title: All the regulated lncRNAs in breast cancer stem cells (BCSCs, CD44+CD24- sorted)MCF-7 cells compared to non-BCSCs (non-CD44+CD24- sorted) MCF-7 cells

first: Liang

last: Jin

summary: Circulating transcriptional landscapes between BCSCs and non-BCSCs were compared using the Affymetrix Human OE LncRNA Microarray with probes for profiling of 63542 human lncRNAs. Goal was to investigate potential lncRNAs involved in BCSCs progression.

overall_design: We used flow cytometry sorting to obtain CD44+CD24- MCF-7 cells and non-CD44+CD24- MCF-7 cells,  extracted the total RNAs of these two kinds of cells, and detected the global expression profile of lncRNAs with Affymetrix Human OE LncRNA Microarray.


title: mRNA-seq of immortailized bone marrow derived macrophages (iBMDM) overexpressing GRA15II

status: Public on Nov 27 2018

city: BEIJING

first: Peiyan

last: Wang

state: 北京

address: NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: Analysis of mRNA-seq reveals difference in gene expression profile of immortalized bone marrow derived macrophages because of GRA15II overexpression

overall_design: Immortalized bone marrow derived macrophages with stable expression of  GRA15II


title: Mucosal transcriptome of rectal biopsies in treatment-naïve, pediatric ulcerative colitits patients

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: Using recal mucosal biopsies, collected prior to treatment in new-onset pediatric ulcerative colitis patients, we performed RNAsequencing to generate transcriptomic profiles linked to pathogenesis, severity, and treatment response.

overall_design: Biopsies were obtained from 206 new-onset patients during diagnostic colonoscopy, using the Qiagen AllPrep RNA/DNA MiniKit. PolyA-RNA selection, fragmentation, cDNA synthesis, adaptor ligation, TruSeq RNA sample library preparation (Illumina, San Diego, CA), and paired-end 75bp sequencing was performed.  Reads were quantified by kallisto [32], using Gencode v24 as the reference genome and Transcripts per Million (TPM) as an output. We included 14,085 protein-coding mRNA genes with TPM above 1 in 20% of the samples in our downstream analysis.

first: Ted

last: Denson

first: Yael

last: Haberman-Ziv


title: Single-cell gene expression data from Ventricular-Subventricular Zone (V-SVZ) cells

status: Public on Jan 01 2019

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

summary: We performed large-scale single cell profiling of V-SVZ cells, following separate dissections of the lateral and septal walls of 8-10 week old male and female mice.

overall_design:
Using an automated microwell array platform and commercially available mRNA capture beads, we generated single-cell RNA-seq profiles of dissociated V-SVZ cells without any prior cell sorting or filtering.

The rows of each of the *Basic.txt files annotate the cell type for each cell in each of the two corresponding single-cell gene expression matrix files.

first: Dogukan

last: Mizrak

first: Jinzhou

last: Yuan

middle: A

first: Hanna

middle: M

last: Levitin


title: CD34mono GEP

status: Public on Feb 07 2019

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

country: Japan

institute: Jichi Medical University Saitama Medical Center

summary: The differences in the gene expression profiles among CD34+ cells, conventional monocytes, and CD34mono.

overall_design: We analyzed human CD34+mono, CD34+cells, and conventional monocyes from G-CSF mobilized grafts (n=3), with Clariom™ S Assay (Thermo Fisher Scientific).


title: Generation of human oogonia from induced pluripotent stem cells in vitro

status: Public on Dec 18 2018

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Human in vitro gametogenesis may transform reproductive medicine. Human pluripotent stem cells (hPSCs) have been induced into primordial germ cell-like cells (hPGCLCs); however, further differentiation to a mature germ cell has not been achieved. Here, we show that hPGCLCs differentiate progressively into oogonia-like cells during a long-term in vitro culture (approximately 4 months) in xenogeneic reconstituted ovaries with mouse embryonic ovarian somatic cells. The hPGCLC-derived oogonia display hallmarks of epigenetic reprogramming-genome-wide DNA demethylation, imprint erasure, and extinguishment of aberrant DNA methylation in hPSCs-and acquire an immediate precursory state for meiotic recombination. Furthermore, the inactive X chromosome shows a progressive demethylation and reactivation, albeit partially. These findings establish the germline competence of hPSCs and provide a critical step toward human in vitro gametogenesis.

overall_design: RNA-seq analysis of human iPSC, iMeLC, PGCLC and aggregate cultured cells oogonia-like cells.

first: Chika

last: Yamashiro

first: Kotaro

last: Sasaki

first: Yoji

last: Kojima

first: Tomonori

last: Nakamura

first: Ikuhiro

last: Okamoto

first: Shihori

last: Yokobayashi

first: Yusuke

last: Murase

first: Yukiko

last: Ishikura

first: Kenjiro

last: Shirane

first: Hiroyuki

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Altered Placental transcriptome in first trimester affected by in vitro fertilization and embryo transfer (IVF-ET) treatments

status: Public on Nov 08 2018

city: Beijing

first: Liang

last: Zhao

state: Beijing

address: No. 31, Xinjiekou East Street, Xicheng District, Beijing

department: Department of Obstetrics and Gynecology

institute: Beijing Jishuitan Hospital

summary: We used microarrays to detail the global gene expression in human placental tissues in first trimester from patients subject to in vitro fertilization and embryo transfer and normal pregnancy

overall_design: Human placental Tissues in first trimester from patients subject to in vitro fertilization and embryo transfer and normal pregnancy were for RNA extraction and hybridization on Affymetrix microarrays.

first: Li

middle: F

last: Sun


title: Glucagon receptor blocked liver gene signature

status: Public on Nov 09 2018

city: Tarrytown

first: Haruka

address: 777 Old Saw Mill River Rd

institute: Regeneron

summary: Liver RNA-seq in lean or diet-induced obese mice administered with glucagon receptor blocking antibody

overall_design: C57BL/6J male mice that had been on regular chow or high fat diet for 4 months were administered with glucagon receptor blocking antibody REGN1193 or isotype control antibody at 10 mg/kg for 3 weeks.


title: NLRP2 promotes proinflammatory and chemotactic responses in proximal tubular epithelial cells

status: Public on Dec 04 2018

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: In this study, we investigated the functional role of NLRP2 in proximal tubular epithelial cells by overexpressing it in human conditionally immortalized cells obtained from urine of a healthy subject.  We found that NLRP2 markedly upregulates proinflammatory and chemotactic responses as well as downregulates interferon-mediated signaling pathways.

overall_design: mRNA profiles of conditionally immortalized proximal tubular epithelial cells (ciPTEC) stably overexpressing NLRP2 protein (NLRP2_over) and ciPTEC transfected with an empty vector (control, CTRL) were generated by deep sequencing, in biological duplicate, using Illumina HiSeq2000

first: Marianna

middle: N

last: Rossi

first: Antonia

last: Pascarella

first: Ivan

last: Caiello

first: Anna

last: Taranta

first: Laura

middle: R

last: Rega

first: Elena

last: Levtchenko

first: Francesco

last: Emma

first: Fabrizio

last: De Benedetti

first: Giusi

last: Prencipe


title: Genome-wide analysis of human reconstructed adipose tissue, human reconstructed connective tissue and native fat

status: Public on Dec 13 2018

city: Québec

first: Julie

last: Fradette

state: Québec

department: Chirurgie

country: Canada

institute: Université Laval

summary: We used adipose-derived human stromal/stem cells to reconstruct an adipose tridimensional model. To determine to what extend the in vitro model is representative of its native counterpart, transcriptomes were analysed.

overall_design: Total RNA obtained from human reconstructed adipose tissue, human reconstructed connective tissue and native fat were analysed

first: Marie-Eve

last: Ouellette

first: Jean-Christophe

last: Berube

first: Jean-Michel

last: Bourget

first: Maud

last: Vallée

first: Yohan

last: Bosse


title: Human decidual macrophage clustering

status: Public on Oct 11 2018

first: Xiangxiang

last: Jiang

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: First trimester decidual macrophages were clustered into three subpopulations by CCR2 and CD11c

overall_design: The mRNA libraries of first trimester decidual macrophage subpopulations and monocytes were sequenced by illumina hiseq 2000 in triplicates. And SRA Study accession was SRP091948. BioProject accession was PRJNA350204.

first: Hongmei

last: Wang


title: The gene expression profiles of human multiple myeloma cell lines transfected with miR-10a mimic

status: Public on Sep 30 2018

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary:
In multiple myeloma (MM), abnormal plasma cells interact with bone marrow (BM) stromal cells and vascular cells among others.  Bone marrow stromal cells (BMSCs) interact with MM cells in the bone marrow (BM), and also create a permissive microenvironment for MM cell growth and survival. Recent evidence indicated that extracellular vesicles (EVs)-mediated MM cell-BMSC communication plays an important role in the MM microenvironment. In this study, we investigated the biological property of the EVs and EV-miRNAs derived from BMSCs, aiming to establish the emerging strategies to target MM microenvironment to prevent tumor growth and spread.
We found that the MM-BMSC-EVs enhanced the cell proliferation of RPMI8226. The EV-miRNA expression was different between MM-BMSCs and Normal-BMSCs, and some miRNAs, including miR-10a, were significantly up-regulated in the MM-BMSC-EVs. We then visualized with an in vitro model the uptake of Cy3-labeled miR-10a into RPMI8226 via EVs. To identify the function of miR-10a in MM cells, miR-10a mimic was transfected into RPMI8226 cells.

overall_design: Parental cells (RPMI8226, KMS-11, U266, IM-9) were cultured for 24 hours under normoxic conditions (20% O2). MM cell lines (2 × 10^4 cells) were transfected with miR-10a mimic (Ambion), or scrambled control (Negative Control 1; Ambion) by using HiPerFect (Qiagen). Total RNA from each sample (RPMI8226, RPMI8226-miR-10a, KMS-11,KMS-11-miR-10a, U266, U266-miR-10a) was processed for hybridization onto GeneChip® human Gene 2.0 ST Array (Affymetrix) according to the manufacturer's protocol and scanned.


title: RNAseq quantitative analysis of ion channel mRNA expression in microbead occlusion model

status: Public on Oct 01 2018

city: Nashville

first: Lauren

middle: Katie

last: Wareham

state: Tennessee

address: 2213 Garland Avenue, MRBIV 11435a

department: Vanderbilt Eye Institute

institute: Vanderbilt University Medical Center

summary: The purpose of this study was to utilize RNAseq to determine if there are changes in ion channel mRNA expression in the retina of C57BL/6 mice subjected to the Microbead Occlusion Model. Whole retina was isolated from 2 month old mice that received intracameral injections of either saline or 15-um-diameter microbeads. Total RNA was isolated from the retinas and subjected to RNA sequencing using Illumina HiSeq 2500. Fold change in mRNA expression was compared between saline- and microbead-injected samples. We then analyzed these data for changes in expression of potassium channels, such as tandem-pore domain K+ channels, inwardly rectifying K+ channels, and the Na+/K+-ATPase.

overall_design: Retinal mRNA profiles of saline- and microbead-injected C57BL/6 mice  were generated by whole genome sequencing using Illumina NovaSeq6000

first: Rebecca

last: Sappington

first: Rachel

last: Fischer


title: High Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune Checkpoint Cancer Therapy

status: Public on Oct 30 2018

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Using complementary forms of high dimensional profiling we define differences in CD45+ cells from syngeneic mouse tumors that either grow progressively or eventually reject following immune checkpoint therapy (ICT). Unbiased assessment of gene expression of tumor infiltrating cells by single cell RNA sequencing (scRNAseq) and longitudinal assessment of cellular protein expression by mass cytometry (CyTOF) revealed significant remodeling of both the lymphoid and myeloid intratumoral compartments. Surprisingly, we observed multiple subpopulations of monocytes/macrophages distinguishable by the combinatorial presence or absence of CD206, CX3CR1, CD1d and iNOS, markers of different macrophage activation states that change over time during ICT in a manner partially dependent on IFNγ. Both the CyTOF data and additional analysis of scRNAseq data support the hypothesis that macrophage polarization/activation results from effects on circulatory monocytes/early macrophages entering tumors rather than on pre-polarized mature intratumoral macrophages. Thus, ICT induces transcriptional and functional remodeling of both myeloid and lymphoid compartments.

overall_design: Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted live CD45+ tumor infiltrating cells into droplets and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v1 according to manufacturer’s protocol (10x Genomics).  The generated scRNAseq libraries were sequenced using an Illumina HiSeq2500.

first: Matthew

last: Gubin

first: Ekaterina

last: Esaulova

first: Jeffrey

middle: P

last: Ward

first: Olga

last: Malkova

first: Daniele

last: Runci

first: Pamela

last: Wong

first: Takuro

last: Noguchi

first: Cora

middle: D

last: Arthur

first: Wei

last: Meng

first: Elise

last: Alspach

first: Ruan

middle: V

last: Medrano

first: Catrina

last: Fronick

first: Michael

last: Fehlings

first: Evan

middle: W

last: Newell

first: Robert

middle: S

last: Fulton

first: Kathleen

last: Sheehan

first: Stephen

middle: T

last: Oh

last: Schreiber


title: In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages

status: Public on Dec 31 2018

city: Maastricht

first: Masoud

last: Zamani Esteki

state: Limburg

address: P. Debyelaan 25

department: Clinical Genetics

country: Netherlands

institute: Maastricht University Medical Center

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Although chromosomal instability (CIN) is a common phenomenon
in cleavage-stage embryogenesis following in vitro
fertilization (IVF), its rate in naturally conceived human
embryos is unknown. CIN leads to mosaic embryos that contain
a combination of genetically normal and abnormal cells,
and is significantly higher in in vitro-produced preimplantation
embryos as compared to in vivo-conceived preimplantation
embryos. Even though embryos with CIN-derived
complex aneuploidies may arrest between the cleavage and
blastocyst stages of embryogenesis, a high number of
embryos containing abnormal cells can pass this strong selection
barrier. However, neither the prevalence nor extent of
CIN during prenatal development and at birth, following IVF
treatment, is well understood. Here we profiled the genomic
landscape of fetal and placental tissues postpartum from
both IVF- and naturally conceived children, to investigate the
prevalence and persistence of large genetic aberrations that
probably arose from IVF-related CIN. We demonstrate that
CIN is not preserved at later stages of prenatal development,
and that de novo numerical aberrations or large structural
DNA imbalances occur at similar rates in IVF- and naturally
conceived live-born neonates. Our findings affirm that human
IVF treatment has no detrimental effect on the chromosomal
constitution of fetal and placental lineages.

overall_design:
We applied haplarithmisis that allows scrutinizing the allelic architecture of human fetal and placental genomes in both IVF and naturally conceived newborns. Specifically, we employed single nucleotide polymorphism (SNP) genotypes of the entire genomes of father, mother, placenta and umbilical cord blood of 111 families, of which 62 and 49 quartets were from natural and IVF pregnancies, respectively. The naturally conceived pregnancies were further subdivided based on birthweight at delivery, with 16 families categorized as ‘appropriate birth weight for gestational age’ (AGA) and 10 families with ‘small birth weight for gestational age’ (SGA). We employed all DNA samples within a quartet to classify copy number variations (CNVs) found exclusively in a single sample or a few to all samples within a quartet.
The data is provided in quartest structure, including Father, Mother, cord  blood and placenta.

first: Triin

last: Viltrop

last: Tšuiko

first: Airi

last: Tiirats

first: Mariann

last: Koel

first: Margit

last: Nõukas

last: Žilina

first: Katre

last: Teearu

first: Heidi

last: Marjonen

first: Hanna

last: Kahila

first: Jeroen

last: Meekels

first: Viveca

last: Söderström-Anttila

first: Anne-Maria

last: Suikkari

first: Aila

last: Tiitinen

first: Reedik

last: Mägi

first: Sulev

last: Kõks

first: Nina

last: Kaminen-Ahola

first: Ants

last: Kurg

first: Thierry

last: Voet

first: Joris

last: Vermeesch

first: Andres

last: Salumets


title: Leprosyl whole blood transcriptome

status: Public on Oct 20 2018

city: Los Angeles

first: Rosane

last: Teles

state: California

address: 10833 Le Conte Ave, CHS 52-121

department: Medicine

institute: UCLA

summary: Transcriptome profiles of the peripheral whole blood of leprosy patients with different clinical forms

overall_design: Whole blood  from leprosy blood were collected and RNA sequencing was performed on a total of 58  samples

first: R

middle: L

last: Modlin

first: A

last: Geluk

first: M

last: Pelegrini


title: Primordial follicle formation involves dynamic conversion of RNA regulatory proteins (RIP-seq data set)

city: Mishima

first: Yuzuru

last: Kato

state: Shizuoka

address: 1111 Yata

department: Division of Mammalian Development

institute: National Institute of Genetics

summary: Long-term reproductive ability in mammalian females is sustained by the successive consumption of the finite pool of primordial follicles, the most primitive ovarian follicles that arise from cystic-oocytes during oogenesis. However, mechanisms underlying the formation of primordial follicles are largely unknown. Here we show that dynamic conversion of RNA-regulatory proteins precedes the formation of primordial follicles in mice. We find that, whereas stress granules dominate in cystic-oocytes, those are replaced by processing-bodies prior to the formation of primordial follicles that coincide with the expression of an evolutionally conserved RNA-binding protein, DDX6. Targeted deletion of Ddx6 disrupts processing-body assembly and perturbs cyst-breakdown. Furthermore, these events are orchestrated by an RNA-binding protein, ELAVL2. Our data suggest that cystic-oocytes switch post-transcriptional mechanism for upcoming formation of primordial follicles.

overall_design: Potentially ELAVL2 associated mRNAs in mouse P0 ovary were identified by RIP-Seq

first: Yumiko

last: Saga


title: Primordial follicle formation involves dynamic conversion of RNA regulatory proteins

type:
Other
Expression profiling by array

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

overall_design: Refer to individual Series


title: Natural selection has contributed to functional immune response differences between human hunter-gatherers and agriculturalists

status: Public on Sep 27 2018

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: The shift from a hunter-gatherer (HG) to an agricultural (AG) mode of subsistence is believed to have been associated with profound changes in the burden and diversity of pathogens across human populations. Yet, the extent to which the advent of agriculture impacted the evolution of the human immune system remains unknown. Here we present a comparative study of variation in the transcriptional responses of peripheral blood mononuclear cells (PBMCs) to bacterial and viral stimuli between the Batwa, a rainforest hunter-gatherer, and the Bakiga, an agriculturalist population from Central Africa. We observed increased divergence between hunter-gatherers and farmers in the transcriptional response to viruses compared to that for bacterial stimuli. We demonstrate that a significant fraction of these transcriptional differences are under genetic control, and we show that positive natural selection has helped to shape population differences in immune regulation. Unexpectedly, we found stronger signatures of recent natural selection in the rainforest hunter-gatherers, which argues against the popularized notion that shifts in pathogen exposure due to the advent of agriculture imposed radically heightened selective pressures in agriculturalist populations.

overall_design: Gene expression profiles of peripheral blood mononuclear cells (PBMCs) that were simulated with the viral ligand Gardiquimod (GARD), the bacterial ligand lippopolysacharide (LPS), or a match un-stimulated control (CTL)

first: Genelle

last: Harrison

first: Joaquin

last: Sanz

first: Jonathan

last: Boulais

first: Michael

middle: J

last: Mina

first: Jean-Christophe

last: Grenier

first: Yumei

last: Leng

first: Vania

last: Yotova

first: Anne

last: Dumaine

first: Christina

last: Bergey

first: Stephen

last: Elledge

first: Erwin

last: Schurr

first: Luis

last: Quintana-Murci

first: George

middle: H

last: Perry

middle: B

last: Barreiro


title: Microarray analysis of Elavl2 knockout ovaries

last: Kato

summary: Elavl2 knocout female mice show oocyte loss-phenotype shortly after birth. To reveal the involvement of Elavl2 in oogenic gene expression, embryonic and newborn ovaries were subjected to microarray analysis

overall_design: Gene expression analysis using whole ovaries


title: A consensus hypoxia signature in breast cancer

status: Public on Dec 26 2018

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: We exposed a panel of 32 breast cancer cell lines or normal human mammary epithelial cells to 20% or 1% O2 concentration for 24h. Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with DNase I (Ambion). All samples had a RIN value of >9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

overall_design: 32 breast cancer cell lines exposedto standard tissue culture conditions normoxic (20% O2) or hypoxic (1% O2) conditions.

first: Daniele

last: Gilkes


title: RNA-Seq of LRRK2 G2019S Parkinson’s iPSC-derived astrocytes

status: Public on Sep 22 2018

city: Cardiff

first: Frank

last: Wessely

address: Maindy Road

department: UK DRI

country: United Kingdom

institute: Cardiff University

summary: Non-neuronal cell types such as astrocytes can contribute to Parkinson’s disease (PD) pathology. The G2019S mutation in leucine-rich repeat kinase 2 (LRRK2) is one of the most common known causes of familial PD. To characterize its effect on astrocytes, we developed a protocol to produce midbrain-patterned astrocytes from human induced pluripotent stem cells (iPSCs) derived from PD LRRK2 G2019S patients and healthy controls. In order to understand the effect of this mutation on astrocyte function, we compared the gene expression profiles of iPSC-derived midbrain-patterned astrocytes from PD patients with those from healthy controls.

overall_design: Bulk RNA-Seq profiles of human iPSC-derived midbrain-patterned astrocytes from 7 donors, including 4 patients with Parkinson's disease who carry the LRRK2 G2019S mutation, and 3 healthy control individuals

first: Heather

last: Booth

first: Natalie

last: Connor-Robson

first: Federica

last: Rinaldi

first: Jane

last: Vowles

first: Cathy

last: Browne

first: Samuel

middle: G

last: Evetts

first: Michele

last: Hu

first: Sally

middle: A

last: Cowley

first: Caleb

last: Webber

first: Richard

last: Wade-Martins


title: Wound healing mechanisms in pathogenesis control in natural SIV host species

status: Public on Sep 20 2018

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

sample_organism:
Chlorocebus aethiops
Macaca mulatta

platform_organism:
Chlorocebus aethiops
Macaca mulatta


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to clarithromycin

status: Public on Sep 07 2018

city: Seattle

first: Shuyi

last: Ma

state: Washington

address: 1900 9th Avenue

department: Department of Pediatrics

institute: University of Washington

summary: To understand the response of M. tuberculosis (MTB) to the first-line drug clarithromycin, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of clarithromycin (no drug, 20μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.

first: Jenny

last: Lohmiller

first: David

last: Sherman


title: Wound healing mechanisms in pathogenesis control in natural SIV host species [monocytes]

summary: We devised a systems biology approach to investigate the early host response to high-dose rectal SIV transmission, by transcriptomic comparative analysis of a natural reservoir host SIV model species, African green monkeys (AGMs – Chlorocebus sabaeus, N=28) and a pathogenic model, rhesus macaques (RMs - Macaca mulatta, N=24).on rectal tissues for both AGMs and RMs.

overall_design: To investigate if AGM macrophages have a stronger wound healing profile compared to RM, we carried out mRNA sequencing on sorted M1 and M2 monocytes. Specifically, longitudinal blood samples were taken at D7, D14 and D28 post inoculation from two AGMs and four RMs

first: Fredrik

last: Barrenas

first: Kevin

last: Raehetz

first: Jan

last: Kristoff

last: Green

first: Lynn

last: Law

first: Steve

last: Bosinger

first: Guido

last: Silvestri

first: Ivona

last: Pandrea


title: Wound healing mechanisms in pathogenesis control in natural SIV host species [rectal tissue]

overall_design: Serial necropsies were performed at time points as early as one-day post-infection, and RNA-Seq was performed on rectal tissues for both AGMs and RMs.


title: Transcriptome Expression Data from Resected Operative Ileal Mucosa Specimens in a cohort of patients with Crohns Disease

status: Public on Aug 21 2018

city: St. Louis

first: Kelly

middle: Colleen

last: Cushing

address: 660 S Euclid Ave

department: Gastroenterology

institute: Washington University

summary: Affymetrix human whole transcriptome array (HTA 2.0) completed on patients with Crohn's disease undergoing their first ileocolic resection

overall_design: Mucosal biopsies from uninflamed operative tissue specimens were obtained and RNA extraction followed by transcriptomic analysis was performed.

middle: C

last: Mclean

first: Keely

last: McDonald

middle: K

last: Gustafsson

first: Kathryn

last: Knoop

first: Devesha

last: Kulkarni

first: R

last: Sartor

first: Rodney

last: Newberry


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to P218

last: Ma

summary: To understand the response of M. tuberculosis (MTB) to the first-line drug P218, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of P218 (no drug, 0.1μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.

last: Lohmiller

middle: R

last: Sherman


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to linezolid

status: Public on Aug 04 2018

summary: To understand the response of M. tuberculosis (MTB) to the drug linezolid, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of linezolid (no drug, 4μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.


title: ANXA10 induction by interaction with tumor-associated macrophages promotes the growth of esophageal squamous cell carcinoma

status: Public on Aug 17 2018

city: Kobe

first: Himiko

last: Kodaira

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

summary:
Tumor-associated macrophages (TAMs) have important roles in the progression, angiogenesis and motility of various cancers. To study the effects of TAMs on the tumor microenvironment of ESCCs, we constructed an in vitro system for the differentiation of peripheral blood monocyte (PBMo)-derived macrophages into TAM-like PBMo-derived macrophages.
We established a co-culture assay using a human ESCC cell line and TAM-like PBMo-derived macrophages and we performed a cDNA microarray analysis between monocultured and co-cultured ESCC cell lines. Our qRT-PCR confirmed that in the co-cultured ESCC cell lines, CYP1A1, DHRS3, ANXA10, KLK6 and CYP1B1 mRNA were highly up-regulated; AMTN and IGFL1 mRNA were down-regulated. We observed that a high ANXA10 expression was closely associated with the depth of invasion and high numbers of infiltrating CD68+ and CD204+ TAMs. ESCC patients with high ANXA10 expression were significantly correlated with poor disease-free survival (p = 0.0216). ANXA10 knockdown using siRNA significantly suppressed the cell growth of TE-8 and TE-9 ESCC cells by inhibiting Akt and Erk1/2 signaling pathways. We confirmed that ANXA10 overexpression induced the cell growth of TE-15 ESCC cells by activating Akt and Erk1/2 phosphorylation. These results suggest that ANXA10 induced by TAMs in the tumor microenvironment is associated with aberrant growth and a poor prognosis in human ESCC tissues.

overall_design: PBMos were cultured with macrophage-colony stimulating factor (M-CSF) for 6 days to induce macrophages. We added 50% condition media of human ESCC cell line (TE-8 and TE-9) to culture for 2 days to induce TAM-like polarization. We established co-culture assay using human ESCC cell line (TE-8 and TE-9) and TAM-like macrophages and performed cDNA microarray analysis between monocultured and co-cultured ESCC cell lines.

first: Hiroshi

last: Yokozaki


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to sulfamethoxazole

first: Shuyi

summary: To understand the response of M. tuberculosis (MTB) to the drug sulfamethoxazole, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of sulfamethoxazole (no drug, 12.5μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.

first: Jenny


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to dapsone

summary: To understand the response of M. tuberculosis (MTB) to the drug dapsone, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of dapsone (no drug, 25μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.

first: David


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to SQ109

status: Public on Aug 07 2018

summary: To understand the response of M. tuberculosis (MTB) to the drug SQ109, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of SQ109 (no drug, 3μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.


title: Identification of INSL4-regulated gene program in non-small cell lung cancer cells

status: Public on Nov 20 2018

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

summary: Gene expression profiling was performed to identify INSL4-regulated gene program in non-small cell lung cancer A549 cells.  We compared gene expression profiles of A549 cells transduced with lentiviruses expressing scrambled shRNA control or INSL4 shRNA. Our analysis revealed INSL4-regulated gene program that are involved in the regulation of cell cycle, growth and survival.

overall_design: Two biological replicates for each sample group were included in this study.  Specifically, A549 cells were transduced with pLKO.1 lentiviruses expressing scrambled shRNA control or INSL4 shRNA and two independent cultures were set up for each group. RNAs were then harvested for microarray analysis.


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Anti-TB drugs

sample_organism:
Mycobacterium tuberculosis
Mycobacterium tuberculosis H37Rv


title: Expression Data from epicardial  (EAT) and subcutaneous adipose tissue (SAT) in patients with coronary artery disease

status: Public on Oct 04 2018

city: Worcester

first: Timothy

middle: P

last: Fitzgibbons

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

summary:
We took samples of subcutaneous adipose tissue from the sternum (SAT) and epicardial adipose tissue (EAT) from a site adjacent to the right coronary artery in cases with coronary disease and controls without coronary disease.
Cases had significant coronary disease and were undergoing coronary artery bypass surgery.  Controls all had coronary angiograms and did not have significant coronary disease.

overall_design: Case control study

first: Tim


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Ethambutol

summary: To understand the response of M. tuberculosis (MTB) to the first-line drug ethambutol, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of ethambutol (no drug, 2.45μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to BTZ043

summary: To understand the response of M. tuberculosis (MTB) to the drug BTZ043, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of BTZ043 (no drug, 0.006μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Delamanid

status: Public on Aug 02 2018

summary: To understand the response of M. tuberculosis (MTB) to the drug delamanid, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of delamanid (no drug, 0.09μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.


title: Expression data from free fatty acid polarized bone marrow Gr1- myeloid cells

city: Würzburg

first: Hao

address: versbacherstr 7-9

country: Germany

institute: institute for systemsimmunology, wurzburg university

summary:
Free fatty acids accumulate in tumor microenvironment which facilitate the polarization of bone marrow derived myeloid cells into tumor associated macrophages. However, the underlying mechanism is still unclear.
Here we use microarray to detail the impact of variant free fatty acids on the maturation of bone marrow derived myeloid cells.

overall_design: Bone marrow isolated from Balb/c mice were cultured in the presence of 40 ng/ml GM-CSF plus variant 0.2 mM stearate (SS), oleate (SO) or BSA control. On day7, Gr1- myeloid cells were purified and lysed for for RNA extraction and hybridization on Affymetrix microarrays. .

first: Rainer

last: Glauben


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Sutezolid

summary: To understand the response of M. tuberculosis (MTB) to the drug sutezolid, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of sutezolid (no drug, 5.6μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.


title: The gene expression profiles of human bone marrow stromal cells derived from multiple myeloma patients

status: Public on Jul 14 2018

first: Tomohiro

last: Umezu

summary:
Bone marrow stromal cells (BMSCs) and their exosomes are a promising area of cancer therapy.
Multiple myeloma (MM) is refractory hematologic malignancy. Bone marrow stromal cells (BMSCs) interact with MM cells in the bone marrow (BM), and also create a permissive microenvironment for MM cell growth and survival. Recent evidence indicated that exosome-mediated MM cell-BMSC communication plays an important role in the MM microenvironment. In this study, we investigated the biological property of the exosomes and exosomal miRNAs derived from BMSCs, aiming to establish the emerging strategies to target MM microenvironment to prevent tumor growth and spread.

overall_design: Human BMSCs of healthy donors were purchased from Lonza (Normal-BMSCs). BM samples were obtained from multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS) patients in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (MM-BMSCs) and MGUS patients (MGUS-BMSCs) were isolated using the classical plastic adhesion method. BMSCs (2 × 10^4 cells) were transfected with -miR-10a mimic (Ambion), or scrambled control (Negative Control 1; Ambion) by using HiPerFect (Qiagen).Total RNA from each sample (Normal-BMSCs, MM-BMSCs and MGUS-BMSCs) was processed for hybridization onto GeneChip® human Gene 2.0 ST Array (Affymetrix) according to the manufacturer's protocol and scanned.


title: Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

status: Public on Sep 01 2018

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: We identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade.

overall_design: TSS-Seq was used to map the transcription initiation sites with single base resolution in A.thaliana seedlings (Col-0 with or without cold treatment);

first: Peter

last: Kindgren

first: Ryan

last: Ard

first: Sebastian

last: Marquardt


title: *Possible corruption in count data files-update in progress* Disease-specific oligodendrocyte lineage cells express immunoprotective and adaptive immunity genes in multiple sclerosis

status: Public on Aug 25 2018

city: Stockholm

last: van Bruggen

state: Stockholm

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

summary:
Single-cell RNA-seq of a mouse model of MS uncovers new oligodendrocyte populations, putative disease markers and suggests new mechanisms underlying the pathogenesis of disease.
In Multiple Sclerosis (MS), oligodendrocytes (OLs) are damaged during an immune system attack targeting myelin. It remains unclear how different OL lineage cells respond to inflammatory autoimmune demyelination in MS. We performed single-cell transcriptomics analysis of OL lineage cells from the spinal cord of mice induced with experimental autoimmune encephalomyelitis (EAE), which mimics certain aspects of MS. We found unique OLs and OL precursor cells (OPCs) in EAE, including populations expressing genes involved in antigen processing and presentation via major histocompatibility complex (MHC) Class I and II, but also in immunoprotection. We further uncovered several genes specifically alternatively spliced in OL lineage cells in EAE, including Mbp, Mobp and Pdgfa. Strikingly, we identified a substantial number of genes known to be susceptibility genes for MS, so far mainly associated with immune cells in the context of this disease, to be expressed in the OL lineage cells. Finally, we found that disease-specific oligodendroglia are present in human MS brains. Our results suggest that OL and OPCs are not passive targets but instead active immunomodulators in MS. The disease-specific OL lineage cells, for which we identify several biomarkers, may represent novel direct targets for immunomodulatory therapeutic approaches in MS.

overall_design: Mouse lines used in this study included C57BL/6NJ wild type mice, Pdgfra-Cre-LoxP- GFP and Pdgfra-H2B-GFP knock-in mice. Experimental Autoimmune Encephalomyelitis mice were generated by subcutaneous injection with an emulsion in MOG35-55 in complete Freud’s adjuvant (CFA) (EK-2110 kit from Hooke Laboratories) followed by the administration of pertussis toxin in PBS (0,2μg per animal), for two consecutive days (all according to manufacture’s instructions). Spinal cords and cerebellum were collected at the chronic stage of the disease with clinical score=3 representing limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analysed in this study. Additional animals were injected subcutaneously with a CFA emulsion (CK-2110 kit from Hooke Laboratories) and used as controls.

first: Gonçalo

last: Castelo-Branco

first: Ana

middle: M

last: Falcão

first: Sueli

last: Marques

first: Eneritz

last: Agirre

first: Mandy

last: Meijer

first: Sarah

last: Jäkel

first: André

middle: O

last: Cacais

first: Darya

last: Vanichkina

first: Elisa

last: Floriddia

first: Charles

last: ffrench-Constant

first: Anna

last: Williams


title: Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [RIP-seq]

status: Public on Jun 29 2018

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Haploinsufficiency and aneuploidy are two phenomena, where alteration of gene dosage causes severe cellular defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between males and females are buffered through the action of dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates two-fold upregulation of the single male X chromosome via Histone H4 lysine 16 acetylation (H4K16ac). The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to its function on the X, targets dosage-sensitive autosomal genes involved in patterning and morphogenesis. We show that the precise regulation of these genes by MSL2 is required for proper development of the fly wing. This set of dosage sensitive genes maintained such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via deposition of H4K16ac. We propose that MSL2-mediated H4K16ac is an evolutionarily conserved process mediating gene-by-gene dosage compensation across flies and mammals.

overall_design: Genome-wide RNA interaction profiles (FLASH; Fast cloning of RNA After some Sort of affinity purification for High-throughput sequencing) of MSL2 and MLE in Drosophila melanogaster third instar larvae. Males and females separated, 2 biological replicates each.

first: Claudia

middle: I

last: Valsecchi

first: Giuseppe

last: Semplicio


title: Inhibition of EGFR signaling downregulates K-RAS mutated activity

status: Public on Aug 29 2018

city: Vienna

first: Herwig

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

summary: KRAS mutations are the ost abundand driver mutations found in lung adenocarcinoma patients. Unfortunately, there are no clinical approved inhibitors available, to directly target mutant forms of KRAS. The aim of the study was to unravel the impact of upstream Egfr activation in signaling of mutated K-ras. We found that upregulation of G12D mutant Kras induced genes was significantly impaired when Egfr was knocked out. Our data suggests that signaling of mutant Kras depends on upstream activation. This finding may be exploited therapeutically by targeting EGFR in KRAS mutant patients.

overall_design: We isolated mouse alveolar type II cells and induced the Kras G12D mutation, with and without concomitant Egfr knockout, in vitro. Cells lysates were analyzed 5 days following transgene induction.

first: Emilio

last: Casanova


title: Transcriptional Response of Mycobacterium tuberculosis H37Rv to Verapamil

first: Shuyi

last: Ma

summary: To understand the response of M. tuberculosis (MTB) to the drug verapamil, we performed transcriptomics on MTB bacilli exposed to the drug.

overall_design: Bacteria were harvested at 0,1 day after being exposed to concentrations of verapamil (no drug, 176μM) as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.

first: Jenny

last: Lohmiller

first: David

last: Sherman


title: Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [RNA-seq mouse]

overall_design: RNA sequencing of mouse embryonic stem cells of control and two indiviual msl2 knock out cell lines


title: Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: Transcriptomic profiling of MDA-MB-231 cells treated with TNFɑ [40 ng/ml] ± Apigenin [40 μM].

status: Public on Sep 28 2018

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: The effects of TNFɑ [40 ng/ml] ± Apigenin [40 μM] were evaluated in MDA-MB-231 cells using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc assessing for mRNAs and long intergenic non-coding RNA transcripts.

overall_design: 12 Samples

last: Bauer

first: Karam

last: Soliman


title: Transcriptome comparison between WT and GPS2 liver knockout (LKO) livers and GPS2 NCOR PPARa cistrome and epigenome analysis in livers.

status: Public on Mar 12 2019

city: Huddinge

first: Rongrong

last: Fan

address: Hälsovägen 7c

summary: Obesity-associated lipid overload triggers non-alcoholic fatty liver diseases (NAFLD), which in part may be driven by alterations of regulatory transcription networks and hepatocyte-selective epigenomes. Here we demonstrate that G protein pathway suppressor 2 (GPS2), a subunit of the nuclear receptor corepressor (NCOR)/ histone deacetylase 3 (HDAC3) complex, is a central component of such networks and accelerates the progression of non-alcoholic steatohepatitis (NASH). In hepatocyte-specific Gps2 knockout mice, loss of GPS2 alleviated the development of diet-induced steatosis and fibrosis and caused activation of lipid catabolic genes. By determining differential cistromes, epigenomes and transcriptomes in wild-type, single and double knockout mice, we identified the lipid-sensing nuclear receptor PPARa as a direct target of GPS2. We also provide evidence that in hepatocytes, unlike in macrophages, GPS2 acts in concert with the NCOR subunit of the corepressor complex. By analyzing the liver transcriptomes of human patients, we found that GPS2 expression positively correlated with the expression of NASH/fibrosis signature genes. Collectively, our data suggest that the GPS2-PPARa partnership in hepatocytes may influence the development of NASH/fibrosis in mice and in humans.

overall_design: Transcriptome signatures of GPS2-regulated genes between WT and LKO livers was assessed through RNA-seq analysis. Epigenomic status of Gps2, Ncor and Smrt LKO vs WT livers was analyzed using histone markers H3K4me3 and/or H3K27ac ChIP-seq. GPS2, NCOR and PPARa cistrome was analyzed in Gps2, Ncor and Ppara WT/KO livers respectively.

first: Ning

last: Liang

first: Anastasius

last: Damdimopoulos

first: Eckardt

last: Treuter


title: Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [ChIP-seq Dmel]

overall_design: ChIP-seq profiles of various histone modfications and DNA binding proteins in Drosophila melanogaster.. Males and females separated, third instar larvae.


title: Detailing Novel Epigenetic Events Associated with Diet-Induced Obesity in the Rat

status: Public on Jun 20 2018

city: Pullman

first: Zhihua

last: Jiang

state: WA

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

summary: We applied Whole Transcriptome Termini Site Sequencing (WTTS-seq) to detect differences in use of alternative polyadenylation sites between diet-induced obesity rats and control rats. Our finding clear showed that a nutritionally complete high fat diet would affect pre-translational alternative polyadenylation events on hypothalamic transcripts that both stimulate and counter regulate body weight.

overall_design: Eight adult male Long-Evans rats (Harlan, IN) were divided into obesity group and control group. Control group were maintained on standard rodent chow (3.41 kcal/g, 0.51 kcal/g from fat). Obesity group received ad libitum access to a nutritionally complete high fat diet (41 kcal/g, 1.71 kcal/g from fat). Following 36 days of diet exposure, all rats were euthanized and brain tissue collected for RNA isolation. Total RNA samples derived from eight male Long-Evan rats were used to construct WTTS-seq libraries. Therefore, this submission involved a total of 8 libraries.

first: Julianna

middle: N

last: Brutman

first: Xiang

last: Zhou

first: Yangzi

last: Zhang

first: Jennifer

last: Michal

first: Jon

middle: F

last: Davis


title: Facultative dosage compensation of developmental genes on autosomes in Drosophila and mammals [ChIP-seq mouse]

first: Asifa

last: Akhtar

first: Claudia

last: Valsecchi

first: Giuseppe

last: Semplicio


title: Metabolic pathways-associated lncRNA expression profiles of 6 human samples derived from patients with gastric cancer

status: Public on May 09 2018

city: Ningbo

first: Junming

last: Guo

address: 818 Fenghua Road

department: Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology

institute: Ningbo University

summary: Detection and analysis of metabolism pathway related to lncRNAs expression profile in gastric cancer.

overall_design: A six chip study using total RNA extracted from three gastric cancer tissues and three paracancerous tissues.


title: Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer

status: Public on Mar 13 2018

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah


title: Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer [RNA-seq]

summary: Steroid hormone receptors are simultaneously active in many tissues and capable of altering each other's function. Estrogen receptor ɑ (ER) and glucocorticoid receptor (GR) are expressed in the uterus and their ligands have opposing effects on uterine growth. In endometrial tumors expressing high levels of ER, we surprisingly found that expression of GR is associated with poor prognosis. Dexamethasone reduced normal uterine growth in vivo; however, this growth inhibition was abolished in estrogen-induced endometrial hyperplasia. We observed low genomic binding site overlap when ER and GR are induced with their respective ligands; however, upon simultaneous induction they co-occupy more sites. GR binding is significantly altered by estradiol with GR recruited to ER bound loci that become more accessible upon estradiol induction. Gene expression responses to co-treatment were more similar to estradiol, but with novel regulated genes. Our results suggest phenotypic and molecular interplay between ER and GR in endometrial cancer.

overall_design: ChIP-seq, ATAC-seq, and RNA-seq data collected from endometrial cancer cell lines induced with dexamethasone, estradiol, or the combination

first: Jay

first: Jeffery

last: Vahrenkamp


title: RNA-seq analysis comparing normal mouse melanocyte stem cells to the melanoma tumor derived from them upon Braf:Pten mutations

status: Public on Sep 23 2017

city: New York

first: Qi

last: Sun

state: NY

address: 550 1st Avenue, Smilow 410

department: Dermatology

institute: New York University

summary: We found that mouse melanocyte stem cells give rise to melanoma whose signatures highly mimicks human melanoma

overall_design: Melanocyte stem cells with Braf:Pten mutations were isolated from mouse back skin and transplanted into nude mice to form tumor. The tumor cells were harvested and compared with the non-transformed melanocyte stem cells for RNA-seq analysis

first: Mayumi

last: Ito


title: RNA-seq in neutrophils from patients with intracranial aneurysms

status: Public on Dec 01 2017

city: Buffalo

first: Hui

last: Meng

address: 875 Ellicott Street

institute: University at Buffalo

summary: In this study, we explored transcriptional differences in human neutrophils from patients with intracranial aneurysms and a demographic and comorbidity paired population of controls

overall_design: We compared differentially expressed genes among neutrophils from 11 blood samples from patients with intracranial aneurysms and 11 blood samples from paired controls. We used an independent, unpaired, corroboration cohort of 5 intracranial aneurysm patients and 5 control patients to confirm our findings.

first: Vincent

last: Tutino

first: Yijun

first: James

last: Jarvis

first: Kaiyu


title: Rad53 checkpoint kinase couples leading and lagging strand DNA synthesis

status: Public on Feb 11 2018

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: In response to DNA replication stress, DNA replication checkpoint is activated to maintain fork stability, a process critical for maintenance of genome stability. However, how DNA replication checkpoint regulates replication forks remain elusive. Here we show that Rad53, a highly conserved replication checkpoint kinase, functions to couple leading and lagging strand DNA synthesis. In wild type cells under HU induced replication stress, synthesis of lagging strand, which contains ssDNA gaps, is comparable to leading strand DNA. In contrast, synthesis of lagging strand is much more than leading strand, and consequently, leading template ssDNA coated with ssDNA binding protein RPA was detected in rad53-1 mutant cells, suggesting that synthesis of leading strand and lagging strand DNA is uncoupled. Mechanistically, we show that replicative helicase MCM and leading strand DNA polymerase Pole move beyond actual DNA synthesis and that an increase in dNTP pools largely suppresses the uncoupled leading and lagging strand DNA synthesis. Our studies reveal an unexpected mechanism whereby Rad53 regulates replication fork stability.

overall_design: We synchronized yeast cells (Wile type and other mutant cells) at G1 and released into early S phase in the presence of BrdU, and hydroxyurea (HU). We then performed BrdU immunoprecipitation using anti-BrdU antibodies following single-strand DNA library preparation and sequencing. We also performed protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for MCM6 and Pol ɛ. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.

first: Chuanhe

last: Yu

first: Haiyun

last: Gan

first: Zhiguo


title: Identification of distinct molecular signatures in AIP mutation-positive familial isolated pituitary adenomas

status: Public on Apr 13 2018

city: London

first: Sayka

last: Barry

address: Charterhouse SQ

department: Endocrinology

institute: QMUL

summary:
The aim of this study was to perform comparative gene expression analysis of AIP mutation-positive, AIP mutation-negative familial and sporadic somatotroph tumours to discover the genes/pathways responsible for the aggressive phenotype.
Gene expression analysis was performed on 25 pituitary samples (five normal pituitary, six AIPpos GH, three AIPneg GH, four sporadic GH, two AIPneg familial NFPA and five sporadic NFPA adenomas) using the Affymetrix human Gene Chip HG-U133 Plus 2.0 array.

overall_design: In order to identify differentially expressed genes both functional non-functional pituitary tumours were compared with normal pituitary samples. Four samples (one AIPpos GH2, one sporadic GH3, one AIPneg familial NFPA2 and one sporadic NFPA5) did not pass the Affymetrix quality control assessment therefore, omitted for further analysis.

first: Eivind

last: Carlsen

first: Emanuela

last: Gadaleta

first: Ajanthah

last: Sangaralingam

first: Claude

last: Chelala

first: Tomasz

last: Radon

first: Tatjana

last: Crnogorac-Jurcevic

first: Dan

last: Berney

first: Plamena

last: Gabrovska

first: Laura

last: Hernández Ramírez

first: Márta

last: Korbonits


title: Next Generation RNA Sequencing reveals defects in nuclear and chloroplast mRNA maturation of Arabidopsis thaliana lefko2 mutant

status: Public on Sep 01 2017

city: Athens

first: Polydefkis

last: Hatzopoulos

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary:
Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. Therefore, we examined the splicing efficiency of plastid and nuclear genes in lefko2 mutant.
Methods: The lefko2 mutant is represented by the Salk T-DNA collection unicode SALK_044699/emb1692 and was obtained from the Nottingham Arabidopsis Stock Centre (NASC, Nottingham, UK). Embryo development in homozygous lefko2 plants is ceased abruptly arresting embryogenesis upon globular-to-heart stage transition. Total RNA was extracted using plant RNA kit spin columns with an on-column DNase treatment from heart-stage lefko2 mutant and wild-type Arabidopsis embryos. The quantity and integrity of the RNA was assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2000 instrument at BGI (Beijing Genomics Institute). Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10).  RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”. Differential alternative splicing events were detected for lefko1 and wild-type using rMATS and visualized using the Integrative Genomics Viewer (IGV) tool.
Results: RNA-seq uncovered an outstanding number of coding or non-coding novel transcripts in lefko2 mutant embryos. Splicing defects were observed in numerous nuclear and plastid genes of lefko2 embryos compared to wild type. Among them, intron retention (IR) events were the most prominent. Further, the fidelity of 5’ splice site (5’SS) donor and 3’SS acceptor splicing was highly disturbed in lefko2 embryos. To less extend, exon skipping (ES) defects were also detected.
Conclusions: Detailed nuclear and chloroplast splicing events were widely observed in lefko2 aborted mutant embryos demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns and chloroplast group II introns.

first: Gerasimos

last: Daras


title: RNA-seq analysis of cymopol and algal extracts in the intestine

status: Public on Dec 03 2017

first: Tongjun

last: Gu

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

summary: A natural product algal extract and its major component, cymopol, have demonstrated anti-oxidant and anti-inflammatory activity in vitro and in vivo. RNA transcript levels of Nqo1 and Hmox1 were discovered in multiple organs following oral gavage of 2 doses of the extract and cympopol for 3 consecutive days.  The highest change in gene expression was noted in the digestive tract.

overall_design: Examination of a high-dose and a low-dose of both a nonpolar (NP) algal extract and cymopol

first: Hendrik

last: Luesch

first: Michelle

last: Bousquet


title: Early transcriptional changes in response to low dose radiation exposure

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: One of the most likely risks astronauts on long duration space missions face is exposure to ionizing radiation associated with highly energetic and charged heavy (HZE) particles.  Since access to medical expertise on such a mission is limited at best, early diagnosis and mitigation of such exposure is critical.  In order to accurately determine the time since exposure and dosage of exposure, dose- and time-dependent “biomarkers” are needed.  Therefore, we performed a dose- and time-course transcriptional analysis for radiation exposure at 0, 0.15, 0.30, and 1.5 Gy with corresponding time points at 1 hour (hr) post-exposure as well as 2 hr and 6 hr using Affymetrix® Human PrimeArrayTM chips.  The analysis of our data suggests a set of sensitive genetic biomarkers specific to each radiation level as well as generic radiation response biomarkers. Upregulated biomarkers can then be used within lab-on-a-chip (LOC) systems to detect exposure to ionizing radiation.

overall_design: A total of 100 human samples representing radiation exposure at levels 0 Gy, 0.15 Gy, 0.30 Gy and 1.5 Gy at time points 1 hour (hr), 2 hr, and 6 hr post-exposure were constructed.  Blood samples were extracted from ten human volunteers, and were irradiated.  Leukocytes were extracted, and gene expression was measured.  Samples for all ten volunteers were measured at 1 hr and 2 hr for all four dose levels, while samples from volunteers 1,2,3,4, and 7 were measured at 6 hr, resulting in 10 replicates at 1 hr and 2 hr for each dosage, and 5 replicates at 6 hr post-exposure.  Thus, a total of 25 samples at each of the four radiation levels were sampled, yielding the total of 100 samples.

first: Robert

last: Flight

first: Brigitte

last: Fasciotto

first: John

middle: W

last: Eaton

first: Phani

last: Patibandla

first: Sabine

last: Waigel

first: Dazhuo

last: Li

first: Xiaohong

last: Kirtley

first: Palaniappan

last: Sethu

middle: S

last: Keynton


title: Genomic and epigenomic characterization of regenerating hepatocytes

status: Public on Jan 24 2018

city: Philadelphia

first: Amber

last: Wang

state: Pennsylvania

address: 3400 Civic Center Blvd, SCTR 12-164

department: Genetics

institute: University of Pennsylvania

summary: To gain a deeper understanding of the genetic basis of liver repopulation after injury, we utilize an innovative technique to profile the expression changes and chromatin landscape during the regenerative response. We utilize the Fah-/- mouse, a model for hereditary tyrosinemia deficient in fumarylacetoacetate hydrolase (FAH), that undergoes repopulation with FAH-expressing hepatocytes. We employ translating ribosome affinity purification followed by RNA-sequencing (TRAP-seq) and assay for transposase accessible chromatin using sequencing (ATAC-seq) to specifically isolate regenerating hepatocytes and performed high-throughput sequencing to identify the dynamic genomic and epigenomic changes during liver repopulation.

overall_design: A total of 16 mice was used for the TRAP-seq study (n=4, quiescent; n=3, 1-week injury; n=6, 4-week injury; n=3, 4-week severe injury). A total of 7 mice was used for the ATAC-seq study (n=2, quiescent; n=4, 1-week injury)

first: Kirk

middle: J

last: Wangensteen

first: Julia

middle: Y

first: Klaus

middle: H

last: Kaestner


title: Forced differentiation in vitro leads to stress-induced activation of DNA damage response in hiPSC-derived chondrocyte-like cells

status: Public on Dec 14 2017

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Human induced pluripotent stem cells (hiPSCs) constitute an important breakthrough in regenerative medicine, particularly in orthopedics, where more effective treatments are urgently needed. Despite the promise of hiPSCs only limited data on in vitro chondrogenic differentiation of hiPSCs are available.
Therefore,the global gene expression profile of chondrocyte-like cells derived from hiPSCs (ChiPS) were compared to the hiPSCs (GPCCi001-A cell line) and to two cell lines of mature chondrocytes: HC-402-05a (Merck Millipore, Germany) (HC) and primary articular cartilage chondrocytes (ACC).

overall_design:
GPCCi001-A cells were generated from primary human dermal fibroblasts in reprogramming process using Stemcca-tetO lentiviral vector coding transcription factors responsible for pluripotency (Oct 4, Sox2, c-Myc and Klf4). GPCCi001-A cells express markers characteristic for pluripotent SCs and possess capacity to form embryoid bodies with the derivatives of three primary germ layers. The experiment was performed in triplicate. We performed global gene expression analysis using the Affymetrix platform—to better understand the processes directing cell fate during chondrogenic differentiation in vitro (hiPSC,HC and ACC served as a control).

This series includes GPCCi001-A and ChIPS samples re-used from GSE106239.

first: Ewelina

last: Stelcer

first: Katarzyna

last: Kulcenty

first: Karol

last: Jopek

first: Tomasz

last: Trzeciak

first: Magdalena

last: Richter

first: Wiktoria

last: Suchorska


title: Assessment of Variant Abundance by Massively Parallel Sequencing for PTEN and TPMT

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

summary: Determining the pathogenicity of human genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes will likely require generalizable, scalable assays. Here we describe Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance in a single experiment. We applied VAMP-seq to quantify the abundance of many thousands of single amino acid variants of two proteins, PTEN and TPMT, in which functional variants are clinically actionable.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design:
Barcoded single amino acid variant libraries of EGFP-fused PTEN or TPMT were recombined into HEK293T cells previously engineered to contain a Bxb1 recombination site at the AAVS1 locus. Upon sorting cells for EGFP expression, genomic DNA was extracted. Barcodes were amplified and counted with Illumina sequencing. Barcodes were associated back to the corresponding PTEN or TPMT variant by comparison with a barcode-variant map previously created by sequencing the variant library plasmids using PacBio sequencing.

Copyright 2018 University of Washington. Data and Scores are owned by the University of Washington. Permission is hereby granted to use, reproduce, and distribute the Data and Scores for noncommercial academic research purposes only, provided that (i) credit for source and copyright are included with each copy and (ii) a link to the original material is provided whenever the material is published elsewhere on the Web. For questions regarding use by non-profit entities or commercial purposes contact: Douglas Fowler, dfowler@uw.edu

first: Douglas

last: Fowler

first: Jay

last: Shendure


title: AtWRKY1 regulates light and nitrogen signalling pathways

status: Public on Aug 01 2017

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

summary: When light and exogenous nitrogen levels are limiting, the AtWRKY1 transcription factor mediates regulatory crosstalk between nitrogen and light signaling pathways in an energy conservation mechanism. Transcriptome experiments were performed for WT and wrky1 mutant lines under no treatment; N treatment; light treatment; or combination treatment.

overall_design: 14 samples consisting of three replicates, 2 samples consisting of 2 replicates. WT (Col-0) and wrky1 mutant lines: steady treatment is on full MS media under long day; N treatment (KCl control or KNO3 + NH4NO3 treatment); light treatment (normal light control or dark treatment); combination treatment is N and light.

first: Manpreet

last: Katari

first: Rebecca

last: Grinberg

first: Sachin

last: Heerah

first: Gloria

last: Coruzzi


title: Transcriptome Analyses of Two Hybrid Citrus Cultivars in Seedlings Etiolation

status: Public on Jun 13 2017

city: chengdu

first: bo

last: xiong

address: NO.211 Huimin

institute: Sichuan Agricultural University

summary: Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30 (sequencing error rate, 0.1%). 124,952 unigenes were finally generated with a mean length of 1,189 bp. Of these unigenes, 98,904 (79.15%), 105,408 (84.35%), 42,016 (33.62%), 78,872 (63.12%), 72,068 (57.67%), 72,464 (57.99%), 72464 (57.99%) and 46,308 (37.06%) had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes (DEGs) in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Functional classification of the DEGs in two cultivars using GO term indicated that biological process, cellular component and molecular function were three major groups. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan, and advance our knowledge of the genes involved in the complex regulatory networks of seedling etiolation.

sample_organism: (Citrus unshiu x Citrus sinensis) x Citrus reticulata

overall_design: Examination of 3 different stages of etiolation leaves of Huangguogan and Shiranuhi.

first: Bo

last: Xiong

first: Zhihui

last: Wang


title: Circular RNA profile of human cervical squamous cell carcinoma

status: Public on Aug 16 2017

city: Jinan

first: Jun

last: Jiao

address: Wenhuaxi Road

institute: Shandong University

summary: Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs, which drew little attention in the past. Recently, limited data showed their promising future to act as biomarkers in human cancer, but the characteristics and functions remain largely unknown in human cervical cancer. In this study,  we demonstrated the expression profile of circRNAs in cervical squamous cell carcinoma(SCC) patients with circRNA microarray, and identified a large number of circRNAs possibly expressed in SCC.

overall_design: 5 cervical squamous cell carcinoma tissues and 5 paired-paracancerous cervical tissuses.

first: Baoxia

last: Cui


title: Expression profiling in exosomal miRNAs secreted from human bone marrow stromal cells

status: Public on May 12 2017

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: The aging of bone marrow stromal cells (BMSCs) lead to decreased ability to maintain hematopoiesis, however, effects of aging on BMSC-derived exosomes in bone marrow microenvironment remain unclear. The aim of this study is therefore to determine the age-related change of BMSC-derived exosomal miRNAs.

overall_design: Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors:  62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. The exosomes from culture medium of BM-MSCs were isolated by Total Exosome Isolation Reagent (Invitrogen). Exosomal miRNA profiling was done using a TaqMan low-density array (ABI), and Student’s t-test was used to determine statistical significance for comparisons between young and old groups using R software.


title: Transcriptional response to early life stress in male and female mouse brain

status: Public on Jun 28 2017

city: Princeton

first: Catherine

middle: Jensen

last: Pena

state: NJ

address: Washington Road

department: Neuroscience

institute: Princeton University

summary: This study explored the interaction of early life and adult stress on transcriptional and chromosomal states in a 2x2 design. Male and female mice were subjected to early life stress (ELS) or were standard-reared (Std), were housed normally through adolescence, and were then exposed to 10 days of control (Ctl) or chronic social defeat stress (CSDS: males only) or 3 days of sub-threshold variable stress (STVS: females only) conditions in adulthood. Long-lasting transcriptional alterations were assessed in the ventral tegmental area (VTA), nucleus accumbens (NAc), medial prefrontal cortex (PFC), and ventral hippocampus (HIP, males only) in adulthood.

overall_design: All male brain tissue for RNA-seq came from one cohort of adult mice. All female brain tissue for RNA-seq came from a separate cohort of adult mice. Male VTA samples for H3K4me1 ChIP-seq came from a third cohort of adult mice. Brain regions were punched from adult mouse brain and flash frozen. Punches from 3 mice were pooled per sample before RNA extraction (male VTA and male NAc) or for HeK4me1 ChIP (male VTA). Samples represent individual mice for female VTA, NAc, and PFC, and male PFC and HIP. H3K4me1 ChIP samples are matched to corresponding Input. RNA-seq was performed using Illumina TruSeq kits according to protocol and read at 100-125 bp. Library multiplexing was counterbalanced across groups. ChIP-seq and Input libraries were prepared with NEB Ultra kits with Illumina adaptors according to protocol and read at 100-bp.

first: Eric

last: Nestler

last: Peña

first: Immanuel

last: Purushothaman

first: Eddie

last: Loh

first: Aarthi

last: Ramakrishnan


title: Expression profiling in exosomal miRNAs of human bone marrow stromal cells derived from multiple myeloma patients

status: Public on Jun 08 2018

summary:
Bone marrow stromal cells (BMSCs) and their exosomes are a promising area of cancer therapy.
Multiple myeloma (MM) is refractory hematologic malignancy. Bone marrow stromal cells (BMSCs) interact with MM cells in the bone marrow (BM), and also create a permissive microenvironment for MM cell growth and survival. Recent evidence indicated that exosome-mediated MM cell-BMSC communication plays an important role in the MM microenvironment. In this study, we investigated the biological property of the exosomes and exosomal miRNAs derived from BMSCs, aiming to establish the emerging strategies to target MM microenvironment to prevent tumor growth and spread.

overall_design: Human BMSCs of elderly (68 and 72 years old) healthy donors were purchased from Lonza (Normal-BMSCs). BM samples were obtained from multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS) patients in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (MM-BMSCs) and MGUS patients (MGUS-BMSCs) were isolated using the classical plastic adhesion method. The exosomes from culture medium of BM-MSCs were isolated by Exoquick-TC (SBI). Total RNA from each exosome fractions (2 Normal-BMSCs, 6 MM-BMSCs and 3 MGUS-BMSCs) was extracted by the miRneasy mini kit (Qiagen). The exosomal miRNA profiling was done using a TaqMan low-density array (ABI), and Student’s t-test was used to determine statistical significance for comparisons between young and old groups using R software.


title: Transcriptomal analysis revealed that the metabolism and structure of porcine Longissimus Dorsi muscle were changed by constant heat stress

status: Public on Jun 11 2017

city: Beijing

first: Yue

last: Hao

address: No.2 Yuanmingyuan West Road

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: To characterize the changes of mRNAs in skeletal muscle responding to heat stress, the mRNA expression profiles of longissimus dorsi muscles of pigs raised under constant heat stress (30°C, n=8) or control temperature (22 C, n=8) for 21 days were analyzed by Illumina high-throughput sequencing. There were 78 genes differentially expressed, of which 37 were up-regulated and 41 down-regulated by constant heat stress. In summary, 5,247 novel genes and 6,108 novel transcribed units in the skeletal muscle were identified. Furthermore, 30,761 and 31,360 AS events were observed in CON and H30 libraries, respectively. The differentially expressed genes in the muscle were involved in glycolysis, lactate metabolism, lipid metabolism, cellular defense, and stress responses. The expression levels of those genes were associated with the parameters of meat quality, indicating that heat stress affected meat quality by regulating genes associated with nutrition metabolism and muscle development.

overall_design: Characterize and compare expression profiling of the mRNA transcriptome in 2 groups of porcine skeletal muscle.

first: Xianhong

last: Gu


title: Role of epigenetics in adaptive evolution of an asexual snail

status: Public on Aug 18 2017

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next generation sequencing of esophageal squamous cell carcinoma (ESCC) cell line KYSE-180 single cell transcriptomes for radio-resistance analysis

status: Public on Jun 01 2017

city: Hangzhou

first: Ling

last: Yang

address: 34th, Yanguan alley

institute: Hangzhou cancer institute

summary: Purpose: Single cell RNA-seq could observe heterogeneity of cell transcriptomes. The goals of this study are to compare the changes of  ESCC cell line KYSE-180 RNA profiles in response to different doses of radiotherapy and to analyze the radio-resistance related genes.

overall_design: Methods: Cultured KYSE-180 cells accepted accumulative irradiation doses of 0 Gy, 12 Gy or 30 Gy, respectively. Single cell libraries were generated by Smart-seq 2 kit, sequenced using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript expression level with TopHat followed by DESeq2/Monocle.

first: Hongjin

last: Wu

first: Xiaoyan

last: Zhang

first: Shixiu


title: The gene expression profiles of human bone marrow stromal cells

summary:
Evidence suggests that the bone marrow microenvironment (niches) support hematopoietic stem cells (HSCs). The cell-cell interaction between bone marrow mesenchymal stromal cells (BMSCs) and HSCs plays a crucial role in hematopoiesis.
The aging of BMSCs lead to decreased ability to maintain hematopoiesis. We used microarray to determine the age-related change of BMSCs.

overall_design: Human BMSCs of young (yBMSC s, age of donors: 19 and 20 years) and elderly (eBMSC s, age of donors: 68 and 72 years) donors were purchased from Lonza. BM samples were obtained from MM patients (age of donors:  62 and 77 years) in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648).  BMSCs derived from MM patients (mmBMSCs) were isolated using the classical plastic adhesion method. Total RNA from each sample (yBMSCs, eBMSCs and mmBMSCs) was processed for hybridization onto GeneChip® human Gene 1.0 ST Array (Affymetrix) according to the manufacturer's protocol and scanned.


title: Role of epigenetics in adaptive evolution of an asexual snail (Lake Lytle)

summary: We examined adaptive morphological divergence and epigenetic variation in genetically impoverished asexual populations of a freshwater snail, Potamopyrgus antipodarum from distinct environments.  These populations exhibit environment-specific adaptive divergence in shell shape and significant genome wide DNA methylation differences among differentially adapted lake and fast water flow river populations. The epigenetic variation correlated with adaptive phenotypic variation in rapidly adapting asexual animal populations. This provides one of the first examples of environmentally-driven differences in epigenetics that associates with adaptive phenotypic divergence.

overall_design: To examine the association between this adaptive divergence and epigenetic differences, we sampled at least 30 individuals from a “river” site characterized by constantly fast water current speeds due to input from underground springs (Ritter Island, Snake River, ID) and from a “lake” site with no water current (Lake Lytle, Rockaway Beach, OR).  Shell spire height and aperture length were measured as an index of adaptive foot size and shell shape differences. On these same samples, we dissected foot tissue from individuals for the analysis of epigenetic variation.

first: Jennifer

last: Thorson

first: Mark

last: Smithson

first: Daniel

last: Beck

first: Ingrid

last: Sadler-Riggleman

last: Nilsson

last: Dybdahl


title: The whole human genome expression data from Huh7 cells

status: Public on Apr 17 2017

first: SHUAI

last: HUANG

address: Nanwei Road NO2

institute: Institute of Materia Medica,Chinese Academy of Medical Sciences/Peking Union Medical College

summary: Botanic drug CA regulated the genes expression in tumor cells. We used microarrays to detail the differentiation genes expression treated with CA or not.

overall_design: The Huh7 cells were untreated, or treated with 50 μM or 100 μM of CA for 24 hrs.

first: Huang

last: Shuai

first: Han

last: Yan-Xing


title: The miRNA expression profiling in Huh7 cells

summary: Botanic drug CA regulated the miRNAs expression in tumor cells. We used microarrays to detail the differentiation miRNAs expression in Huh7 cells treated with CA or not.

overall_design: The Huh7 cells were untreated, or treated with 25 μM or 50 μM of CA for 24 hrs.


title: Distinct NSun methylases control cytosine-5 methylation of messenger, mitochondrial and transfer RNA: implications for human diseases

status: Public on Feb 14 2017

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine


title: Distinct NSun methylases control cytosine-5 methylation of messenger, mitochondrial and transfer RNA: implications for human diseases [miCLIP & Bisfulfite-Seq HEK293]

summary: Aberrant post-transcriptional methylation is implicated in a wide range of human diseases, yet the specific enzymes responsible for site- and substrate-specific methylation remain largely unknown. Here, we use our recently developed catalysis-dependent RIP sequencing approach (miCLIP) and RNA bisulfite sequencing to map C5-methylcytosine (m5C) in the human transcriptome. We identified two novel m5C methylases NSun3 and NSun6, both of which have strong substrate specificity. In contrast to the previously characterized NSun2, which displays some preference to methylating transfer RNAs (tRNA), NSun6 predominantly targeted 3’ UTRs of messenger RNAs (mRNA), and NSun3 mainly methylated mitochondrial RNAs (mtRNA). Consistent with the miCLIP-predicted RNA target specificity, whole exome sequencing identified NSUN3 loss-of-function mutations in a patient presenting with combined respiratory chain complex deficiency. Functional studies of the patient fibroblast cell line revealed that loss of the NSun3 protein resulted in severe mitochondrial translation defects, which were rescued by expression of wild-type NSun3. In summary, our results reveal how highly conserved NSun m5C methylases partition their substrate specificities to remodel the sequences of particular ribonucleotide classes.

overall_design: Identification of Nsun3 and Nsun6 methylation targets by miCLIP and bisulfite sequencing in Embryonic kidney (HEK293) cells

first: Shobbir

last: Hussain


title: Whole genome and miRNA expression profiling in Huh7 cells

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


title: Cell density effects on normal astrocytes and glioma cells

status: Public on Mar 10 2017

city: Bethesda

first: Jayne

last: Stommel

address: 10 Center Drive

institute: National Cancer Institute

summary: Glioma cells and normal astrocytes were plated at low and high density to compare density-dependent gene expression.

overall_design: Primary glioma cells were splated at either sparse plating density (5x104 cells/mL) or dense (3x105 cell/mL).  NHAs were plated at either sparse plating density (3.5x105 cells/55cm2 dish) or dense (5.2x106/55cm2 dish) at a final conc of 5x104 cells/mL and 3x105 cell/mL.  Cells were incubated for 5 days prior to RNA harvest.


title: RNA-Sequencing for Additional Molar Germs Transcriptomes at Stages of Early Development in Miniature Pigs

status: Public on Jan 24 2017

first: Fu

last: Wang

address: Tian Tan Xi Li No.4, P. R. China

institute: Capital Medical University

summary: The molecular mechanisms of the regulatory network of mRNAs and long non-coding RNAs during sequential formation of additional molars remain poorly characterized in diphyodont mammals. The diphyodont miniature pig has proved to be a valuable model for studying human molar morphogenesis. Here, we performed RNA-seq on miniature pigs at three molar developmental stages to examine their differential gene expression profiles and potential regulatory networks during additional molar morphogenesis. Many new unannotated genes plus putative long non-coding RNAs were identified. Our data provide fundamental knowledge and a basis for understanding the molecular mechanisms governing cascade initiation of additional molars.

overall_design: Additional molar germs mRNA profiles from early developmental stages at E50, E60 and E70 in Miniature pigs' were generated by deep sequencing using Illumina Hiseq 2000

first: Songlin


title: Expression data from additional molar germs at stages of early development in miniature pigs

summary:
We identified the spatiotemporal pattern of cascade initiation of additional molars in miniature pig,where second molar (M2) initiated from the posterior-free end of the dental lamina over the first molar (M1) at E60 when M1 progressed to the late bell stage. Similarly, third molar (M3) budded off from the posterior-free end of the dental lamina over M2, which reached bell stage at PN20. However, the molecular mechanisms of the regulatory network during sequential formation of additional molars remain poorly characterized in diphyodont mammals.
We performed microarrays on miniature pigs at three molar developmental stages to examine their differential gene expression profiles and potential regulatory networks during additional molar morphogenesis.

overall_design: Miniature pigs' additional molar germs samples from early developmental stages at E50, E60 and E70 were selected for RNA extraction and hybridization on Affymetrix microarrays in biological triplicates. The differentially expressed genes between the 3 different stages were screened, then differentially expressed genes with significance were chosen for significant GO and pathway enriching.  The differential genes and functions with significant expression tendencies were predicted using STC for further Path-Net, Signal-Net and Dynamic-Gene-Net analysis for Signal-Net to determine significant pathways and identify the key differentially expressed genes during early additional molars development. Additional  molar germs from three key stages were chosen to determine the spatiotemporal control mechanisms of cascade initiation of these molars. The E50 stage corresponding to M1 at cap stage without M2 initiation and the E60 stage targeting M1 at bell stage followed by M2 initiation. The E70 stage as a control, when M1 progresses to late bell stage but M2 changes little.


title: Comprehensive characterization of DNA methylation changes in Fuchs Endothelial Corneal Dystrophy

status: Public on Feb 04 2017

city: San Francisco

first: Selene

last: Clay

state: California

address: 1001 Potrero Ave Rm 210

department: Ophthalmology

institute: University of California, San Francisco

type: Methylation profiling by genome tiling array

summary:
Transparency of the human cornea is necessary for vision.  Fuchs Endothelial Corneal Dystrophy (FECD) is a bilateral, heritable degeneration of the corneal endothelium, and a leading indication for corneal transplantation in developed countries.  While the early onset, and rarer, form of FECD has been linked to COL8A2 mutations, the more common, late onset form of FECD has genetic mutations linked to only a minority of cases.  Epigenetic modifications that occur in FECD are unkonwn.  Here, we report on and compare the DNA methyhlation landscape of normal human corneal endothelial (CE) tissue and CE from FECD patients using the Illumina Infinium HumanMethylation450 (HM450) DNA methylation array.  We show that DNA methylation profiles are distinct between control and FECD samples.  Differentially methylated probes (10,961) were identified in the FECD samples compared with the control samples, with the majority of probes being hypermethylated in the FECD samples.  Genes containing differentially methylated sites were disproportionately annotated to ontological categories involving cytoskeletal organization, ion transport, hematopoetic cell differentiation, and cellular metabolism.  Our results suggest that altered DNA methylation patterns may contribute to loss of corneal transparency in FECD through a global accumulation of sporadic DNA methylation changes in genes critical to basic CE biological processes
Methylation of DNA is a key epigenetic mark that occurs in aging tissues.  Altered DNA methlyation patterns have been observed in several late onset, and progressive ocular diseases including macular degeneration, glaucoma, and cataracts.  While DNA methylation changes also occur in the common, late onset corneal dystrophy, FECD, has not been previously studied.  Fuchs Endothelial Corneal Dystrophy (FECD) is a bilateral, heritable degeneration of the corneal endothelium, and a leading indicatioin for corneal transplantation in developed countries.  Our study examined and compared the genome-scale DNA methylation profiels of corneal endothelial tissue from normal control and FECD patients using the Illumina Infinium HumanMethylation450 (HM450) DNA methylation array.  We show that DNA methylation profiles are distinct between control and FECD samples.  Differentially methylated probes (10,961) were identified in the FECD samples compared with the control samples, with the majority of probes being hypermethylated in the FECD samples.  Genes containing differentially methylated sites were disproportionately annotated to ontological categories involving cytoskeletal organization, ion transport, hematopoetic cell differentiation, and cellular metabolism.  Our findings suggest that alterations in DNA methylation may contribute to FECD pathogenesis by modifying the expression of genes with critical biological roles in the corneal endothelium.  Our study has important clinical implications as FECD is a leading indication for corneal transplantationin the geriatric population.  The effective medical treatment of FECD is a major unmet clinical challenge.  Our findings suggest altered DNA methylation as a novel candidate therapeutic target in FECD

overall_design: Illumina Infinium HumanMethylation450 DNA methylation array: 15 cases (9 used), 4 control

first: Emily

last: Khuc

first: Russel

last: Bainer

first: Marie

last: Wolf

last: Weisenberger

first: Jacquelyn

last: Kemmer

first: Valerie

last: Weaver

first: David

middle: G

last: Hwang

first: Matilda

last: Chan


title: Dynamic regulation of chromatin signatures during Drosophila embryonic glial differentiation

status: Public on Nov 20 2016

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine