encodes GC-A)-deficient mice. To clarify the cause of lactation-induced cardic hypertrophy in Npr1-/-,  we performed the gene expressions analysis using nulliparous (NP) or postpartum lactating wild-type (Npr1+/+) and Npr1-/- mice.
Numerous genes were altered in the postpartum lactating period both in Npr1+/+ and Npr1-/-. Additionally, the involvement of inflammatory responce in the cardiac hypertrophy in lactating-Npr1-/- mice was clarified bythe gene ontology analysis.

overall_design: Gene expressions of female mice heart were examined in nulliparous (NP) and lactating (Lactation) Npr1+/+ and Npr1-/- mice. Four independent mice were utilized for analysis.

first: Takeshi

last: Hasegawa


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, SphK1-/- and SphK2-/- fibroblasts Transcriptomes

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary: In numerous forms of organ injury, interstitial fibrosis is a final common pathway. Despite recent epidemiological studies, therapies to focus on fibrosis and to delay progressive renal failure are limited. Previously our group showed that sphingosine kinase 2 deficient-mice (SphK2-/-) develop less fibrosis in folic acid-induced or unilateral ischemia-reperfusion injury (IRI)-induced kidney fibrosis models. Sphingosine 1-phosphate (S1P) is produced by two sphingosine kinase isoforms (SphK1 and SphK2). S1P is involved in diverse functions, but the role of S1P produced by SphK2 is gathering attention as treatments focused on epigenetics have been developed. SphK2 is primarily located in the nucleus and S1P produced by SphK2 inhibits histone deacetylase (HDAC) and changes in histone acetylation status, which can lead to an altered target gene expression. We identified that bone marrow stromal cell antigen-1 (Bst1/CD157) is a gene related with kidney fibrosis based on the combination of genome-wide analysis and in vivo screening. SphK2 regulates Bst1 expression and Bst1-/- mice develop less fibrosis after unilateral IRI and are protected against renal bilateral IRI. Bone marrow chimera experiments further revealed the importance of Bst1 expression on hematopoietic cells. Furthermore we identified the role of Bst1 expression in neutrophils for inducing renal ischemia-reperfusion injury and fibrosis.

overall_design: Renal fibroblast's mRNA profiles of wild type (WT), SphK1-/- and SphK2-/- mice were generated by deep sequencing.

first: Tsuyoshi

last: Inoue

first: Youichiro

last: Wada

first: Mark

middle: D

last: Okusa


title: miR-21-5p-driven gene expression in human colorectal DLD-1 cells.

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: Gene expression analysis of stable miR-21-5p-overexpressing DLD-1 cells (DLD-1-miR-21) and its control cells (DLD-1-miR-Vec).

overall_design: To establish stable miR-21-overexpressing DLD-1 (DLD-1-miR-21) and corresponding vector-overexpressing (DLD-1-miR-Vec) cell lines, parental DLD-1 cells were transfected with a plasmid encoding human miR-21 or its control vector (pCMV-MIR) using the PolyJet transfection reagent. Stable clones were selected with 1 mg/mL G418 for 2 months. Single clones were selected based on expression of the green fluorescent protein (GFP) reporter and then pooled together for subsequent experiments.


title: Expression data from 2D and 3D HepG2 cells

city: Durham

first: Sreenivasa

last: Ramaiahgari

state: NC

address: 111 TW Alexander drive

department: National Toxicology Program

institute: NIEHS

summary:
Expression data from HepG2 cultured in 2D monolayer cultures and 3D Matrigel cultures
We performed this study to understand differences in gene expression profiles of 2D and 3D HepG2 cultures

overall_design: RNA samples were collected from 2D monolayer cells cultured for 3 days and 3D HepG2 cultured for 3-,7-,14-,21- and 28-days

first: Bob

last: van de Water


title: Characterization of SFPQ role in ovarian cancer cell lines

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

country: Italy

institute: CRO Aviano

summary: SFPQ is a multifunctional nuclear protein first identified as a splicing factor, that participates in several cellular activities, including RNA transport, apoptosis and DNA repair. Here we report that SFPQ is a key mediator of platinum sensitivity in Epithelial Ovarian Cancer cell lines.

overall_design: GEP experiments were performed in human ovarian cancer cell lines silenced for SFPQ, with Agilent platform. Bioinformatics analyses were performed by Gene Springs

first: Ilenia

last: Pellarin

last: Pellizzari

first: Gustavo

last: Baldassarre

first: Barbara

last: Belletti


title: Transcriptional profiling of neurons in the thalamus of a Slc17a6-TRAP (JX883) mouse line

first: Laura

last: Kus

summary: TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain.  Using this technique we obtained RNA-Seq data from actively translating transcripts present in neurons in the thalamus of adult Slc17a6-EGFP/Rpl10a (JX883) mice.  Slc17a6 is also known as Vglut2.  This work was supported by a grant from the National Institute on Drug Abuse P30DA035756 to N.H.

overall_design: TRAP-Seq of neurons in the thalamus of adult Slc17a6-EGFP/Rpl10a (JX883) control mice.

first: Jie

last: Xing

last: Li


title: Translocation driven high expression of NOTCH2 in glomus tumors of the upper digestive tract

city: Boulogne

first: Jean-François

last: Emile

state: Ile-de-France

address: 9 avenue Charles de Gaulle

department: Pathology

institute: Hopital Ambroise Paré

summary: Glomus tumors (GT) are perivascular tumors mostly occurring in the distal extremities. Rare cases occur in the digestive tract and may be misdiagnosed with neuroendocrine or gastrointestinal stromal tumors. We aimed to specify the features of GT of the upper digestive tract.  We investigated two cases using whole exome sequencing (WES) and RNA-sequencing, and present clinical, histological, phenotypic and molecular features of 16 cases.  WES did not reveal any commonly involved cellular pathway. By contrast, RNA-sequencing disclosed a t(1:5)(p13;q32) translocation between MIR143HG and NOTCH2 in both cases. The deducted fusion protein sequence corresponded to the NOTCH2 intracellular domain known as NICD2, which acts as transcription factor.  These data were confirmed by high expression of the transcripts of genes targeted by NOTCH cellular pathway (HES and HEY gene families). In our retrospective multicentric series of 16 GT of upper digestive tract MIR143HG-NOTCH2 translocation was detected in 14 (88%) cases. By contrast, it was present in only 2/6 (33%) GT of the distal extremities.   Most digestive GT raised from the stomach (n=13), and the others from duodenal (2) or oesophagous (1). All digestive GT were positive for α-smooth muscle actin and transgelin, and negative for cytokeratin AE1/AE3, chromogranine, DOG1, KIT and S100. Most cases were positive for H-caldesmon (n=14) and/or for synaptophysin (n=10). Desmin, CD34 or CD56 were positive in only one case each. Nuclear expression of NOTCH2 was detected in the 14 cases containing the fusion transcripts.  The present study shows that MIR143HG-NOTCH2 translocation is present in most digestive GT. This fusion transcript is associated with activation of the NOTCH2 pathway and may drive tumor development. Detection of nuclear NOTCH2 expression may be helpful for diagnosis.

overall_design: Examination of fusion transcript of 2 glomus tumors of the upper digestive tract

first: Nicolas

last: Girard


title: Whole Blood MicroRNA Biomarkers for Blood-stage of Imported Falciparum Malaria through Integrated mRNA and miRNA Expression Profiling [miRNA]

city: beijing

first: Yang

last: Zou

address: Xicheng District road 95 Yongan

institute: Beijing Friendship Hospital Affiliated to the Capital University of Medical Sciences.

summary: human blood mRNA and miRNA expression profile in imported falciparum malaria vs. health.

overall_design: To explore the in vivo function of miRNAs blood-stage of imported falciparum malaria patients, we used Primeview microarrays to examine the occurrence of human mature mRNAs and miRNA4.0 microarrays to examine the occurrence of human mature miRNAs in whole blood specimens obtained from 6 Chinese imported falciparum malaria and 6 normal subjects, respectively.

first: Jingjing


title: Whole Blood MicroRNA Biomarkers for Blood-stage of Imported Falciparum Malaria through Integrated mRNA and miRNA Expression Profiling [mRNA]


title: Characterization of Whole Genome DNA Methylation Profile Associated with Post-Traumatic Stress Disorder in OIF/OEF Veterans [bisulfite-converted DNA]

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Emerging knowledge suggests that post-traumatic stress disorder (PTSD) is causally associated with epigenetic changes although its molecular underpinnings are still largely elusive. We postulate that differentially methylated probes mined from peripheral whole blood could be candidates for potential PTSD diagnostic signatures. Working within the Systems Biology PTSD Biomarker Consortium (SBPBC), we investigated a training set comprising of 48 PTSD male veterans (CAPS > 40) and 51 age/ethnicity matched controls (CAPS < 20). Agilent whole genome array detected ~5,600 differentially methylated CpG islands (CpGI) annotated to ~2,800 differentially methylated genes (DMG). The majority (84.5%) of these DMGs was hypermethylated in PTSD veterans. Thereof ~30% promoter-bound DMGs were used for functional analysis. Taking cues from the clinical information, the curated networks were enlisted into four major clusters, namely PTSD-associated complications, PTSD-relevant endocrine signaling, nervous system development and nervous system functions. Enduring impacts of PTSD was manifested by differentially methylated genes enriching networks associated with LTP, fear memory architecture and complications linked to insulin resistance and innate immunity.  These networks were further validated by an independent test set comprising of 31/29 PTSD+/- veteran selected using aforementioned screening protocol. Two independent assay platforms presented technical validations. Probing the combined 83/83 PTSD+/- cohort, whole genome array from Illumina, Inc. validated most of the networks of interest. Methylation statuses of eight DMGs relevant to PTSD and comorbidities were confirmed by targeted bisulfite sequencing. This list presents a potential set of PTSD biomarkers of translational potential.

overall_design: Working within the Systems Biology PTSD Biomarker Consortium (SBPBC), we investigated a training set comprising of 48 PTSD male veterans (CAPS > 40) and 51 age/ethnicity matched controls (CAPS < 20). Agilent whole genome array detected ~5,600 differentially methylated CpG islands (CpGI) annotated to ~2,800 differentially methylated genes (DMG). A second study for further validation was conducted by an independent test set comprising of 31/29 PTSD+/- veteran. In this study, Bisulphite converted DNA from the 159 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip ,v1.0

first: Rasha

last: Hammamieh

first: Nabarun

last: Chakraborty

first: Seid

last: Muhie

first: Ruoting

first: Raina

last: Kumar

first: Bernie

last: Daigle

first: Yuanyang

last: Zhang

first: Duna

last: Abu Amara

first: Stacy-Ann

last: Miller

first: Seshamalini

last: Srinivasan

first: Rachel

last: Yehuda

first: Linda

last: Petzold

first: Frank

last: Doyle

first: Owen

last: Wolkowitz

first: Sindy

last: Mellon

first: Charles

last: Marmar

first: Marti

last: Jett


title: Genome-wide single nucleotide polymorphism array analysis unveils the origin of heterozygous androgenetic complete moles

city: Chiba

first: Hirokazu

last: Usui

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

department: Department of Reproductive Medicine

institute: Graduate School of Medicine, Chiba University

summary:
Heterozygous CHMs have been believed as synonymous with dispermic moles (two sperm origin). The possibility of diploid sperm origin has not been considered. We assessed whether heterozygous CHMs would be of dispermic or diploid sperm origin.
In all the cases, centromeric zygosity was random, i.e., mixed status. Theoretically, if the heterozygous CHMs were of diploid sperm origin, the centromeric status will be all homozygous or all heterozygous. Thus, all the analyzed heterozygous CHMs were considered to be of dispermic origin. Three cases showed the trisomy while we did not notice them with STR analysis. Diploid sperm fertilization can be rare during the development of heterozygous androgenetic CHM.

overall_design: The villous genomic DNA of the thirteen heterozygous CHMs was further analyzed using the single nucleotide polymorphism array. B allele frequency (BAF) plotting was used to determine the centromeric zygosity status of all chromosomes to discriminate dispermic origin from diploid sperm origin.

first: H

first: K

last: Nakabayashi

last: Maehara

last: Hata

first: M

last: Shozu


title: Comparison of the lymphocyte before and after the activation.

city: Fukuoka

first: Akiko

last: Fujimura

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Cancer Therapy and Research

institute: Graduate School of Medical Sciences Kyushu University

summary: Immunotherapy using activated lymphocytes has recently been developed, but there is not yet the biomarker which can predict curative effect. In our recent study, we found that random migration is significantly increased in activated lymphocyte. Furthermore, it is suggested that random migration may affect cytotoxicity. Therefore we considered that migration of lymphocyte may become the effect prediction biomarker of Immunotherapy. And then we analyzed the gene which fluctuated by lymphocyte activation to search the molecules which positive regulate migration of lymphocyte.

overall_design: To search the molecules which positively regulate migration of lymphocyte,we prepared a lymphocyte from the human peripheral blood and compared the gene expression before and after the activation.

first: Hideya

last: Onishi

first: Takashi

last: Morisaki

last: Nakagawa


title: Small noncoding RNA levels in plasma from breast cancer patients and healthy controls

city: Auckland

first: Annette

last: Lasham

address: 85 Park Road

country: New Zealand

institute: University of Auckland

summary: Plasma small noncoding RNA levels were measured in breast cancer patients and healthy control women, to determine whether any of these were associated with either patient prognosis, or as diagnostic markers for breast cancer.

overall_design: RNAs were extracted from plasma from 30 breast cancer patients and from 10 healthy, control women. The levels of small noncoding RNAs were quantitated using Affymetrix microarrays

first: Sandra

last: Fitzgerald

first: Tamsin

last: Robb

first: Peter

last: Tsai

first: Michael

last: Black

first: Liam

last: Wiliams

first: Nicholas

last: Knowlton

first: Sunali

middle: Y

last: Mehta

first: Gavin

last: Harris

first: Andrew

middle: N

last: Shelling

first: Cherie

last: Blenkiron

first: Cristin

middle: G

last: Print


title: TF ChIP-seq from CH12.LX (ENCSR973SOG)

status: Public on Aug 30 2019

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
USF1 ChIP-seq mouse CH12 produced by the Snyder lab

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


title: Transcriptomic analysis of Col and arf7 responding to auxin in hypocotyl

city: Qingdao

first: feng

last: zhang

state: Shandong

address: 72 Binhai Road

institute: shandong university

summary: The goal of this study is to clarify the function of ARF7 in the pathway of auxin inducing the process responding to gravity in hypocotyl. We isolated total RNA from the hypocotyls of 4-day-old Col-0 and arf7 seedlings that were grown in the darkness. New genes act downstream of ARF7 after responding to auxin treatment, responding to gravity, are discovered.

overall_design: We isolated total RNA from the hypocotyls of 4-day-old Col-0 and arf7 etiolated seedlings with or without auxin treatment.

first: Feng

last: Zhang

first: ZhaoJun

last: Ding


title: Histone ChIP-seq from E14TG2a.4 (ENCSR857MYS)

summary:
PSU mouse E14Tg2a.4 H3K9me3 ChIP-seq

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


title: TF ChIP-seq from CH12.LX (ENCSR906QEK)

summary:
TCF12 ChIP-seq mouse CH12 produced by the Snyder lab

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


title: Whole Blood MicroRNA Biomarkers for Blood-stage of Imported Falciparum Malaria through Integrated mRNA and miRNA Expression Profiling

first: Yang

last: Zou

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: TF ChIP-seq from HepG2 (ENCSR854JES)

summary:
POLR2G ChIP-seq on HepG2

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


title: Severe sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA

city: Bethesda

first: Heejin

last: Choi

state: Maryland

address: 50 South drive, Building 50, Room 3131

institute: NIH

summary: Purpose: piRNAs are a class of germline-specific, small non-coding RNAs required to maintain genome integrity and preserve RNA homeostasis essential for male gametogenesis. During mouse spermatogenesis, male germ cells transcribe piRNAs at pre-pachytene anad pachytene stages of development from genetically distince loci. The most well-studied and conserved function of pre-pachytene piRNAs is repression of transposons to ensure the integrity of the germline genome. In contrast to pre-pachytene piRNAs, the mode of action and function of pachytene piRNA is much less understood. To investigate and characterize the functional importance of pachytene piRNAs in spermatogenesis and male fertility, we have used CRISPR/Cas9 and established mutant mice which have deleted a bi-directional promoter of the pachytene piRNA cluster on Chr18. Mutant mice have a male sterile  phenotype with acrosome overgrowth and defective motility.

overall_design: Methods: Testes mRNA and ncRNA profiles of P28 wild-type (+/+), heterozygous (+/-), and homozygous (-/-) mice were generated by deep sequencing , in triplicate, using Illumina's TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer instruction. The fragment size of RNAseq libraries was verified using the Agilent 2100 Bioanalyzer and the concentrations were determined using Qubit instrument. The libraries were loaded onto the Illumina Hiseq 3000 for 2X50 bp paired end read sequencing. The fastq files were generated using the bcl2fastq software for further analysis.

first: Cameron

last: Palmer

first: Jurrien

last: Dean


title: TF ChIP-seq from CH12.LX (ENCSR806JZK)

summary:
MEF2A ChIP-seq mouse CH12 produced by the Snyder lab

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


title: TF ChIP-seq from E14TG2a.4 (ENCSR779CZG)

summary:
PSU mouse E14Tg2a.4 NANOG ChIP-seq

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


title: TF ChIP-seq from K562 (ENCSR764OXF)

summary:
RBM39 ChIP-seq in K562

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


title: TF ChIP-seq from K562 (ENCSR814AJH)

summary:
SRSF9 ChIP-seq in K562

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


title: TF ChIP-seq from MEL cell line (ENCSR705HGT)

summary:
USF1 ChIP-seq mouse MEL produced by the Snyder lab

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


title: TF ChIP-seq from CH12.LX (ENCSR743ZJL)

summary:
IRF4 ChIP-seq mouse CH12 produced by the Snyder lab

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


title: Histone ChIP-seq from skeletal muscle myoblast (ENCSR596NOF)

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


title: TF ChIP-seq from K562 (ENCSR598GER)

summary:
CCAR2 ChIP-seq in K562

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


title: TF ChIP-seq from CH12.LX (ENCSR980YXJ)

summary:
NRF1 ChIP-seq mouse CH12 produced by the Snyder lab

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


title: TF ChIP-seq from ES-E14 (ENCSR531HWD)

summary:
CHD2 ChIP-seq mouse ES-E14 produced by the Snyder lab

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


title: Histone ChIP-seq from tibial artery (ENCSR535GFO)


title: TF ChIP-seq from body of pancreas (ENCSR572DUJ)


title: TF ChIP-seq from E14TG2a.4 (ENCSR392DGA)

summary:
PSU mouse E14Tg2a.4 POU5F1 (OCT4) ChIP-seq

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


title: TF ChIP-seq from E14TG2a.4 (ENCSR362VNF)

summary:
PSU mouse E14Tg2a.4 CTCF ChIP-seq

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


title: TF ChIP-seq from K562 (ENCSR506KWJ)

summary:
XRCC5 ChIP-seq in K562

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


title: TF ChIP-seq from K562 (ENCSR462QZZ)

summary:
eGFP-ZNF395 ChIP-seq on human K562

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


title: TF ChIP-seq from MEL cell line (ENCSR349JDH)

summary:
TCF12 ChIP-seq mouse MEL produced by the Snyder lab

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


title: Control ChIP-seq from E14TG2a.4 (ENCSR326ULS)

summary:
PSU mouse E14Tg2a.4 Control ChIP-seq

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


title: TF ChIP-seq from K562 (ENCSR283ZRI)

summary:
POLR2G ChIP-seq in K562

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


title: TF ChIP-seq from HepG2 (ENCSR247XFV)

summary:
KIAA1967 ChIP-seq on HepG2

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


title: TF ChIP-seq from K562 (ENCSR581CVA)

summary:
HNRNPH1 ChIP-seq in K562

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


title: TF ChIP-seq from CH12.LX (ENCSR293WTN)

summary:
ELF1 ChIP-seq mouse CH12 produced by the Snyder lab

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


title: Histone ChIP-seq from E14TG2a.4 (ENCSR212KGS)

summary:
PSU mouse E14Tg2a.4 H3K4me3 ChIP-seq

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


title: TF ChIP-seq from K562 (ENCSR189YMA)

summary:
eGFP-VEZF1 ChIP-seq on human K562

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


title: TF ChIP-seq from HepG2 (ENCSR145CXH)

summary:
TARDBP ChIP-seq in HepG2

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


title: TF ChIP-seq from H1 (ENCSR160ZLP)

summary:
ChIP-seq on human H1-hESC KDM5A

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


title: TF ChIP-seq from K562 (ENCSR158RYZ)

summary:
eGFP-ZBTB40 ChIP-seq on human K562

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


title: TF ChIP-seq from HepG2 (ENCSR151NQL)

summary:
AGO2 ChIP-seq in HepG2

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


title: TF ChIP-seq from MEL cell line (ENCSR033OWC)

summary:
ELF1 ChIP-seq mouse MEL produced by the Snyder lab

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


title: TF ChIP-seq from HepG2 (ENCSR066FXN)

summary:
HNRNPH1 ChIP-seq in HepG2

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


title: TF ChIP-seq from K562 (ENCSR072VUO)

summary:
SAFB ChIP-seq in K562

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


title: TF ChIP-seq from HepG2 (ENCSR031URL)

summary:
XRCC5 ChIP-seq in HepG2

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


title: TF ChIP-seq from K562 (ENCSR018MSO)

summary:
eGFP-ZNF148 ChIP-seq on human K562

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


title: PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to identify genes induced upon type I and II interferon response and how loss of PRC2/EZH2 impacts their induction.
Methods: mRNA-seq from cells treated with universal type I IFN alpha/beta  or IFN gamma. miRNA-seq from GBM-derived tumor samples.

overall_design: mRNA-seq from cells treated with IFN alpha/beta or IFN gamma, each with two independent replicates.

first: Haridha

last: Shivram

first: Vishwanath


title: Histone ChIP-seq from mammary epithelial cell (ENCSR016JWS)

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


title: Histone ChIP-seq from E14TG2a.4 (ENCSR032JUI)

summary:
PSU mouse E14Tg2a.4 H3K4me1 ChIP-seq

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


title: EWS-FLI1 modulated alternative splicing of ARID1A reveals novel oncogenic function through the BAF complex

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: There is a long-established connection between epigenetic reprogramming and the local function of the spliceosome. Recently the oncogenic potential of this connection has also been recognized. Recent work has demonstrated that EWS-FLI1 recruits the BRG1/BRM-associated factor (BAF) complex, however, the specific BAF subunits that interact with EWS-FLI1 and the role of the BAF complex in oncogenesis remains unknown. Within the BAF complex, the AT-rich interactive domain-containing protein 1A (ARID1A, BAF250a) gene encodes a central scaffold. EWS-FLI1 is a well-described transcriptional regulator that also has a role in modulating RNA splicing. While EWS-FLI1 alters the splicing of many mRNA isoforms, the role of splicing modulation in ES oncogenesis remains unknown. Here we report a direct connection between the EWS-FLI1-induced transcriptome and the EWS-FLI1 protein interactome to reveal a novel interaction with a specific isoform of ARID1A that has a direct impact on oncogenicity. We report a novel feed-forward cycle of EWS-FLI1 and ARID1A-L facilitating ES growth through splicing modulation and protein stability that may lead to improved cancer-specific drug targeting.

overall_design: 2 replicates each of WT, shEWS-FLI1 (EF) and shARID1A in TC32 and A4573 cell lines

first: Saravana

last: Selvanathan

first: Murat

last: Tuğrul

first: Eleni

last: Tomazou

first: Heinrich

last: Kovar

first: Alexander

last: Grego

first: Tabari

last: Baker

first: J

last: Hogg

first: Mark

last: Simpson

first: Mona

last: Batish

first: Brian

last: Crompton

first: Kimberly

last: Stegmaier

first: Aykut

last: Üren

first: Jeffrey

last: Toretsky


title: Histone ChIP-seq from GM08714 (ENCSR000FCL)

first: ENCODE

last: DCC

summary:
H3K4me3 GM08714 (ICF) ChIP-Seq

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


title: Identification of potassium phosphite responsive miRNAs and their targets in potato

city: Mar del Plata

first: Mariana

middle: Laura

last: Feldman

state: Buenos Aires

address: Funes 3250 4to nivel

country: Argentina

institute: IIB-CONICET- Univ. Nac. de Mar del Plata

summary: The use of phosphites in disease control management and abiotic stress has proven to be effective. Although the mechanisms underlying their effect remain unclear, it has been postulated that miRNAs could be involved. In order to understand these mechanisms we performed NGS sequencing in potato leaves treated or not with KPhi to identify miRNAs responsive to this biocompatible compound. The aim of the present work is to identify miRNAs that are involved in the regulation of potato defense responses after phosphite treatment.

overall_design: miRNAs differential expression between potassium phosphite treated and non treated potato plants. Three biological replicates were made for each treatment.

first: M

last: Rey-Burusco

first: Gustavo

last: Daleo

middle: L


title: Single-cell sequencing of Klinefelter testicular biopsies

city: Münster

first: Sandra

last: Laurentino

address: Domagkstr. 11

institute: University of Münster

summary: We have evaluated the transcriptome of different testicular cell types, including germ cells, at single cell level in a testicular biopsy of a man with Klinefelter syndrome (XXY karyotype)

overall_design: A testicular biopsy was enzymatically digested and single-cell RNAseq libraries were obtained using 10X genomics platform (10x Genomics Chromium Single Cell Reagent Kit v2). The libraries were sequenced on a NovaSeq600 sequencer (Illumina) using 2x150 bp paired-end sequencing.

first: Laura

last: Heckmann

first: Sara

last: Di Persio

first: Xiaolin

last: Li

first: Gerd

last: Meyer zu Hörste

first: Joachim

last: Wistuba

first: Jann-Frederik

last: Cremers

first: Jörg

last: Gromoll

first: Sabine

last: Kliesch

first: Stefan

last: Schlatt

first: Nina

last: Neuhaus


title: Myositis muscle

city: Boston

first: Steven

last: Greenberg

state: MA

address: 60 Fenwood Road

department: Neurology

country: USA

institute: Brigham and Women's Hospital

summary:
Expression profiling of human myositis muscle samples
This study was designed to compare expression signatures among the various types of inflammatory myopathy, dermatomyositis (DM), inclusion body myositis (IBM), necrotizing myopathy (NM), nonspecific myopathy (NS), and polymyositis (PM) compared to normal (NL) muscle.

overall_design: Muscle samples from human biopsies with DM, IBM, NM, NS, PM, or normal were studied for gene expression to identify differentially expressed genes.


title: Xist RNA-dependent Polycomb recruitment through the B and C repeats results in mild relaxation of X-linked transcriptional silencing

status: Public on Aug 28 2019

city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

country: France

institute: Institut Curie

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


title: RNAseq on Xist-tetOP FL, ΔA, ΔB+C cell lines, with 2 days of differentiation, without or with DOX induction

summary: Xist RNA has been established as the master regulator of X-chromosome inactivation in female eutherian mammals but its mechanism of action remain unclear. By creating novel Xist mutants at the endogenous locus in mouse embryonic stem cells, we dissect the role of most of the conserved A-F repeats. We find that transcriptional silencing can be uncoupled from Polycomb repressive complex 1 and 2 (PRC1/2) recruitment, which requires repeats B and C. Xist ΔB+C specifically looses interaction with PCGF3/5 subunits of PRC1, while binding of other Xist partners are largely unaffected. However, a slight relaxation of transcriptional silencing in Xist ΔB+C indicates a role for PRC1/2 proteins in early stabilization of gene repression. Distinct structural modules within the Xist RNA are therefore involved in the convergence of independent chromatin modification and gene repression pathways, with Polycomb recruitment only being of moderate relevance in the initiation of silencing.

overall_design: RNAseq on Xist-tetOP FL, ΔA, ΔB+C cell line, after 2 days of differentiation, in presence or absence of  DOX, in replicates.

first: Ana

last: Raposo

first: Jan

middle: J

last: Zylicz

first: Christel

last: Picard

first: Vanessa

last: Borges Pires

first: Yanyan

last: Qi

first: Laurène

last: Syx

first: Howard

last: Chang

first: Edith

last: Heard

first: Simão

last: Teixeira da Rocha


overall_design: Native ChIPseq on H3K27me3 and H2AK119Ub on  Xist-tetOP ΔB+C cell line, after 2 days of differentiation, with or without DOX induction, in replicates.


title: Single-cell transcriptomic map of the human and mouse bladders

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: A comprehensive cellular anatomy of normal human bladder is vital to address the cellular origins of benign bladder disease and bladder cancer. The physiological function and pathological changes of bladder are associated with its cell type. To investigate the classification and underlying function of bladder cells, we conducted single-cell RNA sequencing (scRNA seq) of 12,423 cells from human bladder and 12,884 cells from mouse bladder. Here, we show a single-cell transcriptomic map of the human and mouse bladders, including 16 clusters of human bladder cells and 15 clusters of mouse bladder cells. Homology and heterogeneity of human and mouse were compared and analyzed by our study, and indicated that there were both conservative and heterogeneous aspects of human and mouse evolution. We also discovered two novel types of human bladder cells; one type is ADRA2A+ and HRH2+ interstitial cells which may be associated with nerve conduction and allergic reactions; the other type is TNNT1+ epithelial cells that may be different from other epithelial cells in biological function. Collectively, this analysis provides a resource for the discovery of novel cell type, specific transcription factors, signaling receptors, and genes dataset that will help us to study the relationship between cell types and diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Primary bladder samples from 3 patients and  C57BL/6 mice were used for single cell RNA sequencing by 10X Genomics

first: Jinling

last: Liao

first: Yang

last: Chen

first: Chunlin

last: Zou

first: Haiying

last: Zhang

first: Jiwen

last: Cheng

first: Deyun

last: Liu

first: Tianyu

last: Li

first: Qingyun

first: Jiaping

first: Xiaobo

last: Yang

first: Yu

last: Ye

first: Zhiguang

last: Huang

first: Xinyang

last: Long

first: Rirong

first: Zengnan

last: Mo


title: Pathway-Associated Gene Expression in Gastrointestinal Cell Lines Under Conditions of Culture Age, Dexamethasone Exposure, and miRNA Overexpression

status: Public on Aug 26 2019

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

summary: Adherent cell layers were grown on permeable membrane inserts culture system using multiple GI cell lines.

overall_design: 1. Caco2 cell lines grown to 30 days an treated with DEX and Control.  2. Additional GI cell lines HEPG2 (hepatocellular adenocarcinoma), HT29 (colorectal adenocarcinoma), CCD18Co (colon fibroblast). 3. CRL1790 (fetal colon epithelial-like line) transfected with miRNA mimic over-expression system.

first: Simon

last: Turkington

first: Sarah

last: Abey

first: Wendy

last: Henderson