title: Expression analysis on endothelial cells migrated into matrigel reconstituted with microfibrillar-associated protein 5 (MFAP5) protein

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Ovarian cancer is the fifth most common form of cancer in women in the United States. Among different types of ovarian cancer, epithelial ovarian cancer is the most common and is highly lethal; however, prognostic and predictive markers, which can be used to predict chemoresponse and patient survival, have not been thoroughly explored. One critically important yet often overlooked component to the tumor progression process is the tumor microenvironment. Primarily composed of fibroblasts and extracellular matrix proteins (ECM) as well as endothelial cells and lymphocytic infiltrate, the tumor microenvironment has been shown to directly affect cell growth, migration, and differentiation through secreted proteins, cell-cell interactions and matrix remodeling (Tlsty and Coussens, 2006). The tumor microenvironment has the potential to promote tumor initiation of normal epithelial cells and facilitate progression of malignant cells, thereby, presenting a unique approach to diagnosing, understanding and treating cancer. Using a whole-genome oligonucleotide array platform to perform transcriptome profiling on the fibroblastic stromal component microdissected from a series of advanced stage high-grade serous ovarian adenocarcinomas, we identified a transcriptome signature for the ovarian cancer-associated fibroblast (CAF). We further functionally characterized one of the identified genes, MFAP5, and we showed that stromal MFAP5 is a prognostic marker associated with poor patient survival. In addition, to investigate the signaling mechanism and the effect of MFAP5 treatment on ovarian cancer angiogenesis, transcriptome profiling was performed on mouse endothelial cells migrated into matrigel reconstituted with recombinant MFAP5 protein.

overall_design: From an in vivo study, endothelial cells migrated into matrigel plugs reconstituted with or without recombinant MFAP5 proteins were harvested. Total RNA was isolated from control samples and MFAP5-treated samples. Followed by cDNA synthesis, IVT and biotin labeling, samples were then hybridized onto Affymetrix Mouse Genome 430 2.0 microarrays. For each treatment group, three independent samples were prepared for the microarray experiment.

first: Sze

last: Leung

first: Tsz

first: Samuel

middle: C

last: Mok


title: LncRNA and transcriptomic analysis of fetal membrane revealed potential targets involved in oligohydramnios

status: Public on Dec 30 2019

city: Guangzhou

first: hongchang

last: huang

state: Guangdong

address: International Biotech Island

country: China

institute: Forevergen Biosciences Co.,Ltd

summary: The challenge of oligohydramnios study is multiple causes of oligohydramnios. Long noncoding RNAs (lncRNAs) is a set of RNAs that has been proved to function in multiple biological process. Currently, little is know about their expression and possible role in oligohydramnios.  Total RNA was isolated from fetal membranes ressected from oligohydramnios pregnant women (OR) and normal amniotic fluid control (Normal).RNA-sequencing (RNA-seq) obtain that a total of 801 lncRNAs and 367 mRNAs were differentially expressed in OR. Of which, 638 lncRNAs and 189 mRNAs were upregulated, and 163 lncRNAs and 178 mRNAs were downregulated. Of these lncRNAs, 566 of them were intergenic lncRNA, 351 were intronic antisense lncRNA，and 300 natural antisense. The differentially expressed lncRNA were primary located in chromosome 2, 1 and 11. KEGG enrichment pathways revealed the differential expressed mRNAs were enriched in pathway in cancer, Ras signaling pathway, TNF signaling pathway, focal adhesion, and chemokine signaling pathway. The qRT-PCR result confirmed that LINC00515 and RP11-388P9.2 were upregulated in OR. Furthermore, the constructed lncRNA-miRNA-mRNA regulatory network revealed TNR, CFTR, ABCC2, ABCA12, and COL9A2 as the candidate targets of LINC00515 and RP11-388P9.2. A wide range of lncRNAs were alert in OR, in particularly, LINC00515 and RP11-388P9.2 were confirmed to be uprgulated in OR, and their predicted downstream targets were transport and tissue growth and development associated. Further study focused on the role of differential expressed lncRNAs such as LINC00515 and RP11-388P9.2 would provide more insight into the pathophysiology in OR

overall_design: Total RNA was isolated from fetal membranes ressected from oligohydramnios pregnant women (five OR samples) and normal amniotic fluid control (five Normal samples).

first: Hui

last: Chen

first: Jian-ping

last: Zhang

first: Yu-hua

last: Ou


title: Global transcriptome analysis identifies genes regulated by FDP

status: Public on Dec 31 2019

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

country: Germany

institute: Max Planck Institute for Plant Breeding Research

type: Expression profiling by genome tiling array

summary: Flowering of Arabidopsis is induced at the shoot meristem by environmental and endogenous signals.  FLOWERING LOCUS T (FT) protein is a systemic signal that induces rapid flowering in response to long summer days (LDs) whereas gibberellin (GA) growth regulators trigger flowering by default in short days (SDs). Mutations in the bZIP transcription factor FDP, which physically interacts to FT, cause late flowering and dwarfism. In order to study the genetic pathways affected by FDP, we compared the global transcriptome changes of Col-0 plants carrying a fusion of the strong ubiquitously expressed CaMV35S promoter to an FDP DsRNAi construct (35S::FDP dsRNA).

overall_design: Col-0 wt and 35s::FDP dsRNA plants were grown under LD conditions during 9 days. Aerial parts of each genotypes were harvested at the end of the light period (ZT16). Biological triplicates of each genotype were used for the Tiling Array experiments.

first: Maida

last: Romera-Branchat

first: Seonghoe

last: Jang

first: Aimone

last: Porri

last: Andrés

first: Pedro

last: Madrigal

first: José

middle: L

last: García-Martínez

first: Isabella

last: Nougalli

first: George

last: Coupland


title: Long noncoding RNAs expression profile in patients with rheumatoid arthritis

city: Weifang

first: Donghua

last: Xu

state: Shandong

address: Yuhe Road No.2428

department: Department of Rheumatology and Immunology

institute: Weifang Medical University

summary: Long noncoding RNAs (lncRNAs) belong to a new class of noncoding RNAs. Emerging evidence has shown that lncRNAs play a crucial role in the regulation of autoimmunity. During the past few years, the modifying effects of lncRNAs in rheumatoid arthritis (RA) have drawn much attention. However, the underlying molecular mechanisms involved in RA pathogenesis remain largely unknown. Herein, we aim to investigate the expression profile of lncRNAs in patients with RA and identify promising targets for RA diagnosis and treatment.Microarray screening and real-time PCR of lncRNAs were performed in the serum from 3 RA patients and 3 healthy controls. Significantly differentially expressed lncRNAs were selectively verified in 43 RA patients and 40 healthy controls by real-time PCR. LncRNA-mRNA co-expression and gene-pathway networks were assured in the bioinformatics analysis.After microarray analysis, there were a total of 73 up-regulated and 61 down-regulated lncRNAs as well as 128 up-regulated and 37 down-regulated mRNAs in the serum of RA patients. After validated by real-time PCR, 5 of these lncRNAs were found to be significantly up-regulated in the serum of RA patients including RNA143598, RNA143596, HIX0032090, IGHCgamma1, and XLOC_002730. Significant association was observed between these lncRNAs and the disease course, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) as well as anti-cyclic citrullinated peptide (anti-CCP) antibody. Computational analysis revealed that 55 of the differentially expressed mRNAs were associated with 41 lncRNAs involved in signaling pathways of toll like receptors (TLRs), nuclear factor-kappa B (NF-κB), and cytokine, especially the IRF3/IRF7 mediated signaling transduction.

first: Hongying

last: Lu

first: Shushan

last: Yan

first: Lanyu

last: Liu

first: Xiaoodong

last: Wang

first: Jihong

first: Weijun

last: Gu

first: Xixing

last: Hou


title: Co-expression of microrna and mrna in cytogenetically normal acute myeloid leukemia patients [miRNA]

city: Setia Alam

first: Ezalia

last: Esa

address: NIH

department: Haematology unit

country: Malaysia

institute: Institute for Medical Research

summary: The study integrated both miRNA and mRNA profiles to explore novel miRNA-mRNA interactions that affect the regulatory patterns in de novo CN-AML.  A total of 637 significant negative correlations (FDR <0.05) were reported. Network analysis revealed a cluster of 12 miRNAs that represents the majority of the mRNA targets. Within the cluster, five miRNAs; miR-495-3p, miR-185-5p, let-7i-5p, miR-409-3p, and miR-127-3p were suggested to play a pivotal role in the regulation of CN-AML as they are associated with negative regulation of myeloid leukocyte differentiation, negative regulation of myeloid cell differentiation, positive regulation of haematopoiesis, and hematopoiesis and its regulation. Three novel interactions in CN-AML were predicted, let-7i-5p:HOXA9, miR-495-3p:PIK3R1 and miR-495-3p:CDK6 which are responsible in regulating myeloid cell differentiation in CN-AML.

overall_design: nCounter platform was utilised to profile both miRNA and mRNA using a similar set of patient samples (n = 24). The miRNA-mRNA network was constructed and underlying biological functions of mRNAs were predicted by gene enrichment. Finally, the interaction pairs were assessed by TargetScan.

first: Ariwibawa

middle: K

last: Hashim

first: Zubaidah

last: Zakaria

first: Alifah

middle: N

last: Hassan

first: Yuslina

middle: M

last: Yusoff

first: Nor

middle: R

last: Kamaluddin

first: Ahmad

middle: Z

last: Rahman

first: Elsa

middle: H

last: Mohamed

first: Chang

last: Meng

first: Rashidah

first: Indhira

last: Subbiah

first: Ehram

last: Jamian

first: Caroline

last: Ling

first: Lim

middle: S

last: Min

first: Lau

middle: P

last: Choon

first: Pung

middle: Y

last: Fen

first: Shamsul

last: Zain


title: Co-expression of microrna and mrna in cytogenetically normal acute myeloid leukemia patients [mRNA]

first: Ezalia


title: Co-expression of microrna and mrna in cytogenetically normal acute myeloid leukemia patients

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

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

overall_design: Refer to individual Series


title: Neurod2 RNA-Seq

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

type: Expression profiling by high throughput sequencing

summary: Neurod2 expression was knocked down in primary cortical neurons from mouse and RNA-Seq was performed.

overall_design: Two separate shRNAs against Neurod2 (shNEurod2-1 and shNeurod2-2) and a non-silencing shRNA (NS) were transfected into primary neurons prepared from E14.5 mouse cortex at plating by the nucleofection method, total RNA was extracted at 4 days in vitro and total RNA was prepared for RNA-Seq analysis.

middle: I

last: Dunn


title: Direct Conversion of Mouse Fibroblasts into Neural Stem Cells by Chemical Cocktail Requires Stepwise Activation of Growth Factors and Nup210

city: Shanghai

first: Lin

last: Cheng

state: Shanghai

address: 808 Building of Sci-Tech, 197 Ruijin 2nd Rd

institute: Shanghai Jiao Tong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neural stem cells (NSCs) are valuable for both basic research and clinical application. We previously reported a chemical cocktail that could reprogram somatic cells into neural progenitor cells. However, the process of chemical induction is complex and the underlying mechanism remains largely elusive. Here, we identified a new culture condition that greatly promotes the efficiency of NSC generation directly from mouse fibroblasts based on our reported chemical cocktail. Transcriptome and epigenome analyses during the reprogramming process demonstrated that growth factors including IL6, FGF5 and LIF were dynamically activated and contributed to the chemical cocktail induced cell fate changes. Interestingly, fibroblast-to-NSC conversion requires the synergistic action of these growth factors. Moreover, the reprogramming capacity of both chemical cocktail and growth factors require nucleoporin Nup210 to activate endogenous neural transcription factors SoxB1 family to initiate NSC fate. Our study not only provides a novel protocol to generate NSC directly from mouse fibroblasts, but also reveals an important role of growth factors in chemical-induced cellular reprogramming.

overall_design: mRNA profile and epigenetic analysis of fibroblasts treated chemical cocktail at different timepoints

first: Yuewen

last: Tang


title: Small RNA sequencing of mouse muscle and heart samples after small hairpin RNA delivery

city: Seattle

first: Paul

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

department: Medicine

country: USA

institute: University of Washington

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) is a promising gene therapy strategy for targeting dominant mutations. This therapy leverages small hairpin RNAs (shRNAs) to knock down gene expression; however, delivery of too much shRNA can disrupt the processing of endogenous microRNAs (miRNAs), and lead to toxicity. In this study, we sought to understand the effect that excessive shRNAs have on muscle miRNAs by transducing several constructs in mice and performing small RNA sequencing on their muscle and liver tissues. We found that shRNA expression was highest in the heart, and that when shRNAs accumulated to about 27% of total small RNAs, mice experienced substantial cardiomyopathy. At this level in the heart, shRNAs in other muscle tissues were only ~1.8-7.6% of total miRNAs. Regardless of treatment, the predominant heart microRNAs remained stable across samples, while the lower-expressed miR-451 – one of the only microRNAs processed in a Dicer-independent manner – changed in direct correlation with shRNA level and toxicity. Our data suggest that certain muscle miRNAs compete with exogenous shRNAs, leading to the observed cardiomyopathy, and that the mechanism of cardiotoxicity in these mice in response shRNA treatment was in contrast to what has been previously shown in the liver. Quantifying microRNA profiles after excessive shRNA delivery illuminates the host response to rAAV-shRNA, allowing for safer and more robust therapeutic gene knockdown, and gives us insight into the basic functions of muscle microRNAs.

overall_design: Small RNA sequencing of mouse liver and five muscle tissues (Diaphragm, Heart, Gastrocnemius, Quadriceps and Tibialis Anterior) in biological triplicate in three groups:  uninjected mice, those with small hairpin RNAs (shRNAs) against the Beta-galactosidase gene with a 19nt stem or 21nt stem.  Tissues were harvested 2 weeks, 6 weeks or 12 weeks after adeno-associated virus 6 delivery (AAV6-shRNA).  All conditions had a minimum of 3 samples.

first: Meredith

last: Course


title: Loss of Lamin A/C in myeloid cells promotes lung metastasis through Gfi-1 and C/EBPe-mediated granulocytic differentiation

status: Public on Dec 28 2019

city: Bethesda

first: Hiroki

last: Ishii

state: Maryland

address: Building 37, Room 3134, 37 Convent Dr.

institute: National Cancer Institute

summary: The immune suppressive tumor microenvironment contributes to metastatic spread. In particular, tumor-associated myeloid cells, which differ from normal myeloid cells, suppress cytotoxic T lymphocyte-mediated anti-tumor immunity. However, the underlying molecular mechanisms for tumor-associated myeloid lineage differentiation and functional properties are not well understood. Here we report a lack of Lamin A/C, a nuclear lamina protein associated with chromatin remodeling, in tumor-associated granulocytic myeloid cells. Using mouse models of myeloid specific Lamin A/C knockout, and mouse models of triple negative breast cancer (TNBC), we discovered that the loss of Lamin A/C drives CD11b+Ly6G+ granulocytic lineage differentiation. Mechanistically, loss of Lamin A/C increased H3K4me3 and led to the up-regulation of transcription factors C/EBPe and Gfi-1, which are critical for granulocytic lineage differentiation. In addition, loss of Lamin A/C changes the production of inflammatory chemokines and decreases anti-tumor immunity, leading to increased lung metastasis. Our data provide mechanistic understanding of myeloid lineage differentiation and function in the immune suppressive microenvironment in TNBC metastasis.

overall_design: CD11b+Ly6C+ or CD11b+Ly6G+ myeloid cells were sorted from spleens of wt or myeloid-specific Lmna knockout mice by the FACSAria flow cytometer. Total RNA was extracted from sorted cells, and RNA-seq was performed to clarify the influence of loss of Lamin A/C in myeloid cells on myeloid differentiation.

first: Li

last: Yang


title: Single cell RNA sequencing for mouse femoral artery

status: Public on Dec 27 2019

first: Fei

last: Li

address: 320 Yue-Yang Road Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

summary: Rapid regeneration of smooth muscle after vascular injury is essential for maintaining proper artery function. The current view holds that pre-existing smooth muscle proliferate and expand in responding to vascular injury, contributing to virtually all new smooth muscle cells. Whether resident vascular stem cells for smooth muscle exist remains controversial and their putative functional role for artery repair and regeneration is elusive. Here we performed cell fate mapping and single cell RNA sequencing to identify Sca1+ vascular stem cells (VSCs) residing in the adventitial layer of artery wall.

overall_design: To examine the cellular components of Sca1+ cells, individual cells were isolated from the femoral artery by enzymatic digestion and processed for single-cell RNA-sequencing technology.

first: Bin

last: Zhou

first: Dong

last: Gao

first: Juan


title: Human Primordial Germ Cells are Specified from Lineage Primed Progenitors

status: Public on Dec 29 2019

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

summary: In vitro gametogenesis is the process of making germline cells from human pluripotent stem cells.  The foundation of this model is the quality of the first progenitors called primordial germ cells (PGCs), which in vivo are specified during the peri-implantation window of human development. Here, we show using human embryo attachment culture that hPGC specification begins at day 12 post fertilization. Using single cell RNA-sequencing of hPGC-like cells (hPGCLCs) differentiated from pluripotent stem cells we discovered that hPGCLC specification involves resetting pluripotency towards a transitional state with shared characteristics between naïve and primed pluripotency followed by differentiation into lineage primed TFAP2A+ progenitors.  Applying the germline trajectory to TFAP2C mutants reveals that TFAP2C functions in the TFAP2A+ progenitors upstream of PRDM1 to regulate the expression of SOX17.  This serves to protect hPGCLCs from crossing the Weismann’s barrier to adopt somatic cell fates and therefore is an essential mechanism for successfully initiating in vitro gametogenesis.

overall_design:
We applied single cell RNA-sequencing (scRNA-seq) with 10x Genomics to hESCs, iMeLCs and aggregate cells at D1-4 with two biological replicates in UCLA1 and UCLA2 cell lines, respectively. In total, we sequenced 85,309 cells with high quality to uncover the germline trajectory and explored the progenitors involved in establishing germline cell fate. Moreover, we performed scRNA-seq of TFAP2C -/- cells at 6 time points (hESCs, iMeLCs, aggregates at D1, D2-D4, 19,808 cells sequenced) and compared this to the single cells from UCLA1 wild type cells which is the genetic background used to make TFAP2C mutant.

We applied ChIP-seq to hESCs, iMeLCs, and day 4 aggregates using anti-TFAP2C antibodies and to ITGA6/EPCAM-isolated day 4 hPGCLCs using anti-H3K27ac antibodies. Two biological replicates were included for each sample.

first: Amander

last: Clark


title: Histamine H3 receptor agonist regulates the expression of inflammation-related genes in kidney and heart of ANS-treated mice

status: Public on Dec 26 2019

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: We found the impaired renal function accompanied with severe cardiac dysfunction in mice co-treated with angiotensin II, nephrectomy and salt (ANS), and identified the increased level of plasma histamine in ANS-treated mice. Interestingly, pro-inflammatory genes were increased in kidneys of ANS-treated animals, which were down-regulated by histamine H3 receptor (H3R) agonist. Purpose: To evaluate the molecular mechanisms underlying the effect of the H3R agonist on the ANS-induced renal and cardiac inflammation, we performed a comprehensive analysis of ANS-mediated gene expression changes with/without H3R agonist in kidneys and hearts using RNA sequencing (RNA-Seq). Results: To investigate differentially expressed genes (false discovery rate (FDR) p<0.05, fold change >2) among three groups, we performed pairwise comparisons of RNA-Seq data using the CLC Genomics Workbench software. In comparison with the control of kidney group, 1,283 (1,010 up- and 273 down-regulated) unique genes were significantly changed in the ANS-treated group. Meanwhile, the data set of ANS-treated kidneys with H3R agonist revealed significant changes in 234 (65 up- and 169 down-regulated) genes as compared with the control groups. In case of hearts, the ANS-treated group revealed that 85 (66 up- and 19 down-regulated) unique genes were significantly changed compared to the control groups. Furthermore, in comparison with the ANS-treated with H3R agonist group, one up-regulated gene was significantly changed in the ANS-treated group.

overall_design: Renal and cardiac mRNA profiles of control (Sham), angiotensin II, nephrectomy and salt (ANS)-treated and ANS-treated with H3R agonist mice were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Kazuyaki

last: Noguchi

first: Akiyoshi

last: Fukamizu


title: Transcriptomic profiling of mouse lung tumor cells in response to CDK7 inhibitor treatment

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary: We performed RNA sequencing analysis on the mouse lung tumor cells treated with CDK7 inhibitor YKL in vitro

overall_design: RNA-sequencing from DMSO/YKL treated mouse tumor cells

first: Hua

last: Zhang

first: Dayanne

last: Castro

first: Kwok-Kin

last: Wong


title: Identification of PRDM15 cistrome in the mouse ESCs

status: Public on Dec 25 2019

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Genome-wide binding sites of PRDM15 were identified in mouse ESCs

overall_design: ChiP-Seq analysis was performed to identify PRDM15 binding sites in mESCs

first: Slim

last: Mzoughi


title: Single-cell transcriptomic profiling of mouse lung tumor in response to CDK7 inhibitor, anti-PD-1 and combination treatment (Experiment 2)

summary: We performed single-cell RNA sequencing (scRNAseq) analysis on the mouse lung tissues from small cell lung tumor-bearing mice treated with CDK7 inhibitor YKL, anti-PD-1 and combination treatment

overall_design: Single-cell RNA-sequencing libraries of mouse tissues using 10x Genomics technology.


title: Single-cell transcriptomic profiling of mouse lung tumor in response to CDK7 inhibitor, anti-PD-1 and combination treatment (Experiment 1)


title: Identification of PRDM15 cistrome in the mouse embryo (6.5 d.p.c)

summary: Genome-wide binding sites of PRDM15 were identified in 6.5 d.p.c embryos

overall_design: ChiP-Seq analysis was performed to identify PRDM15 binding sites in 6.5 d.p.c mouse embryos


title: Transcriptional profiling of grizzly bear skeletal muscle before and during hibernation

city: Berlin

first: Xintian

middle: Arthur

last: YOU

address: Robert-Roessle-str. 10

institute: Max-Delbrueck-Center for Molecular Medicine

summary: We report transcriptional changes in grizzly bear muscle during hibernation (February) as compared to before (October). We used Gastrocnemius muscle biopsies taken during Febrary (hibernation) and the October before (activity) for mRNA extraction followed by 454, paired-end and single-end Illumina sequencing. Resulting reads were later mapped to human homologs and used for further analysis.

overall_design: mRNA profiling for bear skeletal muscles using 454 and Illumina sequencing

last: You

first: Yongbo

last: Wang


title: Yeast heat shock response at 37C, 42C and 46C

status: Public on Dec 24 2019

city: Munich

first: Evi

last: Berchtold

address: Amalienstr. 17

department: Institute for Informatics

institute: Ludwig-Maximilians-University Munich

summary: Life is resilient because living systems are able to respond to elevated temperatures with an ancient gene expression program called the heat shock response (HSR). Our global analysis revealed a modular HSR dependent on the severity of the stress in yeast. Interestingly, at all temperatures analyzed, the transcription of hundreds of genes is upregulated among them the molecular chaperones, which protect proteins from aggregation. However, for approximately 90% of the regulated genes, the function under stress remained enigmatic. Surprisingly, the majority of these upregulated genes is translated but only for a small fraction this results in raised proteins levels. In this context, increased translation is required to counter-balance elevated protein turnover at elevated temperatures. This anaplerotic reaction together with the molecular chaperone system allows yeast to buffer proteotoxic stress. When the capacity of this system is exhausted at extreme temperatures, translation is stopped via phase transition and growth stops.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Overall 18 samples (including 2 control samples at 25C) are measured in triplicates or duplicates

first: Moritz

last: Mühlhofer


title: Whole transcriptome sequencing of 6.5 d.p.c embryos

summary: Whole transcriptome sequencing of 6.5 d.p.c emrbyos

overall_design: RNA was isolated from 6.5 d.p.c emrbyos resulting from intercrosses between Prdm15lacZ/+ mice


title: ChIP-seq analysis of wild-type or PAC1-/- T cells with anti-H3K27-ac

status: Public on Dec 22 2019

city: Beijing

first: Dan

last: Lu

address: #38 Xueyuan Rd

institute: Peking University

summary: To analyze the effects of PAC1 on acetylation of H3K27 in exhausted CD8+ T cells, we isolated CD8+ T cells from spleen of wild-type or PAC1-/- mice post LCMV Cl13 infection and performed ChIP-seq with anti-H3K27-ac.

overall_design: Two replicates for each group, including wild-tpe, Pac1-/- and input

first: Yuxin

last: Yin


title: PRDM15 loss-of-function causes brain malformations through defective embryonic anterior-posterior patterning


title: Crebl2 regulates cell metabolism in muscle and liver cells

city: Heidelberg

first: Marcel

last: Tiebe

state: Germany

address: Humboldtstr., 18

institute: DKFZ Heidelberg


title: Microarray of CLOCK knockdown in GSC272 cells

status: Public on Dec 21 2019

city: CHICAGO

first: Peiwen

last: Chen

state: IL

address: 303 East Superior Street, Suite 6-512

institute: Northwestern University

summary: We used microarrays to study the global gene expression and identified differentially expressed genes in CLOCK inducibel shRNA knockdown GSC272 cells, aiming to identify genes and pathways that are regulated by CLOCK.

overall_design: CLOCK knockdown cells were generated by an inducible shRNA CLOCK knowdown system. The samples used in the microarray analysis were in duplicate.

first: Ronald

middle: A

last: DePinho


city: Tokyo

first: Kenji

last: Shimizu

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: Gene expression profile of T cell after TCR stimulation with or without PD-1 engagement was measured by cap analysis of gene expression (CAGE). This experiment provided insight into how PD-1 modulates gene expression.

overall_design: Total RNA was isolated from DO11.10 T hybridoma cells or mouse primary CD4+ T cell after TCR stimulation with or without PD-1 engagement.

first: Daisuke

last: Sugiura

first: Il-mi

last: Okazaki

first: Takumi

last: Maruhashi

first: Yujiro

last: Takegami

first: Chaoyang

last: Cheng

first: Soichi

last: Ozaki

first: Taku


title: Oscillatory cAMP Signaling Rapidly Alters H3K4 Methylation

status: Public on Dec 23 2019

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 show that cAMP affects gene expression by altering H3K4me3 marks. Note, "Control" samples are untreated with cAMP.

overall_design: Examination of nascent transcription and H3M4me3 marks in control, cAMP treated  or cAMP treated then washed out primary Schwann cells

first: Wang

last: Gaofeng

first: Sant

last: David Wayne

first: Huff

last: Tyler


title: Transcriptome  of juvenile zebrafish treated with the  aromatase inhibitor exemestane and solvent control

status: Public on Dec 20 2019

city: Wuhan

first: Zhen-Xia

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: To reveal the transcriptomic changes during the sex differetiation in larval zebrafish, we treated the lavarl fish with aromatase inhibitors (EM, CAS: 107868-30-4, 100 μg/L), as well as solvent as a control, and sampled them after the exposure.

overall_design: PolyA+ RNA-seq were performed on 6 samples, each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates, with 25 fish per replicate. The exposure treatments included (1) DMSO (10 μL/L), (2) EM + DMSO. The exposure periods were 32 days for zebrafish.

first: Yi-Xuan

last: Tu

first: Lu

first: Zhuang

last: Yang

first: Run-Ze

last: Li


title: Delineating functional enhancers (cis-regulome) in LPS-activated murine splenic B cells

city: Cincinnati

first: Harinder

last: Singh

state: OH

address: 3333 Burnet Ave

department: Immunobiology

institute: CCHMC

summary: LPS activated murine splenic B cells (aB) were subjected to FAIRE-Seq, STARR-Seq, Hi-C, ChIP-seq, Nascent-RNA-seq and RNAseq to compile cis-regulome.

overall_design: Splenic B cells were isolated from C56BL/6J mice (6-8 weeks of age) using B cell isolation kit from Miltenyi (Catalog # 130-090-862) and cultured in complete RPMI with 10% FCS. Purified B cells (250,000 cells/ml) were activated with LPS (10ug/ml, Salmonella typhimurium, Sigma Catalog # L6143). At 72h post-activation B cells were subjected to FAIRE-Seq, Hi-C, ChIP-seq, Nascent-RNA-seq (EU pulse-labeling) and RNAseq. STARR-Seq was performed by transfecting FAIRE-Seq plasmid library at 48h or 60h post LPS-activation. RNA was isolated at 72h post-activation and processed for STARR-Seq. STARR-Seq_24h refers to transfection of library at 48h and STARR-Seq_12h refers to transcfection at 60h. By computational integration of FAIRE-seq and STARR-seq datasets (HOMER peak calls) we identified approximately 10,000 functional enhancers in LPS-activated B cells. These enhancers were connected to active promoters identified by RNA-seq using Hi-C. Integrated datsets yielded a functional mammalian cis-regulome for activated B cells. Cis-regulome was further analyzed using ChIP-seq for 3 histone marks H3K4me1, H3K4me3 and H3K27ac. Nascent RNA-Seq was used for localizing eRNAs and determining rates of gene transcription. Resting B-cells (rB) were used as controls.

first: Virendra

last: Chaudhri


title: Profiling of small RNA in Norway spruce embryonic calli and male gametophytes

city: Uppsala

first: Miyuki

last: Nakamura

address: Ulls Grand1

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Transcriptome analysis of small RNA was performed using pollen and embryonic callus, and vegetative tissues, needles of Picea abies to address differences in small RNA profiles between reproductive tissues and vegetative tissues in gymnosperm.

overall_design: 5 different tissues or conditions with 2 biological replications.


title: Anti-masculinization induced by aromatase inhibitors in adult female zebrafish

status: Public on Dec 19 2019

last: Chen

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

overall_design: Refer to individual Series


title: Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients

city: Utrecht

first: Menno

last: Creyghton

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Speciation is associated with substantial rewiring of the regulatory circuitry underlying the expression of genes. Determining which of these changes are biologically relevant and underlie the emergence of the human brain or its unique susceptibility to neural disease has been challenging. Here we annotate changes to gene regulatory elements at cell type resolution in the brains of multiple primate species spanning most of primate evolution. We identify a unique set of regulatory elements that emerged in hominins prior to the separation of humans and chimpanzees. We demonstrate that these hominin gains disproportionally affect oligodendrocyte function after postnatal development and are preferentially affected in the brains of autism spectrum disorder patients. Our data provide a roadmap of regulatory rewiring across primate evolution providing insight into the genomic changes that underlie the emergence of the brain and its susceptibility to neural disease.

sample_organism:
Callithrix jacchus
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: ChIP-sequencing for H3K27ac, ATAC-sequencing and RNA-sequencing of primate brain samples

first: B

last: Castelijns

first: M

last: Baak

first: I

last: Timpanaro

first: C

last: Wiggers

middle: W

last: Vermunt

first: P

last: Shang

last: Kondova

first: V

last: Bianci

first: W

last: de Laat

first: N

last: Geijsen


title: Nickel induced transcriptional changes persist post exposure through epigenetic reprograming (ChIP-seq & RNA-seq datasets)

city: Charlottesville

first: Zhenjia

last: Wang

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

summary: Nickel is an occupational and environmental toxicant associated with a number of diseases. Our earlier studies showed that Ni-induced alterations to global gene expression persist even after the termination of exposure. A number of earlier studies suggest epigenome as a target of Ni. However, the genome wide dynamics of epigenetic modifications that potentially drive Ni-induced long-term transcriptional changes remain elusive.

overall_design: In this study, we performed a comprehensive analysis of the transcriptome and the epigenome of human epithelial cells during and after termination nickel exposure.

first: Chongzhi

last: Zang

first: Suresh

last: Cuddapah


title: RNA-seq  of adult zebrafish gonads in two sexes

first: Zhen-Xia

summary: To reveal the different of transcriptomic between the two sexes of adult zebrafish.

overall_design: Ribo-Zero RNA-seq were performed on 4 samples from different sex with 2 replicates.

first: Yi-Xuan

last: Tu

first: Lu

first: Li


title: CRISPR-mediated modeling and functional validation of candidate tumor suppressor genes in small cell lung cancer

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: Small cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer that remains among the most lethal of solid tumor malignancies. Recent genomic sequencing studies have identified many recurrently mutated genes in human SCLC tumors. However, the functional roles of most of these genes remain to be validated. Here, we adapt the CRISPR-Cas9 system to a well-established murine model of SCLC to rapidly model loss-of-function mutations in candidate genes identified from SCLC sequencing studies. We show that loss of the gene p107 significantly accelerates tumor progression. Notably, compared with loss of the closely related gene p130, p107 loss results in fewer but larger tumors, as well as earlier metastatic spread. In addition, we observe differences in proliferation and apoptosis, as well as altered distribution of initiated tumors in the lung, resulting from loss of p107 or p130. Collectively, these data demonstrate the feasibility of using the CRISPR-Cas9 system to model loss of candidate tumor suppressor genes in SCLC, and we anticipate that this approach will greatly facilitate efforts to investigate mechanisms driving tumor progression in this deadly disease.

overall_design: RNA sequencing was performed on tumors isolated from SCLC tumor-bearing mice, in which tumor formation was initiated by deletion of Trp53 and Rb1. These tumors harbored CRISPR-mediated mutations in either p107 (8 tumors) or p130 (8 tumors). All samples within each genotype are biological replicates.

first: Sheng

last: Ng

first: William

last: Rideout III

first: Elliot

last: Akama-Garren

first: Arjun

first: Kim

last: Mercer

first: Jason

last: Schenkel

first: Roderick

middle: T

last: Bronson

first: Tyler

last: Jacks


title: Whole transcriptome sequencing of mESCs

first: Diana

last: Low

summary: Investigation of the ability of  WT or mutant hPRDM15 to restore the transcriptional changes induced by deletion of the endogenous mouse Prdm15

overall_design: OHT (50nM) was added to the medium O/N to delete endogenous mouse Prdm15 from isogenic Prdm15flf::RCM2. These lines were ectopically expressing either Wt or mutated human PRDM15, or empty vector as a control.

first: Slim

last: Mzoughi

first: Heike

last: Wollman


title: Nickel induced transcriptional changes persist post exposure through epigenetic reprograming (RNA-seq dataset)

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

first: Suresh

first: Chongzhi

first: Vinay

last: Tanwar

first: Cynthia

last: Jose


title: Loss of Rab11 synergizes with oncogenic Ras to alter growth and metabolism in intestinal cancer models

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Cancer in the intestinal tract is governed by multiple pathways including Wnt, Ras, P53 and Hippo. The GTPase Rab11 regulates endosomal protein trafficking and in a previous report we showed that loss of Rab11 in enterocytes caused intestinal inflammation and hyperplasia in mice and flies. We show here that this inflammation may cooperate with cancer promoting pathways in the intestinal tract. First, lower Rab11 protein staining was observed in 63 out of 70 human colon cancer tissues and patients of age older than 70 had particularly consistent lower Rab11 level. Second, tissue specific knockout of Rab11a in the mouse intestinal epithelium enhanced the formation of intestinal adenocarcinoma after AOM feeding. Third, by using the Drosophila midgut as an experiment model, we show that loss of Rab11 synergizes with the oncoprotein RasV12 to promote cancer-related phenotypes. Fourth, the target genes of this synergistic interaction include the JAK-STAT pathway ligand Upd3 and the IGF pathway antagonist ImpL2. The expression of Upd3 promotes intestinal stem cell proliferation, while ImpL2 suppresses the metabolism of surrounding tissues. Our results demonstrate that a reduced Rab11 function may contribute to intestinal cancer progression by enhancing the growth and metabolic defects initiated by other tumor promoting pathways.

overall_design: Differential gene expression analysis from Drosophila melanogaster midgut mRNA profiling of wild type control flies and Rab11 RNAi flies driven by Myo1AGal4, using Illumina and Ion Torrent

first: Yingchao

last: Nie

first: Tony

last: Ip


title: DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [Colo320 cell line]

status: Public on Dec 18 2019

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

type: Methylation profiling by genome tiling array

summary: Promoter hypermethylation divides colon cancers into subtypes with and without a CpG island methylator phenotype (CIMP). Here, we performed genome-wide DNA methylation profiling of colonic normal and tumor tissues to dissect development of CpG hypermethylation in colon carcinogenesis. This identified age-environment related versus genetically driven CpG hypermethylation, the latter being associated with CIMP cancers. We found a strong association between BRAFV600E mutation and downregulation of the DNA demethylases TET1 and TET2. Expression of BRAFV600E in CIMP cancer cells suppressed TET1 transcription, which was sufficient to establish hypermethylation at CIMP genes promoters, including that of TET2. This phenotype was reverted by the BRAFV600E inhibitor vemurafenib. Thus, BRAFV600E, via impairment of cytosine de-methylation, is a genetic driver of CIMP in colon tumorigenesis.

overall_design: Colo320 cells stably expressing oncogenic BRAF (BRAFV600E) or GFP. Bisulfite-converted DNA were hybridised to the Illumina HumanMethylation850 BeadChip (EPIC array)

first: Kaspar

last: Truninger

first: Primo

last: Schär


title: Transcriptome responses to nitrogen starvation and oxygen limitation during fed-batch cultivation of Aurantiochytrium sp. T66

city: Trondheim

first: Tonje

middle: Marita Bjerkan

last: Heggeset

address: Postboks 4760 Torgarden

department: Industry

country: Norway

institute: SINTEF

summary: Thraustochytrids of the genera Schizochytrium and Aurantiochytrium accumulate oils rich in the essential, marine n3 fatty acid docosahexaenoic acid (DHA). DHA production in Aurantiochytrium sp T66 was studied with the aim to provide more knowledge about factors that affect the DHA-productivities and the contributions of the two enzyme systems used for fatty acid synthesis in thraustochytrids, fatty acid synthetase (FAS) and PUFA-synthase. Fermentations with nitrogen starvation, which is well-known to initiate lipid accumulation in oleaginous organisms, were compared to fermentations with nitrogen in excess where lipid accumulation was obtained by oxygen limitation. The specific productivities of fatty acids originating from FAS were considerably higher under nitrogen starvation than with nitrogen in excess, while the specific productivities of DHA were the same at both conditions. Global transcriptome analysis showed significant up-regulation of FAS under N-deficient conditions, while the PUFA-synthase genes were only marginally upregulated. Neither of them was upregulated under O2-limitation where nitrogen was in excess, suggesting that N-starvation mainly affects the FAS and may be less important for the PUFA-synthase. The transcriptome analysis also revealed responses likely to be related to the generation of reducing power (NADPH) for fatty acid synthesis.

overall_design: mRNA sequencing of Aurantiochytrium sp T66 samples harvested at 4 different cultivation condition in biological triplicates

first: Helga

last: Ertesvåg

first: Bin

last: Liu

first: Inga

last: Aasen


title: Bonn Dataset 2 of meta-analysis on AML classification, Affymetrix HG-U133 2.0

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type:
Expression profiling by array
Third-party reanalysis

summary:
The present dataset ("dataset 2") is a subset of a large metastudy on AML classfication.
In total, three datasets were generated, each containing data of a different platforms: dataset 1 (Affymetrix HG-U133 A microarrays), dataset 2 (Affymetrix HG-U133 2.0 microarrays) and dataset 3 (RNA-seq). Dataset 2 was generated using the following strategy: All data sets published in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) on 20 September 2017 were reviewed for inclusion. Basic criteria for inclusion were the cell type under study (human peripheral blood mononuclear cells (PMBCs) and/or bone marrow samples) as well as the species (Homo sapiens). Furthermore, GEO SuperSeries were excluded to avoid duplicated samples. We filtered the datasets for data generated with the Affymetrix Human Genome U133 Plus 2.0 Array (GLP570) and excluded studies with small sample sizes (< 50 samples). We then applied a disease-specific search, in which we filtered for acute myeloid leukemia, other leukemia and healthy or non-leukemia-related samples.  The results of this search strategy were then internally reviewed and data were excluded based on the following criteria: (i) exclusion of duplicated samples, (ii) exclusion of studies that sorted single cell types (e.g. T cells or B cells) prior to gene expression profiling, (iii) exclusion of studies with inaccessible data. Other than that, no studies were excluded from our analysis. In total, the datasets contained samples from the following GSE Series:  GSE12417, GSE25571, GSE37642, GSE6269, GSE67684, GSE10358, GSE10792, GSE11083, GSE12187, GSE12662, GSE13159, GSE13351, GSE13501, GSE13576, GSE14062, GSE14468, GSE14615, GSE15061, GSE15434, GSE16015, GSE16214, GSE17855, GSE18323, GSE18497, GSE19314, GSE21029, GSE21261, GSE21545, GSE22707, GSE22762, GSE22845, GSE26713, GSE27383, GSE27562, GSE28460, GSE34205, GSE35784, GSE42038, GSE42057, GSE43777, GSE46480, GSE47051, GSE49695, GSE50772, GSE60926, GSE61804, GSE62156, GSE63270, GSE66002, GSE6751, GSE67596, GSE68720, GSE68735, GSE68790, GSE68833, GSE6891, GSE70536, GSE7440, GSE76705, GSE7757, GSE78132, GSE79545, GSE87072, GSE9960.   All CEL-files were downloaded from GEO and imported into R. Robist Multichip Average (RMA) expression measures were calculated using the R package affy.

overall_design: [Dataset_2_matrix.txt]  RMA-normalized expression table of 54675 probes and 8348 samples

first: Stefanie

last: Warnat-Herresthal

first: Thomas

last: Ulas

middle: L


title: Bonn Dataset 1 of meta-analysis on AML classification, Affymetrix HG-U133 A

summary:
The present dataset ("dataset 1") is a subset of a large metastudy on AML classfication.
In total, three datasets were generated, each containing data of a different platforms: dataset 1 (Affymetrix HG-U133 A microarrays), dataset 2 (Affymetrix HG-U133 2.0 microarrays) and dataset 3 (RNA-seq). Dataset 1 was generated using the following strategy: All data sets published in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) on 20 September 2017 were reviewed for inclusion in the present study. Basic criteria for inclusion were the cell type under study (human peripheral blood mononuclear cells (PMBCs) and/or bone marrow samples) as well as the species (Homo sapiens). Furthermore, GEO SuperSeries were excluded to avoid duplicated samples. We filtered the datasets for data generated with the Affymetrix Human Genome U133 A Array (GLP96) and excluded studies with small sample sizes (< 50 samples). We then applied a disease-specific search, in which we filtered for acute myeloid leukemia, other leukemia and healthy or non-leukemia-related samples.  The results of this search strategy were then internally reviewed and data were excluded based on the following criteria: (i) exclusion of duplicated samples, (ii) exclusion of studies that sorted single cell types (e.g. T cells or B cells) prior to gene expression profiling, (iii) exclusion of studies with inaccessible data. Other than that, no studies were excluded from our analysis. In total, the datasets contained samples from the following GSE Series:  GSE10255, GSE1159, GSE12417, GSE12995,  GSE13425, GSE14471, GSE14895, GSE16129, GSE25571,  GSE26281, GSE33315,  GSE34860,  GSE37642, GSE43176, GSE4698, GSE51082, GSE6269, GSE67684, GSE83449, GSE8879, GSE9006, GSE9476.  All CEL-files were downloaded from GEO and imported into R. Robist Multichip Average (RMA) expression measures were calculated using the R package affy.

overall_design: [Dataset_1_matrix.txt]  RMA-normalized expression table of 22283 probes and 2379 samples


title: Nickel induced transcriptional changes persist post exposure through epigenetic reprograming

first: Zhenjia

last: Wang


title: Androgen-induced modulation of XBP1s is functionally driving part of the AR transcriptional program

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

institute: Radboud University

summary: Prostate cancer development and progression is largely dependent on androgen receptor (AR) signaling. AR is a hormone-dependent transcription factor, which binds to thousands of sites throughout the human genome to regulate expression of directly responsive genes, including pro-survival genes that enable tumor cells to cope with increased cellular stress. ERN1 and XBP1 – two key players of the unfolded protein response (UPR) – are among such stress-associated genes. Here, we show that XBP1 levels in primary prostate cancer are associated with biochemical recurrence in five independent cohorts. Patients who received AR targeted therapies had significantly lower XBP1 expression, whereas expression of the active form of XBP1 (XBP1s) was elevated. In vitro results show that AR-induced ERN1 expression led to increased XBP1s mRNA and protein levels. Furthermore, ChIP-seq analysis revealed that XBP1s binds enhancers upon stress stimuli regulating genes involved in UPR processes, eIF2 signaling and protein ubiquitination. We further demonstrate genomic overlap of AR and XBP1s binding sites, suggesting genomic conversion of the two signaling cascades. Transcriptomic effects of XBP1 were further studied by knockdown experiments, which lead to decreased expression of androgen-responsive genes and UPR genes. These results suggest a two-step mechanism of gene regulation, which involves androgen-induced expression of ERN1, thereby enhancing XBP1 splicing and transcriptional activity. This signaling cascade may prepare the cells for the increased protein folding, mRNA decay and translation that accompanies AR-regulated tumor cell proliferation.

overall_design: XBP1s ChIP-seq was performed in LNCaP prostate cancer cells. LNCaP cells were cultured in hormone-deprived medium for three days and then treated with vehicle (DMSO), R1881 for 24 hours or Thapsigargin (Tg) for 3 hours prior to ChIP-seq .

first: Wilbert

last: Zwart


title: Different Diets Change the Bovine Milk Extracellular Vesicle-miRNA Expression

status: Public on Dec 17 2019

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

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

summary: Given that different diets could alter cow milk yield and composition, the effects of different feed formula on milk extracellular vesicle (EV) miRNAs were detected. Cow milk EVs contained various small RNAs, including miRNAs, snRNAs, tiRNAs, Cis-regulatory elements, and piRNAs. Two hundred and seventy-six known bos taurus miRNAs were identified by sequencing in bovine milk EVs. There were 13 immune-related miRNAs in the top 20 miRNAs in milk EVs. Nine differently expressed known miRNAs were detected in responding to different feed formulations. Cow milk EVs are abundant of small RNAs, especially miRNAs, which might be closely related to the development of maternal mammary gland and neonatal immune maturity.

overall_design: Exploration the EV-miRNA profiling changes of bovine milk responding to two different diets

first: Suyu

last: Quan

first: Xuemei


title: Molecular basis for autosomal-dominant renal Fanconi syndrome caused by HNF4A

status: Public on Dec 16 2019

city: Zürich

first: Soeren

last: Lienkamp

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zürich

summary: A specific missense mutation in the DNA binding domain of HNF4A, R85W, causes Fanconi renotubular syndrome (FRTS). To confirm results found in Drosophila, a direct reprogramming approach was applied. Induced renal epithelial tubular cells (iRECs) were generated using transcription factors Hnf1b, Pax8 and either HNF4A WT or HNF4A R85W. RNA Seq analysis of reprogrammed cells shows mitochondrial dysfunction caused by the R85W mutation.

overall_design: 9 samples: 3 replicates of MEFs (mouse embryonic fibroblasts), 3 replicates of iRECs (induced renal epithelial tubular cells) reprogrammed with Hnf1b, Pax8 and Hnf4a R85W and 3 replicates of iRECs reprogrammed with Hnf1b, Pax8 and Hnf4a WT.

first: Valentina

last: Marchesin

first: Albert

last: Pérez-Martí

first: Gwenn

last: Le Meur

first: Roman

last: Pichler

first: Kelli

last: Grand

first: Enriko

middle: D

last: Klootwik

first: Robert

last: Kleta

first: Matias

last: Simons


title: DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [BrafV637E knock-in ]

first: Faiza

last: Noreen

overall_design: Genomic DNA isolated from small intestine of Braf wild type (WT) mice or from hyperplastic (HP) tissue of BrafV637E knock-in mice was subjected to sonication followed by incubation with monoclonal 5-methyl-cytidine (5mC) antibody, and subsequently purification and amplification, labeling and hybridization to the NimbleGen 3x720K DNA methylation Promoter array, according to NimbleGen protocol.

first: Kaspar

last: Truninger

first: Roland

last: Rad

first: Primo

last: Schär


title: Chromatin maturation of the HIV provirus in primary resting CD4+ T cells

city: Huddinge

first: Peter

last: Svensson

address: Hälsovägen 7C

department: Biosciences and Nutrition

institute: Karolinska Institutet

summary: Human immunodeficiency virus (HIV) infection is a chronic condition, where viral DNA integrates into the genome. The fate of the provirus determines the infection course. Latently infected cells form a persistent, heterogeneous reservoir. The reservoir that reinstates an active infection comprises cells with intact provirus that can be reactivated.   We confirmed that latent cells from patients exhibited active transcription throughout the provirus. To find transcriptional determinants, we characterized the establishment and maintenance of latency during proviral chromatin maturation in primary CD4+ T-cells for four months after HIV infection. As heterochromatin (marked with H3K9me3 or H3K27me3) gradually stabilized, the provirus became less accessible and lost activation potential. In a subset of infected cells, active marks (i.e., H3K27ac) remained detectable, even after prolonged proviral silencing. After T-cell activation, the proviral activation occurred uniquely in cells with H3K27ac-marked proviruses. Our observations suggested that, after transient proviral activation, cells were actively returned to latency.

overall_design: ChIP examination of H3K27ac histone modifications in primary CD4 T-cells before and after activation.

first: Birgitta

last: Lindqvist

first: Sara

last: Akusjärvi

first: Marios

last: Dimitriou

first: Anders

last: Sönnerborg

first: J


title: RNA-seq, ChIP-seq and single cell RNA-seq of human skin Langerhans cells

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

summary: Langerhans cells (LCs) in the epidermis promote immune homeostasis, efficiently activating tolerogenic and immunogenic T cell responses. To understand genomic programming in human Langerhans cells we performed whole transcriptome (bulk RNA-seq and single cell RNA-seq) profiling and analysis of H3K4Me3 and H3K27Ac histone modifications across LC genome in primary human cells from 6 independent donors. Primary LCs were either unstimulated and stimulated with TNF-alpha. Additionally we performed a CRISPR editing experiment for IRF4

overall_design: Primary human skin Langerhans cells from independent 3 donors were isolated by migration from epidermal sheets, and either immediately processed for sequencing or exposed to TNF-alpha signalling (2h and 24h). Matched samples from donors LC1 to LC3 were used for time-course stimulation bulk RNA-sequencing, H3K4Me3 and H3K27Ac ChIP sequencing. Additionally 150 unstimulated cells from donor 4 and 1000 unstimulated cells from donor 5 were subjected to single cell RNA-sequencing following encapsulation with Drop-seq. For IRF4 editing experiment primary human migrated LCs were subjected to nucleofaction with purified S. pyogenes Cas9 (spCas9) complexed with a modified single guide RNAs (sgRNAs) targeting IRF4. scRNA-sequencing using DropSeq encapsulation was carried out on 1000 control and 1000 edited primary LCs cells from donor 6 at 48h time point.

middle: E

first: Harinder

last: Singh


title: Herpes Simplex Virus blocks host transcription termination via the bimodal activities of ICP27.

status: Public on Dec 15 2019

city: Irvine

first: Yongsheng

last: Shi

address: 811 Health Sciences Rd

institute: University of California, Irvine

summary: Infection by viruses, including Herpes Simplex virus-1 (HSV-1), and cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII). The underlying mechanisms, however, remain unclear. Here we demonstrate that, in HSV-1-infected cells, the viral immediate early factor ICP27 is necessary and sufficient for inducing DoTT. Mechanistically, ICP27 directly binds to the essential mRNA 3’ processing factor CPSF, induces the assembly of a dead-end 3’ processing complex, and blocks mRNA cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3’ processing for HSV-1 and a subset of host genes. Our results suggest that the bimodal activities of ICP27 play a key role in HSV-1-induced host shutoff and that CPSF is a common host factor targeted by multiple viruses. The mechanism described here may have implications for understanding other virus- and cell stress-mediated regulation of transcription termination.

overall_design: (1) 4SU-seq: explore the effect of ICP27 and HSV-1 on transcription termination; (2) CLIP-seq: examination of RNA binding sites of ICP27.

first: Xiuye

last: Wang

first: Elmira

last: Forouzmand


title: Single cell and genetic analyses reveal conserved cell populations and signaling mechanisms of stomach and intestinal stromal stem cell niches

status: Public on Dec 14 2019

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay Street. Room 16.9709

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

summary: Stomach and intestinal epithelial cells are maintained by the activity of stem cells located in the isthmus and crypt, respectively1,2. Recent studies have demonstrated a surprisingly conserved role for Wnt signaling in stomach and intestinal development and stem cells3,4. Although accumulating evidence suggests that intestinal stromal cells secrete Wnt ligands to promote stem cell renewal5-10, the source of stomach Wnt ligands is still unclear. Moreover, how these gastrointestinal stem cell niche signals are produced is currently unknown. By performing single cell analysis of gastrointestinal stromal cells, we identified cell populations with transcriptome signatures that are conserved between the stomach and intestine. In close proximity to gastrointestinal epithelial cells, these cells highly expressed pericyte markers and Wnt ligands. They also were enriched for Hh signaling, which plays a key role in gut development11,12. A recent study has shown that intestinal pericryptal cells co-express Hh target and Wnt ligand genes8. To define their relationship, we analyzed mice with Hh gain of function in the pericyte-like stromal cells conserved between the stomach and intestine, and found increased levels of Wnt ligands, supporting Hh regulation of stromal Wnt ligand expression. Moreover, utilizing Sufu and Spop double knockout mice, which stabilized GLI2, a key Hh mediator in the gut, we were able to map GLI2 binding sites genome-wide and analyze super enhancers. This work demonstrates GLI2 activation of stromal Wnt ligands through enhancers that are conserved between the stomach and intestine. To determine the significance of Wnt secreting gastrointestinal stromal cells, we genetically inhibited Wnt secretion from the perictye-like or broad stromal cells, demonstrating their roles in gastrointestinal regeneration and development, respectively. Our work not only identifies the conserved gastrointestinal stromal niche cell populations but also reveals their underlying signaling and epigenetic mechanisms.

overall_design: Identification and comparison of the stromal composition in the stomach and the intestine

first: Ji-Eun

first: Lijiang

last: Fei

first: Wen-Chi

last: Yin


title: Genetic analyses reveal the signaling and transcriptional mechanisms of stomach stromal stem cell niches.

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

overall_design: Refer to individual Series


title: All-trans retinoic acid enhances, and a pan-RAR antagonist counteracts, the stem cell promoting activity of EVI1 in acute myeloid leukemia

status: Public on Dec 13 2019

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

country: Austria

institute: Medical University of Vienna

summary: Ecotropic virus integration site 1 (EVI1), whose overexpression characterizes a particularly aggressive subtype of acute myeloid leukemia (AML), enhanced anti-leukemic activities of all-trans retinoic acid (atRA) in cell lines and patient samples. However, the drivers of leukemia formation, therapy resistance, and relapse are leukemic stem cells (LSCs), whose properties were hardly reflected in these experimental setups. The present study was designed to address the effects of, and interactions between, EVI1 and retinoids in AML LSCs. We report that Evi1 reduced the maturation of leukemic cells and promoted the abundance, quiescence, and activity of LSCs in an MLL-AF9-driven mouse model of AML. atRA further augmented these effects in an Evi1 dependent manner. EVI1 also strongly enhanced atRA regulated gene transcription in LSC enriched cells. One of their jointly regulated targets, Notch4, was an important mediator of their effects on leukemic stemness. In vitro exposure of leukemic cells to a pan-RAR antagonist caused effects opposite to those of atRA. In vivo antagonist treatment delayed leukemogenesis and reduced LSC abundance, quiescence, and activity in Evi1high AML. Key results were confirmed in human myeloid cell lines retaining some stem cell characteristics as well as in primary human AML samples. In summary, our study is the first to report the importance of EVI1 for key properties of AML LSCs. Furthermore, it shows that atRA enhances, and a pan-RAR antagonist counteracts, the effects of EVI1 on AML stemness, thus raising the possibility of using RAR antagonists in the therapy of EVI1high AML.

overall_design: Gene expression profiles of solvent or atRA-treated Evi1high and Evi1low leukemic stem cell enriched cells (LSCe), in triplicate for Evi1high and duplicate for Evi1low LSCe, using Illumina HiSeq 3000

first: Chi

last: Nguyen

first: Hubert

last: Hackl


title: Transcriptional changes during hepatic ischemia-reperfusion in the rat

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: Ischemia-reperfusion (IR) injury, a ubiquitous consequence of liver transplantation, is a cause of early graft rejection and increased morbidity. At present, there are no effective strategies to reduce hepatic IR injury. Molecular mechanisms that promote cell survival under these circumstances are largely undefined. We examined changes in global gene expression at early reperfusion times to identify potential IR-mediated protective responses. Using a rat model of 30 minutes of 70% warm ischemia followed by reperfusion, RNA for microarray analysis was extracted from the non-ischemic and the ischemic-reperfused lobes at four reperfusion times: 0 (no reperfusion), 0.5, 2, and 6 hours. Differentially expressed genes and pathway analyses were used to identify IR-induced events. The transcriptome of the reperfused lobes was unique and discrete at each reperfusion time, showing no evidence of sustained changes of the gene expression alterations seen at 30 minutes of reperfusion. At all reperfusion times, a significant portion of gene expression changes in the reperfused lobes were present in the non-ischemic lobes. However, the earliest reperfusion time, 30 minutes, showed a marked increase in the expression of a set of immediate-early genes (c-Fos, c-Jun, Atf3, Egr1) that was exclusive to the reperfused lobe. Similarities of gene expression changes in the reperfused and the non-ischemic lobes at each time suggest that hemodynamics and/or circulating factors are potent stimuli in an IR model. However, early reperfusion events appear to reflect a cell-autonomous response that may be protective, thereby representing potential targets to ameliorate IR injury.

overall_design: Livers were harvested from bioloigical triplicate samples at 4 reperfusion times (0hr, 0.5hr, 2hr, 6hr) after 30 minutes of 70% warm ischemia.  3 sham animals were matched to each time point. RNA was extracted from the reperfused, ischemic, and sham livers using the RNeasy Isolation Kit (Qiagen).  RTA-1_0 Rat Assays (Affymetrix Rat transcriptome 1.0) were used.

first: Valerie

last: Zabala

first: Joan

middle: M

last: Boylan

first: Paul

last: Thevenot

first: Anderson

last: Frank

first: Dewahar

last: Sentoor

first: Varun

last: Iyengar

first: Hannah

first: Ari

last: Cohen

first: Philip

last: Gruppuso


title: Gene expression profile of 22RV1 prostate cancer cells upon SPINK1 knockdown

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: Serine Peptidase Inhibitor, Kazal type 1 (SPINK1) overexpression represents the second-largest prostate cancer (PCa) subtype associated with increased risk of biochemical recurrence and poor prognosis. To determine the pathways regulated by SPINK1 in 22RV1 prostate cancer cells, we performed shRNA mediated knockdown of SPINK1 using lentiviral constructs. Scrambled shRNA was used as a control. pGIPZ constructs against SPINK1 (shSPINK1-1, shSPINK1-2, shSPINK1-3) and control shScrambled construct were purchased from Dharmacon.

overall_design: Global gene expression profile of 22RV1 shSPINK1 cells compared to 22RV1 shScrambled control cell. Two color Experiment, Organism: Homo sapiens, Agilent's Human Whole Genome 8x60k GE Microarray (AMADID-72363).

first: Ritika

last: Tiwari

first: Nishat

last: Manzar

first: Vipul

last: Bhatia

first: Anjali

last: Yadav

first: Bushra

last: Ateeq


title: Neuronal subtype expression profiles from adult mouse cortex

city: South San Francisco

first: Brad

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Neurons were dissociated and purified from adult (~3 months) mouse brains. We used four strains with genetic markers that enabled live sorting. Thy1-GFP labels a subset of excitatory neurons; VIP-tdTomato, SST-tdTomato and PVALB-tdTomato labels different subsets of inhibitory neurons.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0016304

overall_design: RNA from different neuronal subtypes sorted from adult mouse cortex using fluorescence activated cell sorting

first: Melanie

last: Huntley

first: Jesse

last: Hanson


title: Genetic analyses reveal the signaling and transcriptional mechanisms of stomach stromal stem cell niches. [RNA-Seq]

first: Tae-Hee

last: Kim

summary: We demonstrate the conserved Hh-GLI2-mediated chromatin and transcriptional regulation of both stomach and intestinal stromal stem cell niche signals. Analyses of H3K27ac marks demonstrate GLI2-mediated transcription regulation of stem cell niche signals such as Wnt ligand genes, through enhancers conserved between the stomach and intestine.

overall_design: RNA-Seq of E17.5 wildtype and Sufu;Spop double knockout stomach in biological duplicates

first: Sabrina

last: Coquenlorge-Gallon

first: Wen-Chi

last: Yin


title: Enteric Nervous System Derived IL-18 Orchestrates Mucosal Barrier Immunity [DropSeq]

status: Public on Dec 12 2019

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street, TAC S-569

department: Department of Immunobiology

institute: Yale University

summary:
Using DropSeq single cell RNA sequencing, we report that neuronal derived-IL-18 is required for goblet cell expression of intestinal antimicrobial protein expression
Mucosal barrier immunity is essential for the maintenance of the commensal microflora and combating invasive bacterial infection. Although immune and epithelial cells are thought to be the canonical orchestrators of this complex equilibrium, here we show that the enteric nervous system (ENS) plays an essential and non-redundant role in governing the anti-microbial protein (AMP) response. Using confocal microscopy and single-molecule fluorescence in situ mRNA-hybridization (smFISH) studies, we observed that intestinal neurons produce the pleiotropic cytokine IL-18. Strikingly, deletion of IL-18 from the enteric neurons alone, but not immune or epithelial cells, rendered mice susceptible to invasive Salmonella typhimurium (S.t.) infection. Mechanistically, unbiased RNA sequencing and single cell sequencing revealed that enteric neuronal IL-18 is specifically required for homeostatic goblet cell AMP production. Together, we show that neuron derived IL-18 signaling controls tissue wide intestinal immunity and has profound consequences on the mucosal barrier and invasive bacterial killing.

overall_design: Colons from littermate steady state Il18f/f and Il18f/fHand2Cre+ mice were digested and single cell suspension generated and DropSeq conducted. Sample 5 is collected from Il18f/f mice (n=2 combined) and Sample 6 is collected from Il18f/fHand2Cre+ mice (n=2 combined).


title: Deregulation of the three-dimensional epigenome in endocrine resistant breast cancer

status: Public on Dec 11 2019

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

summary: Around 35% of Estrogen Receptor (ER) positive patients develop resistance and relapse, highlighting the need to further understand the mechanisms underpinning endocrine resistance in breast cancer. Here, we study 3-dimensional (3D) epigenome remodelling in endocrine resistant breast cancer cells. We show that chromatin interactions both within and between topologically associating domains (TADs) frequently change in resistant breast cancer cells and that alterations in active (A-type) and inactive (B-type) chromosomal compartments are associated with decreased ER binding and atypical interactions and gene expression. Finally, we identify differentially interacting ER-bound regions that preferentially connect active enhancers and promoters associated with altered expression of ER-regulated genes. Importantly, interactions specifically associated with endocrine resistance, often occur coincidently with hypermethylation of ER binding. Our results demonstrate that 3D epigenome remodelling is a key mechanism of endocrine resistance that consists of differential chromatin interactions and aberrant DNA methylation at ER-regulated enhancer regions.

overall_design: Hi-C was conducted in endocrine-sensitive breast cancer cells (MCF7) at three time-points during long-term culture: time zero (T0), time point mid and late time point (> 6 months)


title: ERRBS-Seq of XpY*x and XmY*x murine CD4+ T cells

city: Pittsburgh

first: Amr

last: Sawalha

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

type: Methylation profiling by high throughput sequencing

summary: Most autoimmune diseases have a higher incidence in women than men due to differences in sex hormones, sex chromosomes, or both. Female (XX) and male (XY) sex chromosome complements differ in parent-of-origin of the X chromosome, with females inheriting one each from the mother and father, while males inherit only one from the mother2. Here, we discovered that the paternal X (Xp) had higher DNA methylation than the maternal X (Xm) in autoantigen specific CD4+ T lymphocytes, potentially suppressing X gene expression in XX. Using the “Four Core Genotypes” model, the transcriptomes of autoantigen specific CD4+ T lymphocytes showed higher expression of many X genes in XY- than XX. Expression of toll-like receptor 7 (Tlr7) and forkhead box P3 (FoxP3), two X chromosome genes important in autoimmunity, was higher in XY- than XX, confirming genome wide methylation and transcription data. Thus, parent-of-origin differences in DNA methylation of X genes can lead to sexual dimorphisms in gene expression during autoimmunity.

overall_design: Enhanced reduced representation bisulfite sequencing of autoantigen specific CD4+ T cells from paternally imprinted XpY*x and maternally imprinted XmY*x mice on SJL background. Mice were induced at 8-12 weeks of age by subcutaneous injection of PLP peptide 139-151 (200 ug/mouse, Mimotopes) emulsified in Complete Freund’s adjuvant, supplemented with Mycobacterium tuberculosis H37Ra (200ug/mouse; Difco Laboratories), over draining auxillary and inguinal lymph nodes one time on Day 0. Mice were sacrificed 12 days after induction. Auxillary, brachial, and inguinal lymph nodes  were  collected and processed into single cell suspensions. Single cell suspensions were resuspended in autoMACS Buffer (90uL/ 107 cells, Miltenyi Biotec). The cells were incubated with CD3 and CD4 microbeads (10 uL/10^7 cells, Miltenyi Biotec) for 15 min at 4°C. Cells were washed with and resuspended in autoMACS buffer (500 uL/10^8cells) then sorted on an autoMACSTM Separator (Miltenyi Biotec) by positive selection. Samples were quick frozen in liquid nitrogen and stored at -80°C until DNA isolation.  Genomic DNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen).

middle: H

first: Patrick

last: Coit


title: Genetic analyses reveal the signaling and transcriptional mechanisms of stomach stromal stem cell niches. [ChIP-Seq]

overall_design: Examination of Gli2, H3K27ac, and H3K36me3-bound DNA in E17.5 Sufu;Spop double knockout mouse stomach


title: Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [WGS]

summary: Endocrine therapy resistance invariably develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine resistant breast cancer cells and that the differential interactions are enriched for genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. Importantly, new 3D chromatin interactions often occur coincidently with hypermethylation and loss of ER binding. Additionally, alterations in active (A-type) and inactive (B-type) chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer.

overall_design: Hi-C, WGS, WGBS, ChIP-seq and RNA-seq were conducted in endocrine-sensitive breast cancer cells (MCF7) and its two endocrine-resistant derivatives - tamoxifen-resistant (TAMR) cells and fulvestrant-resistant (FASR) cells.


title: Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [ChIP-seq]


title: Sex chromsomes affect gene expression of immunized CD4+ T cells in SJL

status: Public on Dec 10 2019

city: Los Angeles

first: Yuichiro

last: Itoh

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throughput RNA sequencing to analyze the transciptomes of CD4+ T cells stimuated with anti-CD3/CD28 from XX and XY- mice using the “four core genotypes” mouse model. We found higher expression of several X genes in the XY- genotype compared to XX, suggesting a difference in DNA methylation of these genes between Xp and Xm. In a hypothesis driven targeted approach, we investigated two immunomodulatory X genes, Tlr7 and FoxP3 and found that the promoter regions of both genes had more DNA methylation on the Xp than Xm, and that both genes had higher expression in autoantigen stimulated CD4+ T cells from XY- compared to XX mice. This study provides new insights regarding how sex chromsomes affect gene expression and cause sex differences in autoimmune disease.

overall_design: Female mice from the "four core genotypes" mouse model (XX and XY-) were gonadectomized at 4-6 weeks old and subsequently immunized with PLP 139-151 peptide emulsified in complete fraunds adjuvant, suppplemented with myobacterium tuberculosis H27Ra for 10 days. Auxillary, brachial, and inguinal draining lymph nodes were collected and processed into single cell suspensions. Cells were stiumulated with PLP 139-151 for 36 hours. Stimulated cells were sorted for CD4+ T cells using the EasySep Mouse CD4+ T cell isolation kit (STEMCELL), and RNA was isolated for analysis by high throughput RNA sequencing.

first: Lisa

last: Golden

first: Noriko

first: Rhonda

last: Voskuhl


title: Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [RNA-seq]


title: Vascular PPARb/d Promotes Tumor Angiogenesis and Progression

city: Nice

first: Kay-Dietrich

last: Wagner

address: 28 Avenue Valombrose

department: Institute of Biology Valrose

country: France

institute: INSERM

summary: PPARβ/δ has been suggested to be involved in the regulation of the angiogenic switch in tumor progression. However, until now it is not clear to what extent the expression of PPARβ/δ in tumor endothelium influences tumor progression and metastasis formation. We addressed this question using transgenic mice with an inducible conditional vascular-specific overexpression of PPARβ/δ. Following specific over-expression of PPARβ/δ in endothelial cells, we induced syngenic tumors. We observed an enhanced tumor growth, a higher vessel density, and enhanced metastasis formation in the tumors of animals with vessel-specific overexpression of PPARβ/δ. In order to identify molecular downstream targets of PPARβ/δ in the tumor endothelium, we sorted endothelial cells from the tumors and performed RNA sequencing.We show here that PPARβ/δ activation, regardless of its action on different cancer cell types, leads to a higher tumor vascularization which favors tumor growth and metastasis formation.

overall_design: Endothelial cells were isolated from tumors of Tie2-CreERT2;PPARβ/δ-flox+/− mice induced with Tamoxifen and the respective vehicle-treated controls, RNA was isolated from the endothelial cells and subjected to Ilumina mRNA HiSeq

first: Nicole


title: Human Tfh cell RNA bulk sequencing

city: Berkeley

first: Chenling

last: Xu

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

summary: We RNA bulk sequenced human Tfh cells sorted from healthy control and MS patient CSF.

overall_design: We isolated CSF leukocytes from patients with multiple sclerosis and healthy controls. Leukocytes were stained with antibodies to identify Tfh cells and Tfh cells were flow sorted. RNA was isolated from sorted Tfhs and prepared for bulk sequencing.

first: David

last: Schafflick


title: Enteric Nervous System Derived IL-18 Orchestrates Mucosal Barrier Immunity [RNA-seq]

summary:
Using RNA sequencing, we report that neuron derived-IL-18 is required for intestinal antimicrobial protein expression
Mucosal barrier immunity is essential for the maintenance of the commensal microflora and combating invasive bacterial infection. Although immune and epithelial cells are thought to be the canonical orchestrators of this complex equilibrium, here we show that the enteric nervous system (ENS) plays an essential and non-redundant role in governing the anti-microbial protein (AMP) response. Using confocal microscopy and single-molecule fluorescence in situ mRNA-hybridization (smFISH) studies, we observed that intestinal neurons produce the pleiotropic cytokine IL-18. Strikingly, deletion of IL-18 from the enteric neurons alone, but not immune or epithelial cells, rendered mice susceptible to invasive Salmonella typhimurium (S.t.) infection. Mechanistically, unbiased RNA sequencing and single cell sequencing revealed that enteric neuronal IL-18 is specifically required for homeostatic goblet cell AMP production. Together, we show that neuron derived IL-18 signaling controls tissue wide intestinal immunity and has profound consequences on the mucosal barrier and invasive bacterial killing.

overall_design: For Bulk RnaSeq experiments proximal colons were removed from: 1) Il18f/f and Il18f/fHand2Cre+, 2) Il18f/f and Il18f/fVillinCre+, and 3) Il18f/f and Il18f/fFLK1Cre+ littermate mice and RNA extracted.


title: Enteric Nervous System Derived IL-18 Orchestrates Mucosal Barrier Immunity

overall_design:
Refer to individual Series. Key for bulk RNA sequencing samples:

Hand2 Experiment: WT_PRX_5 = IL18f/f Hand2Cre- Prox Colon 1, WT_PRX_6 = IL18f/f Hand2Cre- Prox Colon 2, KO_PRX_7 = IL18f/f Hand2Cre+ Prox Colon 1, KO_PRX_8 = IL18f/f Hand2Cre+ Prox Colon 2.

Villin Experiment: V1 = IL18f/f Vil1Cre- Prox Colon 1, V3 = IL18f/f Vil1Cre- Prox Colon 2, V2 = IL18f/f Vil1Cre+ Prox Colon 1, V4 = IL18f/f Vil1Cre+ Prox Colon 2.

Flk Experiment: F5 = IL18f/f FlkCre- Prox Colon 1, F6 = IL18f/f FlkCre- Prox Colon 2, F7 = IL18f/f FlkCre+ Prox Colon 1, F8 = IL18f/f FlkCre+ Prox Colon 2

Key for single cell sequencing data from littermate steady state animals:
Sample_5 = Il18f/f (n=2 combined), Sample_6 = Il18f/f Hand2Cre+ (n=2 combined).


title: Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis

summary: Cerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids the diagnosis of CNS diseases, but our understanding of CSF leukocytes remains superficial. Here, using single cell transcriptomics, we identified a specific border-associated composition and transcriptome of CSF leukocytes. Multiple sclerosis (MS) – an autoimmune disease of the CNS – increased transcriptional diversity in blood, but increased cell type diversity in CSF including a higher abundance of cytotoxic phenotype T helper cells. A new analytical approach, named cell set enrichment analysis (CSEA) identified a cluster-independent increase of follicular T helper (TFH) cells potentially driving the known expansion of B lineage cells in the CSF in MS. In mice, TFH cells accordingly promoted B cell infiltration into the CNS and the severity of MS animal models. Immune mechanisms in MS are thus highly compartmentalized and indicate ongoing local T/B cell interaction.

overall_design: We used a 5 v.s. 5 Case-Control design for the single cell RNAseq experiment. Each donor provided 2 samples from the cerebrospinal fluid and PBMC.

first: Maike

last: Hartlenert

first: Andreas

last: Schulte-Mecklenbeck

first: Tobias

last: Lautwein

first: Jolien

last: Wolbert

first: Gerd

last: Horste


title: Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [Hi-C]


title: Transcriptome data from human endocrine cells recovered from mouse grafts with pre-engraftment controls

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: We examined the transcriptomes of alpha and beta cells recovered from mouse sub-renal capsule grafts of human islets as compared to alpha and beta cells from the same islet preps pre-engraftment. We found that after three to four weeks in the graft the human islets were still glucose responsive, secreting insulin following glucose challenge. In addition, gene expression was largely unchanged from the pre-engraftment control samples.

overall_design: Bulk and single-cell RNA-Seq analysis of human endocrine cells recovered from mouse engraftment

first: Sambra

last: Redick

first: Linda

last: Leehy

first: Ann

middle: R

last: Rittenhouse

last: Blodgett

first: Alper

last: Kucukural

first: Manuel

last: Garber

first: Leonard

last: Shultz

first: Dale

last: Greiner

first: Jennifer

middle: P

last: Wang

last: Harlan

first: Rita

last: Bortell

first: Agata

last: Jurczyk


title: Sex chromosomes affect gene expression of healthy CD4+ T cells in B6 gonadal females.

first: Yuichiro

last: Itoh

summary: To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throughput RNA sequencing to analyze the transciptomes of CD4+ T cells stimuated with antiCD3/CD28 from XX and XY- mice using the “four core genotypes” mouse model. We found higher expression of several X genes in the XY- genotype compared to XX, suggesting a difference in DNA methylation of these genes between Xp and Xm. In a hypothesis driven targeted approach, we investigated two immunomodulatory X genes, Tlr7 and FoxP3 and found that the promoter regions of both genes had more DNA methylation on the Xp than Xm, and that both genes had higher expression in autoantigen stimulated CD4+ T cells from XY- compared to XX mice. This study provides new insights regarding how sex chromsomes affect gene expression and cause sex differences in autoimmune disease.

overall_design: Female mice from the "four core genotypes" mouse model (XX and XY-) were gonadectomized at 4-6 weeks old. At 8-12 weeks old, auxillary, brachial, and inguinal draining lymph nodes were collected and processed into single cell suspensions and sorted for CD4+ T cells using the EasySep Mouse CD4+ T cell isolation kit (STEMCELL). Cells were stiumulated with  anti-CD3/CD28 Dyna Beads for 36 hours and RNA was isolated for analysis by high throughput RNA sequencing.

first: Lisa

last: Golden

first: Noriko

first: Rhonda

last: Voskuhl


title: Sex chromsomes affect gene expression of healthy CD4+ T cells in B6 gonadal males

summary: To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throughput RNA sequencing to analyze the transciptomes of CD4+ T cells stimuated with antiCD3/CD28 from XXSry and XY-Sry mice using the “four core genotypes” mouse model. We found higher expression of several X genes in the XY- genotype compared to XX, suggesting a difference in DNA methylation of these genes between Xp and Xm. In a hypothesis driven targeted approach, we investigated two immunomodulatory X genes, Tlr7 and FoxP3 and found that the promoter regions of both genes had more DNA methylation on the Xp than Xm, and that both genes had higher expression in autoantigen stimulated CD4+ T cells from XY- compared to XX mice. This study provides new insights regarding how sex chromsomes affect gene expression and cause sex differences in autoimmune disease.

overall_design: Male mice from the "four core genotypes" mouse model (XXSry and XY-Sry) were gonadectomized at 4-6 weeks old. At 8-12 weeks old, auxillary, brachial, and inguinal draining lymph nodes were collected and processed into single cell suspensions and sorted for CD4+ T cells using the EasySep Mouse CD4+ T cell isolation kit (STEMCELL). Cells were stiumulated with  anti-CD3/CD28 Dyna Beads for 36 hours and RNA was isolated for analysis by high throughput RNA sequencing.


title: Sex chromosomes affect gene expression of autoantigen specific CD4+ T cells in B6 gonadal males.

summary: To determine the role of sex chromsomes in sex differences of autoimmune disease, we used high throughput RNA sequencing to analyze the transciptomes of autoantigen specific CD4+ T cells from XX and XY- mice using the “four core genotypes” mouse model. We found higher expression of several X genes in the XY- genotype compared to XX, suggesting a difference in DNA methylation of these genes between Xp and Xm. In a hypothesis driven targeted approach, we investigated two immunomodulatory X genes, Tlr7 and FoxP3 and found that the promoter regions of both genes had more DNA methylation on the Xp than Xm, and that both genes had higher expression in autoantigen stimulated CD4+ T cells from XY- compared to XX mice. This study provides new insights regarding how sex chromsomes affect gene expression and cause sex differences in autoimmune disease.

overall_design: Male mice from the "four core genotypes" mouse model (XXSry and XY-Sry) were gonadectomized at 4-6 weeks old and subsequently immunized with MOG 35-55 peptide emulsified in complete fraunds adjuvant, suppplemented with myobacterium tuberculosis H27Ra for 10 days. Auxillary, brachial, and inguinal draining lymph nodes were collected and processed into single cell suspensions. Cells were stiumulated with  MOG 35-55 and IL-12 for 36 hours. Stimulated cells were sorted for CD4+ T cells using the EasySep Mouse CD4+ T cell isolation kit (STEMCELL), and RNA was isolated for analysis by high throughput RNA sequencing.


title: Rainbow trout IgM+ B cells preferentially respond to thymus-independent antigens but are activated by CD40L

city: Valdeolmos

first: Pedro

last: Perdiguero

state: Madrid

address: Ctra. de Algete a El Casar Km 8.1

department: Animal Health Research Centre

country: Spain

institute: CISA-INIA

summary: To further investigate the differential effects exerted by TD and TI-1 antigens on trout IgM+ B cells, RNA sequencing (RNA-seq) was performed on FACS isolated splenic IgM+ B cells that had been stimulated with TNP-KLH or TNP-LPS for 24 h, or on control unstimulated splenic IgM+ B cells

overall_design: 9 samples; 3 biological replicates per treatment including unstimulated IgM+ B-cell as control and TNP-KLH and TNP-LPS stimulated IgM+ B-cells

first: Aitor

last: Granja

first: Alba

last: Martín-Martín

first: Patricia

last: Díaz-Rosales

first: Irene

last: Soleto

first: Carolina

last: Tafalla


title: mRNA-seq of gonads from adult zebrafish treated with aromatase inhibitor and control

status: Public on Dec 07 2019

city: Wuhan

first: Zhen-Xia

last: Chen

address: No.1 Shizishan Street

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

summary: To explore the transcriptional effects of aromatase inhibitors on sex differentiation of zebrafish, we exposed 3-month-old zebrafish (AB strain) to the third generation aromatase inhibitor Exemestane (CAS: 107868-30-4) and characterized transcript abundance among testes and ovaries after 32 days of drug exposure. After the drug treatment, we dissected zebrafish gonads, isolated polyA+ RNA and performed high-throughput RNA-Seq analysis.

overall_design: We performed RNA-Seq analysis on 16 gonad samples in 2 biological replicates with 8 samples each. Eight samples of each replicate included two sexes (female and male) in four different treatments: (1) 50ug/L Exemestane, (2) 100ug/L Exemestane, (3) 200ug/L Exemestane, (4) control. Replicates were performed simultaneously. Each sample was from gonads of one individual. Gonads were dissected from adult zebrafish with clearly identified sex after 32 days of drug exposure. We isolated total RNA from the samples, purified polyA+ mRNA, and generated stranded pair-end mRNA libraries.

first: Qiwei

last: Cheng

first: Li

first: Lu

first: Run-Ze

last: Li


title: Dynamic transcriptomic and metabolic profiling reveal synthetic characters and regulators of apocarotenoids biosynthesis in Crocus sativus

status: Public on Dec 09 2019

city: Shanghai

first: Xianghui

address: No. 325 Guohe Rd

department: Department of Pharmaceutical Botany, School of Pharmacy

institute: Second Military Medical University

summary:
Background: Crocus sativus L. belongs to the Iridaceae family and its dried stigma, called saffron, is one of the world’s most expensive spice. C. sativus is also a famous medicinal plant on account of producing significant pharmaceutical apocarotenoids like crocins, crocetin, picrocrocin and safranal. These metabolites have been reported to play important pharmacological efficiency towards many diseases. However, the regulatory mechanism of saffron apocarotenoids biosynthesis and stigma specific accumulation remains poorly understood.
Results: In this work, we performed deep transcriptomic sequencing and dynamic metabolomic profiling of different developmental stage stigmas, and firstly integrated the dynamic changes of apocarotenoids with dynamic transcriptomic data. As a result, a co-expression network was constructed, and 41 pathway genes, 5 TF genes were identified as hub genes probably participating in apocarotenoid biosynthesis, validated by qRT-PCR. The reliability of these results was validated by previous research of several genes, which were also screened out by the co-expression network.
Conclusions: This work provides novel insights into the mechanism by which the apocarotenoids is synthesized and regulated. Such gene-to-apocarotenoid landscapes associated with different developmental stigma are fundamental of deeply understanding the biosynthesis and metabolic engineering of saffron apocarotenoids in the C. sativus and other plant.

overall_design: Total RNA profiles of RED, -2DAY, 0DAY stage stigmas from Crocus. sativus were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Hexin

last: Tan


title: Mechanical sensing protein PIEZO1 regulates bone homeostasis via osteoblast-osteoclast crosstalk

city: ShangHai

first: Lijun

last: Wang

state: China

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: Wolff’s law and the Utah Paradigm of skeletal physiology state that bone architecture adapts to mechanical loads. These models predict the existence of a mechanostat that links strain induced by mechanical forces to skeletal remodeling. However, how the mechanostat influences bone remodeling remains elusive. Here, we find that Piezo1 deficiency in osteoblastic cells leads to loss of bone mass and spontaneous fractures with increased bone resorption. Furthermore, Piezo1-deficient mice are resistant to further bone loss and bone resorption induced by hind limb unloading, demonstrating that PIEZO1 can affect osteoblast-osteoclast crosstalk in response to mechanical forces. At the mechanistic level, in response to mechanical loads, PIEZO1 in osteoblastic cells controls the YAP-dependent expression of type II and IX collagens. In turn, these collagen isoforms regulate osteoclast differentiation. Taken together, our data identify PIEZO1 as the major skeletal mechanosensor that tunes bone homeostasis.

overall_design: Cortical bones of 6-week WT and  Prx1Cre; Piezo1fl/fl mice were collected and ground with liquid nitrogen to extract the RNA.

first: Weiguo

last: Zou