title: ripseq experiment for rfl8 targets - Functional characterization of the pentatricopeptide repeat protein PPR RFL8

first: Véronique

last: BRUNAUD

summary: blanc09_ripseq_rfl8-ripseq experiment for rfl8 targets-Which mitochondrial transcripts are bound by RFL8 protein? -The RIPseq approach to find the mitochondrial transcripts attached by RFL8 protein via co-immunoprecipitation of 3HA tag fused in C-terminal of RFL8 protein

overall_design: 6 samples with 3 biological replicats. normal vs transgenic comparaison

first: Veronique

last: Brunaud

first: Hakim

last: Mireau

first: Sandrine

last: Blazergue


title: In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response (Bronchoalveolar lavage)

status: Public on Feb 09 2021

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

type: Expression profiling by high throughput sequencing

summary: Single cell transcriptome, TCR and BCR sequencing of FACS-sorted CD45+ cells of the bronchoalveolar lavages of COVID-19 ICU patients

overall_design: Sequencing of RNA, TCR and BCR was performed from FACS-sorted CD45-positive cells from the bronchoalveolar lavage of 2 COVID-19 ICU patients (one at 2 different time points), using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit

first: Caroline

last: Tizian

first: Andrey

last: Kruglov

first: Marta

last: Ferreira-Gomes

first: Gitta

middle: A

last: Heinz

first: Katrin

last: Lehmann

first: Gabriela

last: Guerra

first: Frederik

last: Heinrich

first: Mir-Farzin

last: Mashreghi


title: In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response (Activated B cells, set 1)

summary: Single cell transcriptome and BCR sequencing of FACS-sorted activated B cells of the peripheral blood of COVID-19 ICU patients and healthy controls

overall_design: Sequencing of RNA and BCR was performed from FACS-sorted activated B cells (CD38high CD27high) from the peripheral blood of 9 COVID-19 ICU patients (one at 2 different time points) and 3 healthy controls, using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit


title: In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response (Activated B cells, Set 2)

overall_design: Sequencing of RNA and BCR was performed from FACS-sorted activated B cells (CD38high CD27high) from the peripheral blood of 4 COVID-19 ICU patients, using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit


title: Epigenome Dysregulation Resulting from NSD1 mutation in Head and Neck Squamous Cell Carcinoma

status: Public on Feb 08 2021

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Epigenetic dysregulation has emerged as an important mechanism of oncogenesis. To develop targeted treatments, it is important to understand the epigenetic and transcriptomic consequences of mutations in epigenetic modifier genes. Recently, mutations in the histone methyltransferase gene NSD1 have been identified in a subset of head and neck squamous cell carcinomas (HNSCCs) – one of the most common and deadly cancers. Here, we use whole (epi)genome approaches and genome editing to dissect the downstream effects of loss of NSD1 in HNSCC. We demonstrate that NSD1 mutations are directly responsible for the loss of intergenic H3K36me2 domains, followed by the loss of DNA methylation, and gain of H3K27me3 in the affected genomic regions. We further show that those regions are enriched in cis-regulatory elements, and that subsequent loss of H3K27accorrelates with reduced expression of their target genes. Our analysis identifies genes and pathways affected by the loss of NSD1 and paves the way to further understanding the interplay among chromatin modifications in cancer.

overall_design: WGBS, RNA-seq, and ChIP-seq for histone H3 post-translational modifications in human head and neck squamous cell carcinoma cell lines

first: Nargess

last: Farhangdoost

first: Cynthia

last: Horth

first: Bo

last: Hu

first: Eric

last: Bareke

first: Xiao

last: Chen

first: Yinglu

last: Li

first: Mariel

last: Coradin

first: Benjamin

last: Garcia

first: Chao

last: Lu


title: In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response

first: Pawel

last: Durek

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

overall_design: Refer to individual Series


title: In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response (Measles-reactive T cells)

summary: Single cell transcriptome and TCR sequencing of FACS-sorted Measles-reactive memory T cells of the peripheral blood of a healthy donor

overall_design: Sequencing of RNA and TCR was performed from FACS-sorted Measles-reactive memory T cells (CD4+CD45RO+CD154+) from the peripheral blood of 1 healthy donor, using the 10X Genomics platform with the Single Cell 5’ Library & Gel Bead Kit

first: Weijie

last: Du

first: Jun

last: Dong


title: MreCD are required for correct cell shape, biofilm architecture and interspecies competition in Streptococcus mutans

status: Public on Jan 29 2021

city: Jonesboro

first: Robert

middle: Colquhoun

last: Shields

state: Arkansas

address: Lab Science East

department: Biological Sciences

country: USA

institute: Arkansas State University

summary: RNA-seq was utilized to compare the transcriptomes of wild-type and ΔmreCD S. mutans strains

overall_design: Streptococcus mutans mRNA profiles were generated for a wild-type control strain and a strain lacking the mreCD genes, by deep sequencing, in triplicate

middle: C


title: Cellular and molecular characterization of the dural sinuses as a neuroimmune interface [whole dura]

status: Public on Jan 27 2021

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Meningeal immunity is critical to appropriate CNS function. Here we perform single cell RNA-sequencing to investigate how brain and meningeal stromal populations regulate immune trafficking and retention in young and old mice.

overall_design: 10 young (2 months) and 10 old (24 months) mice were sacrificed with euthasol and dural meninges were collected. Dura were dissociated with collagenase 8 to obtain a single cell suspension and sorted by FACS to obtain all DAPI-Singlets.

first: Justin

last: Rustenhoven

first: Taitea

last: Dykstra


title: Comprehensive Profiling of Cancer Cells and Their Microenvironment in Advanced NSCLC

status: Public on Jan 24 2021

city: Suzhou

first: Yixin

address: No.218,Xinghu Street

country: China

institute: singleron

summary: Using single-cell RNA sequencing (scRNA-seq) profiles gene expression pattern of each individual cell to characterize of the entire tumor ecosystem

overall_design:
42 Samples were collected by diagnostic procedures including transcutaneous needle biopsy, bronchoscopy or superficial lymph node biopsy for scRNA_seq

*** Submitter states that raw data are not available for this Series due to patient privacy concerns and human genetic resources policy in China.

first: Jue

last: Fan


title: Cellular and molecular characterization of the dural sinuses as a neuroimmune interface


title: CD4+ T cells From Children With Active Juvenile Idiopathic Arthritis Show Altered Chromatin Features Associated With Transcriptional Abnormalities (ATAC-seq)

status: Public on Jan 05 2021

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

summary: We used a multi-omics approach in an attempt to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA.  We demonstrate that active JIA is associated with distinct alterations in CD4+ T cell chromatin, as assessed by ATAC-seq studies.  However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved in JIA CD4+ T cells.  However, overlapping CTCF binding, ATACseq, and RNAseq data with known JIA genetic risk loci demonstrated the presence of genetic influences on the observed transcriptional abnormalities and identified candidate target genes.  These studies demonstrate the utility of multi-omics approaches for unraveling some of the most vexing questions regarding the pathobiology of autoimmune diseases.

overall_design: The distinct alterations in CD4+ T cell chromatin was assessed by ATAC-seq studies.

first: Evan

last: Tarbell

first: Kaiyu

last: Jiang

first: James

middle: N

last: Jarvis


title: CD4+ T cells From Children With Active Juvenile Idiopathic Arthritis Show Altered Chromatin Features Associated With Transcriptional Abnormalities


title: CD4+ T cells From Children With Active Juvenile Idiopathic Arthritis Show Altered Chromatin Features Associated With Transcriptional Abnormalities (RNA-seq)

overall_design: The distinct alterations of the gene expression in  CD4+ T cell  was assessed by RNA-seq.


title: Role of SWI/SNF-Related, Matrix Associated, Actin Dependent Regulator of Chromatin A4 (SMARCA4) core complex in epithelial innate response

status: Public on Jan 01 2021

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin


title: Comparison of gene expression in Maize tissues at different dev stages.

status: Public on Dec 14 2020

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

country: France

institute: INRAE

summary: ngs2017_06_amaizing-amaizing_b73_ww-Geneatlas - Co-expression analysis of B73 genes across tissues

overall_design: 33 samples with 3 biological replicates. organ comparison

first: Clémentine

last: Vitte

first: Johann

last: Joets

first: Sylvie

last: Coursol

first: Stéphanie

last: Pateyron

first: Ludivine

last: Soubigou-Taconnat

first: Marie-Laure

middle: L

last: Martin-Magniette

first: Peter

last: Rogowsky

first: Olivier

last: Turc


title: Comparison of MDSC subtypes from spleen and tumor of mice with RM-1 tumors

status: Public on Oct 23 2020

city: Austin

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

summary:
Myeloid derived suppressor cells (MDSC) in the tumor microenvironment suppress T-cell mediated immune surveillance that clears tumor cells.  As such, MDSC promote tumor growth.   There are two subtypes of tumor MDSC, CD11b+Ly6ChiLy6G- monocytic MDSC (M-MDSC) , and CD11b+Ly6ClowLy6Ghigh granulocytic MDSC (G-MDSC).  Cells with these markers also exist in the spleen of tumor bearing mice or in the spleen of mice with tissue-specific inflammation.  Some have argued that the tumor MDSC is an activated version of the spleen MDSC, implying that they are similar to one another.  Here we isolated the MDSC subtypes from the RM-1 tumors and from the spleen of mice with prostatic inflammation (n=4 per subtype per tissue, 16 total samples).  We then analyzed  RNA from these cells to determine how the transcript profile was altered by  tissue location and MDSC subtype.
Platform: Affymetrix Mouse Gene 1.0 ST v1 Genechip

overall_design: To generate tumor MDSC  1 x106 RM-1 tumor cells were injected into the peritoneal cavity of C57Bl/6J mice. 7 d later, tumor-derived MDSC were harvested from ascites by serial lavage with sterile PBS and MDSC subtypes were isolated by fluorescence-activated cell sorting (n=4 pools of cells from 2-3 mice each). To generate activated peripheral MDSC from the spleen, POET-3 mice were injected with 5 x 106 activated OT-I cells to induce prostate inflammation. 6 days later the mice were killed, spleens harvested, and MDSC subsets were isolated by fluorescence-activated cell sorting (n=4 mice).   RNA was isolated and used for transcript profiling using Affymetrix microarrays.

first: Timothy

last: Ratliff


title: Riboseq analysis of the rfl8 mutant-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

status: Public on Apr 27 2021

summary: blanc09_ripseq_rfl8-riboseq analysis of the rfl8 mutant-Which mitochondrial transcripts are bound by RFL8 protein? -Does the RFL8 loss impact on mitochondrial translation?

overall_design: 4 samples with 2 biological replicates. genotype comparison

first: Hakim

last: Mireau


title: botrytisxn - Nitrogen nutrition and pathogen susceptibility: priming by metabolism.

status: Public on Oct 22 2020

summary: aap_bap_nitropath_2014-botrytisxn - impact of nitrogen nutrition on the response of plants to biotic stress-Comparison of Arabidopsis responses to Botrytis infection in relation to nitrogen nutrition (sufficient vs limited).

overall_design: 32 samples with 3 biological replicats. normal vs disease comparison

first: Mathilde

last: Fagard


title: Role of SWI/SNF-Related, Matrix Associated, Actin Dependent Regulator of Chromatin A4 (SMARCA4) core complex in epithelial innate response (RNA-seq)

summary: We examine the epigenetic role of the SWI/SNF Related, Matrix Associated, Actin Dependent Regulator of Chromatin A4 (SMARCA4) in the epithelial response to RSV infection.  Wild type and SMARCA4 silenced cells were subjected to short read illumina RNA Seq in the absence or presence of RSV infection. Cells were infected for 0, 16 h or 24 h prior to RNA seq.

overall_design: wild type small airway epithelial cells were infected 0, 16 or 24 h prior to RNA seq.  SMARCA4 depleted cells were infected for 0, 16 or 24 h prior to RNA seq.

first: Xiaofang

last: Xu


title: Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 associate with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients

status: Public on Sep 30 2020

city: Shanghai

first: Zilu

last: Wen

address: No. 2901, Caolang Road, Jinshan District, Shanghai

institute: SHANGHAI PUBLIC HEALTH CLINICAL CENTER

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Accurate diagnosis of complete inactivation of tuberculosis lesions is still a challenge with respect to sputum-negative tuberculosis. RNA-sequencing was conducted to uncover potential lncRNA indicators of metabolic activity in tuberculosis lesions.
Methods: Lung tissues with high metabolic activity (PET-high) and low metabolic activity (PET-low) demonstrated by fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) were collected from five sputum-negative tuberculosis patients for RNA-sequencing. Differentially expressed mRNAs and lncRNAs were identified, and their correlations were evaluated to constructed lncRNA-mRNA co-expression network. Afterwards, cis- or trans-targets of differentially expressed lncRNAs were predicted, followed by establishing lncRNA-target-pathway network, in which lncRNAs and mRNAs with high degrees were measured by quantitative real-time PCR using samples collected from 11 patients. Prediction efficiencies of lncRNA indicators were assessed by receiver operating characteristic curve analysis, Bioinformatics analysis was performed for potential lncRNAs.
Results: In total, 386 mRNAs and 44 lncRNAs were identified to be differentially expressed. Differentially expressed mRNAs in lncRNA-mRNA co-expression network were significantly associated with the fibrillar collagen, platelet-derived growth factor binding, and leukocyte migration involved in inflammatory response. One cis-target gene and 440 trans-target genes were predicted for differentially expressed lncRNAs. Seven genes (C1QB, CD68, CCL5, CCL19, MMP7, HLA-DMB, and CYBB) and two lncRNAs (ENST00000429730.1 and MSTRG.93125.4) were validated to be significantly up-regulated. The area under the curve of ENST00000429730.1 and MSTRG.93125.4 was 0.750 and 0.813, respectively.
Conclusion: Two lncRNAs ENST00000429730.1 and MSTRG.93125.4 might be considered as potential indicators of metabolic activity in tuberculosis lesions for sputum-negative tuberculosis.

overall_design: Examination of  different Inc-mRNA expressions in 5 lung tissues.

first: Lin

last: Wang

first: Hui

last: Ma

first: Liwei

last: Wu

last: Chen


title: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability

status: Public on Dec 20 2020

city: Manchester

first: Xiangyu

middle: Jack

last: Ge

address: Oxford road

country: United Kingdom

institute: University of Manchester

summary: Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis, and there loci have been shown to be enriched in immune cell-specific enhancers, we add Synovial fibroblasts (FLS), the local stromal cells of joints to this analysis.  We integrated ChIP-seq, Hi-C, Capture Hi-C, ATAC-seq and RNA-seq datasets from FLS , with genetic fine-mapping of RA loci. From this we identified putative casual variants, enhancers and genes for 30-60% of RA loci and demonstrated that FLS regulatory elements accounts for up to 24% of RA heritability.  We also examined the effects of TNF stimulation on the chromatin landscape of FLS, and we found there are significant alterations in the organization of topologically associated domains, chromatin interactions and the expression of several putative causal genes.

overall_design: Examine the enrichment of RA signals in FLS functional elements, assign putative gene targets for these RA signals in FLS, and quantify the effects of TNF stimulation on FLS.

first: Mojca

last: Frank-Bertoncelj

first: Kerstin

last: Klein

first: Amanda

last: Mcgovern

first: Tadeja

last: Kuret

first: Miranda

last: Houtman

first: Blaž

last: Burja

first: Raphael

last: Micheroli

first: Miriam

last: Marks

first: Andrew

last: Filer

first: Christopher

middle: D

last: Buckley

first: Gisela

last: Orozco

first: Oliver

last: Distler

middle: P

last: Morris

first: Paul

last: Martin

first: Stephen

last: Eyre

first: Caroline

last: Ospelt


title: Parallel spatial transcriptomics, single-cell and bulk RNA-Seq analysis of the human embryonic HSC niche, the dorsal aorta

status: Public on Sep 17 2020

city: Edinburgh

first: Edie

last: Crosse

address: 5 Little France Road

department: Centre for Regenerative Medicine

institute: University of Edinburgh

summary: Haematopoietic stem cells (HSCs) first emerge in the embryonic aorta-gonad-mesonephros (AGM) region. Studies on model organisms defined intersecting signalling pathways that converge to promote HSC emergence predominantly in the ventral domain of the dorsal aorta. Much less is known about mechanisms driving HSC development in human. Here, to identify secreted signals underlying human HSC development, we combined spatial transcriptomics analysis of dorso-ventral polarised signalling in the aorta with gene expression profiling of sorted cell populations and single cells. Our analysis revealed a subset of aortic endothelial cells with downregulated arterial signature and a predicted lineage relationship with the emerging HSC/ progenitor population. Analysis of the ventrally polarised molecular landscape identified endothelin 1 as an important secreted regulator of human HSC development. The obtained gene expression datasets will inform future studies on mechanisms of HSC development in vivo and on the generation of clinically relevant HSCs in vitro.

overall_design: Two LCM-Seq transcriptome analyses of spatially defined regions around the dorsal aorta (Carnegie Stages (CS) 16-17, N=6); RNA-Seq analysis of hematoendothelial populations from the dorsal and ventral portions of the dorsal aorta (AoV, AoD respectively) (CS15-16, N=2); single cell RNA-Seq analysis of the AoV (N=1) and central portion of the dorsal aorta (N=1).


title: Efficient strategies for microglia replacement in the central nervous system

status: Public on Jul 31 2020

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: Microglia are important immune cells in the central nervous system (CNS). Dysfunctions of gene-deficient microglia contribute to the development and progression of multiple CNS diseases. Microglia replacement by nonself cells has been proposed to treat microglia associated disorders. However, most of attempts are failed due to low replacement efficiencies, such as with the traditional bone marrow transplantation approach. In this study, we develop three efficient strategies for microglia replacement: microglia replacement by bone marrow transplantation (mrBMT), microglia replacement by peripheral blood (mrPB) and microglia replacement by microglia transplantation (mrMT). mrBMT and mrPB allow microglia-like cells to efficiently replace resident microglia in the whole CNS. On the other hand, mrMT achieves microglia replacement in brain regions of interest. In summary, the present study offers effective tactics for microglia replacement with diverse application scenarios, which potentially opens up a window on treating microglia-associated CNS disorders.

overall_design:
Single-cell RNA-seq for normal microglia and microglia (or microglia-like cells) from mrMT, mrBMT and mrPB.

UPDATE [04-18-2025] The raw data for GSM4705329 was removed at the request of the submitter because it was the wrong data.

first: Zhen

last: Xu

first: Yanxia

last: Rao


title: Role of SWI/SNF-Related, Matrix Associated, Actin Dependent Regulator of Chromatin A4 (SMARCA4) core complex in epithelial innate response (ATAC-seq)

first: Allan

last: Brasier

summary: We examine the epigenetic role of the SWI/SNF Related, Matrix Associated, Actin Dependent Regulator of Chromatin A4 (SMARCA4) in the epithelial response to RSV infection.  Wild type and SMARCA4 silenced cells were subjected to ATAC-seq in the absence or presence of RSV infection. Cells were infected for 0 or 24 h prior to RNA seq.

first: Xiaofang

first: Chenyang

last: Dong


title: CD4+ T cells From Children With Active Juvenile Idiopathic Arthritis Show Altered Chromatin Features Associated With Transcriptional Abnormalities (ChIP-seq)

first: Tao

last: Liu

overall_design: We mapped CTCF anchors of chromatin loops with ChIP-seq.

first: Evan

last: Tarbell

first: Kaiyu

last: Jiang

first: James

last: Jarvis


title: High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

status: Public on Oct 12 2020

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

country: Japan

institute: RIKEN Quantitative Biology Center

summary: Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Escherichia coli. The transcriptome, resistance, and genomic profiles for the evolved strains in 48 environments were quantitatively analyzed. By analyzing the quantitative datasets through interpretable machine learning techniques, the emergence of low dimensional phenotypic states within the 192 strains was observed. Further analysis revealed the underlying biological processes responsible for the distinct states. We also report a novel constraint which leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space, and lead to a comprehensive understanding of constraints for antibiotic resistance.

overall_design: Transcriptomes of the 192 evolved strains and the wild-type strain were compared by DNA microarray analysis. All strains were grown on the modified M9 medium and total RNA was isolated from the cells in the exponential growth phase.

first: Tomoya

last: Maeda

first: Junichiro

last: Iwasawa

first: Kotani

last: Hazuki

first: Natsue

last: Sakata

first: Masako

last: Kawada

first: Takaaki

last: Horinouchi

first: Aki

last: Sakai

first: Kumi

last: Tanabe

first: Chikara


title: Microarray based gene expression analysis in Wt and Rab23-/- mice calvaria at embryonic day 15.5

status: Public on Jul 15 2020

city: Helsinki

first: Md. Rakibul

last: Hasan

address: Haartmaninkatu 8

department: Oral and maxillofacial diseases

country: Finland

institute: University of Helsinki

summary: Differential gene expression analysis in Wt and Rab23-/- calvaria to find genes responsible for early suture fusion

overall_design: Total RNA isolated from mouse (3 Wt and 3 Rab23-/-) calvaria (excluding skin and brain)

first: David P.C.

last: Rice

first: Maarit

last: Takatalo


title: AP-1 Regulates Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion during Zebrafish Heart Regeneration

status: Public on Jun 10 2020

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: The zebrafish has emerged as a powerful model to study cardiac regeneration; however, the mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear.  Here, we show that AP-1 transcription factors play an essential role in regulating the cardiomyocyte response.  Using ATAC-Seq, we first find that the cardiomyocyte chromatin accessibility landscape is dynamic following cryoinjury, and that AP-1 motifs are the most highly enriched in regions that gain accessibility during regeneration.  Using a cardiomyocyte-specific dominant-negative approach, we show that AP-1 promotes cardiomyocyte proliferation as well as chromatin accessibility at genes regulating sarcomere disassembly and cardiomyocyte protrusion into the injured area.  We further find distinct temporal requirements for AP-1 during cardiac regeneration.  Altogether, these results indicate that AP-1 plays a key role in the cardiomyocyte response to injury by promoting chromatin accessibility changes, allowing the activation of gene expression programs that support regeneration.

overall_design: Cardiomyocyte(CM)-specific ATAC-Seq from uninjured FACS sorted myl7:nucDsRed+ CMs (2x replicates), regenerating FACS sorted gata4:EGFP+ CMs at 4 days post cryoinjury (dpci, 2x replicates), dominant-negative A-Fos (+) wound border CMs at 4 dpci (3x replicates), A-Fos (-) wound border CMs at 4 dpci (3x replicates), uninjured junba overexpressing CMs (2x replicates), and uninjured junbb overexpressing CMs (2x replicates)

first: Arica

last: Beisaw

last: Guenther

first: Carsten

last: Kuenne

first: Julia

last: Dahlmann

first: Mario

last: Looso

first: Didier

middle: Y

last: Stainier


title: Expression data from primary mouse Emu-myc B-cell lymphoma.

status: Public on Mar 19 2020

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

institute: Charite University Medicine, Berlin

summary: We are interested in genetic programs and mutations which impact on tumor development and sensitivity to anticancer therapies. Utilizing Emu-myc transgenic mice, which spontaneously develop aggressive B-cell lymphomas, we aimed here to study the effects of drug responses in vivo. For that purpose, primary lymphomas from the Emu-myc transgenic mice were transplanted in several immunocompetent recipients and exposed to a single dose Cyclophosphamide (CTX), a standard component of chemotherapeutic regimens used to treat human B-cell lymphomas. Approximately one half of recipient mice are cured with this treatment (Never Relapse Lymphomas, NR), while in other half lymphomas relapse over time (Relapse Prone Lymphomas, RP), allowing us to treat these relapsed mice with progressively shorter durations of remission into full-blown clinical resistance (Resistant Lymphomas, RES). Looking at the differences between NR, RP and RES lymphomas, each in therapy-naive state or after drug challenge, we aimed here to decipher the genetic and biochemical components determining the susceptibility of lymphoma cells to respond to standard chemotherapeutic drugs.

overall_design: Immunocompetent recipient mice, transplanted with an aliquot of primary lymphoma cells explated from transgenic Emu-myc mice, were exposed to a single dose of Cyclophosphamide (CTX), a standard component of chemotherapeutic regimens used to treat human B-cell lymphomas. After obtaining long-term therapy response data in mice, the global expression profiles were obtained from aliquots of these same lymphomas in therapy-naive state, after acute in vivo drug challenge (where lymphomas engrafted in recipient mice were explated 4h after applying single dose CTX treatment) or long-term responses (where the engrafted lymphomas relapsed over time after CTX treatment and were explated from recipient mice). Ultimate therapy resistance mechanisms were analyzed in samples of relapsed lymphomas above, which were submitted to another two rounds of transplantation into new hosts, CTX treatment and relapse.

first: Clemens

last: Schmitt

last: Kase

first: Kolja

last: Schleich

first: Michael

last: Hummel

first: Dido

last: Lenze

first: Jan

middle: R

last: Dörr


title: Immune-checkpoint blockade lacks anti-tumorgenicity in NASH-induced HCC

status: Public on Oct 24 2020

city: Tübingen

first: MENGJIE

last: QIU

address: Otfried-Müller-Str. 37

institute: M3 Forschungszentrum für Malignom, Metabolom und Mikrobiom

summary: Hepatocellular carcinoma (HCC) has dismal treatment responses to systemic therapies and is caused by both, viral and non-viral etiologies, including non-alcoholic steatohepatitis (NASH) 1–5. NASH - triggered by high caloric intake and sedentary lifestyle - has become an important driver for HCC development. Immunotherapy has been recently approved for HCC but stratification of responders versus non-responders has remained an unmet need 5–8. Here, we found a progressive accumulation of non-classical activated CD8+PD-1+ T-cells in livers of NASH-affected patients and mice. PD-L1/PD-1-targeted immunotherapy of NASH-induced HCC administered either at cancer-initiation or after cancer-establishment lacked beneficial effects in mice. On the contrary, PD-1-targeted immunotherapy drove hepatic necro-inflammation and increased liver cancer incidence, tumor number, and nodule size. Anti-CD8 or anti-CD8/anti-NK1.1 treatment suppressed liver cancer development, implicating CD8+ T-cells as liver cancer drivers in the context of NASH. In line, PD-1-/- mice challenged with a NASH-inducing diet displayed early-onset of liver cancer. Mechanistically, PD-1-targeted immunotherapy triggered necro-inflammation and a pro-tumorigenic environment in the context of NASH, increasing the abundance of hepatic TOX+CXCR6+ expressing CD8+PD-1+ TNF+ T-cells. Anti-CD8/anti-PD-1 or anti-TNF/anti-PD-1, but not anti-CD4/anti-PD-1 treatment reverted anti-PD1 treatment-related increase of liver inflammation, NASH severity and tumorigenesis. Gene expression profile and increased abundance of murine hepatic CD8+PD-1+ T-cells were corroborated in human CD8+PD-1+ T cells derived from NASH patients. In a meta-analysis of clinical trials testing PD-1-targeting immune checkpoint inhibitors alone (i.e. pembrolizumab) or in combination in 1656 patients with advanced HCC, immunotherapy was not favorable over to control treatment in non-viral- when compared to viral-related HCC. Similarly, in two clinical cohorts tested, patients with NASH-driven HCC had a significantly worse overall survival with PD-1-targeted immunotherapy than HCC patients with other etiologies. Our data identify non-viral etiologies, particularly NASH, as potentially non-responsive in the context of HCC immunotherapy, providing a strong rational basis for patient stratification.

overall_design: mRNA profiles of liver tissues from 10 patients with different pathological characteristics

first: Dominik

last: Pfister

first: Nicolás

middle: G

last: Núñez

first: Roser

last: Pinyol

first: Olivier

last: Govaere

first: Matthias

last: Pinter

first: Marta

last: Szydlowska

first: Revant

last: Gupta

first: Mengjie

last: Qiu

first: Aleksandra

last: Deczkowska

first: Assaf

last: Weiner

first: Florian

last: Müller

first: Suhail

last: Youssuff

first: Ankit

last: Sinha

first: Ekaterina

last: Friebel

first: Thomas

last: Engleitner

first: Daniela

last: Lenggenhager

first: Danijela

last: Heide

first: Anja

last: Moncsek

first: Kristin

last: Stirm

last: Kosla

first: Sandra

last: Prokosch

first: Ulrike

last: Rothermel

last: Dudek

first: Eleni

last: Kotsiliti

first: Tracy

last: O`Connor

first: Valentina

last: Leone

first: Donato

last: Inverso

first: Jakob

last: Jansen

first: Indrabahadur

last: Singh

first: Monica

last: Yabal

last: Castet

first: Carla

last: Montironi

first: Philipp

middle: K

last: Haber

first: Sara

last: Torrecilla

first: Viktoria

last: Eichwald

first: Manfred

last: Jugold

first: Rupert

last: Ollinger

last: Matter

first: Luigi

last: Terracciano

first: Dina

last: Tiniakos

first: Pierre

last: Bedossa

first: Simon

last: Cockell

first: Ramy

last: Younes

first: Michele

last: Vacca

first: Fabio

last: Marra

first: Jörn

middle: M


title: Signalling molecules involved in the communication between maize seed compartments

status: Public on Feb 04 2020

first: Véronique

last: BRUNAUD

summary: Transcriptomics at maize embryo/endosperm interfaces identifies a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

overall_design: 24 samples with 4 biological replicats. organ comparison

first: José

last: Caius

first: Thomas

last: Widiez

first: Ludivine

last: Taconnat-Soubigou


title: DNA methylation profiling of 82 triple negative breast cancers with BRCA1 promoter methylation or BRCA1 mutation using the Illumina EPIC 850K platform.

status: Public on Jun 11 2020

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiles for 82 triple negative breast cancer (TNBC) samples from the Swedsh Cancerome Analysis Network - Breast (SCAN-B) cohort.

overall_design: Genomic DNA from 82 triple negative breast cancer (TNBC) samples was treated with bisulfite and hybridized to Illumina EPIC 850K arrays using standard protocols. Raw iDat files were processed using the minfi-package in R as well as custom R-scripts to produce normalized beta values. Both raw intensity values from minfi and the final normalized data are included for each sample.

first: Mattias

last: Aine


title: Large genotype and population comparisons in populus nigra-Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

status: Public on Jun 03 2020

summary:
jc2013_sybiopop_2014
Large genotype and population comparisons in populus nigra-Which genes affect biomass yield in poplar ?-Large genotype comparisons: 241 genotype from 11 populations. RNA was extracted from young differentiating xylem and cambium collected on 480 4-year-old trees trialed in a common garden experiment at INRA Orléans. The trees corresponded to corresponding to 2 replicates of 241 genotypes from 11 natural populations. After RNA quantification, the RNA from xylem and cambium from the same tree were pooled and subjected to high-throughput sequencing on an Illumina HiSeq2000 using 100 bp single-read indexing runs. All the samples were sequenced on one Illumina, yielding around 20 million of single-reads per sample.

overall_design: 461 samples with 2 biological replicates. genotype and ecotype comparison

first: Aurélien

last: Chateignier

first: Sandrine

last: Balzergue

first: Vincent

last: Segura

last: Soubigou-Taconnat


title: Protein O-GlcNAcylation Silences Methylated Promoters in Mammalian Genomes

status: Public on May 29 2020

city: St. Louis

first: John

middle: R.

last: Edwards

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

summary: Methylated mammalian promoters are transcriptionally silenced even in the presence of all the factors required for their expression. Repression requires the assembly of a methylation-dependent silencing complex that contains the TRIM28 (also known as KAP1 and TIF1β) protein. An internally controlled interaction screen identified O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase or OGT) as a protein that was complexed with TRIM28 in wild type em-bryonic stem cells but not in Dnmt1-/- cells that had severely demethylated genomes. In the ab-sence of DNA methylation, multiple proteins associated with TRIM28 failed to undergo modifica-tion by N-Acetylglucosamine (GlcNAc). Mass spectrometry identified several of these proteins as known mediators of transcriptional silencing. The most active transposon in the mouse ge-nome is the IAP LTR retrotransposon, which have been previously shown to be repressed by DNA methylation. A Bacteroides O-GlcNAc hydrolase was fused to a catalytically inactive Cas9 and targeted to methylated IAP retrotransposon promoter sequences via IAP-specific guide RNAs; fulminating reactivation of IAP transcription was induced. These data revealed that Glc-NAcylation is directly involved in the transcriptional repression of methylated promoters.

overall_design:
RNA-seq analysis of Dnmt1-/- ES cells and WT ES cells untreated or treated with dCas9-OGA or dCas9-OGA-D242A with four sgRNAs targeting IAP elements.
O-GlcNAc ChIP-seq analysis of WT ES cells

first: Mathieu

last: Boulard

first: Timothy

middle: H

last: Bestor


title: Splicing regulation by the lncRNA ASCO

status: Public on Jan 30 2020

summary: ngs2016-07-asconcrna-splicing regulation by the lncrna asco

overall_design: 9 samples with 3 biological replicates. normal vs rnai mutant comparison,normal vs transgenic comparaison

first: Stephanie

last: Huguet

first: Jérémie

last: Bazin


title: Search for mitochondrial editing defect in an Arabidopsis PPR mutant

status: Public on Mar 30 2020

summary: ngs2019_18_eplus-eplus-search for mitochondrial editing defect in an arabidopsis PPR mutant Annotation, RNA/Small-RNA quantification: editing quantification. The Mito samples were first enriched with mitochondria by a series of multi-speed centrifugations after grinding with mortar at 4°C.

overall_design: 12 samples with 3 biological replicates. gene knock out

first: Alex-avon

last: Alaunay

first: Etienne

last: Delannoy


title: half_edit - A new predictive method for E+ PPR binding

last: BRUNAUD

summary: ngs2018_04_half_edit-half_edit - Is there some transcriptomic defects in these different PPR KO mutants? - Identification of RNA editing defects in 3 differents KO mutants for E+ PPR. Results will be compared to different predictive methods in order to find out which one is the more accurate. Also looking for other transcriptomic defects in a pure-PPR.

overall_design: 15 samples with 1 biological replicate. normal vs transgenic comparison


title: Allelic variation at a major QTL for cell wall related traits and coordinated changes in gene expression in maize

status: Public on Dec 14 2019

summary: ngs2015_12_zeawall2-zeawall2-Address the hypothesis that allelic variation at a major QTL for cell wall related traits gives rise to coordinated changes in gene expression in maize-Two pairs of BC2S2 maize lines carrying F271 or F288 alleles in an 18-20 Mb interval of chromosome 6 in an otherwise F271 genetic background were grown in the field at Mauguio (Hérault, France) in 2015 with two row replicates. Irrigation was applied during the summer to prevent water stress. The bottom third of upstream-ear internodes (without nodes) of three representative plants in each of the two replicates were harvested two days before silking. All samples were immediately frozen in liquid nitrogen and stored at -80°C.

overall_design: 10 samples with 2 biological replicates. allele,genomic comparison

last: Taconnat

first: Sylvie

last: Coursol


title: Electrical and synaptic integration of glioma into neural circuits

status: Public on Oct 02 2019

city: Palo Alto

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive Room 3035

institute: Stanford University

summary: We report single cell RNA-seq data from patient-derived xenografts that were dissociated, FACS sorted into 96-well plates and profiled by Smart-seq2 and sequencing on an Illumina NextSeq500

overall_design: Individual cells from two DIPG cell cultures derived by the Monje lab (DIPG VI and DIPG XIII-FL) were isolated by enzymatic and mechanical digestion followed by FACS sorting. cDNA libraries were generated using Smart-seq2 and  Nextera XT with dual unique indexes. Libraries were sequenced on an Illumina NextSeq500, reads aligned by Bowtie and quantified by RSEM and alayses performed using Seurat.

first: Humsa

middle: S

last: Venkatesh


title: Nascent transcript analysis of glucocorticoid crosstalk with TNF in Beas-2B airway epithelial cells

status: Public on Aug 27 2019

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

summary: This study addressed mechanisms through which glucocorticoids exert repressive effects on pro-inflammatory TNF signaling using Global Run-on Sequencing (GRO-seq) in Beas-2B airway epithelial cells treated with dexamethasone and/or TNF for 10 or 30 minutes.

overall_design: Duplicate samples for each of the treatment conditions [vehicle (ethanol), TNF (20 ng/ml), dexamethasone (100 nM) or TNF+dex] at each time point (10 or 30 minutes) were sequenced and included in the analyses..

first: Margaret

last: Gruca

first: Mary

last: Allen

first: Vineela

last: Kadiyala

first: Tengyao

last: Song

first: Fabienne

last: Gally

first: Arnav

last: Gupta

first: Miles

last: Pufall

first: Robin

last: Dowell

first: Anthony

last: Gerber


title: Resistance mechanisms to SYK inhibition in AML

status: Public on Jan 16 2020

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary: Targeted therapy studies with small molecules against kinases, such as spleen tyrosine kinase (SYK), are underway in patients with acute myeloid leukemia (AML) and show promising initial results. Identifying the potential mechanism of resistance and finding new drug combinations to overcome them, however, is essential for the long-term success of these targeted agents. Here, we conducted a genome-scale ORF resistance screen and identified activation of the RAS/MAPK/ERK signaling pathway as one major mechanism of resistance to SYK inhibition. This finding was validated in AML cell lines with innate and acquired resistance to a SYK inhibitor and in AML samples from patients who developed resistance to SYK inhibition. In order to circumvent this resistance, we demonstrate the synergistic activity of a MEK Inhibitor in combination with a SYK inhibitor in RAS mutated cells, as well as in entospletinib-resistant AML cells.

overall_design: RNA-seq transcriptome profiling of naïve MV4-11 cell lines and of Entospletinib resistant MV4-11 cell lines,  treated in triplicate with  Entospletinb (700 mM) vs.  DMSO (<0.001%), for 8 h and separately for 24 h. Generation of Entospletinib Resistant Cells: To generate cells that were resistant to SYK inhibition, MV4-11 were treated for 5 months with gradually increasing concentrations of entospletinib (500 nM to 5 µM). Cells were considered entospletinib-resistant when they were able to remain 90-100% viable in the presence of this 10-fold higher than IC50 concentrations of entospletinib.

first: Kimberly

last: Stegmaier


title: RNA-Seq on mpk8 and tcp14 mutants on dry and imbibited seeds - Dormancy release by phosphorylation

status: Public on Jul 23 2019

first: Véronique

last: BRUNAUD

summary: ngs2016_10_dormancy - RNA-Seq on mpk8 and tcp14 mutants on dry and imbibited seeds-Comparison of the expression of genes in wild seeds and in mpk8 and tcp14 mutants on dry seeds and at a precise imbibition time (24h, 25°C) and in the dark.-Dry harversted seed: WT, mpk8, tcp14, 24h of imbibition in dark at 25°C: WT, mpk8, tcp14.

overall_design: 18 samples with 3 biological replicats. gene knock out

first: Juliette

last: Puyaubert

first: Ludivine

last: Soubigou-Taconnat


title: Comparison of WT and JNK3 KO (MAPK10-/-) gene expression in gastrocnemius muscle after hindlimb ischemia (HLI)

status: Public on Aug 15 2019

city: Boston

first: Shashi

last: Kant

address: 4 Blackfan Circle, Room 614

department: Cardiovascular Medicine

institute: Brigham Women's Hospital

summary: JNK3 deficiency leads to upregulation of growth factors such as Vegfa, Pdgfb, Pgf, Hbegf and Tgfb3 in ischemic muscle. In order to ascertain the molecular mechanisms responsible for the accelerated blood flow recovery in Mapk10-deficient mice, a micro-array analysis of gastrocnemius muscle from these mice was performed after HLI. We observed a significant up-regulation of several growth factors known to improve blood flow recovery in the Mapk10-/- muscle compared to WT

overall_design: In order to ascertain the molecular mechanisms responsible for the accelerated blood flow recovery in Mapk10-deficient mice, a micro-array analysis of gastrocnemius muscle from these mice was performed after hindlimb ischemia (HLI).

first: Siobhan

last: Craige

first: Kai

last: Chen

first: Michaella

last: Reif

first: John

middle: F

last: Keaney Jr


title: Single cell RNA-Seq analysis of the human embryo dorsal aorta

status: Public on Sep 17 2020

first: Edie

last: Crosse

summary: Single cell RNA-Seq exploration of the human dorsal aorta, the hematopoietic stem cell (HSC) developmental niche, to explore heterogeneity of the HSC microenvironment and elucidate lineage trajectories of nascent hematopoietic stem/progenitor cells (HSPCs) from endothelium.

overall_design: Single cell analysis of the ventral portion of the dorsal aorta (AoV), the site of hematopoietic stem cell (HSC) emergence, containing 2379 CD34-enriched cells from 1 carnegie stage (CS) 16 embryo. The second datset includes dorsal aorta cells from the trunk of a separate CS16 embryo from which a hematoendothelial subset of cells are analysed.

middle: I

first: Stanislav

last: Rybtsov

first: Anahi

last: Binagui-Casas

first: Richard

middle: A

last: Anderson

first: Kristina

last: Kirschner

first: Tamir

last: Chandra

first: Alexander

last: Medvinsky


title: CoBATCH for high-throughput single-cell epigenomic profiling [heart in situ ChIP]

status: Public on Jul 15 2019

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

summary: we develop a robut low input cell and high throughput single cell ChIP method used for both native and fixed in vitro cultured cells and intact tissue

overall_design: we fused Protein A to the N-terminal of Tn5 to generated Protein A-Tn5 fusion enzyme, the ProteinA-Tn5-complex is enriched through specific antibodies to genomic regions and Tn5 generates indexed chromatin fragments ready for the library preparation and sequencing

first: Qianhao

last: Wang

first: Shanshan

last: Ai

first: Xianhong

last: Yu

first: Yaxi

last: Liu

first: Jiejie

last: Zhang

first: Aibin

last: He


title: CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP]

overall_design: we fused Protein A to the N-terminal of Tn5 to generated Protein A-Tn5 fusion enzyme, the ProteinA-Tn5-complex is enriched through specific antibodies to genomic regions and Tn5 generates indexed chromatin fragments ready for the library preparation and sequencing; ROC - receiver operating characteristic.


title: CoBATCH for high-throughput single-cell epigenomic profiling [embryo in situ ChIP]


title: CoBATCH for high-throughput single-cell epigenomic profiling [EC_CoBATCH_Pol_II]


title: CoBATCH for high-throughput single-cell epigenomic profiling [bulk in situ ChIP]


title: CoBATCH for high-throughput single-cell epigenomic profiling [EC_CoBATCH_H3K36me3]


title: Transcriptome-wide gene-expression analysis of colonic epithelium from enteroendocrine cell-deficient mice

status: Public on Jul 13 2019

city: Dallas

first: Luis

last: Sifuentes-Dominguez

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatrics

institute: University of Texas Southwestern Medical Center

summary: The goal of this study is to study the consequence of EEC loss on the colonic epithelium through tissue specific deletion of the transcription factor Ngn3.

overall_design: colonic epithelial cells from 12-13 week old wild-type (Ngn3 f/f) and colonic enteroendocrine deficient (CDX2 Ngn3 f/f) animals were used for RNASeq.

first: Ezra

last: Burstein


title: validation of pilot transcriptomic study - Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

status: Public on Jun 20 2019

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

institute: INRAE

summary: jc2013_sybiopop_2014-validation of pilot transcriptomic study-Which genes affect biomass yield in poplar

overall_design: 24 samples with 1 biological replicat. genotype and ecotype comparison

first: Ludivine

last: Taconnat

first: Sandrine

last: Balzergue

first: Vincent-

last: Segura

first: Odile

last: Rogier


title: transition-Transcriptome of floral transition

status: Public on Apr 17 2019

summary: ngs2015_01_transition-transition-Identification of transcripts and long non-coding transcripts in wild-type mature rosette leaves of Arabidopsis thaliana during a photoperiodic switch inducing floral transition.-Arabidopsis thaliana Col-0 plants were grown in soil, in growth chamber under white fluorescent light, under short-day (8 hours light/16 hours dark, SD) or long-day (16 hours light/8 hours dark, LD) conditions. Temperature in SD was 21°C during the light period and 18°C during the dark, humidity (65%) remained constant. In LD, temperature (21°C) and humidity (70%) remained constant. Plants were cultured for 4 weeks in individual pot, in SD then transferred in LD. Plants were analysed at different time points before transfer (T0) and after two, three and five days of transfer (T2, T3, T5). The second pair of leaves was collected before dusk, at Zeitgeber time 15 (ZT15) considering ZT 0 the switched on of the light. Three biological replicates were performed. The floral transition occurs between T0 and T5 based on AP1:GUS marker, a inflorescence meristem is not yet visible during this developmental window at the center of the rosette.

overall_design: 12 samples with 3 biological replicates. time course

first: Valerie

last: Gaudin


title: transilice - Effects of silicon (Si) supply on leaf and root transcriptomes

status: Public on Feb 22 2019

summary: ngs2017_08_brasilice-transilice - What are the genes with modulated expression in response to brassica napus treatment (1.7mM, One week, root supply)-Brassica napus were grown on hydropnic conditions using Hoagland nutrient solution containing or not 1.7 mM of Si

overall_design: 12 samples with 3 biological replicates. treated vs untreated comparison

first: José

last: Caius

first: Philippe

last: Etienne

last: Laine

last: Taconnat-Soubigou

last: Brunaud


title: Global gene expression in mouse thymic tissue or lymphocytes from young or aged mice, and during induced regeneration

status: Public on Jun 04 2019

city: Jupiter

first: Mathew

last: Pipkin

state: Florida

address: 130 Scripps Way

department: Immunology and Microbiology

institute: Scripps Research Institute

summary: The thymus begins to atrophy early in life, but maintains the capacity for transient robust re-growth in response to chemical or physical androgen ablation in males.  In mice, at age 5 weeks the thymus remains near peak size, while by 12 months it has atrophied by  .  In response to castration the thymus re-grows to approximately it's peak size after about 20 days when it begins to rapidly re-atrophy.  This study contains gene expression data from affymetrix microarrays covering thymic cortical and medullary laser capture microdissected tissue as well as FACS sorted cortical and medullary lymphocytes in young and aged mice, as well as timecourse data during castration induced regrowth.

overall_design: 156 samples including thymus from young and aged mice C57BL/6, as well as a time course after regeneration including 18 time points from male C57BL6 mice.  There are 39 samples each in 4 sample types, microdissected thymic cortical and medullary tissue, and FACS sorted thymic cortical and medullary lymphocytes.  Samples were collected at 5 weeks, 12 months, and in 12 month olds at days 6 to 23 post surgical castration.  Replicates are present in 5 week old (5 reps), 12 month (4), day 6 (3), day 7 (2), day 12 (3), day 16 (2), day 17 (3), and day 20 (5) post castration.  Replicate numbers indicate number of replicates in each tissue/cell type.

first: Thomas

last: Venables

first: Ann

middle: V

last: Griffith

first: Alice

middle: T

last: DeAraujo

first: Howard

last: Petrie


title: CoBATCH for high-throughput single-cell epigenomic profiling [native ESC coBATCH]

first: Haiqing

last: Xiong

first: Qianhao

last: Wang

first: Shanshan

last: Ai

first: Xianhong

last: Yu

first: Yaxi

last: Liu

first: Jiejie

last: Zhang

last: He


title: CoBATCH for high-throughput single-cell epigenomic profiling [EC_CoBATCH]

first: Aibin


title: Gene expression profile of endothelial cell cultures exposed to uremic serum from Chronic Kidney Disease patients: role of MAPK signaling pathway

status: Public on Jan 31 2019

city: MEXICO

first: Angélica

middle: Rangel

last: López

state: Cuauhtémoc

address: Avenida Cuauhtémoc 330

country: Mexico

institute: IMSS

summary:
Transcriptome analysis of human coronary arterial endothelial cells (HCAEC) primary cultures exposed to uremic serum from patients with stage 4-5 cardiovascular diseases (CKD) without myocardial  infarction (USI) and stage 4-5 CKD with myocardial infarction (UCI).
Gene expression profile of human coronary arterial endothelial cells (HCAEC) primary cultures exposed to uremic serum from of patients with chronic kidney disease (CKD) that explore which pathways are involved in in the development of cardiovascular disease.  The metabolic pathway significantly represented was the MAPK signaling pathway, suggesting that the effects of uremic toxins present in patients with CDK, on the primary cultures of HCAEC provides a more informative model for the study of molecular mechanisms that lead to the development of endothelial dysfunction secondary to CKD.

overall_design: We analyzed RNA of human coronary arterial endothelial cells (HCAEC) primarycultures supplemented with 20% uremic serum from two groups of patients, group 1: patients with stage 4-5 Chronic kidney disease (CKD) without myocardial infarction (USI) and group 2: stage 4-5 CKD with myocardial infarction (UCI). We used Affymetrix GeneChip® microarray and the LIMMA package (Linear Models for Microarray Data) of the Bioconductor software17 was implemented to identify relevant DEGs between the two groups of Uremic patients.

first: Angelica

last: Rangel-López

first: Minerva

last: Mata-Rocha

first: Oscar

last: Pérez-González

first: Juan

last: Mejía-Aranguré

first: Sergio

last: Juárez-Méndez

first: Ricardo

last: López-Romero

first: Vanesa

last: Martínez

last: Orihuela-Rodríguez

first: Cléto

last: Álvarez-Aguilar

first: Abraham

last: Majluf

first: Dante

last: Amato

first: Ramón

last: Paniagua


title: Analysis of arabidopsis mutants tor/lst8/yak1/maktor

status: Public on May 23 2019

first: Véronique

last: BRUNAUD

summary: ngs2018_05_tor-analysis of arabidopsis mutants tor/lst8/yak1/maktor-Analysis of Arabidopsis insertion and suppressor mutants linked to the TOR signaling pathway.-Comparison of in vitro grown plantlets for lst8, yak1 mutants and double mutants corresponding to suppressor lines. Comparison of in vitro grown plantlets for mutants affected in LST8 interacting proteins (MAKTOR) compared to wild type.

overall_design: 18 samples with 2 biological replicats. gene knock out

first: Ludivine

last: Soubigou-taconnat

first: Christian

last: Meyer


title: Pilot transcriptomic study-  Sybiopop: A systems biology approach to improve poplar biorefinery feedstock by deciphering the genetic architecture of lignocellulosic biomass production and quality

status: Public on Oct 23 2018

summary: jc2013_sybiopop_2014-pilot transcriptomic study - Which genes affect biomass yield in poplar? RNA was extracted from young differentiating xylem and cambium collected on 24 4-year-old trees trialed in a common garden experiment at INRA Orléans. The trees corresponded to corresponding to 2 replicates of 12 genotypes from 6 natural populations. After RNA quantification, the RNA from xylem and cambium from the same tree were pooled and subjected to high-throughput sequencing on an Illumina HiSeq 2000 using 100 bp paired-ends reads indexing runs. All the samples were sequenced on one Illumina lane, yielding around 20 million of single-reads per sample.

overall_design: 24 samples with 1 biological replicats. genotype and ecotype comparison

last: Taconnat

first: Sandrine

last: Balzergue

first: Vincent-

last: Segura

first: Odile

last: Rogier


title: Next Generation Sequencing Facilitates Quantitative Analysis of ES, pMN, MN, and IN Transcriptomes

status: Public on Nov 01 2018

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

summary: In this experiment, we sought to identification the stage specific lncRNAs from the transcriptome of WT cells during differentiation of ESCs into cervical motor neurons

overall_design: one line (Hb9GFP ESC)

first: Jun-An

last: Chen

first: Ya-Lin

last: Lu


title: ATAC-seq on HSV-1 infected primary human fibroblasts (time course)

status: Public on Mar 08 2018

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Buenrostro et al., Nature Methods 2013

overall_design: HFF were infected with HSV-1 strain 17 for 0 to 8 h post infection. ATAC-seq samples were prepared at the indicated times of infection. Two independent biological replicates were analyzed.

first: Thomas

last: Hennig

first: Marco

last: Michalski

first: Andrzej

last: Rutkowski

first: Lara

last: Djakovic

first: Adam

last: Whisnant

first: Marie-Sophie

last: Friedl

first: Bhaskar

last: Jha

first: Marisa

last: Baptista

first: Anne

last: L'Hernault

first: Florian

last: Erhard

first: Lars

last: Dölken

middle: C


title: Subcellular RNA fractions of HSV-1 infected primary human fibroblasts

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Subcellular RNA fractions including total RNA, cytoplasmic RNA, nucleoplasmic RNA and chromatin-associated RNA were prepared and subjected to RNA-seq

overall_design: HFF were infected with HSV-1 strain 17 for 8h (or mock). Subcellular RNA fractions were prepared combinig the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013). Two independent biological replicates were analysed.


title: Chromatin accessibility dynamics across C. elegans development and ageing

status: Public on Jun 01 2018

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

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

overall_design: Refer to individual Series


status: Public on Feb 13 2018

first: Véronique

last: BRUNAUD

summary: ngs2012_02_microd-ngs microd-part2-Effect of dilution on RNA seq sensitivity-One sample of total RNA extracted from whole embryo by laser assisted microdissection was diluted from 5ng to 10pg to check sensitivity of the library construction and subsequent sensitivity of transcript identification by RNA seq.

overall_design: 6 samples with  biological replicats. null

first: Bertrand

last: Dubreucq

first: Ludivine

last: Taconnat

first: Sandrine

last: Balzergue


title: RNA-Seq of epidermis and mesophyll in arabidopsis developing embryos

summary: ngs2014_01_microd-ngs micro d-1-RNA seq of epidermis and mesophyll in arabidopsis developing embryos-comparison of transcript accumulation in epidermis and mesophyll in Total RNA extracted by laser assisted microdissection from developping embryos at late heart stage.

overall_design: 8 samples with 4 biological replicats. organ comparison


title: Receptor tyrosine kinase signaling promotes post-embryonic morphogenesis and survival of glia and neural progenitor cells

status: Public on Nov 20 2018

city: Atlanta

first: Renee

last: Read

state: Georgia

address: 1510 Clifton Rd

department: Pharmacology

institute: Emory University School of Medicine

summary: Glioblastomas (GBMs), which are the most deadly malignant brain tumors of children and adults, infiltrate the brain and grow rapidly, and are resistant to current therapies. Glioblastomas (GBMs) frequently display mutations that activate receptor tyrosine kinases (RTKs), such as EGFR, which are thought to cooperate with additional factors to drive tumorigenesis. To identify and characterize genetic pathways that cooperate with RTKs to drive GBM progression, we performed RNA sequencing on several cell cultures created from surgical specimens from tumors with alterations in RTKs, and these cultures were grown as neurospheres in serum-free media used for normal neural stem/progenitor cell cultures. Under these conditions, GBM cells retain many defining features and mutations found in primary tumors. For comparison, we profiled commercially available human normal neural stem cells (HNPCs), which were grown under the same conditions. Data from these cell cultures was analyzed for transcripts differentially expressed between GBM cells and HNPCs, which showed that GBM cells that show RTK alterations strongly overexpressed the PDGFA and IGF2 secreted factors, which likely cooperate with EGFR to drive tumor progression.

overall_design: Transcriptomic profiling of human glioblastoma neurospheres

middle: D


status: Public on Jun 06 2018

summary: ngs2014_07_hevea-hevea_tpd-seq-RNAseq analysis of latex samples from healthy and Tapping Panel Dryness-affected trees.-Identification of Tapping Panel Dryness (TPD)-affected trees in a polyclonal trials grown under standard condition. Trees were tapped since November 2010 every 2 days. Latex yield and TPD occurrence were monitored as well as latex RNA samples were collected twice a year for further analysis. At the end of the experiment, gene expression in latex of healthy and TPD trees were compared.

overall_design: 21 samples with 3 biological replicates. genotype comparison, normal vs disease comparison

first: Pascal

last: Montoro


title: Stable STIM1 knockdown in human neural precursors derived from hESC line, H9

status: Public on Jun 27 2018

city: Bangalore

first: Gaiti

last: Hasan

state: karnataka

address: GKVK Campus Rd

country: India

institute: NCBS,TIFR

summary: Ca2 + signaling plays a significant role in development of the vertebrate nervous system where it regulates neurite growth as well as synapse and neurotransmitter specification (Rosenberg and Spitzer, 2011). Elucidating the role of Ca2 + signaling in neuronal development has been largely restricted to either small animal models or primary cultures. Here we derived human neural precursor cells (NPCs) from human embryonic stem cells to understand the functional significance of a less understood arm of calcium signaling, Store-operated Ca2+ entry or SOCE, in neuronal development. Human NPCs exhibited robust SOCE, which was significantly attenuated by expression of a stable shRNA-miR targeted towards the SOCE molecule STIM1. Along with the plasma membrane channel Orai, STIM is an essential component of SOCE in many cell types where it regulates gene expression. Therefore, we measured global gene expression in human NPCs with and without STIM1 knockdown. Interestingly, pathways down-regulated through STIM1 knockdown were related to cell proliferation and DNA replication processes whereas post-synaptic signaling was identified as an up-regulated process. To understand the functional significance of these gene expression changes we measured the self-renewal capacity of NPCs with STIM1 knockdown. These demonstrated significantly reduced neurosphere size and number as compared to control cells. Moreover, spontaneous differentiation towards the neuronal lineage was enhanced. These findings demonstrate that STIM1 mediated SOCE in human NPCs regulates gene expression changes, that in vivo are likely to physiologically modulate the self-renewal and differentiation of NPCs.

overall_design: STIM1 knockdown in human embryonis stem cell derived neural progenitor cells (NPCs) by using ShERWOOD-UltramiR short hairpin RNA (shRNA). Hence we designed our RNA seq in such a way that we can compare the differential gene expression data using STIM1 Knockdown (KD) as test group, shRNA non-targetted control (NTC) and wild type NPC (WT) as control groups. Biological triplicates were performed for each sample consisting of RNA isolated from wild type NPCs.

first: G

first: R

last: Gopurappilly

first: B

last: Deb

first: P

last: Chakraborty


title: A novel hippocampal long-range VIP-GABAergic projection to subiculum contributes to fear memory formation through region-specific connectivity

status: Public on Jan 30 2018

city: Quebec

first: Lisa

last: Topolnik

department: Biochemistry, Microbiology and Bio-informatics

institute: Université Laval

summary: We sequenced seven long-range projection vasoactive intestinal peptide (VIP)-expressing interneurons from the mouse CA1 oriens/alveus area using patch-seq technique to determine their molecular identity.

overall_design: Cells were recorded using patch-clamp technique, filled with biocytin for morphological identification and aspirated for next-generation sequencing. Only cells with confirmed axonal projections from the CA1 to subiculum were included.

last: Francavilla

first: V

last: Villette

first: X

last: Luo

first: S

last: Chamberland

first: E

last: Muñoz-Pino

first: O

last: Camiré

first: K

last: Wagner

last: Kis

first: M

last: Vallée

first: A

last: Droit

last: Somogyi

first: L


title: Transcriptome analysis of isoxaben-induced loss of cell wall integrity in Arabidopsis nia1/2 mutant

status: Public on Jan 25 2018

city: Trondheim

first: Thorsten

last: Hamann

address: Høgskoleringen 5

department: Department of Biology

country: Norway

institute: NTNU

summary: Plant cell walls maintain their functional integrity during growth, defense and turgor generation through a dedicated cell wall integrity (CWI) maintenance mechanism. Upon detection of integrity impairment due to cell wall damage (CWD) compensatory responses are activated to maintain CWI. Responses include production of salicylic acid (SA), jasmonic acid (JA) and lignin as well as growth inhibition. Here we investigated the processes responsible for inducing growth inhibition upon CWD in Arabidopsis thaliana seedlings. Genetic studies implicated NITRATE REDUCTASE1 2 (NIA1 2) in the response to CWD. RNAseq-based transcriptomics showed that nearly all the CWD-induced transcript changes detectable in Col-0 were absent in nia1 2 seedlings.

overall_design: Both genotypes (Col-0 and nia1/2) were treated with either isoxaben or DMSO (mock). Three replicates of Col-0 samples and two replicates of nia1/2 samples were analyzed.

first: Nora

last: Gigli-Bisceglia

first: Timo

last: Engelsdorf

first: Lauri

last: Vaahtera


title: Dyw2-DYW2_OTP100: Identification of the transcriptome defects (nuclear and organelles) of the T-DNA KO mutants of DYW2 and OTP100

status: Public on Jan 22 2018

first: Véronique

last: BRUNAUD

summary: ngs2016_08_dyw2-dyw2-Identification of the transcriptome defects (nuclear and organelles) of the T-DNA KO mutants of DYW2 and OTP100-TheT-DNA KO mutations are embryo-ethal for DYW2 and OTP100 so the homozygous mutants were produced by a temporal embryo-specific complementation using the promoter of ABI3. The resulting homozygous mutants were compared to their WT siblings. The T-DNA lines were GK_332A07 for DYW2 and SAIL_784_A11 for OTP100

overall_design: 12 samples with 3 biological replicats. gene knock out

first: Alex-avon

last: Alaunay

first: Ludivine

last: Soubigou-Taconnat

first: Etienne

last: Delannoy


status: Public on Jan 24 2018

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

summary: summary : Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47183 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).

overall_design: RNA from the glomerular compartment of was extracted and processed for hybridization on Affymetrix microarrays, annotated using Human Entrez Gene ID custom CDF version 19.

first: Viji

last: Nair

first: Felix

last: Eichinger

first: Maja

last: Lindenmeyer

first: Clemens

last: Cohen

first: Matthias

last: Kretzler


summary: summary : Tubulointerstitial transcriptome from ERCB subjects with chronic kidney disease and living donor biopsies. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47184 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).

overall_design: RNA from the tubulointerstitial compartment of was extracted and processed for hybridization on Affymetrix microarrays, annotated using Human Entrez Gene ID custom CDF version 19.


title: Transcriptome analysis of isoxaben-induced loss of cell wall integrity in Arabidopsis seedling liquid culture

status: Public on Jan 11 2018

summary: Plant cells are surrounded by walls, which must often meet opposing functional requirements during plant growth and defense. The cells meet them by modifying wall structure and composition in a tightly controlled and adaptive manner. The modifications seem to be mediated by a dedicated cell wall integrity (CWI) maintenance mechanism. Currently the mode of action of the mechanism is not understood and it is unclear how its activity is coordinated with established plant defense signaling. We investigated both the responses to cell wall damage (CWD) compromising CWI and the underlying mechanism in Arabidopsis thaliana. A cellulose biosynthesis inhibitor isoxaben was used as a tool to induce the loss of cell wall integrity. Isoxaben was chosen because it only affects a certain cell type / differentiation stage, and weakens the cell walls indirectly by inhibiting a biosynthetic process, making CWD occurrence dependent on high turgor levels (allowing simultaneous manipulation of the responses by addition of osmotica like sorbitol, mannitol, etc.). Isoxaben treatment causes structural damage, induction of lesion formation, cell death, deposition of lignin and callose as well as production of jasmonic acid and salicylic acid. Isoxaben-resistant mutant ixr1-1 is included to ensure the specificity of the treatment.

overall_design: Both genotypes (Col-0 and ixr1-1) were treated with either isoxaben or DMSO (mock). Three replicates of each sample were analyzed.


title: Gene expression data from the skin of Cdsniep-/-adult mice

status: Public on Jan 12 2018

city: Toulouse

first: Nathalie

last: JONCA

state: France

address: CHU Purpan

institute: INSERM UMR1291 - CNRS UMR 5051 - Université Toulouse III

summary:
Peeling Skin Disease (PSD; OMIM 270300) is an inflammatory ichthyosis due to homozygous loss-of-function mutations in Corneodesmosin (CDSN) and characterized by lifelong patchy peeling of the skin associated with eczema, food allergy and severe itching. The pathophysiology of PSD is still poorly known. The initial event of the disease, the detachment of the SC due to a CDSN deficiency, leads to an impairment of the permeability barrier which could in turn trigger erythema, pruritus and atopic manifestations by mechanisms not entirely elucidated. Cdsn-deficient mouse models are interesting tools to decipher these underlying mechanisms. In order to explore the still poorly known pathophysiological mechanisms of PSD, we analyzed the cutaneous transcriptome of two epidermis-specific Cdsn-deficient mouse models representative of early (occurrence of the permeability defect in Cdsnep-/- E18.5 embryos) and chronic (permanent permeability defect in Cdsniep-/- adult mice) phases of the disease
We used affymetrix microarrays to explore genes expression in the skin of  Cdsniep-/- adult mice which represent the chronic phase of the disease.

overall_design: Cdsniep-/- mice are epidermis-specific Cdsn-deficient and their genotype is KRT14-CreERT2(tg/0)/Cdsnfl/fl. To induce Cdsn inactivation and generate Cdsniep-/- mice (KO), seven to 12-week-old KRT14-CreERT2(tg/0)/Cdsnfl/fl mice were treated by daily topical application  of 4-hydroxytamoxifen (4-OHTam, 100μg/ear/day) on both ears until fifteen continuous days. KRT14-CreERT2(tg/0)/Cdsnwt/wt treated in the same conditions were used as control (WT). Total RNA were then extracted from the skin of ears. Microarray experiments were performed with RNAs from 4 individuals KO and from 4 individuals WT.


title: Gene expression data from the skin of Cdsnep-/- E18.5 embryos

summary:
Peeling Skin Disease (PSD; OMIM 270300) is an inflammatory ichthyosis due to homozygous loss-of-function mutations in Corneodesmosin (CDSN) and characterized by lifelong patchy peeling of the skin associated with eczema, food allergy and severe itching. The pathophysiology of PSD is still poorly known. The initial event of the disease, the detachment of the SC due to a CDSN deficiency, leads to an impairment of the permeability barrier which could in turn trigger erythema, pruritus and atopic manifestations by mechanisms not entirely elucidated. Cdsn-deficient mouse models are interesting tools to decipher these underlying mechanisms. In order to explore the still poorly known pathophysiological mechanisms of PSD, we analyzed the cutaneous transcriptome of two epidermis-specific Cdsn-deficient mouse models representative of early (occurrence of the permeability defect in Cdsnep-/- E18.5 embryos) and chronic (permanent permeability defect in Cdsniep-/- adult mice) phases of the disease
We used affymetrix microarrays to explore genes expression in the skin of  Cdsnep-/- E18.5 embryos which represent the early phase of the disease.

overall_design: Cdsnep-/- mice (KO) are epidermis-specific Cdsn-deficient and their genotype is KRT14-Cre(tg/0)/Cdsnfl/fl. Since the Cdsnep-/- phenotype being lethal at birth, caesarean deliveries were performed at E18.5 embryonic stage. KRT14-Cre(tg/0)/Cdsnwt/wt E18.5 embryos (WT) were used as control. Dorsal skins were harvested after caesarean delivery and were stripped using a Dsquame applicator with D-Squame disk (22 mm diameter) and left on Dermalife medium at 37°C for 4h. Total RNA were then extracted from the total skin. Microarray experiments were performed with RNAs from 4 individuals KO and from 4 individuals WT.


title: Expression data of human melanoma cell lines treated with siRNA targeting SR-BI or with the pharmacologic inhibitor BLT-1

status: Public on Jan 02 2018

city: Wien

first: Katharina

middle: M.

last: Pichler

state: Wien

address: Odoakergasse

department: Department of Orthopedics and Trauma Surgery

country: Austria

institute: Medical University of Vienna

summary:
Melanoma patients with high mRNA levels of the HDL receptor SR-BI (SCARB1) reveal poor survival outcome. The aim of the study was to evaluate the role of SR-BI in cancer progression. Therefore, SR-BI was targeted either by siRNA or by using the SR-BI specific lipid transfer inhibitor BLT-1. The SR-BI knockdown specifically revealed reduced protein glycosylation, STAT5 target gene expression and EMT pathway activation. Thus, SR-BI target genes reflect the metastatic phenotype in melanoma cells.
We used the transcriptome analysis to compare SR-BI depletion to BLT-1 treatment (which specifically blocks SR-BI mediated lipid transfer) in human melanoma cells.

overall_design: Three human metastasizing melanoma cell lines were treated with BLT-1 or SR-BI siRNA. Thereafter total RNA was isolated and an Affymetrix microarray was performed.

last: Kinslechner

first: Mario

last: Mikula


title: An Elongin-Cullin-SOCS-box Complex Regulates Stress-induced Serotonergic Neuromodulation Stress-induced Serotonergic Neuromodulation

status: Public on Nov 01 2017

city: Toronto

first: John

last: Calarco

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: Neuromodulatory cells transduce environmental information into long lasting behavioral responses. However, the mechanisms governing how defined neuronal cell types influence behavioral plasticity are difficult to characterize. Here we adapted the Translating Ribosome Affinity Purification (TRAP) approach in C. elegans to profile ribosome-associated mRNAs from three major tissues and the neuromodulatory dopaminergic and serotonergic cells. We identified elc-2, an Elongin C ortholog, specifically expressed in stress-sensing ADF serotonergic sensory neurons, and found that it plays a role in mediating long-lasting change in serotonin-dependent feeding behavior induced by heat stress. We demonstrate that ELC-2 and the von Hippel-Lindau protein VHL-1, components of an Elongin-Cullin-SOCS-box (ECS) E3 ubiquitin ligase, modulate this behavior after experiencing stress. Also, heat stress induces a transient redistribution of ELC-2, becoming more nuclearly enriched. Together, our results demonstrate dynamic regulation of an E3 ligase, and a role for an ECS complex in neuromodulation and control of lasting behavioral states.

overall_design: RNA-seq data of three tissues and two neuronal subtypes using the Translating Ribosome Affinity Purification Technique in C elegans

first: Xicotencatl

last: Gracida


title: Fenofibrate Prevents Skeletal Muscle Loss in Mice with Lung Cancer

status: Public on Dec 21 2017

city: New York

first: Charles

last: Murphy

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: The cancer anorexia cachexia syndrome is a systemic metabolic disorder characterized by the catabolism of stored nutrients in skeletal muscle and adipose tissue that is particularly prevalent in non-small cell lung cancer (NSCLC). Loss of skeletal muscle results in functional impairments and increased mortality. The aim of the current study was to characterize the changes in systemic metabolism in a genetically engineered mouse model of NSCLC. We show that a portion of these animals develop loss of skeletal muscle, loss of adipose tissue, and increased inflammatory markers mirroring the human cachexia syndrome. Using non-cachexic and fasted animals as controls, we report a unique cachexia metabolite phenotype that includes the               dependent ketone production by the liver. In this setting, glucocorticoid levels rise and correlate with skeletal muscle degradation and hepatic markers of gluconeogenesis. Restoring                                                         prevents the loss of skeletal muscle mass and body weight. These results demonstrate how targeting hepatic metabolism can prevent muscle wasting in lung cancer, and provide evidence for a novel therapeutic strategy.

overall_design: Using an inducible lung cancer model, we characterize the changes in intermediary metabolism that occur during cancer anorexia cachexia syndrome (CACS) in mice. We performed RNA-seq on the livers and gastrocnemius muscle of on non-CACS, CACS, and fasted mice.

first: Marcus

last: Goncalves


title: CoBATCH for high-throughput single-cell epigenomic profiling

status: Public on Jul 15 2019

first: Haiqing

last: Xiong

institute: Peking University

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

overall_design: Refer to individual Series


title: Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations.

status: Public on Oct 17 2017

city: Suita

first: Chiara

last: Furusawa

address: Furuedai

institute: RIKEN Quantitative Biology Center

summary: In adaptive evolution, an increase in fitness to an environment is frequently accompanied by changes in fitness to other environmental conditions, called cross-resistance and sensitivity. Although the networks between fitness changes affect the course of evolution substantially, the mechanisms underlying such fitness changes are yet to be fully elucidated. Herein, we performed high-throughput laboratory evolution of Escherichia coli under various stress conditions using an automated culture system, and quantified how the acquisition of resistance to one stressor alters the resistance to other stressors. We demonstrated that resistance changes could be quantitatively predicted based on changes in the transcriptome of the resistant strains. We also identified several genes and gene functions, for which mutations were commonly fixed in the strains resistant to the same stress, which could partially explain the observed cross-resistance and collateral sensitivity. The integration of transcriptome and genome data enabled us to clarify the bacterial stress resistance mechanisms.

sample_organism: Escherichia coli str. K-12 substr. MDS42

overall_design: To examine the contribution of the gene expression changes to the stress resistances, transcriptome of the parent strain (triplicated) and 55 resistant strains (5 parallel-evolved resistant strains for 11 stresses) were analyzed.

first: Takaaki

last: Horinouchi

first: Shingo

last: Suzuki

first: Kumi

last: Tanabe

first: Chikara


title: Gene expression data from the skin of Cdsn Ko mice


title: The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia

status: Public on Sep 27 2017

city: Boston

first: Eric

last: Severson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital


title: The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia [expression array]

summary: Notch is a major oncogenic driver in T cell acute lymphoblastic leukemia (T-ALL), in part because it binds to an enhancer that increases expression of MYC. Here, we exploit the capacity of activated NOTCH1 and NOTCH3 to induce T-ALL, despite substantial divergence in their intracellular regions, as a means to elucidate a broad, common Notch-dependent oncogenomic program through systematic comparison of the transcriptomes and Notch-bound genomic regulatory elements of NOTCH1- and NOTCH3-dependent T-ALL cells. ChIP-seq studies show a high concordance of functional NOTCH1 and NOTCH3 genomic binding sites that are enriched in binding motifs for RBPJ, the transcription factor that recruits activated Notch to DNA. The interchangeability of NOTCH1 and NOTCH3 was confirmed by rescue of NOTCH1-dependent T-ALL cells with activated NOTCH3 and vice versa.  Despite remarkable overall similarity, there are nuanced differences in chromatin landscapes near critical common Notch target genes, most notably at a Notch-dependent enhancer that regulates MYC, which correlates with responsiveness to Notch pathway inhibitors. Overall, a common oncogenomic program driven by binding of either Notch is sufficient to maintain T-ALL cell growth, whereas cell-context specific differences appear to influence the response of T-ALL cells to Notch inhibition.

overall_design: Examination of the effect of Notch1 and Notch3 activity in two T-ALL cell lines via gene expression and Notch inhibition.

first: Sung

last: Choi

first: Warren

last: Pear

first: Xiaole

last: Liu

first: Jon

last: Aster

first: Stephen

last: Blacklow


title: high temp wt - High temperature Arabidopsis root transcriptome

status: Public on Sep 26 2017

first: Véronique

last: BRUNAUD

institute: INRAE

summary: ngs2015_05_high_temperature_root-high temp wt - characterize changes in root gene expression associated with plant growth at higher temperature - plants were grown at 21°C or 26°C, 16h light (90µE)/8h dark for 10 days before harveting roots.

overall_design: 6 samples with 3 biological replicats. treated vs untreated comparison

first: Dao-xiu

last: Zhou

first: Stephanie

last: Huguet

first: Gregory

last: Vers

first: Ludivine

last: Taconnat-Soubigou


title: Zygotic Genome Activation Occurs Shortly After Fertilization in Maize

status: Public on Sep 05 2017

city: Regensburg

first: Thomas

last: Dresselhaus

address: Universitätsstr. 31

department: Institute of Plant Sciences

institute: Universität Regensburg

summary: Plant material from sperm and egg cells, zygotes 12 and 24 hours after pollination (hap) and apical and basal cells was collected using manual dissection. From these cell types RNA Seq libraries were prepared and gene expression profiles were analysed

overall_design:
Three replicate samples of the cell types: sperm (each 1000 cells) , egg (each 20 cells), zygote 12hap(14,15,15 cells), zygote 24 hap (16,16,17 cells), apical (each 16 cells) and basal (13,13,14 cells) were collected.

Junyi Chen and Nicholas Strieder contributed equally to this work.

first: Junyi

last: Chen

first: Nicholas

last: Strieder

first: Nadia

last: Krohn

first: Philipp

last: Cyprys

first: Stefanie

last: Sprunck

first: Julia

last: Engelmann


title: The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia [ChIP-seq]

first: Eric

last: Severson

overall_design: Examination of the effect of Notch1 and Notch3 activity in T-ALL cell line via dynamic Notch3 binding, and H3K27Ac histone modifications

first: Sung

last: Choi


title: RNA sequencing to compare gene expession in hepatic stellate cells on a soft (400 Pa) and stiff (25000 Pa) polyacrylamide hydrogels

status: Public on Jul 18 2017

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th AVE NE

department: Hormel Institute

institute: University of Minnesota

summary: Primary human hepatic stellate cells (HSCs) isolated from healthy patients were purchased from Sciencell.  They were seeded on either 400 Pa or 25000 Pa polyacrylamide hydrogels for 2 days and collected for RNA isolation.  The goal of this study is to determine genes transcriptionally regulated by a stiff matrix. 2 RNA samples of HSCs on 400 Pa and 3 RNA samples of HSCs on 25600 Pa were sent to the University of Minnesota Genomics Center for RNA sequencing.

overall_design: 2 RNA samples isolated from HSC on 400 Pa stiffness and 3 from HSCs on 25600 Pa stiffness.  They were converted to Illumina sequencing libraries using Illumina’s Truseq Stranded mRNA Sample Preparation Kit.  Truseq libraries were then subjected to cluster using Illumina cBot instrument and sequencing using HiSeq2500

first: Changwei

last: Dou


title: S-adenosylhomocysteine hydrolase participates in DNA methylation inheritance

status: Public on Jul 01 2017

city: Ipswish

first: V K Chaithanya

last: Ponnaluri

state: Massachusetts

address: 240 County Road, 3W031

department: Genome Biology

institute: New England Biolabs

summary: DNA (cytosine-5) methyltransferase 1 (DNMT1) is essential for mammalian development and maintenance of DNA methylation following DNA replication in cells. The DNA methylation process generates S-adenosyl-L-homocysteine, a strong inhibitor of DNMT1. Here we report that S-adenosylhomocysteine hydrolase (SAHH), the only mammalian enzyme capable of hydrolyzing S-adenosyl-L-homocysteine binds to DNMT1 during DNA replication. SAHH activates DNMT1 in vitro and its overexpression in mammalian cells leads to hypermethylation of the genome, whereas its inhibition by adenosine periodate resulted in hypomethylation of the genome. Hypermethylation was consistent in both gene bodies and repetitive DNA elements leading to both down- and up-regulation of genes. Similarly, hypomethylation led to both up- and down-regulation of genes suggesting methylated regions influence gene expression either positively or negatively. Cells overexpressing SAHH specifically up-regulated metabolic pathway genes and down-regulated PPAR and MAPK signaling pathways genes. Therefore, we suggest that alteration of SAHH level in the cell leads to aberrant DNA methylation, altered metabolite levels and gene expression.

overall_design: Examination of two control and two GFP-SAHH overexpressing stable clones

first: V

first: Sriharsa

last: Pradhan


title: Analysis of aerobic and resistance training-induced changes in human vastus lateralis gene expression

status: Public on Jun 30 2016

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

summary: The purpose of this study was to use global gene expression to identify skeletal muscle genes that correlate with exercise-induced Si changes. Longitudinal cohorts from the Studies of Targeted Risk Reduction Intervention through Defined Exercise (STRRIDE) were utilized for vastus lateralis gene expression profiles. Si was determined via intravenous glucose tolerance test pre- and post-training. Pearson product-moment correlation coefficients determined relationships between a) baseline and b) training-induced changes in gene expression and Si after training.

overall_design: Total RNA extracted from human vastus lateralis prior-to and following 8 months of structured aerobic and resistance training

first: Monica

middle: J

last: Hubal

first: William

middle: E

last: Kraus


title: Gene expression profiling in DLBCL primary clinical samples

status: Public on Oct 05 2016

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary: Gene expression profiling was performed for 28 DLBCL primary clinical samples and assignment of activated B-cell-like(ABC)/germinal center B-cell-like (GCB) DLBCL classes, B-cell-associated gene signature (BAGS), and a probability of response to doxorubicin was performed for each sample.

overall_design: 28 DLBCL primary clinical samples for which gene expression was determined with Affymetrix GeneChip HG-U133 Plus 2.0 arrays. Gene expression was normalized together with expression from 34 DLBCL primary clinical samples that have been included in GSE56315.

first: Sara

last: Marques

first: Benyamin

last: Ranjbar

first: Maria

middle: B

last: Laursen

first: Steffen

last: Falgreen

first: Anders

last: Bilgrau

first: Laura

middle: K

last: Jørgensen

middle: N

last: Primo

first: Alexander

last: Schmitz

first: Marianne

last: Ettrup

first: Hans

last: Johnsen

first: Martin

last: Bøgsted

first: Jacob

middle: G

last: Mikkelsen

first: Karen

last: Dybkær


title: Tissue Transcriptome Driven Identification of Epidermal Growth Factor as a Chronic Kidney Disease Biomarker

status: Public on Dec 14 2015

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

summary: We identified EGF as the top candidates predicting kidney function through an intrarenal transcriptome-driven approach, and demonstrated it is an independent risk predictor of CKD progression and can significantly improve prediction of renal outcome by established clinical parameters in diverse populations with CKD from a wide spectrum of causes and stages

overall_design: Chronic Kidney Disease, Lupus nephritis, Focal and Segmental Glomerulosclerosis, Nephropathies, Membranous Glomerulonephritis

first: Wenjun

last: Ju

first: Shahaan

last: Smith

first: Li

last: Zhu

first: Kerby

last: Shedden

first: Peter

last: Song

middle: H

last: Mariani

first: Felix

last: Eichinger

first: Celine

last: Berthier

first: Ann

last: Randolph

first: Jennifer

last: Yi-ChunLai

first: Yan

last: Zhou

last: Hawkins

first: Markus

last: Bitzer

last: Sampson

first: Martina

last: Thier

first: Corinne

last: Solier

first: Gonzalo

last: Duran-Pacheco

first: Guillemette

last: Duchateau-Nguyen

first: Laurent

last: Essioux

first: Brigitte

last: Schott

first: Ivan

last: Formentini

last: Magnone

last: Bobadilla

first: Clemens

last: Cohen

first: Serena

middle: M

last: Bagnasco

last: Barisoni

first: Jicheng

last: Lv

first: Hong

last: Zhang

first: Hai-Yan

last: Wang

first: Frank

last: Brosius

first: Crystal

last: Gadegbeku

first: Matthias

last: Kretzler


title: Methylation analysis of normal and tumor bile duct samples

status: Public on Jul 03 2017

city: Singapore

first: Jing Quan

last: Lim

address: 30 Hospital Boulevard

department: CMR

country: Singapore

institute: National Cancer Centre Singapore

summary: Genome wide DNA methylation profiling of normal and tumor bile duct samples. The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 138 tumor bile duct samples and 4 normal bile duct samples.

overall_design:
Bisulphite converted DNA from the 142 samples were hybridised to the Illumina HumanMethylation450 BeadChip
[April 28, 2025] The fluke-association data (determined to be incorrect) were removed from the Sample records, at the submitter's request.

first: Chern Han

last: Yong

first: Apinya

last: Jusakul


title: CATseq a comparative Arabidopsis Transcriptome - RNA-Seq part

status: Public on Jun 01 2014

city: Gif sur Yvette

first: Véronique

last: BRUNAUD

address: avenue des sciences

summary:
A comparative assessment between both technologies, RNASeq and
microarrays to detect differential expression in Arabidopsis transcriptome.
The sequencing approach use High-throughput sequencing on different Solexa technologies (GAII,HiSeq2000 multiplex or not)
Wild type samples were analyzed from 2 tissus (flower buds and leaves)
which have a very contrasted transcriptomic profile
(i.e very high number of genes differentially expressed).

overall_design: The RNA was extracted from 2 tissus Flower Buds and Leaves from Arabidopsis. The associated GEO series with array part is GSE45345

first: Sandrine

last: Balzergue

first: Eddy

last: Blondet

last: Brunaud

first: Marie-Laure

last: Martin-Magniette

first: Etienne

last: Delannoy


title: Effects of aerobic vs. resistance training on visceral and liver fat stores, liver enzymes, and insulin resistance by HOMA in overweight adults from STRRIDE AT/RT

status: Public on Aug 05 2015

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

summary: The aim of this work was  to compare the effects of AT, RT, and the full combination (AT/RT) on central ectopic fat, liver enzymes, and fasting insulin resistance [homeostatic model assessment (HOMA)]

overall_design:
Pre-training samples reported in this Series.
There are no post training samples - these data are being used as classification data to predict outcome and hence we don't profile post intervention samples.
STRRIDE dataset.

first: William

last: Kraus

middle: A


title: Gene expression profiles of de novo diffuse large B-cell lymphoma samples

status: Public on Dec 31 2019

first: Hanne

last: Due

state: North Region

address: Sdr skovvej 15

department: Department of Hematology

summary:
Gene expression profiling was performed for 21 DLBCL patients. Based on the gene expression profile, each patient was classified into the molecular subclasses: Activated B-cell-like (ABC)/Germinal-center B-cell-like (GCB).
A major clinical challenge of diffuse large B-cell lymphoma (DLBCL) is that up to 40% of patients have refractory disease or relapse after initial response to therapy, due to drug-specific molecular resistance. The purpose of the present study was to investigate microRNA (miRNA) involvement in vincristine resistance in DLBCL which was pursued by functional in vitro analysis in DLBCL cell lines and by clinical analysis of DLBCL patients treated with R-CHOP. MiR-155 was documented to be directly linked to vincristine response in DLBCL cell lines and association between miR-155 and ABC/GCB subclasses and clinical outcome was investigated in primary DLBCL samples.

overall_design: 73 primary DLBCL samples were included in this study. Gene expression profiles were determined with Affymetrix HG-U133 Plus2.0 arrays. Gene expression of the 21 samples was normalized together with expression from 52 DLBCL primary clinical samples that have been included in GSE74266 (n=51) and GSE56315 (n=1).

first: Anna

last: Schönherz

first: Ditte

last: Jespersen

first: Anne

last: Roug

first: Hans

last: Johnsen

first: Martin

last: Bøgsted

first: Karen

last: Dybkær