title: Correlates of protection against SIVmac239 infection in rhesus macaques immunized with chimpanzee-derived adenovirus vectors

status: Public on May 21 2019

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: An efficacious vaccine to HIV-1 remains elusive. We tested two vaccine regimens based on prime-boosting with two chimpanzee-origin adenovirus (Ad) vectors (SAdV) of serotypes SAdV24 and SAdV23 or two distinct human serotype Ad vectors (HAdV), i.e., HAdV5 and HAdV26, expressing Gag and gp160 of SIVmac239 for induction of protection against repeated low dose rectal SIVmac251 challenges in Indian rhesus macaques (RMs). Animals were rendered seropositive to the HAdV vectors prior to vaccination. In RMs with non-controller genotypes, the SAdV vectors achieved significant reduction in viral acquisition. In RMs with controller genotypes, both vaccine regimens reduced set-point and peak viral loads and accelerated viral clearance. In SAdV-vaccinated RMs resistance against infection correlated with levels of circulating envelope (Env)-specific antibody (Ab) titers. In both vaccine groups CD8+T cells controlled viral loads upon infection. Circulating CD4+ and CD8+ T cells showed significant changes in their transcriptome over time following vaccination, which differed between the vaccine groups. T cells from SIV-resistant RMs had unique transcriptional profiles indicating that both follicular T helper (TFH) cell responses and highly activated CD8+ T cells may play a role in protection. Our results demonstrate that SAdV-based candidate AIDS vaccines provide protection from virus acquisition and replication in a stringent SIV challenge model in RMs and may thus outperform HIV-1 vaccines that have undergone large-scale clinical efficacy testing in humans.

overall_design: Samples were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome Arrays. CD4+ and CD8+ T lymphocytes were collected by cell sorting from 103 Rhesus macaques. The data from 21 samples suggested low RNA quality and were excluded.

first: Steven

last: Tuyishime

first: Larissa

middle: H

last: Haut

first: Raj

last: Kurupati

first: James

last: Billingsley

first: Diane

last: Carnathan

first: Zhi

middle: Q

last: Xiang

first: Yan

last: Li

first: Malte

last: Zopfs

first: Qin

last: Liu

first: Xiang

last: Zhou

first: Mark

last: Lewis

last: Bosinger

first: Guido

last: Silvestri

first: Hildegund

last: Ertlicholl


title: RNA binding protein DDX1 is responsible for fatty acid mediated repression of insulin translation

city: Beijing

first: Wen

last: Zhong

address: Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: Previous studies have focused on the combined glucolipoxicity that is presence of high glucose and free fatty acid levels effect on insulin gene expression, but the effect of high FFA and normal glucose level on insulin expression is unkown. Here we observed that palmitate can inhibit insulin translation. And we identified a novel insulin mrna binding protein DDX1 that is responsible for fatty acid mediated insulin translation inhibition. Palmitate treatment causes phosphorylation of DDX1 at S295 and dissociation from insulin mRNA, which decreases insulin translation.

overall_design: we used CLIP-seq to identify target genes and the binding sequences of DDX1 in INS1 cell

first: Zonghong

first: Zhaokui

last: Cai

first: Tao

last: Xu


title: An optimized FAIRE procedure for low cell numbers in yeast.

city: Vestec

first: Alexandru

last: Mizeranschi

address: Průmyslová 595

country: Czech Republic

institute: BIOCEV

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report an optimised low-input FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements) procedure to assay chromatin accessibility from yeast colonies. Sensitivity, specificity and reproducibility of the scaled-down method are comparable to that of regular, higher input amounts, assayed over a 100-fold range. The method enables epigenetic analysis of chromatin structure to be assayed without the need for liquid culture, thus opening the possibility to study wild yeasts that form colonies, or those can be isolated in sufficient amounts in situ, from environmental samples.

overall_design:
FAIRE assays of 8 samples: 4 FAIRE samples based on varying amounts of cells (4 mg, 20 mg, 100 mg and 500 mg) and 4 corresponding input DNA samples. 3 biological replicates per sample.
Please note that each processed narrowPeak file was generated from each sample pair (i.e. FAIRE and input, e.g. *F-R* and *I-R* samples) and is linked to the corresponding FAIRE sample record.

first: David

middle: S

last: Luque

middle: E

first: Otakar

last: Hlaváček

first: Timothy

last: Hughes

first: Ragnhild

last: Aaløkken

first: Libuse

last: Vachova

first: Zdena

last: Palkova

first: Gregor

middle: D

last: Gilfillan


title: Control, Prrc2a conditional knockout, and Fto transgene mouse brain study

status: Public on May 16 2019

first: Bao-Fa

last: Sun

address: Da-Tun Road

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

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomics analysis of gene expression in control, Prrc2a conditional knockout, and Fto transgene mouse brain sample

summary: RNA was isolated from hippocampus sample from 4 weeks old prrc2a flox/flox and prrc2a flox/flox;Olig2-cre or 4 weeks old wt and Fto Tg micemice 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 HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 150 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design:
Examination of gene expressive levels in
prrc2a flox/flox and prrc2a flox/flox; nestin-cre mice.
control and Fto transgene mice.

first: Rong

last: Wu

first: Ang

last: Li

first: Baofa

first: Zengqiang

last: Yuan

first: Yuigui

last: Yang


title: RIP-seq for Prrc2a in mouse brain sample

summary: RNA was isolated from widetype C57BL/6J 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 HiSeq2500 or 3000 (Illumina) in paired-read mode, creating reads with a length of 125 or 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of Prrc2a binding targets in wild type mouse brain


title: m6A peaks in mouse brain sample.

summary: RNA was isolated from 4 weeks old Prrc2a flox/flox whole brain using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen) 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 HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of m6A peaks in 4 weeks old Prrc2a flox/flox mice.


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-Seq of HSCe)

status: Public on May 13 2019

city: Miami

first: Maria

last: Figueroa

state: FL

address: 1501 NW 10th Avenue

department: Biochemistry

country: USA

institute: University of Miami

summary: Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. This reprogramming of aged HSCe globally targets developmental and cancer pathways which are comparably altered in AML of all ages; encompassing loss of 4,656 active enhancers, 3,091 bivalent promoters, and deregulation of several epigenetic modifiers and key hematopoietic transcription factors, such as KLF6, BCL6 and RUNX3. Notably, in vitro downregulation of KLF6 results in impaired differentiation, increased colony forming potential and changes in expression that recapitulate aging and leukemia signatures. Thus, age-associated epigenetic reprogramming may form a predisposing condition for the development of age-related AML.

overall_design: We profiled the human HSCe (Lineage-, CD34+, CD38-) transcriptome with aging. RNAseq was performed on FACS isolated human bone marrow derived HSCe young (18-30yo) and aged (65-75) donors. Donors had no known hematological malignancy. For each age group, 10 biological replicates were used.

first: Emmalee

middle: R

last: Adelman

first: Hsuan-Ting

last: Huang

first: Alejandro

last: Roisman

first: André

last: Olsson

first: Antonio

last: Colaprico

first: Tingting

last: Qin

first: R

middle: C

last: Lindsley

first: Rafael

last: Bejar

first: Nathan

last: Salomonis

first: H

middle: L

last: Grimes


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (ERRBS)

type: Methylation profiling by high throughput sequencing

overall_design: We profiled DNA cytosine methylation in HSCe (DAPI-, Lineage-, CD34+, CD38-) with age. Enhanced reduced representation bisulfite sequencing (ERRBS) was performed on FACS isolated human bone marrow derived HSCe from young (18-30yo) and aged (65-75 yo) donors. Donors had no known hematological malignancy. For each age group, 5-7 biological replicates were used.


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (ChIP-seq)

overall_design: ChIP-sequencing was performed on FACS isolated human bone marrow derived HSCe (Lineage-, CD34+, CD38-) from young (18-30 yo) and aged (65-75 yo) donors. Donors had no known hematological malignancy. ChIP-seq was performed for H3K4me1, H3K4me3, H3K27me3, and H3K27ac on 14,000-35,000 sorted cells per immunoprecipitation, using 4-7 replicates per mark, per age group.


title: circRNA expression in infantile hemangioma (IH) and matched non-tumor tissues

status: Public on May 09 2019

city: Jinan

first: Cong

last: Fu

state: Shandong

address: No. 324, jingwu Road, Huaiyin Dist

institute: Shandong provincial hospital

summary: To determine the circRNA expression profile in IH and matched non-tumor tissues, we uesed circRNA microArray analysis form Arraystar to examine the expression of circRNAs in IH and matched non-tumor tissues.

overall_design: Skin tissues from IH surgery were distributed into two experimental groups: tumor tissue group and normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)


title: Spleen and head kidney differential gene expression patterns in trout with clinical signs of lactococcosis caused by Lactococcus garvieae

status: Public on May 14 2019

city: Madrid

first: Alicia

last: Gibello

state: Madrid

address: Facultad de Veterinaria, Avda. Puerta de Hierro s/n

department: Animal Health

country: Spain

institute: Universidad Complutense de Madrid (UCM)

summary: Lactococcus garvieae is the etiological agent of lactococcosis, a hemorrhagic septicaemia that affects marine and freshwater fish, with special incidence and economic relevance in farmed rainbow trout and with potential zoonotic risks. To characterize the trout immune response at the transcriptomic level on those individuals with clinical signs of lactococcosis, we have performed a microarray analysis using a previously validated immune-focused gene design. The analysis of the transcriptome of spleen and kidney reveals a different pattern of transcription between both immune organs. A correlation between the histopathological examination and the expression patterns of gene sets characterizing immune cell populations was observed for the first time in the spleen. Up-regulation of gene sets key to NK cells, cytotoxic T cells, Th1 and Th2 lymphocytes and macrophages correlated with the inflammatory process and the existence of granulomes containing a high number of macrophages with internalized L. garvieae. On the other hand, cell wall peptidoglican seems to be an important antigen able to induce a complex network of pathways, cytokine production and responses in the host.

overall_design: 3 pools for control spleen samples (9 arrays), 3 pools for L. garvieae-infected spleen samples (9 arrays), 2 pools for control kidney samples (5 arrays), and 3 pools for L. garvieae-infected kidney samples (9 arrays).

first: Rosario

last: Castro

first: Julio

last: Coll

first: Jose

middle: F

last: Fernández-Garayzábal


title: Methylation data from cerebral tumors of WHO grade II and III

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

country: Germany

institute: IZBI

summary:
Stratification provided six methylation subtypes. We characterized them in terms of genetic alterations, functional context, cellular composition, tumor microenvironment and their possible impact for treatment resistance and prognosis.
We here present novel DNA methylation data of an LGG‐cohort collected in the German Glioma Network containing about 85% isocitrate dehydrogenase (IDH) mutated tumors and performed a combined bioinformatics analysis using previously reported genome and transcriptome data.

overall_design: For this study, we screened prospectively recruited patients with a histopathological reference diagnosis of cerebral tumors of WHO grade II and III, known KPS at diagnosis, information on extent of resection by early postoperative neuroimaging, available frozen tissue specimens from the initial operation, and documented clinical outcome. Array‐based DNA methylation data (Illumina 450K arrays) of 122 patient‐matched tumors of the cohort

last: Binder

first: E

last: Loeffler-Wirth

first: L

last: Hopp

first: D

middle: T

last: Jones

first: S

middle: M

last: Pfister

first: A

last: von Deimling

last: Gramatzki

last: Fortenbacher

first: M

last: Kreuz

last: Weber

first: B

last: Hentschel

last: Tatagiba

last: Vatter

last: Westphal

first: G

last: Schackert

first: J

last: Tonn

first: U

last: Schlegel

middle: J

last: Steiger

first: W

last: Wick

last: Weller

last: Loeffler


title: Elucidating the role of the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) and its closest homolog-GALNT6 in mediating aberrant O-glycosylation associated with ovarian cancer dissemination

status: Public on May 07 2019

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

summary: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy, thus understanding molecular changes associated with EOC progression could lead to the identification of essential therapeutic targets. Glycosylation is a post-translational modification (PTM) that participates in major pathophysiology events, including tumorigenesis. Aberrant mucin-type or O-glycosylation in cancer is frequently attributed to altered expression of different N-acetylgalactosaminyltransferases (GalNAc-Ts). We have previously identified the N-acetylgalactosaminyltransferase 3 (GALNT3) gene as a potential EOC oncogene, possibly implicated in aberrant O-glycosylation in EOC cells. Literature reports are suggestive for genetic and functional redundancy between different GalNAc-Ts, and our previous data were indicative for an induction of the GALNT6 expression upon GALNT3 suppression in EOC cells.  Here we show that GALNT3 gene knockout (KO) in the A2780s EOC cells leads to strong GALNT6 upregulation. Moreover, A2780s cell migration, invasion, proliferation and cell cycle analysis were significantly reduced in double GALNT3/T6 gene KO cells compared to single GALNT3 gene KO. Furthermore, MUC1 expression was downregulated in both GALNT3 KO and GALNT3/6 KO, with a more prominent decrease observed in the double KO clone. In vivo studies supported the observed functional redundancy imposed by GALNT6, as animals injected with double GALNT3/T6 KO EOC cell clones displayed a significant increase in survival rates compared to those injected with the control and the GALNT3 KO clones.   Collectively our data strongly suggest for possible functional redundancy of the two GalNAc-Ts (GALNT3 and T6) in EOC, with the perspective to use both of these genes as EOC markers and/or therapeutic targets.

overall_design: To better understand the molecular mechanisms of GALNT3 and GALNT6 genes action in epithelial ovarian cancer (EOC), we employed the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes to identify global gene expression changes upon GALNT3 suppression and double GALNT3/6 suppression in A2780s EOC cells. We compared the gene expression of the selected  CRISPR-Cas9-mediated GALNT3 -knockout clones (GAL3 KO-1 and GAL3 KO-2) and the double gene Knockout GALNT3/6 clones (GAL3/6 KO-1 and GAL3/6 KO-2) against the corresponding control (C) clones .


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia

first: Maria

last: Figueroa


title: Identification of IL-27 as potent regulator of inflammatory osteolysis associated with vitamin E-blended ultra-high molecular weight polyethylene debris of orthopedic implants

status: Public on May 06 2019

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: Osteolysis is a serious postoperative complication of total joint arthroplasty that leads to aseptic loosening and surgical revision. Osteolysis is a chronic destructive process occurs when host macrophages recognize the implant particles and release inflammatory mediators that increase bone-resorbing osteoclastic activity and attenuate bone-formation osteoblastic activity. Although much progress has been made on understanding molecular responses of macrophage to implant particles, pathways/signals initiating osteolysis remain poorly characterized. Transcriptomics and gene-expression profiling of these macrophages may unravel key mechanism in pathogenesis of osteolysis and aid in identifying molecular candidates for therapeutic intervention. To this end, we analyzed the transcriptional profiling of macrophages exposed to UHMWPE particles of the most common components used in bearing materials of orthopedic implants. Regulated genes in stimulated macrophages were involved in cytokine, chemokine, growth factor and receptor activities. Gene enrichment analysis suggested that stimulated macrophages elicited common gene expression signatures for inflammation and rheumatoid arthritis. Among the regulated genes, TNFSF15 and CCL20 were further characterized as molecular targets involved pathogenesis of osteolysis. Treatment of monocyte cultures with TNFSF15 and CCL20 resulted in an increase in osteoclastogenesis and bone-resorbing osteoclastic activity, suggesting their potential contribution to loosening between implant and bone tissue.

overall_design: RNA-seq for macrophages exposed to ultra-high molecular weight polyethylene (UHMWPE) particles and to VE-UHMWPE particles.

first: Mohamad

middle: A

first: Masanari

last: Hamasaki

first: Daisuke

last: Takahashi

first: Norimasa

last: Iwasaki


title: Gene Expression Analysis of Ruditapes philippinarum Haemocytes after Experimental Perkinsus olseni Zoospore Challenge and Infection in the Wild

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

institute: University of Santiago de Compostela

summary: The production of Manila clam (Ruditapes philippinarum) is seriously threatened by the protistan parasite Perkinsus olseni. We characterized and compared gene expression of Manila clam haemocytes in response to P. olseni in a time-course (10 h, 24 h, 8 d) controlled laboratory challenge (LC), representing the first steps of infection, and in a more complex infection in the wild (WI) using a validated oligo-microarray containing 11,232 mostly annotated transcripts. Several immune-genes involved in NIK/NF-kappaB signalling, toll-like receptor signalling and apoptosis were activated at LC-10 h. However, down-regulation of others like lysozyme, histones, cathepsins and heat shock proteins indicated signals of immunodepression, which appeared exacerbated at LC-24 h, where only down-regulated genes were detected. A rebound of haemocytes activity occurred at LC-8 d as shown by up-regulation of genes involved in cytoskeleton organization and cell survival. WI showed a more complex picture and several immune-relevant processes, including cytoskeleton organization, cell survival, apoptosis, encapsulation, cell redox- and lipid- homeostasis were activated, involving the main mechanism of host response. Our results provide useful information, including potential biomarkers, to develop strategies for controlling Manila clam perkinsosis.

overall_design: Gene expression in Manila clams haemocytes naturally infected by P. olseni in a natural bed (wild infection, WI) and after a laboratory challenge (LC) at 10 hours, 24 hours and 8 days after the onset of challenge  was measured.  A total of 16 microarrays were used in the experiments: i) 4 for the WI samples, one control (pool of three different replicates) and three biological replicates for the infected haemocytes; and ii) 12 for the LC samples along the 3 time series: 1 control (pool of three different replicates) and 3 biological replicates at each time.

first: Abul

last: Hasanuzzaman

first: Juan

last: Rubiolo

first: Diego

last: Robledo

first: Antonio

last: Gómez-Tato

first: José

last: Álvarez-Dios

first: Sergio

last: Fernández-Boo

first: Asunción

last: Cao

last: Villalba

first: Belén

first: Paulino

last: Martínez


title: Transcription factor NKX3-1 is required for reprogramming to pluripotency and can replace OCT4 in mouse and human iPSC induction [RNA-seq]

city: Stanford

first: Thach

last: Mai

address: 269 Campus Dr

institute: Stanford University

summary: Resolution of early molecular events preceding endogenous OCT4 activation is critical to understanding the mechanism of reprogramming somatic cells to induced pluripotent stem cells (iPSCs), yet capturing transient regulators at the onset of reprogramming is difficult in heterogeneous populations of asynchronously reprogramming fibroblasts following four-factor transduction. To address this need, we used a heterokaryon system to identify an early and transiently expressed homeobox transcription factor, NKX3-1. Upon knockdown of NKX3-1, iPSC reprogramming is abrogated. Further, we identify that NKX3-1 functions downstream of the IL6-STAT3 regulatory network to activate endogenous OCT4. Importantly, we show that NKX3-1 can substitute for exogenous OCT4 to reprogram both mouse and human fibroblasts at comparable efficiencies generate fully pluripotent stem cells. Our findings establish an essential role for NKX3-1, previously known as a prostate-specific tumor suppressor, in iPSC reprogramming.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq timecourse of heterokaryon reprogramming

first: Jennifer

last: Brady

first: Helen

last: Blau


title: Transcription factor NKX3-1 is required for reprogramming to pluripotency and can replace OCT4 in mouse and human iPSC induction


title: RNAseq transcriptomic profile of glioblastoma stem-like cells derived from U87MG cell line treated with a selective A3 adenosine receptor antagonist (MRS1220) under hypoxia

city: Valdivia

first: Carlos

last: Spichiger

state: Región de los Rios

address: Instituto de Bioquímica y Microbiología, campus Isla Teja, UACh

department: Instituto de Bioquímica y Microbiología

country: Chile

institute: Universidad Austral de Chile

summary: Glioblastoma Multiforme (GBM) is the primary brain tumor with the highest incident and mortality rates worldwide. This is because therapies are not effective, mainly due to tumor recurrence after surgical resection and chemotherapeutic treatment. Recurrence is mainly produced by a tumoral cell sub-population called Glioblastoma Stem-like Cells (GSCs), which are primarily responsible for chemo-resistance and tumor infiltration. We previously showed that in this sub-population, adenosine regulates chemo-resistance through its A3AR. The importance of this study lies in the confirmation that the adenosine/A3AR axis is a plausible therapeutic target to attack different features of GBM, including chemo-resistance and cell migration/invasion of GSCs.

overall_design:
Total RNA isolated from U87MG-GSCs treated with vehicle (DMSO) and MRS1220 (10 µM) under hypoxia was analysed by RNA-seq using the high-throughput sequencing system HiSeq2500 (Illumina).
Two paired-end RNAseq analyses were performed. In the first sequencing analysis, the equipment only released the reverse reads; these reads are the "single" files. With the same samples (the same libraries), the sequencing was repeated, obtaining both reads -- reverse and forward; these reads are the "pair" files. The counts obtained in the single and paired-end analyses were added and used for the determination of differential expression.

first: Angelo

last: Torres

first: Claudia

last: Quezada


title: Transcriptome of locally advanced colorectal tumours

status: Public on May 02 2019

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Here, we report the genomic-scale characterization of locally advanced colon cancer transcriptome. Paraffin embedded samples was used to asses differences between normal colon, primary colon tumor an lymph node metastasis.

overall_design: Total RNA was isolated from three location from each recruited patient: normal colon, colon tumor and lymp node metastasis.

first: Michal

last: Mikula

first: Agnieszka

last: Paziewska

first: Maria

last: Kulecka

first: Michalina

last: Dabrowska

first: Katarzyna

last: Paczkowska

first: Jerzy

last: Ostrowski


status: Public on May 01 2019

city: Shanghai

first: Yiqing

last: Zhu

address: 800 Xiang Yin Road

department: department of medical genetics

institute: Second military medical university

summary: Detect lncRNA/mRNA expression profiling for 10 human lung samples from NSCLC patients to elucidate the dysregulation of lncRNAs and mRNA in tumorigenesis

overall_design: five paired expriments:  lung adenocarcinam Vs. adjacent normal lung tissue samples

first: Ye

last: Xiong

first: Yan

last: Shang


title: Effect of mTORC1 and 2 inhibition on myofibroblast global gene expression

city: London

first: Manuela

last: Plate

state: Greater London

address: 5, University Street, Rayne Institute

department: UCL Respiratory

country: United Kingdom

institute: UCL

summary:
Background: Mechanistic target of rapamycin (mTOR) is a nodal serine/threonine protein kinase critical for the control of fundamental cellular processes. Dysregulated mTOR signalling has been shown in cancer, COPD and idiopathic pulmonary fibrosis (IPF). mTOR forms the catalytic subunit of 2 protein complexes: mTORC1 and mTORC2 which differ in upstream inputs, downstream effects and sensitivity to the allosteric inhibitor rapamycin.
Aim: To compare the effects of the mTORC1 inhibitor rapamycin with an ATP-competitive inhibitor of mTORC1/2, AZD8055, on TGFβ1 induced transcriptional responses during myofibroblast differentiation by RNA-Seq analysis.
Methods: Primary human lung fibroblasts were treated with TGFβ1 for 24h to induce myofibroblast differentiation and extra cellular matrix (ECM) production in the presence of rapamycin or AZD8055. Fibroblasts were also treated with rapamycin or AZD8055 without TGFβ1. Total mRNA was analysed by RNA-Seq.
Results: On a global transcriptomic level, TGFβ1 significantly affected the expression of ~4,200 genes by more than 1.5 fold, of which ~1,100 changes were reversed by pan-mTORC1/2 inhibition, while being insensitive to rapamycin. Only 15 gene changes were reversed exclusively by rapamycin. Analysis of the rapamycin-insensitive, mTOR sensitive myofibroblast transcriptome revealed ECM-receptor interaction, metabolism and actin cytoskeleton regulation as major affected pathways.
Conclusions: Our data support the conclusion that therapeutic approaches aimed at interfering with TGFb1 induced myofibroblast differentiation and ECM production require dual mTOR1/2 inhibition and may, in part, explain the lack of clinical efficacy of everolimus in the context of IPF.

overall_design: Primary human lung fibroblasts were treated with TGFβ1 for 24h in the presence of rapamycin or AZD8055. Each treatment was done in quadruplicates, for a total of 16 samples. Untreated cells were used as control. Paired-end RNA sequencing was performed with the NextSeq sequencing platform (Illumina, San Diego, CA, USA). Each sample was run on 4 different lanes.

last: Platé

first: Hannah

middle: V

last: Woodcock

first: Paul

last: Mercer

first: Rachel

last: Chambers


title: RNA-seq and m6A-seq of AML cells with FTO knockdown or inhibition

status: Public on May 04 2019

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

overall_design: Refer to individual Series


title: Gene expression-profiling to predict distant metastasis in locoregionally advanced nasopharyngeal carcinoma

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Gene expression patterns can be used as prognostic biomarkers in various types of cancer. We aimed to identify a gene expression pattern for individual distant metastatic risk assessment in patients with locoregionally advanced nasopharyngeal carcinoma (LA-NPC).

overall_design: Using Affymetrix Human Gene 2.0 ST GeneChips, we profiled the gene expression between 24 LA-NPC tumor tissues with distant metastasis after radical treatment  and 24 LA-NPC tumor tissues without distant metastasis after radical treatment to identify distant metastasis-related genes.

first: X

last: Tang

first: Y

last: Li

first: N

last: Liu

first: J


title: Sequencing of mRNA with N6-methyladenosine (m6A) modification in AML cells upon DMSO or FTO inhibitor treatment

status: Public on Apr 29 2019

summary: To identify the potential mRNA targets of FTO inhibitor, we conducted m6A-seq with mRNA samples enriched from AML cells upon DMSO and FB23-2 (FTO inhibitor) treatment

overall_design: AML cells (herein is MONOMAC-6) were treated with DMSO and 5uM FTO inhibitor FB23-2 for 72 hours. Polyadenylated RNAs (poly(A) RNAs) were extracted with FastTrack MAG Maxi mRNA isolation kit (Life technology) and randomly fragmented with RNA fragmentation reagents (Ambion). m6A antibody (Synaptic Systems) was used to immunoprecipitate m6A RNA. Final library preparation was constructed with TruSeq Stranded mRNA Sample Prep Kit (Illumina) and the library was quantified by BioAnalyzer High Sensitivity DNA chip. The m6A-seq was conducted on the Illumina HiSeq 2500.

first: Rui

last: Su

first: Lei

last: Dong

first: Zijie

last: Zhang

first: Caiguang

last: Yang


title: ALK7 signaling manifests a homeostatic tissue barrier necessarily abrogated during tumorigenesis and metastasis

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

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


title: Implication of G-quadruplexes in mitochondrial gene expression and genome replication

status: Public on Apr 30 2019

city: Seattle

first: Ting

last: Wang

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

summary: Single-stranded DNA or RNA sequences rich in guanine (G) can adopt non-canonical structures known as G-quadruplexes (G4). G4 in the mitochondrial genome are heavy-strand enriched and have been associated with the formation of deletion breakpoints that cause mitochondrial diseases. However, the functional role of G4 structures in mitochondria remains unclear. Here, we have identified RHPS4 as a G4-specific ligand that localizes to mitochondria and causes replication pausing, with mitochondrial DNA (mtDNA) depletion occurring at higher dosage. We further show that RHPS4 interferes with mitochondrial transcript elongation at low doses, leading to respiratory complex depletion. These unprecedented observations suggest that G4 motifs modulate mitochondrial transcription and replication efficiency. Using the differential effects of high vs low RHPS4 dosing, we characterized gene expression pathway responses to mitochondrial transcription inhibition or mitochondrial genome depletion. Importantly, a human mtDNA mutation that increases G4 formation potential strongly enhanced the RHPS4-mediated mitochondrial respiratory defect. We propose that abnormal G4 dynamics may contribute to mtDNA instability and gene expression defects, particularly in the presence of mitochondrial mutations that enhance the G4 formation.

overall_design: Total RNA was extracted from the mouse embryonic fibroblasts (MEFs) stimulated with 0um (n=3), 2um (n=3), and 10um (n=2) RHPS4. Total stranded RNA libraries (ribo-depleted) were generated and sequenced on the Illumina NextSeq 500 NGS platform. RNA-seq data was analyzed for differentially expressed genes between groups of samples.

first: Brett

last: Kaufman


title: RNA seq with AML (NB4) cells upon FTO inhibition

summary: To determine the potential targets of FTO and identify treatment significance of FTO inhibition in AML, we conducted transcriptome wide RNA seq with NB4 cells upon DMSO and FTO inhibitors (FB23 and FB23-2) treatment.

overall_design: NB4 cells were treated with FB23, FB23-2 and DMSO for 48 hours. Total RNA were isolated from the harvested cells and poly(A)+ RNA were enriched with NEBNext Poly(A) mRNA Magnetic Isolution Module. RNA-seq was performed on Illumina Hiseq system.

first: Yue

last: Huang


title: RNA Expression Data from Bovine Ovarian Granulosa Cells from High or Low Androgen-Content Follicles

city: Lincoln

first: Sarah

last: Romereim

state: NE

address: 3940 Fair Street

department: Animal Science

institute: University of Nebraska-Lincoln

summary:
Excessive androgen production is a hallmark of human and bovine ovarian disorders, and our lab has identified a naturally-occurring bovine model with excess follicular fluid androstenedione (A4) without a proportional estrogen increase. Granulosa cell populations from both the control, Low A4 follicles and the abnormal, High A4 follicles were isolated. Total RNA was extracted from those granulosa cells and submitted to the University of Nebraska Medical Center Microarray Core Facility for transcriptome quantification using Affymetrix Bovine GeneChip Gene 1.0 ST Arrays.
The orignal Affymetrix .CEL files and the normalized linear expression data are included in this submission.

overall_design: There are two populations of granulosa cells analyzed including control granulosa cells from low androstenedione-content follicles (Low A4 GC, mean A4 = 1.9 ng/mL, n = 4) and granulosa cells from high androstenedione-content follicles (High A4 GC, mean = 356 ng/mL, n = 4).

first: Adam

last: Summers

first: William

last: Pohlmeier

first: Jennifer

last: Wood

first: John

last: Davis

first: Andrea

last: Cupp

first: Alexandria

middle: P

last: Snider


title: High fat diet accelerates Barrett esophageal carcinogenesis by inducing a distinct IL-8 dependent immune reaction through alteration of the microbiome

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

institute: Technische Universität München

summary: Barrett Esophagus (BE) is a risk factor for the development of esophageal adenocarcinoma (EAC). As endemic obesity emerges as a risk factor for increasing numbers of EAC we utilized our IL-1b mouse model of BE to understand the impact of a high fat diet (HFD) on disease progression.  Indeed, increased dysplasia development in HFD treated IL-1b mice correlated with an accelerated cytokine response with specific upregulation of IL-8 in esophageal tissue, which could be confirmed by specific overexpression of IL-8 in the BE mouse model. Consequently we observed an influx of immature myeloid cells and neutrophils resulting in a decrease of regulatory NK T cells. HFD led to a specific shift in the gut microbiome, similar to that in human BE patients, being responsible for a specific inflammatory phenotype with elevated IL-1b and IL-8 which could be eliminated under germ free conditions and lead to an increased influx of cardia (Lgr5) stem cells into the esophagus giving rise to dysplasia.

overall_design: Our mouse model of BE in which overexpression of IL-1b in the squamous esophagus induces chronic inflammation leads to metaplasia and dysplasia at the squamo-columnar junction (SCJ) in the mouse gastro-esophageal junction resembles the human disease. The impact of a high fat diet (HFD) and corresponding increase of specific upregulation of IL-8 in esophageal tissue on disease progression was investigated by comparing the gene expression profiles of mice overexpressing IL-1b and IL-8 and mice overexpressing IL-1b being fed with HFD or chow diet.

first: Frederik

last: Wein


title: RNA seq with AML cells (NB4) upon FTO knockdown

first: Jianjun

last: Chen

summary: To identify the potential targets genes of FTO in acute myeloid leukemia (AML), we peroformed RNA-seq of NB4 cells with or without FTO knockdown based on Illumina Hiseq system.

overall_design: NB4 cells were infected with pLKO.1-shFTO and pLKO.1-shNS lentivirus and the positive cells were selected with 1ug/ml puromycin 72 hours post lentivirus infection. After two generation of selections, the NB4 cells were harvested and RNA samples were extracted for sequencing.

first: Rui

last: Su


title: Comparing CTEPH to Control and IPAH pulmonary arteries

status: Public on Apr 27 2019

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary:
Samples surgically extracted from CTEPH pulmonary arteries were compared to post-transplant pulmonary arteries from IPAH and failed donor pulmonary arteries from controls
The goal was to determine if altered gene expression in CTEPH associated with development of chronic thrombi

overall_design: CTEPH samples were compared to IPAH and control

first: Anna

last: Hemnes


title: Characterization of the ALK7 signaling pathway in PanNET, using cell lines that either express constitutively active ALK7 (ALK7-CA) or treated with activin B

first: Nadine

last: Fournier

summary: Herein we report that the TGFß superfamily receptor ALK7 is a suppressor of tumorigenesis and metastasis, as revealed by functional studies in mouse models of pancreatic neuroendocrine and luminal breast cancer, complemented by experimental metastasis assays. Activation in neoplastic cells of the ALK7 signaling pathway by its principal ligand activin B induces apoptosis. During tumorigenesis, cancer cells use two different approaches to evade this barrier, either downregulating activin B and/or ALK7. Suppressing ALK7 expression additionally contributes to the capability for metastatic seeding. ALK7 is associated with shorter relapse-free survival of various human cancers and distant-metastasis-free survival of breast cancer patients. This study introduces a new mechanistic insight into primary and metastatic tumor development, in the form of a protective barrier that triggers apoptosis in cells that are not ‘authorized’ to proliferate within a particular tissue, by virtue of those cells expressing ALK7 in a tissue microenvironment bathed in its ligand.

overall_design: We performed RNA-seq of ßTC3 and AJ-5257-1 cells subjected to either DOX-inducible expression of ALK7-CA, or treatment with activin B.

first: Iacovos

last: Michael

last: Zangger

first: Douglas

last: Hanahan


title: Reprogramming of Tumor-infiltrating Immune Cells in Early Stage of NSCLC

city: Winston-Salem

first: Qianqian

last: Song

state: NC

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

summary: Comparing the relative proportions of immune cells in tumor and adjacent normal tissue from NSCLC patients demonstrates the early changes of tumor immunity and provides insights to guide immunotherapy design. We mapped the immune ecosystem using computational deconvolution of bulk transcriptome data from the Cancer Genome Atlas (TCGA) and single cell RNA sequencing (scRNA-seq) data of dissociated tumors from early-stage non-small cell lung cancer (NSCLC) to investigate early immune landscape changes occurring during tumorigenesis. Computational deconvolution of immune infiltrates in 44 NSCLC and matching adjacent normal samples from TCGA showed heterogeneous patterns of alterations in immune cells. The scRNA-seq analyses of 11,485 cells from 4 treatment-naïve NSCLC patients comparing tumor to adjacent normal tissues showed diverse changes of immune cell compositions. Notably, CD8+ T cells and NK cells are present at low levels in adjacent normal tissues, and are further decreased within tumors. Myeloid cells exhibited marked dynamic reprogramming activities, which were delineated with differentiation paths through trajectory analysis. A common differentiation path from CD14+ monocytes to M2 macrophages was identified among the 4 cases, accompanied by up-regulated genes (e.g. ALCAM/CD166, CD59, IL13RA1, IL7R) with enriched functions (adipogenesis, lysosome), and down-regulated genes (e.g. CXCL2, IL1B, IL6R) with enriched functions (TNFa signaling via NF-kB, inflammatory response). Computational deconvolution and single cell sequencing analyses have revealed a highly dynamic immune reprogramming that occurs in early stage NSCLC development, suggesting that normalizing both immune compartments may represent a viable strategy for treatment of early stage cancer and prevention of progression.

overall_design: Map the immune ecosystem using computational deconvolution of bulk transcriptome data from the Cancer Genome Atlas (TCGA) and single cell RNA sequencing (scRNA-seq) data of dissociated tumors from from early-stage non-small cell lung cancer (NSCLC) to investigate early immune landscape changes occurring during tumorigenesis

first: Wei

last: Zhang

first: Elizabeth

last: Forbes

first: Guangxu

last: Jin


title: Temporal Transcriptome Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity.

city: Beijing

first: Wen

last: Zhong

address: Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The pancreatic beta cell function failure is the core event of type 2 diabetes mellitus. High levels of free fatty acid and glucose are two main factor that induced pancreatic beta cell function failure. Long term exposure to palmitate can induced pancreatic beta cell apoptoss and impaired insulin secretion in vivo and in vitro, called lipotoxicity. The lipotoxicity often coupled with high glucose, their combination form called glucolipotoxcity. We carried out temporal transcriptome and proteome studies investigating the evolution of molecular events in Ins1 cells stimulated by palmitate for different times. And through compared the transcriptome and proteome between lipotoxicity and glucolipotoxicity explain the mechanism of glucolipotoxicity more harmfull to beta cell.

overall_design: we performed a time-course large-scale transcriptome of INS1 cells induced by 0.5 mM palmitate and 0.5 mM palmitate with 27.8 mM glucose at four time points (8, 16, 24 and 48 h) using MAPS method

first: Zonghong

last: Li

first: Hongyang

last: Liu

first: Junjie

last: Hou


title: Cell layer specific AGO1-loaded sRNA from Arabidopsis thaliana dcl234 triple mutant

status: Public on Apr 24 2019

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

institute: ETH

type: Non-coding RNA profiling by high throughput sequencing

summary: microRNAs (miRNA’s) regulation target gene expression, often transcription factors and as such control entire transcriptional networks. This control is important for various developmental transitions and stress responses in a wide range of eukaryotic organisms. While miRNA-mediated gene regulation has been investigated over time (temporal) and in whole organs or tissues in multiple different organisms highlighting their importance, there has been a distinct lack of focus on spatial resolution of miRNA biology. Here we present at cell-type specific resolution, miRNA loading and miRNA action within the Arabidopsis root. Our results for the first time demonstrate the multiple novel modes of miRNA action and illustrate the widespread nature of miRNA movement, at a genome scale within a complex eukaryotic organ.

overall_design: 5 samples examined corresponding to FLAG-AGO1-IP for plants expressing FLAG-AGO1 under 5 specific root cell layer promoter (columella/pACR4, stele/pSHR, endodermis/pSCR, cortex/pCO2 and epidermis/pWER)

first: Chris

last: Brosnan

first: PeiQi

last: Lim

first: Matthias

last: Hirsch-Hoffmann

first: Nicolas

last: Bologna

first: Olivier

last: Voinnet


title: Transcriptional changes in the breast cancer cell line MCF7 rendered resistant to the cationic drug siramesine

city: Copenhagen

first: Mikkel

last: Rohde

address: Strandboulevarden 49

country: Denmark

institute: Danish Cancer Society

summary: Repurpusing cationic amphiphilic drugs (CADs) may be enhance the effect of chemotherapy in cancer treatment. In order to understand the molecular mechanism, we created cell lines resistant to the CAD siramesine by growing them for 6 months in increasing concentrations of siramesine. Parental and resistant cell lines were subjected to RNAseq and revealed diffentially expressed genes in ca+ and cAMP signalling pathways.

overall_design: Parental and CAD resistand cell lines were profiled by RNAsequencing in dublicate and triplicate using the Illumina 2000 plarform

first: Atul

last: Anand

first: Marja

last: Jäättelä


title: Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [miRNA]

status: Public on Apr 21 2019

city: Davis

first: Keith

last: Dunaway

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

summary: The quality of maternal care in early-life plays a crucial role in mammalian neurodevelopment. Augmented maternal care (AMC) is a well-established rodent model of enhanced neonatal care. Rats that have undergone AMC have improved stress resilience and cognition compared with rats that have experienced normal levels of maternal care or adverse neonatal stress. However, the epigenomic basis of long-lived responses to AMC has not been previously explored. Thus, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to assess DNA cytosine methylation, gene expression, and miRNA expression, respectively. The integrated results identify a suite of 20 prioritized candidates impacted by AMC. Overall, these results identified AMC-induced regulatory differences in genes related to neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation in addition to the expected stress response genes. Together, these unbiased results represent a key progression in understanding the complex mechanisms underlying the early-life mechanisms for AMC programming stress resiliency.

overall_design: DNA methylation and RNA were assayed in augmented maternal care male rats as well as controls.

first: Dag

last: Yasui

first: Annie

last: Ciernia

first: Benjamin

last: Laufer


title: Gene expression changes in Burkitt's lymphoma due to treatment with high density lipoprotein-like nanoparticles (HDL NP)

status: Public on Apr 20 2019

city: Chicago

first: Colby

middle: Shad

last: Thaxton

state: IL

address: 303 E Chicago, Tarry 16-703

department: Urology

institute: Northwestern University

summary: We report changes in gene expression in the Burkitt's lymphoma cell line Ramos, treated with high density lipoprotein-like nanoparticles (HDL NPs) for 48 hours, compared to saline (NT) and natural, human HDL treatment

overall_design: Total RNA, isolated using Qiagen's Rneasy Mini kit, from Ramos cells treated with HDL NPs, human HDL or saline for 48 hours, were run on Illumina HT-12 microarrays

first: Jonathan

last: Rink


title: Cell layer specific AGO1-loaded sRNA from dcl234 triple mutant; Cell layer specific and polysome associated RNA from Col0 and hyl1 mutant roots.


title: Functional genomics of iMEF SDHC-loss stable line

status: Public on Apr 22 2019

city: Rochester

first: John

middle: Andrew

last: Smestad

state: Minnesota

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic


title: Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma [ChIP-seq]

status: Public on Apr 17 2019

city: Strasbourg

first: Irwin

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

summary: Somatic oncogenic mutation of BRAF coupled with inactivation of PTEN constitute a frequent combination of genomic alterations driving development of human melanoma. Mice genetically engineered to conditionally express oncogenic BrafV600E and inactivate Pten in melanocytes following tamoxifen treatment rapidly develop melanoma. While early stage melanomas comprised melanin-pigmented Mitf and Dct-expressing cells, expression of these and other melanocyte identity genes was lost in later stage tumours that showed histological and molecular characteristics of de-differentiated neural crest type cells. Melanocyte identity genes displayed loss of active chromatin marks and RNA polymerase II and gain of heterochromatin marks indicating epigenetic reprogramming during tumour progression. Nevertheless, late stage tumour cells grown in culture re-expressed Mitf and melanocyte markers and Mitf together with Sox10 co-regulated a large number of genes essential for their growth. In this melanoma model, somatic inactivation that the catalytic Brg1 (Smarca4) subunit of the SWI/SNF complex and the scaffolding Bptf subunit of the NuRF delayed tumour formation and deregulated large and overlapping gene expression programs essential for normal tumour cell growth. Moreover, we show that Brg1 and Bptf co-regulated many genes together with Mitf and Sox10. Together these transcription factors and chromatin remodelling complexes orchestrate essential gene expression programs in mouse melanoma cells

overall_design: 4 samples corresponding to genomic occupancy profiling of PolII, epigenetic landscape of H3K27me3 and H3K27ac and fixed sonicated genomic DNA input from mouse melanoma tumors.

first: Patrick

last: Laurette

first: Sebastien

last: Coassolo


title: Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [BiSulfite-seq]


title: Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [RNA-seq]


title: Host response to IAV infections in human patients

status: Public on Apr 15 2019

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary: Using influenza infection as a disease model, we used a systems biology approach to analyse host response and to identify immune pathways that might contribute to disease progression. We recruited influenza patients with varying severity of infection (n=154) and collected peripheral blood samples within 24 hours of their presentation to hospitals. Gene-expression arrays of these samples were analysed using weighted gene co-expression network analysis to detect disease-driving modules. These modules were then ranked based on the weight of their contribution to disease progression and fatality.

overall_design: We recruited patients from 20 hospitals during the period 2009 to 2016. The eligibility criteria included (1) age greater than 18 years and (2) World Health Organization definition of influenza-like illness (fever of 38 C° or higher, cough and illness onset within the last ten days). Eligible patients were assessed by an admitting physician for likelihood of influenza infection. Patients with a high likelihood of infection, based on history and clinical features, were enrolled into the study. Airway samples (nasopharyngeal swab, throat sample or sputum) and a 2.5ml peripheral blood sample (into PAXgene tubes) were obtained in each study participant. Routine investigations were performed, as determined by the admitting physician. Airway samples were tested for bacterial pathogens and common respiratory viruses. Blood samples in PAXgene tubes were later processed for microarray analysis.

last: Tang

first: Robert

last: Geffers


title: Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care

overall_design: Refer to individual Series


title: Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma

status: Public on Apr 16 2019

overall_design:
4 samples corresponding to genomic occupancy profiling of PolII, epigenetic landscape of H3K27me3 and H3K27ac and fixed sonicated genomic DNA input from mouse melanoma tumors.
18 RNA-seq samples after siMitf, siSox10, and 4-OHT induced inactivation of Smarca4 or Bptf along with appropriate siControl and control cell samples.

Refer to individual Series


title: The comparation of transcriptome between MEF and mES

status: Public on Apr 14 2019

first: xiao

last: yang

address: 190 Kaiyuan Ave.

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Next Generation Sequencing  in MEF and mES

overall_design: Collecting mRNA profiles processing with Illumina MiSeq

first: Xiao

last: Yang

first: Hui

last: Zheng


title: Function of 5C medium in somatic cell reprogramming

summary: We induced reprogramming by mES and 5C medium, and collected mRNA profiles of the GFP+ and GFP- reprogramming cells sorted by FACS. We found that 5C iPSCs showed differences with mES iPSCs, with different influences on GFP+ and GFP- cells on MET. And we picked the 5C iPSCs single colony, cultured with naive and primed medium. We showed that 5C iPSCs could be converted to naive and primed state respectively.

overall_design: Sorting GFP+ and GFP- reprogramming cells, converting 5C iPSCs to naive and primed state, collecting mRNA profiles processing with Illumina MiSeq


title: Cell type-specific dysregulation of ERK signaling impairs synaptic plasticity and memory in a mouse model of Noonan syndrome

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary: We report transcriptome data from excitatory and inhibitory neurons of mouse brain.

overall_design: Examination of replicated samples in 2 different cell types, excitatory and inhibitory brain neurons

first: Yong-Seok

last: Lee


title: Transcriptomic analysis of cochleae after hair cell damage

status: Public on Apr 13 2019

first: Lingling

last: Jiang

address: No 19, Xinjiekouwai Street

department: Beijing Key Laboratory of Gene Resource and Molecular Development

institute: Beijing Normal University

summary: Although mammalian hair cells are essentially unable to regenerate after damage, nonmammalian hair cells have a robust capacity for hair cell regeneration. To obtain insights into the mechanism of this difference, we analyzed the transcriptomic changes in the mouse cochleae after gentamicin damage and compared them with those in the chick cochleae collected at the corresponding damage time. The results indicated that 2,243 genes had significantly differential expression between the gentamicin- and saline-treated cochleae.

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Cochlea mRNA profiles of mice and chicken (at 3 days post gentamicin damage) were generated by deep sequencing, using Illumina Hiseq2500.

first: Huanju

last: Bai


title: Identification of human CD4+ TEM and TEMRA cell-specific gene markers

status: Public on Apr 09 2019

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: Memory T cells mount an accelerated response upon antigen re-challenge but are heterogeneous in phenotype and function. Therefore, traditionally memory T cells were classified into central memory (TCM), effector memory (TEM) and terminally differentiated effector memory (TEMRA) cells based on the expression of lymph node homing receptors and CD45 splice variants. However, findings on functional heterogeneity even within these subsets demonstrated the need for more suitable markers to match phenotype and function during T cell differentiation. To improve functional classification of human CD4+ memory T cells we applied bulk and single gene expression profiling and identified a set of surface markers, KLRB1, KLRG1, GPR56 and KLRF1, which facilitate classification into subsets with “low”, “high” or “exhausted” cytokine production. Highest level production of multiple cytokines was observed in T cells co-expressing KLRB1 with KLRG1 and/or GPR56 while additional KLRF1 expression was associated with a decline in cytokine production. The superiority of using KLRF1 expression to define exhausted cytokine producers compared to classical TEMRA identification was best exemplified for intrahepatic T cells in patients with inflammatory liver diseases. These data open up new opportunities for monitoring and treatment of chronic inflammatory diseases driven by cytokine producing CD4+ memory T cells.

overall_design: CD4+ naive, central memory, effector memory and TEMRA cells were sorted from peripheral blood of 8 healthy individuals and 9 patients with end stage  inflammatory disease, total RNA isolated and pooled to obtain 4 samples each for RNA expression analysis.

first: Birgit

last: Sawitzki


title: Transcriptome sequencing analysis of BRAF-mutant melanoma metastases.

status: Public on Apr 06 2019

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Melanoma patients carry a high risk of developing brain metastases, and improvements in survival are still measured in weeks or months. Durable disease control within the brain is impeded by poor drug penetration across the blood-brain barrier, as well as intrinsic and acquired drug resistance. In this study, we used high-throughput pharmacogenomic profiling to identify potentially repurposable compounds against BRAF-mutant melanoma brain metastases. One of the compounds identified was β-sitosterol, a well-tolerated and brain-penetrable phytosterol. We found that β-sitosterol attenuated melanoma cell growth in vitro and significantly inhibited brain metastasis in vivo. Large-scale phosphoproteomic and in silico analyses indicated that the therapeutic potential of β-sitosterol was linked to mitochondrial interference. Mechanistically, β-sitosterol effectively reduced mitochondrial respiration and respiratory capacity in melanoma cells, mediated by a selective inhibition of mitochondrial complex I. This led to increased oxidative stress and apoptosis. Notably, we observed completely abrogated BRAF inhibitor resistance when vemurafenib was combined with either β-sitosterol or a functional knockdown of mitochondrial complex I. Based on its favorable tolerability, excellent brain bioavailability, and capacity to inhibit mitochondrial respiration, β-sitosterol represents a promising candidate for drug repurposing in patients with, or at risk for, melanoma brain metastases.

overall_design: A total of 12 samples were analyzed by transcriptome sequencing (RNA-seq) in this study. The study included metastaic xenograft tumors derived from intracardiac injection of H1_DL2 melanoma cells into 5 mice. Metastases to brain, brain, adrenals, ovaries, and femurs in each mouse were identified by bioluminescence imaging, and metastic tumor cells were collected and counted by cell sorting for GFP fluorescence. Replicate tumor cell samples (triplicates) with the highest number of cells from each organ metastasis were selected for RNA-seq analysis.

first: Frits

last: Thorsen

first: Terje

last: Sundstrøm


title: CTCF occupancy in the mouse telencephalon and medial ganglionic eminence

status: Public on Apr 05 2019

city: London

first: Nathalie

last: Berube

state: Ontario

address: 800 Commissioners Road East

institute: Children's Health Research Institute

summary: In this study, we wanted to compare CTCF binding sites in whole telencephalon vs medial ganglionic eminence (MGE) at embryonic day E13.5.

overall_design: ChIP-sequencing for CTCF and input (no antibody) in embryonic day 13.5 telencephelon and medial ganglionic eminence

first: Adrienne

last: Elbert

first: Michael

last: Levy


title: Ligand-independent CXCR7 Activation of MAPK Signaling leads to Prostate Cancer Enzalutamide Resistance

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

institute: Emory University

summary: The standard of care for patients with advanced form of prostate cancer, castration-resistant, now includes enzalutamide, a second generation antiandrogen. However, most of the treated patients will develop resistance to enzalutamide based therapy in around a year, succumbing to lethal disease. Investigating the transcriptome of enzalutamide-resistant prostate cancer cell lines, we identified CXCR7 as one of the most upregulated genes suggesting its role in advanced prostate cancer. CXCR7, known as an atypical G-coupled receptor, is engaged in many physiological and pathological processes. Here we show that in prostate cancer CXCR7 is tightly regulated by androgen receptor (AR), which directly binds to CXCR7 gene promoter and enhancer and represses its transcription. In turn, CXCR7 in prostate cancer reduces enzalutamide toxicity and promotes cell survival and invasiveness. We identified that CXCR7 forms an integral complex with ARRB2 and activates ERK1/2, eliciting pro-survival MAPK pathway. Enzalutamide treatment combined with MAPKK specific inhibitor, trametinib, reversed enzalutamide resistance in prostate cancer in vitro and in vivo. Taken together our findings highlight the critical role of CXCR7 in enzalutamide-resistant prostate cancer and open an avenue for developing novel anti-CXCR7 therapies to improve survival in patients with advanced prostate cancer.

overall_design: genetic_modification_design; MDV3100 resistant or sensitive LNCap or C4-2B lines were continuously selected under 1 μM (C4-2B) or 10 μM (LNCaP) enzalutamide. DMSO used as control.

first: Jonathan

last: Zhao


title: Effect of CXCR4 knockdown in CAFs on gene expression

status: Public on Apr 03 2019

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Cancer associated fibroblasts were used for siRNA mediated knockdown of CXCR4. Control and knockdown CAFs were used to generate RNA and cDNA that was used for gene expression analysis

overall_design: gene expression array analysis with affymetrix arrays

first: Kith

last: Pradhan


title: Long-term expansion and differentiation of adult murine epidermal stem cells in three-dimensional organoid cultures

status: Public on Apr 01 2019

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Mammalian epidermal stem cells maintain homeostasis of skin epidermis and contribute to its regeneration throughout adult life. While two-dimensional mouse epidermal stem cell cultures have been established decades ago, a long-term, feeder cell- and serum-free culture system recapitulating murine epidermal architecture has not been available. Here we describe an epidermal organoid culture system that allows long-term, genetically stable expansion of adult epidermal stem cells. Our epidermal expansion media combines atypically high calcium concentrations, activation of cyclic AMP, FGF and R-spondin signaling with inhibition of BMP signaling. Organoids are established robustly from adult mouse skin and expand over at least 6 months, while maintaining the basal-apical organization of the mouse interfollicular epidermis. The system represents a powerful tool to study epidermal homeostasis and disease in vitro.

overall_design: We establish an organoid culture system for long-term expansion of mouse epidermal stem cells. Using histological methods as well as low-coverage multiplexed RNA sequencing, we show that cultured organoids resembled interfollicular epidermis. We analyzed a total of 23 samples, including 6 controls that are isolated from the skin of mice. None-passaged as well as cultured organoids were compared with replicates. Differences growth factors and small molecules that allow expansion of organoids were compared with replicates.

first: Kim

last: Boonekamp

first: Kai

last: Kretzschmar

first: Dominique

last: Wiener

first: Priyanca

last: Asra

first: Sepideh

last: Derakhshan

last: Basak

first: Hans

last: Clevers


title: Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

institute: Aix-Marseille Université

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


title: An Adversarial DNA N6-methyladenine-Sensor Network Preserves Polycomb Silencing

status: Public on Apr 11 2019

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

summary: Adenine N6 methylation in DNA (6mA) is widespread among bacteria and phage and is detected in mammalian genomes, where its function is largely unexplored. Here we show that 6mA deposition and removal are catalyzed, respectively, by the Mettl4 methyltransferase and Alkbh4 dioxygenase, and that 6mA accumulation in genic elements corresponds with transcriptional silencing. Inactivation of murine Mettl4 depletes 6mA and causes sublethality and craniofacial dysmorphism in incross progeny. We identify distinct 6mA sensor domains of prokaryotic origin within the MPND deubiquitinase and ASXL1, a component of the Polycomb repressive deubiquitinase (PR-DUB) complex, both of which act to remove monoubiquitin from histone H2A (H2A-K119Ub), a repressive mark. Deposition of 6mA by Mettl4 triggers the proteolytic destruction of both sensor proteins, thereby preserving H2A-K119Ub levels. Expression of the bacterial 6mA methyltransferase Dam, in contrast, fails to destroy either sensor. These findings uncover a native, adversarial 6mA network architecture that preserves Polycomb silencing.

overall_design: Analysis of 6mA, Asxl1, MPND distribution by ChIP-seq and 6mA MeDIP-seq in wild-type and Mettl4 knockout (KO) mouse ES cells.  RNA-seq profiling in wild-type and Mett; 4  KO mouse ES cells.  analysis of E9.5 wild-type and Srap1 KO embryos.

first: Soo-mi

last: Kweon

first: Yibu

last: Chen


title: Expression data from human dermal fibroblast subpopulations

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

summary:
Fibroblasts are the main dermis-resident cells, yet they remain poorly characterized. Fundamentally, fibroblasts originate from the same population of mesenchymal cells but fibroblast subpopulations have been identified. Papillary and reticular fibroblasts were characterized based on their respective location in the papillary and reticular dermis. Here, we identified a new subset of fibroblasts, located in human papillary dermis and displaying specific features such as their organization into cell clusters.
We used microarrays to detail the gene expression profiles of the novel fibroblast subpopulation we have identified compared to papillary and reticualr fibroblasts and notably the relative contribution of the different fibroblast subpopulations to the extracellular matrix of the dermis.

overall_design: Three different patients were used in the study. For each patient, three samples were analyzed: single cells from papillary dermis (SC), cell clusters (C) and single cells from reticular dermis (R). Each sample has been duplicated. The experimental design results in a total of 18 samples.

first: Gallic

last: Beauchef

first: Christelle

last: Guere

first: Katell

last: Vié

first: Florence

last: Ruggiero

first: Pauline

last: Nauroy


title: Direct Induction of the Three Pre-Implantation Blastocyst Cell Types from Fibroblasts

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

summary: ATAC-seq, RNA-seq and ChIP-seq in induced TSC and PSC 72 hours past Doxycyclin induction

overall_design:
MEFs, ESCs and TSCs were used as controls, and cells in reprogramming by different factors were harvested at day 3 of reprogramming and subjected to ATAC-seq, RNA-seq and ChIP-seq.

This series contains the re-analysis of GSM1576854, GSM1576855 and GSM1576856 from GSE64684.

first: Mohammad

last: Jaber

first: Hana

last: Benchetrit

first: Shulamit

last: Baror-Sebban

first: Valery

last: Zayt

first: Oren

last: Ram

first: Michal

last: Inbar

first: Yossi

last: Buganim


title: Characterization of the Filovirus-Resistant Cell Line SH-SY5Y Reveals Redundant Role of Cell Surface Entry Factors

status: Public on Mar 31 2019

city: Hannover

first: Rui

last: Costa

state: Niedersachsen

address: Carl Neuberg Strasse 1

department: Gastroenterology Hepatology and Endocrinology

institute: Medizinische Hochschule Hannover

summary: Filoviruses infect a wide range of cell types with the exception of lymphocytes. The intracellular proteins cathepsin B and L, two-pore channel 1 and 2, and bona fide receptor Niemann–Pick Disease C1 (NPC1) are essential for the endosomal phase of cell entry. However, earlier steps of filoviral infection remain poorly characterized. Numerous plasma membrane proteins have been implicated in attachment but it is still unclear which ones are sufficient for productive entry. To define a minimal set of host factors required for filoviral glycoprotein-driven cell entry, we screened twelve cell lines and identified the nonlymphocytic cell line SH-SY5Y to be specifically resistant to filovirus infection. Heterokaryons of SH-SY5Y cells fused to susceptible cells were susceptible to filoviruses, indicating that SH-SY5Y cells do not express a restriction factor but lack an enabling factor critical for filovirus entry. However, all tested cell lines expressed functional intracellular factors. Global gene expression profiling of known cell surface entry factors and protein expression levels of analyzed attachment factors did not reveal any correlation between susceptibility and expression of a specific host factor. Using binding assays with recombinant filovirus glycoprotein, we identified cell attachment as the step impaired in filovirus entry in SH-SY5Y cells. Individual overexpression of attachment factors T-cell immunoglobulin and mucin domain 1 (TIM-1), Axl, Mer, or dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) rendered SH-SY5Y cells susceptible to filovirus glycoprotein-driven transduction. Our study reveals that a lack of attachment factors limits filovirus entry and provides direct experimental support for a model of filoviral cell attachment where host factor usage at the cell surface is highly promiscuous.

overall_design: In total, 13 different total RNA samples were subjected to microarray analysis according to a single-color design.

first: Francisco

last: Zapatero-Belinchon

first: Erik

last: Dietzel

first: Olga

last: Dolnik

first: Katinka

last: Döhner

first: Barbara

last: Hertel

first: Barbora

last: Veselkova

first: Anneke

last: Klintworth

first: Stefan

last: Pöhlmann

first: Michael

last: Manns

first: Thomas

last: Krey

first: Sandra

last: Ciesek

first: Beate

last: Sodeik

first: Stephan

last: Becker

middle: v

last: Hahn

first: Jared

last: Kirui

last: Pietschmann

first: Gisa

last: Gerold


title: Development of the embryonic head: Modelling the impact of WNT signalling activity on the differentiation of epiblast cells to neural progenitors [Dkk]

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

summary: The modulation of WNT activity is critical for the specification of the anterior (head) tissue progenitors in the multipotent early epiblast and the repression of WNT activity enhances the ectoderm lineage potency of the epiblast cells and poises the activation of endogenous WNT activity that drives neurogenesis during head morphogenesis.

overall_design: For the microarray analysis, E7.75 embryos were collected and dissected along the antero-posterior axis. Dkk+/+ and Dkk-/- strains were used in this experiment.

first: Pierre

last: Osteil

first: Patrick

last: Tam


title: WNT signalling activity on epiblast cells

overall_design: Refer to individual Series


title: Epigenetic profiling in Utx germline conditional knockouts and F1 offspring

city: New Haven

first: Bluma

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

summary: Susceptibility to cancer is highly heritable, but much of this heritability remains unexplained.  Some "missing" cancer heritability may be mediated by epigenetic changes in the parental germ line that do not involve transmission of genetic variants from parent to offspring.  These data describe the finding that deletion of the chromatin regulator Utx (Kdm6a) in the mouse male germ line results in an elevated tumor incidence in genetically wild type offspring.  This effect increases following passage through two successive generations of Utx male germline deletion, but is lost following passage through a wild type germ line.  We find widespread redistribution of the H3K27me3 mark in Utx mutant germ cells, and further define approximately 200 regions marked by H3K27me3 that exhibit increased DNA methylation, both in sperm of Utx mutants and in somatic tissue of their progeny.  These hypermethylated regions are located in functional enhancers and may alter regulation of genes involved in cancer initiation or progression. The results indicate that epigenetic changes in the male germ line can profoundly impact cancer susceptibility in adult offspring.

overall_design: ChIP-seq, RRBS, and RNA-seq in cKO sperm and spermatids and in offspring bone marrow. ChIP-seq control spermatids.

first: David

last: Page


title: Gadd45a modulates aversive learning through post-transcriptional regulation of memory-related mRNAs

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: Learning is essential for survival, and is controlled by complex molecular mechanisms including regulation of newly synthesized mRNAs that are required to modify synaptic functions. Despite of the well-known role of RNA-binding proteins (RBPs) in mRNA functionality, their detailed regulation during memory consolidation is poorly understood. This study focuses on the brain function of the RBP Gadd45α (Growth arrest and DNA damage-inducible protein 45 alpha, encoded by the Gadd45a gene). Here, we find that hippocampal memory and long-term potentiation are strongly impaired in Gadd45a-deficient mice, a phenotype accompanied by reduced levels of memory-related mRNAs. The majority of the Gadd45α-regulated transcripts show unusually long 3´ untranslated regions (3´UTRs) that are destabilized in Gadd45a-deficient mice via a transcription-independent mechanism, leading to reduced levels of the corresponding proteins in synaptosomes. Moreover, Gadd45α can bind specifically to these memory-related mRNAs. Our study reveals a new function for extended 3´UTRs in memory consolidation and identifies Gadd45α as a novel regulator of mRNA stability.

overall_design: Gene expression profiling by RNA-seq of hippocampi from wild type and Gadd45a-knockout mice subjected to the passive avoidance (PA) test

first: Alejandro

last: Aparisi Rey

first: Christof

last: Niehrs

first: Beat

last: Lutz


title: Cigarette smoking effect on pancreatic duct epithelial cells

status: Public on Mar 24 2019

city: Guangzhou

first: Liang

middle: Jia

last: Zhang

address: 651 Dongfeng Road East, Yuexiu District,

country: China

institute: SYSUCC

summary: Analysis of different expression of microRNAs in immortalized human pancreatic duct epithelial cells treated with cigarette smoke condensate. Cigarette smoking plays vital role in tumorigenesis and development of pancreatic ductal adenocarcinoma. Results provide insight in the machenisms involved in PDAC initiation and progression.

overall_design: MicroRNA expression in immortalized human pancreatic duct epithelial cells (HPDE6-C7) treated with cigarette smoke condensate (CSC)or DMSO for 48 h were measured. Three independent experiments were performed for each treatment.

first: Jialiang

first: DongXin

last: Lin


title: Gene expression profile in the cuprizone-induced demyelination mouse model

status: Public on Mar 30 2019

city: Daejeon

first: Yun Hee

last: Kang

address: 77 Gyeryong-ro 771 beon-gil, Jung-gu

department: Eulji Biomedical Science Research Institute

institute: Eulji University School of Mdicine

summary: Myelin abnormalities, oligodendrocyte damage, and concomitant glia activation are common in demyelinating diseases of the central nervous system (CNS). The neurotoxicant cuprizone (CPZ) has been extensively used to create a mouse model of demyelination. However, the changes of miRNA expression and effects on behavior of cuprizone treatment have not been clearly reported. We have analyzed the behavioral changes of mice given a diet containing 0.2% cuprizone for 6 weeks. To evaluate the changes of gene expression in CPZ-induced demyelination compared with control, we performed the GeneChip® mouse Gene 2.0 ST Array.

overall_design: We analyzed cerebellum from 2 subjects using the GeneChip® Mouse Gene 2.0 ST Array platform. Array data export processing and analysis were performed using Affymetrix® GeneChip Command Console® Software (AGCC).

first: Seung Ro

last: Han

first: Myung-Shin

last: Lee

first: Seung-Hoon


title: Human cochlear gene expression

status: Public on Mar 19 2019

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: Rainbow Blvd.

department: Otolaryngology Head and Neck Surgery

institute: University of Kansas School of Medicine

summary:
Transcriptome analysis of human inner ear tissue
Hearing loss is common and caused by a wide range of molecular and cellular pathologies. Current diagnosis of hearing loss depends of a combination of physiologic testing, patient history and in some cases genetic testing.  Currently no biopsy or equivalent procedure exists to diagnose inner ear disorders.  The goal of this study was to determine if miRNAs could be identified in human perilymph potentially leading to the development of biomarkers for inner ear disease. Analysis of miRNAs was carried out by evaluating miRNA targets in a cochlear transcriptome library (GSE128505) derived from human inner ear tissue harvested during surgery in which the inner ear is removed.

overall_design:
Basilar membrane, cochlear lateral wall and modiolous harvested at time of transcochlear approach to skull base meningioma
Total RNA isolated and analyzed with Affymetrix Human Transcriptome 2.0 array; Data was processed with the Affymetrix console

first: Staecker

last: Hinrich


title: The Transcriptome Analysis of THP-1 Macrophage Infected with ΔM5447 or Wt Mycobacterium smegmatis by Next Generation Sequencing

status: Public on Mar 29 2019

city: dalian

first: liqiu

last: jia

state: liaoning province

address: No.9 West Section Lvshun South Road

institute: Dalian Medical University

summary: Purpose: The goals of this study are systematic analysis of cellular pathway in THP-1 Macrophage which infected with wild type mycobacterium smegmatis (Wt) or MSMEG_5447 gene defected Mycobacterium smegmatis( ΔM5447) at 24h postinfection. Method: THP-1 Macrophages mRNA profiles infected with Wt orΔM5447 at 24h postinfection  were generated by deep sequencing, in duplicate, using Illumina HiSeq platform and human transcriptome (RefSeq transcriptome index hg19) is a reference sequence. Results: In total, 497 differentially expressed genes (DEGs) was identified in ΔM5447-infected macrophages relative to the Wt-infected macrophages which including 173 up-regulated genes and 324 down-regulated genes using adjusted p-value<0.05 as the threthold criteria. The DEGs of THP-1  macrophages infected with ΔM5447 strain was enriched in inflammatory related pathway. Conclusion: Our study find that the THP-1  macrophages infected with ΔM5447 strain display decreased inflammatory response, MSMEG_5447 may play an essential role in inflammatory response.

overall_design: THP-1 Macrophages mRNA profiles infected with Wt orΔM5447 at 24h postinfection  were generated by deep sequencing, in duplicate, using Illumina HiSeq,  platform, Wt as control sample.

first: Liqiu

last: Jia

first: yufang

last: Ma


title: Genome-wide maps at the base-pair level, of chromatin regions enriched for H3 me3 marks in mouse glioma neurospheres (NS)

status: Public on Mar 18 2019

city: Ann Arbor

first: Maria

last: Castro

state: Michigan

address: 1150 W. Medical Center Drive MSRB II, Room 4570C

department: Dept. of Neurosurgery and Dep. of Cell and Developmental Biology

institute: University of Michigan

summary: We generated data from over four billion bases of sequence from chromatin immunoprecipitated using H3K4me3 or H3K27me3 specific antibodies. We generated genome-wide maps of chromatin regions enriched for the two H3 marks described above. Chromatin source were neurospheres harboring mutant or wild-type IDH1. Our data demonstrated that lysine 4 and lysine 27 trimethylation effectively discriminates between genes that are either expressed or repressed. Therefore, reflecting the impact of mIDH1 on the NS transcriptome.

overall_design: Examination of 2 different histone modifications in 2 neurospheres types (wt-IDH1 and mIDH1).

first: Pedro

middle: R

last: Lowentein


title: Genome-wide analysis of MNase digestibility in wild type or Lsh depleted murine embryonic fibroblasts

status: Public on Mar 28 2019

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

summary: We report here differences in MNase digestibility comparing murine embryonic fibroblasts (MEFs) with and without Lsh. In the first set of samples we compare primary MEFs derived from Lsh+/+ (pMEF_WT5) or Lsh-/- (pMEF_KO6) day 13.5 gestation embryos. In a second set we compare MEFs form conditional Lsh knockout mice before (GC-OHT-NC) or after 48 hours of tamoxifen inducible cre-recombinase expression (GC-OHT-2D). In a third set we compare Lsh knockout (Lsh cko) MEFs before (IAA-0h) and after 72 hours of IAA induced proteolytical degradation of Lsh (IAA-3D). In a fourth set we compare Lsh knockout MEFs before (IAA-0h-2) and after 7 hours of IAA induced proteolytical degradation of Lsh (IAA-7h) or after 24 hours (IAA-24). Lsh depletion leads to specific changes in chromatin accessibility at potential enhancer sites.

overall_design: Genome-wide maps of MNase digestiblity in MEFs in the presence or absence of Lsh.

first: Jianke

last: Ren

first: Richard

last: Finney

first: Maggie

first: Kathrin

last: Muegge


title: Toll-like receptors 2 and 4 control adaptive β-cell expansion in diet-induced obesity

status: Public on Mar 21 2019

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Adult pancreatic β cells are refractory to proliferation, a roadblock for the treatment of insulin-deficient diabetes. Consumption of energy-dense Western or high-fat diet (HFD) triggers mild adaptive β cell mass expansion to compensate for peripheral insulin resistance; however, the underlying molecular mechanism remains unclear. Here we show that Toll-like receptors (TLR) 2/TLR4 act as molecular “brakes” for diet-induced β cell replication in both mice and humans. The combined loss of TLR2/TLR4, but not individually, dramatically increases facultative β, not α, cell replication, leading to progressively enlarged islet mass and hyperinsulinemia in diet-induced obesity. Mechanistically, loss of TLR2/TLR4 increases β cell proliferation and nuclear abundance of Cyclin D2 and CDK4 in an extracellular signal-regulated kinase (ERK)-dependent manner. These data reveal a novel mechanism governing adaptive β cell mass expansion in diet-induced obesity and suggest that selective targeting of TLR2/TLR4 pathways may hold promise for reversing β cell failure in diabetic patients.

overall_design: Pancreatic islets were isolated from wild type and Tlr2/Tlr4 double knockout mice after high-fat diet intervention for 5 wks or 7 months and subjected to genome wide expression profiling.

first: Yewei

last: Ji

first: Sun

last: Shengyi

first: Neha

last: Shrestha

first: Laurel

last: Darragh

first: Jun

last: Shirakawa

first: Yan

last: Xing

first: Yi

last: He

first: Bethany-Ann

last: Carboneau

first: Geun-Hyang

last: Kim

first: Hana

first: Shu

last: Xin

first: Duo

last: An

first: Minglin

first: Jose

last: Oberhozler

first: Scott

last: Soleimanpour

first: Maureen

last: Gannon

first: Chengyang

last: Liu

first: Ali

last: Naji

first: Rohit

last: Kulkarni

first: Yong

last: Wang

first: Sander

last: Kersten

first: Ling

last: Qi


title: miR-155 enhances PRC2 activity via polycomb-like protein Phf19 to sustain T cell antitumor immunity

status: Public on Mar 11 2019

first: Luca

last: Gattinoni

address: 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute


title: Type I interferon gene expression response to chemotherapy

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

summary: Neoadjuvant and adjuvant chemotherapies provide survival benefits to breast cancer patients by delaying distant relapses or inducing cure, but the mechanism is not fully clear. Here, we performed a gene expression analysis to demonstrate that estrogen-receptor (ER)-negative murine 4T1 mammary adenocarcinoma cells treated by chemotherapy in vitro activate the IFNß/IFNAR/IRF7 pathway to elicit a T cell-dependent immune response that maintains cancer cells in a dormant state in vivo.

overall_design: 10e6 4T1 tumor cells were plated one day prior treatment. For methotrexate (MTX) selection, cells were treated with the dosage close to IC85 directly added into the culture medium. The MTX-containing medium was replaced at the 2nd and 3rd days post starting and then every 2 to 3 days. The in vitro treatment was then continued for up to 2 weeks until single colonies of surviving cells were visible. The resulting surviving cells were the MTX-resistant ones, that we named MR20 compared to the MTX-sensitive WT untreated cells.

first: Qiang

last: Lan

first: Mauro

last: Delorenzi

first: Girieca

last: Lorusso

first: Curzio

last: Rüegg


title: Regulation of mesenchymal stem to transit amplifying cell transition in the continuously growing mouse incisor [Microarray Expression]

status: Public on Mar 12 2019

city: London

first: Paul

middle: T.

last: Sharpe

state: Please select one below:

address: Guy's hospitial

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

summary:
Regulation of transit amplifying cell formation from self-renewing stem cell is fundamental process for cell replacement in a controlled way. Here we analyse the properties of a population of mesenchymal TACs in the continuously growing mouse incisor to identify key components of the molecular regulation that drives proliferation.
Using gene microarray profiling, we show that the polycomb repressive complex 1 acts as a global regulator of the TAC phenotype by its direct action on the expression of key cell cycle regulatory genes and also by regulating Wnt/b-catenin signalling activity.
Analysing the properties of mesenchymal transit amplifying cells population and identifing key components of the molecular regulation that drives proliferation.

overall_design: Gene expression data from Ring1b deletion samples than control samples. Three biological replicates for each condition.

first: Zhengwen


title: SALL3 regulates propensity of human induced pluripotent stem cells to differentiate into distinct cell lineages

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

institute: National Institute of Health and Sciences

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


title: miR-155 enhances PRC2 activity via polycomb-like protein Phf19 to sustain T cell antitumor immunity [ChIP-Seq]

summary: The microRNA miR-155 is essential for CD8+ T cell antiviral and antitumor immunity but the mechanisms behind its activity remain unresolved. Here, we show that miR-155 increased CD8+ T cell antitumor function by restraining T cell senescence and functional exhaustion through epigenetic silencing of key drivers of effector differentiation. miR-155 enhanced the function of polycomb repressor complex 2 (PRC2) indirectly by promoting the expression of the PRC2 cofactor Phf19 via AKT signaling. Phf19 orchestrated a transcriptional program extensively shared with miR-155 to enhance T cell engraftment, polyfunctionality, and antitumor immunity. These effects were dependent on the histone-binding capacity of Phf19 which is critical for the PRC2 recruitment to chromatin. These findings establish miR-155–Phf19–PRC2 as a pivotal axis regulating CD8+ T cell differentiation. Targeting the microRNA–polycomb-group protein circuitry is a promising route to potentiate cancer immunotherapy through epigenetic reprogramming of CD8+ T cell fate.

overall_design: We compared the H3K27me3 binding  profiles of Pmel-1 CD8+ T cells overexpressing with miR-155 or Controls 5 days after transduction.

first: Yun

last: Ji


title: Regulation of mesenchymal stem to transit amplifying cell transition in the continuously growing mouse incisor


title: Singing female songbirds: Female-specific gene networks in the song area HVC

city: Seewiesen

first: Meng-Ching

last: Ko

state: Bayern

address: Eberhard-Gwinner-Str. 6a

department: Behavioral Neurobiology

institute: Max Planck Institute for Ornithology

summary:
In this data set, we compared the expression data of song nuclei HVC,  visual cortex entopallium, and the molecular layer of the cerebellum dissected from females and males of 3 songbird species (S. canaria, U. cyanocephalus, P. bicolor) to identify sex-specific stimulated gene expression.
Testosterone-treated male and female canaries were also included in order to study whether testosterone effect on transcriptomes is sex-specific.
Finally, testosterone-treated female canaries were compared with a rare group of spontaneously singing female canaries to study whether testosterone stimulation would be different from natural stimulation.

sample_organism:
Serinus canaria
Ploceus bicolor
Uraeginthus cyanocephalus

overall_design:
A total of 36 Female and 30 male HVC, 35 female and 30 male entopallium, and 12 female and male cerebellum (molecular layer) from 3 songbird species (S. canaria, U. cyanocephalus, P. bicolor) were sampled. The transcriptomes were compared by 2 approches: 1) male-to-female from the same species/breeding status/testosterone treatment,
2) HVC-to-entopallium of the same group. The differential expression was analyzed using ChipInspector (Genomatix) with group-wise exhaustive method, False Discovery Rate was set to zero and the minimum significant probe coverage was set at 10.
ChipInspector carries out significance analysis on the single probe level (not provided), instead, the normalized transcript level data are included in the Sample tables.

first: Carolina

last: Frankl-Vilches

first: Antje

last: Bakker

first: Manfred

last: Gahr


title: Gene expression alteration in mouse primary chondrocytes by cyclic tensile strain.

status: Public on Mar 13 2019

city: TOKYO

first: Taku

last: Saito

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

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

summary: To investigate effects of excessive mechanical loading on chondrocytes.

overall_design: Primary chondrocytes were isolated from 6-day-old C57BL/6J mice, and were subjected to cyclic tensile strain (0.5 Hz, 10% elongation) for 30 min. Total RNA was isolated from the mouse primary chondrocytes before and 24 hours after the cyclic tensile strain loading.

first: Song

middle: H

last: Chang


title: MicroRNA expression profiles between high and low TET1 expressers with AML

status: Public on Mar 05 2019

city: Hangzhou

first: Jinghan

last: Wang

address: No.79 Qingchun Road, Hangzhou 310003 Zhejiang, People’s Republic of China

institute: Department of Hematology, The First Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, P.R. China

summary: To obtain the biologic insight of TET1 expression,we analyzed microRNAs expression profiles from 12 AML patients with high TET1 expression and 12 cases with low TET1 expression.

overall_design: We selected 12 AML patients with high TET1 expression and 12 cases with low TET1 expression to assess the differences of microRNA expression. As a result, we identified 199 differently expressed microRNAs including 111 downregulated and 88 upregulated in high TET1 expressers.

first: Jie

last: Jin


title: Next Generation Sequencing Facilitates Quantitative Analysis of IFNα Stimulated Transcriptomes in HepG2, SETD2-KO, STAT1-KO and STAT1-K525ARe HepG2 cells

city: shanghai

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

summary:
Purpose: Using RNA-seq to analyze the different expressions induced by IFNα among the SETD2-KO HepG2 cells, STAT1-KO HepG2 cells and STAT1-K525A-Re HepG2 cells and HepG2 control cells
Methods: mRNA profiles of HepG2 control cells and SETD2-KO cells, STAT1-KO cells, STAT1-K525A-Re cells were generated by deep sequencing, using BGISEQ-500RS. The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).

overall_design: Examination of 2 different RNA-seq analysis in 4 cell types.

first: Xuetao

last: Cao

first: Kun

last: Chen