title: Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

city: Xi'an, Shaanxi

first: liu

middle: ying

last: dong

address: Shaanxi

department: College of Animal Science and Technology

institute: Northwest University of Agriculture and Forestry Science and Technology

summary: We applied whole genome bisulfite Sequencing data and profiled genome-wide DNA methylation distribution in four germ cell types during spermatogenesis.

overall_design: Whole-genome DNA methylation modifications of mouse spermatogenesis was deeply sequenced using Illumina HiSeq X10 system.

first: Yingdong

last: Liu

first: Yanping

last: Zhang

first: Wenqiang


title: Ultra-low-input native ChIP-seq data of four germ-cell types during mouse spermatogenesis

status: Public on Jul 17 2020

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We applied ultra-low-input native ChIP-seq and profiled genome-wide H3K9me3 distribution in four germ cell types during spermatogenesis.

overall_design: Whole-genome H3K9me3 modifications of mouse spermatogenesis was deeply sequenced using Illumina HiSeq X10 system.


title: ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer (RNA-Seq)

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

type: Expression profiling by high throughput sequencing

summary: Interleukin 6 (IL6) signaling has been associated with an aggressive and metastatic phenotype in multiple solid tumors including breast cancer, but its mechanism of action in mediating tumor progression and treatment response is not clear. By exploiting a clinically relevant intraductal xenograft model of estrogen receptor a positive (ER+) breast cancer, we demonstrate that IL6 increases both primary tumor growth and distant metastases. In pre-clinical models and clinical specimens, signal transducer and activator of transcription 3 (STAT3) mediates IL6-induced activation of a metastatic gene program from enhancers shared with ER and its pioneer factor FOXA1. However, STAT3 drives transcription independent of ER and FOXA1 function from these enhancers, and the IL6/STAT3 pathway is therefore resistant to ER-targeted therapies, decoupling these two important oncogenic pathways. This demonstrates that ER/FOXA1 and IL6/STAT3 are two parallel, but functionally independent and actionable pathways controlling breast cancer progression.

overall_design: RNA-seq in human breast cancer cell lines in response to short-term interleukin 6 (IL6) treatment

first: Rasmus

last: Siersbaek

first: Igor

last: Chernukin

middle: S


title: IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer


title: Daily rhythms of Plasmodium chabaudi, showing that 60% of those are intrinsic to the parasite

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

country: USA

institute: University of Texas Southwestern Medical Center

summary: Malarial rhythmic fevers are the consequence of the synchronous bursting of red blood cells (RBCs) upon completion of the malaria parasite asexual cell-cycle. Here we hypothesized that an intrinsic clock in the parasite underlies the modulo-24h rhythms of RBC bursting. We show that parasite rhythms are plastic and slow down to match rhythms of hosts with long circadian period. We also demonstrate that malaria rhythms persist even when host food intake is evenly spread across 24h, suggesting that host feeding cues are not required for synchrony. Moreover, we find that the parasite population remains synchronous and rhythmic even in an arrhythmic clock mutant host. Thus, we propose that parasite rhythms are generated by the parasite, possibly to anticipate its rhythmic changing environment.

sample_organism:
Plasmodium chabaudi
Mus musculus

platform_organism:
Plasmodium chabaudi
Mus musculus

overall_design: mRNA-seq circadian profiles were generated from Plasmodium chabaudi infected mouse blood. Multiple host conditions tested, from normal light/dark cycles, complete darkness, long period mutants, spread-out feeding and arrhythmic mutants

first: Filipa

last: Rijo-Ferreira

first: Victoria

middle: A

last: Acosta-Rodriguez

first: John

middle: H

last: Abel

first: Izabela

last: Kornblum

first: Ines

last: Bento

first: Elizabeth

middle: B

last: Klerman

first: Maria

middle: M

last: Mota

first: Joseph

last: Takahashi


title: Leveraging genetic variation to identify divergent functions of distinct NF-kB factors on the activity of regulatory elements in macrophages

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: CMM

institute: University of California, San Diego

summary: Genetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of the regulatory elements. However, it is unclear which motifs are prone to impact transcriptional regulation if mutated. Current motif analysis tools either prioritize TFs based on motif enrichment without linking to a function or are limited in their applications due to the assumption of linearity between motifs and their functional effects. We present MAGGIE, a novel method for identifying motifs mediating TF binding and function. By leveraging measurements from diverse genotypes, MAGGIE uses a statistical approach to link mutations of a motif to changes of an epigenomic feature without assuming a linear relationship. We benchmark MAGGIE across various applications using both simulated and biological datasets and demonstrate its improvement in sensitivity and specificity compared to the state-of-the-art motif analysis approaches. We use MAGGIE to gain novel insights into the divergent functions of distinct NF-κB factors in pro-inflammatory macrophages, revealing the association of p65-p50 co-binding with transcriptional activation and the association of p50 binding lacking p65 with repression. The Python package for MAGGIE is freely available at https://github.com/zeyang-shen/maggie

overall_design: p65 and p50 ChIP-seq for BMDMs (bone marow-derived macrophages) from C57BL/6J mice stimulated with KLA for 1 hour.

first: Marten

last: Hoeksema

first: Zeyang

last: Shen


title: Studying diet induced liver carcinogenesis

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

summary: The scope of this project is to study, using state-of-the-art systems in the liver following den induced liver cancer with dietary modification (high fat diet and sugar water - HFD+SW).

overall_design: Male C57BL/6J mice were challenged with an IP injection of Diethylnitrosamine (DEN) at day 15;  Mice were fed HFD+SW, and were culled at 30 weeks.

first: Fiona

last: Oakley

first: Quentin

last: Anstee


title: RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [Non-synchronized RNA-seq]

city: BEIJING

first: Haili

last: Qian

address: 17 South Panjiayuan Lane, Chaoyang District

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: The processing of RNAs by chromatin-associated proteins (CAPs) is highlighted by the latest findings. However, whether and how CAP-RNA interactions regulate cancer biology remain underdefined. Using modified fCLIP-seq technology, we show that, cancer metastasis-associated antigen 1 (MTA1), a well-known oncogenic chromatin modifier, binds bulk transcripts, preferentially at splicing-responsible motifs, influencing the abundance and alternative splicing (AS) of target transcripts, preferentially those encoding mitosis regulators. MTA1 orchestrates the fluctuant pre-mRNA AS kinetics of mitosis regulators, such as ATRX and MYBL2, during mitosis. MTA1 overexpression causes a defective mitotic arrest, leading to aberrant chromosome segregation, and CIN occurrence in cancer cells and clinical tumors, which eventually contributes to tumorigenesis. Hence, we present MTA1 as a pivotal RNA-binding CAP linked to mitosis control in tumorigenesis.

overall_design: RNA-seq experiments performed on MTA1-knockout and control samples from non-synchronized HCT116 cells. Each was performed with three replicates.

first: Yi

last: Zhang


title: Linkage of genetic drivers and strain-specific germline variants confound mouse cancer genome analyses

city: München

first: Sebastian

last: Mueller

address: Ismaninger Strasse 22

department: Institut für Molekulare Onkologie und Funktionelle Genomik

country: Germany

institute: Klinikum rechts der Isar

summary:
Cell cultures were isolated from primary pancreatic cancers (PPTs) of KPC mice and subjected to array comparative genomic habridization (aCGH) for the investigation of copy nummber profiles.
We generated primary pancreatic cancer cell cultures from KPC mice (n=4).

overall_design: Investigated mouse genotypes are: KPC (n=4).

last: Lange

first: Roland

last: Rad


title: The effect on the lack of ILCs on the colon of mice exposed to DSS colitis

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: Anti CD90 was used to deplete ILCs in Rag mice prior to the induction of colitis. After 6 days the mice were culled and RNASeq performed on RNA extracted from the Colon

overall_design: 12 mice, 6 were treated with DSS and 6 control mice

first: J

middle: R

first: T

last: Castro-Dopico

first: M

last: Clatworthy


title: RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [fCLIP-Seq]

overall_design: fCLIP-seq experiments performed on MTA1 protein. IgG was performed with the same steps as control.


title: RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [Synchronized RNA-seq]

overall_design: RNA-seq experiments performed on MTA1-knockout and control samples from synchronized HCT116 cells. Each was performed with three replicates.


title: Effect of ILCs depletion on Macrophages in a mouse model of colitis

first: John

summary: Anti CD90 was used to deplete ILCs in RAG mice at point of iniation of DSS colitis in Rag mice. After 6 days the Macrophages were sorted from the colon and compared by using RNASeq to mice in which ILCs had not been repleted but still had colitus induced.

overall_design: All mice recived were RAG KO mice and reciveed DSS. 6 recived anti CD90 and the remaining 6 recived an isotype control

middle: W

last: Dennison


title: miRNA-mRNA interaction network in liver of hybrid yellow catfish (Pelteobagrus fulvidraco × P. vachelli) fed high fat diets

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

summary:
Background: Yellow catfish (Pelteobagrus fulvidraco) is one of the important aquaculture species in China. In recent years, due to the high breeding density, the increasing frequency of feeding, and the excessive addition of feed fat, the excessive deposition of body fat in cultured yellow catfish has become more frequent. MicroRNAs (miRNAs) are an important gene expression regulatory signal molecule that regulates liver fat synthesis and transport and play an important role in fat deposition. However, there is a little research on the mechanism of fatty liver caused by excessive deposition of liver fat.

Results: After 60 days of high-fat stress, the growth and feed conversion rate of hybrid yellow catfish (Pelteobagrus fuIvidraco♀×P. vachelli♂) were significantly inhibited, and hepatosomatic index, viscerosomatic index, hepatic triglyceride and cholesterol, and red lipid droplets in liver tissues were increased. Through high-throughput sequencing, we constructed miRNA libraries of high-fat stress at 60d, identified 346 conserved miRNAs and 410 novel miRNAs, among which 13 differentially expressed miRNAs were screened between high-fat diet group and normal-fat diet group. Also, we constructed mRNA transcriptome libraries after high-fat stress. Potential target genes for differentially expressed miRNAs were identified by bioinformatics analysis. Seven miRNA-mRNA pairs were screened. The expression of differential miRNA and mRNA and potential binding sites were analyzed by qRT-PCR and dual luciferase assay. Hybrid yellow catfish could promote the oxidative degradation of liver glucose, reduce fatty acid peroxidation, regulate antioxidant enzyme activity and response of immune and inflammatory to relieve fat deposition and liver stress.

Conclusions: The disorders of fat metabolism in liver not only result in feed wastage, increase metabolic burden of yellow catfish, but also cause immune function damage, resulting in a variety of nutritional diseases. The development of this study is to understand the molecular mechanism of hepatic fat deposition in yellow catfish. It has important biological significance for improving protection of liver against stress and healthy culture.

sample_organism: Tachysurus fulvidraco x Tachysurus vachelli

overall_design: The normal fat diet (NFD) and the high fat diet (HFD) were set according to experimental requirements.

first: Fanyi

last: Tao

first: Wenjin

last: Bao

first: Jie

last: He

first: Ming

last: Liang

first: Cong

first: Xiahong

last: Li

first: Deju

last: Chen

first: Pao

last: Xu


title: RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing

first: Haili

last: Qian

type: Expression profiling by genome tiling array


title: RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [ChIP-Seq]

overall_design: ChIP-seq experiments performed on MTA1 protein. Input was performed with the same steps as control.

first: Yi

last: Zhang


title: DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells [2]

status: Public on Jul 16 2020

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

summary: RNA-DNA hybrids form throughout the chromosome during normal cell growth and under stress conditions. When left unresolved, RNA-DNA hybrids can slow replication fork progression, cause DNA breaks, increase mutagenesis, and reduce gene expression. To remove hybrids, all organisms use ribonuclease H (RNase H) to specifically degrade the RNA portion of RNA-DNA hybrids. Here we show that, in addition to chromosomally encoded RNase HII and RNase HIII, Bacillus subtilis NCIB 3610 encodes a previously uncharacterized RNase HI protein, RnhP, on the endogenous plasmid pBS32. Like other RNase HI enzymes, RnhP incises Okazaki fragments, ribopatches, and a complementary RNA-DNA hybrid. We show that while chromosomally encoded RNase HIII is required for pBS32 hyper-replication, RnhP compensates for loss of RNase HIII activity on the chromosome. Consequently, loss of RnhP and RNase HIII impairs bacterial growth. We show that the decreased growth rate can be explained by laggard replication fork progression near the terminus region of the right replichore resulting in SOS-dependent inhibition of cell division. We conclude that B. subtilis NCIB 3610 encodes functional RNase HI, HII, and HIII, and pBS32-encoded RNase HI contributes to replication fork progression and chromosome stability while RNase HIII is important for chromosome stability and plasmid hyper-replication.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: Assessment of sequencing coverage across the chromosome for WT and RNase H deficient cells in a ppsA-E deletion background

first: Daniel

last: Kearns

first: Lyle

last: Simmons


title: DNA sequencing coverage in wild type and RNase H deficient Bacillus subtilis cells

platform_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10


title: Transcriptome-wide analysis of apical shoot development during growing season in Pinus canariensis

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

institute: University of Göttingen

summary: The shoot apical meristem is responsible of seasonal length increase in plants. In woody plants transition from primary to secondary growth is also produced during seasonal apical growth. These processes are controlled by different families of transcription factors. Using a previously constructed Pinus canariensis transcriptome, we designed a genomic microarray to measure the levels of transcription during apical growth. The identification of differentially expressed genes was performed by mean of a time-course analysis.

overall_design: mRNA samples were collected at 5 dates during the growing season in Pinus canariensis, supported by microscopical observation of developmental activity: April 15th, April 30th, May 22nd,  July 3rd and September 11th. Three biological replicates were collected for each time sampled, and therefore 15 mRNA samples were hybridazed in a one-color microarray experiment.

first: Carmen

last: Collada

first: Alvaro

last: Soto


title: A central role of glutamine in Chlamydia infection

city: Wuerzburg

first: Thomas

last: Rudel

state: Bavaria

address: Am Hubland

department: Chair of Microbiology

institute: University of Wuerzburg

summary: RNA Seq in HUVEC after infecting with Chlamydia

overall_design: HUVEC after infecting with Chlamydia

first: Karthika

last: Rajeeve

first: Apoorva

last: Baluapuri

first: Elmar

last: Wolf


title: Transcriptomic profile of high and low fertile HF crossbred bulls.

city: Bangalore

first: Arumugam

last: Kumaresan

state: Karnataka

address: Hosur Road

department: Veterinary Gynaecology and Obstetrics

country: India

institute: National Dairy Research Institute

summary: To identify the transcriptomic differences in spermatozoa derived from high and low fertile crossbred bulls.

overall_design: Microarray Gene expression Study : Agilent Bos Taurus 8x60k Microarray: AMADID: 29411

first: A


title: Tet2 deletion mediated DNA methylation changes in the mouse mammary gland

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

summary: We used enhanced reduced representation bisulfite sequencing (ERRBS) analysis to dertemine global DNA methylation perturbed by loss of TET2 in the mouse mammary gland.

overall_design: Detarmine differential DNA methylation profiles of three Tet2 wild-type (WT) and two Tet2 knockout (KO) animals using ERRBS analysis.


title: High throughput sequencing of transcripts from normal and Bardet-Biedel Syndrome mouse adipose tissue after treatment with Glucosyl Ceramide Synthase inhibitor (GCSi) Genz667161

city: Framingham

first: Herve

last: Husson

state: Massachusetts

address: 49 New York Ave

department: Rare and Neurologic Diseases Research

institute: Sanofi Genzyme

summary: The goal of this study was to compare Next Generation mRNA Sequencing (RNA-seq) data obtained from adipose tissue from Wt, untreated Bbs2-/-, and GCSi treated Bbs2-/- male mice.

overall_design: Comparison of RNA expression of 20 most altered canonical pathways and more specifically, sphingolipid, adipogenic and inflammatory pathways in  WT vs Bbs2-/-, and in Bbs2-/- vs  Bb2-/- mice treated with GCSi.

first: Hervé

first: Brenda

last: Richards


title: Requirement for LIM kinases in acute myeloid leukemia

city: Heidelberg

first: Stefan

last: Fröhling

address: Im Neuenheimer Feld 460

institute: German Cancer Research Center ans National Center for Tumor Diseases

summary: Acute myeloid leukemia (AML) is an aggressive disease for which only few targeted therapies are available. Using high-throughput RNA interference (RNAi) screening in AML cell lines, we identified LIM kinase 1 (LIMK1) as a potential novel target for AML treatment. High LIMK1 expression was significantly correlated with shorter survival of AML patients and coincided with FLT3 mutations, KMT2A rearrangements, and elevated HOX gene expression. RNAi- and CRISPR-Cas9-mediated suppression as well as pharmacologic inhibition of LIMK1 and its close homolog LIMK2 reduced colony formation and decreased proliferation due to slowed cell cycle progression of KMT2A-rearranged AML cell lines and patient-derived xenograft (PDX) samples. This was accompanied by morphologic changes indicative of myeloid differentiation. Transcriptome analysis showed upregulation of several tumor suppressor genes as well as downregulation of HOXA9 targets and mitosis-associated genes in response to LIMK1 suppression, providing a potential mechanistic basis for the anti-leukemic phenotype. Finally, we observed a reciprocal regulation between LIM kinases (LIMK) and CDK6, a kinase known to be involved in the differentiation block of KMT2A-rearranged AML, and addition of the CDK6 inhibitor palbociclib further enhanced the anti-proliferative effect of LIMK inhibition. Together, these data suggest that LIMK are promising targets for AML therapy.

overall_design: shRNA-mediated knockdown of LIMK1 in THP-1 cells

first: Patrizia

last: Jensen

first: Claudia

last: Scholl


title: Genome-wide maps of E2A binding peaks in Embryonic stem cells and Neural progenitor cells

city: Beijing

first: Yang

last: Li

address: Xueyuan Road 38,Haidian District

institute: Peking University

summary:
Background:  E2A, encoded by the TCF3 gene locus, belongs to the E protein transcription factor family, which also includes HEB (TCF12) and E2-2 (TCF4), has been suggested to play an important role in leukemogenesis. However, far less is known about the function of E2A in cell-fate regulation of hESCs. Therefore,  further understanding of E2A in self-renewal and differentiation of embryonic stem cells may be influenced.
Methods: The mRNA profiles of wildtype and E2A knockout embryonic stem cells were generated by RNA-seq technique, in triplicate for each group, using IIIumina Hiseq 2500.
Results: A comprehensive human transcriptome map of wild type and E2A knockout embryonic stem cells was provided. Function enrichment, network characteristics and disease association of the differentially expressed genes were analyzed.
Conclusion: The dataset could serve as a baseline resource for investigating the potential effects and mechanism of E2A in embryonic stem cells.

overall_design: Examination of E2A binding peaks in Embryonic stem cells and Neural progenitor cells

first: Yi

last: Siqi

first: Huang

last: Xiaotian

first: Zhou

last: Yuan

first: Li

last: Yang


title: Gene expression profiling of Notch1-overexpressing renal progenitors

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

summary:
Notch1 overexpression in renal progenitors leads to morphologic changes. In this study we investigate the possible mechanisms that lead to cell transformation.
We found that several genes involed in proliferation, apoptosis, cell polarity and cell division.

overall_design: Renal progenitor cells were infected with a lentivirus overexpressing the intracellular domain of Notch1 (NICD1) or a mock control.

first: Anna

middle: J

last: Peired

first: Paola

last: Romagnani


title: Identification of Host-derived Circular RNAs that Display Pro- and Anti-Viral Activities in Flavivirus-Infected Cells

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

type: Non-coding RNA profiling by high throughput sequencing

summary: Viruses subvert macromolecular pathways in the infected host to aid in viral gene amplification or to counteract innate immune responses. Recently, roles for host-encoded non-coding RNAs, such as microRNAs, have been found to encode pro- and anti-viral functions. One class of non-coding RNAs are circular RNAs that are generated by a nuclear back-splicing mechanism of pre-mRNAs. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circular RNAs were up-regulated or down-regulated in infected cells. Identified circular RNAs displayed both pro- and anti-viral effects.

overall_design: Total RNA sequencing analyses of Huh7 hepatoma cells that were either HCV-infected (triplicates) or mock-infected (9 replicates) for 48 hours.

first: Tzu-Chun

last: Chen

first: Marc

last: Talló-Parra

first: Sebastian

last: Kadener

first: René

last: Böttcher

first: Gemma

last: Pérez-Vilaró

first: Pakpoom

last: Boonchuen

first: Kunlaya

last: Somboonwiwat

first: Peter

last: Sarnow


title: Different effects of constitutive and induced microbiota modulation on microglia in a mouse model of Alzheimer’s disease

status: Public on Jul 15 2020

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: It was recently revealed that gut microbiota promote amyloid-beta (Aβ) burden in mouse models of Alzheimer’s disease (AD). However, the underlying mechanisms when using either germ-free (GF) housing conditions or treatments with antibiotics (ABX) remained unknown. In this study, we show that GF and ABX-treated 5x familial AD (5xFAD) mice developed attenuated hippocampal Aβ pathology and associated neuronal loss, and thereby delayed disease-related memory deficits. While Ab production remained unaffected in both GF and ABX-treated 5xFAD mice, we noticed in GF 5xFAD mice enhanced microglial Aβ uptake at early stages of the disease compared to ABX-treated 5xFAD mice. Furthermore, RNA-sequencing of hippocampal microglia from SPF, GF and ABX-treated 5xFAD mice revealed distinct microbiota-dependent gene expression profiles associated with phagocytosis and altered microglial activation states. Taken together, we observed that constitutive or induced microbiota modulation in 5xFAD mice differentially controls microglial Aβ clearance mechanisms preventing neurodegeneration and cognitive deficits.

first: Charlotte

last: Mezö

first: Nikolaos

last: Dokalis

first: Omar

last: Mossad

first: Jana

last: Neuber

first: Bahtiyar

last: Yilmaz

first: Daniel

last: Schnepf

first: Mercedes

last: Gomez de Agüero

first: Stephanie

middle: C

last: Ganal-Vonarbung

first: Andrew

last: Macpherson

first: Melanie

last: Meyer-Luehmann

last: Staeheli

first: Thomas

last: Blank

first: Marco

last: Prinz

last: Erny


title: Leptomeningeal metastatic cells outcompete macrophages for iron through Lipocalin-2

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

summary: The tumor microenvironment plays a critical regulatory role in cancer progression, especially in metastases to the central nervous system. Cancer cells inhabiting the cerebrospinal spinal fluid (CSF)-filled leptomeningeal space face substantial microenvironmental challenges including inflammation and sparse extracellular iron. Unlike CSF leukocytes, we find that cancer cells within the CSF express the iron-binding protein LCN2 and its receptor SCL22A17. Employing mouse models of LM, we find that the LCN2/SLC22A17 system is necessary to support leptomeningeal cancer cell growth. We find that infiltrating CSF macrophages generate inflammatory cytokines that induce cancer cell LCN2 expression. This LCN2/SLC22A17 system provides cancer cells superior access to limiting extracellular iron, allowing LCN2-expressing cancer cells to outcompete CSF macrophages for this resource. Finally, pharmacologic interruption of these interactions prevents cancer cell growth within the leptomeninges.

overall_design: Leptomeningeal metastatic cells were depleted for Lipocalin-2 with two lentiviral shRNAs or control shRNA and along with Parental cells subjected for transcriptomic analysis

first: Yudan

last: Chi

first: Adrienne

last: Boire


title: Immune dysfunction in intermediate hyperglycaemia and diabetes patients in tuberculosis

city: London

first: Clare

last: Eckold

state: London

address: 10 Logan Place

institute: (None)

summary: People living with diabetes have an increased risk of developing active tuberculosis. The effects of diabetes (HbA1c ≥6.5%) and intermediate hyperglycaemia (HbA1c 5.7-6.5%), on this transcriptomic signature were investigated by RNA-seq, to enhance understanding of immunological susceptibility in diabetes-tuberculosis comorbidity.Diabetes increased the magnitude of gene expression change in the host transcriptome in tuberculosis, characterised by an increase in innate, and decrease in adaptive immune responses.  Strikingly, patients with intermediate hyperglycaemia and tuberculosis exhibited blood transcriptomes much more similar to diabetes-tuberculosis patients than to uncomplicated tuberculosis patients. Aberrant transcriptomes unveil a susceptibility mechanism of DM patients to TB of enhanced inflammation and reduced interferon responses.

overall_design: Whole blood was collected from patients with TB-only, TB-DM, TB-IH, DM-only and healthy controls in  four field sites; South Africa, Peru, Romania and Indonesia. Total 249 patient samples

first: Jacqueline

last: Cliff

first: Hazel

last: Dockrell

first: Vinod

last: Kumar

first: Reinout

last: van Crevel


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT,cop1 and cor27cor28 mutant Transcriptomes

city: Shanghai

first: hongtao

last: LIU

address: #300 Fenglin Road

institute: CAS center for excellence in Molecular plant sciences

summary: Analysis of gene expression level. The hypothesis tested in the present study was that cor27cor28 mutant affects multiple genes expression which regulated by COP1

overall_design: mRNA profiles of 7 day old wild type (Col_0),cop1-6 and cor27cor28 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq Xten

first: Xu

last: Li

first: Hongtao

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and HY5 mutant Transcriptomes

summary: Analysis of gene expression level. The hypothesis tested in the present study was that hy5 mutant affects multiple genes expression which regulated by COR27 and COR28

overall_design: mRNA profiles of 7 day old wild type (Col_0) and hy5(hy5-215) mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq Xten


city: Dalian

first: Weifeng

last: Mao

address: 9 Lvshun South Rd,

institute: Dalian Medical University

summary: We perform RNA-seq in CH12F3 and Lig4-/- CH12F3 cells.   The results show the deficiency of Lig4 triggers RIG-I-like receptor,   NOD-like receptor, IL-17 signaling, Cytosolic DNA-sensing pathway,   and Toll-like receptor signaling pathways. As these pathways   play impotant roles in immune resposne, the RNA-seq results   suggest Lig4 may regulate the immune repsonse in CH12F3 cells.

overall_design: Perform RNA-seq of CH12F3 and Lig4-/- CH12F3 cells

first: Xingjie

last: Gao

first: Ying

last: Wang

first: Jingkai

last: Zhang


title: Single-cell sequencing of BALF reveals immune response of COV2019 infection

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

overall_design:
We analyzed the single-cell transcriptome expression profiles (scRNA-seq) for COVID-19 patient

NOTE: Raw data is not provided due to patient privacy.


title: RNA Seq analysis of Chlamydia trachomatis D serovar in axenic culture

first: Thomas

last: Rudel

summary:
Chlamydia trachomatis D serovar was grown in axenic culture with G6P or G6P with glutamine. The data reveal the
early transcriptonal regulation in the bacteria.

first: Karthika

last: Rajeeve

first: Apoorva

last: Baluapuri

first: Elmar

last: Wolf

first: Rajeeve

last: Sivadasan


title: Loss of function of the mitochondrial peptidase PITRM1 induces Alzheimer’s disease-like pathology and immune perturbations in human cerebral organoids

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

summary: Mutations in pitrilysin metallopeptidase 1 (PITRM1), a mitochondrial protease involved in mitochondrial precursor processing and degradation, result in a slow-progressing syndrome characterized by cerebellar ataxia, psychotic episodes, and obsessive behavior, as well as cognitive decline. To investigate the pathogenetic mechanisms of mitochondrial presequence processing, we employed cortical neurons and cerebral organoids generated from PITRM1 knockout human induced pluripotent stem cells (iPSCs). PITRM1 deficiency strongly induced mitochondrial unfolded protein response (UPRmt) and enhanced mitochondrial clearance in iPSC-derived neurons. Furthermore, we observed increased levels of amyloid precursor protein and amyloid β in PITRM1 knockout neurons. However, neither cell death nor protein aggregates were observed in 2D iPSC-derived cortical neuronal cultures. On the other hand, over time, cerebral organoids generated from PITRM1 knockout iPSCs spontaneously developed pathological features of Alzheimer's disease (AD), including the accumulation of protein aggregates, tau pathology, and neuronal cell death. Single-cell RNA sequencing revealed a perturbation of mitochondrial function in all cell types in PITRM1 knockout cerebral organoids, whereas immune transcriptional signatures were substantially dysregulated in astrocytes. Importantly, we provide evidence of a protective role of UPRmt and mitochondrial clearance against impaired mitochondrial presequence processing and proteotoxic stress. Here, we propose a novel concept of PITRM1-linked neurological syndrome whereby defects of mitochondrial presequence processing induce an early activation of UPRmt that, in turn, modulates cytosolic quality control pathways. Thus, our work supports a mechanistic link between mitochondrial function and common neurodegenerative proteinopathies.

overall_design: 4 human cerebral organoids generated from PITRM1-WT and PITRM1-KO iPSCs. For each condition, we prepared single-cell suspensions with a pool of 4 organoids each, all with similar sizes (Day 60).

first: Maria

last: Perez

first: Dina

last: Ivaniuk

first: Vasiliki

last: Panagiotakapoulou

first: Gabriele

last: Di Napoli

first: Stefanie

last: Kalb

first: Dario

last: Brunetti

first: Rawaa

last: Al-Shaana

first: Stephan

last: Kaeser

first: Sabine

last: Fraschka

first: Mathias

last: Jucker

first: Massimo

last: Zeviani

first: Carlo

last: Viscomi


title: Gene expression profiles of MIN6 cells treated with vehicle (PBS) or Maidong polysaccharide extract (MPE) for 3 days

city: Shatin

first: Ronald

last: Wang

address: Prince of Wales Hospital

department: Obstetrics & Gynaecology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: In this study, we investigated the role of MPE in pancreatic β-cell function. To examine whether MPE protects β-cell function and study the underlying mechanisms, we treated MIN6 β cells with MPE to explore changes in gene expressions in vitro by microarray analysis.

overall_design: MIN6 cells treated with either PBS or MPE for 3 days were analyzed.


title: BRAF inhibition in melanoma is associated with the dysregulation of histone methylation and histone methyltransferases

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Linker-mediated PCR for global integration site analysis in splenic human CD4-positive T cells of HIV1-GFP-infected humanized mice

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

summary: To comprehensively compare the HIV-1 integration sites between viral producing cells (GFP+ cells) and non-producing cells (GFP- cells), linker-mediated PCR is performed by using the samples obtained from HIV1-GFP-infected humanized mice. Additionally, to reactivate latently infected cells, viral non-producing cells (GFP- cells) were stimulated with PMA and ionomycin ex vivo. Then, the viral integration sites in potential latently infected cells (GFP-_GFP+ cells) and the cells with dead/inactivated proviruses (GFP-_GFP- cells) were analyzed by linker-mediated PCR.

overall_design: GFP+ cells (n=13) and GFP- cells (n=13) were sorted from the splenic human CD4-positive T cells of HIV1-GFP-infected humanized mice at 2 weeks post-infection. GFP- cells were stimulated with PMA and ionomycin ex vivo, and then GFP+ cells (GFP-_GFP+ cells; n=6) and GFP- cells (GFP-_GFP- cells; n=6) were sorted. By using these samples, linker-mediated PCR was performed to describe genome-wide HIV-1 integration sites.

first: Shumpei

last: Nagaoka

first: Jumpei

last: Ito

first: Benjy

last: Tan

first: Saiful

last: Islam

first: Yorifumi

last: Satou


title: Temporal transcriptomic analysis of human pancreatic exocrine cells in 3D suspension culture

status: Public on Jul 18 2020

city: Jette

first: Jonathan

last: Baldan

address: Laerbeeklaan 103

institute: Vrije Universiteit Brussel


title: Digital RNA-Seq for transcriptome analysis in splenic human CD4-positive T cells of mock-infected humanized mice and GFP-positive and GFP-negative CD4-positive cells of HIV1-GFP-infected humanized mice

summary: Transcriptome analysis of digital RNA-sequencing (dRNA-Seq) data reveals the differentially expressed genes between GFP-positive and GFP-negative cells.

overall_design: GFP-positive cells and GFP-negative cells were sorted from the splenic human CD4-positive T cells of HIV1-GFP-infected humanized mice (n=6) at 2 weeks post-infection. The splenic human CD4-positive T cells were also sorted from mock-infected mice (n=7). By using these samples, dRNA-Seq was performed to performe transcriptome analysis (3 technical replicates for 3 infected mice and 3 mock-infected mice; 1 technical replicate for 3 infected mice and 4 mock-infected mice).

first: Eiryo

last: Kawakami

first: Shinji

last: Nakaoka

first: Koichi

last: Ashizaki

first: Katsuyuki

last: Shiroguchi


title: Next Generation Sequencing of  human BRAF melanoma cell lines treated with vemurafenib for 20 days

summary:
Purpose: The goals of this study are to compare NGS-derived transciptomes from human melanoma cell lines before and after vemurafenib in order to compare to a mouse model of melanoma using doxycycline that permits control of mutant BRAF expression. Treatment with doxycycline leads to loss of mutant BRAF expression and tumor regression, but tumors reoccur after a prolonged period of dormancy.
Results: We found conserved expression changes in histone methyltransferase genes (HMT), including Enhancer Of Zeste 2 Polycomb Repressive Complex 2 Subunit (EZH2), Suppressor Of Variegation 3-9 Homolog 1(SUV39H1), Suppressor Of Variegation 3-9 Homolog 2 (SUV39H2), ASH2 Like, Histone Lysine Methyltransferase Complex Subunit (ASH2L), SET And MYND Domain Containing 2 (SYMD2), and Protein arginine methyltransferase 5 (PRMT5) and histone deacetylases (HDACs) HDACS 7, 9,10, and 11.

overall_design: human melanoma mRNA profiles before and afer 20 days of exposure to vemurafnib

middle: L

first: James

middle: P

last: Robinson


title: Migration arrest of chemoresistant leukemia cells mediated by MRTF-SRF pathway

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Dormant chemotherapy-resistant leukemia cells can survive for an extended period before relapse. Nevertheless, the mechanisms underlying the development of chemoresistance in vivo remain unclear. Using intravital bone imaging, we characterized the behavior of murine acute myeloid leukemia (AML) cells (C1498) in the bone marrow before and after chemotherapy with cytarabine. Proliferative C1498 cells exhibited high motility in the bone marrow. Cytarabine treatment impaired the motility of residual C1498 cells. However, C1498 cells regained their migration potential after relapse. RNA sequencing revealed that cytarabine treatment promoted MRTF-SRF pathway activation. MRTF inhibition using CCG-203971 augmented the anti-tumor effects of chemotherapy in our AML mouse model, as well as suppressed the migration of chemoresistant C1498 cells. These results provide novel insight into the role of cell migration arrest on the development of chemoresistance in AML, as well as provide a strong rationale for the modulation of cellular motility as a therapeutic target for refractory AML.

overall_design: We conducted RNA-seq experiment with three untreated and three cytarabine-treated mice 21 days after AML cell injection as triplicates.

first: Erika

last: Yamashita

first: Junichi

last: Kikuta


title: Tissue-Biased Expansion of DNMT3A-Mutant Clones Associated with Conserved Epigenetic Alterations

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

summary: DNA methyltransferase 3A (DNMT3A) is the most frequently mutated gene in clonal hematopoiesis (CH) and serves as a key tumor suppressor in the hematopoietic system. Somatic mutations in DNMT3A arise in hematopoietic stem and progenitor cells (HSPCs) many years before malignancies develop, but how they prime cells for transformation remains unknown, partly due to our inability to compare mutant to equivalent wild-type cells before frank disease. To overcome this challenge, we derived multiple normal and DNMT3A-mutant lymphoblastoid cell clones from a germ-line mosaic individual in whom these cells co-existed for nearly six decades. Although arising early in gestation, mutant cells dominated the blood, but not other tissues. Deep sequencing revealed similar mutational burdens and mutational signatures across normal and mutant clones. In contrast, epigenetic profiling uncovered focal erosion of DNA methylation at oncogenic regulatory regions in mutant clones. These regions overlapped with those sensitive to DNMT3A loss after DNMT3A ablation in HSPCs and with those present in leukemia samples. These results suggest that DNMT3A is responsible for maintaining a conserved DNA methylation pattern that is maintained for decades and across cell types and states. Erosion of this pattern confers a distinct competitive advantage, increasing the likelihood of malignant transformation

overall_design: Analysis of DNA methylation in human umbilical cord CD34+cells after KO of DNMT3A

first: Ayala

last: Tovy


title: Impact of human miR-887-3p on gene expression in human pulmonary microvascular endothelial cells

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: We report the results of RNA sequencing of total RNA isolated from human pulmonary microvascular endothelial cells after transfection with human miR-887-3p or a negative control siRNA, both in triplicate.

overall_design: Examination of HPMEC gene expression after exposure to miR-887-3p vs control.

first: Andrew

last: Goodwin

first: E

last: Hazard

first: Hongkuan

last: Fan

first: Pengfei

last: Li

first: Perry

last: Halushka


title: Genome-wide maps of chromatin state in rat IUGR islets at 2 time points

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

institute: Bioinformatics Core, IBI, UPen

summary: Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes in adulthood. A rat model of IUGR induced by bilateral uterine artery ligation at day 18 of gestation, which reduces the blood supply and critical substrates to the fetus, was used to assess the alterations of genome-wide histone modifications in IUGR islets. At 2 and 10 weeks of age, pancreatic islets were isolated and chromatins were extracted for ChIP-Seq study. Chromatin state of H3K4me3, H3K27me3, and H3K27Ac modifications was compared in the study.

overall_design: Examination of 3 different histone modifications in 2 experimental conditions (IUGR and Control) and 2 time points (2 and 10 weeks of age).

first: Yu

last: Lien

first: Rebecca

last: Simmons

middle: Z

first: Xueqing

last: Lu


title: Aurothioglucose Enhances Pro-Angiogenic Pathway Activation in Lungs from Room Air and Hyperoxia-exposed Newborn Mice

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: Acute neonatal muring hyperoxia exposure to evaluate the impact of the TXNRD1 inhibitor aurothioglucose on pulmonary response and gene expression.

overall_design: Day 0 Neonatal C57/Bl6 mice were intraperitoneally injected with 25 mg/kg of aurothioglucose or saline, followed by >95% oxygen exposure for 72hrs or room air.

first: Katelyn

last: Dunigan-Russell

first: Vivian

middle: Y

last: Lin

first: Mary

last: Silverberg

first: Stephanie

last: Wall

first: Rui

first: Anusha

last: Sridhara

first: Cassidy

last: Delany

first: Qian

first: Trent

middle: E

last: Tipple


title: Evaluation of Tmem184b dependent gene expression changes during sensory neuron differentiation in vitro

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

summary: Our objective was to evaluate the gene expression changes occuring in early sensory neuron development that were lost in the absence of Tmem184b and restored upon its reintroduction into mutant neurons in culture.

overall_design: Embryonic DRG neurons were cultured from wild type (4 mice) or from Tmem184b mutant mice (5 mice) with or without lentiviral restoration of Tmem184b. We collected RNA at Day 0 (day of culture) and day 14 (end of experiment). For mutant samples, neurons from each mouse were evaluated at Day 0, Day 14 without rescue, and Day 14 with rescue. Total RNA was extracted nad transcripts were evaluated using RNAseq.

first: Erik

last: Larsen


title: RNAseq measurement of cortisol induced gene expression change under knockout of Klf9

city: Bar Harbor

first: Joel

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

summary: We found that a frameshift deletion introduced into exon 1 of zebrafish klf9 eliminates the DNA binding domain and significantly reduces expression of the mature transcript. RNA-seq shows that klf9 is required for the pro-inflammatory transcriptomic effects of chronic cortisol treatment. klf9 is one of a core set of genes consistently found to be upregulated by chronic cortisol exposure.

overall_design: We used CRISPR-Cas9-mediated mutation of klf9 and RNA-seq to assess Klf9-dependent gene expression in both normal and cortisol-treated larvae.

first: Ian

last: Gans

first: Ellen

middle: I

last: Hartig

first: Shusen

last: Zhu

first: Andrea

last: Tilden

first: Lucie

last: Hutchins

first: Nathaniel

last: Maki

first: James

middle: A

last: Coffman


title: RNAseq measurement of cortisol induced gene expression change under knockout of glucocorticoid receptor (nr3c1)

middle: H

summary: We found that GR mediates most of the effects of the treatment, and paradoxically, that the transcriptome of cortisol-treated larvae is more like that of larvae lacking a GR than that of larvae with a GR, suggesting that the cortisol-treated larvae develop GR resistance.

overall_design: To assess the role of the Glucocorticoid Receptor (GR) in such programming, we used CRISPR-Cas9 to produce a new frameshift mutation, GR369-.


title: Autonomous neutrophil ageing in the lung governed by the pulmonary microbiome

city: Los Angeles

first: Eun-Cheon

last: Lim

state: California

address: 116 N. Robertson Blvd., Pacific Theatres Building.Suite 903

department: Surgery

institute: Cedars-Sinai Medical Center

summary: We used cellular indexing of transcriptomes and epitopes-based single cell RNA sequencing (CITE-scRNAseq) coupled with adoptive transfer approaches to determine tissue contribution to neutrophil diversity.

overall_design: Bone marrow, blood, liver and lung were isolated from WT mice. Cells were hashed, and DAPI-Ly6G cells were FACS sorted from these tissues. Cells were then processed (10X chromium)

first: E

first: Z

last: Peng

first: D

last: Cao

first: A

last: Victor

last: Bernstein

first: L

last: Veiras

first: J

middle: F

last: Giani

first: S

last: You

first: H

last: Koefler

first: X

last: Cui

middle: M

last: Underhill

first: K

last: Okwan-Duodu


title: Kynurenine engages Serotonin Receptor 1b in osteoblasts to reinforce Acute Myeloid Leukemia

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

summary: We performed RNAseq analysis of primary human osteoblasts co-cultured with the human THP-1 AML cell-line and, in parallel, RNAseq analysis on the THP-1 AML cells exposed to the human primary osteoblasts.

overall_design: 2 osteoblasts samples co-cultured with the human THP-1 AML cell-line were compared to 2 untreated osteoblasts samples to identify differentially expressed genes;  2 THP-1 AML samples exposed to the human primary osteoblasts were compared to 2 untreated THP-1 AML samples to identify differential expressed geens.

first: Stavroula

last: Kousteni

first: Junfei


title: miR-552-3p modulates transcriptional activities of FXR and LXR to meliorate hepatic glycolipid metabolism disorder

city: Shanghai

first: Jing

last: Chen

state: Shanghai

address: 501 Haike Road

department: Center for Drug Safety Evaluation and Research

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: According to our previous discovery that miR-552-3p could regulate the gene expression both in cytoplasm and nucleus. Furthermore, we found the sequence in miR-552-3p was similar with cis-elements of NR1 subfamily, the important regulator of glycolipid metabolism, suggesting miR-552-3p may play a pivotal role in metabolism.   To find the genes regulated by miR-5523-p, RNA-seq was used and the difference expression genes in HepG2 cells transfected with miR-552-3p or negative control was detected. Meanwhile, to found which genes are regulated by cytoplasmic miR-552-3p or nuclear miR-552-3p, importin8 expression was silenced by siRNA in the HepG2 cell and the effect of miR-552-3p on the genes expression was detected.   The results of this study are showed the genes regulated by miR-552-3p and distinguish which genes are regulated by the cytoplasmic miR-552-3p or nuclear miR-552-3p.

overall_design: The HepG2 cells was transfected with miR-552-3p mimics(1nM) or negative control(1nM), under condition with importin8 siRNA(30nM) or negative control(30nM). After 72h, the cell was lysed by trizol and the total RNA was extracted.Each group was given two experiments.

first: Lei

last: Fan

first: Jin

last: Ren


title: Environmental enrichment during abstinence from cocaine self-administration opposes gene network expression changes associated with the incubation effect

city: Tempe

first: Janet

middle: Leigh

last: Neisewander

address: 427 E. Tyler Mall Life Sciences E-Wing

department: School of Life Sciences

institute: Arizona State University

summary: Environmental enrichment (EE) is a robust intervention for reducing cocaine-seeking behaviors in animals when given during abstinence. However, the mechanisms that underlie these effects have not been well-established. We investigated the adult male rat transcriptome using RNA-sequencing (RNA-seq) following differential housing during abstinence from cocaine self-administration for either 1 or 21 days. Rats housed for 21 days of abstinence in EE displayed a significant reduction in cocaine-seeking behavior compared to rats housed in isolation. RNA-seq of the nucleus accumbens shell revealed hundreds of differentially regulated transcripts between rats of different abstinence length and housing environment, as well as within specific contrasts such as enrichment (isolated 21 days vs. enriched 21 days) or incubation (isolated 1 day vs. isolated 21 days). Ingenuity Pathway Analysis affirmed several pathways as differentially enriched based on housing condition and abstinence length including RELN, the Eif2 signaling pathway, synaptogenesis and neurogenesis pathways. Additionally, multiple pathways reversed their directionality between enrichment and incubation contrasts, potentially indicating oppositional roles across housing and abstinence length. Together, these findings reveal novel mechanisms potentially involved in the protective effects of EE against cocaine seeking, which may inform efforts to develop new pharmacological and gene therapies for treating cocaine use disorders.

overall_design: 12 samples from cocaine self-administering adult male rats. Following self-administration, animals were placed into abstinence for 1 or 21 days in either isolation or enriched environment (n=3/group). Following abstinence, animals experienced a 1-hr cue reactivity test and were immediately euthanized and brain tissue extracted. RNA-seq analysis was performed on nucleus accumbens shell.

first: Gregory

last: Powell

first: Annika

last: Vannan

first: Ryan

last: Bastle

first: Melissa

last: Wilson

first: Michela

last: Dell'Orco

first: Nora

last: Perrone-Bizzozero


title: Next Generation Sequencing of  mouse melanoma tumors generated with a repressible  BRAF construct

first: Aaron

last: Sarver

summary:
Purpose: The goals of this study are to compare NGS-derived transciptomes from engineered mouse tumors with activated BRAF (primary), repressed BRAF (simulating drug treatment- dormant) and tumors which escape dormant state (recurrent)
Results: We found conserved expression changes in histone methyltransferase genes (HMT), including Enhancer Of Zeste 2 Polycomb Repressive Complex 2 Subunit (EZH2), Suppressor Of Variegation 3-9 Homolog 1(SUV39H1), Suppressor Of Variegation 3-9 Homolog 2 (SUV39H2), ASH2 Like, Histone Lysine Methyltransferase Complex Subunit (ASH2L), SET And MYND Domain Containing 2 (SYMD2), and Protein arginine methyltransferase 5 (PRMT5) and histone deacetylases (HDACs) HDACS 7, 9,10, and 11.

overall_design: Genetically Engineered mouse was designed to    grow BRAFV600E dependent primary melanomas.  BRAFV600 construct was    designed so that it could be turned off resulting in tumor dormancy.  After    a period of time the tumors escaped the dormant state and began to grow    again generating recurrent tumors.

first: James

last: Robinson


title: Genome-wide analysis of gene expression in white adipose tissue in angiotensinogen overexpression transgenic and wild type male B6 mice

city: Lubbock

first: Naima

last: Moustaid-Moussa

address: 1301 Akron Street

department: Nutritional Sciences & Obesity Research Institute

institute: Texas Tech University

summary: Investigation of differential gene regulation with overexpression of angiotensinogen in white adipose tissue. We hypothesized that angiotensinogen overexpression will disrupt metabolic homeostasis of adipocytes leading to obesity and related chronic diseases. Results indicate that angiotensinogen overexpression differentially regulate genes related metabolic functions in adipose tissue.

overall_design: Total RNA was obtained from white adipose tissue from wild type and transgenic mice where angiotensinogen was specifically overexpressed in the adipose tissue.


title: Inter-individual variability in lymphocyte stimulation and transcriptomic response predicts mycophenolic acid sensitivity in healthy volunteers

city: Indianapolis

first: Kimberly

middle: S.

last: Collins

state: IN

address: 950 W Walnut Street E202

institute: Indiana University School of Medicine

summary: Mycophenolic acid is an immunosuppressant commonly used to prevent renal transplant rejection and treat glomerulonephritis. Despite its widespread use, there is a clinical need to reduce solid-organ transplant rejection and improve rates of complete therapeutic response in autoimmunity. Single-cell RNA-sequencing (n=6) in lymphocytes was performed at baseline, post-stimulation, and post-mycophenolate treatment. This study identifies a polygenic transcriptomic signature in lymphocyte sub-populations predictive of mycophenolate response.

overall_design: Lymphocytes were sequenced at baseline (after Ficoll Isolation), post-stimulation (antibodies to CD3/CD28), and post-MPA treatment (1 µg/mL).

first: Michael

last: Eadon


title: Role of microRNAs in Mediating Angiotensin II Effects on Inflammation and ER stress

summary: We aim to identify the role of Renin Angiotensin pathway by identifying novel genes and microRNAs altered by overexpressing angiotensiogen specifcally in the adipose tissue

overall_design: We used mice model where angiotensiongen was specifically was altered in adipose tissue using ap2 promoter as previously described in Massiera F, Bloch-Faure M, Ceiler D, et al. . FASEB J. 2001; 15:2727–2729


title: Hypoxanthine phosphoribosyl transferase 1 is upregulated, predicts clinical outcome and controls gene expression in breast cancer

city: El Paso

first: Shrikanth

last: Gadad

address: 5001 El Paso Drive

department: Department of Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center El Paso

summary: Hypoxanthine phosphoribosyl transferase 1 (HPRT1) is traditionally believed to be a housekeeping gene; however, recent reports suggest that it is upregulated in several cancers and associates with clinical outcome. Like several cancer testis (CT) genes, HPRT1 is found on chromosome X, and encodes the HPRT enzyme, which functions in recycling nucleotides to supply for DNA and RNA synthesis in actively dividing cells. Here, we have used genome wide expression to interrogate its expression across all known cancer types and elucidated its functional role in breast cancer. We observed elevated HPRT1 RNA levels in malignant tissues when compared to normal controls, indicating its potential as a diagnostic and prognostic marker. Further, in breast cancer, subtype specific analysis showed that its expression was highest in basal and triple-negative breast cancer, and HPRT1 knockdown in breast cancer cells suggested that HPRT1 positively regulates genes specific to cellular and DNA repair pathways. Collectively, our results essentially highlight the importance and change the way HPRT1’s function is studied in biology, and warrants careful examination of its role in cancer.

overall_design: HPRT1 was knocked down using two distinct siRNA oligos in three cell lines, MCF-10A (immortalized mammary epithelium), MCF-7 (Estrogen receptor positive breast cancer cell line), MDA-MB-231 (Estrogen receptor, progesterone receptor and HER2 negative breast cancer cell line)

middle: S


title: Cross validated serum exosomal microRNAs for the detection of oropharyngeal squamous cell carcinoma

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

summary:
Exosomes were purified from 250 ul serum using ExoQuickTm. The presence of particles consistent in size with exosomes (60-150nm) was confirmed using a Nanosight LM10.   miRNA was extracted from exosomes  using an miRNeasy Serum/Plasma kit (Qiagen, #217184). miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a custom high throughput TaqMan® OpenArray® Human microRNA panel  (Life technologies). The panel consisted of probes for 110 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v20.
The poor prognosis and rising incidence of HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) highlight the need for improved methods for detection of this cancer. Molecular biomarkers offer potential for this. The potential for circulating miRNAs as biomarkers in some other cancers has been shown, but circulating miRNAs have not been well validated in OPSCC. This study therefore used stabilised nested cross validation to investigate whether circulating miRNAs could be used to differentiate OPSCCs from healthy controls and patients with gastro-oesophageal reflux disease.

overall_design: OpenArray high throughput real time PCR of microRNAs -- 19 patients healthy patients, 20 patients with gastro-oesophageal reflux disease (GORD) and without cancer, 19 patients with  locally advanced HPV-positive oropharyngeal squamous cell carcinoma (OPSCC)

first: George

last: Mayne

first: Charmaine

last: Woods

first: Nuwan

last: Dharmawardana

first: Tingting

last: Wang

first: S

last: Krishnan

first: J

last: Hodge

first: A

last: Foreman

last: Boase

last: Carney

first: David

last: Watson

first: Eng

last: Ooi

middle: J


title: IPSC-derived neuronal cultures expressing the Alzheimer's disease associated rare TREM2 R47H variant enables the construction of an Aβ-induced gene regulatory network

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: Recently, genes associated with immune response and inflammation have been identified as genetic risk factors for late-onset Alzheimer's disease (LOAD). One of them is the rare p.Arg47His (R47H) variant within triggering receptor expressed on myeloid cells 2 (TREM2), which has been shown to increase the risk for developing AD 2-3-fold. Here, we report the generation and characterization of a model of LOAD using lymphoblast-derived iPSCs from patients harbouring the R47H mutation in TREM2 (AD TREM2 iPSCs), as well as from control individuals without dementia (CON iPSCs). iPSCs efficiently differentiate into mature neuronal cultures and comparative global transcriptome analysis identified a distinct gene expression profile in AD TREM2 neuronal cultures. Furthermore, manipulation of the iPSCderived functional neuronal cultures with an Aβ-S8C dimer highlighted metabolic pathways, phagosome and immune response as the most perturbed pathways in AD TREM2 neuronal cultures. Through the construction of an Aβ-induced gene regulatory network, we were able to identify an Aβ signature linked to protein processing in the endoplasmic reticulum (ER) which emphasised ER-stress, as a potential causal role in LOAD. Overall, this study has shown that our AD-iPSC based model can be used for in-depth studies to better understand the molecular mechanisms underlying the etiology of LOAD and provides new opportunities for screening of potential therapeutic targets.

overall_design: The transcriptomes of human iPSC-derived neuronal cultures were compared between Aß-S8C dimer stimulation and control condition by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Wruck

last: Wasco

first: Martins

last: Soraia

first: Bohndorf

last: Martina

first: Adjaye

last: James


title: Deciphering molecular mechanisms of MEIS1-mediated prostate tumor suppression through RNAseq and ChIPseq - ChIPseq data

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S Wolcott Ave., RM5051

department: Pathology

institute: University of Illinois at Chicago

summary: In order to identify direct gene targets and pathways regulated by MEIS1 in prostate cells and identify mechanisms of observed tumor suppression with MEIS1 expression, we performed Chromatin Immunoprecipitation and sequencing (ChIP-seq) of MEIS1 in the CWR22Rv1-LV-MEIS1 line. Also, given the dependence of HOXB13, and to enable determination of HOXB13-dependent vs. HOXB13-independent MEIS1 DNA binding, we performed parallel MEIS1 ChIP-seq in the CWR22Rv1-HOXB13ko-LV-MEIS1 line.  LV-MEIS1 denotes cells with exogenous lentiviral expression of MEIS1, and they still express endogenous HOXB13. Knockout of HOXB13 was achieved by CRISPR and validated with western blotting. HOXB13ko-LV-MEIS1 denotes cells where the same lentiviral expression of MEIS1 was infected into the HOXB13ko cells, so these cells are positive for MEIS1 expression and negative for HOXB13.

overall_design: MEIS1 immunoprecipitation was performed in triplicate for the LV-MEIS1 condition and was performed in duplicate for the HOXB13ko-LV-MEIS1 condition. Non-immunoprecipitated DNA was used as an input DNA control when calling peaks. Replicates in each condition were pooled using MACS2 to call peaks against the input DNA control.

first: Calvin

last: VanOpstall


title: Comprehensive transposon insertion sequencing screen in Francisella tularensis LVS

city: Boston

first: Simon

middle: L

last: Dove

state: MA

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

summary: We used transposon insertion sequencing (Tn-Seq) to identify the genes that are required for in vitro growth and intramacrophage growth of the live vaccine strain of F. tularensis (LVS).

sample_organism: Francisella tularensis subsp. holarctica LVS

overall_design: Illumina sequencing was used to identify the location of transposon insertions by sequencing transposon-genomic DNA junctions. Included are 3 samples from transposon libraries grown on solid media, 1 sample from the transposon library grown in liquid media, and one sample from the transposon library after 24 hours of growth in murine-macrophage-like cells

first: Kathryn

last: Ramsey


title: RNA sequencing of healthy and diseased (idiopathic pulmonary hypertension) human pulmonary artery smooth muscle cells

city: La Jolla

first: Paul

last: Insel

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: UC San Diego

summary: We performed RNA-seq to analyze gene expression in human PASMCs (Pulmonary arterial smooth muscle cells) isolated from subjects without disease and from subjects with IPAH (idiopathic pulmonary hypertension)

overall_design: Four biological replicates each in two groups a) Healthy subjects b) IPAH patients

first: Matthew

middle: W

last: Gorr

first: Krishna

last: Sriram


title: Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: While the cerebral cortex is organized into six excitatory neuronal layers, it is unclear whether glial cells show distinct layering. Here, we developed a high-content pipeline, the Large-area Spatial Transcriptomic (LaST) map, which can quantify single-cell gene expression in situ. Screening 46 candidate genes for astrocyte diversity across the mouse cortex, we identified superficial, mid, and deep astrocyte identities in gradient layer patterns that were distinct from those of neurons. Astrocyte layer features, established in early postnatal cortex, mostly persisted in adult mouse and human cortex. Single cell RNA sequencing and spatial reconstruction analysis further confirmed the presence of astrocyte layers in the adult cortex.  Satb2 and Reeler mutations that shifted neuronal post-mitotic development were sufficient to alter glial layering, indicating an instructive role for neuronal cues. Finally, astrocyte layer patterns diverged between mouse cortical regions. These findings indicate that excitatory neurons and astrocytes are organized into distinct lineage-associated laminae.

overall_design: Gene expression analysis of purified astrocyte, non-astrocyte and bulk tissue from manually dissected upper and deep layers of the mouse cerebral cortex using RNA-sequencing. Astrocytes were purified from 14 day old transgenic animals harboring the Aldh1l1-GFP reporter via flow cytometry.

first: Omer

last: Bayraktar

first: Giovanni

last: Coppola

last: Rowitch


title: The effect of PLK1 inhibitor BI6727 on transcriptomic profile of Transforming Growth Factor β 1 (TGFB1) -mediated gene expression in mouse myofibroblast

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

summary: To determine the underlying mechanisms of PLK1 inhibitor BI6727 alleviating TGFB1-induced the differentiation of myofibroblast, we performed RNA-seq to define the global gene expression of embryonic mouse fibroblast (NIH/3T3 cell line) that treated with BI6727 or vehicle (DMSO) with or without TGFB1 stimulation.

overall_design: We designed the experiment to three groups. In Group A, NIH/3T3 was resuspended in DMEM complete medium and cultured at 37℃ as the control. In group B, TGFB1 (1ng/ml) was added additionally. In Group C, TGFB1 (1ng/ml) and BI6727 (5μM) was added additionally. Each group has two replicates. 72 hours later, cells were collected after PBS washing for extraction of total RNA.

first: Jizhang

last: Yu

first: Heng

last: Xu


title: Expression data of PRDM14 overexpression in WT, Suz12 KO and Ctbp1/2 DKO ESCs

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

institute: Kwansei Gakuin University

summary: The pluripotency-associated transcriptional network is regulated by a core circuitry of transcription factors. The PR domain-containing protein, PRDM14, maintains pluripotency by  activating and repressing transcription in a target gene-dependent manner. However, the mechanisms underlying dichotomic switching of PRDM14-mediated transcriptional control remains elusive. Here, we identified C-terminal binding protein 1/2 (CtBP1/2) as components of the PRDM14-mediated repressive complex. CtBP1/2 binding to PRDM14 depends on CBFA2T2, a core component of the PRDM14 complex. The loss of Ctbp1/2 impaired the PRDM14-mediated transcriptional repression required for pluripotency maintenance and primed to naïve pluripotency transition. Furthermore, CtBP1/2 also interacted with the PRC2 complexes, and the loss of Ctbp1/2 impaired the PRC2 and H3K27me3 enrichment at the target genes upon PRDM14 overexpression. These results suggest that evidence that the target gene-dependent transcriptional activity of PRDM14 is regulated by partner switching to ensure transition from primed to naïve pluripotency.

overall_design: We anlalyzed 8 samples on two strip of microarray detected by GeneAtlas.


title: Effects of SPOP mutation in DU145 cells

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

summary: We aimed at analyzing the transcriptome changes associated with SPOP mutation in DU145 cells

overall_design: Trascriptome of DU145 cells upon SPOP mutation using pMCV6-Entry expressing vectors were compared to wild type SPOP cells. Experiments were conducted in triplicate

first: Rihan

last: El Bezawy


title: RNA sequencing of mouse glomerular endothelial cells and implications of their heterogeneity in Alport syndrome

first: Brendan

last: Grubbs

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary:
Background: Recent transcriptomic studies of total glomerular and isolated glomerular endothelial cells (GEC) provide much needed insight into the potential associations between expression of specific genes and dysfunctional endothelium in the development of diabetic kidney disease. Similarly, many studies on Alport syndrome (AS) mice, including our own, suggest that damage to GEC can contribute to disease progression. However, the underlying cellular and molecular pathways and associated transcriptional identity of the cells remain either limited or non-existent.
Methods: We used a model of endothelial-specific tdTomato reporter mouse for the feasibility of isolating the GEC from kidneys of WT and AS mice. To generate a snapshot of GEC specific transcriptional profiles and to elucidate gene expression changes in AS, we performed transcriptome-wide RNA-seq analysis of GEC from AS-TektdT mice and control WT-TektdT mice at 4-month of age.
Results: We identified two subpopulations of GEC (dimtdT and brighttdT) based on the fluorescence intensity of the TektdT signal. Gene expression analysis showed vast heterogeneity in the two subpopulations, including in the expression of endothelial specific genes. In AS, dimtdT and brighttdT GEC had remarkably heterogeneous profiles in matrix associated genes (Svep1, Itgβ6), metabolic activity (ApoM, Pgc1α) and immune modulation (Apelin, Icam1) compared to WT. Additionally, we confirmed the expression data of these genes in biopsy samples from AS and FSGS patients.
Conclusions: Our findings suggest the presence of two subpopulations of GEC that develop distinct responses in metabolic and inflammatory immune activity in AS. In depth understanding of the pathologic role of GEC in the progression of AS could lead to novel targets for intervention.

overall_design: Gene expression profiles of glomerular endothelial cells derived from wild type and Alport syndrome mice at 4 month of age were generated by RNA sequencing.

first: Hasmik

last: Soloyan

last: Thornton

first: Valentina

last: Villani

first: Georgina

last: Gyarmati

first: Patrick

last: Khatchadourian

first: Janos

last: Peti-Peterdi

first: Roger

last: De Filippo

first: Laura

last: Perin

first: Sargis

last: Sedrakyan


title: Expression data of murine dermal macrophages

city: Freiburg

first: Aaron

last: Forde

address: Breisacher Str. 115

institute: Medical Center University of Freiburg

summary:
Dermal macrophages were sorted from the ears of CCR2-/- mice that were uninfected, injected with PBS or injected with S.aureus strain Newmann
107 CFU/ml live S. aureus was injecetd in 10µl PBS.

overall_design: Dermal macrophages were sorted 3 weeks after the injection of PBS or S.aureus. We aimed to dertermine long lasting changes in gene expression in tissue resident dermal macrophages as a result of infection with S.aureus

first: Reinhild

last: Feuerstein


title: RNA sequencing of mammary tumors induced in MTB-IGFIR transgenic mice fed 20% ISP, 1% ISP, or 20% Casein

city: Guelph

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

summary: Epidemiologic studies demonstrate that women from cultures that consume high levels of dietary soy have reduced breast cancer rates compared to women from cultures where soy consumption is typically much lower. The types of soy products consumed can also differ with Asian cultures consuming primarily minimally refined soy products while Western cultures often consume more highly refined soy products such as isolated soy protein (ISP). Our previous work showed that lifetime exposure to a diet containing 20% ISP promoted mammary tumor development in MTB-IGFIR transgenic mice. In this study, lifetime exposure to lower levels of ISP were evaluated (5% ISP and 1% ISP) to determine whether more moderate levels of ISP could protect against mammary tumorigenesis.  A standard rodent diet, Teklad 2018 was also included in this study and Teklad 2018 contains a less refined form of soy, namely soybean meal. MTB-IGFIR mice fed ISP diets, independent of the concentration, displayed increased mammary tumor incidence and reduced tumor latency compared to MTB-IGFIR mice fed a 20% casein diet. Unexpectedly, MTB-IGFIR mice fed Teklad 2018 were completely protected against mammary tumor development. Although RNA sequencing of mammary tumors from ISP or casein fed mice did not identified gene expression patterns associated with the ISP diets, the ISP diets consistently promoted the expression of contractile related proteins in pubertal mammary glands. Therefore, lifetime exposure to ISP may alter gene expression in pubertal mammary glands rendering them more susceptible to transformation. Based on these findings women may want to avoid highly refined soy products such as ISP and switch to less refined forms of dietary soy until additional studies can be performed.

overall_design: Mice were exposed to 20% isolated soy protein (ISP), 1% ISP, 20% casein or Teklad 2018 throughout embryonic and postnatal development (lifetime exposure). For mice fed the Teklad 2018 diet, mammary glands were collected at postnatal day (PND100), lymph node removed, and RNA extracted prior to sending for RNA sequencing. For MTB-IGFIR mice fed the 20% ISP, 1% ISP or 20% casein diets, mice were switched to the appropriate diet containing 100mg/kg of doxycycline at PND100. Mammary tumors were collected when the tumors reached approximately 10% of the mouse's body weight. RNA was extracted and sent to Genome Quebec for RNA sequencing


title: Deciphering molecular mechanisms of MEIS1-mediated prostate tumor suppression through RNAseq and ChIPseq

first: Donald

last: Vander Griend

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

overall_design: Refer to individual Series


title: RNA sequencing of pubertal mammary glands and mammary tumors from MTB-IGFIR transgenic mice fed diets containing different levels of isolated soy protein


title: Effect of ionizing radiation on transcriptome during neural differentiation of hESC

city: Bethesda

first: Igor

last: Panyutin

state: MD

address: 10 Center DR., room 1C401

department: Radiology Imaging Sciences

institute: NIH/CC

summary:
Differentiation of hESCs to neural lineages was used as a model for early embryonic brain development in order to assess the effect of their exposure to low (17 mGy) and high (572 mGy) doses of radiation on gene expression.
Exposure of hESC to the low dose did not result in changes in gene expression at any of the time points, whereas exposure to the high dose resulted in downregulation of some major neurodifferentiation markers on days 6 and 10. Gene ontology analysis showed that pathways related to nervous system development, neurogenesis, and generation of neurons were among the most affected.
Conclusion: exposure to a low dose of 17 mGy was well tolerated by hESCs while exposure to 572 mGy significantly affected their genetic reprogramming into neuronal lineages.

overall_design: Transcriptomes were assessed by RNA sequencing during neural differentiation at three time points in control and irradiated samples in three biological replicates. The first time point was when the cells were still pluripotent (day 0), the second time point was during the stage of embryoid body formation (day 6), and the last time point was during the stage of neural rosette formation (day 10).


title: Establishment of patient-derived tumor xenografts from Asian gastric adenocarcinoma is characterized by clonal selection and bias in molecular subtypes

first: Vincent

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

institute: 4HF Biotec

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


title: A model of molecular characteristics to classify WHO Grade III glioma patients

city: Beijing

first: tao

middle: bo

last: zhang

address: No. 17 South Panjiayuan, Chaoyang District

institute: Cancer Hospital

summary: Combing WHO classification and molecular characteristics to analysis gliomas more and more important. But Grade III glioma samples have a big difference within the group had not been reported as far as we know. In this study, we proposed a model to evaluate diagnosis and prognosis of Grade III glioma patients, and two independent datasets indicated that the model has a good predictive ability. Therefore, this strategy provides a new method to assist diagnosis and treatment of Grade III glioma patients.

overall_design: There are 225 samples. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray.

first: Botao

last: Zhang

first: Shujun

last: Cheng

first: Lin

last: Feng


title: Whole genome bisulfite sequencing data of Russian wheat aphid biotypes SA1 and SAM

city: Stellenbosch

first: Pieter

middle: Herodus

last: du Preez

state: Western Cape

address: LAB239, JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

summary:
The aim for this study was to compare the differences in the methylome of 2 Russian wheat aphid biotypes that are genealogically linked, but at opposite ends of the virulence scale. We studied genic as well as intergenic methylation in all three available contexts in the Bismark pipeline, CpG, CHG and CHH. We were also interested to see how methylation patterns in the Russian wheat aphid compares to that of other investigated insects. Specifically the ratio of genic to intergenic methylation and to what extent contexts other than CpG are methylated.

Grant number: CPR20110615000019459
Funding body: National Science Foundation ZA
Grantholders name: Anna-Maria Botha-Oberholster

overall_design: Comparing the methylation from 3 pooled sample (100 aphids) each of two Russian wheat aphid biotypes

first: N

last: Burger

first: Anna-Maria

last: Botha-Oberholster


title: The impact of YTHDF2 knockout on the distribution of 5-methylcytosine in RNA

city: Riverside

first: Weifeng

last: Gu

address: 900 University Ave

department: Molecular, Cell and Systems Biology

institute: University of California at Riverside

summary: 5-methylcytosine is an important epigenetic modification found in both DNA and RNA. Transcriptome-wide mapping of 5-methylcytosine revealed that, after CRISPR-Cas9-mediated knockout of YTHDF2 gene, 545 sites displayed significant changes in 5-methylcytosine levels, with the majority of 5-methylcytosine sites in ribosomal RNA exhibiting substantially increased levels of methylation. Our data demonstrateda broader role of YTHDF2 in the post-transcriptional regulation of RNA.

overall_design: Combine RNA bisulfite conversion with next-generation sequencing to monitor the variation of 5-methylcytosine in the transcriptome of HEK293T and isogenic cells with YTHDF2 gene being knocked out.

first: Xiaoxia

last: Dai

last: Li

first: Jie

first: Changjun

last: You

first: Gwendolyn

last: Gonzalez

first: Weili

last: Miao

first: Junchi

last: Hu

first: Lijuan

last: Fu

first: Yanhui

last: Xu

first: Yingsheng

last: Wang


title: Next generation sequencing identifies circulating microRNAs in cardiac arrest patients

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: The goal of this study is to identify circulating microRNAs with prognostic value in a large cohort of comatose survivors of out-of-hospital cardiac arrest. We performed RNA-Seq for short RNAs in plasma, collected 48 hours after return of spontaneous circulation, of 50 cardiac arrest patients including 25 good neurological outcome at 6 months (cerebral performance category 1) and 25 poor neurological outcome including death at 6 months (cerebral performance category score 5). The sequencing generated on average 18.5 million reads per sample. After mapping the reads and counting to relevant entries in miRBase 20, we found 236 microRNAs detected in all 50 samples with TPM above or equals to 1. 11 microRNAs were differentially expressed between 2 groups with False Discovery Rate (FDR) < 5%.

overall_design: Plasma microRNA profiles of 50 cardiac arrest patients, including 25 good neurological outcome (cerebral performance category score 1, CPC1) and 25 bad neurological outcome (cerebral performance category score 5, CPC5) at 6 months.

first: Antonio

last: Salgado-Somoza

first: Lu


title: Deciphering molecular mechanisms of MEIS1-mediated prostate tumor suppression through RNAseq and ChIPseq - RNAseq data

first: Donald

last: Vander Griend

summary: We conducted RNA-sequencing to determine MEIS1-mediated gene regulation in prostate cancer cells because phenotypic data has demonstrated that expression of MEIS1 is sufficient to slow tumor growth and metastatic colonization in vitro and in vivo.  These analyses compared global gene expression of CWR22Rv1-Control and CWR22Rv1-LV-MEIS1, as well as the HOXB13ko and HOXB13ko-LV-MEIS1 cells to precisely delineate MEIS1 and HOXB13-regulated genes.  Importantly, inclusion of HOXB13ko lines enabled determination of HOXB13-associated gene regulation, as well as identification of significant changes between LV-MEIS1 vs. Control that are HOXB13-independent and thus unrelated to tumor suppression. Are samples are from CWR-22Rv1 cells. Control denotes cells with constitutive expression of Cas9, but with no gRNA provided. Control cells have nearly undetectable levels of endogenous MEIS1 expression, but do express HOXB13. LV-MEIS1 denotes cells with exogenous lentiviral expression of MEIS1, and they still express endogenous HOXB13. HOXB13ko denotes cells where HOXB13 was knocked out using CRISPR, 6 cell clones were isolated with confirmed HOXB13 knockout by western blot and pooled together into one line, so these cells lack both MEIS1 and HOXB13. HOXB13ko-LV-MEIS1 denotes cells where the same lentiviral expression of MEIS1 was infected into the HOXB13ko cell pool, so these cells are positive for MEIS1 expression and negative for HOXB13.

overall_design: mRNA from all four cell line derivatives (Control, LV-MEIS1, HOXB13ko, and HOXB13ko-LV-MEIS1) was sequenced in triplicate

first: Calvin

last: VanOpstall


title: STAP-1 is Required for Maintenance of Leukemic Stem Cells in Chronic Myeloid Leukemia.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The family of signal transduction adapter proteins (STAPs) has been reported to be involved in a variety of intracellular signaling and transcriptional molecules. We originally cloned STAP-2 as a c-fms interacting protein and found the effects on chronic myeloid leukemia (CML) leukemogenesis. STAP-2 binds to BCR-ABL, up-regulates BCR-ABL phosphorylation and activates its downstream molecules. In this study, we evaluated the role of STAP-1, another member of the family, in CML pathogenesis. The expression of human STAP-1 is aberrantly upregulated in CML stem cells (LSCs) in patient bone marrow. Using experimental model mice, we revealed that deletion of STAP-1 prolonged survival of CML mice with the induced apoptosis of LSCs. The impaired phosphorylated status of STAT5 by STAP-1 ablation results in downregulation of anti-apoptotic genes, BCL-2 and BCL-xL. Interestingly, transcriptome analyses indicate that STAP-1 affects several signaling pathways related to BCR-ABL, JAK2 as well as PPARγ. This adaptor protein directly binds not only BCR-ABL, also STAT5 proteins, showing synergistic effects of STAP-1 inhibition on the treatment with BCR-ABL or JAK2 tyrosine kinase inhibitor. It is known that the inhibition of BCR-ABL alone cannot eliminate CML LSCs. Our results have identified STAP-1 as a regulator of CML LSCs and support the evidence as a novel therapeutic target for CML cure.

overall_design: To gain further understanding of effects of STAP-1, we performed a gene expression analysis using RNA-sequence (RNA-seq), using WT and STAP-1 KO CML LSCs. Putative differentially expressed genes generated by RNA-seq were identified (2 fold change cut-off).

first: Jun

last: Toda


title: Expression data from 27 Asian gastric patient-derived xenograft (PDX) models

first: Vincent

last: Vuaroqueaux

summary: There is a strong need to develop patient-derived xenograft (PDX) tumor models for studying new treatment options for gastric cancer (GC). With low engraftment success, few collections of GC PDX have been reported and molecular basis of the model establishment remain largely unknown.   Here we established n=27 PDX models from n=100 GC tumors and compared their characteristics to GC patient tumors based on the recent work done by ACRG and TCGA, to evaluate the representativeness and relevance of the collection for drug testing.   We show that MSI, CIN and MSS/TP53- tumors were preferentially established as PDX, while MSS/EMT and EBV not and that PDX models retained histology and molecular subtypes of parental tumors. By using synapse database, we identified 48 druggable alterations that could be investigated with the collection. Counting alterations for these 48 genes in PDX compared to TCGA tumors revealed models frequently classified with heavily altered tumors but well preserved genomic alteration patterns specific of each GC subtype.  The molecular analysis of n=8/27 tumors and corresponding PDX at passage P1, P2 and P3 revealed variations in somatic alteration content both at single nucleotide and chromosomal level in highly unstable MSI and CIN tumors, with changes occurring mainly at P1. In two cases, we show likely emergence of rare subclones carrying known oncogenic alterations in KRAS and PIK3CA.   Significance. This study presents a resource of fully annotated GC PDX models for anticancer agent testing. We show that beside close resemblance of PDX with parental tumors, not all subtypes are established, and that the clonal selection plays a key role the establishment of certain tumors. This may have a bearing on translation of observations into the clinic and underline the need to frequently survey the molecular characteristics of the PDX models.

overall_design: total RNA samples were extracted from 4 tumor samples per patient-derived xenograft model using the mirVana kit (Ambio) following the manufacturer's recommendations. After standard quality controls RNA were subjected to Affymetrix HGU133 Plus2.0 microarray hibridization.

first: Anne-Lise

last: Peille

first: Swee-Seong

last: Wong

first: Jason

last: Ting

first: Kerstin

last: Klinger

first: Bruno

last: Zeitouni

first: Manuel

last: Landesfeind

first: Woo

last: Kim

first: Hyuk-Joon

last: Lee

first: Seong-Ho

last: Kong

first: Isabella

last: Wulur

first: Steven

last: Bray

first: Peter

last: Bronsert

first: Nina

last: Zanella

first: Greg

last: Donoho

first: Han-Kwang

last: Yang

first: Heinz-Herbert

last: Fiebig

first: Christoph

last: Reinhard

first: Amit

last: Aggarwal


title: Transcriptome profiling of wildtype C57BL/6 mouse with metformin treatment

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

institute: Peking University

summary:
Background: Metformin, one of the first-line medication for the treatment of type 2 diabetes and gestational diabetes, has recently be suggested for targeting cardiovascular disease, cancer and aging. Therefore, current understanding of the mechanism of this drug is incompletely understood, and the function of multiple tissues, other than liver metabolism alone, may be influenced.
Methods: The wildtype healthy mice treated with metformin were compared with controls (treated with double distilled water). The transcriptome changes with/without metformin treatment were probed by using high-throughput RNA-seq techniques
Results: A comprehensive mouse transcriptome map with metformin treatment across ten tissues including aorta, eyeball, brain, adipose tissue, heart, kidney, liver, skeletal muscle, stomach and testis, was provided. Function enrichment, network characteristics and disease association of the differentially expressed genes were analyzed. We also compared our expression profiles with related microarray data in order to find conditions that share similar expression profiles with metformin treatment.
Conclusions: This dataset could serve as a baseline resource for investigating the potential beneficial or adverse effects of metformin across different tissues.

overall_design: Wildtype healthy C57BL/6 mice were treated with either metformin (treatment group) or double distilled water (control group). The mRNA profiles across 10 tissues (including aorta, eyeball, brain, adipose tissue, heart, kidney, liver, skeletal muscle, stomach and testis) were generated RNA-seq technique, in triplicate for each group, using Illumina HiSeq 2500.

first: Jichun

first: Qinghua

last: Cui


title: Sympathetic nerves and arrector pili muscles form a dual component niche to regulate hair follicle stem cells

city: cambridge

first: Ya-Chieh

last: Hsu

address: 7 Divinity Avenue, SF 312

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Piloerection (goosebump) requires concerted actions of the hair follicle, the arrector pili muscle (APM), and the sympathetic nerve, providing a model to study interactions across epithelium, mesenchyme, and nerves. Here, we show that APMs and sympathetic nerves form a dual component niche to modulate hair follicle stem cell (HFSC) activity. Sympathetic nerves form synapse-like structures with HFSCs and regulate HFSCs through norepinephrine, whereas APMs maintain sympathetic innervation to HFSCs. Without norepinephrine signaling, HFSCs enter a deep quiescence state by down-regulating cell cycle machinery and mitochondria metabolism, while up-regulating quiescence regulators Lhx2, Foxp1, and Fgf18. During development, HFSC progeny secrets Sonic Hedgehog (SHH) to direct the formation of this APM-sympathetic nerve niche, which in turn controls hair follicle regeneration in adults. Our results reveal a reciprocal interdependence between a regenerative tissue and its niche at different stages, and illustrate that nerves can modulate stem cell quiescence through synapses and neurotransmitters.

overall_design: The sympathetic nerves influence hair follicle stem cells through binding of norepinephrine to the adrenergic receptor beta 2 (Adrb2). Deletion of Adrb2 specifically from hair follicle stem cells using the K15-crePGR reporter allows us to uncover molecular changes downstream of adrenergic signaling. Hair follicle stem cells (CD34+, a6+, Sca1-) from control and K15-CrePGR; Adrb2 fl/fl mice were isolated using FACS.

first: Meryem

last: Gonzalez-Celeiro

first: Yulia

last: Shwartz


title: RNA sequencing of PND55 mammary glands of mice fed 20% ISP, 1% ISP, 20% casein or Teklad 2018

first: Roger

last: Moorehead

overall_design: Mice were exposed to 20% isolated soy protein (ISP), 1% ISP, 20% casein or Teklad 2018 throughout embryonic and postnatal development (lifetime exposure). 4th mammary glands were collected, lymph node removed, and RNA extracted prior to sending for RNA sequencing.


title: Transcriptional response of Pseudomonas aeruginosa PAO1r to bacteriophage phiYY infection

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

department: Department of Clinical Laboratory

institute: Third Military Medical University

summary: Explore the genome-scale phage–host interactions across different developmental infection stages

sample_organism:
Pseudomonas aeruginosa
Pseudomonas phage phiYY

overall_design: Samples were taken from thePAO1r Lysates infected with phage phiYY at six internal time (6,12,18 min). Three independent experiments were performed