title: Arnt2 tunes activity-dependent gene expression through NCoR2-mediated repression and Npas4-mediated activation

status: Public on Apr 11 2019

city: Boston

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

summary:
ChIP-, ATAC-, and RNA-seq data
Neuronal activity-dependent transcription is tuned to ensure precise gene induction during periods of heightened synaptic activity, allowing for appropriate responses of activated neurons within neural circuits. The consequences of aberrant induction of activity-dependent genes on neuronal physiology are not yet clear. Here, we demonstrate that, in the absence of synaptic excitation, the basic-helix-loop-helix (bHLH)-PAS family transcription factor ARNT2 recruits the NCoR2 co-repressor complex to suppress neuronal activity-dependent regulatory elements and maintain low basal levels of inducible genes. This restricts inhibition of excitatory neurons, maintaining them in a state that is receptive to future sensory stimuli. By contrast, in response to heightened neuronal activity, ARNT2 recruits the neuronal-specific bHLH-PAS factor NPAS4 to activity-dependent regulatory elements to induce transcription and thereby increase somatic inhibitory input. Thus, the interplay of bHLH-PAS complexes at activity-dependent regulatory elements maintains temporal control of activity-dependent gene expression and scales somatic inhibition with circuit activity.

overall_design:
DIV7 cortical cultures were dissected from e16.5-17 pups and treated with depolarizing KCl for NGS assays.

Please note that the stimulus and viral treatment information for GSM3443013-GSM3443034 samples has been updated on Oct 15th, 2019.

first: Nikhil

last: Sharma

first: Elizabeth

last: Pollina

first: M


title: SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

status: Public on May 01 2019

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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: Reduced Representation Bisulphite Sequencing of WT and AICDA KO iPCS clones

status: Public on Apr 03 2019

city: New York

first: Ritu

last: Kumar

address: 1300 York Avenue

department: Surgery

country: USA

institute: Weill Cornell Medicine

summary: We report AICDA facilitates naïve pluripotency of mouse iPSCs by suppressing FGF/ERK signaling. In the absence of AICDA iPSCs fail to achive naïve pluripotent state and display chracteristics of EpiSCs and are primed for differentiation.

overall_design: IPSC clones from WT and AICDA KO fibroblasts were reprogrammed using OSKM.

first: Bill

last: Ding


title: Transcriptome profiling of MIR148A-TKO and wild-type hESC-derived cells on day 4 of cardiac differentiaton

status: Public on Apr 22 2019

city: Suzhou

first: Xing

last: Fang

state: Jiangsu

address: 708 Renmin Rd

department: Institute for Cardiovascular Science

institute: Soochow University

summary: To gain global insights into the transcriptomic response associated with MIR148A family knockout, we performed RNA sequencing (RNA-Seq) on hESC-differentiated cells on day 4 of cardiac differentiation for both WT and MIR148A-TKO groups. RNA-Seq analysis identified a total of 1837 differentially expressed genes in MIR148A-TKO and wild-type hESC-derived cells on day 4 of cardiac differentiaton. Furthermore, Gene Ontology enrichment analysis indicated knockout of all MIR148A family members inhibited lateral mesodermal and cardiac differentiation.

overall_design: RNA-seq analysis of cells derived from both the MIR148A-TKO and wild-type hESCs on day 4 of cardiac differentiation.

first: Zhen-Ao

last: Zhao

last: Lei

first: Shijun

last: Hu


title: Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers

status: Public on Apr 15 2019

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas


title: Retapamulin-assisted Ribo-seq reveals the alternative bacterial proteome

status: Public on Mar 04 2019

city: Chicago

first: Alexander

last: Mankin

state: Illinois (IL)

address: 900 S. Ashland Avenue Room 3056

department: Pharmacognosy

institute: University of Illinois at Chicago

summary: Unorthodox rules of extracting genetic information enable proteome expansion without increasing the genome size. The use of alternative translation initiation sites achieves this goal by allowing production of more than one protein from a single gene. Although several such examples have been serendipitously found in bacteria, genome-wide experimental mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin treatment followed by Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the annotated Escherichia coli genes but, strikingly, it also revealed putative alternative internal start sites in a number of genes. Experimental evidence demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose translation is initiated at an internal in-frame and out-of-frame start sites, can be functionally important and contribute to the ‘alternative’ bacterial proteome. In addition to proteome expansion, the internal start sites may play regulatory role in gene expression.

overall_design: 4 samples of Ribo-seq data were analyzed. In this study we compared the distribution of ribosome density in BWK or BL21 strains of Escherichia coli, with or without Retapamulin treatment.

first: Sezen

last: Meydan

first: James

last: Marks

first: Dorota

last: Klepacki

first: Virag

first: Pavel

last: Baranov

first: Andrew

last: Firth

first: Tonu

last: Margus

first: Amira

last: Kefi

first: Nora

last: Vázquez-Laslop

middle: S


title: Open chromatin profiling of human mast cells

status: Public on Mar 17 2019

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

summary: Here, we used Omni-ATAC-seq to identify open chromatin regions in human peripheral blood-derived MCs and tonsillar MCs

overall_design: Cells were left untreated or sensitized overnight with myeloma-IgE (0.5 μg/ml) and treated with anti-IgE (1 μg/ml) for 2h or 24h. Select samples were pretreated with BAPTA-AM (30 min, 20 μM) or DMSO before anti-IgE treatment. For IL-33-mediated activation, cells were treated with 10 ng/ml recombinant hIL-33.

first: Gokhan

last: Cildir


title: Transcriptomic profiling of human peripheral blood-derived mast cells

summary: Here, we characterized the transcriptome of MCs under steady state, immunoglobulin E (IgE)-sensitized and anti-IgE-treated conditions.

overall_design: MCs were left untreated or sensitized overnight with myeloma-IgE (0.5 μg/ml) and treated with anti-IgE (1 μg/ml) for 2h. RNA was isolated with Trizol and RNeasy columns and RNA-seq was performed.


title: Impact of dieldrin on transcription in Jurkat T cells

status: Public on Mar 18 2019

city: Paris cedex 15

first: Christian

last: MUCHARDT

address: 25 rue du Dr-Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur Paris

summary: Dieldrin is a pesticide with a suspected impact on chromatin. Here, we have exposed Jurkat cells to dieldrin for 30 min. and examined by next generation sequencing the impact on transcription. This impact was compared to that of DMSO (solvent of the dieldrin) and that of PMA.

overall_design: Jurkat cells were exposed to either DMSO, 100microM dieldrin, or 100microM PMA for 30 min. Total RNAs were isolated with a phenol-chloroform-based protocole. Stranded libraries were prepared by random priming, enrichched in poly(A), and then sequenced with a paired end protocole. A second series of  libraries were also prepared with RNAs from DMSO and dieldrin-treated cells using a rRNA-depletion approach rather than a poly(A) enrichment. These libraries were sequences alike.

first: Saliha

last: Azébi

first: Etienne

last: Kornobis

last: Muchardt


title: Molecular characterizaion of neuroendocrine-like bladder cancer

status: Public on Mar 23 2019

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

summary: Neuroendocrine bladder cancer is an aggressive variant of bladder cancer with significant metastatic potential and high risk of mortality. Diagnosis of these tumors is currently dependent on morphological criteria and staining for neuroendocrine markers. Using machine learning and multiple validation cohorts in different clinical settings, we developed a model that identifies tumors with transcriptomic profiles consistent with NE bladder cancers with an absence of NE features by morphological criteria. Early and accurate identification of these patients by genomic analysis may improve outcomes through treatment intensification and adaptation of standard treatment regimens.

overall_design: In this study, we used transcriptome-wide expression profiles to generate a single-sample classifier to identify neuroendocrine-like muscle-invasive bladder tumors.  The classifier was validated on six independent cohorts, including a radical cystectomy cohort of 256 bladder cancer cases.

first: José

middle: B

last: da Costa

first: Ewan

middle: A

last: Gibb

first: Trinity

middle: J

last: Bivalacqua

first: Yang

last: Liu

first: Htoo

middle: Z

last: Oo

first: David

middle: T

last: Miyamoto

first: Mohammed

last: Alshalalfa

first: Jonathan

last: Wright

first: Marc

last: Dall’Era

last: Douglas

first: Joost

middle: L

last: Boormans

first: Michiel

last: Van der Heijden

first: Chin-Lee

last: Wu

first: Bas

middle: W

last: van Rhijn

first: Shilpa

last: Gupta

first: Petros

last: Grivas

first: Kent

last: Mouw

first: Paari

last: Murugan

first: Ladan

last: Fazli

first: Seong

last: Ra

first: Badrinath

middle: R

last: Konety

first: Roland

last: Seiler

first: Siamak

last: Daneshmand

first: Omar

middle: Y

last: Mian

first: Jason

last: Efstathiou

first: Yair

last: Lotan

first: Peter

middle: C

last: Black


title: Competition for energy between immunity and homeothermy triggers trade-offs and regulates host defense strategies

status: Public on Mar 07 2019

city: San Francisco

first: Joni

last: Nikkanen

address: 555 Mission Bay Blvd S

institute: UCSF

summary: Activation of immunity via LPS injection causes an energetic trade-off with the somatic maintenance program of homeothermy, resulting in hypometabolism and hypothermia. To better understand the pathways involved in this trade-off, genome-wide expression profiling was performed on livers of mice housed at 2 different ambient temperatures (22°C and 30°C) with tissue collected at several timepoints post-LPS injection (0, 4, 12, 24hours). Our analysis revealed that regardless of ambient temperature, LPS reprograms host metabolism with distinct metabolic programs engaged to support entry and recovery from the hypometabolic state.

overall_design: Analysis of livers from mice at 22°C (RT) or 30°C (TN) at 0, 4, 12, 24 hours post-LPS injection.

first: Kirthana

last: Ganeshan

first: Ajay

last: Chawla


title: Genome-wide analyses of chromatin state in human mast cells reveal molecular drivers and mediators of allergic and inflammatory diseases

first: John

last: Toubia


title: Function of Epithelium BRG1 in colitis and CAC II

status: Public on Mar 01 2019

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

summary: Here we show that epithelial BRG1, the catalytic subunit of SWI/SNF complex is critical for colitis and colitis-associated-cancer. Depletion of BRG1 in colonrectal epithelial cells make mice develop Spontaneous colitis. To dissect underlying mechanism, we conducted gene expression profile analysis (RNA-Seq) by using primary colonrectal epithelial cells isolated from BRG1CTRL and BRG1IEC-KO(Tamoxifen induced BRG1 knock-out) mice to gain molecular insights into the affected biological processes. To this end, colorectal epithelial cells were isolated after 7 days of tamoxifen treatment, on which day BRG1-depleted mice showed little morphological defects in colon in comparison with control littermates. IECs were isolated by EDTA isolation buffer. Each sample contains pooled mRNA from 3 mice, and was subjected to Hiseq RNA-Seq, performed by Guangzhou RiboBio Co., Ltd. (Guangzhou, China)using IlluminaHiSeq 3000 platform.

overall_design: Genome-wide expression profiling of primary colon epethelial cells isolated form BRG1CTRL and BRG1IEC-KO(Tamoxifen induced BRG1 knock-out) mice，1 weeks prior to cell collection BRG1F/F and Villin-CreERT2，BRG1F/F mine were treated with tamoxifen.

first: yongfeng

first: Jun

last: Qin


title: RNA sequencing of WT and AICDA KO iPCS clones

first: Ritu

last: Kumar

first: Todd

last: Evans


title: A genome-wide assessment of the ancestral neural crest gene regulatory network

status: Public on Mar 30 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: The neural crest is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional profiles and chromatin accessibility of neural crest cells in the basal sea lamprey, in order to gain insight into the ancestral state of the neural crest gene regulatory network (GRN) at the dawn of vertebrates. Transcriptome analyses reveal clusters of co-regulated genes during neural crest specification and migration that show high conservation across vertebrates for dynamic programmes like Wnt modulation during the epithelial to mesenchymal transition, but also reveal novel transcription factors and cell-adhesion molecules not previously implicated in neural crest migration. ATAC-seq analysis refines the location of known cis-regulatory elements at the Hox-α2 locus and uncovers novel cis-regulatory elements for Tfap2B and SoxE1. Moreover, cross-species deployment of lamprey elements in zebrafish reveals that the lamprey SoxE1 enhancer activity is deeply conserved, mediating homologous expression in jawed vertebrates. Together, our data provide new insight into the core elements of the GRN that are conserved to the base of the vertebrates, as well as expose elements that are unique to lampreys.

sample_organism:
Lampetra planeri
Petromyzon marinus

platform_organism:
Lampetra planeri
Petromyzon marinus

overall_design: RNA-seq datasets from Tahara stage (T)18 (3 replicates), T20 (2 replicates) and T21 (3 replicates) dissected lamprey (P. marinus) dorsal neural tubes, count table generated with featureCounts, normalised count table generated with DESeq2. Dissected T20  lamprey (P. marinus) head (2 replicates) and whole embryo (2 replicates) RNA-seq datasets which have been merged. Transcriptome from dorsal neural tube, head and embryo RNA-seq datasets generated with cufflinks/cuffmerge.  ATAC-seq datasets from T20 (3 replicates) and T21 (3 replicates) dissected lamprey (P. marinus) dorsal neural tubes, and T23 (3 replicates) dissected lamprey (P. marinus) heads. Consensus lamprey (P. marinus)  ATAC-seq peakset, from peaks called by MACS2.  ATAC-seq datasets from T20 (3 replicates) and T21 (4 replicates) dissected lamprey (L. planeri) dorsal neural tubes, and T23 (3 replicates) dissected lamprey (L. planeri) heads. Consensus lamprey (L. planeri)  ATAC-seq peakset, from peaks called by MACS2.

first: Dorit

last: Hockman

first: Vanessa

last: Chong-Morrison

first: Stephen

last: Green

first: Daria

last: Gavriouchkina

first: Ivan

last: Candido-Ferreira

first: Irving

last: Ling

first: Ruth

middle: M

last: Williams

first: Chris

last: Amemiya

first: Jeramiah

last: Smith

first: Marianne

middle: E

last: Bronner


title: Maturation of human telomerase RNA component from an extended precursor

status: Public on Mar 28 2019

city: Stanford

first: Caitlin

last: Roake

state: California

address: CCSR 1150, 269 Campus Drive

institute: Stanford

summary: Here, we develop nascent RNAend-Seq, in which we isolate nascent RNA and sequence the 3' ends of RNA precursors. Using a pulse-chase experimental design, we follow extended precursors of the telomerase RNA component (hTR) and show that the mature telomerase RNA derives from these species with slow kinetics compared to other small non-coding RNAs. The human disease causing gene PARN further delays maturation of the hTR precursor in PARN- mutant cancer cell lines. Disruption of the poly(A)polymerase PAPD5 in PARN-mutant cells restores normal processing kinetics and levels of mature hTR. Unexpectedly, neither PARN nor PAPD5 is required for hTR processing. Instead, PAPD5 and PARN set the hTR maturation rate by controlling precursor adenylation.

overall_design: Examination of hTR 3' ends in HeLa and hES cells and in nascent RNA. For all nascent RNA experiments, two replicates performed per time point.

first: Lu

last: Chen

first: Grazia

last: Raffa

first: Ananya

last: Chakravarthy

first: Steve

last: Artandi


title: Expression data from ependymal cell cultures treated with EGF

city: Durham

first: Khadar

last: Abdi

state: NC

address: 300 North Duke St.

department: DMPI

institute: Duke University

summary:
We identified that EGF blocks differentiation of radial glial progenitors into multiciliated cells.
We evaluated global changes to ependymal cell culture gene expression profiles during EGF treatment during differentiation.

overall_design: Radial glial cells were cultured with or without EGF to make ependymal cells  (2 weeks).

first: K

first: C

last: Kuo


title: Dynamic Erasure of Random X-Chromosome Inactivation during iPSC Reprogramming

status: Public on Feb 08 2019

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis and the derivation of induced pluripotent stem cells (iPSCs). X-chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. While XCI has long been studied and provided important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. In this work, we use allele-resolution transcriptomic approaches to study XCR during mouse iPSC reprogramming in order to elucidate the timing and mechanisms of chromosome-wide reversal of gene silencing. Our findings reveal a sequential hierarchy of gene reactivation from the inactive X-chromosome (Xi). We show that gene reactivation initiates before the activation of late pluripotency genes and complete silencing of the long non-coding RNA (lncRNA) Xist, and is completed late in reprogramming. We reveal that the gene-specific timing of reactivation correlates with the genomic distance to genes that escape inactivation and with differential targeting by pluripotency transcription factors (TFs). We also show that histone deacetylases restrict XCR in reprogramming intermediates and that the severe hypoacetylation state of the Xi persists until late reprogramming stages. Therefore, randomly inactivated X-linked genes possess different degrees of epigenetic memory, the reversal of which may involve the combined action of chromatin regulators, pluripotency transcription factors and chromatin topology. Taken together, our study provides the chromosome-wide dynamics of gene reactivation from the randomly inactivated X-chromosome and a framework for understanding how transcription factors induce dynamic reversal of stable epigenetic memory by overcoming repressive chromatin barriers.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Transcriptome profiles of female Mus Musculus/Mus Castaneus mouse embryonic fibroblasts induced to reprogramming by overexpression of dox inducible Oct4, Sox2, Klf4, cMyc cassette were generated by next generation sequencing using NextSeq 500 platform. In total  7 samples were analyzed including: cells collected at Day 2 after dox treatment; Day 8 SSEA1+, Day 10 SSEA1+, Day 13 SSEA1+, Day 15 SSEA1+, iPSCs SSEA1+/GFP+, ESCs SSEA1+/GFP+.

first: Adrian

last: Janiszewski

first: Irene

last: Talon

first: Juan

last: Song

first: Natalie

last: De Geest

first: San

middle: K

last: To

first: Greet

last: Bervoets

first: Jean-Christophe

last: Marine

first: Florian

last: Rambow


title: Sorting leukemia initiating cells from adult and neonatal leukemia

status: Public on Jan 29 2019

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

summary: The defining characteristics of leukemia, such as lineage and genetics, are associated with a typical age of onset.  Understanding mechanisms of leukemia age specificity could improve disease models to develop new therapies.  We used heterochronic transplantation of murine leukemia driven by MLL-AF9 to investigate the relative contribution of the age of the cell-of-origin or the hematopoietic microenvironment to the lineage fate of leukemia initiating cells (LICs).  We show that the neonatal hematopoietic niche supports the development of infant-like mixed lineage B-cell/myeloid leukemia, while a mature niche promotes adult-like pure acute myeloid leukemia (AML) from identical cells of origin.  We attribute this to inhibition of B-lymphoid fate in multipotent progenitor-like LICs by Ccl5 from adult bone marrow (BM) stroma, and implicate glycogen synthase kinase-3 (GSK-3) signaling in the myeloid fate specification in mouse and human MLL-driven leukemia.  These findings connect maturation and aging of the hematopoietic system to leukemia age specificity.

overall_design: Study of transcriptional differences between adult and neonatal leukemia initiating cells

first: Robert

middle: G

last: Rowe

last: da Rocha


title: Function of Epithelium BRG1 in colitis and CAC

first: Yongfeng

last: Liu

summary: Here we show that epithelial BRG1, the catalytic subunit of SWI/SNF complex is critical for colitis and colitis-associated-cancer. Depletion of BRG1 in colonrectal epithelial cells make mice develop Spontaneous colitis. To dissect underlying mechanism, we conducted gene expression profile analysis (RNA-Seq) by using primary colonrectal epithelial cells isolated from BRG1CTRL and BRG1IEC-KO(Tamoxifen induced BRG1 knock-out) mice to gain molecular insights into the affected biological processes. To this end, colorectal epithelial cells were isolated after 14 days of tamoxifen treatment, on which day BRG1-depleted mice showed little morphological defects in colon in comparison with control littermates. IECs were isolated by EDTA isolation buffer. Each sample contains pooled mRNA from 3 mice, and was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.

overall_design: Genome-wide expression profiling of primary colon epethelial cells isolated form BRG1CTRL and BRG1IEC-KO(Tamoxifen induced BRG1 knock-out) mice，2 weeks prior to cell collection BRG1F/F and BRG1ERT2-F/F mine were treated with tamoxifen.

first: Jun

last: Qin


title: Effect of sulforaphane and 5-aza-2'-deoxycytidine on melanoma cell growth

status: Public on Feb 28 2019

city: Little Rock

first: Ravi

middle: W.

last: Sun

state: Arkansas

address: 4301 W Markham St

department: Department of Otolaryngology - Head and Neck Surgery

institute: University of Arkansas for Medical Sciences

summary:
Background: UV exposure-induced oxidative stress is implicated as the driving mechanism for melanoma. Increased oxidative stress results in DNA damage and epigenetic modifications. We wondered whether a low dose of antioxidant could attenuate the oxidative stress of and help cells respond to epigenetic modification treatment at a lower dose. Sulforaphane (SFN) is a natural bioactivated product of the cruciferous family and is known as an antioxidant. We investigated the combinational effect of SFN and epigenetic modification drug, 5-aza-2'-deoxycytidine (DAC), on metastatic melanoma growth.
Methods: Cell growth characteristics, RNA-seq and histone post-translational modification markers (PTMs) were compared in single and combination treatments.
Results: We found increased cell growth inhibition and changes in gene expression profiles which includes a key immuno-regulator cytokine, C-C motif ligand 5 (CCL-5) gene expression upon combinational treatments. There was no significant difference in detectable histone PTMs between treatments.
Conclusions: These results indicate a potential combinational effect of a dietary antioxidant and an FDA-approved epigenetic drug in controlling melanoma growth. The long-term goal of the current study is to find the therapeutic role of the dietary antioxidant SFN as a supporting drug for targeted epigenetic treatment with DAC in controlling melanoma growth.

overall_design: mRNA profiles of mouse B16F10 melanoma cells treated with DMSO (control) , DAC, SFN, or combination treatment (DAC + SFN) were generated by deep sequencing using illumina's NextSeq 500 instrument (75bp SE reads). Three independent biological repeats were performed for all sample groups.

first: Tung-chin

last: Chiang

first: Brian

last: Koss

first: L

last: Su

first: Charity

last: Washam

first: Stephanie

middle: D

last: Byrum

first: Aaron

last: Storey

first: Alan

last: Tackett


title: Chromatin profiling of human mast cells

first: John

last: Toubia

summary: Here, we characterized the steady state, immunoglobulin E (IgE)-sensitized and anti-IgE-mediated chromatin reorganization in human peripheral blood-derived MCs

overall_design: Cells were left untreated or sensitized overnight with myeloma-IgE (0.5 μg/ml) and treated with anti-IgE (1 μg/ml) for 2h. H3K27ac CHIP-seq or H3K4me3 CHIP-seq was performed.

first: Gokhan

last: Cildir


title: Expression data from wild-type and MURC knockout male mouse hearts

status: Public on Jan 19 2019

city: Kyoto

first: Masahiro

last: Nishi

address: Kajii-cho 465, Kawaramachi Hirokoji, Kamigyo

department: Cardiology

country: Japan

institute: Kyoto prefectural university of medicine

summary:
Muscle-restricted coiled-coil protein (MURC)/Cavin-4, which is a component of caveolae, is involved in the pathophysiology of dilated cardiomyopathy and cardiac hypertrophy.
We used microarrays to examine the gene expression of mouse hearts perturbed by MURC deficieny.

overall_design: Left ventricule tissue from 10–13-week-old wild type (WT) and MURC knockout (KO) male mouse hearts were collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the gene expression data perturbed by MURC dificiency to understand pathophisiology of heart disease.

first: Takehiro

last: Ogata


title: Comparison of NK cells and ILC1 in lean versus obese mouse livers by RNASeq

status: Public on Mar 13 2019

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

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

institute: Imperial College London

summary: Mice were weaned onto standard RM1 diet or onto a highly palatable obesogenic diet (824018 – ‘45% AFE fat) supplemented with condensed milk. After 12 weeks, mice were killed, and liver NK cells (Lin- NK1.1+ CD49a- CD49b+) or ILC1 (Lin- NK1.1+ CD49a+ CD49b-) were sorted. Total RNA was extracted from sorted cells, cDNA generated and RNASeq performed.

overall_design: Cells from the livers or 3 lean and 3 obese mice were sorted, with liver NK cells and ILC1 isolated from each mouse, for a total of 12 samples


title: Genome-wide assay of BRG1 regulated genes in inflamed colon epithelial cells

summary: Here we focus on the function of BRG1 in colitis and colitis-associated-cancer, in the aim of finding the direct target genes of BRG1 which may response for the phenotype we observed in BRG1 conditional knock-out mice, ChIP-Seq assay is used. The cells used for ChIP-Seq is colon epithelial cells which isolated from DSS treated mice.

overall_design: To mimic the status of BRG1IEC KO mice, wild-type mice were treated with 2% DSS for 3 days and IECs were isolated by EDTA isolation buffer, and each sample contains pooled IECs from 5 mice. Flash frozen cells were then sent to Active Motif, Inc. for chromatin extraction and followed by immunoprecipitation using anti-BRG1 antibody (Abcam, cat # ab110641).


title: The age of the hematopoietic microenvironment specifies lineage in MLL-rearranged leukemia [Ccl5]

city: Boston

first: Edroaldo

last: Lummertz da Rocha

overall_design: Primary neonatal murine leukemia treated with ccl5 or under control conditions

last: Rowe


title: Identification of transcriptional network regulated by FGFR1 fusion kinase in stem cell leukemia and lymphoma (SCLL)

status: Public on Feb 12 2019

city: Augusta

last: Cowell

state: GA

address: 1410 Laney-Walker Blvd

institute: Augusta University

summary:
Purpose: Oncogenic transformation of hematopoietic stem cells by chimeric fusion kinases causing constitutive activation of FGFR1 leads to a stem cell leukemia/lymphoma (SCLL) syndrome, accompanied by widespread dysregulation of gene activity. The goals of this study are to use NGS-derived transcriptome profiling (RNA-seq) to identify genes regulated by FGFR1 fusion kinase in SCLL.
Methods: Three different cell models for SCLL, respectively BBC2 (B cell lymphoblastic leukemia/lymphoma), ZNF112 (B cell lymphoblastic leukemia/lymphoma) and BCRF8C (myloid leukemia) were treated with selective FGFR1 kinase inhibitor,then the total RNA from treatment and viechel control were isolated for RNA-Seq analysis.
Results: A global gene experssion change is generated, and provides fundamental information for demostration of molecular mechanisms in FGFR1 driven leukemogenesis.

overall_design: comparasion of the transcriptomes of SCLL lines with and without the inhibition of FGFR1

first: Tianxiang

last: Hu


title: RNA-seq using the Cel-Seq2 method, of wild type and 35-polyglutamine (polyQ35) expressing C. elegans worms treated with RNAi toward anc-1,  or left untreated (EV) gene expression profiles.

status: Public on Feb 15 2019

city: Jerusalem

first: Ehud

last: Cohen

address: The Hebrew University of Jerusalem, Ein Kerem

department: Biochemistry and Molecular Biology

country: Israel

institute: The Hebrew University of Jerusalem

summary:
Purpose: We observed protein homeostasis modulations when anc-1 is knocked-down. We wanted to measure changes in gene expression profiles following this manipulation.
Methods: We treated wild type (strain N2) or polyQ35-YFP (strain AM140) nematodes, which express toxic aggregative proteins that challenge their protein homeostasis, with anc-1 RNAi until day six of adulthood, and compared their gene expression levels to those of untreated worms.
Results: The knockdown of anc-1 leads to modified expression levels of hundreds of genes. There is an enrichment of transcription factors and protein homeostasis modulators, such as E3 ubiquitin ligases.
Conclusions: anc-1 regulates protection from toxic aggregative proteins, at least partially, by regulating the expression of genes that encode protein homeostasis factors.

overall_design: Wild type strain, three repeats; polyQ35-YFP strain, four repeats. Each repeat has two conditions: untreated (EV), and RNAi toward anc-1.

first: Amir

last: Levine


title: Neutrophil and whole blood RNAseq from Generalised Pustular Psoriasis patients and healthy individuals

status: Public on Jan 18 2019

first: Francesca

last: Capon

address: Great Maze Pond

department: Genetics and Molecular Medicine

institute: King's College London

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

overall_design: Refer to individual Series


title: Neutrophils RNAseq from Generalised Pustular Psoriasis patients and healthy individuals

summary: NeutrophilsRNAseq

overall_design: 8 affected  and 11 healthy individuals

first: Marta

last: Vergnano

first: Marika

last: Catapano


title: The age of the hematopoietic microenvironment specifies lineage in MLL-rearranged leukemia [MLL_AF9]

overall_design: Study of transcriptional differences between MLL-AF9 transformed hematopoietic stem and progenitor cells in pro-myeloid and pro-lymphoid cells culture conditions

first: Robert

last: da Rocha


title: mRNA sequence  Analysis of Apocynin treated MKN45

status: Public on Jan 27 2019

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

institute: kanazawa university

summary: Noxo1, a component of NADPH oxidase 1 (NOX1) complex, is upregulated in gastric cancer cells in a inflammation-dependent manner, and plays an important role in tumorigenesis (Oncogene, 33: 3820, 2014). To examine the mechanism of NOX1/ROS signaling in tumorigenesis, MKN45 gastric cancer cells were treated with apocynin, an inhibitor for NOX, and their gene expression was examined by RNA sequencing. Based on expression data, Sox2 was shown to be suppressed by apocynin, suggesting a role of Sox2 in a inflammation-associated gastric tumorigenesis.

overall_design: Total mRNA expression profiles of Apocynin administrated MKN45 in 2 trials.

first: Masanobu

last: Oshima

first: Yoichi

last: Yamada

first: Kanae

last: Echizen


title: The age of the hematopoietic microenvironment specifies lineage in MLL-rearranged leukemia


title: Single Cell RNA seq of Genetically Engineered Mouse Models of Pancreatic Adenocarcinoma

status: Public on Jan 25 2019

city: Houston

first: Abdel

middle: Nasser

last: Hosein

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: We report the scRNAseq profiles of three mouse models of pancreatic cancer: KIC, KPfC, KPC.  Analyses demonstrate the existence of 2 molecular subtypes of cancer cells, 2 molecular subtypes of cancer associated fibroblasts, and 2 molecular subtypes of cancer associated macrophages.

overall_design: Untreated mice were sacrificed at various time points prior to scRNA library generation: normal mouse at 60 days, early KIC mouse at 40 days, late KIC mouse at 60 days, late KPfC mouse at 60 days and KPC mouse at 6 months.

middle: N

first: Rolf

last: Brekken


title: Single cell RNA-seq of 25 thousand epithelial cells from xenografts of triple-negative breast cancers

status: Public on Feb 26 2019

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: Patient derived xenografts (PDX) were created from two triple-negative breast cancers (PDX-110 and PDX-332) taken at the time of surgery from drug-naive patients. Freshly sorted epithelial cells were profiled by single-cell RNA-seq (scRNA-seq) using a 10X Genomics Chromium System.

overall_design: Transcriptional profiling was completed for 10,060 total epithelial cells from PDX-110 and 14,681 total epithelial cells from PDX-322.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

last: Visvader


title: Whole blood RNAseq from Generalised Pustular Psoriasis patients and healthy individuals

summary: Whole blood RNAseq

overall_design: 9 affected individuals and 7 controls


title: Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures

status: Public on Dec 31 2018

city: Atlanta

first: Steven

last: Sloan

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

summary: We report a method for deriving oligodendrocyte lineage cells from human pluripotent stem cells (hPSCs) in three-dimensional (3D) culture called human oligodendrocyte spheroids (hOLS). To characterize oligodendrocyte-lineage cells in hOLS, we isolated O4+ cells by immunopanning and performed deep single cell RNA sequencing. We sequenced 295 cells and compared their profiles to unsorted cells isolated from primary human fetal cortex, primary human adult cortex, and hCS. Clustering of all cells using the t-distributed stochastic neighbor embedding (tSNE) approach revealed a distinct populations of SOX10+ oligodendrocytes, within which the O4+ cells derived from hOLS clustered most closely to oligodendrocyte progenitor cells (OPCs) and mature oligodendrocytes from the primary human adult cortical tissue. Additionally, subpopulations of OPCs, newly formed oligodendrocytes, and myelinating oligodendrocytes derived were observed in the hOLS-derived cluster. To further assess the state of oligodendrocyte-lineage cells in hOLS, we performed a Monocle analysis which revealed a spectrum of oligodendrocyte-lineage stages in hOLS ranging from dividing cells that closely resembled primary OPCs to mature cells that closely resembled primary oligodendrocytes.

overall_design: Examination of gene expression in single oligodendrocyte-lineage cells derived from human pluripotent stem cells in three-dimensional culture

first: Rebecca

last: Marton


title: Opposing chromatin remodeler activities control initiation frequency and start site selection

status: Public on Jan 01 2019

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

country: Switzerland

institute: University of Geneva

summary: Using an integrated analysis of chromatin remodeler binding in unperturbed cells and nucleosome displacement activity upon rapid remodeler depletion or degradation, we investigate the interplay between these enzymes and their functional consequences. We show that many promoters are acted upon by multiple remodelers that operate either cooperatively or in opposition to determine the precise location of the key transcription start site-associated +1 nucleosome. Functional assays indicate that +1 nucleosome positioning reflects a trade-off between maximizing RNA Polymerase II recruitment and minimizing transcription initiation at incorrect sites. Interestingly, in the absence of any remodeling activity +1 nucleosomes largely maintain their positions. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to productive transcription initiation.

overall_design: Nucleosome occupancy, TBP binding, RNA Pol II and transcription initiation sites were measured upon depletion of chromatin remodelers of budding yeast.

first: Drice

last: Challal

first: René

last: Dreos

first: Stefano

last: Mattarocci

first: Maria

last: Bruzzone

first: Philipp

last: Bucher

first: Domenico

last: Libri

first: David

last: Shore


title: Function of BRG1 in colitis and colitis-associated-cancer

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM


title: snRNAs as regulators of alternative splicing

city: Madison

first: Heidi

last: Dvinge

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: UW-Madison

summary: In this study we investigated snRNA-mediated modulation of pre-mRNA splicing across the human transcriptome. We first quantified the relative abundance of snRNAs across a comprehensive range of healthy adult and fetal tissues, revealing a surprising variation in the relative snRNA levels both inter- and intra-tissue. To study the role of snRNAs in cancer-relevant splicing, we used breast cancer as a model, since it exhibits a high rate of aberrant splicing48, but a low frequency of mutations in the splicing machinery52. We observed fluctuations in snRNA adundance across the majority of patients, across all breast cancer subtypes. To investigate the impact of snRNA levels using a controlled system, we knocked down snRNAs in vitro, to analyze splicing both transcriptome-wide and at the level of individual exons and introns. Depletion of each specific snRNA resulted in differential splicing across more than a thousand exon junctions within mRNA transcripts. Knock-down of U1 and U2 levels was primarily associated with changes in exon inclusion rates, whereas U4 and U6 depletion predominantly caused incomplete intron removal and a resulting retention of introns in the mature mRNA. Rather than being driven by a single factor, the observed splicing changes were associated with multiple other splicing-relevant features and mechanisms, including mRNA transcription, intron size, and nucleotide composition. The snRNA-mediated changes to the splicing program were enriched within genes encoding components of core cellular pathways and processes, including multiple aspects of RNA and protein metabolism, and thereby have the potential to impact cell growth and identity. The exons and introns that were sensitive to snRNA levels displayed a high variability in splicing in vivo across primary breast cancer samples, indicating that snRNA dysregulation may contribute to aberrant splicing in cancer. We suggest that the cellular composition of snRNAs constitutes a previously unrecognized layer of splicing regulation within the cell, and that variations or disruptions in the relative abundance of the snRNAs can affect the transcriptome of both healthy and malignant cells.

overall_design: snRNAs were knocked down using chemically modified antisense oligos. Cells were harvested after 48h, and the polyA-selected RNA was sequenced.

first: R

last: Bradley

first: H


title: Simultaneous profiling of transcriptome and chromatin accessibility in single nucleus

status: Public on Feb 05 2019

city: La Jolla

first: Song

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: Here we describe SNARE-seq, a droplet-based method to simultaneously profile gene expression and chromatin accessibility in each of thousands of single nuclei. Employing this method, we profiled 1047 nuclei from human cell line mixture, 5081 and 10309 nuclei from neonatal and adult mouse brain.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single nuclei RNA-seq and ATAC-seq co-assay for BJ, H1, K562 and GM12878 cell mixture, and wild type neonatal and adult mouse brain cerebral cortex.

first: Kun

last: Zhang


title: Metformin reverses gene expression signautres in hyperglycaemics endothelial cells

status: Public on Feb 01 2019

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

institute: Baker Heart and Diabetes Institute

summary: Metformin is a well tolerated and often prescribed treatment for type 2 diabetes. However, the effect of metformin on gene expression in endothelial cells remains unknown. We used RNA-seq to profile gene expression in primary human aortic endothelial cells stimulated with metformin in normoglycaemic and hyperglycaemic conditions. We identified novel pathways in hyperglycaemic endothelial cells that may be involved in the development of endothelial dysfunction. Hyperglycaemic endothelial cells expressed interferon-response pathway genes such as MX1 and IFI27. Transcription factor analysis implicates the activation of STAT1 and IRF1. Co-treatment of hyperglycaemic cells with metformin prevented glucose-dependent changes in gene expression, including interferon response genes. Indeed, the effects of metformin in endothelial cells were dependent on glucose levels. In normoglycaemic cells, metformin subtly regulated changes in gene expression. In contrast, metformin was strongly associated with the reversal of gene expression changes induced by hyperglycaemia.

overall_design: Human aortic endothelial cells were stimulated with DMSO (control), metformin (2 mM), D-glucose (30 mM) or metformin and  D-glucose (2 mM and 30 mM respectively) for 64 hours. Study performed in triplicate.

first: Haloom

last: Rafehi

first: Jun

last: Okabe

first: Mark

last: Zeimann

first: Ishant

last: Khurana

first: Scott

last: Maxwell

first: Hari

last: KN

first: Antony

last: Kaspi


title: Dynamic networks of lymphatic vessels interconnect nodes of neighboring hair follicles across the skin

city: Madrid

first: Mirna

middle: Alicia

last: Perez-Moreno

state: Madrid

address: 3rd Melchor Fernandez Almagro st

department: Epithelial Cell Biology

country: Spain

institute: CNIO

summary: Dermal lymphatics form a network that connects all the hair follicles in skin and localize in proximity to the Hair Follicle Stem Cell. RNA sequencing analyses of isolated dermal lymphatics at two different time points of the hair follicle cycle (P55 and P70) indicate the existence of dynamic signaling networks associated with lymphatic remodeling, immune trafficking, and HF signaling.

overall_design: Prox1CreERT2; ROSA26-LSL-eYFP mice of P55 (Mid Telogen) and P70 (Late telogen) were sacrificed and eYFP positive cells were isolated from the backskin.

first: Daniel

last: Peña-Jimenez

first: Coral

last: Fustero-Torre

last: Pérez-Moreno


title: Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts

status: Public on Jan 02 2019

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

institute: CHUV

summary: X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X  chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single cellRNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. In this framework we integrated an original method to identify and exclude doublets of cells. In fibroblast cells, we have identified 55 genes as escapees including five novel escapee genes. Moreover, we observed that all genes exhibit a variable propensity to escape XCI in each cell and cell type and that each cell displays a distinct expression profile of the escapee genes. A metric, the Inactivation Score—defined as the mean of the allelic expression profiles of the escapees per cell—enables us to discover a heterogeneous and continuous degree of cellular XCI with extremes represented by “inactive” cells, i.e., cells exclusively expressing the escaping genes from the active X chromosome and “escaping” cells expressing the escapees from both alleles. We found that this effect is associated with cell-cycle phases and, independently, with the XIST expression level, which is higher in the quiescent phase (G0). Single-cell allele-specific expression is a powerful tool to identify novel escapees in different tissues and provide evidence of an unexpected cellular heterogeneity of XCI.

overall_design: Single-cell RNA seq study on 935 human fibroblasts and 48 lymphoblastoid cells from 5 female individuals, in order to investigate the X chromosome nactivation mechanism on a single cell level and to identify escapee genes

first: Marco

last: Garieri

first: Geogios

last: Stamoulis

first: Xavier

last: Blanc

first: Emilie

last: Falconnet

first: Pascale

last: Ribaux

first: Christelle

last: Borel

first: Stylianos

last: Antonarakis


title: Porcine DRG pain genes analysis  Transcriptomics analysis of the caudal dorsal root ganglia   of tail amputated pigs reveals long-term alterations in gene expression associated with wound healing, inflammation and neuropathic pain

city: Edinburgh

first: Dale

middle: Andrew

last: Sandercock

state: Midlothian

address: Roslin Institute Building

department: Animal and Veterinary Science

institute: Scotland's Rural College (SRUC)

summary:
Tail amputation by tail docking or as an extreme consequence of tail biting in commercial pig production has serious implications for animal welfare. Tail amputation causes peripheral nerve injury that might be associated with chronic lasting pain. The aim of this study was to investigate the short- and long-term effects of tail amputation in pigs on caudal DRG gene expression at different stages of development, particularly in relation to genes associated with nociception and pain. Microarray analysis was used to analyse whole DRG transcriptomes from tail amputated and sham-treated pigs 1, 8 and 16 weeks following tail treatment at either 3 or 63 days of age (8 pigs/treatment/age/time after treatment; n=96). Tail amputation induced marked changes in gene expression (up and down) compared to sham-treated intact controls for all treatment ages and time points after tail treatment. Sustained changes in gene expression in tail amputated pigs were still evident approximately 4 months after tail injury.  Gene correlation network analysis revealed two gene coexpression clusters associated with amputation.  Gene ontology (GO) enrichment analysis found the genes in Cluster A (124 genes) and Cluster B (61 genes) to be associated with both ‘inflammatory pain’ and ‘neuropathic pain ’. Key families of ion channels and receptors were significantly down-regulated  compared to shams in Cluster A, in particular voltage-gated potassium channels and GABA receptors which are both linked to increased peripheral nerve excitability after axotomy. Up-regulated functional gene families in Cluster B were linked to transcription regulation, inflammation, tissue remodelling and regulatory neuropeptide activity. DRG gene expression profiles appear to reflect sustained tissue inflammation and repair (ca. 4 months) and pain signal modulation consistent with adaptive, compensatory responses linked to injury induced increases in peripheral somatosensory neuronal excitability in the tail stump.   Tail amputation causes acute and sustained changes in peripheral somatosensory nerve function involving key mediators of inflammatory and neuropathic pain which have implications for long-term tail stump pain. The findings of this study may have ramifications for the effects of tail amputation in other species.
We used microarray to investigate the effects of tail amputation on gene expression in the dorsal root ganglia of caudal nerves in pigs at 2 treatment ages and 3 time points after tail treatment

overall_design: 8 pigs/treatment/treatment age/time after treatment. 2 x tail treatments (tail amputated, sham amputated); 2 x tail treatment age (3 days, 63 days); 3 x time after tail treatment ( 1, 8  and 16 weeks)

middle: A

first: Jennifer

last: Coe

first: Alison

last: Downing

last: Barnett

first: Ajit

middle: J

last: Nirmal

first: Tom

last: Freeman

first: Pierpaolo

last: Di Giminiani

first: Sandra

last: Edwards


title: Oviposition by Spodoptera exigua on Solanum dulcamara alters the plant's response to herbivory and impairs larval performance [L1]

status: Public on Dec 11 2018

city: Berlin

first: Daniel

last: Geuss

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Biology

country: Germany

institute: Freie Universität Berlin

summary: Plant resistance traits against insect herbivores are extremely plastic. Plants respond not only to the herbivory itself, but also to oviposition by herbivorous insects. How prior oviposition affects plant responses to larval herbivory is largely unknown. Combining bioassays and defense protein activity assays with microarray analyses and metabolite profiling, we investigated the impact of preceding oviposition on the interaction of Solanum dulcamara with the generalist lepidopteran herbivore Spodoptera exigua at the levels of the plant's resistance, transcriptome and metabolome. We found that oviposition increased plant resistance to the subsequently feeding larvae. While constitutive and feeding-induced levels of defensive protease inhibitor activity remained unaffected, pre-exposure to eggs altered S. dulcamara's transcriptional and metabolic response to larval feeding in leaves local and systemic to oviposition. Particularly, genes involved in phenylpropanoid metabolism were stronger expressed in previously oviposited plants, which was reflected by reciprocal changes of primary metabolites upstream and within these pathways. Our data highlight that plants integrate signals from non-threatening life stages of their natural enemies to optimize their response when they become actually attacked. The observed transcriptional and metabolic reshaping of S. dulcamara's response to S. exigua herbivory suggests a role of phenylpropanoids in oviposition-primed plant resistance.

overall_design: Four treatment groups with 3 replicates each were analyzed in S. dulcamara plants grown from seeds from two different locations in Germany (Erkner, Siethen) and from one location in The Netherlands (Friesland). Plants were either untreated controls (control), oviposited by S. exigua (eggs), fed upon by S. exigua (feeding), or oviposited and fed upon by S.exigua (eggs+feeding). This is the analysis of the L1-leaf, that was systemic to the oviposited leaf but locally fed by larvae in case of the feeding and eggs-feeding treatments.

first: Tobias

last: Lortzing

first: Jens

last: Schwachtje

first: Joachim

last: Kopka

first: Anke

last: Steppuhn


title: Oviposition by Spodoptera exigua on Solanum dulcamara alters the plant's response to herbivory and impairs larval performance [L0]

overall_design: Four treatment groups with 3 replicates each were analyzed in S. dulcamara plants grown from seeds from two different locations in Germany (Erkner, Siethen) and from one location in The Netherlands (Friesland). Leaves were either untreated controls (control), oviposited by S. exigua (eggs), fed upon by S. exigua (feeding), or oviposited and fed upon by S.exigua (eggs+feeding)


title: ImmGen ULI: Male-Female Immune Differences

status: Public on Jan 10 2019

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Primary RNA Seq data for 11 diverse immunocyte populations from male and female mice of varying ages stimulated with different dose of IFN and sequenced using ImmGen's standard ultra-low input RNA-seq pipeline

overall_design:
RNASeq data for 11 cell populations from male and female mice generated by ImmGen labs to study sexual differences in the immune system (companion ATACseq datasets are found in GSE100738). These mice comprised of varying ages, including 6-8weeks and 2- 20months old. In addition, mice were stimulated with 1K and 10K Type 1 interferon to understand sex specific responses.

contributor: Immunological Genome Project Consortium


title: Comparative Transcriptomics Unravels Prodigiosin’s Potential Cancer-Specific Activity Between Human Small Airway Epithelial Cells and Lung Adenocarcinoma Cells

status: Public on Dec 09 2018

city: Singapore

first: Bala

last: Davient

address: 60 Nanyang Dr

country: Singapore

institute: Singapore Centre for Environmental Life Sciences Engineering

summary: Objective: Non-small cell lung cancer (NSCLC) is extremely lethal upon metastasis and requires safe and effective systemic therapies to improve a patient’s prognosis. Prodigiosin (PG) appears to selectively and effectively target cancer but not healthy cells. However, PG’s cancer-specific activity has remained elusive until recently. Methods: PG’s cancer-specific performance was compared to Docetaxel (DTX), Paclitaxel (PTX), and Doxorubicin (DOX) against human lung adenocarcinoma (A549) and human small airway epithelial cells (HSAEC). Combination of PG with DTX, PTX, or DOX in a 1:1 ED50 ratio was also evaluated. MTT assay was used to determine the post-treatment cell viability. RNA-sequencing was used for comparative transcriptomics analysis between A549 and HSAEC treated with 1.0μM PG for 24 h. Results: PG reduced A549 cell viability by four-folds greater than HSAEC. In comparison to DTX, PTX and DOX, PG was ∼1.7 times more toxic toward A549, and 2.5 times more protective toward HSAEC. Combination of PG in 1:1 ED50 ratio with DTX, PTX, or DOX failed to exhibit synergistic toxicity toward A549 or protection toward HSAEC. In A549, genes associated in DNA replication were downregulated, while genes directly or indirectly associated in lipid and cholesterol biogenesis were upregulated. In HSAEC, co-upregulation of oncogenic and tumor suppressive genes was observed. Conclusion: An overactive lipid and cholesterol biogenesis could have caused A549’s autophagy while a balancing-act between genes of oncogenic and tumor-suppressive nature could have conferred HSAEC heightened survival. Overall, PG appears to be a smart chemotherapeutic agent that may be both safe and effective for NSCLC patients.

overall_design: HSAEC, A549 and HCT116 cells derived from American Type Culture Collection (ATCC) were subjected to 1.0µM PG treatment for 24 hours in vitro (biological triplicates). Total RNA was extracted and mRNA was purified with the Illumina® TruSeq® Stranded messenger RNA Sample Prep Kit. The library preparation output which was cDNA fragments were paired-end sequenced at read lengths of 100 nucleotides via the Illumina® HiSeq 2500 (Illumina) platform.

first: Jessica

last: Ng

first: Qiang

last: Xiao

last: Li


title: microRNA responses of LPS and IL-10 stimulated primary human monocyte-derived macrophages over a short time-course

city: GULDFORD

first: RACHEL

last: SIMMONDS

state: Surrey

address: FHMS UNIVERSITY OF SURREY, STAG HILL CAMPUS

institute: University of Surrey

summary: Lipopolysaccharide stimulated primary human monocyte-derived macrophages at 2, 4 and 8hrs, IL-10 at 4hrs, IL-10+LPS at 4hrs

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Dual label approach with each test sample was labelled with Hy3, and a “common reference” sample (obtained by combining equal quantities of RNA from each of the six experimental data points) was labelled with Hy5. Pooled donor approach: each test sample was pooled from 4 independent experiments with different human donors

first: Rachel

last: Simmonds

first: Marc

last: Feldmann


title: Gene expression comparison of exhausted CD8 T cells after PD-L1 blockade alone or PD-L1 blockade combined with LPS

status: Public on Dec 01 2018

city: Chicago

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

summary: CD8 T cells after combined treatment exhibit a distinct molecular signature

overall_design: We FACS-sorted exhausted CD8 T cells from chronically infected mice (lifelong model of LCMV Cl-13 infection) given PD-L1 antibody alone or PD-L1 antibody with LPS

last: Penaloza-MacMaster


title: VEGAS: A Platform for Continuous Directed Evolution in Mammalian Cells (RNAseq)

status: Public on Dec 04 2018

city: Chapel Hill

first: Justin

middle: Gregory

last: English

address: 120 Mason Farm Rd., 2113 Genetic Medicine Bldg

department: Pharmacology

institute: UNC Chapel Hill

summary: Sindbis virus is a mutagenic ssRNA arbor virus. The structural genome component of this virus can be exchanged for any transgene of < 6kb in size. Here we sequence transgenic elements inserted to the virus. Our EGFP transgene was analyzed as a function of time during viral replication to quantify the mutagenic rate of the virus. Our nanobody transgene was analyzed to assess cDNA library complexity and identity.

overall_design: In this study we packaged transgenic virus carrying either EGFP or a library of nanobody cDNA sequences obtained from a 5HT2A receptor immunized llama. The EGFP packaged virus was applied to BHK21 (hamster) cells harboring the plasmid pCMV-SSG, a mammalian expression plasmid to drive constitutive production of the sindbis virus structural genome (SSG). This allows the virus to freely proliferate in the transfected culture. We collected virus from cell culture at 3, 6, 24, and 36 hours after infection and amplified the EGFP transgene. The amplicons were sequenced and sequence integrity of individual nucleotide positions was determined. The nanobody-containing Sindbis genome was directly amplified without culturing and sequenced. The resulting sequences were aligned to the FASTA files provided in this submission to determine if the FASTA deposited nanobody sequences were present in the originating viral titer.


title: The hepatic integrated stress response to asparaginase corresponds with transcriptional signatures that differ with age.

status: Public on Dec 25 2018

city: New Brunswick

first: Tracy

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers, The State University of New Jersey

summary: Clinical reports describing increased liver toxicity in adult versus pediatric patients treated with the anti-leukemic drug asparaginase suggest that hepatic stress responses differ with age. We utilized RNA sequencing to comparatively examine the liver transcriptomes of juvenile (2 wk old) and adult (8 and 16 wk old) mice following chronic exposure to asparaginase.  Liver RNA from 2 and 16 week old mice were sent Sulzberger Columbia Genome Center for cDNA library preparation and sequencing at the same time as liver RNA from 8 week old mice (GSE92364). Asparaginase exposure altered the liver transcriptomes only modestly whereas age had a massive global influence. Unbiased exploration into the effect of age on drug responses revealed that the integrated stress response (ISR) represented a common, core molecular signature regardless of age. ISR engagement in juveniles corresponded with transcriptional signatures of downregulated lipid biosynthesis and increased sequestration of iron. In contrast, adults showed ISR activation alongside upregulation of Saa1 and Saa2 inflammatory markers, serine/glycine metabolism, and folate cycle suggesting mitochondrial stress. We also observed sporadic enrichment in RNA gene signatures reflecting altered nucleotide metabolism of adults in response to the drug. Taken together, our data show that maturity to adulthood does not alter the ISR gene signature to asparaginase. Instead, age-related changes in cellular resource capacity and turnover may be the determining factor in guiding hepatic stress responses to asparaginase.

overall_design: RNA-seq analysis of livers of 2, 8, and 16 wk old mice that were exposed chronically to asparaginase (3 international units per gram body weight daily over 7 days for 2- and 16- wk old mice and over 8 days for 8 wk old mice) or equivolume excipient (phosphate buffered saline).  All mice were on the C57BL/6J genetic background for at least 8 generations. Three mice were used for each genotype and treatment (Total = 18 samples).

first: William

last: Belden

first: Inna

last: Nikonorova


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and dek33 mutant Transcriptomes

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

summary: Analysis of  gene expression level. The hypothesis tested in the present study was that dek33 mutant affects oil body accumulation and ABA synthesis . Results provide important information of the gene expression level regulation of  lipid storage body and ABA synthesis pathway associated genes.

overall_design: Endosperm mRNA profiles of 15 DAP wild type and dek33 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Weiwei

last: Qi


title: Mouse Genome-Wide Association and Systems Genetics Identifies Lipoma HMGIC Fusion Partner (Lhfp) as a Regulator of Bone Mass

status: Public on Oct 30 2018

city: Charlottesville

first: Charles

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Bone mineral density (BMD) is a strong predictor of osteoporotic fracture. It is also one of the most heritable disease-associated quantitative traits. As a result, there has been considerable effort focused on dissecting its genetic basis. Here, we performed a genome-wide association study (GWAS) in a panel of inbred strains to identify associations influencing BMD. This analysis identified a significant (P=3.1 x 10-12) BMD locus on Chromosome 3@52.5 Mbp that replicated in two seperate inbred strain panels and overlapped a BMD quantitative trait locus (QTL) previously identified in a F2 intercross. The association mapped to a 300 Kbp region containing four genes; Gm2447, Gm20750, Cog6, and Lhfp.  Further analysis found that Lipoma HMGIC Fusion Partner (Lhfp) was highly expressed in bone and osteoblasts and its expression was regulated by local expression QTL (eQTL) in multiple tissues. A co-expression network analysis revealed that Lhfp was strongly connected to genes involved in osteoblast differentiation. To directly evaluate its role in bone, Lhfp deficient mice (Lhfp-/-) were created using CRISPR/Cas9. Consistent with genetic and network predictions, bone marrow stromal cells (BMSCs) from Lhfp-/- displayed increased osteogenic differentiation. Lfhp-/- mice also had elevated BMD due to increased cortical bone mass. In conclusion, we used GWAS and systems genetics in mice to identify Lhfp as a regulator of osteoblast activity and bone mass.

overall_design: Bones and osteoblast-derived from bone marrow stromal cells were profiles using RNA-seq from CC0016/GeniUnc mice (N=3 biological replicates per sample type)


title: Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Transcriptome

first: Virginia

last: Ruiz-Ferrer

address: Ramiro de Maeztu, 9

department: Environmental Biology

institute: CSIC

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Transcriptome [RNA-Seq]

summary:
Purpose: The goal of this study is to compare the transcriptome profilling (RNA-seq) of inflorescences infected with tobacco ratle virus (TRV) to mock inoculated inflorescences (negative controls), in Arabidopsis plants
Methods: Inflorescences of systemically TRV infected or mock-inoculated plants were collected from more than 40 independent Arabidopsis plants, at 14 days post-inoculation (dpi). TRV and mock mRNA profiles were generated by deep sequencing by Illumina HiSeq 2000. The sequence reads that passed quality filters (SOAPnuke) were analysed by Burrows-Wheeler (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Genes and isoforms were quantified by RSEM sofware package. qRT-PCR validation was performed using TaqMan and SYBR Green assays.
Results: Here we report   a significant repression of DNA methylation genes in inflorescences of Arabidopsis plants infected with Tobacco rattle virus (TRV) that coincides with dynamic changes in methylation at the whole genome level. Arabidopsis mutants deficient in DNA methylation were more resistant to this virus in early colonized tissues but more susceptible at later time points of infection, indicating that DNA methylation was critical to control both proliferation and antiviral defense. We found that TRV interference with DNA methylation leads to changes in the methylation and trancriptional status of transposable elements (TEs), including TEs located in the promoter of disease resistance genes that were significantly repressed in plants exposed to TRV. Activation of both TEs and their nearby disease resistance genes was altered in a range of hypo- and hyper-methylated Arabidopsis mutants, indicating that perturbations in DNA methylation contributes to modulate their expression in infected plants.
Conclussion: Our study showed that TRV interferes with DNA methylation to alter the transcriptional silencing of TEs, which in turn compromises the expression of neighboring disease resistance genes.

overall_design: TRV and mock mRNA profiles were generated from Arabidopsis inflorescences by deep sequencing with Illumina HiSeq 2000.

first: Cesar

last: Llave


title: Gene expression profiling U87 cells knocking down Glud1 under low glucose treatment

status: Public on Oct 23 2018

city: Guangzhou

first: Xiongjun

last: Wang

address: 230 Wai Huan Xi Road

institute: Guangzhou University

summary: U87 cells (shGlud1 and shNT) were treated with low glucose for 6 hours, then mRNA were extracted for high-throughput sequencing

overall_design: shGlud1 v.s. shNT, in duplicate

last: Yang


title: Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Methylome. [MethylC-seq]

summary:
Purpose: The goal of this study is to compare the whole genome bisulfite sequencing of inflorescences infected with tobacco ratle virus (TRV) to mock inoculated inflorescences (negative controls), in Arabidopsis plants
Methods: Inflorescences of systemically TRV infected or mock-inoculated plants were collected from more than 40 independent Arabidopsis plants, at 14 days post-inoculation (dpi). TRV and mock mRNA profiles were generated by deep sequencing by Illumina HiSeq 2000. The sequence reads that passed quality filters (SOAPnuke) were analysed by Burrows-Wheeler (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Genes and isoforms were quantified by RSEM sofware package. qRT-PCR validation was performed using TaqMan and SYBR Green assays.
Results: We show a significant repression of DNA methylation genes in Arabidopsis infected with Tobacco rattle virus (TRV) that coincides with changes in methylation at the whole genome level. Loss of de novo methylation and/or maintenance of CHH methylation caused a phenotype of high resistance in early colonyzed tissues, whereas defects in  CHG methylation correlated with hypersusceptibility to TRV as the infection progresses. Reactivation of several transposable elements (TEs) during TRV infection inversely correlated with the expression of nearby disease resistance genes. Transcript accumulation of both TEs and TRV-responsive disease resistance genes was altered in hypo- and hyper-methylated mutants.
Conclussion: Our study showed that TRV interferes with DNA methylation to alter the transcriptional silencing of TEs, which in turn compromises the expression of neighboring disease resistance genes.

overall_design:
TRV and mock mRNA profiles were generated from Arabidopsis inflorescences by deep sequencing with Illumina HiSeq 2000.
MethylC-seq samples were collected from inflorescences of systemically tobacco ratle virus (TRV) infected plants or mock-inoculated plants (negative controls) at 14 days post-inoculation (dpi). Inflorescences from more than 40 independent Arabidopsis plants were pooled per sample.


title: The signaling pathways and target genes regulated by miR-330-3p in non-small cell lung cancer (NSCLC)

status: Public on Oct 17 2018

city: Wuhan

first: Chunhua

last: Wei

address: 1277 JieFang Avenue

institute: Huazhong University of Science and Technology

summary: The underlying mechanisms of miR-330-3p in the progresion of NSCLC have not been well investigated. Thus we design this expirment tying to find out the pathways and target genes involved in NSCLC metastasis.

overall_design: Total RNA was extracted from A549 cells transfected with lentivirus knocking down miR-330-3p and vector, respectively. Isolations and microarray analyses were performed using the Human OneArray.


status: Public on Oct 16 2018

city: Amsterdam

first: Cun

address: Plesmanlaan 121,

department: Division of Molecular Carcinogenesis

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Hep3B and Huh7 cells pre-treated with XL413 for 10 days to induce senescence prior to sertraline treatment for 24 hours. For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software.

overall_design: RNA seq data of Hep3B-control, Hep3B-sertraline, Hep3B-XL413, Hep3B-XL413-sertraline, Huh7-control, Huh7-sertraline, Huh7-XL413, Huh7-XL413-sertraline cells, to check gene expression signatures

first: Cor

last: Lieftink


title: CDC7 inhibition induces a senescence-like state in Hep3B and Huh7 cells

summary: Purpose: to check senescence gene expression signature in XL413 treated liver cancer cells. Methods: Hep3B and Huh7 cells are treated with XL413 for 4 days. For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software. The FRIDMAN_SENESCENCE_UP gene set was used to assess the enrichment of senescence-associated genes in the XL413-treated versus control cells.

overall_design: RNA seq data of Hep3B-control, Hep3B-XL413, Huh7-control, and Huh7-XL413 cells, to check senescence gene expression signature


title: Comparison of Pseudomonas responsive gene expression after histone methyltransferase RNAi in C. elegans

status: Public on Oct 20 2018

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: UMASS Medical School

summary:
We resport the changes in gene expression occuring after Pseudomonas exposure in C. elegans with low s-adenosylmethionine, or RNAi of two H3K4 methyltransferases
Using a C. elegans model of low SAM, we previously found that transcriptional responses response to a bacterial pathogen failed and these bacterial-response genes did not show normal H3K4me3 close to the transcriptional start sites, (Ding et al. 2015 Cell Metabolism).  We also found the HMT set-16/MLL was required for full induction, whereas set-2/SET1 appeared dispensable (Ding et al. 2015 Cell Metabolism).  We hypothesized that animals with low SAM might fail to transcriptionally respond to stress and that the HMTs may also have distinct roles in modulating stress responses.  In our present study, we set out to compare induction of transcriptional responses and survival upon stress exposure between C. elegans with reduced SAM (sams-1(RNAi)) and animals with limited H3K4me3 function, set-2/SET1, and set-16/MLL RNAi.  Because distinct stresses may rely on different transcriptional activation mechanisms, we also compared whole-genome expression patterns in three stresses: pathogenic bacteria (PA14), xenotoxic (R24) and heat in response to each RNAi.

overall_design:
C. elegans were grown on RNAi plates, then exposed to Pseudomonas for 6 hours

Please note that the raw data files for the following two samples have been updated with the correct files on 10/25/2019
GSM3438436 Control OP50 rep 2
GSM3438443 Control PA14 rep 1


title: Highly structured homolog pairing reflects functional organization of the Drosophila genome

city: Cambridge

first: Anton

last: Goloborodko

state: Massachusetts

address: 77 Massachusetts Ave., E25-524

department: Physics

institute: MIT

summary: Trans-homolog interactions encompass potent regulatory functions, which have been studied extensively in Drosophila, where homologs are paired in somatic cells and pairing-dependent gene regulation, or transvection, is well-documented. Nevertheless, the structure of pairing and whether its functional impact is genome-wide have eluded analysis. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, discovering that homologs pair relatively precisely genome-wide in addition to establishing trans-homolog domains and compartments. We also elucidated the structure of pairing with unprecedented detail, documenting significant variation across the genome. In particular, we characterized two forms: tight pairing, consisting of contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional role genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing.

overall_design: This submission contains four Hi-C experiments on a Drosophila cell line: 2 biological replicates of Hi-C on a wild type sample, 2 biological replicates of Hi-C on a mock RNAi sample, 2 biological replicates of Hi-C on a Slmb RNAi sample, 2 biological replicates of Hi-C on a Top2 RNAi sample. The submission also contain 4 biological replica of a RNA-Seq experiment on a Wild Type sample.

first: Jumana

last: AlHaj Abed

first: Jelena

last: Jerceg

first: Son

last: Nguyen

first: Ruth

last: McCole

first: Wren

last: Saylor

first: Geoffrey

last: Fudenberg

first: Bryan

last: Lajoie

first: Job

last: Dekker

first: Leonid

last: Mirny

first: Chao-ting

last: Wu


title: Interleukin 2 distinctly activates human basophils in skin disorders

status: Public on Oct 01 2018

city: Xuzhou

first: Hui

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

summary: Basophils are important effector cells in allergic inflammation, anti-parasitic immune response and skin disorders. A number of activators including interleukin 3 (IL-3) and IgE have been identified in the regulation of human basophils expressing mediators such as histamine and leukotriene C4 (LTC4) and cytokines, including IL-4 and IL-13. Human basophils express high levels of IL-2 receptors. However, the function of the IL-2 pathway in basophils remains unknown. Here, we identify that IL-2-stimulated human basophils in vitro express a variety of inflammatory cytokines and chemokines including IL-5, IL-13, GM-CSF and CCL-17. Of note, one of the top regulated cytokines, IL-5, was for the first time identified to be expressed in human basophils and was distinctly regulated by IL-2, independently of IL-3 and IgE. Immunofluorescence analysis of skin specimens from bullous pemphigoid and eczema revealed that infiltrating basophils in skin lesions widely express IL-5 and GM-CSF. Together, our findings reveal IL-2 as a novel regulator of human basophils to express IL-5 and GM-CSF in skin disorders. This adds a new layer to support the importance of basophils in skin disorders.

overall_design: Human basophils were pre-enriched from PBMCs from buffy coat by Magnetic-activated cell sorting (MACS) positive sorting using rat anti-human CRTH2 microbeads. Next, basophils were further purified by FACS sorting of FSClowSSClowCD4-CRTH2high populations.Purified basophils at a density of 2×105 cells/well in a 96-well plate were cultured either with or without human IL-2 (10 ng/mL) (n = 3) (10 ng/mL) for 24 hours. Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8×60K V2 microarray according to the manufacture’s instruction.

first: Shuli

last: Zhao


title: The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos

summary: Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focused on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first addressed the long-standing question of whether pairing extends genome-wide and, to this end, developed a haplotype-resolved Hi-C approach that uses a new strategy to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This approach revealed striking genome-wide pairing in Drosophila embryos. Moreover, we discovered pairing to be surprisingly structured, with trans-homolog domains and interaction peaks, many coinciding with the positions of analogous cis features. We also found a significant correlation between pairing and the chromatin accessibility mediated by the pioneer factor Zelda.  Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered more than a century ago.

overall_design: This submission contains data from a Hi-C experiment on Early Drosophila embryos (2 biological replicates).

first: Nezar

last: Abdennur

first: Maxim

last: Imakaev

first: Eric

last: Joyce

first: Niroshini

last: Senaratne

first: Mohammed

last: Hannan

first: Guy

last: Nir


title: miR-205-5p Inhibits Human Endometriosis Progression by Targeting ANGTP2 in Endometrial Stromal Cells

status: Public on Dec 19 2018

first: min juan

last: liu

address: gong ye da dao No.253

institute: ZhuJiang Hospital of Southern Medical University

summary: the newly identified miR-205-5p-ANGPT2-AKT/ERK axis illustrates the molecular mechanism of endometriosis progression and may represent a novel diagnostic biomarker and therapeutic target for disease treatment.

overall_design: Agilent miRNAs microarray 21.0 for normal endometrium (n=3) and ectopic endometrium (n=3) was established and analyzed by GeneSpringGX software 11.0 (Agilent)

first: Chen-Fei

last: Zhou

first: Min-Juan

last: Liu

first: Wei

last: Wang

first: Sha

first: Yu-Xin

last: Huang

first: Guo-Bin

last: Chen

first: Li-Min

first: Dong-Xian

last: Peng

first: Xue-Feng

first: Xu-Zi

last: Cai

first: Xiao-Xuan

last: Li

first: Wan-Qin

last: Feng

first: Ying

last: Ma


title: ChIP-seq analysis of CFP1 and related molecules

status: Public on Oct 15 2018

city: London

first: Kamil

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

summary: We report a ChIP-seq analysis of the CpG binding protein CFP1 and related proteins to study regulation of chromatin in transcribed genes in erythroblasts and EBV-transformed B-lymphoblasts. We generated multiple ChIP datasets and compared these to publicly available ChIP datasets.

overall_design: Comparison of ChIP-seq results in two haematopoietic cell types.

first: Louie

last: van de Lagemaat

first: Douglas

last: Vernimmen


title: Oviposition by Spodoptera exigua on Solanum dulcamara alters the plant's response to herbivory and impairs larval performance

first: Daniel

last: Geuss

address: Albrecht-Thaer-Weg 6

institute: Freie Universität Berlin


title: Genome-wide copy number analysis by Array CGH for the analysis of clonality of thoracic tumors

status: Public on Sep 20 2018

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

type: Genome variation profiling by genome tiling array

summary: Multiple synchronous and metachronous lung tumors are frequently encountered in patients with lung cancer. For treatment purposes it is important to determine, whether or not tumors are clonally related. In other words, whether multiple tumors in a patient are either metastases or multiple primaries. Previous reports show considerable discordance between histopathological and molecular comparison of tumor pairs. The purpose of this study is to compare genome-wide copy number analysis to the classical histological and clinicopathological routine for clonality analysis in a prospective cohort of patients with synchronous or metachronous tumors, of which at least one site occurred in the thorax.

overall_design: Two-colour experiment experiment,tumor vs reference. Multiple cases with 2 or more tumors per case.

first: Julien

middle: P

last: Vincenten

first: Hendrik

middle: F

last: van Essen

first: N

last: Bulkmans

first: Oscar

last: Krijgsman

first: Katrien

last: Grünberg

first: Birgit

middle: I

last: Witte

first: Egbert

last: Smit

first: Bauke

last: Ylstra

first: Erik

last: Thunnissen


title: ChIP-seq from lung (ENCSR240ZWZ)

status: Public on Sep 21 2018

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Effect of adenosine on the gene expression profile of cumulus cells in vitro cultured as cumulus-oocyte complexes for 6 h

status: Public on Sep 12 2018

city: Quebec

first: Francois

last: Richard

state: Quebec

address: 2425 rue de l'agriculture

department: Sciences animales

institute: Université Laval

summary: Changes in gene expression induced by adenosine treatment in cumulus cells using Agilent EmbryoGENE microarray slides. Bovine cumulus-oocyte complexes in vitro-cultured for 6 h using adenosine and compared to non-treated (control). After culture, COC were were washed and cumulus cells were used for microarray analysis

overall_design: Four pools of cumulus cells treated by adenosine were hybridized against four pools of control cumulus cells in a dye-swap design.

first: Julieta

last: Caballero

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Marc-André

last: Sirard

first: François


title: Integrated network analysis reveals genotype-phenotype correlations in Williams syndrome

status: Public on Nov 06 2018

city: Kyoto

first: Ryo

last: Kimura

address: Yoshida-Konoe-cho

department: Anatomy and Developmental Biology

institute: Kyoto University Graduate School of Medicine

summary: Williams Syndrome (WS) is a rare neurodevelopmental disorder caused by heterozygous deletions in a chromosome 7q11.23 region typically encompassing 26-28 genes. WS patients exhibit a wide spectrum of symptoms, including cardiovascular disease, intellectual disability, visuospatial deficits and hypersociability a behavioral profile that contrasts with autism spectrum disorder (ASD). However, the relationship between neuropsychiatric phenotypes and dysregulated gene networks caused by the 7q11.23 deletion is unknown. We report results from a large-scale integrated transcriptome analysis of peripheral blood in clinically evaluated subjects with WS, ASD and matched controls. We identified significantly differential expressed genes in WS as compared with ASD or controls, even after removing genes spanning the 7q11.23 region. Using weighted gene co-expression network analysis (WGCNA), we found that three co-expression modules were upregulated in WS, and were significantly associated with the intermediate phenotypes such as anxiety and attention problems. Notably, these three co-expression modules were only composed of genes located outside of 7q11.23 critical region. One module was associated with immune systems and B cell proliferation. Its top hub gene, BCL11A, is implicated in ASD and chromatin modification. Another module was enriched with genes associated with astrocytes and oligodendrocytes, and the third module was associated with RNA processing and neurons. MicroRNA (miRNA) profiling revealed differentially expressed miRNAs whose targets were enriched in each co-expression module associated with WS. These results identify genes and potential driver miRNAs, located outside of 7q11.23 critical region, that are novel candidates for mediating the neuropsychiatric phenotypes in WS.

overall_design: We profiled gene expression from 32 WS patients, 32 ASD patients and 30 controls using peripheral blood.

first: Masatoshi

last: Hagiwara


title: Effect of FSH on the gene expression profile of cumulus cells in vitro cultured as cumulus-oocyte complexes in presence of adenosine for 6 h

summary: Changes in gene expression induced by FSH in cumulus cells treated with adenosine using Agilent EmbryoGENE microarray slides. Bovine cumulus-oocyte complexes in vitro-cultured for 6 h using adenosine. The effect of FSH was compared with control as non-treated cumulus-oocyte complexes. After culture, COC were were washed and cumulus cells were used for microarray analysis

overall_design: Four pools of cumulus cells treated by FSH were hybridized against four pools of control cumulus cells in a dye-swap design.


title: The pancreatic cancer stem cell marker CD44v6 affects transcription, translation and signaling: consequences on exosome composition and delivery II

status: Public on Aug 25 2018

city: Heidelberg

first: Jan

last: Provaznik

state: Baden-Wuerttemberg

address: Meyerhofstr. 1

department: Genomics Core Facility

institute: EMBL Heidelberg

summary:
The miRNA profile between different pancreatic adenocarcinoma cells (A818.4, Capan-1) and different colorectal carcinoma cells (SW948, HT-29).

The impact of a knockdown (kd) of function-relevant cancer stem cell markers (CD44v6, Tspan8, CD151, claudin7) on the miRNA profile. The kd cell miRNA profiles were compared with the wt cell as well as between the different kd miRNA profiles.

overall_design: This series includes whole cell miRNA profiles of A818.4, Capan-1, SW-948 cells that are wildtype or CD44v6 or Cld7 KD and exosome miRNA profiles of wildtype A818.4 and Capan-1 cells.

first: Hanxue

last: Sun

first: Sanyukta

last: Rana

first: Zhe

last: Wang

first: Kun

last: Zhao

first: Martina

last: Schnölzer

first: Thilo

last: Hackert

first: Qingjie

last: Lv

first: Margot

last: Zöller


title: The pancreatic cancer stem cell marker CD44v6 affects transcription, translation and signaling: consequences on exosome composition and delivery I

summary:
The miRNA profile between different pancreatic adenocarcinoma cells (A818.4, Capan-1) and different colorectal carcinoma cells (SW948, HT-29).

The impact of a knockdown (kd) of function-relevant cancer stem cell markers (CD44v6, Tspan8, CD151, claudin7) on the miRNA profile. The kd cell miRNA profiles were compared with the wt cell as well as between the different kd miRNA profiles.

These analyses were important to define joint miRNA that could be of functional relevance and be of potential interest as therapeutic targets.

overall_design: miRNA analysis of pancreatic cancer cell lines A818.4 and Capan-1 subjected to Tspan8, CD151 and CD44v6 knockdown compared to wildtype controls. Cld7 knockdown was assesed in HT-29 cells. All samples are whole cell miRNA preparations.


title: Identification of microRNAs and their target genes in Moringa oleifera leaf and callus

status: Public on Aug 31 2018

first: Stefano

last: Pirro

address: Chartehouse Square

department: Molecular Oncology

institute: Barts Cancer Institute, Queen Mary University of London

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aims to identify the differential expression of conserved and novel miRNAs and their target genes in M. oleifera leaf, callus and cold stress treated callus by high-throughput small RNA sequencing.

overall_design: miRNAs from normal and stressed callus from Moringa oleifera, as well as leaves, were sequenced by using an Illumina NextSeq 500 System

first: Ivana

last: Matic

first: Arianna

last: Guidi

first: Letizia

last: Zanella

first: Angelo

last: Gismondi

first: Rosella

last: Cicconi

first: Roberta

last: Bernardini

first: Vittorio

last: Colizzi

first: Antonella

last: Canini

first: Maurizio

last: Mattei

first: Andrea

last: Galgani


title: Mycobacterium tuberculosis Sensor Kinase DosS Modulates the Autophagosome in a DosR-independent Manner [I]

status: Public on Aug 22 2018

city: Covington

first: Uma

middle: S

last: Gautam

state: LA

address: 18703 Three Rivers Road

department: Bacteriology and Parasitology

institute: TNPRC

summary: Transcriptional profiling of RNA samples from un-infected Rhesus Bone Marrow Derived Macrophages (RhBMDMs) exposed to IMDM complete media used as control were compared to RNA from RhBMDMs infected for 24 hr with 'dos' mutants of Mtb viz. MtbΔdosR, MtbΔdosS, or MtbΔdosT

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Microarray Experiment, Mtb dos mutants infected RhBMDMs vs. uninfected RhBMDMs for 24 hr. 2 replicates

first: Deepak

last: Kaushal


title: Mycobacterium tuberculosis Sensor Kinase DosS Modulates the Autophagosome in a DosR-independent Manner [II]

summary: Transcriptional profiling of bacterial RNA samples from infected Rhesus Bone Marrow Derived Macrophages (RhBMDMs) compared to RNA isolated from respective in vitro grwon cultures viz M. tuberculosis H37Rv or  Isogeneic mutant MtbdosS

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: In this experiment we have compared Mtb transcriptomics in vivo, using samples derived from infected macrophages, compared to Mtb cultured in-vitro. 0 hr time point. 3 replicates


title: Mycobacterium tuberculosis Sensor Kinase DosS Modulates the Autophagosome in a DosR-independent Manner

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

sample_organism:
Mycobacterium tuberculosis
Macaca mulatta

platform_organism:
Macaca mulatta
Homo sapiens
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: Refer to individual Series


title: Endogenous RAC1 P29S in mouse melanocytes

status: Public on Aug 10 2018

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

institute: The Francis Crick Institute

summary: We studied the effects of long-term endogenous expression of the melanoma oncogene RAC1 P29S using melanocyte cultures isolated from transgenic mice

overall_design: Transgenic mice with a conditional knock-in of the P29S mutation in the endogenous Rac1 locus were generated and crossed onto C57BL/6J, Tyr-CreER;Trp53fl/fl mice. Melanocytes were isolated from the dorsal skin of neonatal mice and cultured using the protocol developed by others (Godwin et al. Current Protocols in Cell Biology, 1.8.1-1.8.20, 2014). Melanocytes were recombined by 4OH-tamoxifen treatment. Three independent melanocyte cultures from Tyr-CreER+/-;Trp53fl/fl;Rac1LSL-P29S/wt mice were used and compared to two independent cultures from Tyr-CreER+/-;Trp53fl/fl;Rac1wt/wt mice. The spontaneously immortalised C57BL/6J melanocyte cell line melan-a was used as the third independent replicate for the Rac1 wt/wt group.

first: Daniel

last: Lionarons

first: Julian

last: Downward


title: Seed composition traits: comparative genomic hybridization analysis in glycine max fast neutron mutants

status: Public on Aug 16 2018

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

summary: Ten mutants with altered seed composition traits were identified in a soybean fast neutron population (Bolon et al. 2014). These mutant lines were maintained to an advanced generation (ranging between M5 and M9) and compared to their wild-type parent (M92-220-Long) using CGH to identify the causative region/gene associated with the seed composition changes.

overall_design: Ten samples were analyzed, each identified as a soybean fast neutron lines with altered seed composition traits. Each sample was compared to its wild type parent (M92-220-Long) using Agilent CGH arrays.

first: Adrian

last: Stec


title: RNA sequencing of Dorsal Root Ganglia upon axonal injury, in presence or absence of NAC (N-acetyl cysteine), and upon H2O2 nerve treatment

status: Public on Jul 06 2018

city: Columbus

first: Ilaria

last: Palmisano

state: Ohio

address: 460 West 12th Avenue

institute: Ohio State University

summary:
Purpose: A) compare the response to an axonal injury in the peripheral vs central nervous system B) clarify the mechanism of Reactive Oxygen Species-dependent axonal regeneration

Results: we found that after peripheral axonal injury there is a higher number of differentially expressed genes with respect to central injury. Moreover,inflammation related genes and regeneration-associated genes were differentially regulated after peripheral injury and H2O2, but less after central injury. Signalling pathways and biological processes related to injury-dependent nerve regeneration were reduced with the addition of NAC at the time of sciatic injury compared to vehicle.

overall_design: Method: RNA-seq from sciatic L4-L6 DRG tissue 24 hours after the following treatments: a) spinal cord dorsal column injury b) laminectomy c) sciatic nerve injury  in presence of saline d) sham in presence of saline, e) sciatic nerve injury in presence of 30 mM NAC (N-acetyl-cysteine), f) sham in presence of 13 mM H2O2. Pool of sciatic DRGs from 2 mice were used for each sample. DRG were collected in RNase later reagent, and crushed with RNase free micropestle for RNA extraction.

first: Arnau

last: Hervera

first: Matt

middle: C

last: Danzi

first: Simone

last: Di Giovanni


title: lncRNA/mRNA expression profiling of miR-200c-overexpressing MDA-MB-231 cells

status: Public on Aug 28 2018

first: baiyao

last: wang

state: Guangdong province

address: 1838 guangzhou dadaobei road

department: Department of Radiation Oncology

institute: Nanfang Hospital, Southern Medical University, Guangzhou, China

summary: MiR-200c is a well-studied miRNA that is involved in stemness, the epithelial-mesenchymal transition, chemoresistance, radioresistance, and invasion/metastasis of various cancer cells. To obtain an overview of the lncRNA/mRNA regulated by miR-200c signaling in breast-cancer cell lines, we performed global lncRNA/mRNA-expression profiling on MDA-MB-231-pGIPZ and MDA-MB-231-miR-200c cells.

overall_design: Three independent cell-culture replicates from the total population of MDA-MB-231-pGIPZ and MDA-MB-231-miR-200c stable transfectants were used to generate total RNA. Total RNA was extracted using Trizol.

first: Baiyao

last: Wang

first: Yawei

last: Uuan