title: A MYC2, MYC3, MYC4-dependent transcription factor network regulates touch responses in plants

status: Public on Oct 29 2019

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Plants are continuously exposed to environmental triggers, including mechanical stimulation. Our results demonstrate that jasmonic acid (JA)-signalling not only plays a key role in touch-induced developmental changes, but also in the very early gene expression changes. Using multi-omics, we show that the JA-activated transcription factors MYC2/MYC3/MYC4 co-regulate touch-induced gene expression of 266 genes. MYC2/3/4 particularly activate top touch-induced genes, which peak around 25 minutes and then rapidly decline by 40-60 minutes. ChIP-seq shows that MYC2 dynamically binds hundreds of touch-induced promoters within 25 minutes. Furthermore, promoter activation assays confirm that MYC2 directly activates touch-induced promoters. By combining these data, we identified a core MYC2/3/4-dependent ‘touch regulon’, containing many previously-unknown MYC2 targets like bHLH19 and ERF109. bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/3/4 initiate a hierarchical network of downstream transcription factors. Finally, hormone profiling shows that the rapid touch-induced accumulation of JA/JA-isoleucine is directly controlled by MYC2/3/4 in a positive amplification loop regulating JA-biosynthesis genes.

overall_design: one biological sample for ChIP-seq

first: Alex

last: Van Moerkercke

first: Owen

last: Duncan

first: Mark

last: Zander

first: Jan

last: Šimura

first: Martyna

last: Broda

first: Robin

last: Vanden Bossche

first: Mathew

last: Lewsey

first: Sbatie

last: Lama

first: Karam

last: Singh

first: Karin

last: Ljung

first: Alain

last: Gooseens

first: Harvey

last: Millar

first: Olivier

last: van Aken


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and cd36-/- murine peritoneal macrophage Transcriptomes

status: Public on Oct 28 2019

city: Milwaukee

first: Yiliang

last: Chen

state: WI

address: 8727 W Watertown Plank Rd

country: USA

institute: Blood Research Institute, Versiti

type: Expression profiling by high throughput sequencing

summary: Oxidized LDL induce macrophages to turn into foam cells in a CD36 dependent manner. The Goal of this study is to compare transcriptome profile by RNA-seq among WT/CD36 knockout macrophages treated with or without oxLDL. We detected re-organization of lipid metabolisms as well as immune activation by oxLDL.

overall_design: Peritoneal macrophages were isolated from WT or CD36 knockout mice and cultured in vitro. Cells then treated with 20μg/ml oxLDL or media (control) for 8h. We triplicate each condition (i.e. WT-control, WT-oxLDL, CD36 KO-control, CD36 KO-oxLDL).

first: Roy

middle: L

last: Silverstein


title: Mouse colon tumor gene expression of  epithelial, stromal and infiltrating myeloid cells.

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: High T cell infiltration in colorectal cancer (CRC) correlates with a better disease outcome and immunotherapy response. This is observed in only a small subset of CRC patients. A better understanding of the factors influencing tumor T cell responses in CRC could inspire novel therapeutic approaches to achieve broader immunotherapy responsiveness. Numerous cell types and factors within the tumor microenvironment (TME) have been described as T cell suppressive within multiple mouse and human cancers. The influence of the TME on T cell infiltration and response in CRC is currently a matter of intense investigation. Here we investigated gene expression of different cell types isolated from mouse colon tumors or control tissue in order to find potential T cell suppressive cues present within these tumors.

overall_design: Comparison of samples from sorted neutrophils, monocytes, epithelial and stromal cells from mouse colon tumor or blood of tumor bearing or healthy mice.

first: Markus

last: Germann

last: Zangger

first: Freddy

last: Radtke


title: Tagger–a Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice [TU-Tag-RNA-seq]

status: Public on Oct 30 2019

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

summary: We developed a knock-in mouse line that combines four enrichment tools to study gene regulatory networks of the brain and other complex tissues. As a result, chromatin, nascent RNA, translating mRNA and mature miRNA can be purified from specific cell populations. Specifically, we developed "Tagger" – a Cre and/or Flp recombinase-dependent mouse model that expresses four proteins to enable purification of distinct populations of cellular nucleic acids from specific cell types. Upon activation by cell type-directed recombinases, cells of a desired population express: 1) exogenous uracil phoshoribosyltransferase (UPRT) for tagging nascent total RNA with thiol groups upon administration of 4-thiouracil (4TU, TU-Tag), 2) epitope-tagged large ribosomal subunit protein 22 (Rpl22) to co-immunoprecipitate (co-IP) ribosome-bound mRNA (RiboTag), 3) epitope-tagged Argonaute 2 (Ago2, a component of the RNA-induced silencing complex) to co-IP mature miRNA (AgoTag), and 4) nucleus-directed mKate2 red fluorescent protein, providing good tissue penetrating transmission properties for in vivo imaging and a fluorescent nuclear tag (NucTag) for FACS enrichment of nuclei for chromatin studies.

overall_design: For functional validation, Tagger mice were bred to neuron-directed Cre lines: vGluT2-Cre, Gad2-Cre and PV-Cre, producing vGluT2-Tagger, Gad2-Tagger and PV-Tagger mice, respectively. Then, TU-Tag RNA-seq, RiboTag RNA-seq, AgoTag small RNA-seq and NucTag MeDIP-seq from specific cell types and respective controls/input was generated.

first: Lech

last: Kaczmarczyk

first: Stefan

last: Bonn

first: Walker

middle: S

last: Jackson


title: A chimeric IDD4 repressor constitutively induces immunity in Arabidopsis with the potential application for crop improvement

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: We report the transcriptome composition of idd4SRDX lines compared to Columbia wild-type plant

overall_design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of idd4SRDX lines

first: Ronny

last: Völz

first: Soon-Kap

last: Kim

first: Jianing

last: Mi

first: Kiruthiga

middle: G

last: Mariappan

first: Anna

last: Siodmak

first: Salim

last: Al-Babili

first: Heribert

last: Hirt


title: Dermatomyositis skin transcriptomic signature

status: Public on Oct 27 2019

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

summary: Dermatomyositis is a cutaneous and muscular auto-immune condition associated with specific autoantibodies. MDA5 antibody-associated DM has higher mortality. We demonstrate here for the first time using skin microarray analysis that MDA5+ DM is associated with a greater type I interferon skin signature than MDA5- DM, mainly involving the IFN- κ member produced by skin keratinocytes

overall_design: We planned to identify genes associated with dermatomyositis as compared to healthy donnors on skin samples. Dermatomyositis sample allow also to investigate gene expression associated with their serological status.

first: Charles

last: CASSIUS

first: Reyhan

last: AMODE

last: DELORD

first: Maxime

last: BATTISTELLA

first: Justine

last: POIROT

first: Alexandre

last: HOW-KIT

first: Clemence

last: LEPELLETIER

first: Marie

last: JACHIET

first: Adèle

last: DE MASSON

first: Laure

last: FRUMHOLTZ

first: Florence

last: CORDOLIANI

first: Sylvie

last: DUBANCHET

first: Antionio

middle: J

last: ALBERTI

first: Marine

last: MERANDET

first: Martine

last: BAGOT

first: Armand

last: BENSUSSAN

first: Jean-David

last: BOUAZIZ

first: Hélène

last: LE BUANEC


title: Investigating the Interleukin-22 regulated transcriptome in normal and APC-mutant small intestinal epithelial organoids

status: Public on Oct 25 2019

city: Dundee

first: Mahima

last: Swamy

state: Angus

address: Dow Street

department: MRC Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: University of Dundee

summary:
Purpose: to investigate the effects of the cytokine Interluekin-22 (IL-22) on small intestinal epithelial cells, using organoids.
Methods: WT or Apc(Min/Min) organoids (day 3) were stimulated with IL-22 (2ng/ml) for 3 hours, and submitted for transcriptomic profiling.
Results: The main function of IL-22 in small intestinal epithelial cells is to activate an antimicrobial immune response and defence against infection and stress. Further, we found that loss of Apc lead to a complete loss of response to IL-22

overall_design: Transcriptome profiling (RNA-seq) was performed on Wild-type (WT) and Adenomatous Polyposis Coli (APC) mutant small intestinal epithelial organoids untreated or treated with IL-22 for 3 hours.  3 independent biological replicates were used for each group.

first: Yu

last: Chen


title: OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: We performed evolution of Escherichia coli K12 MG1655 to study how the system adapt to iron toxicity. RNA-Seq was performed to examine the underlying transcriptional rewiring.

overall_design: Growth of E. coli with various supplements was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.


title: Genome-wide analysis of the transcriptional profile of sphingolipid-related genes KD astrocytes during EAE in NOD mice.

city: Boston

first: Chun-Cheih

last: Chao

state: MA

address: 60 Fenwood road BTM 10032

department: Neurology

institute: Brigham and Women's Hospital

summary: We reported that knockdown of sphingolipid metabolism in astrocytes has impact to interfere EAE pathological progressing in NOD mice

overall_design: shControl-targeted (n=3),  shB4galt6-targeted (n=3), shUgcg-targeted (n=3), shCers5-targeted (n=3), shCers6-targeted (n=3) and shPla2g4a-targeted (n=3) mice.

first: Emily

middle: C

last: Tjon

first: Francisco

last: Quintana


title: A critical insulin TCR contact residue selects high affinity and pathogenic insulin specific T cells

city: Salt Lake City

first: Matt

last: Bettini

state: Utah

address: 15 North Medical Drive East, EEJMRB RM 1820

institute: University of Utah

summary: Type 1 Diabetes (T1D) is an autoimmune mediated disease that culminates in the targeted destruction of insulin producing β cells. CD4 responses in non-obese diabetic mice are dominated by InsB9-23 specificity, and mutation of the key TCR contact residue within the epitope prevents diabetes development. However, it is not clear how insulin self-antigen controls the selection of autoimmune and T regulatory cells.  Here we demonstrate that mutation of insulin epitope results in escape of highly pathogenic T cells.  We observe an increase in antigen reactivity, clonality and pathogenicity of insulin specific T cells that develop in the absence of cognate antigen. Using single TCR system, we demonstrate that Treg development is greatly diminished in mice with Y16A mutant epitope. Collectively, these results suggest that the tyrosine residue at position 16 is necessary to constrain TCR reactivity for InsB9-23 by both limiting the development of pathogenic T cells and supporting the selection of regulatory T cells.

overall_design: InsB9-23 expanded T effector Transfer: 3 islet T effector NOD-WT samples, 3 islet T effector NOD-Y16A samples, 3 Splenic NOD-WT samples, 3 Splenic NOD-Y16A samples

first: Matthew

first: Maria

first: Marissa

last: Scavuzzo

first: Malgorzata

last: Borowiak


title: SIX4 acts as a master regulator of genes associated with the malignant phenotype of non-small cell lung cancer cells

status: Public on Oct 26 2019

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

country: China

institute: The Affiliated Hospital of Southwest Medical University

summary: In this work, we evaluated SIX4, a member of the Homeobox gene, acts as a master regulator of oncogenes with the explicit function in the malignant phenotype of NSCLC cells. And SIX4 is a potential candidate of molecular marker for NSCLC.

overall_design:
In this study, the expression of the SIX4 gene in tumors and matching normal lung tissues from 38 NSCLC patients was assessed by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC). Subsequently, the SIX4 gene was stably transfected into two human NSCLC cell lines (A549 and PC9) using the lentiviral system. The malignancy-associated phenotype, including proliferation, migration, and invasion, was assessed in the SIX4-transfected cells and controls using carboxyfluorescein diacetate succinimidyl ester (CFSE), growth curves, wound healing, and Matrigel assays. To further elucidate the mechanism underlying the biological function of SIX4, RNA-seq was performed to check the mRNA expression. Bioinformatics tools were utilized to analyze the contribution of SIX4 co-expressed genes to the malignant phenotype of NSCLC cells.
This dataset includes the RNA-seq data.

first: Xiaoping

last: Tang

first: Yingcheng

last: Yang

first: Xueqin

last: Song

first: Xu

last: Liu

first: Xiaoyang

last: Wang

first: Fang

last: Huang

first: Yan

last: Li

first: Feng

first: Haisu

last: Wan


title: miRNA microarray in the synovial tissue 14 days after anterior cruciate ligament transection (ACLT)

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

summary: To investigate changes in miRNA expression in the synovial tissue, miRNA microarray was performed at day 14 after ACLT and revealed that several miRNA expressions were changed more than 1.5-fold. We chose to analyze the role of miR-21 in joint pain after ACLT because it had the highest signal intensity among the increased miRNAs. Quantitative PCR confirmed that miR-21 expression in synovial tissue was significantly increased 14 days after ACLT.

overall_design: ACLT or sham surgery induced gene expression in synovial tissue of rat was measured at 7 days after surgery.

first: Naoya

last: Hoshikawa


title: Transcriptional characterization of lymph node (LN) naïve CD4+ T cells in infant and adult C57BL/6 mice.

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: RORg+ and Helios+ Tregs in the colon are phenotypically and functionally distinct, but their origins and relationships are poorly understood. In monocolonized and normal mice, single-cell RNAseq revealed sharing of TCR clonotypes between these Treg populations, potentially denoting a common progenitor. In a polyclonal Treg replacement system, naïve conventional CD4+ (Tconv) cells, but not pre-existing tTregs, could differentiate into RORg+ pTregs upon interaction with gut microbiota. A smaller proportion of Tconv converted into Helios+ pTregs, but these dominated when the Tconv originated from pre-weaning mice. T cells from infant mice were predominantly immature, insensitive to RORg-inducing bacterial cues and to IL6, and showed evidence of higher TCR-transmitted signals, also characteristics of recent thymic emigrants (RTE). Correspondingly, transfer of adult RTE or Nur77high Tconv mainly yielded Helios+ pTregs, recapitulating the infant/adult difference. Thus, CD4+ Tconv can differentiate into both RORg+ and Helios+ pTregs, providing a physiological adaptation of colonic Tregs as a function of the age of the cell or of the individual.

overall_design: Gene expression profiles of LN naïve CD4+ T cells from infant and adult mice. Each biological replicate is one mouse and 3 biological replicates were obtained per experimental group.

first: Alvin

last: Pratama

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Transcriptional signatures derived from murine tumor-associated macrophages predict  outcome in breast cancer patients

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)

summary: Macrophages are frequently the most abundant immune cells in murine and human cancers. Studies in various transgenic mouse tumor models have revealed pro-tumor functions of tumor-associated macrophages (TAMs), but despite their association with poor clinical outcome in human patients, molecular signatures for the prediction of clinical outcome in humans are still missingbeen demonstrated. Here we generated molecular signatures from F4/80+CD11b+ TAMs from two transgenic breast cancer models: K14cre;Cdh1flox/flox;Trp53flox/flox (KEP), which resembles human invasive lobular carcinoma (ILC) and MMTV-NeuT (NeuT), which resembles HER2-overexpressing breast cancer. Determination of truly specific TAM transcriptome signatures in breast cancer required relationship analysis with healthy mammary gland tissue macrophages (MTMs), since comparison with macrophages from tissues overestimated TAM-specific gene expression. Furthermore, translation of the TAM signatures to outcome prediction in patients required consideration of the breast cancer subtype. TAM signatures derived from the KEP, but not the NeuT model reliably predicted outcome in ILC patients. Collectively, we show that a transgenic mouse tumor model can be utilized to derive a TAM-based signature for human breast cancer outcome prediction and provide a generalizable strategy for determining and applying specific molecular signatures of immune cells to, in principle, any cancer provided the murine model reflects the human disease.

overall_design: Analysis of changes in the expression of mRNAs in tow different murine breast cancer models.

first: Sander

last: Tuit

first: Camilla

last: Salvagno

first: Theodore

last: Kapellos

first: Cheei-Sing

last: Hau

first: Lea

last: Seep

first: Marie

last: Oestreich

first: Kathrin

last: Klee

first: Karin

middle: E

last: de Visser

first: Thomas

last: Ulas


title: CDK2 kinase activity is a regulator of male germ cell fate

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: The ability of men to remain fertile throughout their lives depends upon establishment of a spermatogonial stem cell (SSC) pool from gonocyte progenitors, and also maintaining the proper balance between SSC renewal and spermatogenic differentiation throughout life. Depletion of SSCs causes infertility with a Sertoli Cell Only Syndrome (SCOS) phenotype. We previously created a mouse strain in which an inhibitory phosphorylation site (Tyr15) of Cyclin-dependent kinase 2 (Cdk2) was altered. Juvenile males homozygous for this allele (Cdk2Y15S) initiate the first round of spermatogenesis, which originates from prospermatogonia, but meiocytes arrest due to chromosomal defects resembling those in Cdk2-/- mice. Subsequent waves of spermatogonial differentiation and meiosis were largely absent, leading to an SCOS-like phenotype. Here, we demonstrate that Cdk2Y15S/Y15S mice possess mitotically active GFRa1+ SSC-like cells, but they are impaired in their ability to differentiate. Marker analysis and single cell RNA-seq revealed defective differentiation of gonocytes into SSCs. Biochemical and genetic data demonstrated that Cdk2Y15S is a gain-of-function allele causing deregulated kinase activity, and its phenotypic effects could be reversed by mutating the Thr160 positive regulatory site in cis. These results demonstrate that precise temporal regulation of CDK2 activity in male germ cell development and in the cell cycle is critical for long-term spermatogenic homeostasis.

overall_design: P3 animals (Cdk2<+/+>, Cdk2<+/YS> and Cdk2<YS/YS>) were sacrificed and their gonads were detunicated to prepare single cell samples as described below.

first: Priti

last: Singh

first: Ravi

last: Patel

first: Andrew

last: Grimson

first: John

last: Schimenti


title: Genome-wide CRISPR screen reveals cancer cell resistance to NK cells induced by NK-derived IFN-gamma

status: Public on Oct 24 2019

city: ROCKVILLE

first: Eric

last: Long

state: MD

address: 5625 FISHERS LN RM 4S-12A

department: Molecular & Cellular Immunology Section

institute: National Institute of Allergy and Infectious Diseases

summary: The anti-leukemia activity of NK cells helps to prevent relapse during hematopoietic stem cell transplantation in leukemia patients. However, the factors that determine sensitivity or resistance of leukemia cells in the context of NK-mediated cytotoxicity are not well established. Here we performed a genome-wide CRIPSR screen in the human chronic-myelogenous-leukemia (CML) cell line K562 to identify genes that regulate vulnerability of leukemia cells to killing by primary human NK cells. Distribution of guide RNAs (gRNAs) in K562 cells that survived co-incubation with NK cells showed that loss of NCR3LG1, which encodes the ligand of the natural cytotoxicity receptor NKp30, protected K562 cells from killing. In contrast, loss of genes that regulate pathways for antigen-presentation and interferon-gamma-signaling increased the vulnerability of K562 cells. Addition of IFN-gamma neutralizing antibody increased the susceptibility of K562 cells to NK-mediated killing. Upregulation of MHC class I on K562 cells after co-incubation with NK cells was dependent on IFNGR2. Analysis of RNA-seq data from The Cancer Genome Atlas (TCGA) showed that low IFNGR2 expression in cancer tissues associated with improved overall survival in acute myeloid leukemia (AML) and Kidney Renal Clear Cell Carcinoma (KIRC) patients. Our results showing that upregulation of MHC class I by NK-derived IFN-gamma leads to resistance to NK cytotoxicity suggest that targeting IFN-gamma responses might be a promising approach to enhance NK cell anti-cancer efficacy.

overall_design: Cas9-expressing K562 cells were transduced with GeCKO V2 lentivirus libraries at a low MOI of 0.3 and selected in puromycin for 7 days. 50 × 106 transduced K562 cells were incubated with IL-2 -activated NK cells at an E to T ratio of 0.3:1. Percentages of surviving K562 cells were monitored. If needed, extra NK cells were added until only 10% of K562 cells had survived. To recover surviving K562 cells, dead cells were removed by Dead Cell Removal Kit (Miltenyi Biotec) followed by depletion of NK cells using EasySep™ Human CD56 Positive Selection Kit (Stemcell Technologies). In the screen with low selection pressure, recovered K562 cells were refreshed in complete media for 48 hours before genomic DNA extraction. To achieve higher selection pressure, recovered K562 cells were further cultured up to 50 × 106 cells, which were selected again by 2 rounds of co-incubation with NK cells.  Control K562 cells were kept in the same culture conditions without exposure to NK cells. Two biological repeats were performed in the screen under low selection pressure, and two technical repeats were performed in the screen with high selection pressure.

first: Xiaoxuan

last: Zhuang

first: Daniel

middle: P

last: Veltri

middle: O


title: Tagger–a Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice [Ribo-Tag-RNA-seq]

first: Vikas

last: Bansal

first: Lech

last: Kaczmarczyk

first: Stefan

last: Bonn

first: Walker

last: Jackson


title: Tagger–a Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice [Ago-Tag-sRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing


title: Serum Dioxin and DNA Methylation in the Sperm of Operation Ranch Hand Veterans Exposed to Agent Orange

city: Providence

first: Karl

middle: T

last: Kelsey

state: Rhode Island

address: 40 Ship St

department: Epidemiology

institute: Brown University

summary:
Purpose: We studied dioxin exposures and DNA methylation in sperm in 37 men from the Air Force Health Study
Methods: We compared methylation levels in subjects with no, low, medium, and high dioxin levels using EWAS and looking at regions of DNA. We compared our results to those from a Russian study
Results: No loci were found to be significantly associated with dioxin exposure in the EWAS when controlling for false discovery rate. Region H19 was found to have significant associations. Five of our loci of interest overlapped with significant findings from the Russian study

overall_design: 450K methylation array run on sperm cells from men in Air Force Health Study

first: Matthew

last: Rytel

first: Edward

last: Dere

first: Rondi

last: Butler

first: Melissa

last: Eliot

first: Susan

middle: M

last: Huse

first: E

middle: A

last: Houseman

first: Devin

last: Koestler

first: Kim

last: Boekelheide


title: Expression data from roots of WT and fit plants exposed to either Fe sufficient or Fe deficient conditions for 72 hours

city: Hanover

first: Mary Lou

last: Guerinot

state: NH

address: 78 College St

department: Biological Sciences

institute: Dartmouth College

summary: PMID: 15539473. We compared the gene expression in roots between WT and fit mutant under +Fe and -Fe conditions using ATH1 microarray analysis to explore which genes are affected by the loss of FIT function.

overall_design: RNA was harvested from root tissues from WT and fit plants grown on B5 for 2 weeks and then transferred to either +Fe or -Fe conditions for 3 days. Two biological replicates were prepared per genotype and per condition.

first: Sun

last: Kim

first: Mary


title: Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

summary: Patients with germline APC mutations are recognized by hundreds of adenoma polyps in colon, which will give rise to adenocarcinoma inevitably. Over 700 germline APC mutations have been reported to be the leading cause of adenomatous polyposis. However, the underlying mechanism of APC mutation triggered colonic cancer remains mysterious. Here, using a modified STRT-seq protocol, we analyzed over 4000 single cells from the four matching adenomatous polyposis, adenocarcinoma, adjacent normal colon tissue and one lymphatic metastasis from four adenomatous polyposis patients with APC mutations.   We identified the main cell types existed in human intestine such as B cells, mast cells, T cells, macrophage cells, endothelial cells, stromal cells and epithelial cells. And the proportional changes of various cell types during the development of adenoma were showed. The transcriptomic similarities and differences between adenoma, adenocarcinoma and adjacent normal tissue were comprehensively investigated. For better understanding the tumor progression process, we also take advantage of other genomic signatures, such as SNV and CNV. We found that the gene expression signatures of adenoma and adenocarcinoma were largely similar when compared with adjacent normal tissue. But the mutation accumulation was indeed observed during the progression from adenoma to adenocarcinoma. To summarized, our work will help us accurately investigate the pathogenic mechanism and heterogeneity of APC inactive mutation triggered colonic cancer, which will also help us better understand the non-familial colorectal cancers

overall_design:
Single cell transcriptome profiles of matching adenomatous polyposis, adenocarcinoma, adjacent normal colon tissue and one lymphatic metastasis from four adenomatous polyposis patients with APC mutations were generated by next generation sequencing using illumina 4000. For each sample, we also extracted the genomic DNA for whole genome sequencing by using illumina 4000.
Please note that the *txt files (linked to each sample records) provide the barcode sequence and corrsponding sample names.  For example,  file 'FAP3_SA_R2.txt' provided the barcode sequence and sample names for FAP3_SA_R2_*fastq.gz.

first: Li

last: Jingyun

last: Wang


title: Functional classification of chromatin associated lncRNAs via histone modification specific PIRCh-seq analysis

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Many long noncoding RNAs (lncRNAs) regulate gene transcription through binding to histone modifying complexes, therefore a comprehensive study of chromatin associated RNA in a histone modification specific manner is critical to understand their regulatory mechanisms. In this study, we developed a new method named Profiling Interacting RNAs on Chromatin followed by deep sequencing (PIRCh-seq), and profiled chromatin associated transcriptome on 3 cell types, mouse v6.5 embryonic stem cells (mESC), mouse embryonic fibroblasts (MEF) and mouse neuronal precursor cells (NPC), with antibodies attached to histone H3 and 6 active and repressive histone modifications. Compared with existing methods, PIRCh-seq identifies chromatin associated RNAs with significant lower nascent transcription, and classifies chromatin enriched lncRNAs into 6 functional groups based on the patterns of their attachment to nucleosome with specific chemical modifications. Further analysis showed that lncRNAs were also enriched with different modified chromatin in different cell types, suggesting lncRNAs’ regulation may also be cell type specific. By integrating profiles of RNA secondary structure from icSHAPE and RNA m(6)A modification, we noticed that RNA bases attached with chromatin tend to be more single stranded. These results provide a unique resource to globally study the functions of chromatin associated lncRNAs and elucidates the basic mechanisms of chromatin-RNA association.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we developed a new method named Profiling Interacting RNAs on Chromatin followed by deep sequencing (PIRCh-seq), which enriches chromatin associated RNAs at a histone modification specific manner and classifies functional lncRNAs based on the patterns of their attachment to nucleosome with specific chemical modifications. Compare to existing chromatin-RNA association detection techniques, PIRCh-seq efficiently reduces the influence of nascent transcripts with significantly lower number of intronic reads. Through performing PIRCh-seq with histone H3 and a number of different histone modification specific antibodies on different cell-types, we identify cell type specific relationship between lncRNAs and epigenetics. We found chromatin associated lncRNAs can be classified into 6 functional groups, based on their association with chromatin under histone modifications, and is partly conserved among several cell types. We also discovered lncRNAs were associated with different chromatin modifications in different cell types, indicating lncRNAs’ regulation may also be cell type specific. In addition, we found that bases on lncRNAs attached with chromatin tends to be more single stranded. In total, the PIRCh-seq data provides insights into global functional and mechanistic study of chromatin associated lncRNAs.

first: Jingwen

last: Fang

first: Qing

last: Ma

first: Ci

last: Chu

first: Bebei

last: Huang

first: Lingjie

last: Li

first: Pengfei

last: Cai

first: Pedro

last: Batista

first: Pengcheng

last: Du

first: Howard

middle: Y

last: Chang


title: Effects of a male meiotic driver on male and female transcriptomes in the house mouse

city: Zurich

first: Anna

last: Lindholm

address: Winterthurerstrasse 190

department: Department of Evolutionary Biology and Environmental Studies

institute: University of Zurich

summary: We investigated effects of the t haplotype in house mice, an autosomal male meiotic driver, on genome-wide gene expression patterns in males and females. We analysed gonads, liver and brain in adult sibling pairs differing in genotype, allowing us to identify t-associated differences in gene regulation. In testis, only 40% of differentially expressed genes mapped to the approximately 708 annotated genes comprising the t haplotype. Thus much of the activity of the t haplotype occurs in trans, and as up-regulation. Sperm maturation functions were enriched among both cis and trans acting t haplotype genes. Within the t haplotype, more down-regulation and differential exon usage was observed. In ovaries, liver, and brain, the majority of expression differences mapped to the t haplotype, and were largely independent of the differences seen in the testis. Overall, we found widespread transcriptional effects of this male meiotic driver in the house mouse genome.

overall_design:
We compared the transcriptomes of gonads, liver and brain of male and female siblings pairs (one of the genotype +/t, the other +/+) of house mice reared in the lab until sexual maturity, using RNA-seq.
These are wild house mice  (Mus musculus domesticus) descended from animals wild-caught from an intensively studied free-living population in Illnau, Switzerland [PMID: 23762510]

first: Andreas

last: Sutter

first: Sven

last: Kuenzel

first: Diethard

last: Tautz

first: Hubert

last: Rehrauer


title: Single cell transcriptomic analysis (InDrops) of mouse CD4+ T cells isolated from colon

first: CBDM

last: Lab

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation (InDrops)

first: Alvin

last: Pratama

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Loss of Pitx2c predisposes to arrhythmia and atrial fibrillation pathologies via structural and metabolic dysfunction

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: RNAseq profiling of embryonic zebrafish hearts was performed to identify differentially expressed genes downstream of Pitx2c.

overall_design: Embryonic hearts were dissected from wild-type, pitx2c mutants, and pitx2c gain-of-function (OE) embryos at 56 hpf

last: Guenther

first: Michelle

last: Collins

first: Didier

last: Stainier


title: The ETS transcription factor ELF1 regulates a critical, broadly antiviral program distinct from the type I interferon response

city: New York

first: Meike

last: Dittmann

address: 430 East 29th Street, room 313

institute: NYU Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next Generation RNA Sequencing Analysis of AMPK Wild Type,  AMPKα-KO and AMPKα1-2A U2OS cell Transcriptomes

city: Houston

first: Yongji

last: Zeng

state: Texas

address: One Baylor Plaza

department: Medicine

institute: Baylor Collge of Medicine

summary:
Purpose: The goals of this study are to compare NGS-derived U2OS transcriptome profiling (RNA-seq) To get insight into the downstream signaling of AMPK and to evaluate protocols for optimal high-throughput data analysis
Methods: RNA was extracted by using the Direct-zol™ RNA Miniprep Plus Kit (Zymo Research) and evaluated the purity and concentration of the RNA by ultraviolet spectroscopy (NanoDrop). RNA integrity numbers (RIN) were evaluated using the Agilent 2100 Bioanalyzer. RNA sequencing libraries were constructed using 1000 ng of total RNA from each sample and the TruSeqV2 kit from Illumina following manufacturer’s protocol. Illumina NextSeq sequencing and NGS data acquisition were conducted at the UNMC Genomics Core Facility. The libraries were subjected to 75 bp paired-end high-output sequencing using a NextSeq500 sequencer to generate approximately 33.3 to 41.6 million reads per sample. Fastq files were generated using the bc12fastq software, version 1.8.4 and provided to the UNMC Bioinformatics Core facility for further analysis. The original fastq format reads were trimmed and filtered using the fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30). The trimmed fastq files were processed by our facility’s newly developed standard pipeline utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at both gene and isoform levels. TPM values were used for comparison results (student’s t-test) for all the available genes. The Benjamini-Hochberg (BH) adjusted p values  were also provided to adjust for multiple testing-caused false discovery rate (FDR) with significant level of adjusted p value of ≤ 0.05. Comparative analysis of parental U2OS (control) vs. AMPKα-KO and control vs. AMPKα1-2A was performed using Ingenuity Pathway Analysis (IPA) to examine canonical pathways similarly altered in each to designate effects due to dysregulation of CDK1 phosphosites.
Results: Comparative analysis of parental U2OS (control) vs. AMPKα-KO and control vs. AMPKα1-2A was performed using Ingenuity Pathway Analysis (IPA) to examine canonical pathways similarly altered in each to designate effects due to dysregulation of CDK1 phosphosites. Canonical pathways influencing actin dynamics such as actin cytoskeleton signaling, ILK signaling, and regulation of actin-based motility by Rho were predicted to be significantly activated. The expression of a multitude of genes involved in promoting cellular movement and migration were increased and several inhibitors of cell movement were diminished in AMPKα-KO and α1-2A cells compared to controls. By examining alterations of downstream gene expression, upstream analysis pinpointed numerous possible upstream regulators. Most of the highestscoring upstream effectors were analogously modulated between AMPKα-KO and α1-2A compared to controls, indicating that loss of phosphorylation of AMPK by CDK1 is comparable to AMPK knockout for alterations seen in these particular pathways. We previously detected stark reduction of p-Histone H3 (S10) in both the AMPKα-KO and α1-2A cells, which led to speculate that this was possibly due to either phosphatase dysregulation leading to hyperdephosphorylation, or perturbation of kinase signaling leading to inadequate phosphorylation of Histone H3. Interestingly, there were eight significantly up- or down-regulated phosphatases found to be changed mutually between the AMPKα-KO and α1-2A cells compared to controls. Furthermore, between the two treatments, the expression levels of ten kinases and two mitosis-associated kinases significantly changed compared to controls.
Conclusions: Our study represents the first detailed analysis of AMPK Wild Type, AMPKα-KO and AMPKα1-2A U2OS cell Transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that that CDK1 regulates AMPK control of mitotic entry and progression. It remains to be determined which signaling networks or processes CDK1-phosphorylated AMPK utilizes to drive these events.

overall_design: Investigated the transcriptome of U2OS Wild Type,  AMPKα-KO and AMPKα1-2A cells by next generation RNA sequencing (RNA-seq) to investigate the downstream signaling of AMPK.

first: Jixin

last: Dong

first: Seth

last: Staffer


title: DNaseI hypersensitivity mapping/DNaseI high-throughput sequencing (DHS-Seq) in Saccharomyces cerevisiae

status: Public on Oct 23 2019

first: Zlata

last: Gvozdenov

address: 240 Longwood Ave

department: BCMP

summary: We report the application of DHS-Seq and digital genomic footprinting to study chromatin changes and transcription factor-DNA binding upon long-term Hsp90 depletion utilizing the temperature-sensitive allele G170D. By generating about 86 and 85.6 million reads for wild type and mutant, we were able to reconstitute the chromatin accessibility and the transcription factor-DNA binding maps under regular conditions and under conditions where Hsp90 was long-term inactivated. We find that there is a global reduction of transcription factor binding sites with concurrent loss of open chromatin upon Hsp90 inactivation. This data was used in conjunction with our previous work involving DHS-Seq studies and short-term Hsp90 depletion (GEO GSE88875) to distinguish the affected transcription factor networks and the chromatin changes upon short- and long-term Hsp90 depletion. We identified two different modes of Hsp90 operation on transcription factor activities – short-term inactivation of Hsp90 altered transcription factor DNA binding activities, whereas long-term Hsp90 inactivation affected the steady-state levels of transcription factors. Overall, this study shows that Hsp90 regulates multiple transcription factor protein families and modulates chromatin architecture on a genome-wide scale.

overall_design: DHS-Seq for WT and the Hsp90 temperature-sensitive strain with allele G170D.

first: Brian

last: Freeman


title: Tagger–a Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice

city: Tübingen

first: Vikas

last: Bansal

address: Otfried Müller Strasse 23

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

type: Methylation profiling by high throughput sequencing


title: DNA binding of ELF1 in A549 cells

state: New York

address: 430 E 29th Street

department: Microbiology

institute: NYU School of Medicine

summary: The goal of this study was to analyze the DNA binding landscape of ELF1 in A549 cells. We found that ELF1 mostly binds promoters of genes, close to transcription start sites. We used the promoter-bound genes from our ChIP-seq data and intersected it with differentially expressed genes upon ELF1 overexpression in A549 cells to identify a set of ELF1 regulated target genes.

overall_design:
Examination of ELF1 DNA binding landscape at steady-state or under IFN-beta stimulation.
Examination of ELF1 DNA binding landscape in wild-type A549 cells.

first: Mohammad

last: Sadic

first: Uwe

last: Schaefer


summary: Induction of vast transcriptional programs is a central event of innate host responses to viral infections. Here we report a unique transcriptional program with potent antiviral activity, driven by E74-like ETS transcription factor 1 (ELF1). Using high-content microscopy to quantify viral infection over time, we found that ELF1 inhibits eight diverse RNA and DNA viruses uniquely at multi-cycle replication. Elf1 deficiency results in enhanced susceptibility to influenza A virus infections in mice. ELF1 does not feed-forward to induce interferons, and ELF1’s antiviral effect is not abolished by the absence of STAT1 or by inhibition of JAK phosphorylation. Accordingly, comparative expression analyses by RNAseq revealed that the ELF1 transcriptional program is distinct from interferon signatures. Thus, ELF1 provides an additional layer of the innate host response, independent from the action of type I interferons.

overall_design: A549 cells were not-transduced or transduced with empty vector, ELF1-WT, or ELF1-R8A mutant. Indicated cultures were stimulated with interferon beta for 6 hours or 48 hours. All samples were harvested simultaneously and analyzed by RNA-Seq.

first: Brad

last: Rosenberg


title: Discovery of Specialized NK Cell Populations Infiltrating Human Melanoma Metastases

first: Yuheng

last: Lu

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

summary: NK cells contribute to protective anti-tumor immunity, but little is known about the functional states of NK cells in human solid tumors.  To address this issue, we performed single-cell RNA-seq analysis of NK cells isolated from human melanoma metastases, including lesions from patients who had progressed following checkpoint blockade.  This analysis identified major differences in the transcriptional programs of tumor-infiltrating compared to circulating NK cells.  Tumor-infiltrating NK cells represented seven clusters with distinct gene expression programs indicative of significant functional specialization, including cytotoxicity and chemokine synthesis programs.  In particular, NK cells from three clusters expressed high levels of XCL1 and XCL2, which encode two chemokines known to recruit XCR1+ cross-presenting dendritic cells into tumors.  In contrast, NK cells from two other clusters showed a higher level of expression of cytotoxicity genes.  These data reveal key features of NK cells in human tumors and identify NK cell populations with specialized gene expression programs.

overall_design: Matching samples were collected from blood and tumor-infiltrating NK cells in 5 patients with melanoma metastasis.

first: Kai

middle: W

last: Wucherpfennig


title: Murine Th2, Th9, and iTreg transcriptome

city: Seoul

first: Gap Ryol

last: Lee

address: 35 Baekbeom-ro, Mapo-gu

department: Department of Life Science

country: South Korea

institute: Sogang University

summary: Transcriptional profiling of mouse Th2, Th9, and iTreg cells. Transcriptomes were compared with that of naïve CD4 T cells. Goal was to screen subset-specific genes.

overall_design: Transcriptional profiling of mouse Th2, Th9, and iTreg cells were compared with that of naïve CD4 T cells. Biological replicates: 1 Naïve vs Th2, 1 Naïve vs Th9, 1 Naïve vs Treg.

first: G


title: Analysis of single cell gene expression profile in human iPSC-derived lt-NES cells

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

summary: We performed single-cell total RNA-seq of iPSC-derived neuroepitherial-like stem cells using RamDA-seq methods. We observed hetelogeneity and classified it based on differentiation potential.

overall_design: Single cell RNA-Seq profiling of 88 iPSC-derived neuroepitherial-like stem cells.


title: TIP60/KAT5 is required for neuronal viability in hippocampal CA1

city: Shanghai

first: Haifang

last: Wang

address: NO 320, Yue Yang Road

institute: Institute of Neuroscience

summary: We aimed at investigating the function of TIP60 in the in the mammalian hippocampus. For this, we used mice with a forebrain-specific deletion of Tip60 upon tamoxifen injection (Tip60 cKO). RNA-sequencing was applied to examine the transcriptome changes in the CA1 region upon Tip60 deletion. We observed massive transcriptional changes and identified a neurodegeneration-related signature at a time when there are no obvious morphological changes in Tip60 cKO mice. Later on these mice develop extensive neurodegeneration in hippocampal CA1.

overall_design: We profiled gene expression levels through RNA-Seq to compare Tip60 cKOs to control mice 10 days after tamoxifen injections.

first: Inga

last: Urban


title: Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability (22RV1 RNA-seq)

city: North Chicago

first: Xin

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties.  RNA-seq analysis revealed that ABBV-744 elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.

overall_design: mRNA profiles of 22RV1 cells treated with ABBV-075, ABBV-744, or Enzalutmide in the presence or absence of DHT were generated by deep sequencing, in duplicate, using Illumina HiSeq3000.

first: Emily

last: Faivre


title: Shox2 deficiency leads to a unique loss of the palatine process of the maxilla

city: chengdu

first: Jue

last: Xu

address: 18# 3rd section, Renmin South Road

institute: Sichuan University

summary: In order to profile genome-wide effect of Shox2 in regulating osteogenesis in the developing palate, we further performed RNA-Seq on the anterior palatal tissues from E14.5 Shox2Cre/-;Nkx2.5F/F embryos and controls, respectively.

overall_design: Examination of mRNA level in E14.5 anterior hard palatal tissues from  Shox2Cre/+;Nkx2.5F/F and Shox2Cre/-;Nkx2.5F/F mice.

first: Zhen

last: Huang

first: YiPing

last: Chen


title: Shox2 regulates osteogenesis and patterns the hard palate during palatogenesis


title: Effect of linoleic acid on gut-derived Bifidobacterium breve DSM 20213: a transcriptomic approach

city: Piacenza

first: Maria Luisa

last: Callegari

state: Piacenza

address: via Emilia Parmense

department: DISTAS

country: Italy

institute: Università Cattolica del Sacro Cuore

summary: we investigated the effect of linoleic acid on the metabolism Bifidobacterium breve DSM 20213 by means of transcriptomic approach

sample_organism: Bifidobacterium breve DSM 20213 = JCM 1192

overall_design: Examination of samples grown in two different conditions: MRS-cys and MRS-cys-linoleic acid


title: Transcriptional basis of CD4 T cel help for memory CD8 T cell formation

first: Tomasz

last: Ahrends

address: 1230 York Ave

institute: The Rockefellere University

summary: CD4+ T-cell help is required for the generation of CD8+ cytotoxic T lymphocyte (CTL) memory. We here reveal how “help” signals delivered during priming impact memory differentiation of CTLs, as informed by genome-wide analyses. “Help” signals promoted the IL-15-dependent maintenance of central memory (TCM) cells. However, they had a much larger impact on the generation of effector memory (TEM) cells and their gene expression program . CD4+ T-cell help created TEM cells that produced Granzyme B and IFNg after antigen-independent recall with IL-12 and IL-18. Furthermore, “helped” memory CTLs expressed the effector program characteristic of “helped” primary CTLs upon recall with MHC class I-restricted antigen only, due to both epigenetic imprinting and sustained mRNA expression of relevant genes . Thus, CD4+ T-cell help delivered during priming creates CD8+ TEM cells with innate and help-independent recall capacities.

overall_design: Whole transcriptome analysis of effector and central memory CD8 T cells primed in the presence or absence of CD4 T cell help.

first: Jannie

last: Borst


title: Epigenetic basis of CD4 T cel help for memory CD8 T cell formation

summary: We report here the effects of CD4 T cell help during priming on the acquistion of specific epigenetic program by memory CD8 T cells.

overall_design: Examination of 2 different histone marks in heled and non-helped memory CD8 T cells.


title: Shox2 is necessary for lineage-specific chromatin accessibility in the anterior palate

summary: Being a transcription factor, Shox2 binds to specific DNA sites to regulate gene expression via modulating chromatin status. To investigate the impact of Shox2 on the chromatin accessible landscape in the anterior hard palate, we subjected FACS-sorted Shox2+ cells from the palate of E14.5 Shox2Cre/+;Nkx2.5F/F;R26RmTmG and Shox2Cre/-;Nkx2.5F/F;R26RmTmG mice to ATAC-Seq analysis.

overall_design: Examination of Shox2 cell linage in Shox2 deficiency palate and the control palate


title: Distinct mechanisms of acquired resistance to oncogenic kinase inhibition in cancer cells revealed using a single-step, high-dose selection scheme

city: South San Francisco

first: Kenneth

last: Finn

state: CA

address: 1170 Veterans Blvd

institute: Calico Labs

summary: Despite the remarkable clinical efficacy demonstrated by molecularly-targeted cancer therapeutics, the benefits are typically temporary due to the emergence of acquired drug resistance.  This has spurred a massive effort by the cancer research community to identify mechanisms used by cancer cells to evade treatment.  Among the various methodologies developed and employed to identify such mechanisms, the most commonly used approach has been to model acquired resistance by exposing cancer cells in culture to gradually increasing concentrations of drug over an extended period of time.  Here, we employed a less commonly used variation on this approach wherein resistant cells are selected by immediately exposing cancer cells to a continuous, high concentration of drug.  Using this approach, we isolated clones representing three distinct mechanisms of resistance to inhibition of MET kinase activity from a single clonally-derived cancer cell line.  The emergent clones had acquired resistance through engagement of alternative receptor tyrosine kinases, either through upregulation of FGF3 or HB-EGF, or increased MAPK signaling through an activating V600E mutation in BRAF.  Importantly, these mechanisms were not identified using the conventional ‘ramp-up’ approach in previous studies that employed the same cell line.  These results suggest that the particular nature of the selection scheme employed in cell culture modeling studies can determine which potential resistance mechanisms are identified, and which ones may be missed, highlighting the need for careful consideration of the specific approach used to model resistance in cultured cells.

overall_design: Total RNA was collected and analyzed from each of six crizotinib resistant subclones derived from GTL-16 cells (GTL-16_A, GTL-16_B, GTL-16_C, GTL-16_D, GTL-16_E, GTL-16_F), as well as from parental GTL-16 cells.  For each, triplicate samples were collected for analysis.

first: Scott

last: Martin

first: Jeff

last: Settleman


title: RNA Sequencing Allows for Differential Gene Expression Analysis of Infrequently Dividing and Frequently Dividing (IDC/FDC) Oral Epithelial Stem Cells

status: Public on Oct 22 2019

city: Durham

first: Kevin

middle: Matthew

last: Byrd

state: North Carolina

address: 4134 Brenmar Lane

department: Pathology and Laboratory Medicine

institute: The University of North Carolina

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare palatal epithelial basal cell transcriptomes between infrequently and frequently dividing cells (IDC/FDCs).
Methods: RNA was isolated from 200-1000 palatal basal epithelial cells and libraries prepared using the SoLo RNA-Seq library preparation kit (NuGEN). mRNA profiles of 14-day doxycycline chased K5-tTA;tetO-H2B-GFP (containing populations of slow-cycling GFP-HI and fast-cycling GFP-LO) mice were generated with 6 matched samples using an Illumina HiSeq4000. RNA Sequencing Allows for Differential Gene Expression Analysis of infrequently dividing and frequently dividing cells (IDC/FDC). RNA-seq fastq files were trimmed and aligned to the latest mouse genome, mm10 (GRCm38/GCA_000001635.2) using BBMap. A matrix of the data was generated using featureCounts. RNAseq data was analyzed with DESeq2. All statistical analyses were performed using R version 3.4.1 and RStudio version 1.0.143. Validation was performed using lineage tracing and immunofluorescence immunohistochemistry.
Results: Using an optimized data analysis workflow, approximately 2% of the transcripts showed differential expression between the GFP-HI and GFO-LO palatal basal epithelial cell with a p value <0.05. Analysis of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to oral epithelial stem cell, such as Lrig1 and Igfbp5 as followed up on in the associated manuscript.
Conclusions: Our study represents the first detailed analysis of palatal basal epithelial stem cell transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show GFP-LO infrequently dividing cells are express a distinct transcriptional profile compared to frequently dividing neighbor cells such as Lrig1 and Igfbp5.

overall_design: Palatal epithelial basal cell mRNA profiles of 14-day doxycycline chased K5-tTA;tetO-H2B-GFP mice were generated with 6 matched samples using an Illumina HiSeq4000.


title: RNA sequencing (RNA-Seq) in Saccharomyces cerevisiae

city: Boston

first: Zlata

last: Gvozdenov

institute: Harvard Medical School

summary: Genomic events including gene regulation and chromatin status are controlled by transcription factors.  Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family.  Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure.  Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern.  Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function whereas prolonged Hsp90 inactivation led to a significant decrease in the steady-state transcription factor protein levels.  Intriguingly, despite the broad chaperone-impact on a variety of transcription factors, the operational influence of Hsp90 was at the level of chromatin with only a mild effect on gene regulation.  Thus, Hsp90 selectively governs the transcription factor process overseeing local chromatin structure.

overall_design: RNA-Seq for WT and the Hsp90 temperature-sensitive strain with allele G170D.

first: Brian

last: Freeman


title: Prevalent cytidylation and uridylation of precursor miRNAs in Arabidopsis

city: Nanchang

first: Jianbo

last: Song

state: Jiang Xi

address: Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China

institute: Jiang Xi Agricultural University

summary: A key step in microRNA (miRNA) biogenesis is the processing of a primary precursor RNA by the microprocessor into a precursor miRNA (pre-miRNA) intermediate. In plants, little is known about the processes that act on pre-miRNAs to influence miRNA biogenesis. Here, we performed 3’ RACE-seq to profile pre-miRNA 3’ ends in Arabidopsis. 3’ end heterogeneity was prevalent and the three microprocessor components promoted 3’ end precision. Extensive cytidylation and uridylation of precise and imprecise pre-miRNA 3’ ends were uncovered. The nucleotidyl transferase HESO1 uridylated pre-miRNAs in vitro and was responsible for most pre-miRNA uridylation in vivo. HESO1, NTP6 and NTP7 contribute to pre-miRNA cytidylation. Tailing of pre-miRNAs tended to restore trimmed pre-miRNAs to intact lengths to promote further processing. In addition, HESO1-mediated uridylation led to the degradation of some imprecisely processed pre-miRNAs. Thus, we uncovered widespread cytidylation and uridylation of pre-miRNAs and demonstrated diverse functions of pre-miRNA tailing in plants.

overall_design: 3' RACE-seq in Arabidopsis


title: Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage [RNA-Seq]

city: Setagaya

first: Kazuhiko

last: Nakabayashi

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: Although Tead4 is well-known to be critical for blastocyst development and trophoblast lineage differentiation, the higher-order chromatin organization around this gene remains poorly understood. We assayed long-range chromosomal interactions on the Tead4 promoter in mouse embryonic stem (ES) cells and trophoblast stem (TS) cells using the circular chromosome conformation capture (4C)-seq technique. We observed frequent overlaps of genomic regions interacting with the Tead4 promoter and open chromatin regions identified by FAIRE-seq in TS cells. By systematic reporter assays using ES and TS cells, we identified five genomic fragments possessing a TS-specific enhancer activity to the Tead4 promoter, consisting of two intra- and three inter-chromosomal loci relative to the Tead4 gene on chromosome 6. We established five mouse lines deleted with one of the five enhancer elements using CRISPR/Cas9 genome editing, and evaluated the effect of each of the enhancer deletions on the Tead4 gene expression at the blastocyst stage. We observed 35-50% decrease of the Tead4 expression in the blastocysts with heterozygous or homozygous deletion of an inter-chromosomally located enhancer on chromosome 19 compared to that in wild-type blastocysts, whereas the other four deletions did not affect the Tead4 expression level. Our results demonstrate that inter-chromosomal enhancer-promoter interaction bears a critical role in assuring the appropriate level of Tead4 gene expression at the trophoblast lineage specification.

overall_design: RNA-seq was performed for the blastocystes homozygously or heterozygously deleted with the Region M on chromosome 19 and for the wild-type blastocysts. RNA-seq was also performed for the C57BL/6 mouse-derived ES and TS cells.

first: Junko

last: Tomikawa


title: CD4+ T-cell help creates effector memory CTLs with innate and help-independent recall capacities

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin state in Shox2-domained anterior and Shox2-free posteior palatal tissues in the developing palate.

summary: To characterize the anterior palate-specific chromatin landscape of the distal Shox2-binding sites, we conducted Shox2 ChIP-Seq again in parallel with H3K27ac ChIP-Seq on the Shox2+ domain anterior palate and the Shox2- posterior palate. Integrative analysis of the Shox2 and H3K27ac ChIP-Seq datasets and aggregate plots of binding signals of H3K27ac in the anterior and posterior palate, respectively, versus the summits of Shox2 binding sites showed close association of Shox2 binding peak with enriched H3K27ac in the anterior palate but not the posterior palate, indicate that Shox2 occupancy is highly related to active enhancer elements.

overall_design: Examination of Shox2-binding peaks in anterior palate and the H3K27ac-enriched peaks in anterior and posteior palate


title: 53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science


title: 53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination (END-seq)

institute: Center for Excellence in Molecular Cell Science

summary: 53BP1 activity drives genome instability and embryonic lethality in BRCA1-deficient cells by inhibiting homologous recombination (HR).53BP1’s anti-recombinogenic functions require phosphorylation-dependent interactions with two effector complexes, PTIP and RIF1/Shieldin. While RIF1/Shieldin is thought to block 5’-3’ nucleolytic processing of DNA ends, it remains unclear how PTIP antagonizes HR. Here we show that mutation of the PTIP interaction site in 53BP1 (S25A) increases Shieldin association with DNA damage. Despite excessive Shieldin “end-blocking” activity, the mutant protein allows end resection sufficient to rescue the lethality of BRCA1D11 mice. End resection in BRCA1D1153BP1S25A mice is rewired in a manner driven by DNA2 since Shieldin blocks EXO1-mediated nucleolytic processing. Despite ample resection, mutant cells fail to complete HR, as 53BP1/Shieldin also inhibits RNF168-mediated loading of PALB2/RAD51 onto ssDNA post-resection. As a result, BRCA1D1153BP1S25A mice exhibit hallmark features of HR insufficiency, including increased developmental neuronal apoptosis, premature aging and hypersensitivity to PARP  inhibitors. Disruption of Shieldin or forced targeting of PALB2 to ssDNA in BRCA1D1153BP1S25A cells restores RNF168 recruitment, RAD51 nucleofilament formation, and PARPi resistance. Our study supports a model in which RIF1/Shieldin and PTIP associate independently with 53BP1 to regulate distinct end-resection pathways, and reveals a critical function of 53BP1/Shieldin post-resection that limits RNF168-mediated loading of RAD51.

overall_design: WT, 53BP1-/-, BRCA1-/-,BRCA1-/- 53BP1-/-, 53BP1_S25Aand BRCA1-/- 53BP1_S25A MEFs expressing inducible AsiSI were processed for ENDseq analysis at DSB sites.

first: Elsa

last: Callen

first: Dali

last: Zong

first: Nancy

last: Wong

first: Andre

last: Stanlie

first: Lavinia

last: Dumitrache

first: Andrea

last: Byrum

first: Carlos

last: Mendez-Dorantes

first: Paula

last: Martinez

first: Andres

last: Canela

first: Yaakov

last: Maman

first: Amanda

last: Day

first: Michael

last: Kruhlak

first: Maria

last: Blasco

first: Jeremy

last: Stark

first: Nima

last: Mosammaparast

first: Peter

last: McKinnon

last: Nussenzweig


title: Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage [FAIRE-Seq]

first: Kazuhiko

last: Nakabayashi

overall_design: FAIRE-seq was performed for mouse TS and ES cells.

first: Junko

last: Tomikawa


title: 53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination (ChIP-seq)

first: Wei

last: Wu

overall_design: RPA ChIP-seq in WT, 53BP1-/-, BRCA1-/- MEFs at DSB sites upon induction of AsiSI. Rad51 ChIP-seq profile in WT, BRCA1-/- and BRCA1-/- 53BP1_S25A MEFs with or without FHA-PALB2 at AsiSI-induced DSB sites

first: Elsa

last: Callen

first: Dali

last: Zong

last: Wong


title: Sequencing of all RNA species by next generation sequencing of wildtype and GCNAKO Drosophila ovaries

city: Dallas

last: Buszczak

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary:
Purpose: To identify significantly different individual mRNA species or genetic pathways in the GCNAKO mutant  sample when compared to the wildtype sample.  GCNA is encoded by CG14814 (Flybase ID: FBgn0023515).

Method: Total RNA was extracted using the Qiagen miRNEasy kit, followed by on column DNAse digest using the Qiagen DNAse digest kit. We used the miRNEasy kit to ensure collection of small RNA species as well as total RNA.

RNA was collected from three independent bological replicates of freshly dissected Drosophila ovaries ( 100 ovaries per replicate), collected from 1-3 day old female Drosophila. Ovaries were flash frozen in liquid nitrogen after dissection to preserve the RNA species and prevent degradation. RNAse free conditions were maintained throughout the extraction protocol. RNA quality was tested by the sequencing core before sequencing the RNA.

overall_design: Whole trasncriptome or total RNA profiles were generated of 1-3 day old Drosophila ovaries by next generation sequencing using the Illumina HiSeq 2500 .

first: Varsha

last: Bhargava


title: GR cistromes reprogramming by High Fat Diet [ChIP-seq H3K27ac]

city: Munich

first: Nina

middle: Henriette

last: Uhlenhaut

state: Bavaria

address: Ingolstädter Landstraße 1,  Neuherberg

department: Molecular Endocrinology

institute: HelmholtzZentrum München - IDC

summary: We mapped the genome-wide profiles of Histone H3K27 acetylation (two time points, ZT0 and ZT12) by using ChIP-Seq in livers from control mice and mice fed High Fat Diet (HFD) for 12 weeks

overall_design: C57BL/6J mice were fed High Fat Diet (Research Diet, D12331) and control diet (Research Diet, D12329) for 12 weeks. Mice were sacrificed by cervical dislocation at ZT0 (6 am) and at ZT12 (6 pm), liver collected and snap frozen. ChIP was performed as previously described (Uhlenhaut et al. 2012). Sheared chromatin was immunoprecipitated with anti-H3K27ac antibody (Abcam, ab4729). Two replicates per condition and time point were used, for a total of 8 ChIP-seq samples.

first: Ashfaq

last: Mir

first: Fabiana

last: Quagliarini


title: RNA sequencing of mouse placenta in control and protein restricted pregnancies

city: Calgary

first: Malcolm

last: Eaton

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: We used RNA sequencing to identify differentially expressed genes in whole mouse placentas. Pregnant mice were fed either a 20% or 6% protein (isocaloric) two-weeks before mating and throughout pregnancy. Placental lysates are derived from C57BL/6 conceptuses at E16.5 of gestation.

overall_design: Examination of RNA expression in mouse placenta at E16.5. Samples were same-sex litter mates from n=5 pregnancies.

first: Matthew

last: Workentine


title: RUNX2/CBFB modulates the response to MEK inhibitors through activation of receptor tyrosine kinases in KRAS mutant colorectal cancer

city: Amsterdam

first: Evert

last: Bosdriesz

address: De Boelelaan 1111

department: Computer Science

country: Netherlands

institute: VU University Amsterdam

summary: Investigation of the transcriptional consequences of RUNX2 and CBFB loss in the presence and absence of the MEK inhibitor selumetinib in LoVo ERN1 knockout KRAS mutant colorectal cancer cells.

overall_design: RNA-seq comparison of LoVo ERN1 KO, LoVo ERN1/RUNX2 double KO, and LoVo ERN1/CBFB double KO cells treated with 1 uM selumetinib or vehicle.

first: T

last: Sustic

first: E

first: C

last: Lieftink

first: L

middle: F

last: Wessels

first: R

last: Bernards


title: Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage [4C-Seq]

first: Kazuhiko

last: Nakabayashi

overall_design: 4C-seq for the Tead 4 gene promoter was performed for TS and ES cells.

last: Tomikawa


title: Molecular effects of ISRIB during asparagine deprivation

city: New Haven

first: Don

last: Nguyen

state: CT

address: 310 Cedar St BML 338

department: Pathology

institute: Yale University

summary: The integrated stress response (ISR) is a conserved pathway which is activated by cells that are exposed to stress. In lung adenocarcinoma (LUAD), activation of the ATF4 branch of the ISR by particular oncogenic mutations has been linked to the regulation of amino acid metabolism. In the present study, we provide evidence for ATF4 activation across multiple stages and molecular subtypes of human LUAD. In response to extracellular amino acid limitation, LUAD cells with diverse genotypes broadly induce ATF4 in an eIF2α dependent manner, which can be blocked pharmacologically using the integrated stress response inhibitor (ISRIB). Although suppressing eIF2α or ATF4 can trigger different biological consequences, adaptive cell cycle progression and cell migration are particularly sensitive to inhibition of the ISR. These phenotypes specifically require the ATF4 target gene asparagine synthetase (ASNS), which maintains protein translation independently of the mTOR/PI3K pathway. Moreover, NRF2 protein levels and oxidative stress can be modulated by the ISR downstream of ASNS. Finally, we demonstrate that the ISR via ASNS controls the biosynthesis of select proteins, including the cell cycle regulator cyclin B1, which are associated with poor LUAD patient prognosis. Our findings uncover new regulatory layers of the ISR pathway and its control of proteostasis in lung cancer cells as they adapt to metabolic barriers during tumor progression.

overall_design: PC9 cells treated with vehicle or ISRIB in the presence or absence of asparagine for 6 or 24 hr including biological triplicates

first: Alexandra

last: Albert

middle: X


title: GR cistromes reprogramming by High Fat Diet [ChIP-seq: GR day/night]

summary: We mapped the genome-wide binding profiles of GR throughout the day/night cycle (ZT0-ZT4-ZT8-ZT12-ZT16-ZT20) by using ChIP-Seq in livers from control mice and mice fed High Fat Diet (HFD) for 12 weeks

overall_design: C57BL/6J mice were fed High Fat Diet (Research Diet, D12331) and control diet (Research Diet, D12329) for 12 weeks. Mice were sacrificed by cervical dislocation every 4 hours along the day, liver collected and snap frozen. ChIP was performed as previously described (Uhlenhaut et al. 2012). Sheared chromatin was immunoprecipitated with anti-GR antibody (Santa Cruz, sc-1004X), anti-PPARalpha antibody (Santa Cruz, sc-9000), and a mixture of anti-Stat5a/b (RD System, AF2168) and anti-Stat5a/b (pY694/Y699) (Cell Signaling, 9351). Two replicates per condition and time point were used, for a total of 24 GR (ZT0-ZT20, control/HFD), 4 PPAR alpha (ZT12, control/HFD), and 4 STAT5 (ZT12, control/HFD) ChIP-seq samples.


title: GR cistromes reprogramming by High Fat Diet [RNA-seq]

overall_design: Male C57BL/6J mice were fed either control diet (11 kcal% fat w/sucrose, Research Diets D12329) or High Fat Diet (58 kcal% fat w/sucrose, Research Diets D12331) for 12 weeks. At 17 weeks of age, mice were sacrificed by cervical dislocation, and livers were collected at the indicated 4h intervals (ZT0,4,8,12,16,20). Dexamethasone (Sigma, D2915) was administered at ZT0 and at ZT12 as a single i.p. injection of 10mg/kg after 12 weeks of high fat or control diet. Mice were sacrificed by cervical dislocation 4h later. Hepatocyte-specific Alb-Cre x GRflox/flox (Opherk et al. 2004) and controls were placed on HFD or control diet for 12 weeks. Livers were collected after cervical dislocation at the indicated 4h intervals (ZT0,4,8,12,16,20).

first: Kinga

last: Balázs


title: Gene expression data of human normal colon organoids stimulated by IL-17A

status: Public on Oct 21 2019

city: Tokyo

first: Mariko

last: Shimokawa

address: 35, Shinanomachi, Shinjuku-Ku

institute: Keio University

summary: With aging, normal human tissues experience expansion of somatic clones that carry cancer mutations. However, whether such clonal expansion exists in the non-neoplastic intestine remains unknown. Here, from whole exome sequencing of 76 clonal human colon organoids, we identify a unique pattern of somatic mutagenesis in the inflamed epithelium of ulcerative colitis patients. The affected epithelium accumulates somatic mutations in multiple IL-17 signaling-related genes, including NFKBIZ, ZC3H12A, and PIGR, which are rarely identified in colon cancer. Targeted sequencing validates pervasive spread of IL-17 signaling-related mutations. Unbiased CRISPR-based knockout screening in colon organoids illuminates mutation-mediated resistance to IL-17A-induced proapoptotic response. Some of these genetic mutations are known to exacerbate experimental colitis in mice, and somatic mutagenesis in human colon epithelium may be causally linked to the inflammatory process. Our findings highlight a unique genetic landscape adapting to a hostile microenvironment and its potential contribution to the pathogenesis of ulcerative colitis.

overall_design: WT and NFKBIZ-KO organoids generated from 2 human normal colon organoids were stimulated by IL-17A. mRNA were extracted from organoids and hybridized to GeneChip PrimeView Human Gene Expression Array, and scanned using GeneChip Scanner 3000 7G.

first: Kosaku

last: Nanki

first: Masayuki

last: Fujii


title: Both Fallopian Tube and Ovarian Surface Epithelium Can Act as Cell-of-Origin for High Grade Serous Ovarian Carcinoma

city: New York

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: The cell-of-origin of high grade serous ovarian carcinoma (HGSOC) remains controversial, with fallopian tube epithelium (FTE) and ovarian surface epithelium (OSE) both considered candidates. Here, by using genetically engineered mouse models and organoids, we assessed the tumor-forming properties of FTE and OSE harboring the same oncogenic abnormalities. Combined RB family inactivation and Tp53 mutation in Pax8+ FTE caused Serous Tubal Intraepithelial Carcinoma (STIC), which metastasized rapidly to the ovarian surface. These events were recapitulated by orthotopic injection of mutant FTE organoids. Engineering the same genetic lesions into Lgr5+ OSE or OSE-derived organoids also caused metastatic HGSOC, although with longer latency and lower penetrance. FTE- and OSE-derived tumors had distinct transcriptomes, and comparative transcriptomics and genomics suggest that human HGSOC arises from both cell types. Finally, FTE- and OSE-derived organoids exhibited differential chemosensitivity. Our results comport with a dualistic origin for HGSOC and suggest that the cell-of-origin might influence therapeutic response.

overall_design: mRNA profiles of five (5) independent tumors from FTE-derived PTPT organoids (T-FT) and 3 tumors from OSE-derived organoids (T-O) were generated by deep sequencing. Pooled normal OSE (N-O) and FTE (N-FT) samples (3 each) were profiled as controls.

first: Shuang

last: Zhang

first: Benjamin

last: Neel


title: GR cistromes reprogramming by High Fat Diet [ChIP-seq: GR DEX]

first: Nina

last: Uhlenhaut

summary: We mapped the genome-wide binding profiles of GR by using ChIP-Seq in livers from mice fed control or HFD diet after acute exogenous ligand (DEX) administration.

overall_design: Male C57BL/6J mice were fed either control diet (11 kcal% fat w/sucrose, Research Diets D12329) or High Fat Diet (58 kcal% fat w/sucrose, Research Diets D12331) for 12 weeks. At 17 weeks of age, Dexamethasone (Sigma, D2915) was administered at ZT0 and at ZT12 as a single i.p. injection of 10mg/kg. Mice were sacrificed by cervical dislocation 1h later. ChIP was performed as previously described (Uhlenhaut et al. 2012). Sheared chromatin was immunoprecipitated with two different anti-GR antibody (Santa Cruz, sc-1004X and ProteinTech, 24050-AP). Two replicates per condition and time point were used, for a total of 12 GR (ZT0,ZT12, control/HFD) ChIP-seq samples.

first: Ashfaq

last: Mir

first: Fabiana

last: Quagliarini


title: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations [in situ Hi-C]

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

summary: Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. Seemingly complex patterns of enhancer-gene connections in this dataset can largely be explained by a simple quantitative Activity-by-Contact (ABC) model, in which the effect of a candidate enhancer on a target gene is predicted by the intrinsic activity of the enhancer multiplied by the contact frequency between the enhancer and promoter. This ABC score can identify regulatory enhancer-gene connections and predict their quantitative effects from DNase-Seq, H3K27ac ChIP-seq, and Hi-C measurements. The ABC model can explain even complex regulatory phenomena including the ability of an enhancer to “skip” over one gene to regulate a more distant one. Our approach provides a foundation for dissecting mechanisms of enhancer-gene regulation and predicting enhancer-gene connections across cell types.

overall_design: In situ Hi-C was used to probe the three-dimensional structure of the genome in V6.5 mES cells mouse ES cells in four technical replicates

first: Charles

last: Fulco

first: Joseph

last: Nasser

first: Thouis

middle: R

last: Jones

first: Glen

last: Munson

first: Drew

last: Bergman

first: Vidya

last: Subramanian

first: Sharon

last: Grossman

first: Rockwell

last: Anyoha

first: Tejal

last: Patwardhan

first: Tung

middle: H

first: Michael

last: Kane

last: Doughty

first: Elizabeth

last: Perez

first: Neva

last: Durand

first: Elena

last: Stamenova

first: Erez

middle: L

last: Aiden

first: Eric

middle: S

last: Lander


title: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations [ATAC-Seq]

city: Cambridge

state: MA

address: 415 Main Street

institute: Broad Institute

overall_design: ATAC-seq was used to profile NCCIT cells in 2 technical replicates.

last: Nguyen

first: Benjamin

middle: C

first: Jesse

last: Engreitz


title: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations

overall_design: Refer to individual Series


title: Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage

first: Kazuhiko

last: Nakabayashi


title: Transcriptomic profiles of Pseudomonas aeruginosa PAO1 grown in the presence or absence of mucins or mucin-glycans

status: Public on Oct 20 2019

first: Katharina

last: Ribbeck

state: Massachusetts

address: 21 Ames St

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: We use high-throughput sequencing to profile the response of the opportunistic mucosal pathogen Pseudomonas aeruginosa to mucins and mucin-glycans from the mucosal niche. We find that P. aeruginosa undergoes a genome-wide phenotypic shift in response to mucins and their attached glycans. Specifically, nearly all virulence pathways are downregulated in response to these host-produced factors. This study provides a framework for understanding how the host environment regulates bacterial function.

overall_design: Examination of differential gene expression in Pseudomonas aeruginosa in response to mucin and mucin sugars

first: Kelsey

last: Wheeler


title: Comparison of gene expression profiles between S100A4-positive and -negative cells isolated from the Peyer's patches

city: Fukuoka

first: Takehito

last: Uruno

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary: To identify gene products expressed in S100A4-producing cells in Peyer's patches, we used transgenic mice expressing enhanced green fluorescent protein (EGFP) under the control of the mouse S100A4 promoter (S100A4-GFP mice) and analyzed gene expression profiles using microarray.  As a result, we found that S100A4-producing cells expressed many genes characteristic of LysoMac/DCs and ILC3s.

overall_design: S100A4-positive and -negative cells were sorted from the Peyer's patches of S100A4-GFP mice using BD FACSAria II, and the gene expression profiles were compared between them.

first: Kazufumi

last: Kunimura

first: Yoshinori

last: Fukui


title: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations [RNA-Seq human]

overall_design: We examined the effects of using siRNAs to inhibit GATA1. We performed RNA sequencing on K562 cells transfected with siRNAs targeting GATA1 (2 siRNAs) or non-targeting controls (2 siRNA). We generated RNA sequencing libraries from 4 biological replicates for each siRNA and with matched siRNA dose between GATA1-targeting and non-targeting conditions.

first: Charles

last: Fulco

first: Joseph

last: Nasser

first: Thouis

last: Jones

first: Glen

last: Munson

first: Drew

last: Bergman

first: Vidya

last: Subramanian

first: Sharon

last: Grossman

first: Rockwell

last: Anyoha

middle: K


title: Expression data from invasive melanoma cells

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

summary: Melanoma cell lines were established and used for Affymetrix Human Gene 1.0 ST Array

overall_design: Selected invasive melanoma cell populations were compared to those in the original cell lines.

first: Margit

last: Balázs


title: Impact of cognitive performance and normal aging on transcriptomic changes in the prefrontal cortex of rats

city: Philadelphia

first: Vinay

last: Parikh

state: PA

address: 1701 N. 13th Street, Weiss Hall

department: Psychology

institute: Temple University

summary: We investigated how cognitive stimulation impacts gene expression in the prefrontal cortex (PFC), a brain region known to regulate higher cognitive functions including the control of attention, in young and aged rats.

overall_design: 2x2 design: 2 (cognitive performance [2 levels: performing, non performing) x 2 (age [2 levels: young, old])

first: Yin-Fei

last: Tan

first: Eric

last: Ross

first: Michael

last: Slifker

first: Surbhi

last: Joshi

first: Mathieu

last: Wimmer

last: Duggan


title: RNA-seq of etv2 mutant knock-in heterozygous and homozygous zebrafish embryos

status: Public on Oct 19 2019

city: Tampa

first: Saulius

last: Sumanas

state: FL

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

summary: Zebrafish etv2^Gt(2A-Gal4)ci32 line was generated using CRISPR-Cas9 mediated NHEJ approach which has 2A-Gal4 sequence inserted with the exon 5 of etv2 gene thus interrupting etv2 coding sequence. Heterozygous and homozogous embryos were subjected to bulk RNA-seq

overall_design: 3 batches of 15-20 heterozygous and homozygous embryos were frozen at the 15-somite and 24 hpf stages. Total 12 samples were sequenced: triplicate samples of Heterozygous and homozygous embryos at 15-somite and 24 hpf stages

first: Brendan

last: Chestnut


title: Cistromic reprogramming of the diurnal glucocorticoid hormone response by high fat diet

first: Nina

last: Uhlenhaut

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


title: Age-associated Changes in the Transcriptome of SCA7 Mice

city: La Jolla

first: Theresa

last: Gaasterland

address: 9600 Gilman Drive MS 0202

department: Scripps Institution of Oceanography

institute: University of California San Diego

summary: Atxn7 repeat expansion mutations lead to ataxia phenotypes. Total cerebellar RNA from mice with normal Atxn7 repeat lengths and expanded repeats (92 CAG) were sequenced to compared gene expression changes at 12 and 29 weeks of age in normal vs. expanded repeats.

overall_design: Comparison of gene expression in cerebellum of mice to examine effects of repeat expansion in the Atxn7 gene.  Repeats of normal length and length 92 CAG, at age 12 weeks and 29 weeks were compared (4 conditions). Each condition was sampled in triplicate, with tissue from three mice pooled in each sample.

first: Terry

first: Albert

last: La Spada

first: Chenchen

last: Niu

first: Colleen

last: Stoyas


title: Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage [ChIP-Seq]

first: Kazuhiko

last: Nakabayashi

institute: National Research Institute for Child Health and Development

summary: Although Tead4 is well-known to be critical for blastocyst development and trophoblast lineage differentiation, the higher-order chromatin organization around this gene remains poorly understood. We assayed long-range chromosomal interactions on the Tead4 promoter in mouse embryonic stem (ES) cells and trophoblast stem (TS) cells using the circular chromosome conformation capture (4C)-seq technique. We observed frequent overlaps of genomic regions interacting with the Tead4 promoter and open chromatin regions identified by FAIRE-seq in TS cells. By systematic reporter assays using ES and TS cells, we identified five genomic fragments possessing a TS-specific enhancer activity to the Tead4 promoter, consisting of two intra- and three inter-chromosomal loci relative to the Tead4 gene on chromosome 6. We established five mouse lines deleted with one of the five enhancer elements using CRISPR/Cas9 genome editing, and evaluated the effect of each of the enhancer deletions on the Tead4 gene expression at the blastocyst stage. We observed 35-50% decrease of the Tead4 expression in the blastocysts with heterozygous or homozygous deletion of an inter-chromosomally located enhancer on chromosome 19 compared to that in wild-type blastocysts, whereas the other four deletions did not affect the Tead4 expression level. Our results demonstrate that inter-chromosomal enhancer-promoter interaction bears a critical role in assuring the appropriate level of Tead4 gene expression at the trophoblast lineage specification.

overall_design: ChIP-seq for H3K27ac, H3K4me1, TEAD4, KLF5 were performed for TS cells.

first: Junko

last: Tomikawa


title: The impact of depletion of iron or manganese on the transcriptome of Streptococcus mutans

city: Gainesville

first: Jessica

last: Kajfasz

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: Iron and manganese are micronutrientients that serve as important co-factors necessary for enzymatic function.  In the host environment, access to metals can be highy restricted.  Here, we wanted to identify the transcriptomic response when S. mutans UA159 is grown in media depleted of iron, manganese, or both.

overall_design: Streptococcus mutans UA159 was grown in the chemically defined medium FMC, either under metal replete conditions (control), or with iron, manganese, or both metals omitted from the recipe.  Cultures were grown to mid-exponential phase (OD600 = 0.4) and harvested for transcriptional profiling

first: Tridib

last: Ganguly

first: Jose

last: Lemos


title: eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide

status: Public on Oct 18 2019

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: BG 49 RM 2C08, 49 Convent Dr.

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development,

institute: National Institutes of Health

summary: The translation pre-initiation complex (PIC) scans the mRNA for an AUG codon in favorable context. Previous findings suggest that the factor eIF1 discriminates against non-AUG start codons by impeding full accommodation of Met-tRNAi in the P site of the 40S ribosomal subunit, necessitating eIF1 dissociation for start codon selection. Consistent with this, yeast eIF1 substitutions that weaken its binding to the PIC increase initiation at UUG codons on a mutant his4 mRNA and particular synthetic mRNA reporters; and also at the AUG start codon of the mRNA for eIF1 itself owing to its poor Kozak context. It was not known however whether such eIF1 mutants increase initiation at suboptimal start codons genome-wide. By ribosome profiling, we show that the eIF1-L96P variant confers increased translation of numerous upstream open reading frames (uORFs) initiating with either near-cognate codons (NCCs) or AUGs in poor context. The increased uORF translation is frequently associated with reduced translation of the downstream main coding sequences (CDS). Initiation is also elevated at the NCCs initiating N-terminal extensions on GRS1 and ALA1 mRNAs, and at a small set of main CDS AUG codons with especially poor context, including that of eIF1 itself.  Thus, eIF1 acts throughout the yeast translatome to discriminate against NCC start codons and AUGs in poor context; and impairing this function enhances the repressive effects of uORFs on CDS translation and alters the ratios of protein isoforms translated from near-cognate versus AUG start codons.

overall_design:
We examined the effect of sui1-L96P on global translational efficiencies (TEs) by ribosome footprint profiling of isogenic WT and sui1-L96Pstrains. The study includes 8 samples, comprised of 4 mRNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates of sui1Δ mutant strains harboring plasmid-borne sui1-L96P or the WT SUI1 allele. The 4 ribosome footprint profiling samples were deposited to GEO previously (GSM2895472-GSM2895475 in the GSE108334 records).

Please note that wig files were generated from both replicates and are linked to the corresonding *_1 sample records.

first: Fujun

last: Zhou

first: Hongen

last: Zhang

first: Shardul

middle: D

last: Kulkarni

first: Alan

middle: G

last: Hinnebusch


title: Characterization of the developmental landscape of murine RORγt+ iNKT cells

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

summary: Invariant natural killer T cells (iNKT) expressing the retinoic acid receptor-related orphan receptor γt (RORγt) and producing IL-17 represent a minor subset of CD1d-restricted iNKT cells (iNKT17) in C57BL/6J (B6) mice. We aimed in this study to define the reasons for their low distribution and the sequence of events accompanying their normal thymic development. We found that RORγt+ iNKT cells have higher proliferation potential and a greater propensity to apoptosis than RORγt- iNKT cells. These cells do not likely reside in the thymus indicating that thymus emigration, and higher apoptosis potential, could contribute to RORγt+ iNKT cell reduced thymic distribution. Ontogeny studies suggest that mature HSAlow RORγt+ iNKT cells might develop through developmental stages defined by a differential expression of CCR6 and CD138 during which RORγt expression and IL-17 production capabilities are progressively acquired. Finally, we found that RORγt+ iNKT cells perceive a strong TCR signal that could contribute to their entry into a specific Th17 like developmental program influencing their survival and migration. Overall, our study proposes a hypothetical thymic developmental sequence for iNKT17 cells, which could be of great use to study molecular mechanisms regulating this developmental program.

overall_design:
We investigate the transcriptional difference of iNKT cells between mice expressing from B6 mice vs Balbc mice
Klibi J
Li S
Amable L
Joseph C
Brunet S
Delord M
Parietti V
Jaubert J
Marie J
Karray S
Eberl G,
Lucas B
Toubert A
Benlagha K.

first: J

last: Klibi

first: S

last: Li

first: L

last: Amable

first: C

last: Joseph

last: Brunet

first: M

first: V

last: Parietti

last: Jaubert

last: Marie

last: Karray

first: G

last: Eberl

first: B

last: Lucas

first: A

last: Toubert

first: K

last: BenlaghaÂ


title: Duodenal tissues and mesenteric lymph nodes from  wild-type (BALB/c) and MIF deficient mice were compared in the steady state and at day 5 following infection with the gastrointestinal helminth parasite Heligmosomoides polygyrus

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary:
We have found that macrophage migration inhibitory factor (MIF) is essential for the development of effective immunity to the intestinal helminth Heligmosomoides polygyrus, even following vaccination which induces sterile immunity in wild-type mice.
In the context of a Type 2 infection, MIF plays a critical role in polarizing macrophages into the protective alternatively-activated phenotype, and that STAT3 signaling may make a previously unrecognized contribution to immunity to helminths.

overall_design: Tissues from two different sites (duodenum in small intestine, and mesenteric lymph nodes) from  wild-type (BALB/c) and MIF deficient mice were compared in the steady state and at day 5 following infection with the gastrointestinal helminth parasite Heligmosomoides polygyrus.  Samples were named using a three letter scheme; firstly, B or M to indicate Balb/c or MIF-KO, U or I for naive or infected, and D or M for duodenal gut tissue or mesenteric lymph nodes.  Numbers following the three letters are internal identifiers of replicates.

first: Rick

last: Maizels

first: Danielle

last: Smyth


title: Macrophage migration inhibitory factor (MIF) is essential for Type 2 effector cell immunity to an intestinal helminth parasite


title: Gene expression analysis in heart from wild-type or ADAM12 knockout mice under heart failure condition.

city: suita

first: yuto

last: nakamura

address: yamada-oka, 2-2

department: metabolic medicine

institute: Osaka university

summary:
To investigated global changes caused by pressure overload-induced heart failure in ADAM12 knockout mice using a microarray analysis.
A disintegrin and metalloproteinase (ADAM) 12 is has long been considered to promote cardiac dysfunction based on according to the finding report that a small molecule ADAM12 inhibitor, KB-R7785 ameliorated cardiac function in a transverse aortic constriction (TAC) model by inhibiting the through inhibition of proteolytic activation of HB-EGF signaling. HoweverOn the other hand, this compound has poor selectivity for ADAM12, and the role of ADAM12 inon cardiac dysfunction has not yet been investigated usingby genetic loss-of-function mice.   Anoperation. ADAM12 deficiency resulted in significantly more expanded cardiac fibrosis accompanied byaccompanying with increased collagen-related gene expression in their failing hearts. The results of a genome-wide transcriptional analysis suggested a strongly enhanced highly elevated focal adhesion- and fibrosis-related signaling pathway in ADAM12 knockout hearts.   The present results study revealed that the loss of ADAM12 enhanced focal adhesion and canonical TGF-β signaling by regulating the abundance of the integrin β1 and TGF-β receptors.

overall_design: To evaluate heart RNAs two weeks after TAC surgery in order to observe characteristic changes in the genes of signaling elements. Three biological replicates from each genotypes were used. The analysis was performed using Affymetrix Mouse Clariom D (MTA 1.0) array.

first: Yuto

last: Nakamura

first: Shunbun

last: Kita

first: Yoshimitsu

last: Tanaka

first: Shiro

last: Fukuda

first: Yoshinari

last: Obata

first: Tomonori

last: Okita

first: Yusuke

last: Kawachi

first: Yuri

last: Shimizu-Tsugawa

first: Yuya

last: Fujishima

first: Hitoshi

last: Nishizawa

first: Atusko

last: Sehara

first: Norikazu

last: Maeda

first: Iichiro

last: Shimomura