title: Tumor-Infiltrating Regulatory T Cell Accumulation in the Tumor Microenvironment is Mediated by IL33/ST2 Signaling

status: Public on Sep 30 2019

city: Boston

first: JAE WON

last: CHO

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: The objective of this study is to compare transcriptional features in tumor-infiltrating (TI) regulatory T (Treg) cells with TI CD4+ conventional T (Tconv) cells, splenic Treg cells of tumor-bearing mice, splenic Tconv cells of tumor-bearing mice, splenic Treg cells of normal mice, or splenic Tconv cells of normal mice.

overall_design: A total of 5 × 10^5 TC-1 cells were intravenously injected into the tail vein of mice. At 3 weeks after tumor inoculation, tumor-bearing mice were sacrificed. The spleen and tumor from tumor-bearing mice and spleen of normal mice were harvested and processed into single cells. CD4+ T cells were enriched using a CD4+ T cell isolation kit by negative selection. Pure CD4+GFP+ Treg and CD4+GFP- Tconv populations were obtained through sorting using a FACSAria II.

first: Jimin

last: Son

first: Jae-Won

last: Cho

first: Hyo

last: Park

first: Jihyun

last: Moon

first: Seyeon

first: Hoyoung

last: Lee

first: Jeewon

first: Gamin

last: Kim

first: Su

middle: M

first: Sergio

middle: A

last: Lira

first: Andrew

last: McKenzie

first: Hye

middle: Y

first: Cheol

last: Choi

first: Yong

middle: T

last: Lim

first: Seong

first: Su-Hyung

first: Eui-Cheol

last: Shin

first: Insuk

first: Sang-Jun

last: Ha


title: Expression data from monocytes treated with complement factor H

status: Public on Oct 01 2019

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

summary:
Monocyte maturation plays an important role in many physiological and patological processes includning cancer. Complement factor H is a complemnt inhibitor but has been shown to also have various cellular functions.
We used microarrays to detail the global programme of gene expression underlying maturationn of monocytes upon FH stimulation and identified distinct classes of up-regulated genes during this process.

overall_design: Monocytes were isolated from blood of 6 healthy volunteers and incubated with purified Factor H for 48h. Afterwords, RNA was extracted and hybridization performed using Affymetrix microarrays

first: Karolina

last: Smolag-Klosowska

first: Anna

last: Blom


title: The role of the Calcium-Sensing receptor in colorectal cancer

status: Public on Nov 26 2019

city: vienna

first: luca

last: iamartino

state: Please Select

address: Waehringer Guertel 18-20

country: Austria

institute: Institute of Pathophysiology and Allergy Research

type: Expression profiling by high throughput sequencing

summary: The Calcium-Sensing receptor (CaSR) is a G proteins-coupled receptor involved in calcium homeostasis. The CaSR regulates cell proliferation and apoptosis and has been suggested to play an antitumor role in colorectal cancer. However it is down-regulated during carcinogenesis and in more malignant tumors its expression is lost.

overall_design: We stably transfected with a lentiviral system a colorectal cancer cell line (HT29) to over-express the CaSR: HT29CaSR-GFP. As control we transfected the HT29 with a vector containing only GFP, generating thus the HT29GFP cells. We tested whether the CaSR has an impact on gene transcription and whether its stimulation via a CaSR specific positive allosteric modulator, namely NPS-R568 (here indicated as R568), would further enhance CaSR effects. We treated either the HT29CaSR-GFP and the HT29GFP with 1µM of R568 or with 0.1% DMSO (as untreated control) for 48 hours. With three biological replicates per each condition we performed the RNAseq.

first: Luca

last: Iamartino

first: Taha

last: Elajnaf

first: Katharina

last: Gall

first: Teresa

last: Manhardt

first: Petra

last: Heffeter

first: Michael

last: Grush

first: Sophia

last: Derdak

first: Sabina

last: Baumgartner-Parzer

first: Martin

last: Schepelmann

first: Enikö

last: Kallay


title: CROP-seq analysis of TCR stimulation using the 10x Genomics platform

status: Public on Oct 08 2019

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
T cell receptor (TCR) signaling in Jurkat cells was investigated using the CROP-seq method for CRISPR single-cell sequencing. In CROP-seq, genetic perturbations are introduced into single cells in a pooled fashion, and single-cell RNA-seq is used to determine the transcriptional response to the CRISPR-induced perturbation in a large number of single cells in parallel. Importantly, the CROP-seq vector makes individual guide-RNAs detectable using standard single-cell RNA-seq technology.

The dataset presented here is based on CROP-seq in combination with single-cell RNA-seq using the 10x Genomics v2 chemistry. It recapitulates a previously published CROP-seq dataset (Datlinger et al. 2017 Nature Methods; GEO: GSE92872) that used the Drop-seq protocol as the single-cell RNA-seq readout. Additional information on CROP-seq are available from the following website: http://crop-seq.computational-epigenetics.org/ .

overall_design: Cas9-expressing Jurkat cells were transduced using a lentiviral vector with a guide-RNA library targeting candidate regulators of TCR signaling, including signaling proteins and transcription factors. After 10 days of cell expansion with antibiotic selection for guide-RNA expressing cells, cells were stimulated with anti-CD3 and anti-CD28 antibodies (which induces potent TCR stimulation) or left untreated (control samples). Stimulated und unstimulated cells were subjected to single-cell RNA-seq using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) followed by Illumina HiSeq 4000 sequencing. The sequencing data were analyzed using standard methods. To identify the guide-RNAs in each cell, a reference genome was created by extending the genome with the sequences of all used guide-RNAs.

first: Paul

last: Datlinger

first: Andre

middle: F

last: Rendeiro

first: Christian

last: Schmidl

first: Thomas

last: Krausgruber

first: Nikolaus

last: Fortelny


title: Simultaneous analysis of open chromatin, promoter interactions and gene expression in stimulated T cells implicates GWAS SNPs with causal genes

status: Public on Oct 31 2019

city: Manchester

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

country: United Kingdom

institute: Univeristy of Manchester

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide association studies have identified genetic variation contributing to complex disease risk but assigning causal genes and mechanisms has been more challenging, as disease-associated variants are often found in distal regulatory regions with cell-type specific behaviours. Here, the simultaneous correlation of ATAC-seq, Hi-C, Capture Hi-C and nuclear RNA-seq data, in the same stimulated T-cells over 24 hours, allowed the assignment of functional enhancers to genes. We show how small magnitude changes in DNA interaction and activity dynamics are correlated with much larger changes to dynamics in gene expression and that the strongest correlations are observed within 200 kb of promoters. Using rheumatoid arthritis as an exemplar T-cell mediated disease, we demonstrate interactions of expression quantitative trait locus SNPs with target genes and confirm assigned genes or show complex interactions for 20% of disease associated loci. Finally, we confirm one of the putative causal genes using CRISPR/Cas9.

overall_design: Examine dynamics between open chromatin, chromosome interactions and gene expression in stimulated T cells over 24 hours

first: Jing

last: Yang

first: Amanda

last: McGovern

first: Kate

last: Duffus

first: Peyman

last: Zarrineh

first: Andrew

middle: P

last: Morris

first: Antony

last: Adamson

first: Peter

last: Fraser

first: Magnus

last: Rattray

first: Stephen

last: Eyre


title: H3K4me2 ChIP-seq upon GSK inhibiton

status: Public on Sep 29 2019

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

country: USA

institute: University of Massachusetts Boston

summary: We show in prostate cancer cells that LSD1 co-localizes with FOXA1 and active enhancer markers (H3K4me2), and that LSD1 inhibition globally disrupts FOXA1 chromatin binding.

overall_design:
LNCaP cells were treated with vehicle or DHT and together with or without GSK2879552 for 24 hrs

Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Shuai

last: Gao

first: Dong

last: Han

first: Sujun

last: Chen

first: Housheng

middle: H

last: He


title: AR ChIP-seq with DHT induction and GSK treatment

summary: The major pioneer factor activity of FOXA1 in PCa is to facilitate AR recruitment to androgen-regulated enhancers. Therefore, we hypothesized that the decreased FOXA1 binding and enhancer availability by LSD1 inhibition may result in the impairment of subsequent AR recruitment to enhancers. To globally test this hypothesis, we performed AR ChIP-seq in LNCaP cells treated with an LSD1 inhibitors. Consistent with previous reports, DHT treatment can dramatically induce AR binding to chromatin. Significantly, LSD1 inhibitor treatment in presence of DHT stimulation markedly decreased the total number of AR binding peaks and their  intensity. We further assessed the impact of LSD1 inhibition on overall AR transcriptional output using RNA-seq data.

overall_design: AR ChIP-Seq were performed in LNCaP cells treated with vehicle, DHT (10nM at 4h), DHT (4h) with pretreated GSK2879552 (50µM for 4h), or DHT (4h) with pretreated GSK2879552 (48h)


title: A global overview of translation efficiency and ribosome occupancy at nucleotide resolution in HEK293 cells

status: Public on Oct 09 2019

city: Glasgow

first: Sarah

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research

summary: Looking at ribosome distribution and translational efficiency in control conditions in HEK293 cell line. Combining this information with our other datasets from HEK293 cells has allowed us to look at ribosome occupancy of specific groups of mRNAs

overall_design: Ribosome Profiling conducted in HEK293 cells treated with control siRNA. Ribo-zero treated total RNA for the same samples is also included.

middle: L


title: RNA-seq of Whole Cortex and FACS-Sorted Glia Populations from Curpizone-challenged and unchallenged mice and mice undergoing EAE.

status: Public on Sep 20 2019

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

summary: We report a time-series analysis of the changes in gene expression that occur in a cuprizone-fed murine model for demyelination without autoimmunity. Wildtype and LRP1 knockout mice were either fed cuprizone or left untreated and whole cortex samples were sequenced before cuprizone feeding, and at 3, 5, and 5.5 weeks after administration of cuprizone. We find that a number of inflammatory genes that are differentially expressed in wildtype mice are not in knockout mice at later time points. We also report a dataset that includes RNA-seq samples of glia cell populations FACS-sorted from cortices of wild type or LRP1 knockout mice undergoing EAE.

overall_design:
1. RNA-seq on mice from two different genotypes subject to two different treatments and over four time points (0, 3, 5, and 5.5 weeks) 2. RNA-seq on two distinct FACS-sorted populations of cells from mice from two different genotypes subject to the same experimental conditions.

Sequencing performed at UVa Genome Analysis & Technology Core,
Office of Research Core Administration.
University of Virginia Health System,
P.O. Box 800741,
Charlottesville, VA 22908-0741

first: Alban

last: Gaultier

first: Anthony

last: Fernandez-Castaneda


title: Comparative analysis of gene expression between overexpression and deficiency of signal peptide peptidase in Arabidopsis thaliana

status: Public on Sep 01 2019

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

country: Japan

institute: Tokyo University of Agriculture

summary:
Signal peptide peptidase (SPP) plays an essential role in among all eukaryotes. The knock out lines of A. thaliana SPP (AtSPP) is lethal and the substrates of AtSPP are not identified. Based on the situation, we constructed the plants with AtSPP over-expressed and knock down to investigate the role of AtSPP.
We also used the data to find the candidate substrates of AtSPP, which regulates intermembrane proteolysis, would have crucial physiological functions as well as control the gene expression encoding the substrates.

overall_design: Wild type (Col-0) and AtSPP mutants were grown on a half strength of MS medium containing 0.8% agar. Seven days seedlings were collected and subjected to the analysis.

first: Kenta

last: Kusunoki

first: Masako

last: Hosh

last: Tamura

first: Tomiko

last: Asakura


title: RNA-Seq with DHT induction and/or GSK treatment at 24, 48 hrs and 2 weeks

overall_design: LNCaP cells were treated with vehicle or DHT and together with or without GSK2879552 for 24, 48 hrs or 2 weeks.


title: Long-term Y-27632 treatment promotes senescence of primary human dermal fibroblasts by increasing IGFBP-5

status: Public on Aug 19 2019

city: Jinan

first: Xunwei

last: Wu

state: Shandong

address: 44-1 Wenhua West Road

department: School of Stomatology

country: China

institute: Shandong University

summary:
Purpose: Y-27632, a well-characterized Rho-associated kinase (ROCK) inhibitor, has been shown to play an important role in regulation of cell growth in multiple types of cells, the regulation appeared to be cell specific.  To further understand its molecular mechanisms, we performed RNA-seq analysis of HDF at 12 hours and 48 hours after Y-27632 treatment.
Methods: Total RNAs were isolated from dermal cells with/without Y-27632 treatment for 12 hours or 48 hours respectively. Then mRNAs were purified from above total RNA using poly-T oligo-attached magnetic beads. After sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA), the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Results: We sequenced 12 of 229 differential expressed genes 48 hours after Y-27632 treatment and found genes which by GO analysis are negative regulators of cell growth ). Of these 12 genes, the expression level of 4 genes, IGFBP1, IGFBP-5, HNF4A and NKD1, changed significantly at both 12 hours and 48 hours of Y-27632 treatment. This results, validated by RT-qPCR analysis  showed that the expression of IGFBP-5 (Insulin Growth Factor Binding Protein 5) increased by 1.5 fold after 12 hours of treatment, and increased more than 10-fold after 48 hours. Expression of the other 3 genes didn’t change significantly after Y-27632 treatment
Conclusions:RNA-seq analysis of gene expression profile in HDFs collected from 12 hours and 48 hours treatment of Y-27632. From these analyses we found the IGFBP-5, a negative regulation of cell proliferation, whose expression increased with the duration of Y-27632 treatment (7-fold increase after the first 24 hours

overall_design: RNA-seq analysis of gene expression profile in HDFs collected from 12 hours and 48 hours treatment of Y-27632 vs untreated controls.

first: Xiangyong

last: Li


title: DART-seq: an antibody-free method for global m6A detection

status: Public on Sep 23 2019

city: D

first: Kate

last: Meyer

state: NC

address: 307 Research Drive Box 3711

department: Biochemistry

institute: Duke University School of Medicine

summary: m6A is a widespread RNA modification which plays important roles in the regulation of gene expression. Methods for the global detection of m6A rely on immunoprecipitation of methylated transcripts using m6A antibodies. However, these methods are costly and require large amounts of input RNA, making them prohibitive for many experiments. Here, we describe DART-seq, an antibody-free method for m6A detection which enables transcriptome-wide mapping of m6A residues using low amounts of input material. DART-seq can be used to obtain global m6A maps using as little as 10 nanograms of total RNA and at single-molecule resolution. This method offers several improvements over current techniques and will facilitate detection of m6A in limiting cell and tissue types.

overall_design:
Transcriptome-wide m6A profiling in HEK293T cells.

Please note that each bed file was generated from all repliates and is linked to the corresponding first replicate sample records.

middle: D


title: Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins

status: Public on Aug 13 2019

city: Huddinge

first: Maria

last: Eriksson

address: Karolinska Institutet, Biosciences and Nutrition, NEO Halsovagen 7

department: BioNut

institute: Karolinska Institutet

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

overall_design: Refer to individual Series


title: Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins [RNA-Seq]

summary:
Purpose: Hutchinson-Gilford progeria syndrome (HGPS) is the result of a defective form of the lamin A protein called progerin. While progerin is known to disrupt the properties of the nuclear lamina, the underlying mechanisms responsible for the pathophysiology of HGPS remain less clear. Previous studies in our laboratory have shown that progerin expression in murine epidermal basal cells results in impaired stratification and halted development of the skin. Stratification and differentiation of the epidermis is regulated by asymmetric stem cell division.
Methods: Primary keratinocytes were isolated from HGPS and wild-type mice, and processed for FACS. Isolated keratinocytes were incubated with anti-α6-integrin (CD49f) and anti-CD45 (30-F11) antibodies. Samples were sorted into basal (CD45neg/CD49fhigh) and suprabasal (CD45neg/CD49flow) populations using a FACScalibur flow cytometer. After sorting, RNA was extracted and subjected to cDNA synthesis, ligation of adapters and amplification of indexed libraries. The indexed cDNA libraries were sequenced on the Illumina HiSeq 2000. The generated sequence reads were mapped to the mouse genome (mm10) using Galaxy software. Sequences were aligned to the reference genome using TopHat (Trapnell et al., 2009) and differential expression analysis was done using Cufflinks (Trapnell et al., 2012).
Results: Here, we show that expression of progerin impairs stem cells ability to maintain tissue homeostasis as a result of altered cell division. Quantification of basal skin cells showed an increase in symmetric cell division that correlated with progerin accumulation in HGPS mice. Investigation of the mechanisms underlying this phenomenon revealed a putative role of Wnt/β-catenin signaling. Further analysis suggested an alteration in the nuclear translocation of β-catenin involving the inner and outer nuclear membrane proteins, emerin and nesprin-2.
Conclusions: Taken together our results suggest a direct involvement of progerin in the transmission of Wnt signaling and normal stem cell division. These new insights into the molecular mechanisms of progerin may help develop new treatment strategies for HGPS.

overall_design: Skin suprabasal and basal mRNA profiles of 4-day old wild type (WT) and bitransgenic HGPS (BT) mice were generated by sequencing using Illumina HiSeq2000.

first: Hafdis

last: Helgadottir


title: Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins [Affymetrix]

summary:
Hutchinson-Gilford progeria syndrome (HGPS) is the result of a defective form of the lamin A protein called progerin. While progerin is known to disrupt the properties of the nuclear lamina, the underlying mechanisms responsible for the pathophysiology of HGPS remain less clear. Previous studies in our laboratory have shown that progerin expression in murine epidermal basal cells results in impaired stratification and halted development of the skin. Stratification and differentiation of the epidermis is regulated by asymmetric stem cell division.
In this dataset, we include the expression data using Affymetrix array. The samples were obtained from basal and suprabasal keratinocyes from 4-day old wild-type and bitransgenic (BT) mice.

overall_design: 12 samples were analyzed. We generated the following pairwise comparisons:  bt_low vs wt_low; bt_high vs wt_high;wt_high vs wt_low; bt_high vs bt_low. Unpaired, 2-sided student's t-test and FDR was used to compare the groups. Array: MTA-1_0, mm10.


title: Pregnancy enables expansion of autoreactive regulatory T cells in an animal model of multiple sclerosis

status: Public on Jul 30 2019

city: Hamburg

first: Manuel

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Disease activity of autoimmune disorders such as multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE) is temporarily suppressed by pregnancy. However, whether disease amelioration is due to non-specific immunomodulation or mediated by antigen-specific regulation of disease-causing conventional T cells (Tcon) and immuno- suppressive regulatory T cells (Treg), remains elusive. In the present study, we systematically analyzed changes of the T cell receptor (TCR) β repertoire driven by EAE and pregnancy using TCR sequencing. We demonstrate that EAE, but not pregnancy, robustly increased TCR repertoire clonality in both peripheral Tcon and Treg. Notably, pregnancy was required for the expansion of Treg harboring the dominant EAE-associated TRBV chain 13.2 and increased the frequency of EAE-associated clonotypes within the Treg compartment. Our findings indicate that pregnancy supports the expansion of Treg clonotypes that are equipped to recognize EAE- associated antigens. These Treg are thereby particularly suited to control corresponding encephalitogenic Tcon responses and likely contribute to pregnancy-associated protection in autoimmunity.

overall_design: T cell receptor (TCR) sequencing of CD4+Foxp3+ regulatory T cells and CD4+Foxp3- conventional T cells from pregnant and non-pregnant, EAE and naive mice.

first: Jan

middle: B

last: Engler

first: Nina

last: Heckmann


title: Molecular Fingerprints of Borderline Changes of Kidney Allografts is Influenced by Donor Category

status: Public on Jul 18 2019

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

summary: The fate of transplanted kidneys is substantially influenced by the graft quality as transplantation of kidneys from elderly and expanded criteria deceased donors (ECD) is associated with higher occurrence of delayed graft function, rejection and inferior long term outcome. Little is known about early molecular fingerprints of these events in different donor categories. Borderline changes represent the most frequent histological finding early after kidney transplantation. Therefore,  transcriptomic profiles of early case biopsies diagnosed as borderline changes were studied in ECD, standard criteria deceased donors (SCD) and living donor (LD) kidney transplantation using  RNA microarray (Agilent SurePrintG3). The increased transcripts typical for ECD as compared to LD (n=437) showed enrichment of extracellular matrix (ECM) -receptor interaction (p=0.004) and complement and coagulation pathways (p=0.004) and GO terms related to platelet activation, blood coagulation, regulation of cell cycle, acute inflammatory response, wound healing or defense response (p<0.001).   Gene annotation analysis of transcripts with increased expression in ECD grafts compared to SCD (n=244) showed the highest enrichment of inflammatory response (p=0.013), response to wounding (p=0.001) and defense response (p=0.005) and ECM-receptor interaction pathway (p=0.043). Comparative gene expression overlaps of ECD, SCD and LD using Venn’s diagrams found 62 up- and 16 down-regulated genes in ECD compared to both LD and SCD. Shared increased transcripts in ECD vs. both SCD and LD included, thrombospondin 2 (THBS2), angiopoietin-like 4 (ANGPTL4), collagens (COL6A3, COL1A1), chemokines CCL13 or interleukin IL11 and most significant down-regulated transcripts included proline rich 35 (PRR35) and fibroblast growth factor 9 (FGF9).  Transcriptomic profile of higher inflammation and extracellular matrix remodeling in early borderline changes in the ECD kidney allografts suggest mechanisms how ischemia/reperfusion injury aggravates alloimmune response in the presence of chronic vascular changes.

overall_design: The experiments were performed with total RNA derived from the renal graft biopsy samples of 21 different patients who had undergone a kidney transplantation.  Only the patients with  diagnosis of borderline changes as a first pathology in the early indication biopsy (<14 days after transplantation)  were included in the study.  RNA profiles of  patients with borderline changes who received grafts from expanded criteria donors (ECD), standard criteria donors (SCD) and living donors (LD) were compared. As microarray platform,  Agilent SurePrintG3 Human Gene Expression v3 8x60K Array was used.

first: Zdenek

last: Krejcik

first: Michaela

last: merkerova-Dostalova

first: Jiri

last: Klema

first: Viktor

last: Stranecky

first: Janka

last: Slatinska

first: Jana

last: Maluskova

first: Eva

last: Honsova

first: Ondrej

last: Viklicky


title: SirT7 auto-ADPribosylation regulates glucose starvation response through macroH2A1.1 (ChIP-seq)

status: Public on Aug 07 2019

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

institute: Rutgers University

summary: Sirtuins are key players in the response to oxidative, metabolic and genotoxic stress, and are involved in genome stability, metabolic homeostasis and aging. Originally described as NAD+-dependent deacetylases, some sirtuins are also characterized by poorly understood mono-ADP-ribosyltransferase (MADPRT) activity. Here we report that the deacetylase SirT7 is a dual sirtuin as it also features auto-MADPRT activity. Molecular and structural evidence suggests that this novel activity occurs at a second previously undefined active site that is physically separated in another domain. Specific abrogation of this activity alters SirT7 chromatin distribution, suggesting a role for this modification in SirT7 chromatin binding specificity and localization. Our studies uncover an epigenetic pathway by which ADP-ribosyl-SirT7 is recognized by the ADP-ribose reader macroH2A1.1, a histone variant involved in chromatin organization, metabolism and differentiation. Glucose starvation (GS) boosts this interaction and promotes SirT7 re-localization intergenic regions in a macroH2A1-dependent manner, which is required for specific up- or downregulation of a subset of nearby genes upon GS in primary cells and in vivo in the livers of calorie-restricted (CR) Wt and SirT7-/- mice. The level of expression of these genes decreases with age in SirT7-deficient mice, reinforcing the link between Sirtuins, CR and aging. Our work provides a novel perspective about sirtuin duality and suggests a key role for SirT7/macroH2A1.1 axis in mammalian glucose homeostasis, calorie restriction signaling and aging.

overall_design: Chromatin from 14.5 day WT and SirT7-/- MEFs was subjected to ChIP using antibodies raised against SIRT7, macroH2A1.1, and H3K27me3, and subjected to high-throughput sequencing.

first: Lourdes

last: Serrano

first: Nicolás

middle: G

last: Simonet

first: Alejandro

last: Vaquero


title: Development of a PD-L1-expressing orthotopic liver cancer model

status: Public on Aug 06 2019

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: This study sought to explore the functional significance of PD-L1 expression in tumor cells in the tumor microenvironment.

overall_design: The mouse liver cancer cell line BNL-MEA was transfected with PD-L1 plasmids and stable clones expressing PD-L1 were selected. An orthotopic HCC model was generated by implanting the cells into the subcapsular space of BALB/c mice.

first: Chiun

first: Da

middle: Liang

last: Ou


title: Gene expression profiling of Trop2+ and Trop2- luminal epithelial cells and stromal cells from young adult and old mouse prostates

status: Public on Aug 01 2019

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

state: CA

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

summary: We set out to determine if distinct prostate luminal epithelial cell-types exhibited age-related differences in their gene expression profiles. We used fluorescence activated cell sorting to isolate Trop2+ and Trop2- luminal cells and EpCAM- CD49f- stromal cells from dissociated preparations of prostate tissue taken from young adult (3 months) and old (24 months of age) mice. RNA was extracted from sorted cells to evaluate differences in gene expression.

overall_design: RNA sequencing of Trop2+ and Trop2- luminal cells and stromal cells isolated from 3 month and 24 month old mouse prostates. Experiments were performed using biological triplicates for stromal cells and duplicates for luminal subsets. Sequencing was performed on Illumina HiSeq 3000.

middle: S


title: Analysis of copy number alterations from a lncRNA perspective reveals ALAL-1 a mediator of NSCLC immune evasion.

status: Public on May 17 2019

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Analysis of the transcriptomic changes after ALAL-1 knockdown in HCC95 cells.

overall_design: Inhibition of the lncRNA ALAL-1 in lung cancer cells (HCC95) treated with TNFalpha. Each experimental condition was performed in triplicates.

first: Huarte

last: Maite

first: Athie

last: Alejandro


title: Gene expression profiling of basal and luminal epithelial cells from young adult and old mouse prostates

summary: We set out to determine if prostate epithelial cell-types exhibited age-related differences in their gene expression profiles. We used fluorescence activated cell sorting to isolate basal and luminal cells from dissociated preparations of prostate tissue taken from young adult (3 months) and old (24 months of age) mice. RNA was extracted from sorted cells to evaluate differences in gene expression. We found significant enrichment for progenitor genes in old luminal cells including an immune/inflammatory profile that overlapped with a previously identified CD38-lo human prostate luminal progenitor signature. This study demonstrates a luminal progenitor signature in old mouse prostate.

overall_design: RNA sequencing of basal and luminal cells isolated from 3 month and 24 month old mouse prostates. Experiments were performed using biological triplicates, with each replicate pooled from 2 mice of the same age. Sequencing was performed on Illumina HiSeq 3000.


title: Apatinib preferentially inhibits Gefitinib-resistant lung cancer cells by inducing cell cycle arrest and inhibiting VEGFR signaling pathway

status: Public on May 15 2019

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

institute: Mayo Clinic

summary: Targeted therapy for patients with EGFR mutations by tyrosine kinase inhibitors (TKIs) has provided a significant benefit to patients. However, gradually developed resistance to the therapy becomes a major challenge in clinical practice. Herein, we report that Apatinib, an anti-angiogenic drug, strongly and specifically inhibits Gefitinib-resistant cancer cells but not their parental sensitive cells. Gefitinib-resistant lung cancer cell line (PC9GR) was established from its parental sensitive line (PC9) with a traditional EGFR mutation after long time exposure to Gefitinib. The established PC9GR cells had over 250 fold increased resistance to Gefitinib than its sensitive parental PC9 cells. Apatinib demonstrated much stronger (~5 fold) growth inhibition on PC9GR cells than on PC9 and other lung cancer cell lines. This inhibition was mostly achieved through cell cycle rest in G1 phase as demonstrated by transcriptome and protein expression data. Oral intake of Apatinib in mouse model significantly inhibited establishment and growth of PC9GR implanted tumors. VEGFR2 phosphorylation in PC9GR tumors after Apatinib treatment was significantly reduced along with less micro-vessel formation. Apatinib may provide a benefit to patients with acquired resistance to TKI treatment.

overall_design: RNA sequencing was performed on PC9, PC9GR, and both after apatinib treatment, three replicates in each condition, to detect differentially expressed genes and involved pathways.

first: Yongan

last: Song


title: Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

status: Public on Jun 01 2019

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: We engineered m6A methyltransferase or demethylases with CRISPR-Cas9 to achieve site-specific editing of m6A. The resultant m6A editors can be programmed with a guide RNA, allowing functional comparison of single site methylation in different mRNA regions.

overall_design: Examination of m6A methylation patterns after targeted methylation of Actin and targeted demethylation of Malat1.

first: Xiao-min

last: Liu

first: Shu-Bing

last: Qian


title: SNP arrays of BT474 Latpatinib and/or Trastuzumab resistant cell lines for copy number analysis.

status: Public on Jun 21 2019

city: New York

first: Kathleen

last: Burke

state: NY

address: 475 Main St., Apt 12H

department: Pathology

institute: Memorial Sloan Kettering Cancer Center

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

summary:
Targeting HER2 with lapatinib (L), trastuzumab (T), or the LT combination, is effective in HER2+ breast cancer (BC), but de novo and acquired resistance commonly occur.
The purpose of this experiment was to investigate the somatic alterations found in Lapatinib and/or Trastuzumab resistant cells lines.

overall_design: SNP arrays of BT474 cell derivative genomic DNA was performed using HumanOmni2.5-8 BeadChip Kit.

first: Sophie

last: Xu


title: Comparison of NK cell developmental stages in bone marrow of Tbx21 WT versus KO mice

status: Public on Mar 20 2019

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

institute: Imperial College London

summary: Bone marrow cells were isolated from wild type and Tbx21 knockout mice. iNK (Lin- NK1.1+ CD11b- CD27+) and mNK1 (Lin- NK1.1+ CD11b+ CD27+) were sorted from WT and Tbx21 KO mice. mNK2 (Lin- NK1.1+ CD11b+ CD27-) were sorted from WT mice only, since these cells are not present in Tbx21 KO mice.

overall_design: Cells from the bone marrow of three WT and three Tbx21 KO mice were sorted. Each of the WT mice yielded iNK, mNK1 and mNK2. Each of the Tbx21 KO mice yielded iNK and mNK1. Total of 15 samples.


title: RNA Expression in fusiform gyrus of  AD and Control subjects

status: Public on Apr 17 2019

city: South San Francisco

first: Brad

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
RNA was purified from frozen fusiform gyrus tissue sections of autopsy-confirmed Alzheimer's cases and neurologically normal age-matched controls.

89 of the 289 subjects in this study were previously analyzed in GSE95587. For these subjects, the RNA was extracted from fusiform gyrus tissue blocks distinct to those used in GSE95587. The subjects, and the corresponding identifiers in GSE95587, are indicated in the descriptions as "repeated in GSE95587: NA" (for a new subject) or, for example, "repeated in GSE95587: GSM2516875" (for re-analyzed subject).

The ID of this project in Genentech's ExpressionPlot database is PRJ0014902

overall_design: RNA from fusiform gyrus of Alzheimer's or Neurologically Normal post-mortem tissue.

first: Melanie

last: Huntley

first: Oded

last: Foreman

first: Ainhoa

last: Etxeberria


title: Identification of three subtypes of triple negative breast cancer with potential therapeutic implications

status: Public on May 26 2019

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

summary:
Background:
Heterogeneity and lack of targeted therapies represent the two main impediments to precision treatment of triple-negative breast cancer (TNBC) and therefore, molecular subtyping and identification of therapeutic pathways are required to optimize medical care. The aim of the present study was to define robust TNBC subtypes with clinical relevance.
Methods:
Gene expression profiling by means of DNA chips was conducted in an internal TNBC cohort composed of 238 patients. In addition, external data (n = 257), obtained by using the same DNA chip, were used for validation. Fuzzy clustering was followed by functional annotation of the clusters. Immunohistochemistry was used to confirm transcriptomics results: CD138 and CD20 were used to test for plasma cell and B lymphocyte infiltrations, respectively, MECA79 and CD31 for tertiary lymphoid structures, and UCHL1/PGP9.5 and S100 for neurogenesis.
Results:
We identified three molecular clusters within TNBC: one molecular apocrine (C1) and two basal-like-enriched (C2 and C3). C2 presented pro-tumorigenic immune response (immune suppressive), high neurogenesis (nerve infiltration) and high biological aggressiveness. In contrast, C3 exhibited adaptive immune response associated with complete B cell differentiation that occurs in tertiary lymphoid structures, and immune checkpoint upregulation. External cohort subtyping by means of the same approach proved the robustness of these results. Furthermore, plasma cell infiltration, tertiary lymphoid structures and neurogenesis were validated at the protein levels by means of histological evaluation and immunohistochemistry.
Conclusion:
Our work showed that TNBC can be subcategorized in three different subtypes characterized by marked biological features, some of which could be targeted by specific therapies.

overall_design: Subtyping molecular characterization within a breast cancer cohort of 131 TN-IHC by means of gene expression profiling

first: Pascal

last: Jézéquel

first: Kerdraon

last: Olivier

first: Hondermarck

last: Hubert

first: Catherine

last: Guérin-Charbonnel

first: Hamza

last: Lasla

first: Jean-Luc

last: Canon

first: Andrea

last: Gombos

first: Florence

last: Dalenc

first: Suzette

last: Delaloge

first: Jérome

last: Lemonnier

first: Delphine

last: Loussouarn

first: Véronique

last: Verrièle

first: Mario

last: Campone


title: C6 glioblastoma microRNA regulation induced by haloperidol, risperidone and clozapine

city: New Taipei City

first: Mao-Liang

last: Chen

address: No.289, Jianguo Rd., Xindian Dist.,

department: Department of Research

institute: Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

summary: Antipsychotic drugs (APDs) have been reported to ease psychotic symptoms in the clinic. miRNAs have also been identified that can regulate the expression of genes/proteins related to possible molecular mechanisms of drug action. To reveal APD-induced miRNA modulations in glial cells, we analyzed miRNA expression in subchronically APD-treated C6 cells by using a miRNA microarray.

overall_design: C6 cells were subchronically treated with haloperidol, risperidone or clozapine for five days. The final concentrations of haloperidol (2 μg/ml), risperidone (4 μg/ml) and clozapine (25 μg/ml) were calculated based on therapeutic concentrations in clinic. Cells were then harvested for microarray analysis. miRNA expression of APD-treated C6 cells were compared to miRNA expression of untreated control C6 cells. The microarray experiments were performed in two biological repeats.

first: Mao


title: The LIM-homeodomain transcription factor LHX4 is required for the differentiation of retinal rod bipolar cells and rod-connecting cone bipolar cells [P7]

status: Public on Mar 05 2019

first: Xuhui

last: Dong

address: 601 ELMWOOD AVE

institute: University of Rochester

summary: Study the role of the LIM-homeodomain transcription factor LHX4 in the development of retinal bipolar cell subtypes

overall_design: Gene profiles of post-natal day7  (P7) control and Lhx4-null retina were generated using Illumina; SRA project: SRP186424; BioProject: PRJNA523455

first: Lin

last: Gan


title: Gene Expression Profiles Associated with A Simple and Reliable Myeloid Signature for HCC

status: Public on Jul 27 2019

city: Guangzhou

first: Chong

last: Wu

address: 135 Xin Gang Xi Road

institute: Sun Yat-sen University

summary: BACKGROUND & AIMS: Despite the increasing appreciation of the roles that myeloid cells play in tumor progression and therapy, challenges remain in interpreting the balance of the tumor-associated myeloid response and its translational value. We aimed to construct a simple and reliable signature of local myeloid responses in hepatocellular carcinoma (HCC). METHODS: Using in situ immunohistochemistry (IHC), we assessed myeloid features that revealed the distribution of major myeloid subtypes in both the peri- and intratumoral regions of HCC. A signature was constructed using an L1-penalized Cox regression model based on the postsurgery recurrence data from a training subset (n = 244) that was validated in the testing subset (n = 244) and independent internal (n = 341) and external (n = 348) cohorts. Multiplexed immunofluorescence staining, flow cytometry and transcriptomic analyses were performed to examine the immunological deviations associated with the myeloid signature. Further, we built nomograms to provide a more robust and personalized prognosis for HCC patients. RESULTS: A 2-feature-based, myeloid-specific prognostic signature, namely the myeloid response score (MRS), was constructed. The increase in the MRS was associated with a change in the predominant myeloid populations from CD169+ macrophages (Mφs) in MRSlow HCCs to CD15+CD11b+ neutrophils and CD11b+CD169- Mφs in MRShigh tumors, suggesting a shift in the balance of the myeloid response from antitumor to protumor activities. This alteration was also accompanied by the enhancement of CD8+ T cell exhaustion patterns, including impaired cytotoxic potential and elevated programmed cell death protein 1 (PD-1) expression. The MRS and the MRS-based nomograms had higher accuracy for predicting recurrence and patient survival than the Barcelona Clinic Liver Cancer (BCLC) and tumor-node-metastasis (TNM) staging systems and were validated in a multicenter cohort of HCC patients. Moreover, in a separate cohort of 51 patients, we provided evidence that the MRS was associated with the efficacy of sorafenib treatment for recurrent HCC. CONCLUSIONS: We identified and validated a descriptive and prognostic myeloid signature for HCC. HCC tissues with low, intermediate, and high MRS estimates represent tumors with immunocompetent, immunodeficient, and immunosuppressive subtypes, respectively. This technically simple and reliable myeloid signature shows remarkable prognostic potential for HCC after resection and could serve as the basis for the stratification of HCC immune subtypes to aid in a wide range of clinical decisions.

overall_design: To characterize the cellular activities underlying the change in the MRS between tumors, we performed gene expression microarray analysis for 21 HCC samples (MRSlow, n = 10; MRShigh, n = 11).

first: Chao-Qun

last: Liu

first: Limin

last: Zheng


title: Single cell transcriptome profiling of the bone marrow niche at steady state and under stress conditions.

status: Public on Apr 11 2019

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Single-cell RNA-seq analysis of bone marrow niche populations.

overall_design: Single-cell RNA-sequencing libraries of  BM niche.

first: Anastasia

middle: N

last: Tikhonova

first: Aristotelis

last: Tsirigos

first: Iannis

last: Aifantis


title: Next Generation Sequencing Analysis of Beta-actin knockout (KO) and wildtype (WT) Mouse Embryonic Fibroblast (MEFs) Transcriptomes Under Adipogenic Induced Conditions

status: Public on May 07 2019

city: Abu Dhabi

first: Mohamed

last: Al-Sayegh

address: Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: mRNA profiles of beta-actin knockout (KO) and wild-type (WT) MEFs induced to adipocyte-like feature to study how global transcriptome changes during differentiation

overall_design: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the changes of the global gene expression programs in beta-actin knockout (KO) and wild-type (WT) Mouse Embryonic Fibroblasts during adipogenesis. MEFs were induced to adipogenic like feature using growth media supplemented with 10mg/ml Insulin (Ins), 2mM Dexamethasone (Dex), 0.5mM 3-isobutyl-1-methylxanthine (IBMX) and 25mg/ml Ascorbic Acid (AsA).

first: Nizar

last: Drou


title: Genome-wide identification and analysis of long noncodingRNAs in porcine preadipocytes treated with TGF-β1

city: Changchun

first: bao

last: yuan

address: 5333 Xi'an Road

institute: Jilin University

summary: Several studies have revealed thatTGF-β1 may play a key role in epithelial-mesenchymal transition (EMT); however, little is known about the effects of TGF-β1 treatment on porcine preadipocytes. To identify the key lncRNAregulator, two libraries were constructed from porcine preadipocytes were treated with or without 10 ng/mL human recombinant TGF-β1 for 48 h by using the Illumina HiSeqXten platform. RT-qPCR was used to detect the expression of ten differentially expressed lncRNAs, andthe results were consistent with the sequencing results. In addition, the lncRNATargets platform was used to construct an interaction network of lncRNAs and the Smad7 gene.A total of 39 lncRNA transcripts, including 28 upregulated and 11 downregulated transcripts, were significantly differentially expressed in the TGF-β1 group compared with the control group. Functional annotation and enrichment analysisof the host genes revealed that the differentially expressed lncRNAs were related to single-organism process, cell part and cellular process.We constituted the lncRNA/mRNAco-expression network in the TGF-βsignaling pathway.In our study, we systematically investigated the lncRNA contents in porcine preadipocytes were treated with or without 10 ng/mL human recombinant TGF-β1. A total of 8158 lncRNA transcripts were identified, and 39 of these transcripts were significantly differentially expressed between two libraries.

overall_design: Porcine preadipocytes were treated with 10 ng/mL recombinant human TGF-β1or 10 mM citric acid as the negative control (NC)

first: Zhe

last: Zhang

first: Bao

last: Yuan


title: Peritoneal Dialysis Induces Alterations In The Transcriptome Of Peritoneal Cells Before Detectible Peritoneal Functional Changes

status: Public on Jan 24 2019

first: Petra

last: Hruba

address: Videnska 1958

institute: Institute for Clinical and Experimental Medicine

summary: Long-term peritoneal dialysis (PD) is associated with functional and structural alterations of the peritoneal membrane. Inflammation may be the key moment and consequently fibrosis, the end result of chronic inflammatory reaction. The objective of the study was to identify genes involved in peritoneal alterations during PD by comparing transcriptome of peritoneal cells in short- and long-term PD patients. Peritoneal effluent of the long-dwell of stable PD patients was centrifuged to obtain peritoneal cells. Gene expression profiling of peritoneal cells using microarray between short- and long-term PD patients was compared. Based on microarray analysis 31 genes for RT-qPCR validation were chosen. A 4-hour peritoneal equilibration test (PET) was performed on the day after the long dwell. Transport parameters and proteins appearance rates were assessed. Genes involved in the immune system process, immune response, cell activation, leuko- and lymphocyte activation were found to be substantially up-regulated in the long-term group. RT-qPCR validation showed higher expression of CD24 (CD24 molecule), LY9 (lymphocyte antigen 9 ), TNFRSF4 (tumor necrosis factor receptor superfamily, member 4), CD79A (CD79a molecule, immunoglobulin-associated alpha), CCR7 (chemokine (C-C motif) receptor 7), CEACAM1 (carcinoembryonic antigen-related cell adhesion molecule 1) and IL2RA (interleukin 2 receptor, alpha)  in long-term PD patients, CD24 having the best discrimination ability between short- and long-term treatment. A relationship between CD24 expression and genes for collagen and matrix formation was shown. Activation of CD24 provoked by pseudohypoxia due to extremely high glucose concentrations in dialysis solutions might play the key role in the development of peritoneal membrane alterations.

overall_design:
An observational,prospective, cross-sectional cohort study was performed to compare expression profiles of peritoneal cells of patients with short-term (n=20) and long-term peritoneal dialysis (PD) (n=13). Short-term is defined as patients with a PD duration between 0 and 24 months and long-term patients with a PD duration of ≥ 25 months. Peritoneal effluent of the long-dwell (median 9, range 8-13 hours) was centrifuged to obtain peritoneal cells.   As microarray platform,  Illumina HumanHT 12 v4.0 Expression BeadChips (Illumina) was used.
Classification of clinical samples.

first: Alena

last: Parikova

first: Zdenek

last: Krejcik

first: Viktor

last: Stranecky

last: Lavrikova

first: Janka

last: Franekova

first: R

last: Krediet

first: Ondrej

last: Viklicky


title: The Role of CD83 in ovarian cancer cell line SKOV3

status: Public on Jan 14 2019

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed RNA-Seq of CD83 overexpression SKOV3 cells (OV_1, OV_2, OV_3), CD83 knockdown SKOV3 cells (KD_1, KD_2, KD-3), and control SKOV3 cells (NC_1, NC_2, NC_3) using BGISEQ-500 platform (BGI, China).

overall_design: To initiate this study, we developed human CD83 stable overexpression and knockdown sublines of SKOV3 cells, using infection of full length CD83 lentivirus (CD83-OV) and CD83-specific lentiviral shRNA (CD83-KD), respectively. LV5 or LV3 lentivirus, containing GFP and puromycin resistant site, was served as negative control (NC). Polybrene (4 μg/ml) was used to increase the lentivirus infection efficiency. GFP-positive stable transfected cell lines were generated by two rounds of puromycin (1μg/ml) selection.

first: Aalia

last: Batool


title: Gene expression profiles of 35 paired HCC and non-tumor tissues by RNA-seq data

status: Public on Mar 03 2019

first: Ying

last: Jiang

address: Life Science Park Road

institute: National Center for Protein Sciences (Beijing)

summary: This study aims to uncover the transcriptomic variations in HCC

overall_design: RNA-seq reads per sample were mapped to the reference using Tophat v2.0.12. The reference consists of the human reference genome and the Ensembl annotated human transcriptome (GRCh37/hg19 assembly). The overall mapping rate per sample was 92% on average. Next, the mapped reads were processed using cufflinks v2.2.1 with the ‘classic-fpkm’ library normalization method and ‘fr-unstranded’ library type to quantitate gene expression against Ensembl transcript annotation.

first: Li


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats

status: Public on Dec 01 2018

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 1129 Farm Lane

department: Biochemistry and Molecular Biology

institute: Michigan State University

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

overall_design: Refer to individual Series


title: Transcriptome analysis of flowering variation with or without Gibberellin (GA) in two inbred lines of korea radish

status: Public on Jan 31 2019

city: Daejeon

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

country: South Korea

institute: KRIBB

summary: We analyze that the flowering integrators, FT and SOC, change to  expression by GA treatment

overall_design: After vernalization for a certain period of time, we observed changes with or without GA treatment in two inbred lines of radish

first: HyeSun

last: Cho


title: The LIM-homeodomain transcription factor LHX4 is required for the differentiation of retinal rod bipolar cells and rod-connecting cone bipolar cells

status: Public on Feb 23 2019

first: Xuhui

last: Dong

overall_design: Gene profiles of post-natal day 6 (P6) control and Lhx4-null retina were generated using Illumina

first: Lin

last: Gan


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats [RNA-Seq]

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist that elicits a broad spectrum of dose-dependent effects in the liver, including hepatic lipid accumulation coupled with inflammation. To determine the role of inflammatory lipid mediators in TCDD-mediated hepatotoxicity, eicosanoid metabolism was investigated in female Sprague-Dawley (SD) rats. Rats were gavaged with sesame oil vehicle or 0.01-10 µg/kg TCDD every 4 days for 28 days. Hepatic RNA-Seq data from female SD rats was compared with data from female C57BL/6 mice and functionally annotated to determine key toxicogenomic differences between the two species regarding TCDD exposure. Hepatic RNA-Seq data from female SD rats integrated with untargeted metabolomics of liver, serum, and urine identified dose-dependent changes in linoleic acid (LA) and arachidonic acid (AA) metabolism. TCDD also elicited dose-dependent differential gene expression associated with cyclooxygenase, lipoxygenase, and cytochrome P450 epoxidation/ hydroxylation pathways with corresponding changes in omega-6 (e.g. AA and LA) and omega-3 polyunsaturated fatty acids (PUFAs) as well as their eicosanoid metabolites. Overall, total omega-6 PUFAs increased, while total omega-3 PUFAs decreased. Phospholipase A2 (Pla2g12a) was induced 6-fold consistent with increased AA metabolism, while AA utilization by lipoxygenases Alox5 (2-fold) and Alox15 (10-fold) increased leukotrienes (LTs), important mediators signaling an inflammatory response. More specifically, TCDD increased pro-inflammatory eicosanoids, including leukotriene (LT) B4 (3-fold), and LTB3 (5-fold), known signals for the recruitment of neutrophils to areas of tissue damage. Dose-response modeling of metabolite and gene expression changes suggests the cytochrome P450 hydroxylase/epoxygenase and the lipoxygenase pathways are the most sensitive to TCDD. While several differentially expressed genes (DEGs) associated with eicosanoid biosynthesis contained putative dioxin response elements (pDRE) within their regulatory region, ChIP-Seq analysis showed little AhR enrichment, suggesting TCDD-elicited induction of eicosanoid biosynthesis is not a direct effect of AhR activation.

overall_design: Three biological replicates for rats given dose of sesame oil vehicle or 0.01, 0.03, 0.1, 0.3, 1, 3, or 10 μg/kg.

first: Claire

middle: M

last: Doskey

first: Rance

last: Nault

first: Kelly

middle: A

last: Fader

first: Todd

last: Lydic

first: Jason

last: Matthews

first: Dave

last: Potter

first: Bonnie

last: Sharratt

middle: R


title: Expression data of BRAF inhibitor resistant melanoma cells

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

summary: We generated four drug-resistant melanoma cell lines from paired primary/metastatic cell lines using PLX4720 and used for Affymetrix Human Gene 1.0 ST array

overall_design: 8 Samples

first: Margit

last: Balázs


title: Zebrafish Samples for Loss of ATRX cooperates with p53-Deficiency to promote the Development of Sarcomas and other Malignancies

status: Public on Feb 15 2019

city: Boston

first: Kenneth

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: The SWI/SNF-family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas, gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of  telomeres (ALT) pathway in tumor cells, while it also affects Polycomb repressive complex 2 (PRC2)  silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis, we knocked out atrx in our previously published p53/nf1-deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. Complete inactivation of atrx using CRISPR-cas9 was lethal in developing fish and resulted in an alpha-thalassemia-like phenotype including reduced alpha-globin expression. In p53/nf1-deficient zebrafish neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/- fish, but these fish developed various tumors that were not observed in their atrx+/+ siblings, including epithelioid sarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma and rare types of carcinoma. Most of these cancer types are included in the AACR Genie database of human tumors associated with mutant ATRX, indicating that our zebrafish model reliably reflects a role for ATRX-loss in the early pathogenesis of these types of human cancers. RNA-seq of p53/nf1- and p53/nf1/atrx-deficient tumors revealed that down-regulation of telomerase accompanied ALT-mediated lengthening of the telomeres in atrx-mutant samples. Moreover, inactivating mutations in atrx disturbed PRC2-target gene silencing, indicating a connection between ATRX loss and PRC2 dysfunction in cancer development.

overall_design: Gene expression values were derived from paired end RNA-Seq data that compared zebrafish samples from p53/nf1/atrx-deficient tumors to samples from atrx-wildtype controls (3 vs. 3 samples).

first: Felix

last: Oppel

first: A

middle: T

last: Look


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats [ChIP-Seq]

first: Timothy

last: Zacharewski

overall_design: 5 biological replicates


title: Host-pathogen transcriptomics of Mucor circinelloides spores phagocytosed by mouse macrophages

status: Public on Jan 09 2019

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

institute: Universidad de Murcia

summary: Here, we have studied the first stage of this infection—the interaction of Mucor circinelloides spores with phagocytic cells—from an integrated transcriptomic and functional perspective. Our transcriptomic results showed that a relevant gene network is remodelled in response to phagocytosis, enriched in crucial functions to survive the phagosome, such as nutritional adaptation and response to oxidative stress. An additional transcriptomic analysis of atf1 and atf2 mutants unveiled the complex gene network of secondarily regulated genes involved in the response to phagocytosis. These new insights into the initial phase of mucormycosis define genetic regulators and molecular processes that could serve as pharmacological targets.

sample_organism:
Mus musculus
Mucor lusitanicus

platform_organism:
Mus musculus
Mucor lusitanicus

overall_design:
24 samples are provided and analyzed, comprising 2 replicates (a and b) for each coculture interacting samples and each single culture, which are as follows: Mucor strain R7B cocultured with mouse macrophages (cell line J774A.1) for 5h, strain NRRL cocultured with mouse macrophages (cell line J774A.1) for 5h, wild-type control strain (R7B) cocultured with mouse macrophages (cell line J774A.1) for 5h, Mucor atf1 mutant cocultured with mouse macrophages (cell line J774A.1) for 5h, Mucor atf2 mutant cocultured with mouse macrophages (cell line J774A.1) for 5h, wild-type control strain (R7B) singlecultured in cell media for 5h, Mucor strain NRRL singlecultured in cell media for 5h,  mouse macrophages (cell line J774A.1) singlecultured in cell media (4 replicates) for 5h, strain R7B singlecultured in MMC media for 24h, Mucor atf1 mutant singlecultured in MMC media for 24h, Mucor atf2 mutant singlecultured in MMC media for 24h.

Libraries were prepared with Illumina TruSeq strand-specific mRNA kits and sequenced with an Illumina HiSeq 2500 system to generate 50-bp, first-strand (or reverse) and single-end reads.

last: Perez-Arques

first: Maria-Isabel

last: Navarro-Mendoza

first: Victoriano

last: Garre

first: Francisco-Esteban

last: Nicolas


title: Characterization of embryonic osteoclast precursors

status: Public on Jan 16 2019

city: Durham

first: Yasuhito

last: Yahara

address: Duke Hospital South, 200 Trent Drive, Orange Zone 5th floor

institute: Duke Univ

summary: Embryonically established osteoclast precursors expressing tdTomato reporter gene were analyzed by single cell RNA-sequencing. Data showed that hematopoietic stem cell independent yolk-sac erythromyeloid progenitors produced embryonic osteoclast precursors.

overall_design: Macrophage/ monocyte lineage cells isolated from E14.5 whole body were subjected to the sc RNA-seq. All samples included tdTomato expressing cells derived from E8.5 or E9.5 erythromyeloid progenitors in the yolk-sac.

first: Benjamin

last: Alman


title: A metabolic checkpoint controls hyphal development in Candida albicans via nitric oxide signaling

status: Public on Nov 20 2018

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: We investigated the roles of mitochondrial dynamics in hyphal growth of C. albicans using the small molecule inhibitor MDIVI-1. Strikingly, the small molecule inhibitor represses both the yeast-to hyphae transition and ongoing filamentation, and its effects on morphogenesis can be uncoupled from general growth inhibition. RNAseq experiments of inhibitor-treated cells coupled with Candida mutant analyses suggest the existence of a novel mechanism of action to represses hyphal growth. The inhibitor was protective to host cells, increasing the survival of bone-marrow derived macrophages in ex vivo macrophage-Candida infection assays, suggesting it has potential as a therapeutic.

overall_design: Analysis of RNA-seq  in C. albicans

first: Ana

last: Traven

first: Paul

middle: F

last: Harrrison


title: RNA-seq of heart failure in human left ventricles

status: Public on Nov 14 2018

city: Aurora

first: Mary

middle: E

last: Sweet

state: CO

department: Medicine

institute: University of Colorado Anschutz

summary: The goal of this dataset was to use RNA-seq in human heart tissue to delineate etiology-specific gene expression signatures in heart failure.

overall_design: We performed poly-A enriched RNA-seq in 64 samples from human left ventricle tissue: 14 non-failing donors, 37 dilated cardiomyopathy, and 13 ischemic cardiomyopathy

first: Amrut

middle: V

last: Ambardekar

first: Michael

last: Bristow

first: Luisa

last: Mestroni

first: Matthew

last: Taylor


title: Comparative analysis of mouse decidualization models by using RNA-seq

status: Public on Nov 10 2018

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: There are three well-established mouse models of decidualization: natural pregnancy decidualization (NPD), artificial decidualization (AD) and in vitro decidualization (IVD). In the present study, we analyzed global gene expression changes by using RNA-seq.

overall_design: RNA-seq data were generated from NPD, AD and IVD, respectively.


title: GMUCT sequencing of 4 week old leaves in Arabidopsis ABI3:MTA plants

status: Public on Nov 09 2018

city: Philadelphia

first: Stephen

middle: James

last: Anderson

state: PA

address: 433 South University Avenue

institute: University of Pennsylvania

summary: In order to gain insight into relative stability of transcripts in plants that lacked m6A, we performed global mapping of uncapped and cleaved transcripts

overall_design:
2 replicates of GMUCT in Arabidopsis thaliana ecotype Col-0 ABI3:MTA (mta) plants.
genome-wide mapping of uncapped and cleaved transcripts (GMUCT)

middle: J

first: Xiang

last: Yu

first: Sager

last: Gosai

first: Zachary

first: Rupert

last: Fray

first: Brian

last: Gregory


title: mRNA sequencing of 4 week old leaves in Arabidopsis wild type and ABI3:MTA

summary: In order to gain insight into abundance of transcripts in the presence and absence of m6A, we performed an mRNA sequencing expirement in both mta and Col-0 plants.

overall_design: 2 replicates per genotype of miCLIP-seq in Arabidopsis thaliana ecotype Col-0 wild-type (WT) and ABI3:MTA (mta).

middle: D


title: Profiling of N6-methyladenosine (m6A) in Arabidopsis wild type and ABI3:MTA


title: Profiling of N6-methyladenosine (m6A) in salt-treated and control Arabidopsis

summary: In order to gain insight into m6A in control and salt stress, we performed an miCLIP-sequencing experiment in control and salt treated plants

overall_design: 2 replicates per genotype of miCLIP-seq in Arabidopsis thaliana ecotype Col-0 UBQ10:NTF/ACT2p:BirA Control and salt treated plants


title: Loss of the FAT1 tumor suppressor promotes resistance to CDK4/6 inhibitors via the Hippo pathway

status: Public on Nov 02 2018

city: NEW YORK

first: Sarat

last: CHANDARLAPATY

address: 417 E 68th Street

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

summary: Loss of FAT1 promotes resistance to CDK4/6 inhibitors. This study was to compare the differential mRNA expression of FAT1 crispr cells with parental cells, to identify the underlying mechanisms of resistance.

overall_design: Examnination of differential RNA expression in FAT1 loss cells compared to MCF-7 parental cells.

last: Chandarlapaty

first: Qing

last: Li


title: Genome-wide analysis of liver tissue mRNA expression from Pten-deficient and/or Sav1-deficient mice liver

status: Public on Oct 08 2018

first: Sun-Hye

last: Jeong

address: 291 Daehak-ro

department: Biological science

institute: KAIST

summary: To know the crosstalk between Hippo and AKT pathways in the liver metabolism, we generated liver-specific Pten (AKT signaling), Sav1 (Hippo signaling) and double-knockout mice and analysed the liver mRNA expression globally from 4groups (WT, Pten KO, Sav1 KO and Pten;Sav1 dKO).

overall_design: We sacrificed 3-month-old male mice from 4 groups (WT, Pten KO, Sav1 KO and Pten;Sav1 dKO), and they were deprived of food for 16 h before killing for analyses.

first: Sun

middle: H

first: Dae

last: Lim


title: GMUCT sequencing of 4 week old leaves in salt-treated and control Arabidopsis

summary: In order to gain insight into stability of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

overall_design: 2 replicates per genotype of GMUCT in Arabidopsis thaliana ecotype Col-0 UBQ10:NTF/ACT2p:BirA Control and salt treated plants


title: mRNA sequencing of 4 week old leaves in salt-treated and control Arabidopsis

summary: In order to gain insight into abundance of transcripts in the presence and absence of m6A in control and salt stress, we performed an mRNA sequencing experiment in control and salt treated plants

overall_design: 2 replicates per genotype of mRNA-seq in Arabidopsis thaliana ecotype Col-0 UBQ10:NTF/ACT2p:BirA Control and salt treated plants


title: Identification and analysis of adenine N6-methylation sites in the rice genome

status: Public on Jun 10 2018

city: yichang

first: chao

last: zhou

address: No.8,daxuelu Street

institute: CTGU

type: Methylation profiling by high throughput sequencing

summary: We report the application of 6mA IP-sequencing technology for high-throughput profiling in rice tissues of 12 days' leaf. By obtaining over 20 million high quality clean mapping sequenced reads from immunoprecipitated DNA, we generate genome-wide 6mA maps of rice 12 days' leaf. Using mass spectrometry and immunoprecipitation and validation with analysis of single-molecule real-time sequencing, we observed that about 0.2% of all adenines are 6mA-methylated in the rice genome. 6mA occurs most frequently at GAGG motifs and is mapped to about 20% of genes and 14% of transposable elements (TEs). In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylated cytosine (5mC) at CG sites in gene bodies and is complementary to 5mC at CHH sites in TEs. We show that   OsALKBH1 may be potentially involved in 6mA demethylation in rice. The results suggest that 6mA is complementary to 5mC as an epigenomic mark in rice and reinforces a distinct role for 6mA as a gene-expression associated epigenomic mark in eukaryotes.

overall_design:
Examination of 6mA modification in 12 days' leaves；

The raw data of rice genome PacBio sequencing is available under SRA accession number SRP071598. And the download link is https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP071598 .

first: Chao

last: Zhou

first: D

middle: X


title: RNA-seq analysis of apoptotic HCT116 cells shows widespread mRNA decay and limited noncoding RNA decay.

status: Public on May 01 2018

first: Rui

last: Fu

address: 200 Longwood Ave

department: PCMM

institute: boston children's hospital

summary: Rapid and widespread mRNA decay is a previously unappreciated feature of apoptosis. Previous work showed that apoptotic mRNA decay depends on mitochondrial outer membrane permeabilization (MOMP) and the RNA-processing enzymes, TUT4, TUT7, and DIS3L2. Which RNAs are decayed, however, was not known. Here we present RNA-seq data of TRAIL-induced apoptosis in HCT116 cells showing global decay of mRNAs as well as polyadenylated noncoding RNAs, beginning at the 3’-end.

overall_design: HCT116 cells were treated or untreated with 100ng/ml TRAIL for 2 hrs. Total RNA was then isolated and depleted for rRNA with Ribo-Zero.

first: Xing

first: Judy

last: Lieberman


title: NEXT GENERATION SEQUENCING DETECTS DYSREGULATED PLACENTAL MICRORNAS IN PREECLAMPSIA

status: Public on Sep 12 2018

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

type: Non-coding RNA profiling by high throughput sequencing

summary:
Introduction: To determine the miRNA expression profile in pregnancies complicated by Preeclampsia (PE) and compare it to uncomplicated pregnancies.
Methods: Seventeen placentas from women with PE, [all of them being late onset PE (LOPE)], as well as 17 placentas from uncomplicated pregnancies were analyzed using miRNA NGS. For statistical analyses the MATLAB® simulation environment was applied. The expression of miR-99b and miR-23b were verified using Quantitative Real-Time Polymerase Chain Reaction.
Results: Two miRNAs were found dysregulated in PE complicated placentas. Statistical analysis revealed that miR-99b and miR-23b were under-expressed in complicated placentas as compared to controls.
Discussion: Since specific miRNAs can differentiate complicated from uncomplicated pregnancies, they may be considered as putative PE-specific biomarkers.

overall_design: Blood samples were collected from 17 women with PE (all of them being LOPE) and from 17 with uncomplicated term pregnancies at the time of cesarean section in the 3rd Department of Obstetrics and Gynecology of the National and Kapodistrian University of Athens. Plasma was separated from the collected blood samples, which was used for further analysis. From the 17 pre-eclampsia samples, 5 were used for Next Generation Sequencing (NGS) miRNA expression analysis, as well as from the 17 control samples 5 were similarly used for NGS miRNA analysis. Differentially expressed (DE) miRNAs were further evaluated in all 34 samples, using qRT-PCR in order to confirm DE miRNA expression.

first: Aggeliki

last: Kolialexi


title: Protein-interaction profile sequencing of 4 week old leaves in Arabidopsis ABI3:MTA plants.

first: Stephen

summary: In order to investigate the influence of m6A on RNA secondary-structure and RNA-protein interactions, we performed protein-interaction profile sequencing (PIP-seq)

overall_design: 2 replicates per genotype of protein interaction profile sequencing (PIP-seq) in  Arabidopsis thaliana ecotype Col-0 ABI3:MTA (mta) plants. Each rep is are crosslinked with formaldehyde split into structure-only and protein-bound libraries and further split to be treated by two different RNases (ssRNase and dsRNase).

first: Xiang

first: Sager

middle: G


title: N6-methyladenosine-mediated structural changes are associated with transcript cleavage and stability in Arabidopsis

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

overall_design: Refer to individual Series


title: RNA Seq Profiling of Murine Salivary Glands in the Presence or Absence of Active MCMV Infection

status: Public on Jan 15 2018

city: Bethesda

first: Ilias

last: Alevizos

state: Maryland

address: 10 Center Dr., RM 1N110

institute: National Institute for Dental and Craniofacial Research (NIDCR)

summary: Recent work indicates that salivary glands are able to constitutively recruit CD8+ T cells and retain them as tissue resident memory T cells (TRM), independently of local infection, inflammation or antigen. To understand the mechanisms supporting T cell recruitment to the salivary gland, we compared T cell migration to the salivary gland in mice infected or not with murine cytomegalovirus (MCMV), a herpesvirus that infects the salivary gland and promotes the accumulation of salivary gland TRM. We found that acute MCMV infection increased rapid T cell recruitment to the salivary gland, but that equal numbers of activated CD8+ 44 T cells eventually accumulated in both infected and uninfected glands. T cell recruitment to uninfected salivary glands depended on chemokines and the integrin α4. Several chemokines were expressed in the salivary glands of both infected and uninfected mice and many of these could promote the migration of MCMV-specific T cells in vitro. MCMV infection increased expression of chemokines that interact with the receptors CXCR3 and CCR5, but neither receptor was needed for T cell recruitment to the salivary gland during MCMV infection. Unexpectedly however, the chemokine receptor CXCR3 was critical for T cell accumulation in uninfected salivary glands. Together, these data suggest that CXCR3 and the integrin α4 mediate T cell recruitment to uninfected salivary glands, but that redundant mechanisms mediate T cell recruitment after MCMV infection.

overall_design: Transcriptomic profiling was performed on salivary glands from three MCMV-infected and three naïve mice using total RNA-Seq

first: Sofia

last: Caldeira-Dantas

first: Thomas

last: Furmanak

first: Corinne

last: Smith

first: Michael

last: Quinn

first: Leyla

middle: Y

last: Teos

first: Adam

last: Ertel

first: Drishya

last: Kurup

first: Mayank

last: Tandon

first: Christopher

last: Snyder


title: The role of metallothionenins and Slc genes in accommodation in ABOincompatible transplantation

status: Public on Jan 19 2018

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

institute: Institute for Clinical and Experimental Medicine

summary: Both present hemagglutinins and anti HLA antibodies bind to vascular endothelial cells in kidney transplantation, however in some patients this antibody-endothelial interaction is not associated with obvious tissue injury. Mechanisms of this phenomenon called accommodation remain poorly understood.  Illumina Human HT-12 v4 Expression BeadChips whole renal transcriptome was evaluated in 3-months protocol biopsies with isolated C4d staining in otherwise stable ABO incompatible and HLA incompatible DSA positive kidney grafts (n=18) as well as in C4d negative HLA compatible grafts with normal histological findings (n=8). Top differently regulated genes were further validated using RT-qPCR at the independent patient cohort (n=24). GO terms with the highest fold enrichment revealed by gene annotation analysis of deregulated genes between ABOi and HLAi groups were represented by cadmium ion binding (p<0.01), apical plasma membrane (p<0.01) and anion transmembrane transporter activity (p<0.05). Majority of deregulated genes between both groups belongs to metallothioneins (MT) and solute carrier family (Slc) genes. The decreased expression of 5 Slc family genes (SLC4A1; SLC4A9; SLC17A3; SLC12A3; SLC30A2) and 3 metallothioneins of class1 (MT1F, MT1G and MT1X) in ABOi compared to HLAi group was verified by RT-qPCR. The most deregulated genes in C4d negative compared with C4d positive cohorts were those included in GO term “mitochondrion” which suggests the activation of metabolism in complement activation. In conclusion, hemagglutinin- and anti-HLA antibody-endothelial interactions and complement activation lead to different regulation of metallothioneins and distinct solute carrier family genes, which suggests its specific role in the accommodation phenomenon.

overall_design: The experiments were performed with total RNA derived from the renal graft biopsy samples of 18 different patients who had undergone a kidney transplantation.  Only the patients with C4d positive 3 months protocol biopsies of either after ABO incompatible transplanation or after HLA incompatible transplantation were included in the study.  RNA profiles of C4d positive 3 months protocol biopsies in ABO incompatible patients with excellent graft function and no signs of rejection  were compared with HLA incompatible patients with positive donor specific antibodies and subclinical antibody mediated rejection. As microarray platform,  Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) was used.

first: Ondrej

last: Viklicky

first: Zdenek

last: Krejcik

first: Viktor

last: Stranecky

first: Faikah

last: Gueler

first: Alena

last: Parikova

first: Janka

last: Slatinska

first: Mariana

last: Wohlfahrtova

first: Ilja

last: Striz

first: Jiri

last: Fronek

first: Eva

last: Honsova

first: Jana

last: Maluskova


title: Transcriptome profile of MafB-cKO Sertoli cells.

status: Public on Dec 23 2017

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

summary: MafB is a transcription factor acts as an important regulator of the  development and differentiation of various organs and tissues. MafB is expressed in sertoli, leydig, and germ cells in adult mice testis. However, analysis of MafB cKO mice testis showed no dissruption of spermatogenesis or obvious abnormal structure. Thus, the exact function is unclear. We examined any change in the transcriptome profile of MafB-cKO Sertoli cells. Results of signaling pathway analysis of the downregulated genes was related to immune-function but not spermatogenesis.

overall_design: Examination of 2 samples (cKO and Control). Each sample contains RNA mixed from 3 mice. Paired-end RNA sequencing was performed with NextSeq500 sequencer (Illumina).

first: Satoru

last: Takahashi


title: Asynchronous remodeling is a driver of failed regeneration in Duchenne muscular dystrophy

status: Public on Jan 14 2018

city: DC

first: mamta

last: giri

state: Washington. DC

address: 111 Michigan Ave

department: Center for Genetic Medicine

institute: CNMC

summary:
49 human patient mRNA profiles was generated using HG-U133 Plus 2.0 microarrays. Procesed in Affymetrix Expression console using Plier normalization method and later processed in Partek Genomics Suite. The clustering figure was generated using HCE clustering software.
We sought to determine the mechanisms underlying failure of muscle regeneration that is observed in dystrophic muscle through hypothesis generation using muscle profiling data (human dystrophy and murine regeneration). We found that transforming growth factor β-centered networks strongly associated with pathological fibrosis and failed regeneration were also induced during normal regeneration but at distinct time points. We hypothesized that asynchronously regenerating microenvironments are an underlying driver of fibrosis and failed regeneration. We validated this hypothesis using an experimental model of focal asynchronous bouts of muscle regeneration in wild-type (WT) mice. A chronic inflammatory state and reduced mitochondrial oxidative capacity are observed in bouts separated by 4 d, whereas a chronic profibrotic state was seen in bouts separated by 10 d. Treatment of asynchronously remodeling WT muscle with either prednisone or VBP15 mitigated the molecular phenotype. Our asynchronous regeneration model for pathological fibrosis and muscle wasting in the muscular dystrophies is likely generalizable to tissue failure in chronic inflammatory states in other regenerative tissues.

overall_design: These datasets contained profiles from 6 normal controls, 17 DMD (absence of dystrophin), 11 BMD (present but abnormal dystrophin), 7 LGMD2I (FKRP deficiency, a glycosylation defect), and 8 LGMD2B (DYSF). Patients had a broad range of ages, clinical severity of their disease, and histopathological findings, although all neuromuscular disease patients showed evidence of a dystrophic process (degeneration/regeneration of muscle fibers)

first: Eric

middle: P

last: Hoffman


title: MicroRNA-146a and glucocorticoids in inflamed airway epithelial cells

status: Public on Nov 01 2018

city: Hershey

first: Faoud

last: Ishmael

address: 500 University Dr.

department: Division of Pulmonary and Critical Care Medicine

institute: Penn State College of Medicine

summary: Glucocorticoids are the cornerstone of asthma and other inflammatory disease therapy. Resistance or insensitivity to glucocorticoids presents a substantial and challenging clinical problem. MicroRNAs are emerging as central regulators of inflammation, but it is not clear whether they could augment or attenuate glucocorticoid responses. We aimed to identify microRNAs that regulate cytokine and chemokine expression in airway epithelial cells and whether these miRNAs are subject to the effects of glucocorticoids. MicroRNAomic analyses of primary bronchial epithelial cells and the A549 airway epithelial cell line identified 7 miRNAs that were altered by inflammatory cytokine treatment and 22 that were regulated by glucocorticoids (n=3 for each treatment). miR-146a emerged as a central candidate, whose expression was induced by TNF-alpha and repressed by glucocorticoids. Its role as a candidate in asthmatic inflammation was supported by expression profiling in human asthmatics, which showed that plasma miR-146a expression was elevated in asthma and associated with measures related to worse asthma outcomes, including elevated blood eosinophil counts, higher asthma control questionnaire scores, and need for higher doses of inhaled glucocorticoids. However, transfection of miR-146a in A549 cells treated with TNF-alpha +/- glucocorticoids produced an anti-inflammatory effect and with increased efficacy of glucocorticoids. We propose a model whereby miR-146a is induced by inflammatory conditions as a feedback mechanism to limit inflammation. Glucocorticoids may limit this regulatory pathway by preventing miR-146a expression. Consequently, exogenous administration of miR-146a could be a novel therapeutic strategy to enhance effects of glucocorticoids.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Cultures of the human airway epithelial cell line NuLi-1 were treated with control (n=3), dexamethasone (n=3), TNF-alpha (n=3), or dexamathasone plus TNF-alpha (n=3). Total RNA was isolated from the 12 culture samples for evaluation of microRNA expression levels.


title: RNA-sequencing from wild-type (WT) or Tie2-Ino80 knockout (KO) mouse embryo hearts

status: Public on Nov 21 2017

city: Stanford

first: Devin

middle: Aalpoel

last: King

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

summary:
Purpose: Endothelial cell-specific knockout of the INO80 chromatin-remodeling complex in developing mouse embryos results in defective coronary angiogenesis. Transcriptome analysis on whole hearts was performed to understand how Ino80 regulates the genome to influence angiogenesis.
Methods: mRNA was extracted from whole hearts after surgical removal from embryonic day 13.5 mice, either WT or Tie2-Ino80 KO, and prepped for Illumina sequencing using the NEBNext Ultra RNA Library Prep kit.
Results: Deletion of Ino80 in the two major coronary progenetiors results in intermediate non-compaction phenotypes and an increase in E2F-mediated gene expression and cellular proliferation.
Conclusions: Ino80 normally functions to suppress E2F-mediated proliferation in cardiac endothelial cells in order to promote productive angiogenesis and prevent underdevelopment of the myocardium heart muscle. Loss of this critical chromatin-remodeling function results in human disease phenotypes.

overall_design: mRNA profiles from embryonic day E13.5 mice were generated from WT or Tie2-Ino80-KO whole hearts using deep sequencing with three biological replicates for each. An average of 33.9M and 53.5M reads per replicate were included in the final analysis for the WT and KO samples, respectively.

first: Jae

last: Chung


title: miRNA Expression data from Glioblastoma Multiforme patient tumor samples, healthy brain tissue (partly from GBM patients) and NHA cell line and Human fetal astrocyte cell line

status: Public on Sep 15 2017

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

summary:
Although glioblastoma multiforme is a common brain tumor, there is a need to elucidate underlying mechanisms behind its initiation and progression and identifying key molecular pathways for improving treatment.
Here, we used combined miRNA-mRNA transcriptome analysis to discover novel genes and networks in GBM

overall_design: 16 fresh-frozen glioblastoma multiforme samples and 7 healthy brain tissues were analyzed by using miRNA and whole transcriptome microarray chips. Data was filtered and analyzed

first: Emre

middle: C

last: Tuysuz

first: Omer

last: Bayrak


title: Novel Atherogenic Pathways from the Differential Transcriptiome Analysis of Diabetic Epicardial Adipose Tissue

status: Public on Jan 10 2018

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we performed transcriptome sequencing on the Subcutaneous Adipose Tissue and Epicardial Adipose Tissue of both diabetic and nondiabetic human patients.

overall_design: Examination of transcriptome in human fat samples

first: Gianluca

last: Iacobellis

middle: W

first: Gaofeng

last: Wang


title: Next Generation Sequencing Facilitates Quantitative Analysis of the control 3T3-L1 (3T3-L1-NC) and LIGHT (tnfsf14) overexpression 3T3-L1 cells (3T3-L1-LIGHT) before and after differentiation into beige adipocytes

status: Public on May 22 2018

city: Xuzhou

first: Yanbo

last: Kou

address: Tongshan Road No. 209

institute: Xuzhou Medical University

summary:
Purpose: The goals of this study are to compare NGS-derived 3T3-L1-NC  transcriptome profiling (RNA-seq) to LIGHT overexpression 3T3-L1 cells and find out the DEGs
Methods: mRNA profiles of 3T3-L1-NC and 3T3-L1-LIGHT before and after differentiation into beige adipocytes were generated by deep sequencing, in triplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript isoform level.
Results: Using an optimized data analysis workflow, we mapped about 6.53 Gb data per sample. The average genome mapping rate is 87.27% and the average gene mapping rate is 80.18%. 18,255 genes were identified in which 17,367 of them are known genes and 1,001 of them are novel genes. 13,086 novel transcipts were identified in which 9,304 of them are previously unknown splicing event for known genes, 1,001 of them are novel coding transcripts without any known features, and the remaining 2,781 are long noncoding RNA.
Conclusions: Our study represents the first detailed analysis of the impact of LIGHT on gene expression in process of beige adipocytes biogenesis with biologic replicates, generated by RNA-seq technology.

first: Yugang


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming

status: Public on Feb 20 2018

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg


title: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming  [Pax5-ChIP-Seq-Tet-On]

summary: EBF1 is essential for B cell specification and commitment. To explore the dynamics of EBF1 initiated B cell programming, we performed EBF1 ChIP-seq, ATAC-seq, bisulfite-seq, RNA-seq and several histone ChIP-seq analyses at different stages of the transition from Ebf1-/- pre-pro-B to pro-B triggered by EBF1 restoration. We also performed Pax5 ChIP-seq in Ebf1-/- pre-pro-B cell and EBF1-restored pro-B cell to study the pioneering function of EBF1 that allows other transcription factors to access certain chromatin sites.

overall_design: Pax5 ChIP-Seq analysis in Ebf1-deficient pre-pro-B cell and EBF1-restored pro-B cell.

first: Rui

last: Li

first: Senthilkumar

last: Ramamoorthy

first: Chavez

last: Lukas

first: Rudolf

last: Grosschedl


title: Expression data from Glioblastoma Multiforme patient tumor samples, healthy brain tissue (partly from GBM patients) and NHA cell line and Human fetal astrocyte cell line

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

platform_organism:
Homo sapiens
synthetic construct


title: Gene Expression data from Glioblastoma Multiforme patient tumor samples, healthy brain tissue (partly from GBM patients) and NHA cell line and Human fetal astrocyte cell line

middle: F


title: Arabidopsis AT2G24360 knock-out lines microarray

status: Public on Sep 01 2017

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: STYK knock-out alters the gene expression levels as compared to wild-type

overall_design: Organism : Arabidopsis thaliana , Agilent Custom Arabidopsis Gene Expression  8x60k Array (AMADID: 037661) designed  by Genotypic Technology Private Limited.

first: Ram

last: Rajasekharan

first: Anitha

last: Vijayakumarl


title: Expression data from LIF treated chordoma cell lines U-CH1 and MUG-Chor1

status: Public on Jul 26 2017

summary:
Leukemia Inhibitory Factor is an important cytokine of the IL family. Recent findings suggest it has a crucial role in cancer progression
We used microarray to monitor the global changes in gene expression after LIF treatment for 3 weeks in two chordoma cell lines

overall_design: Chordoma cell lines U-CH1 and MUG-Chor1 were treated 3 times a week with 100ng/mL recombinant human Leukemia Inhibitory Factor. Cells were harvested and microarray was conducted.

first: Mesut

last: Sahin


title: Characterizing protein-DNA binding event subtypes in ChIP-exo data

status: Public on Feb 13 2018

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: Regulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein-protein interactions with other regulators. Each genomic recruitment mechanism may be associated with distinct motifs, and may also result in distinct characteristic patterns in high-resolution protein-DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein-DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5’ to 3’ exonuclease digestion. Since different regulatory complexes will result in different protein-DNA crosslinking signatures, analysis of ChIP-exo sequencing tag patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type, or rely on the presence of DNA motifs to cluster binding events into subtypes. To systematically detect multiple protein-DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype membership of protein-DNA binding events using both ChIP-exo tag enrichment patterns and DNA sequence information, thus offering a principled and robust approach to characterizing binding subtypes in ChIP-exo data. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix detects cooperative binding interactions between FoxA1, ERalpha, and CTCF, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Genome-wide analysis of key regulatory factors in breast cancer progression using ChIP-exo

first: Naomi

last: Yamada

first: William

middle: K

last: Lai

first: Nina

last: Farrell

first: B

last: Pugh


title: Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

status: Public on Sep 13 2017

city: Richland

first: Ryan

middle: Scott

last: McClure

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

summary: Testing of response of hetertrophic partners (Halomonas sp. HL-48 and Marinobacter sp. HL-58) to both axenic and co-culture growth using both glucose and xylose

sample_organism:
Halomonas sp. HL48
Halomonas sp. HL58

platform_organism:
Halomonas sp. HL48
Halomonas sp. HL58

overall_design: Both Halomonas sp. HL-48 and Marinobacter sp. HL-58 were grown either on glucose axenically or in co-culture and on xylose in co-culture.  Halomonas HL-48 was also grown on xylose axenically.  Transcriptomic data was collected under each condition and used to determine each organisms response to the other under both competitive and commensal conditions.

first: Nymul

last: Khan

first: Yukari

last: Maezato

middle: S

first: Colin

last: Brislawn

first: Jennifer

middle: M

last: Mobberley

first: Nancy

last: Isern

middle: B

last: Chrisler

first: Lye

last: Markillie

first: Brett

last: Barney

first: Hyun-Seob

last: Song

last: Nelson

first: Hans

last: Bernstein

first: Meng


title: Role of PhoPQ TCS plays in Shigella virulence

status: Public on Nov 28 2017

city: shanghai

first: Zhiwei

last: Lin

state: shanghai

address: dongan road 131 , xuhui district, Shanghai

institute: School of Basic Medical Science and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University

summary: To explore what important role of PhoPQ TCS plays in Shigella virulence, the Agilent microarray technologies was used to compare the transcriptional profiles of Shigella flexneri 2a 301 and △phoPQ mutant strains at middle-log phase (6 h) or early-stationary phase (10 h) under LB growth conditions.

overall_design: Shigella flexneri 2a 301 and △phoPQ mutant strains were grown at middle-log phase (6 h) or early-stationary phase (10 h) under LB growth conditions with three biological replicates. In total, 12 sample were analyzed

first: Di

last: Qu


title: Gene-expression molecular subtyping of triple-negative breast cancer tumors

status: Public on Aug 27 2017

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)