title: Essential functions of the transcription factors TCF1 and SOX13 in gdT cell development (Sox13hi and Sox13lo)

summary: Innate-like gd T effector subsets are exported from the thymus as “memory-like” cells prewired for rapid, specialized function. Previously, we showed that emergent gd subsets distinguished by TCRg and TCRd usage in the fetal and adult thymus possess distinct global transcriptomes and the subset-specific combinatorial expression of High Mobility Group box transcription factors (HMG TFs) shown as a primary determinant of gd effector differentiation. While the detailed mechanism of HMG TFs cooperativity and counter-regulations are not fully understood, a key feature for IL-17 producing gd T effectors (Tgd17) is predicted to be context-dependent interactions between SOX13 and TCF1 that result in diversified target gene regulation. More SOX13 allow more TCF1 dockings on DNA. TCF1 chromatin occupancy in the Tgd17 gene cluster (V2 set) mimics when the amount of SOX13 is enhanced like the Sox13 transgenic system. Globally 75% of SOX13 binding is overlapped with TCF1 binding and V2 set-specifically 85% of SOX13 targets are overlapped with TCF1 targets. Mostly V2 sets are H3K4me3 (79%) and the genome wide analysis between TCF1 and SOX13 indicate cooperative and active SOX13-dependent-TCF1-modulations on V2 sets.

overall_design: Performed ChIPseq using antibodies specific for TCF1 or SOX13 will establish global positioning of TCF1&SOX13 on chromatin as a basal state of cells undergoing effector programming. ChIPseq for H3K4me3 and H3K27me3, a mark associated with transcriptional activation or repression, will support SOX13-dependent global TCF1- and SOX13-chromatin docking pattern.


title: Below ground attack by root knot nematode Meloidogyne graminicola predisposes rice to blast disease

status: Public on Nov 02 2018

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

type: Expression profiling by high throughput sequencing

summary: Magnaporthe oryzae (rice blast) and the root-knot nematode Meloidogyne graminicola are causing two of the most important pathogenic diseases jeopardizing rice production. Here, we show that root-knot nematode infestation on rice roots leads to important above-ground changes in plant immunity gene expression, which is correlated with significantly enhanced susceptibility to blast disease.

overall_design: Differential expression analysis between controls rice shoots and shoots from root knot nematode (M. graminicola) infected rice at two time points.

first: Tina

last: Kyndt

first: Henok

middle: Y

last: Zemene

first: Ashley

last: Haeck

first: Richard

last: Singh

first: David

last: De Vleesschauwer

first: Simon

last: Denil

first: Tim

last: De Meyer

first: Monica

last: Höfte

first: Kristof

last: Demeestere

first: Godelieve

last: Gheysen


title: Hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes in choriocarcinoma cells

status: Public on Nov 01 2018

city: Shanghai

first: Jiuru

last: zhao

address: Hengshan Road 910#

department: Pathology and Bio-Bank

country: China

institute: International Peace Maternity and Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We report the application of transcriptome sequencing for investigating of the hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes. JAR, JEG-3 and BeWo choriocarcinoma cells were transfected with hsa-miR-371a-5p or hsa-miR-518a-3p inhibitors or control inhibitors. Totally, 237, 132 and 277 genes with > 2 folds change and adjusted P < 0.05 were upregulated in JAR, JEG-3 and BeWo cells respectively after hsa-miR-371a-5p knockdown. Meanwhile, 229, 269 and 191 genes were upregulated in JAR, JEG-3 and BeWo cells respectively after hsa-miR-518a-3p knockdown. The top upregulated genes included many oncogenes or oncogenesis associated ones. Enrichment analysis showed hsa-miR-371a-5p and hsa-miR-518a-3p regulated diverse pathways related to tumorigenesis and metastasis. Our results would be helpful for the searching of early molecular biomarkers and therapeutic targets for gestational trophoblastic neoplasia.

overall_design: Examination of functions of 2 different miRNAs in 3 cell types.

last: Zhao

first: Huijuan

last: Zhang


title: APA modulator_U2OS_RNA-seq

city: Fujisawa

first: Yusuke

last: Nakayama

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Pharmaceutical Research Division

country: Japan

institute: Takeda Pharmaceutical Company Limited

summary: RNA-seq data treated with small molecule compounds that modulate alternative polyadenylation

overall_design: mRNA profiles treated with APA modulator (T4 or T5) for 6 h in U2OS cells

first: Shinsuke

last: Araki


title: Genomic profiling of chromatin accessibility in gd T cells during thymic development

city: Worcester

first: OK HYUN

last: CHO

state: MA

address: 368 Plantation Street

department: Pathology

country: USA

institute: University of Massachusetts Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Innate-like gd T effector subsets are exported from the thymus as “memory-like” cells prewired for rapid, specialized function. Previously, we showed that emergent gd subsets distinguished by TCRg and TCRd usage in the fetal and adult thymus possess distinct global transcriptomes and the subset-specific combinatorial expression of High Mobility Group box transcription factors (HMG TFs) shown as a primary determinant of gd effector differentiation. While the detailed mechanism of HMG TFs cooperativity and counter-regulations are not fully understood, a key feature for IL-17 producing gd T effectors (Tgd 17) is predicted to be context-dependent interactions between SOX13 and TCF1 that result in diversified target gene regulation. Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATACseq) will map chromatin accessibility genome wide. Each read will provide information about the positions of nucleosomes and nucleosome-free regions.

overall_design: For ATAC-Seq, gdT cells were isolated from thymocytes to profile chromatin states of low cell number samples

first: O

middle: H

last: Cho

first: H

middle: M

last: Shin

first: J

last: Kang


title: Transciptome changes in relation to manic episode

status: Public on Oct 31 2018

city: Taipei

first: Ya-Chin

last: Lee

address: Rm 521, No.17, Xu-Zhou Rd.

department: Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University

summary: The present study focused on manic episode in bipolar disorder (BD) patients, and to investigate state-specific transcriptome alterations between acute episode and remission, including mRNAs, long non-coding RNAs (lncRNAs), and miRNAs using Affymetrix Human Transcriptome Array 2.0.

overall_design: Six BD patients were enrolled with clinical and biological samples collected at both acute and remission status following-up for at least two-months. We extracted RNA from two time points and used Affymetrix Human Transcriptome 2.0 array to capture transcriptome data underwent intra-individual comparison.

first: Yu-Lin

last: Chao

first: Chiao-Erh

last: Chang

first: Ming-Hsien

last: Hsieh

first: Kuan-Ting

last: Liu

first: Hsi-Chung

last: Chen

first: Mong-Liang

last: Lu

first: Wen-Yin

first: Chun-Hsin

first: Mong-Hsun

last: Tsai

first: Tzu-Pin

first: Ming-Chyi

last: Huang

first: Po-Hsiu

last: Kuo


title: Divergence of alternative splicing in Arabidopsis

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: We investigated genome-wide variation in AS in Arabidopsis thaliana accessions Col and Ler using RNA-seq. We identified many cis-regulatory elements associated with AS events, among which polypyrimidine tracts (e.g., UCUCUC and CUCUCU) were significantly overrepresented, especially in the exons upstream of each AS event. We found that variation in cis-regulatory element sequences contributed to divergence in AS levels, but not to differential gene transcription between the two Arabidopsis accessions.

overall_design: RNA-seq analysis of alternative splicing in the first leaf of 14 day old seedlings of two Arabidopsis Col and Ler.

first: Mei

last: Yang

first: Guangming

last: He

first: Xingwang

last: Deng


title: A defective pentose phosphate pathway reduces inflammatory macrophage responses during hypercholesterolemia

city: Amsterdam

first: Menno

last: de Winther

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: Academic Medical Center University of Amsterdam

summary: Metabolic reprogramming has emerged as a crucial regulator of immune cell activation but how systemic metabolism influences immune cell metabolism and function remains to be investigated. To investigate the effect of dyslipidemia on immune cell metabolism, we performed in-depth transcriptional, metabolic and functional characterization of macrophages isolated from hypercholesterolemic mice. Systemic metabolic changes in such mice alter cellular macrophage metabolism and attenuate inflammatory macrophage responses. In addition to diminished maximal mitochondrial respiration, hypercholesterolemia reduces the  LPS-mediated induction of the pentose phosphate pathway (PPP) and the Nrf2-mediated oxidative stress response. Our observation that suppression of the PPP diminishes LPS-induced cytokine secretion supports the notion that this pathway contributes to inflammatory macrophage responses. Overall, this study reveals that systemic and cellular metabolism are strongly interconnected, together dictating macrophage phenotype and function.

overall_design: RNA-seq of peritoneal macrophages from female mice placed on a control or high fat diet, stimulated with LPS for 0 or 24 hours.

first: Jeroen

last: Baardman

first: Sanne

middle: G

last: Verberk

first: Koen

last: Prange

first: Michel

last: Weeghel

first: Saskia

last: van der Velden

first: Dylan

last: Ryan

first: Rob

middle: C

last: Wüst

first: Annette

middle: E

last: Neele

first: Dave

last: Speijer

first: Simone

middle: W

last: Denis

first: Maarten

last: Witte

first: Riekelt

last: Houtkooper

first: Luke

middle: A

last: O'Neill

first: Elena

middle: V

last: Knatko

first: Albena

middle: T

last: Dinkova-Kostova

first: Esther

last: Lutgens

middle: P

first: Jan

last: van den Bossche


title: Megadomains and superloops form dynamically during X-chromosome inactivation but are dispensable for silencing and escape

city: Cambridge

first: John

middle: Edward

last: Froberg

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

summary: The mammalian inactive X-chromosome (Xi) is structurally distinct from all other chromosomes and serves as a model for higher order chromosome organization. The Xi lacks strong topologically associated domains and is instead organized into megadomains and superloops mediated in part by the noncoding loci, Dxz4 and Firre. Their functional significance is presently unclear, though one study suggests that they permit Xi genes to escape silencing. Here, we find that megadomains do not form before silencing spreads along the Xi. Deletional analysis shows that Dxz4, but not Firre, is required for megadomains. Surprisingly, however, deleting neither Dxz4 nor Firre impacts Xi silencing or gene escape. Nor does it affect Xi nuclear localization, stability, or H3K27 methylation. Furthermore, ectopic integration of Dxz4 and Xist is not sufficient to form megadomains on autosomes, thereby uncoupling megadomain formation from chromosomal silencing. We conclude that Dxz4 and megadomains are dispensable for Xi silencing and escape.

overall_design:
Hi-C, Hi-C^2, 4C, ATAC-seq, ChIP-seq, RNA-seq
Please note that, to make data access easier, the 'GEO_readme.xls' lists Sample names with expriments and their associated files.


title: Gene expression profiling of human iPSC kidney organoid-derived epithelium

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

summary: The kidney organoid differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. Here the EPCAM+ epithelial fraction was isolated from day 25 kidney organoids using MACS-enrichment and RNA-sequencing libraries generated.

overall_design: RNA-Seq of three replicates of EPCAM+ epithelial fraction isolated from human kidney organoids


title: A facile method for generating tumorigenic cancer stem cell spheroids from diverse cancer cell lines

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

summary: Although cancer stem cells (CSCs) are thought to be responsible for tumor recurrence and resistance to chemotherapy, CSC-related research and drug development have been hampered by the limited supply of patient-derived diverse CSCs. Here, we developed a functional polymer thin film (PTF) platform that promotes conversion of human cancer cell lines to highly tumorigenic spheroids without the use of biochemical or genetic manipulations. Culturing various human cancer cells on the specific PTF, poly(2,4,6,8-tetravinyl-2,4,6,8-tetramethyl cyclotetrasiloxane) (pV4D4), gave rise to numerous multicellular spheroids within 24 hours, with high efficiency and reproducibility. Cancer cells in the resulting spheroids showed an enormous increase in the expression of CSC-associated genes and acquired dramatically increased drug resistance compared with monolayer-cultured controls. These spheroids also showed greatly enhanced xenograft tumor-forming ability and metastasis capacity in nude mice. By enabling the generation of tumorigenic spheroids as a patient-derived CSC substitute, the surface platform described here will likely contribute to CSC-related basic research and drug development.

overall_design: mRNA profiles of 8 day-SKOV3-ssiCSC spheroids and 2D-cultured SKOV3 control were generated by deep sequencing, in duplicate, using Hiseq-2500.

first: Minsuk

first: Seung-Jung

last: Yu

first: Hak-Rae

last: Lee

first: Eunbyeol

first: Eunjung

first: Jin-Yong

last: Kim

first: Sukmo

last: Kang

first: Jieung

last: Baek

first: Daeyoup

first: Sun-Gap

last: Im

first: Sangyong

last: Jon


title: RNA-seq analysis of THP-1 cell line upon knockdown of CHD4

city: Stockholm

first: Julian

last: Walfridsson

country: Sweden

summary: Epigenetic alterations contribute to leukemogenesis in childhood acute myeloid leukemia (AML). We used RNAi screens of AML cells together with non-transformed bone marrow cells and identified CHD4 as being required for AML maintenance. RNAi and CRISPR-Cas9 approaches, showed that CHD4 is essential for cell growth of leukemic cells in vitro, and disease progression in vivo, including primary childhood AML cells. Loss of function of CHD4 arrests AML cells in the G0 phase of the cell cycle, which is associated with downregulation of MYC and its target genes. Conversely, CHD4 suppression is not essential for normal blood cells. Taken together, our results identify CHD4 as a potential therapeutic target in childhood AML.

overall_design: THP-1 cell line were trasnduced with shRNA targeting CHD4 or negative control vectors and RNA was isolated for RNA-seq analysis 72hour post transduction.

first: Yaser

last: Heshmati


title: Stable oxidative cytosine modifications accumulate in cardiac mesenchymal cells from Type2 diabetes patients: rescue by alpha-ketoglutarate and TET-TDG functional reactivation [mouse heart RNA-seq]

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Background: Here, the role of α-ketoglutarate (αKG) in the epi-metabolic control of DNA demethylation has been investigated in therapeutically relevant cardiac mesenchymal cells (CMSCs) isolated from controls and type 2 diabetes donors. Methods & results: Quantitative global analysis, methylated and hydroxymethylated DNA sequencing and gene specific GC methylation detection revealed an accumulation of 5mC, 5hmC and 5fC in the genomic DNA of human CMSCs isolated from diabetic (D) donors (D-CMSCs). Whole heart genomic DNA analysis revealed iterative oxidative cytosine modification accumulation in mice exposed to high fat diet (HFD), injected with streptozotocin (STZ) or both in combination (STZ-HFD). In this context, untargeted and targeted metabolomics indicated an intracellular reduction of αKG synthesis in D-CMSCs and in the whole heart of HFD mice. This observation was paralleled by a compromised thymine DNA glycosylase (TDG) and ten eleven translocation protein 1 (TET1) association and function with TET1 relocating out of the nucleus. Molecular dynamics and mutational analyses showed that αKG binds TDG on Arg275 providing an enzymatic allosteric activation. As a consequence, the enzyme significantly increased its capacity to remove G/T nucleotide mismatched or 5fC. Accordingly, an exogenous source of αKG restored the DNA demethylation cycle by promoting TDG function, TET1 nuclear localization and TET/TDG association. TDG inactivation by CRISPR/Cas9 knockout or TET/TDG siRNA knockdown induced 5fC accumulation thus partially mimicking the diabetic epigenetic landscape in cells of non- diabetic origin. The novel compound (S)-2-[(2,6-dichlorobenzoyl)amino]succinic acid (AA6), identified as an inhibitor of αKG-dehydrogenase, increased the αKG level in D- CMSCs and in the heart of HFD mice eliciting DNA demethylation, glucose uptake and insulin response. Conclusions: In this report we established that diabetes may epigenetically modify and compromise function of therapeutically relevant cardiac mesenchymal cells. Restoring the epi-metabolic control of DNA demethylation cycle promises beneficial effects on cells compromised by environmental metabolic changes.

overall_design: RNA was isolated from mouse heart samples (4 control, 4 high fat diet, and 4 high fat diet + AA6) and sequenced.

first: Francesco

last: Spallotta

first: Chiara

last: Cencioni

first: Sandra

last: Atlante

first: Davide

last: Garella

first: Mattia

last: Cocco

last: Mori

first: Raffaella

last: Mastrocola

first: Stefan

last: Guenther

first: Simona

last: Nanni

first: Valerio

last: Azzimato

first: Sven

last: Zukunft

first: Angela

last: Kornberger

first: Duran

last: Sürün

first: Frank

last: Schnutgen

first: Harald

last: von Melchner

first: Antonella

last: Di Stilo

first: Manuela

last: Aragno

first: Maarten

last: Braspenning

first: Wim

last: Van Criekinge

first: Miles

last: De Blasio

first: Rebecca

last: Ritchie

first: Germana

last: Zaccagnini

first: Fabio

last: Martelli

last: Farsetti

first: Ingrid

last: Fleming

first: Thomas

last: Braun

first: Andres

last: Beiras-Fernandez

first: Bruno

last: Botta

first: Massimo

last: Collino

last: Bertinaria

first: Andreas

last: Zeiher

first: Carlo

last: Gaetano


title: Stable oxidative cytosine modifications accumulate in cardiac mesenchymal cells from Type2 diabetes patients: rescue by alpha-ketoglutarate and TET-TDG functional reactivation [mouse muscle RNA-seq]

first: Carsten

last: Kuenne

overall_design: RNA was isolated from mouse skeletal muscle samples (3 control, 3 high fat diet, and 3 high fat diet + AA6) and sequenced.

first: Francesco

last: Spallotta

first: Chiara

last: Cencioni

first: Sandra

last: Atlante

first: Davide

last: Garella

first: Mattia

last: Cocco

last: Mori

first: Raffaella

last: Mastrocola

first: Stefan

last: Guenther

first: Simona

last: Nanni

first: Valerio

last: Azzimato

first: Sven

last: Zukunft

first: Angela

last: Kornberger

first: Duran

last: Sürün

first: Frank

last: Schnutgen

last: von Melchner

last: Di Stilo


title: Stable oxidative cytosine modifications accumulate in cardiac mesenchymal cells from Type2 diabetes patients: rescue by alpha-ketoglutarate and TET-TDG

last: Kuenne

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A Zeb1 Hdac2 eNOS feedback circuitry identifies early cardiovascular precursors in naïve mouse embryonic stem cells (ChIP-Seq)

summary: Soon after release from stemness, a relevant portion of mouse embryonic stem cells (mES), kept in naïve state by MEK inhibitor, GSK3 inhibitor and LIF (2i/L), expresses endothelial nitric oxide synthase (eNOS) and endogenously synthesizes nitric oxide (NO). In this condition, an eNOS/NO-positive subpopulation (ESNO+) has been recognized by 4-amino-5-methylamino-2′,7′-difluorescein (DAF) fluorescence. Sorted ESNO+ cells expressed high levels of mesendodermal markers and efficiently generated cardiovascular precursors compared to eNOS/NO-negative cells (ESNO-). Mechanistically, the endogenous NO production deter- mined a rapid S-nitrosylation of Hdac2, a post-translational modification that compromised Hdac2 association with the transcription repression factor Zeb1. This condition destabilized Zeb1/chromatin interaction with genomic loci encoding for mesendodermal genes. Remarkably, Zeb1 or Hdac2 targeting activated an unscheduled transcription of mesendodermal lineage-associated genes in naïve mES revealing the Hdac2-Zeb1 pathway important for stemness maintenance in 2i/L. In contrast, eNOS targeting significantly reduced the endogenous NO production preventing the activation of mesendodermal gene transcription.

overall_design: ChIP-Seq experiments of the Zeb1 transcription factor were performed three times on mouse embryonic stem cells (ES). One genomic input sample was generated for control purposes.

last: Spallotta

first: Matteo

last: Savoia

first: Agnese

last: Re

first: Susanne

last: Wingert

first: Maike

last: Rehage

first: Mauro

last: Siragusa

first: Jacob

last: Smith

last: Schnütgen

first: Harald

first: Michael

last: Rieger

first: Fabio

last: Martelli

first: Antonella

last: Riccio

first: Ingrid

last: Fleming

first: Thomas

last: Braun

last: Zeiher

last: Farsetti

last: Gaetano


title: A Zeb1 Hdac2 eNOS feedback circuitry identifies early cardiovascular precursors in naïve mouse embryonic stem cells

first: Carsten

last: Kuenne


title: A Zeb1 Hdac2 eNOS feedback circuitry identifies early cardiovascular precursors in naïve mouse embryonic stem cells (RNA-Seq)

overall_design: ES cell in Mesendodermal and Spontaneous differentiation media

first: Chiara

last: Cencioni

first: Francesco

last: Spallotta

first: Stefan

last: Guenther

last: Sürün

last: von Melchner

first: Andreas

first: Carlo


title: Genomic basis for clinical response to histone deacetylase inhibition in advanced urothelial carcinoma

city: Salt Lake City

first: Sumati

last: Gupta

state: Utah

address: 2000 Circle of Hope

department: Medicine

institute: Huntsman Cancer Institute

summary: Abstract  Background: Histone deacetylase (HDAC) inhibition has shown some efficacy in urothelial carcinoma (UC); the genomic basis for clinical response is not known.  Methods: In two separate phase I clinical trials testing HDAC inhibitors in advanced solid tumors, we identified one patient with advanced UC who had a complete response (CR) to belinostat and one with advanced UC who had a partial response (PR) to panobinostat. The archived tumor of the responders was genomically characterized and studied in comparison to others with UC, in the context of their response to HDAC inhibition on trial. UC cell lines treated with panobinostat were studied to elucidate the mechanisms of benefit.  Results: The two patients who responded to HDAC inhibition had ARID1A and FANCD2 mutations. The patient who had a CR to HDAC inhibition had the highest tumor mutational burden of all tumors. Corroborating the basis of sensitivity, transcriptional profiling of platinum resistant ARID1A mutated HT1197 cells treated with panobinostat revealed downregulation of cyto-proliferative and DNA repair gene sets and upregulation of inflammatory gene sets.  Conclusions: Clinical efficacy of HDAC inhibition in UC may be dependent on overlapping SWI/SNF pathway mutations and DNA repair defects. Tumor mutational burden may predict the depth and duration of benefit.

overall_design: RNASeq analysis of urothelial carcinoma cell lines treated with HDAC inhibitor panobinostat

first: Dan

last: Albertson

first: Timothy

last: Parnell

first: Andrew

last: Butterfield

first: Alexis

last: Weston

first: Lisa

last: Pappas

first: Brian

last: Dalley

first: John

last: Oshea

first: William

last: Lowrance

first: Joshua

last: Schiffman

first: Sunil

last: Sharma

first: Brad

last: Cairns


title: Stable oxidative cytosine modifications accumulate in cardiac mesenchymal cells from Type2 diabetes patients: rescue by alpha-ketoglutarate and TET-TDG functional reactivation [human cells RNA-seq]

first: Carsten

last: Kuenne

overall_design: Human primary cardiac mesenchymal cells (CMSC) from 7 diabetic (D) and 7 non-diabetic (ND) donors were analyzed after few rounds of ex vivo expansion. RNA was isolated and sequenced.

first: Chiara

last: Cencioni

first: Sandra

last: Atlante

first: Davide

last: Garella

first: Mattia

last: Cocco

last: Mori

first: Raffaella

last: Mastrocola

first: Simona

last: Nanni

first: Valerio

last: Azzimato

first: Sven

last: Zukunft

first: Angela

last: Kornberger

first: Duran

first: Frank

last: Schnutgen

first: Harald

first: Antonella

last: Di Stilo

first: Manuela

last: Aragno

first: Maarten

last: Braspenning

first: Wim

last: Van Criekinge

first: Miles

last: De Blasio

first: Rebecca

last: Ritchie

first: Germana

last: Zaccagnini

first: Fabio

last: Martelli

last: Farsetti

first: Ingrid

last: Fleming

first: Thomas

last: Braun

first: Andres

last: Beiras-Fernandez

first: Bruno

last: Botta

first: Massimo

last: Collino

last: Bertinaria

last: Zeiher

last: Gaetano


title: Expression analysis of THP1 cells following shRNA knock-down of RUVBL2

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

country: United Kingdom

institute: UCL GOS ICH

summary: We used an inducible shRNA system and RNA-Seq to examine gene expression changes in acute myeloid leukemia THP1 cells following silencing of RUVBL2. RUVBL2 is a AAA+ ATPase that functions in a number of cellular processes, including chromatin remodeling and trnascriptional control, and is critical for survival of acute myeloid leukemia cells and in vivo disease progression.

overall_design: Total cellular RNA was extracted using the RNeasy Plus Mini Kit from THP1 cells transduced with RUVBL2-specific inducible shRNA, following 4 days exposure to doxycycline or medium controls. In total, 5 pairs of control and doxycycline-treated samples were analysed.

first: Elena

last: Armenteros-Monterroso

first: Jasper

last: de Boer


title: RNA-Seq profiling of days 0, 7 and 18 kidney organoids differentiated from three separate vials of starting material

first: Belinda

last: Phipson

summary: The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. This data has been generated to investigate the reproducibility of the kidney differentiation protocol using RNA sequencing from days 0, 7 and 18 organoids. Organoid differentiations were performed in parallel from three separate vials of starting material. The resulting RNA-seq data was analysed to identify genes with highly variable expression between vials.

overall_design: Gene expression profiling of three day 0 hIPSCs, three day 7 kidney organoids and six day 18 kidney organoids.


title: Understanding the reproducibility and robustness of the kidney organoid differentiation protocol using RNA-seq

summary: The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. Here we investigate the reproducibility of the kidney differentiation protocol using RNA sequencing from day 18 organoids. Organoid differentiations were performed in separate batches, and within one of the batches, from three separate vials. The resulting RNA-seq data was analysed to identify genes with highly variable expression between batches and vials.

overall_design: Gene expression profiling of four day 18 kidney organoids differentiated concurrently, and six day 18 kidney organoids differentiated from three vials of starting material at a later date.


title: RNA-Seq from early time points in the kidney differentiation protocol

summary: The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. Initially the cells are grown in a monolayer in a dish before being pelleted on day seven. We have performed RNA sequencing on three replicates taken at two points before cells are pelleted: day 0, when they are still iPSCs, and day 4 when cells have been exposed to growth factors and have started differentiating.

overall_design: Gene expression profiling of six samples across two time points (Day 0 and Day 4)


title: RNA-Seq profiling of day 7 and day 18 kidney organoids differentiated in two batches

summary: The kidney differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. This data has been generated to investigate the reproducibility of the kidney differentiation protocol using RNA sequencing from day 18 organoids. Organoid differentiations were performed in two separate batches separated in time. The resulting RNA-seq data was analysed to identify genes with highly variable expression between batches.

overall_design: Gene expression profiling of five day 7 kidney organoids and five day 18 kidney organoids from two differentiation experiments.


title: The effect of TAZ-K in neonatal rat cardiomyocytes

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

institute: The University of Tokyo

summary: Accumulating evidence suggests that new cardiomyocytes are generated from existing cardiomyocytes at a low rate throughout life. This limited regenerative capacity is unable to restore cardiac function after substantial cardiac damage; thus, small molecules have been examined for their ability to enhance the replication of existing cardiomyocytes. A novel compound TAZ-K promoted cardiomyocyte proliferation, therefore, we analyzed the effect of TAZ-K on gene expression in neonatal rat cardiomyocytes. Gene expression involved in cell cycle, anti-oxidant and anti-apoptosis was up-regulated. Thus, TAZ-K may have multifaceted effects and provide a treatment strategy that complements current therapies for patients with myocardial infarction.

overall_design: Primary neonatal rat cardiomyocytes were cultured in DMEM media supplemented with 10% FCS. After 24 hours, cardiomyocytes were starved (0.1% FCS) for 6 hours, subsequently treated with vehicle (3 samples) or TAZ-K (10 µM; 3 samples) for 24 hours. Cardiomyocytes were harvested, and total RNA was isolated and utilized for gene expression analysis.

first: Hironori

last: Hara

first: Norifumi

last: Takeda

first: Hiroyuki

last: Aburatani

first: Issei

last: Komuro


title: Gene expression profiling of human iPSC kidney organoid-derived proximal tubules

summary: The kidney organoid differentiation protocol takes induced pluripotent stem cells through to kidney organoid via directed differentiation in approximately 25 days. The cells are grown in a monolayer in a dish for seven days and are subjected to growth factors before being pelleted on day seven. The organoids then continue to differentiate as a 3D structure, with at least 8 distinct kidney cell types identifiable around day 18. Here proximal tubules were isolated from day 25 kidney organoids and RNA-sequencing libraries generated.

overall_design: RNA-Seq of three replicates of proximal tubules isolated from human kidney organoids


title: RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after PTBP1 knockdown in human erythroid cells

status: Public on Oct 30 2018

city: TianJin

first: Hua

middle: Jin

last: Liu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Purpose: The goals of this study are to determine possible  downstream targets of PTBP1 on day8 of  erythroid differentiation with or without PTBP1 knockdown.
Methods:gene expression profiling with or without PTBP1 knockdown in differentiated erythroblasts at day8  were generated by deep sequencing, induplicate, using Illumina GAIIx.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Conclusions: heme metabolism genes were down-regulated after PTBP1 knockdown during erythroid differentiation

overall_design: mRNA profiles of day8 erythroid cells with or without PTBP1knockdown were generated by deep sequencing, in duplicate, using Illumina GAIIx.

first: Lihong

last: Shi

first: Jinhua


title: Transcriptome profiling reveals the EanI/R quorum sensing regulon in Pantoea ananatis LMG 2665T

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

summary:
Background: Pantoea ananatis LMG 2665T synthesizes and utilizes acyl homoserine lactones (AHLs) for signaling. In this strain, short chain AHLs (C4 to C8) are produced by the EanI/R quorum sensing (QS) system that is involved in pathogenicity and biofilm formation. The complete set of genes regulated by the EanI/R system in P. ananatis LMG 2665T is still not fully known. In the present study, RNA-seq was used to analyze the transcriptome profiles controlled by the EanI/R system in this strain by comparing the wild type strain and its QS mutant 2665T ean∆I/R during lag and log stages. The RNA seq data was validated by RT qPCR.
Results: The results showed that the EanI/R regulon in P. ananatis LMG 2665T comprised 144 genes, constituting 3.3% of the whole transcriptome under the experimental conditions in this study. The majority of genes regulated by the EanI/R system included genes for flagella assembly, bacterial chemotaxis, pyruvate metabolism, two component system, metabolic pathways, microbial metabolism and biosynthesis of secondary metabolites.
Conclusions: This is the first study to identify the EanI/R QS regulon in P. ananatis LMG 2665T. Functional analysis of genes regulated the EanI/R system in LMG 2665T could help unveil genes that play a vital role in pathogenesis and survival strategies of this pathogen.

overall_design: mRNA profiles of growth phases (lag and log) in wild type (WT) and mutant generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform.

first: Siphathele

last: Sibanda

first: Divine

last: Shyntum

first: Teresa

last: Coutinho

first: Lucy

middle: N

last: Moleleki


title: Identification of Driver Mutations for Induction of Pancreatic Cancer from Adult Tree Shrew (Tupaia belangeri chinensis) Acinar Cells

city: Kunming

first: Junjun

last: Hao

address: 32 Jiaochang Donglu Kunming

institute: Kunming Institute of Zoology

summary: To investigate gene expression in the tree shrew pancreatic cancer model, tumor samples were analyzed by RNA-seq and the expression profiles were compared to those of human pancreatic cancer samples (n = 30) containing KRAS, TP53, and CDKN2A/B mutations downloaded from The Cancer Genome Atlas (https://tcga-data.nci.nih.gov/) and mouse pancreatic cancer (accession no. GSE87388), which showed similar histological features

overall_design:
comparation of gene expression profile among human, mouse and tree shrew pancreatic cancer. This series contains only tree shrew samples.

Processed data are not available for this series because acceptable data with publicly trackable gene IDs or associated sequence were not provided.

first: Qiu

last: Tu


title: Long Non-Coding RNA-Dependent Mechanism to Control Heme Biosynthesis and Erythrocyte Maturation


title: Transcriptional regulation of lipophorin receptors supports neuronal adaptation to chronic elevations of activity

city: Bethesda

first: Jun

last: Yin

state: Maryland (MD)

address: 35 Convent Drive, Room 1B-1006

department: NINDS

institute: National Institutes of Health

summary: Activity-dependent modifications strongly influence neural development. However, molecular programs underlying their context and circuit-specific effects are not well understood. To study global transcriptional changes associated with chronic elevation of synaptic activity, we performed cell-type-specific transcriptome profiling of Drosophila ventral lateral neurons (LNvs) in the developing visual circuit and identified activity-modified transcripts that are enriched in neuron morphogenesis, circadian regulation, and lipid metabolism and trafficking. Using bioinformatics and genetic analyses, we validated activity-induced isoform-specific upregulation of Drosophila lipophorin receptors LpR1 and LpR2, the homologues of mammalian low-density-lipoprotein receptor (LDLR) family proteins. Furthermore, our morphological and physiological studies uncovered critical functions of neuronal LpRs in maintaining the structural and functional integrities in neurons challenged by chronic elevations of activity. Together, our findings identify LpRs as molecular targets for activity-dependent transcriptional regulation and reveal the functional significance of cell-type-specific regulation of neuronal lipid uptake in experience-dependent plasticity and adaptive responses.

overall_design: LNv neuron-specific mRNA profiling in Drosophila larvae subjected to different visual experiences during development

first: Quan

last: Yuan


title: Human Sandhoff Disease Cerebral Organoids Exhibit Enlarged Size, Increased Cellular Proliferation, and Impaired Differentiation

first: Richard

middle: L

last: Proia

state: MD

address: 9000 Rockville Pk Bldg10-9D08

department: NIDDK

institute: NIH

summary: Sandhoff disease, one of the GM2 gangliosidoses, is a lysosomal storage disorder characterized by the absence of b-hexosaminidase A and B activity and the concomitant lysosomal accumulation of its substrate, GM2 ganglioside. It features catastrophic neurodegeneration and death in early childhood. How the lysosomal accumulation of ganglioside might affect the early development of the nervous system is not understood. Recently, cerebral organoids derived from induced pluripotent stem (iPS) cells have illuminated early developmental events altered by disease processes. To develop an early neurodevelopmental model of Sandhoff disease, we first generated iPS cells from the fibroblasts of an infantile Sandhoff disease patient, then corrected one of the mutant HEXB alleles in those iPS cells with CRISPR/Cas9 genome-editing technology, thereby creating isogenic controls. Next, we used the parental Sandhoff disease iPS cells and isogenic HEXB-corrected iPS cell clones to generate cerebral organoids that modeled the first trimester of neurodevelopment. The Sandhoff disease organoids but not the HEXB-corrected organoids accumulated GM2 ganglioside, and exhibited increased size and cellular proliferation compared with the HEXB-corrected organoids. Whole-transcriptome analysis demonstrated that development was impaired in the Sandhoff disease organoids, suggesting that alterations in neuronal differentiation may occur during early development in the GM2 gangliosidoses

overall_design: Sandhoff disease and corrected cerebral organoids grown for 8 and 10 weeks were analyzed: four samples at each time point, each consisting of 4–6 pooled organoids, for both Sandhoff and corrected. Whole transcriptome from Sandhoff disease and corrected organoids for both time points were generated by deep sequencing on an Illumina HiSeq 2500.

first: Maria

last: Allende


title: Critical modulation of hematopoietic lineage fate by Hepatic Leukemia Factor

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: Hematopoiesis commences with a gradual restriction in lineage potential of multipotent stem/progenitor cells, but the underlying molecular events of this remain incompletely understood. We here identify robust expression of the transcription factor Hepatic Leukemia Factor (Hlf) in multipotent hematopoietic progenitors, which is rapidly lost with differentiation. Prolonged Hlf expression reveals it as a strong negative regulator of lymphoid development and results in a pronounced and reversible differentiation block in the B-cell lineage, while remaining compatible with myeloid fates. Reciprocally, we observe rapid lymphoid commitment upon eduction of Hlf activity. These phenotypes result from Hlf-binding to active enhancers of myeloid-competent cells, induction of myeloid-affiliated transcription and ablation of lymphoid gene programs, with Hlf induction of Nuclear Factor I C (Nfic) as a functionally relevant target gene. Collectively, we establish Hlf as a key regulator of  the earliest lineage-commitment events at the transition from multipotency to lineage restricted progeny.

overall_design: Analysis of the genome wide binding profiles of Hlf in mulitpotent hematopoietic progenitors.

first: Vasileios

last: Ladopoulos


title: Differential analysis of salivary microRNA profiles in healthy and chronic periodontitis patients using Next Generation sequencing technology.

city: Bangalore

first: Nisha

state: Karnataka

address: EPIP Zone, Whitefield

department: Department of Periodontics

country: India

institute: Vydehi Institute of Dental sciences and Research Centre

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of high throughput Illumina sequencing for profiling of small RNAs in saliva of patients who were diagnosed with chronic periodontitis as compared to healthy controls. To date, there is no published literature on salivary microRNA profiling done using the high throughput next-generation sequencing analysis in patients diagnosed with chronic periodontitis. Also, this is the first study of its kind done in an Indian population. The objectives of the study were to profile microRNAs expressed in saliva of patients diagnosed with chronic periodontitis, to identify differentially expressed microRNAs between chronic periodontitis and healthy patients and to identify putative salivary microRNAs which can serve as biomarkers for periodontal disease.

overall_design: Comparative analysis of microRNA profile in saliva of healthy and chronic periodontitis patients.

first: K

middle: J

last: Nisha

first: Presanthila

last: Janam

last: Harshakumar


title: Cry1CvsSf9

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

country: France

institute: INRA

summary: Comparative study of cell lines Sf9 selected to Cry1C

overall_design:
We have 18 microarrays corresponding to 9 dye swaps, there are 3 biological replicates for each comparison.

6 microarrays: We performed dye swap of 3 biological replicates corresponding to the comparison between Sf9 cell lines cycle 8 and Sf9 cell lines cycle 40

6 microarrays: We performed dye swap of 3 biological replicates corresponding to the comparison between Sf9 cell lines cycle 40 and Sf9 cell lines cycle 40 treated with lethal dose 50 (LD) of Cry1C toxin

6 microarrays: We performed dye swap of 3 biological replicates corresponding to the comparison between Sf9 cell lines cycle 40 and Sf9 cell lines cycle 40 treated with lethal dose 80 (LD) of Cry1C toxin

first: Frederique

last: Hilliou

first: Pascal

last: Barbry

first: Kevin

last: Lebrigand

first: Claude

last: Castella


title: RNA Sequencing Facilitates Quantitative Analysis of differentially expressed genes after UCA1 knockdown in human erythroid cells

first: Hua

last: Liu

summary:
Purpose: The goals of this study are to determine possible  downstream targets of UCA1 on day8 of  erythroid differentiation with or without UCA1 knockdown.
Methods:gene expression profiling with or without UCA1 knockdown in differentiated erythroblasts at day8  were generated by deep sequencing, induplicate, using Illumina GAIIx.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Conclusions: heme metabolism genes were down-regulated after UCA1 knockdown during erythroid differentiation

overall_design: mRNA profiles of day8 erythroid cells with or without UCA1 knockdown were generated by deep sequencing, in duplicate, using Illumina GAIIx.

first: Lihong

last: Shi

first: Jinhua


title: Transriptome profiling of mutant p53 skin deficient in AURORA-A KINASE

city: Aurora

first: Enrique

last: Torchia

state: CO

department: Dermatology

institute: University of Denver

summary: We performed next-generation sequencing of RNA to determine the transcriptional changes in hyperplastic mutant p53 skin after the epithelial deletion of the AURORA-A Kinase gene in mice.

overall_design: In this study skin RNA of four experimental groups were sequenced.  Mice with the p53f, p53lslR172H, and KrasLSLG12D knock in alleles were crossed with the K14CreER(T) transgene to generate Loss-Of-Function (LOF) p53 mice (p53f/lslR172H;KraslslG12D;K14CreER) or GOF p53 mice (p53f/lslR172H;KraslslG12D;K14CreER). A floxed Aur-A allele was introduced to GOF or LOF p53 mice to generate Aur-Af/f; GOF or Aur-Af/f; LOF p53 mice. Tamoxifen was given to 8-10wk old mice in the diet for 14 d to induce recombination of floxed alleles. The mice were also co-treated with topical 12-O-tetradecanoylphorbol-13-acetate for 7d. Skin samples were harvested at the end of the study period.


title: Identification of global XBP1s target gene expression in human prostate cancer cells

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

summary: To gain insight into the global XBP1s target gene profile in prostate cancer cells, we performed RNA-seq analysis in LNCaP cells upon either XBP1 siRNA-mediated knockdown (siXBP1) or MKC8866-mediated IRE1α inhibition.

overall_design: Transcriptomics analysis upon two independent modalities to inhibit XBP1s expression in human LNCaP cells

first: Xia

last: Sheng

first: Fahri

last: Saatcioglu


title: Identifying differentially expressed miRNAs in cancer stem cells of laryngeal squamous carcinoma

status: Public on Oct 27 2018

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: To understanding the miRNA expression profiling of cancer stem cells of laryngeal squamous carcinoma, the total RNA of CD133+CD44+ laryngeal cancer stem cells (isolated from LSCC cell line TU-177, named TDP), CD133-CD44- cells (TDN) and parental TU-177 (unsorted TU-177 cells, named TPT) was extracted, followed by miRNA sequencing. Differentially expressed miRNAs were identified.

overall_design: The CD133+CD44+ cells (TDP) and CD133-CD44- cells (TDN) were isolated from TU-177 cells and cultured. Total RNA was extracted using TRizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction. Equal quantities of RNA from 3 samples in one group were mixed. The small RNA library was prepared. The library products were finally sequenced on Illumina HiSeq 2000 platform.

first: Wei

last: Gao

first: Fei

last: Li

first: Binquan

last: Wang

first: Shuxin

last: Wen


title: Arrayed molecular barcoding identifies TNFSF13 as a positive regulator of acute myeloid leukemia-initiating cells

city: Lund

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

institute: Lund University

summary: Dysregulation of cytokines in the bone marrow microenvironment promotes acute myeloid leukemia cell growth. Due to the complexity and low throughput of in vivo stem-cell based assays, studying the role of cytokines in the bone marrow niche in a screening setting is challenging. Herein, we developed an ex vivo cytokine screen using 11 arrayed molecular barcodes, allowing for a competitive in vivo readout of leukemia-initiating capacity. With this approach, we assessed the effect of 114 murine cytokines on MLL-AF9 acute myeloid leukemia mouse cells and identified the tumor necrosis factor ligand superfamily member 13 (TNFSF13) as a positive regulator of leukemia-initiating cells. By using Tnfsf13-/- recipient mice, we confirmed that TNFSF13 supports leukemia-initiation also under physiological conditions. TNFSF13 was secreted by normal myeloid cells but not by leukemia mouse cells, suggesting that mature myeloid bone marrow cells support leukemia cells by secreting TNFSF13. TNFSF13 supported leukemia cell proliferation in an NF-κB-dependent manner by binding TNFRSF17 and suppressed apoptosis. Moreover, TNFSF13 supported the growth and survival of several human myeloid leukemia cell lines, demonstrating that our findings translate to human disease. Taken together, using arrayed molecular barcoding, we identified a previously unrecognized role of TNFSF13 as a positive regulator of acute myeloid leukemia-initiating cells. The arrayed barcoded screening methodology is not limited to cytokines and leukemia, but can be extended to other types of ex vivo screens, where a multiplexed in vivo read-out of stem cell functionality is needed.

overall_design: MonoMac6 cells were grown in RPMI media containing baseline cytokines with or without human APRIL (100 ng/mL) 24 hours

first: Marion

last: Chapellier


title: tRNA modification landscape selectively controls mitochondrial translation efficiency in MERRF

status: Public on Oct 29 2018

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: We identified a novel N1-methyladenosine (m1A) modification in tRNALys with distinct effects on the synthesis and stabilities of the 13 mitochondrial proteins. Moreover, we observed regulated RNA modifications of mitochondrial tRNAs for the control of mitochondrial gene expression. Collectively, our data provide unprecedented insight into the regulation of mitochondrial tRNAs and reveal greater complexity to the molecular pathogenesis of MERRF.

overall_design: Comprehensive biochemical and sequencing analysis of wild-type and MERRF samples treated or not with AlkB demethylase (DM)

first: Molly

last: Evans

first: Wesley

last: Clark

first: Uwe

last: Richter

first: Paula

last: Marttinen

first: Eric

last: Shoubridge

first: Anu

last: Suomalainen

first: Anna

last: Wredenberg

last: Wedell

first: Brendan

last: Battersby


title: Genome-wide maps of ONECUT2 binding sites in 22Rv1 human castration resistant prostate cancer cell

status: Public on Oct 26 2018

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: In order to determine whether ONECUT2 directly regulates the AR transcriptional program, or whether the effect of ONECUT2 is a mere consequence of AR downregulation, we performed ONECUT2 ChIP-sequencing (ChIP-seq) using the 22Rv1 human castration resistant prostate cancer cell line, which expresses high levels of ONECUT2 in comparison to other human prostate cancer cell lines

overall_design: Genome-wide binding profile of ONECUT2 transcription factor in 22Rv1 cell.

first: Micheal

middle: R

last: Freeman

first: Mirja

last: Rotinen


title: Contribution of aerobic metabolism and oxidative stress responses to freeze-drying and storage resistance of Lactococcus lactis subsp. lactis TOMSC161 by using post-genomic approaches

city: Thiverval-Grignon

first: Helene

last: Velly

address: 1 avenue Lucien Bretignieres

summary:
Purpose: Lactococcus lactis is the primary constituent of many industrial starter cultures used in food fermentations. However, this bacterium is exposed to several stressful conditions during the industrial process. L. lactis TOMSC161 has been shown to resist better to freeze-drying and storage when cells are harvested at the late stationary compared to the early stationary phase.

Methods: In this work, the physiological changes that occur during growth (early and late stationary phases) were studied using transcriptomic, proteomic and cytometric approaches in order to elucidate the cell mechanisms involved in the stress tolerance of L. lactis TOMSC161 to freeze-drying and storage processes.

Results: The majority of altered abundances for genes determined by transcriptomic analysis indicated a slowdown at the late stationary phase in general metabolism and in the incomplete reduction of O2 leading to reactive oxygen species (ROS), in comparison to the early stationary phase. Furthermore, the expression of genes involved in general and oxidative stress responses was over-expressed at the late stationary phase when compared to the early stationary phase, thus explaining the better resistance to freeze-drying and the storage of cells harvested after six hours of stationary phase. Superoxide anion detection was performed by flow cytometry and related to the ROS production of starters. Superoxide anion concentration was lower for cells harvested at the late stationary phase when compared to cells harvested at the early stationary phase.

Conclusions: L. lactis TOMSC161 was thus able to develop an oxidative stress “pre-adaptation” during the stationary phase making it possible to better resist freeze-drying and storage stresses and especially oxidative stress.

overall_design: Comparison of genes expression for cells harvested at the early and late stationary phase

first: Marielle

last: Bouix

last: Dugat-Bony


title: Next Generation Sequencing Analysis of control and hnRNPK-/- RKO cells Transcriptomes

city: shanghai

first: Lina

last: Liu

address: Yueyang Road 320

department: Institute for Nutritional Sciences

institute: SIBS，Chinese Academy of sciences

summary: We generated the hnRNPK-/- RKO cells,and collected the cells at 2 days after transfectd with siRNA. Then,we extracted RNAs and performed next generation sequencing. By comparing sequcing data from control and hnRNPK -/- samples, we profiled the alternative splicing events and gene expression regulated by hnRNPK in CRC.

overall_design: RKO cells mRNA profiles of  control and hnRNPK-/- were generated by deep sequencing, using Illumina HiSeq2000.


title: Effects of blackcurrant extract on gene expression on Human Umbilical Vein Endothelial Cells.

status: Public on Oct 25 2018

city: Hirosaki

first: Kayo

last: Horie

address: 66-1 Hon-cho

institute: Hirosaki university

summary: To investigate new health functions by blackcurrant extract (BCE), we compare altered of the genes expression before and after BCE (2.0μg/ml) treatment in Human Umbilical Vein Endothelial Cells (HUVEC).

overall_design: HUVEC were seeded in culture dish and maintain to confluent. Then medium replace with  phenol red-free follicle dermal papilla cell basal medium with or without BCE (2.0μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.


title: Neuronal target-derived gene activation mediated by widespread use of a BMP-activation element

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: In Drosophila, efferent neurons gain access to a target-derived BMP signal in the periphery that is required for differentiation and/or synaptic growth and neurotransmission. This requires transcriptional activity of the BMP-activated Smad transcription factors, but the Smad-bound enhancers and BMP-regulated effector genes they control remain unidentified. In the absence of insight into how BMP signaling controls these fundamental aspects of neuronal development and function, here we test whether Smads act directly at widely-deployed archetypal Smad-binding motifs to directly co-regulate batteries of BMP-responsive genes. To target these motifs for analysis, we employed a bioinformatics approach to identify candidate motifs conforming to the consensus 15bp BMP-Activation Element (BMP-AE). After filtering for high conservation and proximity to neuronally-expressed genes, we prioritized 62 BMP-AEs for analysis. Testing the in vivo enhancer activity of 58 genomic fragments containing these BMP-AEs in transgenic reporters, we show that 61% are functional BMP enhancers in diverse motoneuron and neuropeptidergic neuronal populations, and that the BMP-AE motif itself is required for activity. Moreover, 60% of these functional BMP-AEs were located within 20kb of at least one BMP activated gene, as identified by RNAseq analysis. Finally, we show that the BMP-AE motif plays a conserved activator function in the vertebrate nervous system, by electroporation in the developing chick neural tube. Our results provide evidence that BMP signaling controls neuronal development and function by directly coordinating networks of genes through widespread deployment of conserved, consensus Smad-binding motifs.

overall_design: RNA sequencing expression profiles of witA12/+ and witA12/B11 Drosophila third instar ventral nerve cords.

first: Robin

last: Vuilleumier

first: Douglas

last: Allan


title: Whole transcriptomic sequencing of CD133+CD44+ cancer stem cells from laryngeal squamous carcinoma cell line

first: Yongyan

last: Wu

summary: To understand the gene expression profiling of cancer stem cells of laryngeal squamous carcinoma, the total RNA of CD133+CD44+ laryngeal cancer stem cells (isolated from LSCC cell line TU-177, named TDP), CD133-CD44- cells (TDN) and parental TU-177 (unsorted TU-177 cells, named TPT) was extracted, followed by RNA sequencing. Differentially expression of lncRNA, mRNA, and circRNA was identified.

overall_design: The CD133+CD44+ cells (TDP) and CD133-CD44- cells (TDN) were isolated from TU-177 cells and cultured. Total RNA was extracted using TRizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction, followed by DNase I treatment to remove DNA contamination. Equal quantities of RNA from 3 samples in one group were mixed. The lncRNA library (including lncRNA, mRNA, and circRNA) was prepared. The library products were finally sequenced on Illumina HiSeq 2000 platform.

first: Wei

last: Gao

first: Fei

last: Li

first: Binquan

last: Wang

first: Shuxin

last: Wen


title: Whole-transcriptome profiling of neovascularized corneas reveal miR-204 as a potent biotherapy deliverable by rAAVs

city: Worcester

first: Guangping

state: Massachusetts

address: Albert Sherman Center (AS6-2011)

department: Gene Therapy Center

institute: University of Massachusetts, Medial School

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

overall_design: Refer to individual Series


title: Enhanced glucose uptake in adipocytes despite deteriorating insulin signaling and increased autophagic flux with high fat feeding in mice

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

summary:
Background: Systemic glucose homeostasis is affected by adipose cell function. Still, the cellular events preceding the onset of insulin resistance in adipocytes are not yet resolved. To capture the immediate cellular changes during diet-induced expansion of cell volume and number, we characterized the initial changes in mature adipocytes during a short high fat diet (HFD) intervention.
Methods: C57BL6/J male mice were fed chow diet, and switched to HFD for 2, 4, 6 or 14 days. Systemic glucose clearance was assessed by glucose tolerance test. Adipose tissue was dissected for RNA seq analysis and cell size distribution analyzed using coulter counter technique. Insulin response in isolated adipocytes was measured by glucose uptake and Western blotting of insulin signaling intermediates. Confocal microscopy was used to assess autophagic flux in cells pre-incubated with rapamycin and chloroquine.
Results: Switching to HFD was accompanied by an immediate adipose cell size expansion followed by recruitment of new adipocytes. Despite an increase in both basal and insulin-stimulated glucose uptake in adipocytes, we observed a progressive decrease in insulin-stimulated activation of Protein Kinase B (PKB) Ser473, PKB Thr308 and Akt substrate of 160 (AS160) Tyr642, and onset of systemic insulin-resistance already after two days. Moreover, RNA-seq analysis of adipose tissue revealed marked changes in gene expression at day four, of which the most significant included genes directly involved in autophagy (Trp53Inp2 and Beclin1). Enhanced autophagy was observed in isolated adipocytes from HFD-fed mice, detected as an increased density of LC3-positive puncta by confocal microscopy, and increase of LC3II.
Conclusions: HFD rapidly caused impaired insulin signal transduction in adipocytes, while both basal and insulin-stimulated glucose uptake increased, which support the concept of spare signaling. Interestingly, our data suggests autophagy as one of the early cellular events that could contribute to insulin resistance.

overall_design:
C57BL6/J male mice were fed chow diet, and switched to HFD for 2, 4, 6 or 14 days.
Biological replicates from adipose tissue across 5 time points.

first: Karin

last: Stenkula


title: Characterization of quiescent adult liver stem cells and downstream lineages

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University


title: Characterization of quiescent adult liver stem cells and downstream lineages [RNA-seq]

summary: Understanding the liver stem cells (LSCs) holds great promise for new insights into liver diseases and liver regeneration. By employing single-cell RNA-seq technology with weighted gene co-expression network analyses (WGCNA), we examined transcriptome features of distinct Krt19 lineage-tracing cell types isolated from Krt19CreERT; Rosa26R-GFP reporter mice, and identified gene expression signatures of quiescent and active adult LSCs, as well as their downstream lineage-restricted progenitors and terminally differentiation hepatocytes and cholangiocytes. Importantly, we discovered a novel cell surface LSC marker, CD63, as well as CD56, which distinguished active and quiescent LSCs. Furthermore, we confirmed that CD63+CD56- quiescent LSCs resided in Canals of Hering and peribiliary glands and that these cells could be activated by a combined action of VEGF and bFGF, and subsequently underwent terminal differentiation. These findings define an authentic adult liver stem cells compartment and highlight its contribution to liver homeostasis during pathophysiologic processes.

overall_design: Examination of 39 single cells from adult mouse liver.

first: Yiping

last: Hu

first: Siguang

last: Chen

first: Minjun


title: BATF regulates the expression of Nfil3, Wnt10a and miR155hg for efficient induction of antibody class switch recombination

city: West Lafayette

first: Rosemary

middle: Elizabeth

last: Morman

state: IN

address: 1203 West State Street Rm 181

department: Biology

institute: Purdue University

summary: BATF functions in both T cells and B cells to control the host response to antigen and promote the production of class switched immunoglobulins.  In this study, we demonstrate that BATF expression is increased rapidly, and transiently, immediately following B cell stimulation and use an inducible model of BATF deletion to show that this induction is necessary, and sufficient, to trigger the program of  immunoglobulin class switch recombination (CSR).   We identify two genes (Nfil3 and miR155gh) that are positively regulated and one gene (Wnt10a) that is negatively regulated by BATF during CSR.   All three of these BATF targets play an essential role in CSR and each impacts the expression and/or function of the others.  Our observations allow for the positioning of these targets in a network downstream of BATF induction and upstream of the transcriptional activation of Aicda – the gene encoding the enzyme responsible for immunoglobulin gene rearrangements.   This work extends the knowledge of the molecular control of CSR and, importantly, positions the induction and function of BATF as an early event in this process.

overall_design: B cells were isolated from 4WT and 3Batf KO mouse spleens using MACS columns.  B cells were activated for 6hrs with LPS and IL-4.  Total RNA was harvested for for RNA-seq. All Samples have 2 replicates

first: Patrick

last: Schweickert

first: Stephen

middle: F

last: Konieczny

first: Elizabeth

last: Taparowsky


title: Analysis of Wild Type and B7-H4-/- leukemia initial cells Transcriptomes

first: Fangzhen

last: Xia

address: South Chongqing Road，NO.280

institute: Shanghai  Jiao  Tong  University  School  of  Medicine

summary: The goal of this study are to find the abonormally expressed genes of  B7-H4-/- leukemia inital cells in MLL-AF9 induced AML mice by RNA-seq analysis.Methods:  Lin- festival liver cells were isolated from WT and B7-H4-null mice and infected with MLL-AF9 retroviruses, then transplanted to the lethally  irradiated recipient mice. When AML developed, we isolated the  YFP+/Mac-1+/c-Kit+  bone marrow cells  by FACS and and then  made the RNA-sequence using Illumina. Results:  We  identified 27180 transcripts in wild type and B7-H4-/- leukemia initial cells. 572 transcripts showed differential expression between the WT and B7-H4−/− LICs, with a fold change ≥1.5 and p value <0.01. 271  transcripts were downregulated and 241 transcripts were upregulated.

overall_design: Examination of differentially expressed genes in wild type and B7-H4-null AML LSCs.

first: Junke

last: Zheng


title: RNA-seq of YB5 cells treated with HH1

city: Philadelphia

first: Hanghang

state: PA

address: 3307 N. Broad Street Pharmacy Allied Health Building, Room 339

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary: RNA-seq was performed after YB5 cells were treated with DAC,  HH1 or the combination of the two. RNA-seq was also perfomed after viral transduction using a TET-off dnCDK9 construct

overall_design: Biological triplicates were performed for a total of 48 samples. Fold change of each gene was calculated by comparing change in expression after inhibitor treatment to expression in the control samples

first: Somnath

last: Pandey

first: Meghan

last: Travers

first: Hongxing

last: Sun

first: Yasuyuki

last: Okamoto

first: Takahiro

last: Sato

first: Judit

last: Garriga

first: Bela

last: Patel

first: Jozef

last: Madzo

first: Noël

last: J.-M. Raynal

first: Yi

first: Wayne

last: Childers

first: Magid

last: Abou-Gharbia

last: B. Baylin

first: Cynthia

last: Zahnow

first: Jaroslav

last: Jelinek

first: Xavier

last: Graña

first: Jean-Pierre

last: Issa


title: Usage of Alternative Polyadenylation Sites Differs Dramatically Between Male and Female Xenopus tropicalis.

status: Public on Oct 24 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 our recently released Whole Transcriptome Termini Site sequencing protocol to profile usage of alternative polyadenylation sites in Xenopus tropicalis.

overall_design: Total RNA samples derived from whole body homogenates of individual adult frogs were used to construct WTTS-seq libraries. Four WTTS-seq libraries from two male frogs and two female frogs were involved in this submission.

first: Xiang

last: Zhou

first: Jennifer

last: Michal

first: Yangzi

last: Zhang


title: Effect of SETD1A knockdown on global gene expression in MCF-7 cells

city: Incheon

first: Kwang Won

last: Jeong

address: 191 Hambakmoe-ro, Yeonsu-gu

department: College of Pharmacy

institute: Gachon University

summary: SETD1A is a histone H3K4 methyltransferase and function as a coactivator for nuclear receptors (NRs) and other transcription factors. We performed genome-wide gene expression analysis in non-specific siRNA transfected or SETD1A knockdown MCF-7 cells to investigate global gene expression changes induced by SETD1A knockdown.

overall_design: Differential expresssion profile of transcripts in shNS or shSETD1A expressing cells in presence or absence of beta-estradiol (E2).

first: Ming

last: Jin

first: Kwang


title: Whole-transcriptome profiling of neovascularized corneas reveal miR-204 as a potent biotherapy deliverable by rAAVs [RNA-Seq]

first: Guangping

last: Gao

summary: Current drugs that directly target pro-angiogenic factors to inhibit or reverse corneal neovascularization, the major sight-threatening pathology caused by angiogenic stimuli, require multiple rounds of administration and have limited efficacies. Here we report the profiling of anti-angiogenic corneal microRNAs (miRNAs), and a framework that employs discovered miRNAs as biotherapies deliverable by recombinant adeno-associated viruses (rAAVs). By querying differentially expressed miRNAs in neovascularized mouse corneas induced by alkali-burn, we have revealed 39 miRNAs that are predicted to target more than 5,500 differentially expressed corneal mRNAs. Among these corneal miRNAs, we selected miR-204 and assessed its efficacy as a therapeutic miRNA in injured corneas. Our results show that delivery of miR-204 by rAAV is efficacious and safe for mitigating corneal NV. Overall, our work demonstrates the discovery of therapeutic miRNAs in corneal disorders and their translation into viable clinical vectors.

overall_design: Profiling of mRNAs in normal mouse corneas and corneas injured by alkali burn treatment.

last: Lu

first: Phillip

last: Tai

first: Jianzhong

last: Ai

first: Dominic

last: Gessler

first: Qin

last: Su

first: Qiang

last: Zheng

middle: D

last: Zamore

first: Xun

last: Xu


title: Gene Expression Changes in the LA/BC muscle of a knock-in mouse model of SBMA

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Examining changes in expression in a mouse model of SBMA compared to WT littermates.

overall_design: Mice sacrificed at 14wks of age had LABC isolated and cDNA generated and sequenced on an illumina platform.

first: Zhigang

last: Yu

first: Andrew

last: Lieberman

first: Theresa

last: Wasylenko

first: David

last: Housman


title: Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation

city: Harbin

first: Hui

last: Yuan

state: Heilongjiang

address: XiangFang

department: College of Animal Science and Technology

institute: Northeast Agricultural University

summary: During the long history of chicken domestication, eyelid color, like skin color and shank color, has been one of the unique physical traits of Chinese indigenous chickens that influence consumer behavior. In China, the Lindian chicken, which has colored feathers, is renowned for the appetizing flavor of its meat and eggs, and its eyelid colors varies from deep to light shades, including black, gray, red, and light yellow. To identify the genes controlling eyelid pigmentation, the expression profiles of black and light-yellow eyelids of Lindian chickens were analyzed with transcriptome sequencing. We detected 13,466 genes expressed in the eyelids, among which 14 were differentially expressed. A KEGG pathway analysis showed that tyrosine metabolism and melanogenesis genes were significantly enriched among these DEGs (corrected P < 0.05). Therefore, we infer that melanin metabolism is one of main factors affecting Lindian chicken eyelid pigmentation. In summary, we have identified the melanin genes responsible for eyelid pigmentation of the Lindian chicken, and also provide a valuable resource for the future study of the physical traits of chickens.

overall_design: Examination of 6 mRNA expression in black and light-yellow eyelid of Lindian chickens.

first: Li

last: Leng


title: Analysis of KMT2D Knockdown/Control PC-3 Cell Line

status: Public on Oct 23 2018

city: Guangzhou

first: Shidong

last: Lv

state: State...

address: 1838 Guangzhou North Ave.

institute: Nanfang Hospital


title: Genome-wide maps of chromatin state difference in KMT2D Knockdown/Control PC-3 Cells

summary: KMT2D is a histone methyltransferase for catalyzing the monomethylation of H3K4. The H3K4me1 is prominent on active enhancers and participates in gene expression regulation. Loss of KMT2D in cancer has been approved to impact on a set of gene expression by the reduction of H3K4me1 level. To identify the direct target of KMT2D in prostate cancer, we performed H3K4me1 ChIP-seq with KMT2D knockdown and control PC-3 cells.

overall_design: Examination of the different histone modifications in KMT2D knockdown and control PC-3 cells

first: Liyan

last: Ji


title: Next Generation Sequencing Facilitates Quantitative Analysis of KMT2D Knockdown/Control PC-3 Cell Line Transcriptomes

summary: KMT2D is a histone methyltransferase for catalyzing the monomethylation of H3K4. Previous studies have indentified that H3K4me1 is prominent on active enhancers and participates in gene expression regulation. To further examine the transcriptional changes in response to KMT2D depletion, we performed RNA-seq with KMT2D knockdown and control PC-3 cells by BGISEQ-500

overall_design: Retinal mRNA profiles of KMT2D knockdown and control PC-3 cells were generated by deep sequencing, using BGISEQ-500.


title: CD90 Identifies Adventitial Mesenchymal Progenitor Cells in Adult Humans

city: New York

first: Jason

last: Kovacic

state: NY

address: 1 Gustave L. Levy Place, Box: 1030

institute: Icahn School of Medicine at Mount Sinai

summary: RNAseq of CD90+ cells obtained fresh from human vessels (healthy aorta, diseased aorta and internal thoracic artery).

overall_design: Cross comparison of CD90+ cells from 3 human vascular tissues.

first: Johan

last: Björkegren


title: Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: mRNAs of human and mouse cell lines were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement. mRNAs were fragmented to ~100 nt and treated by Sodium bisulfite solution (pH 5.1) containing Hydroquinone. Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000/3000 (Illumina) in pair-end mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Explore the single-base resolution methylome of 5-Methylcytosine in mammalian transcriptome

first: Ying

last: Yang

first: Yun-Gui

first: Baofa


title: A quantitative model for characterizing the evolutionary history of mammalian gene expression

status: Public on Oct 21 2018

city: Cambridge

first: Jenny

last: Chen

address: 16 Divinity Ave

institute: Harvard

summary: Characterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype. However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein-Uhlenbeck (OU) process. This stochastic process models expression trajectories across time as Gaussian distributions whose variance is parameterized by the rate of genetic drift and strength of stabilizing selection. We use these mathematical properties to identify expression pathways under neutral, stabilizing, and directional selection, quantify the extent of selective pressure on a gene’s expression, and detect deleterious expression levels outside expected evolutionary distributions in single patients. Our work provides a statistical framework for interpreting expression data across species and in disease.

sample_organism:
Dasypus novemcinctus
Canis lupus familiaris
Mustela putorius furo
Oryctolagus cuniculus
Monodelphis domestica

overall_design: RNA-sequencing of 7 tissues (brain, heart, kidney, liver, lung, skeletal muscle, testis) from  rabbit, dog, ferret, cow, armadillo, and opposum

first: Ross

last: Swofford

first: Jeremy

last: Johnson

first: Beryl

middle: B

last: Cummings

first: Noga

last: Rogel

first: Kerstin

last: Lindblad-Toh

first: Wilfried

last: Haerty

first: Federica

last: di Palma

first: Aviv

last: Regev


title: Transcriptomics analysis of gene expression in multiple human and mouse cells and tissues

summary: RNA was isolated from siCTRL, siNSUN2 HeLa or 3T3-L1 cells, human cells (embryonic kidney T cell line 293T; colon cancer cell line HCT116; hepatocellular carcinoma cell line Huh7; embryonic lung fibroblast cell line MRC-5; glioma cell line SNB19), mouse cells (kidney collecting duct cell line M-1; cervical cancer cell line U14) and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

overall_design: Examination of gene expressive levels in mammalian transcriptome

first: Xin


title: Systems biology analysis of the effect and mechanism of Qi Jing Sheng Bai granule on leucopenia in mice

status: Public on Oct 20 2018

first: ai

middle: ping

last: jiang

address: No.151, Libing Rd., Zhangjiang Hi-tech Park, Pudong

institute: Shanghai Biotechnology Corporation

summary: Qi-Jing-Sheng-Bai granule (QJSB) is a new developed traditional Chinese medicine (TCM) formula. In clinical, it has been used for the treatment of leucopenia. However, the therapeutic mechanism needs further solid investigation. In present study, we first tested the effect of QJSB on leucopenia mice induced by cyclophosphamide. QJSB was administered to leucopenia mice for 8 days. Our experiments showed that QJSB significantly increased the number of peripheral white blood cells, platelets and nucleated bone marrow cells. Meanwhile it markedly enhanced the cell viability and promoted the colony formation of bone marrow mononuclear cells. It also reversed the serum cytokines IL-6 and G-CSF disorders. Then, based on the data of transcripts derived from the bone marrow and metabonomic data from plasma, we integrated transcriptomics, network pharmacology and metabolomics technologies to investigate the mode of action of QJSB. We found that QJSB regulates a series of biological processes such as hematopoietic cell lineage, homeostasis of number of cells, lymphocyte differentiation, metabolic processes (including lipid, amino acid and nucleotide metabolism), B cell receptor signaling pathway, T cell activation, NOD-like receptor signaling pathway. In conclusion, QJSB exerts protective effect against leucopenia in mice probably through accelerating cell proliferation and differentiation, regulating metabolism response pathways and modulating immunologic function at system level. The multi-omics approach might achieve a complementary and verified view for the comprehensive evaluation of therapeutic effects and complex mechanisms of QJSB.

overall_design: Four groups: normal group, model group,  QJSB group and leucogen group, each group has three biological replicates.

first: Saisai

last: Tian

first: Pengli

last: Huang


title: A transcriptome analysis of a citrus rootstock Poncirus trifoliata identified genes associated with arbuscular mycorrhizal symbiosis

status: Public on Oct 22 2018

city: Wuhan

first: Jianyong

last: An

state: Hubei Province

address: Shizi shan Street, Hongshan District

institute: Huazhong Agricultural Univeristy

summary: To date, little is known about molecular mechanisms by which woody plants engage symbiosis with arbuscular mycorrhizal (AM) fungi. Here we investigated transcriptome changes in the roots of Poncirus trifoliata (the most common citrus rootstock) that are induced during colonization of an AM fungus Glomus versiforme (Gv). A total of 282 Poncirus genes were differentially expressed in response to Gv colonization, of which 138 could identify homologous genes from the model legume Medicago truncatula that also exhibit similar AM-induced transcriptional changes, while the remaining 144 do not. A high proportion of the AM-responsive Poncirus genes are predicted to be involved in transcription regulation, transport process, cellular organization and protein degradation, implicating these processes in the establishment of AM symbiosis. Promoter-GUS analysis of six AM-induced Poncirus genes [encoding an exocyst subunit (PtrEXO70I), two transcription factors (PtNAC1 and PtPALM1), one chitinase (PtrChit2), one plastid movement associated protein (PtrPMI2) and one lipase (PtrLipase3)] showed that all of them exhibit specific expression in arbuscule-containing root cortical cells, suggesting their potential involvement in establishing AM symbiosis. Notably, down-regulation of the ortholog of PtrExo70I in Medicago by RNAi significantly impaired arbuscule development, indicating that Exo70I is an important host component required for arbuscule development in root cortical cells. This study not only helps identify conserved host genes engaged in AM symbiosis but should also guide future mechanistic studies of potentially Poncirus-specific events during its symbiosis with AM fungi.

overall_design: Six samples, the Poncirus trifoliata (L.) Raf roots inoculated by Glomus versiforme (Gv) or roots from uninoculated control were subjected to RNA-seq analysis with three biological replicates, respectively.

first: Zhiyong

last: Pan


title: Cyclin D1, Id2 and Sox9 are upregulated in a lobular competent COMMA Db clonal derivative’ cells compared to a lobular incompetent clone both in vitro, and in vivo

status: Public on Oct 19 2018

city: Memphis

first: Evan

middle: M.

last: Savage

state: TN

address: 1910 Nonconnah Blvd., Suite

institute: Genome Explorations

summary: Understanding underlying mechanisms responsible for the differentiation and stemness of mouse mammary progenitor cells are paramount to understanding the heterogeneity of mammary development and tumorigenesis. Consequently, studies have isolated and characterized mouse mammary progenitor cell lines such as: COMMA-1D, NSP2 and SP3, but have not parsed the various transcriptomes that play a role in progenitor differentiation and mammary gland development.

overall_design: Using microarray technologies, we analyzed transcriptomes, from Comma Db clonal derivatives, SP3 and NSP2, during different mouse mammary growth phases: In-vitro, In-vivo 5 weeks, and In-vivo 12 weeks.

first: Jabril

first: Corrine

last: Boulanger

first: Tamaro

last: Hudson

first: Gilbert

last: Smith


title: Streptococcus mutans YidC2: regulation and effects on the transcriptome

city: Columbus

first: Sara

last: Palmer

state: Ohio

address: 305 West 12th Avenue

department: College of Dentistry

institute: The Ohio State University

summary: Differential gene expression was determined between wild type Streptococcus mutan and a yidC1 or yidC2 mutant using whole transcriptome RNA sequence.  A significantly greater number of genes were differentially expressed (DE) in the yidC2 mutant (320 DE genes) compared to wildtype, while the yidC1 mutant had only 21 DE genes when compared to wildtype.

overall_design: RNAseq was performed on Streptococcus mtuans UA159 and an isogenic yidC1 or yidC2 mutant using mRNA and the Illumia NextSeq 500 DNA sequencer plateform

first: Ashton

last: Combs

first: Andrew

middle: C

last: Malaney

first: Hsiaochi

last: Chang


title: MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence

city: Porto

first: Jorge

last: Pinheiro

state: Porto

address: Rua Alfredo Allen, 208

department: Host Interaction and Response

country: Portugal

institute: IBMC-Institute for Molecular and Cell Biology, i3S-Institute for Research and Innovation in Health

summary: The foodborne pathogen Listeria monocytogenes (Lm) can cause invasive infection in susceptible animals and humans. To survive and proliferate within hosts, this facultative intracellular pathogen needs to tightly coordinate the expression of a complex regulatory network, including virulence factors. Here, we identify and characterize MouR a novel virulence regulator of Lm. Through RNA-seq transcriptomic analysis, we characterized the MouR regulatory network and demonstrated how MouR positively controls the expression of the Agr system (agrBDCA) of Lm. Resolving MouR 3D structure revealed a dimeric DNA-binding transcription factor belonging to the VanR class of the GntR superfamily of regulatory proteins. We showed that by direct binding to the agr promoter region, MouR ultimately modulates chitinase activity and biofilm formation. Importantly, we demonstrated by in vitro cell invasion assays and in vivo mice infections the crucial role of MouR for Lm full virulence.

overall_design: Transcriptomes of Listeria monoctyogenes EGD-e wild type and mouR deletion mutant strains by RNA-seq, with three biological replicates using Ion Torrent Proton.

first: Johnny

last: Lisboa

first: Rita

last: Pombinho

first: Filipe

last: Carvalho

first: Alexis

last: Carreaux

first: Anna

last: Pöntinen

first: Hannu

last: Korkeala

first: Nuno

last: Santos

first: João

last: Cabral

first: Sandra

last: Sousa

first: Didier

last: Cabanes


title: transcriptomic profiling of HEK293 cells upon individual knockdown of the splicing factors  RBM17, U2SURP or CHERP

status: Public on Oct 17 2018

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: We found that the core spliceosomal proteins RBM17, U2SURP and CHERP form a protein complex regulating alternative splicing and expression of a whole network of RNA binding proteins

overall_design: RNA sequencing of triplicate RNA samples from HEK293 cells treated with siRNAs against RBM17, U2SURP , CHERP or SCRAMBLE sequence

first: A

last: De Maio

first: Hari

middle: K

first: Zhandong

last: Liu

first: H

middle: Y

last: Zoghbi


title: Mechanism of cellular and humoral rejection

status: Public on Oct 16 2018

city: San Francisco

first: Minnie

last: Sarwal

address: 500 Parnassus Ave

institute: UCSF

summary: This study used RNAseq to study the mechanism of cellular and humoral rejection by comparing clinical samples of cellular, humoral, mixed, and normal.

overall_design: Comparison of normal (N=12), cellular (N=13), humoral (12) and mixed (n=4)

first: Anyou

last: Wang

first: Oriol

last: Bestard

first: Tara

last: Sigdel


title: Dose-dependency of heterochromatin domains reveals subtelomeric structuration in budding yeast

status: Public on Oct 15 2018

city: Paris

first: Antonin

last: Morillon

address: 26 rue d'Ulm

institute: Institut Curie

summary: The eukaryotic genome is divided into chromosomal domains of distinct gene activities. Transcriptionally silent chromatin is found in subtelomeric regions leading to telomeric position effect (TPE) in yeast, fly and man. Silent chromatin generally initiates at defined loci and tends to propagate from those sites by self-recruitment mechanisms implying the requirement for processes preventing ectopic spreading of silencing. Barrier elements that can block the spread of silent chromatin have been documented, but their relative efficiency is not known. Here we explore the dose-dependency of silencing factors for the extent of TPE in budding yeast. We characterized genome wide the impact of overexpressing the silencing factors Sir2 and Sir3 on the spreading of Sir3 and its impact on coding and non-coding transcription. We thus reveal that extension of silent domains can reach saturation. Analysis of published data sets enabled to uncover that the extension of Sir3 bound domains stops at zones corresponding to transitions of specific histone marks including H3K79 methylation that is deposited by the conserved enzyme Dot1. Importantly, DOT1 is essential for viability when Sir3 is in excess indicating that this transition actively blocks Sir3 spreading. Our work uncovers previously uncharacterized discrete chromosomal domains associated with specific chromatin features and demonstrates that TPE is efficiently restricted to subtelomeres by the preexisting chromatin landscape.

overall_design: Total RNA-seq in WT, GPD-SIR3, GPD-SIR3-A2Q and SIR3Δ of S. cerevisiae

first: Antoine

last: Hocher

first: Myriam

last: Ruault

first: Marc

last: Descrimes

first: Mickael

last: Garnier

first: Angela

last: Taddei


title: Comparative study of gene expression during early vertebrate development between Xenopus laevis and Sturgeon

city: Woods Hole

first: Esther

middle: Jane

last: Pearl

state: MA

address: 7 MBL Street

department: National Xenopus Resource

institute: Marine Biological Laboratory

summary: Sturgeon and Xenopus is estimated to be separate by about 400 My of evolution. We have collected data on temporal expression profile in Sturgeon in order to compare the level and timing of expression for homologous pairs of genes, commonly referred to as hetero-metry and hetero-chrony. Following up our previously published research on similar comparison between two species of Xenopus separated by estimated 50 My, we are asking whether patterns of expression and signaling cascades of two key developmental periods - gastrulation and neurulation are implemented via conserved molecular basis. Uncovering and describing deviation for the conserved expression program as well as the composition of maternal deposit will provide new insights into vertebrate development both the normal course and developmental abnormalities.

overall_design: mRNA from 24 sturgeon embryo samples each at a different developmental stage

first: Leonid

last: Peshkin

first: Andrey

last: Zaraisky

first: Marko

middle: E

last: Horb

middle: W

last: Kirscher


title: Exercise in adult zebrafish promotes ventricular cardiomyocyte proliferation in the regenerating heart

status: Public on Oct 18 2018

city: Barcelona

first: Josep

middle: V.

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

summary: Exercise promotes a set of physiological adaptations known to provide long-term health benefits and it can play an important role in cardioprotection. However, the mechanisms underlying exercise-induced cardiac adaptation are not fully understood. In the present study, we examined  cardiac adaptive responses to exercise training in the adult zebrafish and in the context of cardiac regeneration.We found that swimming-induced exercise increased cardiomyocyte proliferation and that this response was also found under regenerating conditions, when exercise was performed either prior to and after ventricular cryoinjury (CI). Exercise prior to CI resulted in a mild improvement in cardiac function and lesion recovery over the non-exercise condition.Transcriptomic profiling of regenerating ventricles in cryoinjured fish subjected to exercise revealed a differential regulation of genes related toregeneration as well as other biological processes potentially involved in the exercise response. Taken together, these results suggest that exercise constitutes a physiological stimulus thatmay help promote cardiomiogenic mechanisms of the vertebrate heart and that the zebrafish exercise model may be useful for evaluating the potential cardioprotective effects of exercise.

overall_design: mRNA profiles of adult zebrafish regenerating ventricles at 7 and 14 days post injury that were exercising or not, were compared.

middle: V


title: Comparison of expression profiles of APP-depleted prostate cancer cells (LNCaP)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: This analysis determines the relevanve of APP in prostate cancer as potential novel redox-regulator in androgen-responsive and castration-refractory prostate cancer

overall_design: LNCaP cells either expressing empty vector (pcDNA3.1) or overexpressing wild-type androgenreceptor (AR) were stably transduced with shRNA against APP

first: Vivek

last: Venkataramani

first: Tapio

last: Visakorpi

last: Salinas-Riester


title: FOXO1 Regulates Attachment of the Implanting Blastocyst to the Endometrium at the Window of Receptivity

city: Houaton

first: Rainer

last: Lanz

address: One Baylor Plaza

department: Molecular and Cellular biology

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

overall_design: Refer to individual Series


title: FOXO1 Regulates Uterine Epithelial Integrity and Progesterone Receptor Expression Critical for Embryo Implantation [RNA-seq]

summary: We report the sequencing of the uterine transcriptome sequencing of control and conditional knock-out of the Forkhead box O1 at day 4.5 of murine pseudopregnancy

overall_design: RNA was isolated from day 4.5 Pseudopregnancy adult females. RNA from two females was pooled per sample. Three samples per genotype were sequenced for differential gene expression analysis.

first: Franscesco

last: DeMayo

first: Yasmin

middle: M

last: Vasquez


title: Transcriptome analysis of E. coli and P. aeruginosa expressing endolysin wild type and mutant in vivo

city: Hangzhou

first: Fei

last: Xu

address: 198 Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

summary: We report the different bactericidal ability of endolysin wild type and mutant and explain the pathway of lipopolysaccharide biosynthesis is the dominant factor.

sample_organism:
Pseudomonas aeruginosa
Escherichia coli

platform_organism:
Pseudomonas aeruginosa
Escherichia coli

overall_design: Endolysin wild type and mutant were expressed in E. coli TOP10 and P. aeruginosa PAO1, respectively

first: Wei

last: Liu


title: NUAK2 is a critical YAP target in liver cancer

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: The Hippo-YAP signaling pathway is a critical regulator of proliferation, apoptosis, and cell fate. The main downstream effector of this pathway, YAP, has been shown to be misregulated in human cancer and has emerged as an attractive target for therapeutics. A significant insufficiency in our understanding of the pathway is the identity of transcriptional targets of YAP that drive its potent growth phenotypes. Here, using liver cancer as a model, we identify NUAK2 as an essential mediator of YAP-driven hepatomegaly and tumorigenesis in vivo. By evaluating several human cancer cell lines we determine that NUAK2 is selectively required for YAP-driven growth. Mechanistically, we found that NUAK2 participates in a feedback loop to maximize YAP activity via promotion of actin polymerization and myosin activity. Additionally, pharmacological inactivation of NUAK2 suppresses YAP-dependent cancer cell proliferation and liver overgrowth. Importantly, our work here identifies a specific, potent, and actionable target for YAP-driven malignancies.

overall_design: Chromatin immunoprecipitation was  done for primary hepatocytes of TetO-YAP S127A mice placed on Dox for four days.  Chromatin immunoprecipitation was  performed essentially as previously described  in Galli et al Mol Cell. 2015 Oct 15;60(2):328-37.  Chromatin immunoprecipitation was done for H3K27Ac histone mark, Yap and Tead4 proteins. Input DNA was used as reference for peak calling.

first: Wei-Chien

last: Yuan

first: Brian

last: Pepe-Mooney

first: Giorgio G

last: Galli

first: Michael

middle: T

last: Dill

first: Hai-Tsang

last: Huang

first: Mingfeng

last: Hao

first: Yumeng

last: Wang

first: Han

last: Liang

first: Fernando

last: Camargo