title: Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

status: Public on Jul 14 2018

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary: The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available. Here we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. The method does not require specialized transgenic strains or growth conditions and can be readily applied with minimal troubleshooting. This new capacity removes a major barrier in the field to dissect gene expression mechanisms in the germ line of C. elegans. Consequent discoveries using this technology will be relevant to conserved regulatory mechanisms across species.

overall_design: This series includes four ChIP-seq samples (IGN-H3K27ac and SOM-H3K27ac and IGN-H3K4me3 and SOM-H3K4me3) and two RNA-seq samples (IGN and SOM) performed in C. elegans. The ChIP-seq experiments were performed in duplicate with matching input for normalization, thus there are 16 ChIP-seq sequencing fastq files (8 ChIP and 8 input). The RNA-seq samples were done in duplicate, yielding two sequence files per sample, thus there are 4 RNA-seq sequencing fastq files. We are also submitting 4 combined normalized wig files for ChIP-seq samples (IGN-H3K27ac and SOM-H3K27ac and IGN-H3K4me3 and SOM-H3K4me3) and 4 bigwig files for RNA-seq (2 replicates of IGN RNA-seq and 2 replicates of SOM RNA-seq). Thus, we are submitting 20 fastq files (consisting of 16 fastq files for ChIP-seq and 4 fastq files for RNA-seq) and 8 wig/bigwig files for the series (consisting of 4 wig files for ChIP-seq and 4 bigwig files for RNA-seq).

first: Mei

last: Han

first: Guifeng

last: Wei

first: Catherine

last: McManus

first: LaDeana

last: Hillier


title: Expression data from Arabidopsis thaliana accessions Col-0, Ts-1 and Ga-0 in response to high light stress

status: Public on Jul 10 2018

city: Duesseldorf

first: Roxanne

last: van Rooijen

address: Universitaetsstrasse 1

country: Netherlands

institute: Heinrich Heine University

summary:
Plants have evolved several mechanisms for sensing increased irradiance, involving signal perception by photoreceptors, and subsequent biochemical and metabolic clues to transmit the signals. This retrograde signaling controls nuclear gene expression.
We used microarrays to detail the gene expression response to increased irradiance in three photosynthetically diverse accesssions of Arabidopsis thaliana.

overall_design: Complete Arabidopsis rosettes of three accessions (Col-0, Ts-1, and Ga-0) were harvest after an irradiance increase from 100 to  550 μmol m-2 s-1 on day 25 after sowing. For all three genotypes, rosettes of nine plants per genotype were harvested on the day of the irradiance increase,  1 hour (1h) after the start of the photoperiod and flash-frozen in liquid nitrogen. For the Col-0 accession, nine rosettes were additionally harvested on the day of the irradiance increase 3.5 hours (3.5h) after the start of the photoperiod, and again one day later, at 1 hour after the start of the photoperiod, so 25 hours (25h) after the irradiance increase.

first: Jeremy

last: Harbinson

first: Mark

middle: M

last: Aarts


title: Gene expression profiles of multiple myeloma plasma cell fractions from bone marrow III

status: Public on Sep 27 2018

city: Aalborg

first: Rasmus

middle: Froberg

last: Brøndum

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg University Hospital

summary: Today’s diagnostic tests for multiple myeloma (MM) reflect the criteria of the updated WHO classification based on biomarkers and clinicopathologic heterogeneity. To that end, we propose a new subtyping of myeloma plasma cells (PC) by B-cell subset associated gene signatures (BAGS), from the normal B-cell hierarchy in the bone marrow (BM). To do this, we combined FACS and GEP data from normal BM samples to generate classifiers by BAGS for the PreBI, PreBII, immature (Im), naïve (N), memory (M) and PC subsets. The resultant tumor assignments in available clinical datasets exhibited similar BAGS subtype frequencies in four cohorts across 1302 individual cases. The prognostic impact of BAGS was analyzed in patients treated with high dose melphalan as first line therapy in three prospective trials: UAMS, HOVON65/GMMG-HD4 and MRC Myeloma IX with Affymetrix U133 plus 2.0 microarray data available from diagnostic myeloma PC samples. The BAGS subtypes were significantly associated with progression free (PFS) and overall survival (OS) (PFS, P=3.05e−06 and OS, P=1.06e−11) in a meta-analysis of 926 pts. The major impact was observed within the PreBII and M subtypes conferred with significant inferior prognosis compared to the Im, N and PC subtypes. Cox proportional hazard meta-analysis documented that the BAGS subtypes added significant and independent prognostic information to the TC classification system and ISS staging. BAGS subtype analysis identified transcriptome differences and a number of novel differentially spliced genes. We have identified hierarchal subtype differences in the myeloma plasma cells, with prognostic impact. This observation support an acquired reversible B-cell trait and phenotypic plasticity as a hallmark, also in MM.

overall_design:
Gene expression profiles of multiple myeloma plasma cell fractions from bone marrow were normalized together with B-cell subsets of PreBI, PreBII, Immature, Naive, Memory and Plasma cells obtained using FACS from mononuclear cells isolated from bone marrow of healthy persons.
Normal bone marrow (BM, n=6) was harvested from healthy volunteers. The normal B-cell subsets were directly phenotyped by multiparametric flow cytometry (MFC) and fluorescence-activated cell sorting (FACS) into six distinct B-cell subsets PreBI, PreBII, immature (Im), naïve (N), memory (M) B-cells, and plasma cells (PC) by a highly selected monoclonal antibody panel.

first: Julie

middle: S

last: Bødker

middle: F

first: Karen

last: Dybkær

first: Martin

last: Bøgsted

first: Hans

middle: E

last: Johnsen


title: Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing

status: Public on Aug 11 2018

city: Fuyang

first: Yong

last: Liu

address: Qinghe West Road

country: China

institute: Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province

type: Expression profiling by high throughput sequencing

summary: Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their genetic transcription. This technology is widely used in medicine, animal husbandry and other industries. However, certain deficiencies, such as the poor developmental ability of reprogrammed nuclear transfer (NT) embryos and the low birth rate (less than 5%) of cloned animals, severely restrict the promotion of this technology. Multiple nuclear reprogramming barriers likely exist in the process of somatic nuclear reprogramming. Furthermore, the NT embryos obtained via this technology have transcriptional defects in embryonic development. To address these problems, in this study, two types of NT embryos were constructed using the same genetic background in mice. We detected the full transcriptome of all stages of NT embryos using single-cell RNA-seq and obtained the following results: 1) NT embryos have translation initiation defects during the minor zygotic genome activation (ZGA) period; NT embryos display RNA processing and RNA modification defects during the major ZGA period, and their protein kinase activity in protein phosphorylation exhibits defects during blastocyst formation; and 2) 2003 constant genes cannot be reprogrammed in cumulus cells (CCs) and mouse embryo fibroblast cells (MEFs); of these constant genes, 399/583 reprogramming barrier genes (RBGs) continue to mis-transcribe from the pronuclear stage to the blastula stage, and the same 136 RBGs are found in both the CCs and MEFs. The main functions of these RBGs is to positively regulate certain factors. In conclusion, our study offers full transcriptome blueprints of all stages of CC donor NT embryos, MEF donor NT embryos and in vivo embryos and reveals new transcriptional defects and reprogramming barriers in nuclear reprogramming. These findings provide insight for further mechanism studies investigating somatic nuclear reprogramming.

overall_design: The transcriptomic analyses of in vivo fertilized embryos, cumulus cell NT embryos and MEF NT embryos were systematically performed. First, the dynamic changes in gene transcription during the entire embryonic developmental process from the pronuclear stage to the blastocyst stage were systematically examined in these three types of embryos separately. Then, the differences in the gene transcripts among these embryos and donor cells were intensively explored.

first: Fengrui

last: Wu

first: Wenyong

last: Li


title: Genome-wide analyses of long non-coding RNA expression profiles and functional network analysis in esophageal squamous cell carcinoma

status: Public on Sep 25 2018

city: Changsha

first: Junliang

last: ma

state: Hunan

address: No. 582 Xianjiahu Road, Yuelu District

department: The 2nd Department of Thoracic Surgery

institute: Hunan Cancer Hospital

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

summary: The aim of this study was tantamount to screen and analyze the differential expression profiles of lncRNAs in ESCC, as well as to analyze the differentially expressed lncRNAs function and related acting molecules to further understand the role of lncRNAs in the occurrence and development of ESCC.

overall_design: Genome-wide expression of lncRNAs and mRNAs was determined in 5 pairs of ESCC and matched normal esophageal tissue using microarray. 6 lncRNAs were detected by qRT-PCR to verify the results of the microarray, and the clinicopathological parameters were analyzed in 53 ESCC patients.

last: Ma

first: Bo

last: Tian

first: Min

last: Su

first: Wenxiang

last: Wang

first: Baihua

last: Zhang

first: Jie

first: Zhining

first: Xu

first: Desong

last: Yang

first: Jinming

last: Tang

last: Zhou


title: Comparison of transcriptome responses to isoxaflutole, quizalofop-p-ethyl and mesotrione in the HepaRG cell line

status: Public on Aug 08 2018

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

summary: We provide here the alterations in gene expression profiles of HepaRG cells, a validated model for cellular steatosis, exposed to three concentration of quizalofop-p-ethyl, isoxaflutole and mesotrione

overall_design: Differentiated HepaRGTM cells (HPR 116) were purchased from Biopredic International. The cells were kept in the general purpose medium until day 8, when the culture becomes well organized and includes well-delineated trabeculae and many canaliculi-like structures. Three concentrations of the different pesticide active ingredients (quizalofop-p-ethyl, isoxaflutole and mesotrione ) were then tested from day 8 to day 14. In order to ensure coverage of a wide range of potential biological effects, three concentrations of each active principle were tested; a concentration representative of low environmental exposure (0.1 uM), an intermediate concentration (10 uM) and a high concentration (1000 uM).

first: Charles

middle: A

last: Mein


title: miRNA profiles for mice hearts with lipopolysaccharide (LPS)-induced cardiac dysfunction

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

summary: To investigate the roles of miRNAs in sepsis-induced cardiac dysfunction, we performed microarray analysis to examine microRNA profiles in mice hearts exposed to LPS versus Saline control.

overall_design: C57BL/6 mice were exposed to LPS (i.p 5 mg/kg) or equal volumes of Saline, and heart samples were harvested 7-9 hr post injection (n=6 per group).

first: Hui

first: Junjie

last: Xiao


title: Next generation sequencing facilities quantitative analysis of KMST6 cells expressing AUG-initiated c-Myc and CUG-initiated c-Myc.

status: Public on Aug 04 2018

city: La Jolla

first: Kuniaki

last: Sato

state: CA

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

country: USA

institute: University of California San Diego

summary: To investigate the differences of transcriptional activities between AUG-initiated c-Myc and CUG-initiated c-Myc , we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq).

overall_design: Total RNA extracted from KMST6 fibroblast cells stably expressing AUG-initiated c-Myc, CUG-initiated c-Myc, and empty vector (negative control) was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by Illumina Hiseq 4000. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the sequencing reads were aligned to the human reference GRCh38 genome using Gencode v27 annotations by STAR. Read counts per gene were quantified using the HTSeq Python package.

first: Takaaki

last: Masuda

first: Koshi

last: Mimori


title: Discovering human diabetes-risk gene function with genetics and physiological assays

status: Public on Jul 01 2018

city: Stanford

first: Heshan

last: Peiris

state: California

address: 279 Campus Drive, Beckman Center B300

institute: Stanford University

summary: To delineate the effects of BCL11A (a type 2 diabetes risk gene) in human beta cell function we knockdown BCL11A in primary human beta cells and generated and sequenced RNA-seq libraries from 4 human donors

overall_design: Examination of the effects of BCL11A knockdown in primary human beta cells

first: Seung

last: Kim


title: Specific modulation of HIV RNA splicing and upregulation of anti-inflammatory miR-124 by the new drug candidate ABX464

status: Public on Jun 22 2018

city: Montpellier

first: Jamal

last: Tazi

address: 1919 Route de Mende

country: France

institute: CNRS

summary:
Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used a high-throughput RNAseq approach. Many genome-wide expression studies of HIV infection are based on analyses of total peripheral blood mononuclear cells (PBMCs), which consist of over a dozen cell subsets, including T cells, B cells, NK cells and monocytes
Methods: The CD4 T cells were uninfected or infected with the YU2 strain and were untreated or treated for 6 days with ABX464, followed by high-throughput RNAseq. Each raw dataset of the samples contained between 44 and 105 million single-end reads (50 bp), with an average of approximately 60 million raw reads per sample
Results: Approximately 98% of the total raw reads were mapped to the human genome sequence (GRCh38), giving an average of 60 million human reads per sample for further analyses. The reads that were correctly mapped (approximately 98% of total input reads) to the gene and transcript locations (GTF annotation file)
Conclusions: The MDS of our gene expression data showed, without any outliers, that the different donors segregated well and distributed into the DMSO (untreated) and ABX464 treatments that were infected or uninfected. The displayed variance was donor-dependent (clustered by donor) but treatment-independent (no data structure related to the different treatments), which suggests that the ABX464 molecule did not induce a major difference in CD4 T cell gene expression.

overall_design: We used purified CD4 T cells from the PBMCs of 4 donors. The CD4 T cells were uninfected or infected with the YU2 strain and were untreated or treated for 6 days, followed by high-throughput RNAseq to generate 32 mRNA profiles.

first: Emeric

last: Dubois

first: Laurent

last: Manchon


title: Oxygen Controls Metabolic Flux and Influences Global Acetylation and Methylation in Human Pluripotent Stem Cells

status: Public on Aug 02 2018

city: Melbourne

first: Jarmon

middle: Gerald

last: Lees

state: Victoria

address: Royal Parade

country: Australia

institute: University of Melbourne

summary: Purpose: The goals of this study are to compare the effects of 5% and 20% oxygen culture on human embryonic stem cells, inlcuding the impact on their transcriptomes.

overall_design: mRNA profiles of two human embryonic stem cell lines (MEL1 and MEL2) cultured long term at 5% and 20% oxygen.

middle: G

first: Timothy

last: Cliff

first: Amanda

last: Gammilonghi

first: James

last: Ryall

first: Stephen

last: Dalton

first: David

middle: K

last: Gardner

first: Alexandra

middle: J

last: Harvey


title: Transcriptomic profile of circulating memory CD4 T cells can differentiate between latent tuberculosis individuals and healthy controls

status: Public on Jun 14 2018

first: Bjoern

last: Peters

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Tuberculosis (TB) is responsible for the majority of mortality and morbidity associated with infectious diseases worldwide. The characterization of exact molecular components of immune response associated with protection against TB may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of memory T cells associated with latent infection with Mycobacterium tuberculosis. Transcriptomic profiling using RNA sequencing was performed on memory CD4 T cells isolated from individuals with latent tuberculosis, as well as from tuberculosis negative healthy controls. Overall, we found specific gene signatures in each cell subset that could successfully discriminate between individuals with latent tuberculosis and healthy controls.

overall_design: RNA-sequencing of sorted memory CD4 T cells from cryopreserved PBMC of 20 subjects with latent tuberculosis infection and 19 tuberculosis negative healthy controls

first: Julie

last: Burel

first: Cecilia

last: Lindenstam

first: Gregory

last: Seumois

first: Zheng

last: Fu

first: Jason

last: Greenbaum

first: Alessandro

last: Sette

first: Pandurangan

last: Vijayanand


title: Next generation sequencing facilities quantitative analysis of negative control HCT116 cells and 5MP1-overexpressed HCT116 cells.

first: Kuniaki

last: Sato

summary: To investigate the downstream targets of eIF5 mimic protein 1 (5MP1), also known as Basic Leucine Zipper and W2 domains 2 (BZW2; Ensembl:ENSG00000136261), we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq).

overall_design: Total RNA extracted from HCT116 cells stably expressing 5MP1 and empty vector-transfected negative control HCT116 cells was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by Illumina Hiseq 4000. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the sequencing reads were aligned to the human reference GRCh38 genome using Gencode v27 annotations by STAR. Read counts per gene were quantified using the HTSeq Python package.

first: Takaaki

last: Masuda

first: Koshi

last: Mimori


title: Gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

status: Public on Jun 09 2018

city: HAMILTON

first: Marie

last: Elliot

state: ON

address: 1280 Main Street West

country: Canada

institute: McMaster University

summary: Comparing gene expression of wild type and lsr2 mutants, to determine the effect of Lsr2 on Streptomyces development and metabolism

overall_design: Two replicates per sample per time point (2 for wild type; two for lsr2 mutant)

first: Emma

last: Gehrke


title: OK-seq profile from cycling (S) phase untreated B cells

status: Public on Aug 01 2018

city: Bethesda

first: Andre

last: Nussenzweig

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

summary: In this study, we map sites of replication initiation and breakage in primary cells at high resolution under conditions of replication stress.  We show that replication initiates between transcribed genes within nucleosome-depleted structures established by long asymmetrical poly(dA:dT) tracts flanking the initiation site. Paradoxically, large (>20 bp) homopolymeric (dA/dT) tracts are also preferential sites of polar replication fork stalling and collapse. We propose that the evolutionary expansion of poly(dA:dT) tracts in eukaryotic genomes serves to promote replication initiation, but at the cost of increasing chromosome fragility.

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

last: Wu

first: Xia

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela

first: Haiqing

first: Chrishtophe

last: Redon

first: Steven

last: Pruitt

first: Yan

last: Jaszczyszyn

first: Mirit

last: Aladjem

first: Peter

last: Aplan

first: Olivier

last: Hyrien


title: ChIP-seq profile of RPA in B upon HU treatment

first: Andre

last: Nussenzweig

type: Genome binding/occupancy profiling by high throughput sequencing

first: Anthony

last: Tubbs

first: Sriram

last: Fu


title: Oncogenic KRAS(G12V) and BRAF(V600E) in intestinal organoids

status: Public on Jun 02 2018

city: Berlin

first: Markus

last: Morkel

address: Charitéplatz 1

department: Dept. of Pathology

country: Germany

institute: Charité - Universitätsmedizin Berlin

summary: Goals of the study was to compare transcripional and phenotypic response of mouse intestinal organoid cultures to the KRAS(G12V) or BRAF(V600E)oncogenes.

overall_design:
Two biological  replicates of organoids with transgenic luc-tdTomato, KRAS(G12V)-tdTomato, BRAF(V600E)-tdTomato were analysed by RNA-Seq
By comparing 7-10 x 10E7 50bp paired end reads per library we identify transcriptional alterations in the intestinal epithelium following expression of each oncogene

first: Pamela

last: Riemer


sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: END-seq profile in B,T, and HCT116 untreated and upon HU treatment.

last: Sridharan

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

first: Xia


title: Stem cell functionality is microenvironmentally defined during tumor expansion and therapy response in colon cancer

status: Public on Jul 18 2018

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine

institute: Academic Medical Center

summary: Solid malignancies have been speculated to depend on cancer stem cells (CSCs) for expansion and relapse after therapy. Here we report on quantitative analyses of lineage tracing data from primary colon cancer xenograft tissue to assess CSC functionality in a human solid malignancy. The temporally obtained clone size distribution data support a model in which stem cell function in established cancers is not intrinsically but entirely spatiotemporally orchestrated. Functional stem cells that drive tumour expansion predominantly reside at the tumour edge, close to cancer-associated fibroblasts (CAFs). Hence, stem cell properties change in time depending on the cell location. Furthermore, although chemotherapy enriches for cells with a CSC phenotype, also in this context functional stem cell properties are fully defined by the microenvironment. To conclude, we identified osteopontin (OPN) as a key CAF-produced factor that drives in situ clonogenicity in colon cancer.

overall_design: RNA-Seq was performed to compare gene expression between the edge and the centre of tumors, derived from human colorectal cancer cell lines grown as PDX in nude mice.

first: Kristiaan

last: Lenos


overall_design: EdU-seq profile in B,untreated and upon HU treatment.

last: Wu

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela

first: Haiqing

first: Chrishtophe

last: Redon

first: Steven

last: Pruitt


title: Insights into transcriptional characteristics and homoeolog expression bias of embryo and endosperm in developing grain through mRNA-Seq and Iso-Seq

status: Public on Aug 14 2018

city: beijing

first: Jun

last: Wei

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology, CAS

institute: Institute of Botany, CAS

summary: To analyse the regulation of transcripts in grain embryo and endosperm during  development, we performed RNA-Seq for wheat from 14 and 25 day post anthesis (DPA). And long-read sequencing for mixed whole grains from 14 and 25 DPA was employed to obtain full-length transcripts. A series of differentially expressed genes and tissues-specific genes of embryo and endosperm were identified. Moreover, 4351, 4641, 4516 and 4453 genes with A, B and D homoeoloci were detected in the four tissues. These provide specific gene pools of embryo and endosperm and homoeolog expression bias model in a large scale, which provides new insights into the molecular physiology of wheat.

overall_design: Wheat (Triticum aestivum L.) cultivar Zhou 8425B were field cultivated. Embryo and endosperm (including episperm and pericarp) at 14 and 25 day post anthesis (DPA) were collected respectively for three biological replicates and immediately frozen in liquid nitrogen. They were then stored at -80°C following RNA extraction. Totals RNAs were extracted from each tissue sample using Plant Total RNA Purification Kit (GMbiolab co., Ltd. Taichung, Taiwan) according to the manufacturer’s protocol. Finally, the twelve RNA librarie sequencing based on Illumina HiSeq 4000 platform by paired-end experiments.

first: Yong

middle: X

last: Liu


title: Transcript expression of microdissected xenografted glioblastomas with and without treatment with Lck-I

status: Public on Jun 01 2018

city: Providence

first: Nikos

last: Tapinos

state: RHODE ISLAND

address: 593 Eddy street

department: Neurosurgery

institute: Brown University

summary: Migration of human glioma stem cells (hGSCs) within the brain parenchyma makes glioblastoma one of the most aggressive and lethal tumors. Studies of the cellular and molecular mechanisms underlying hGSC migration are hindered by the limitations of existing migration models. Here we developed a dorsal root ganglion axon-oligodendrocyte-hGSC co-culture to study in real time the migration and interaction of hGSCs with their microenvironment. hGSCs interact with myelinated and non-myelinated axons through the formation of pseudopodia. Isolation of pseudopodia-localized polysome-bound RNA reveals transcripts of Lck, Paxillin, Crk-II and Rac1 that undergo local translation. Inhibition of Lck blocks the activation of this pathway, the formation of pseudopodia and the migration of hGSCs. In vivo intraventricular administration of a Lck inhibitor using an orthotopic xenograft mouse model results in significant inhibition of tumor growth and significant down-regulation of stemness gene expression. Targeting this Lck pathway constitutes a novel treatment paradigm for human glioblastomas.

overall_design: Human glioma stem cells were orthotopically transplanted in the brain of NU/J mice. Following the cell transplantation, 2 mice were treated with intraventricular delivery of Lck-I for 4 weeks through an ALZET pump, while 3 mice received the diluent (Controls). After 4 weeks of continous treatment the tumors were microdissected and total RNA was isolated to perform RNAseq using Illumina HiSeq 2500.  RESULTS: Continuous local treatment with Lck-I for 4 weeks results in significant downregulation of 743 transcripts in human glioblastomas.


title: MLL1 promotes IL-7 responsiveness and survival during B cell differentiation

status: Public on Jun 30 2018

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: B-lymphocyte differentiation is an exquisitely regulated homeostatic process resulting in continuous production of appropriately selected B cells. Relatively small changes in gene expression can result in deregulation of this process, leading acute lymphocytic leukemia, immune deficiency or autoimmunity. Translocation of Mll1 (Kmt2a) often results in a pro-B cell acute lymphocytic leukemia (B-ALL), but little is known about its role in normal B cell differentiation. Using a Rag1-cre knock-in to selectively delete Mll1 in developing lymphocytes, we show that B-cell, but not T-cell homeostasis depends on MLL1. Mll1-/- B progenitors fail to differentiate efficiently through the pro- to pre-B cell transition, resulting in a persistent reduction in B cell populations. Cells inefficiently transit the pre-B cell receptor (pre-BCR) checkpoint, despite normal to higher levels of pre-BCR components and rearranged IgH expression fails to rescue this differentiation block. Instead of IgH rearrangement defects, we find that Mll1-/- pre-B cells exhibit attenuated RAS/MAPK signaling downstream of the pre-BCR, resulting in reduced survival in physiologic levels of IL-7. Genome-wide expression data illustrate that MLL1 is connected to B-cell differentiation and IL-7-dependent survival through a complex transcriptional network. Overall, our data demonstrate that wild type MLL1 is a regulator of pre-BCR signaling and B-cell differentiation, and further suggest that targeting its function in B-ALL may be more broadly effective than previously anticipated.

overall_design: Pro-B cells (fraction B: PI-/IgM-/CD43+/CD24+/BP-1-) cells were sorted from four control (Mll1F/F) and four Mll1 knockout (Rag1-cre;Mll1F/F) female mice at 3 weeks of age.  RNA samples were labeled  fragmented and hybridized to Mouse 430 2.0 Arrays (Affymetrix) .

first: Tao

last: Gan

first: Bin

last: Li

first: Bibhu

middle: P

last: Mishra

first: Patricia

last: Ernst


title: Gene expression data from control and CG32732 KO virgins

status: Public on Jul 26 2018

city: Heidelberg

first: Marcel

last: Tiebe

state: Germany

address: Humboldtstr., 18

institute: DKFZ Heidelberg

summary:
The aim of the experiment was to identify genes whose transcription is regulated by CG32732 in Drosophila virgin adults.
Data are part of the manuscript Phenotypic characterization of SETD3 knockout Drosophila

overall_design: 2 biological replicates from 2 conditions: control adult virgins , CG32732 KO adult virgins ; overall 4 samples

first: Marilena

last: Lutz

first: Dan

last: Levy

first: Aurelio

last: Teleman


title: Analysis of parent-of-origin bias in gene expression levels

status: Public on Jun 15 2018

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: In order to study parent-of-origin effects on gene expression, we performed RNAseq analysis (100bp single end reads) of 165 children who formed part of mother/father/child trios where genotype data was available from the HapMap and/or 1000 Genomes Projects. Based on phased genotypes at heterozygous SNP positions, we generated allelic counts for expression of the maternal and paternal alleles in each individual. This analysis reveals significant bias in the expression of the parental alleles for dozens of genes, including both previously known and novel imprinted transcripts.

overall_design: This submission contains RNAseq data from 165 children from mother/father/child trios studied as part of the 1000 genomes and/or HapMap projects. We provide raw fastq format reads, and processed read counts per gene. Allelic count information can be provided by directly contacting the authors.

first: Bharati

last: Jadhav


title: Identifying Lsr2 binding sites in Streptomyces venezuelae

first: Marie

last: Elliot

summary: The goal of this work was to determine where Lsr2 binds within the S. venezuelae chromosome, and to differentiate between direct versus indirect effects by comparing our ChIP-seq results with RNA-seq results

overall_design: S. venezuelae ChIP-seq data, generated using an Illumina MiSeq platform

first: Emma

last: Gehrke


title: Studying the genetic heterogeneity in mouse dopamine neurons

status: Public on May 31 2018

city: Berkeley

first: Daniel

last: Kramer

state: Ca

address: 291 Life Sciences Addition #3200

institute: UC Berkeley

summary: Midbrain dopamine neurons project to numerous targets throughout the brain to modulate various behaviors and brain states. Within this small population of neurons exists significant heterogeneity based on physiology, circuitry, and disease susceptibility. Recent studies have shown that dopamine neurons can be subdivided based on gene expression; however, the extent to which genetic markers represent functionally relevant dopaminergic subpopulations has not been fully explored. Here we performed single-cell RNA-sequencing of mouse dopamine neurons and validated studies showing that Neurod6 and Grp are selective markers for dopaminergic subpopulations. Using a combination of multiplex fluorescent in situ hybridization, retrograde labeling, and electrophysiology in mice of both sexes, we defined the anatomy, projection targets, physiological properties, and disease vulnerability of dopamine neurons based on Grp and/or Neurod6 expression. We found that the combinatorial expression of Grp and Neurod6 defines dopaminergic subpopulations with unique features. Grp/Neurod6 dopamine neurons reside in the ventromedial VTA, send projections to the medial shell of the nucleus accumbens, and have noncanonical physiological properties. Grp/Neurod6- DA neurons are found in the VTA as well as in the ventromedial portion of the SNc, where they project selectively to the dorsomedial striatum. Grp-/Neurod6 DA neurons represent a smaller VTA subpopulation, which is preferentially spared in a 6-OHDA model of Parkinson’s disease. Together, our work provides detailed characterization of Neurod6 and Grp expression in the midbrain and generates new insights into how these markers define functionally relevant dopaminergic subpopulations with distinct projection patterns, physiology, and disease vulnerability.

overall_design: We collected a total of 384 neurons from 8 different p26-p34 DAT-Cre::Ai9 mice (6 male 2 female) to isolate DA neurons. RNA was captured from each samples neurons on separate fluidigm chips then all samples were pooled before sequencing.

first: Davide

last: Risso

first: Polina

last: Kosillo

first: John

last: Ngai

first: Helen

last: Bateup


title: Lsr2 binding sites and gene expression of wild type and lsr2 mutants of Streptomyces venezuelae during late development in liquid culture

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

overall_design: Refer to individual Series


title: Functional characterization of NSE4A subunit of SMC5/6 complex in Arabidopsis

status: Public on Jun 06 2018

city: Olomouc - Holice

first: Ales

last: Pecinka

address: Slechtitelu 31

department: Centre of Plant Structural and Functional Genomics

country: Czech Republic

institute: Institute of Experimental Botany

summary: The control of genome integrity throughout cellular generations is critical for plant development and the correct transmission of genetic information to the progeny. A key factor involved in this process is STRUCTURAL MAINTAINANCE OF CHROMOSOME 5/6 (SMC5/6) complex, related to cohesin and condensin complexes. Here, we analyzed mRNA abundance changes in the partial loss of function mutant of NON-SMC ELEMENT 4A (nse4a-2 mutant allele), a subunit of SMC5/6 complex, in Arabidopsis.

overall_design: Arabidopsis Col-0 wild-type and nse4a-2 plants were grown under control and zebularine stress conditions, their shoot apices were dissected and analyzed for mRNA abundances using RNA-sequencing.

first: Anna

last: Nowicka

first: Mariana

last: Díaz


title: The zinc finger transcription factor PQM-1 is a mediator of transcellular chaperone signalling and novel regulator of proteostasis in C. elegans

status: Public on Jun 05 2018

city: Leeds

first: Patricija

last: van Oosten-Hawle

state: Please Select

address: Garstang Building 8.53c

department: Faculty of Biological Sciences, School of Molecular and Cell Biology, Garstang 8.53c

institute: UNIVERSITY OF LEEDS

summary: The goal of this RNA-Seq analysis was to identify genes differentially expressed in a C. elegans strain overexpressing HSP-90 in the neurons compared to control (N2) animals. C. elegans overexpressing HSP-90 protein in the neurons activate transcellular chaperone signalling that enhances organismal proteostasis. This study aimed to identify components of the signalling pathway responsible for this effect.

overall_design: Gene expression profile of L4 C. elegans wild type (N2) animals compared to L4 C. elegans overexpressing HSP-90::GFP in the neurons, using a neuron-specific promoter (F25B3.3p), grown at 20C. 3 replicates of each sample.

last: O'Brien


title: RNA-seq of induced brain microvascular endothelial cells from cerebral childhood adrenoleukodystrophy patients and wild-type controls

status: Public on Apr 01 2018

city: Minneapolis

first: Jakub

last: Tolar

state: MN

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota, Twin Cities

summary: The goal of this study is to compare gene expression differences between induced brain microvascular endothelial cells from cerebral childhood adrenoleukodystrophy patients and wild-type controls

overall_design: iPSCs from three clinically confirmed cases of cerebral childhood adrenoleukodystrophy and three wild-type controls were directed to differentiate into brain microvascular endothelial cells, three replicates were sequenced for each cell line

first: Catherine

last: Lee


title: Ikaros target genes in pre-B cell line

status: Public on May 19 2018

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

summary: We showed that the Ikaros transcription factor is essential for the pre-B cell differentiation. We analyzed the transcriptome of a Ikaros deficient pre-B cell line which was reconstituted with an inducible Ikaros-ER fusion protein. To determine the direct Ikaros targets, we did ChIP-sequencing on chromatin from this pre-B cell line, as cell numbers in mice were too limiting for these studies.

overall_design: A Ikaros deficient pre-B cell line was reconstituted with a Tamoxifen inducible Ikaros-ER fusion protein. 24h after Ikaros induced expression we performed an Ikaros ChIP-Seq analysis.

first: B

last: Heizmann

first: P

last: Kastner

first: S

last: Chan


title: Gene expression analysis of parental and sulfasalazine-resistant human oral squamous carcinoma cell line OSC19

status: Public on May 01 2018

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

country: Japan

institute: Nihon University

summary: To identify the genes involving in the resistance to xCT inhibitors, we established the sulfasalazine-resistant clone of an oral squamous cell carcinoma OSC19 cell line, and the resulting sulfasalazine-resistant cells and its parental cells were subjected to cDNA microarray analysis.

overall_design: To establish the sulfasalazine-resistant clone, OSC19 cells were cultured in increasing doses of sulfasalazine up to 800 mM over two months. Total RNAs were isolated from the sulfasalazine-resistant clone and parental OSC19 cells and subjected to cDNA microarray analysis. 4 replicates were examined on each cell lines.

first: Subaru

last: Shintani

first: Hideyuki

last: Saya

first: Osamu

last: Nagano


title: Targeting EZH2 reprograms intratumoral regulatory T cells to enhance cancer immunity

city: San Francisco

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

summary: Regulatory T cells (Tregs) are critical for maintaining immune homeostasis, but their presence in tumor tissues impairs anti-tumor immunity and portends poor prognoses in cancer patients. Here we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency for the histone H3K27 methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8+ and CD4+ effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a novel strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.

overall_design: Comparison of transcriptomes by RNAseq of Ezh2-deficient Tregs (4 biological replicates) versus WT Tregs (5 biological replicates) 4 days after activation in vitro with anti-CD3/anti-CD28-coated beads in the presence of IL2.

first: David

last: Wang

first: Michel

last: DuPage

first: Jeffrey

last: Bluestone


title: mRNA expression from three human gastric cancer cell lines (MKN1, NUGC4 and AZ521) following either 10ug/ml Pam3Cys-Ser-(Lys)4 and FSL-1 or no treatment.

status: Public on Mar 30 2018

city: melbourne

first: Liang

last: Yu

state: vic

address: 27-33 wright street

department: CIIID

institute: Hudson institute of medical research

summary:
Toll-like receptors (TLRs) are key regulators of innate immune responses, and their dysregulation is observed in numerous inflammation-associated malignancies, including gastric cancer (GC). However, the identity of specific TLRs and their molecular targets which promote the pathogenesis of human GC is ill-defined. Here, we sought to determine the clinical utility of TLR2 in human GC. TLR2 mRNA and protein expression levels were elevated in 50% of GC patient tumors across multiple ethnicities. TLR2 was also widely expressed among human GC cell lines, and DNA microarray-based expression profiling was conducted on RNA from NUGC4 and AZ521 cells either non-stimulated or stimulated with a combination of 10g/ml Pam3Cys-Ser-(Lys)4 and FSL-1.
Only NUGC4 and AZ521 were analyzed for publication.

overall_design: DNA microarray-based expression profiling was conducted on RNA from MKN1, NUGC4 and AZ521 cells either non-stimulated or stimulated with a combination of 10ug/ml Pam3Cys-Ser-(Lys)4 (P3C) and FSL-1. (3 treated and 3 non-treated for both lines)

first: Niantao

last: Deng

first: Brendan

last: Jenkins

first: Patrick

last: Tan


title: Investigation of ctitrinin and pigment biosynthesis mechanisms in Monascus purpureus by transcriptomic analysis

status: Public on May 02 2018

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: M. purpureus YY-1 is widely used in food colorant production in China. In our previous study, the whole-genome information of YY-1 was clearly illustrated, which provided useful hints for evolution  esearch and industrial applications. However, the presence of citrinin, which has nephrotoxic, hepatotoxic, and carcinogenic activities, attracts people′s attention to the safety of Monascus products. In order to reduce the harm of citrinin in Monascus related products, in this study, a random mutant of M. purpureus YY-1, with scarce citrinin production (designated as winter) was obtained. To analyze the biosynthesis and regulation mechanism of pigment and citrinin, transcriptomic analysis of M. purpureus YY-1 and winter was performed. Comparative transcriptomic analysis reveals pksCT, the essential gene for citrinin synthesis, showed low expression level in M. purpureus YY-1 and winter, which suggested there might be isoenzymes in M. purpureus YY-1 that were responsible for the citrinin synthesis during evolution. In addition, the expression change of transcription factors may also influence the regulatory network of citrinin synthesis pathway of in M. purpureus. Moreover, the yields of pigments produced by the winter mutant were significantly increased. Repressing central carbon metabolism and improving the acetyl-CoA pool can contribute to the high yield of pigments, and enhanced NADPH regeneration also lead the metabolic flux to pigments in M. purpureus. Investigations on biosynthesis and regulation of citrinin and pigment production in M purpureus will enhance our knowledge of the mechanisms in fungal secondary metabolite biosynthesis.

overall_design: RNA was extracted from cultures of Monascus purpureus YY-1 and its derivate Winter strain during pigment production

first: Bin

last: Liang

first: Shuo


title: Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation

status: Public on Apr 26 2018

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

institute: Broad Institute


title: Transcriptional profiling of bulk tumor samples from implanted T cell low and T cell high mouse pancreatic tumors

status: Public on Apr 30 2018

first: Jinyang

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary:
Purpose: Use RNA-seq strategy to characterize the differentially expressed genes in T cell low and high mouse pancreatic tumors in order to identify factors contributing to the differential abundance of tumor infiltrating T cells.
Methods: Subcutaneously implanted T cell low and high pancreatic tumors were utilized for the preparation of RNA-seq libraries from both bulk tumors.

overall_design: Examination of differentially expressed genes between two biological groups (T cell low v.s. T cell high tumors).

first: Ben

middle: Z

last: Stanger

first: Robert

middle: H

last: Vonderheide

first: Katelyn

middle: T

last: Byrne


title: Differentially expressed circulating miRNAs during interferon therapy for 48 weeks to reduce HBsAg levels in HBeAg negative chronic hepatitis B patients

status: Public on Mar 31 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: In the current single-armed prospective study, HBeAg negative chronic hepatitis B patients with compensated liver function undertook weekly PEG-IFN subcutaneous injection for 48 weeks. Furthermore, serum miRNAs, extracted from sera taken at 24th week, were analyzed to identify predictive biomarkers for HBsAg reduction.

overall_design: Patients: Consecutive adult patients with HBeAg-negative chronic hepatitis B patients were enrolled in the current study. Additional including criteria were serum HBV-DNA < 4-5 log copies/ml and alanine aminotransferase (ALT) < 100 U/l. Patients who have already been prescribed nucleos(t)ides analogues were also included in the current study. Exclusion criteria were evident cirrhosis, psychiatric diseases, absolute neutrophil count < 1.0×109/l, platelet (Plt) < 50×109/l and a history of alcohol or drug abuse. Written informed consent was obtained from each patient. The study was conducted in accordance with the ethical principal of the Declaration of Helsinki and approved by the ethical committee of Kagawa University, Faculty of Medicine.   Study design: The patients were assigned to the single arm in which 180 μg or 90 μg dose of pegylated interferon α-2a (PEG-IFN) was injected subcutaneously once a week for 48 weeks. All patients were followed up until the 96th week. Sera taken at 24 week were subject to miRNA analyses to identify predicting miRNAs for HBsAg drop at 48 week and 96 week.   Efficacy of treatment: The primary end point was defined as 1 log drop of HBsAg levels comparing to those before the treatment initiation. The secondary end point was defined as declines of serum HBV-DNA levels below 2.1 log copies/ml. The efficacy of 48weeks-treatment was evaluated at 48th and 96th week.

first: Koji

last: Fujita

first: Tsutomu

last: Masaki


title: Plasma small RNASeq comparison with Illumina TruSeq and Biooscientific NextFlex

status: Public on Apr 13 2018

city: Boston

first: SAUMYA

last: Das

address: 185 Cambridge Street

institute: MGH

type: Non-coding RNA profiling by high throughput sequencing

summary: Comparison of small RNA sequencing for 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma

first: Ashish

last: Yeri

first: Kendall

last: Jensen


title: RNA-seq of DRG neurons isolated from alum vs. alum+KLH immunized mice

status: Public on Mar 19 2018

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Purpose: we have performed RNA-seq analysis of sensory neurons isolated from alum vs. alum+KLH immunized mice

overall_design: Pooled DRG neurons from mice (10 mice per group) were subjected to RNA-seq analysis

first: Christine

middle: N

last: Metz


title: Frontal cortex transcriptomic analysis of a TDP-43 Q331K knock-in mouse [20month]

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Here we analyse transcriptome profiles within the frontal cortex between wild type, heterozygous and homozygous TDP-43 Q331K knockin mice at 20 months of age (C57BL/6)

overall_design: Transcriptome (RNA-Seq) from 20 month old frontal cortex tissue

first: Matthew

last: White

first: Jemeen

last: Sreedharan


title: RNA-seq and ATAC-seq profiling of T cell low and T cell high mouse pancreatic tumors

status: Public on Apr 28 2018

last: Li


title: Ribosome profiling reveals changes in translational status of soybean transcripts during immature cotyledon development

status: Public on Mar 23 2018

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: To understand translational capacity on a genome-wide scale across three developmental stages of immature soybean seed cotyledons, ribosome profiling was performed in combination with RNA sequencing and cluster analysis. Transcripts representing 216 unique genes demonstrated a higher level of translational activity in at least one stage by exhibiting higher translational efficiencies (TEs) in which there were relatively more ribosome footprint sequence reads mapping to the transcript than were present in the control total RNA sample. The majority of these transcripts were more translationally active at the early stage of seed development and included 12 unique serine or cysteine proteases and 16 2S albumin and low molecular weight cysteine-rich proteins that may serve as substrates for turnover and mobilization early in seed development. It would appear that the serine proteases and 2S albumins play a vital role in the early stages. In contrast, our investigation of profiles of 19 genes encoding high abundance seed storage proteins, such as glycinins, beta-conglycinins, lectin, and Kunitz trypsin inhibitors, showed that they all had similar patterns in which the TE values started at low levels and increased approximately 2 to 6-fold during development. The highest levels of these seed protein transcripts were found at the mid-developmental stage, whereas the highest ribosome footprint levels of only up to 1.6 TE were found at the late developmental stage.  These experimental findings suggest that the major seed storage protein coding genes are primarily regulated at the transcriptional level during normal soybean cotyledon development. Finally, our analyses also identified a total of 370 unique gene models that showed very low TE values including over 48 genes encoding ribosomal family proteins and 95 gene models that are related to energy and photosynthetic functions, many of which have homology to the chloroplast genome.

overall_design: Construction of ribosome profiling libraries using cotyledons from 3 different developmental stages, with two biological replicates. Data was obtained also from two stages of seed coat development.

first: Md

last: Shamimuzzaman

middle: O


title: Exosomal RNA may reflect placenta deficiencies and provide better biomarker in preterm birth.

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Preterm birth (PTB) is defined as childbirth occurring at less than 37 completed weeks or 259 days of gestation. Premature babies have higher rates of cerebral palsy, sensory deficits, learning disabilities and respiratory illnesses that extend into adulthood. This lifelong morbidity results in high economic and social costs to families and communities. PTB is a syndrome initiated by multiple mechanisms, including infection or inflammation, uteroplacental ischaemia or haemorrhage, uterine overdistension, stress, and other immunologically mediated processes. Identifying and monitoring molecular signals in easily accessible body fluids that can diagnose or predict the risk of preterm labor in pregnant women will reduce or prevent PTBs. A number of studies reported the identification of putative biomarkers for PTB including protein, miRNA and hormone from different body fluids such as serum/plasma, cervical vaginal fluid, saliva and amniotic fluids. These putative biomarkers identified can largely be grouped into three main functional categories: inflammatory related molecules, placenta or fetal derived molecules and stress related molecules. In the past few years next generation sequencing (NGS) has become the major platform for miRNA analysis especially with body fluids. However, studies have shown significant sequence bias among different small RNA library preparation protocols. We have modified the small RNA library construction protocol which greatly reduces the sequence bias and increase miRNA coverage in sample. We also adapted a newly developed size exclusion chromatography (SEC) based EV purification protocol which can provide cleaner EVs compared to other methods. We are using these improved approaches to gain more reliable profile of circulating RNA in body fluid as well as its associated EVs. With these new approaches, we explore the possibility of using specific circulating miRNAs, specifically those encapsulated in EVs, as a noninvasive biomarker for PTB by comparing the miRNA profiles in maternal plasma, EV and EV-depleted plasma between individuals who had a spontaneous preterm birth and uncomplicated pregnancies.

overall_design: Blood samples were collected from women who had spontaneous preterm births between 24-34 weeks (n=20) and matched with respect to gestational age and other variables to pregnant women with normal pregnancy (n=50).

first: Shannon

last: Fallen

first: Taek-Kyun

last: Kim


title: Xenopus andrei RNA-Seq

status: Public on Mar 10 2018

city: Williamsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

department: Biology

institute: College of William and Mary

summary: The Xenopus genus is well known for the high degree of polyploidy observed in its constituent species, but there is minimal information about transcriptional changes observed in these highly polyploid vertebrates. Xenopus andrei, an octoploid species within the Xenopus genus, presents a novel system for assessing a polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through late tailbud stages. Additionally, using Trinity, RNA-seq data from all nine stages was pooled to create a draft de novo assembly of the transcriptome. This represents the first published assembly of an octoploid vertebrate transcriptome. This RNA-Seq and transcriptome data will be useful in comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication in vertebrates.

overall_design: Embryos were obtained from one mating of two adult X. andrei frogs. Nine samples are analyzed, each from a different developmental stage.

first: Mark

last: Pownall

first: Ronald

middle: R

last: Cutler

middle: S


title: Gene expression profiling of human musculoskeletal tissue samples

status: Public on Mar 29 2018

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

summary: We profiled gene expression of purified cell types isolated from 5 musculoskeletal tissues: tendon, bone, muscle, cartilage and ligament. We then performed WGCNA to identify tissue-specific transcription factors, signaling pathways and cell surface receptors. The sequencing data for muscle cells is made available here.

overall_design: 3-4 biological replicates from human samples

first: Gabriel

last: Ferguson

first: Ben

last: Van Handel


title: High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions

status: Public on Mar 15 2018

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

institute: University of Groningen

summary: Streptococcus pneumoniae is an opportunistic human pathogen that typically colonizes the nasopharyngeal passage and causes lethal disease in other host niches such as the lung or the meninges. How pneumococcal genes are expressed and regulated at the different stages of its life cycle, as commensal or as pathogen, has not been entirely described. To chart the transcriptional responses of S. pneumoniae, we quantified the transcriptome under 22 different infection-relevant conditions. The transcriptomic compendium exposed a high level of dynamic expression and, strikingly, all annotated pneumococcal genomic features were expressed in at least one of the studied conditions. By computing the correlation of gene expression of every two genes across all studied conditions, we created a co-expression matrix that provides valuable information on both operon structure and regulatory processes. The co-expression data is highly consistent with well-characterized operons and regulons, such as the PyrR, ComE and ComX regulons, and had allowed us to identify a new member of the competence regulon. Finally, we created an interactive data center (www.veeninglab.com/pneumoexpress) that enables users to access the expression data as well as the co-expression matrix in an intuitive and efficient manner, providing a valuable resource to the pneumococcal research community.

overall_design: 17 conditions of 2 biological replicates, totalling in 34 individual samples

first: Jelle

last: Slager

first: Siger

last: Holsappel

first: Jan-Willem

last: Veening


title: Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana).

city: Irapuato

first: Sergio

middle: F.

last: Nigenda-Morales

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: Unit of Advanced Genomics - National Laboratory of Genomics for Biodiversity

country: Mexico

institute: Center for Research and Advanced Studies

summary: We investigated the gene expression changes associated with skin pigmentation variation between Virginia opossum populations inhabiting tropical and temperate environments. We found that gene expression variation in genes with melanocytic and immune functions is associated with the degree of skin pigmentation variation. Further, we found evidence suggesting that the Wnt/ß-catenin signaling pathway might be regulating the depigmentation observed in temperate populations. We present several alternative hypotheses that may explain Gloger’s rule pattern of skin pigmentation variation in the Virginia opossum.

overall_design: Skin samples from 13 Virginia opossums we collected, eight from tropical populations and five from temperate populations. The mRNA was extracted, sequenced (RNA-Seq) and analyzed.

first: Robert

last: Wayne


title: Global Changes in the Transcriptome of Synechocystis sp. Strain PCC 6803 in Response to Ethylene

status: Public on Mar 09 2018

city: Knoxville

first: Brad

middle: M

last: Binder

state: Tennessee

address: 309 Ken and Blaire Mossman Bldg.

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee

summary: Using RNA sequencing, we report that application of ethylene to Synechocystis sp. alters the transcript levels of over 500 genes

overall_design: Cells were maintained in phototaxing conditions for 4 days in the presence or absence of 1 ppm ethylene prior to RNA extraction and analysis

first: Randy

middle: F

last: Lacey


title: Integrated genetic and epigenetic analysis of myxofibrosarcoma

status: Public on Mar 08 2018

city: Tokyo

first: Koichi

last: Ogura

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center

summary: Myxofibrosarcoma (MFS) is a common adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high local recurrence rate and high propensity for local recurrence. Using 41 MFSs as a discovery set, we underwent whole exome sequencing  (N=41), RNA sequencing (N=29), and methylation analysis (N=41). We subsequently performed targeted sequencing of 140 genes in the entire cohort of 99 MFSs to validate the results in the discovery samples. We also combined 17 MFSs data from TCGA to characterize the molecular features of MFS. Fourteen driver genes were identified, including potentially actionable therapeutic targets seen in 37% of cases. There were frequent alterations in p53 signaling (51%; TP53 and MDM2) and cell cycle checkpoint genes (43%; RB1, CDKN2A/CDKN2B, CDK6, and CCND1) genes. Other conceivably actionable driver genes including ATRX, JAK1, NF1, NTRK1 and novel oncogenic BRAF fusion gene were identified and a novel oncogenic BRAF fusion gene, SLC37A3-BRAF, which could potentially be targeted with BRAF inhibitors, and other conceivably actionable driver genes (ATRX, JAK1, NF1, and NTRK1) were identified. Methylation patterns clustered into three subtypes associated with unique combinations of MFS driver mutations. This cluster was also associated with clinical outcomes, and immune cell compositions. Our results provide a valuable genomic resource to enable the design of precision medicine for MFS. Here, based on these analyses, we identified recurrent driver genes, including novel BRAF fusion gene, and novel methylation clusters associated with unique combinations of driver mutations, clinical outcomes, and immune cell compositions.

overall_design: Bisulphite converted DNA from the 50 samples were hybridised to the Illumina Infinium HumanMethylation450 BeadChip

first: Fumie

last: Hosoda

first: Yasuhito

last: Arai

first: Hiromi

last: Nakamura

first: Natsuko

last: Hama

first: Yasushi

last: Totoki

first: Akihiko

last: Yoshida

first: Momoko

last: Nagai

first: Mamoru

last: Kato

first: Erika

last: Arakawa

first: Wakako

last: Mukai

first: Hirofumi

last: Rokutan

first: Akira

last: Kawai

first: Sakae

last: Tanaka

first: Tatsuhiro

last: Shibata


title: Frontal cortex transcriptomic analysis of a TDP-43 Q331K knock-in mouse [5month]

first: Felix

last: Krueger

summary: Here we analyse transcriptome profiles within the frontal cortex between wild type, heterozygous and homozygous TDP-43 Q331K knock-in mice

overall_design: Transcriptome (RNA-Seq) from 5 month old frontal cortex tissue

first: Matthew

last: White

first: Jemeen

last: Sreedharan


title: Lower motor neuron and Frontal cortex transcriptomic analysis of a TDP-43 Q331K knock-in mouse

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

overall_design: Refer to individual Series


title: Lower motor neuron transcriptomic analysis of a TDP-43 Q331K knock-in mouse

summary: Here we analyse transcriptome profiles from laser captured lower motor neurons between wild type, heterozygous and homozygous TDP-43 Q331K knockin mice

overall_design: Transcriptome (RNA-Seq) from 5 month old laser captured lower motor neurons


title: Viral miRNAs alter cellular miRNAs profiles

city: Chicago

first: Afsar

last: Naqvi

address: 801 S Paulina, Room 561B

department: Periodontics

institute: University of Illinois at Chicago

summary: Prevalence of the members of herpesvirus family in oral inflammatory diseases is increasingly acknowledged suggesting their likely role as etiological factor. However, the underlying mechanisms remains obscure. In our recent miRNA profiling of healthy and diseased human tooth pulpal, elevated expression of HHV encoded v-miRs were identified. Based on the fold induction and significance values, we selected three v-miRs namely miR-K12-3-3p (KSHV), miR-H1 (HSV-1), and miR-UL-70-3p (HCMV) to further examine their impact on host cellular functions. We examined their impact on cellular miRNA profiles of primary human oral keratinocytes (HOK). Our results show differential expression of several host miRNAs in v-miR transfected HOK. High levels of v-miRs were detected in exosomes derived from v-miR transfected HOK as well as the latent KSHV infected cell lines. We show that HOK derived exosomes release their contents into macrophages (Mφ) and alter expression of endogenous miRNAs.

overall_design: Total RNA isolated from v-miRs (miR-H1, miR-K12-3-3p and miR-UL70-3p) or control mimic transfected human oral keratinocytes and primary human macrophages. Microarray ananlysis was performed to assess global changes in miRNA profiles using Exiqon miRCury LNA microarray.

first: Jennifer

last: Shango

first: Alexandra

last: Seal

first: Salvador

last: Nares


title: CpG methylation analysis in Mesial temporal lobe epilepsy and Focal cortical dysplasia patients

city: NEW DELHI

first: APARNA

middle: BANERJEE

last: DIXIT

state: AIIMS

address: Room No 7003, 7th Floor, Convegence Block, AIIMS, ANSARI, NAGAR

department: A collaborative project between NBRC & AIIMS

country: India

institute: NATIONAL BRAIN RESERACH CENTRE

type: Methylation profiling by genome tiling array

summary:
CpG methylation analysis of MeDIP DNA using Agilent Human DNA methylation Microarray slides (G4495A, AMADID 023795)
Using methylated DNA immunoprecipitation microarray (MeDIP-chip) and Agilent Human DNA methylation Microarray slides (G4495A, AMADID 023795) we report genomic methylation signatures of tissues resected from Mesial temporal epilepsy (MTLE) and Focal cortical dysplasia (FCD) type II patients undergoing surgery. Control samples were obtained from the non-epileptic post mortem cases without any brain pathology

overall_design: Tissues resected from 2 autopsy, 4 MTLE and 3 FCD type II were used for isolating Genomic DNA. Genomic DNA was extracted using genomic DNA extraction kit (Qiagen, Hilden, Germany), followed by MeDIP using monoclonal mouse anti 5-methylcytidine antibody.  Both the Input and MeDIP DNA was amplified using GenomePlex Complete Whole Genome Amplification (WGA) kit.  WGA amplified sample (MeDIP-WGA), along with their corresponding whole genomic DNA (input), were labeled usingthe SureTag DNA labeling kit (5190-3400, Agilent)and hybridized to Human DNA methylation Microarray slides (G4495A, AMADID 023795)

first: Aparna

middle: B

last: Dixit

first: Devina

last: Sharma

first: Arpna

last: Srivastava

first: Jyotirmoy

last: Banerjee

first: Debasmita

last: Paul

first: Deepak

last: Prakash

first: Manjari

last: Tripathi

first: P

last: Chandra


title: Genome-wide analysis of gene expression and DNA copy number variations in small cell esophageal carcinoma

status: Public on Mar 02 2018

city: Shanghai

first: Juan

last: Wang

address: No. 135 Guowei Road

institute: Shanghai Jiayin Biotechnology Co., Ltd.

type: Genome variation profiling by genome tiling array


title: RNA-seq of Human neck of femur (NOF) fracture hip and osteoarthritic (OA) cartilage

status: Public on Mar 03 2018

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

institute: Newcastle University


title: Expression data from SCEC and corresponding normal samples

summary:
Primary SCEC is a rare malignancy without established treatment strategy. Although previous studies suggested that there were similarities between SCEC and SCLC in clinical manifestation and pathological morphology, genetic studies on this highly malignant tumour remained sparse.
This study was designed to investigate the gene expression profile of SCEC, and compare it with the known expression data of SCLC and EC.

overall_design: De novo expression array analysis was performed on three pairs of frozen tissues of primary SCEC and corresponding normal samples from institutional tissue bank using the Affymetrix HG U133 plus 2.0 array.After individual normalization, primary tumors were submitted to statistical analysis (GeneSpring GX 12.5) for identifying differentially expressed genes (DEGs) as compared with their paired normal tissues.

first: Di

last: Liu

first: Jia-yan

last: Chen

first: Min

last: Fan


title: Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [scATAC-Seq]

first: Jason

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

summary: Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. Using bulk chromatin accessibility profiles to scaffold our single-cell data analysis, we constructed an epigenomic landscape of human hematopoiesis and characterized epigenomic heterogeneity within phenotypically sorted populations to find epigenomic lineage-bias toward different developmental branches in multipotent stem cell states. We identify and isolate sub-populations within classically-defined granulocyte-macrophage progenitors (GMPs) and use ATAC-seq and RNA-seq to confirm that GMPs are epigenomically and transcriptomically heterogeneous. Furthermore, we identified transcription factors and cis-regulatory elements linked to changes in chromatin accessibility within cellular populations and across a continuous myeloid developmental trajectory, and observe relatively simple TF motif dynamics give rise to a broad diversity of accessibility dynamics at cis-regulatory elements. Overall, this work provides a template for exploration of complex regulatory dynamics in primary human tissues at the ultimate level of granular specificity – the single cell.

overall_design: Profiles of single cell epigenomes, assayed using scATAC-seq, across sorted cell types from CD34+ bone marrow.


title: DBP1 in budding yeast

status: Public on Mar 01 2018

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 CENTER DR Room 230, MSC 0609

institute: NICHD

summary: We analyzed the effect of deleting the gene encoding putative RNA helicase DBP1 in budding yeast on translational efficiencies (TEs) genome wide in wild-type or ded1-ts (temperature-sensitive allele of DED1) strains by combining ribosome footprint profiling with RNA-seq analysis of mRNA abundance.  This study includes a total of 32 samples comprised of 16 RNA-Seq samples (mRNA) and 16 ribosome footprint profiling samples (ribo). Experiment 1 includes 8 samples, comprised of 4 RNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of the dbp1Δ  and ded1-ts dbp1Δ mutant strains, cultured in synthetic complete (SC) medium, following shifts in growth temperature from 30°C to 37°C for 2h.  Experiment 2 examines the effect of overexpression of DBP1 in rescuing genome-wide translational defects of a ded1-cs mutant (cold-sensitive allele of DED1) and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1 (dubbed DED1-CS), ded1-cs and ded1-cs overexpressing DBP1 (ded1-cs_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 15°C for 10 min. Experiment 3 examines rescue of translational defects of ded1-ts by DBP1 overexpression and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1(DED1-TS), ded1-ts and ded1-ts overexpressing DBP1 (ded1-ts_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 37°C for 2h.

overall_design: 32 samples

first: Neelam

middle: D

last: Sen


first: Tomas

last: Kloosterman

address: Nijenborgh 7

department: Natural Sciences

summary:
Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39SM in medium without uracil.
Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae'

overall_design: One condition with two strains (D39 and D39SM), including a dye swap


summary:
Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39SM in medium with uracil.
Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae'


title: Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae


title: Expression profiles in Chd7 knockdown oligodendrocyte precursor cells

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Oligodendrocytes are generated from oligodendrocyte precursor cells (OPCs). Chd7 is ATP-dependent chromatin-remodeling enzyme. We performed microarray analysis to examine changes in gene expression between control and Chd7 knockdown OPCs. Results provide insight into the function of Chd7 in oligodendrocyte development.

overall_design: OPCs derived from E15.5 mouse forebrains were infected with control or Chd7 knockdown retrovirus in the presence of fibroblast growth factor 2 (FGF2) and platelet-derived growth factor AA (PDGF-AA). Three days after infection, the virus-infected OPCs were harvested.

first: Toru

last: Doi

last: Ogata

first: Motoshi

last: Nagao


summary:
Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39PcpsT=>C in medium without uracil.
Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae'

overall_design: One condition with two strains (D39 and D39PcpsT=>C), including a dye swap


summary:
Comparing transcriptome by means of DNA microarrays of Streptococcus pneumoniae D39 versus D39PcpsT=>C in medium with uracil.
Details of this experiment are described in a paper with the title 'Interplay between capsule expression and uracil metabolism in Streptococcus pneumoniae'


title: Human iPS-derived astroglia from a stable neural precursor state; improved functionality compared to conventional astrocytic models

status: Public on Feb 15 2018

city: Stockholm

first: Anders

last: Lundin

address: Retzius väg 8

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Characterization of different astrocytes soruces was done using RNAseq including samples from human primary adult brain, astrocytoma, and hiPSC derived astrocytes including neural stem cell origin

overall_design: Full RNAseq (>200nt) of biological triplicates isolated with Illumina TrueSeq Stranded mRNA LT Sample Prep Kit and sequenced using Illumina NextSeq 500 sequencer

first: Maryam

last: Clausen

first: Ricchiuto

last: Piero

first: José

last: Sanchez

first: Ryan

last: Hicks

first: Anna

last: Herland

last: Falk


title: RNA-Seq analysis comparing gene expression changes between Col-0 wild-type (WT) and sig2-2 mutant lines at the whole genome level

status: Public on Feb 21 2018

city: East Lansing

first: Sookyung

last: Oh

state: MI

address: 612 Wilson Road, Rm. 322

department: Plant Research Laboratories

institute: Michigan State Univ.

summary: To understand the transcriptional role of SIGMA FACTOR 2 (SIG2) in Red (R) light-dependent growth and development, RNA-sequencing analysis was perfomed to compare gene expression in a sig2-2 mutant and Col-0 wild-type seedlings grown in R light at two developmental stages (1-day and 7-day).

overall_design: Total RNA was isolated from 1- or 7-d-old whole seedlings of Col-0 WT and sig2-2 mutant lines, grown in Red-light with three biological replicates. Sequencing samples were prepared using the Illumina TruSeq mRNA prep kit, and RNA-seq was performed by the Research Technology Support Facility at Michigan State University using the Illumina sequencing system.

first: Jin

last: Chen

first: Beronda

middle: L

last: Montgomery


title: Transcriptome profile in INT cells modulated by Cryptosporidium parvum RNA transcripts

city: Omaha

first: Xianming

state: NE

address: 2500 california plaza

institute: creighton university

summary: Cryptosporidium parvum is an important opportunistic parasite pathogen for immunocompromised individuals and a common cause of diarrhea in young children in developing countries. Certain parasite molecules can be delivered into host epithelial cells and may act as effector molecules for parasite intracellular development.  This study aims to measure the impact of transfection of two parasite low-protein coding potential RNA transcripts, cdg2_FLc_0220 and cdg7_FLc_1000, on the transcriptome profile in intestinal epithelial cells. Human intestinal epithelial INT (FHs 74 Int) cells were grown to 80% confluence and transfected with the cdg2_FLc_0220 or cdg7_FLc_1000full-length or the empty vector for 48h. Total RNA was collected for the genome-wide analysis. The Agilent SurePrint G3 Human Gene Expression Microarray (G4851B) was used for the genome-wide analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4851B/G4851B).

overall_design: The FHs 74 Int  were grown to 80% confluence for three groups:  pcDNA3.1(+) empty vector (Group CP-A, cells transfected with pcDNA3.1(+) empty vector), pcDNA3.1(+)_cdg2_FLc_0220 full-length (Group CP-B, cells transfected with pcDNA3.1(+)_cdg2_FLc_0220 full-length ) and pcDNA3.1(+)_cdg7_FLc_1000 full-length (Group CP-C, cells transfected with pcDNA3.1(+)_cdg7_FLc_1000 full-length ). 48h later, total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: Transcriptomic analysis of regulatory gene expression profiles by DELLA and LEC1 during embryo development in Arabidopsis thaliana.

city: guangzhou

first: yilong

last: hu

state: guangdong

address: No.723, xingke road, tianhe district

institute: south china botanical gardern, chinese academy of science

summary: To understand how GA functions in regulating embryo development, a genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of dellaq (rga28 gai rgl1 rgl2) and the wild-type (col-0-2) grown in full-spectrum white fluorescent light at 22°C under long day conditions (16 h light/8 h dark). Then we found that GA regulates embryo development via DELLA-LEC1interaction, a subsequent genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of lec1-4 and the wild-type (col-0-1) in the same growth condition. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in dellaq vs col-0-2, lec1-4 vs Col-0-1 subsets, which are referred to as DELLA and LEC1 regulated genes. These data reveal that DELLAs and LEC1 co-target a set of common genes in late embryogenesis, strongly supporting the role of DELLA-LEC1 in embryo development.

overall_design: RNA-seq analysis profiles of wild-type Col, dellaq, lec1-4 and  9DAF seeds  were generated by deep sequencing, in triplicate.

first: Xingliang

last: Hou

first: Yilong

last: Hu


title: An ErbB2/c-Src axis drives mammary tumorigenesis through metabolically directed translational regulation of Polycomb Repressor Complex 2 [array]

status: Public on Jan 31 2018

city: Montreal

first: Harvey

middle: Wilmore

last: Smith

state: Quebec

address: Life Sciences Complex, Room 602, 1160 Pine Avenue West

department: Goodman Cancer Research Centre

institute: McGill University

summary: Perturbations in histone modifications alter transcription and promote carcinogenesis. Breast cancers frequently overexpress the histone methyltransferase EZH2, the catalytic subunit of Polycomb Repressor Complex 2 (PRC2). However, the mechanisms driving EZH2 overexpression are obscure and elucidating the role of PRC2 in breast cancer, which is highly heterogeneous, is challenging given its context-dependent oncogenic and tumor suppressive functions. Here, using genetically engineered mouse, PDX and cell line models, we show that the tyrosine kinase c-Src links energy sufficiency with PRC2 subunit overexpression via control of mRNA translation. In breast cancers initiated by the oncogene ErbB2, c-Src stimulates mitochondrial ATP production to suppress energy stress and permit sustained activation of the mammalian/mechanistic target of rapamycin complex 1 (mTORC1), which increases the translation of mRNAs encoding the PRC2 subunits Ezh2 and Suz12. We show that Ezh2 overexpression and activity are pivotal in ErbB2-mediated mammary tumorigenesis. These results reveal the hitherto unknown c-Src/mTORC1/PRC2 axis, which is essential for ErbB2-driven carcinogenesis.

overall_design:
We used microarrays to analyze transcriptional responses to c-Src ablation in the resulting c-Src-deficient mammary tumors. ErbB2-expressing tumors from mice without conditional Src alleles (hence expressing normal levels of c-Src) were used as the control.
We extracted total RNA from four control tumors (MMTV-NIC/c-Src+/+) and four c-Src-deficient tumors (MMTV-NIC/c-SrcL/L) of equivalent size and subjected the RNA to Affymetrix microarray analysis.

middle: W

first: William

middle: J

last: Muller


title: The psychiatric risk gene NT5C2 regulates AMPK signalling and protein translation in human neural progenitor cells

status: Public on Jan 26 2018

city: Lodon

first: Deepak

middle: P

last: Srivastava

address: 5 Cutcombe Road

department: Department of Basic & Clinical Neuroscience

institute: King's College London

summary:
Background
The cytosolic 5’-nucleotidase II gene (NT5C2, cN-II) is associated with disorders characterised by psychiatric and psychomotor disturbances. Common psychiatric risk alleles at the NT5C2 locus reduce expression of this gene in the foetal and adult brain, but downstream biological risk mechanisms remain elusive.

Methods
Distribution of the NT5C2 protein in the human DLPFC and cortical human neural progenitor cells (hNPCs) was determined using immunostaining, publicly available expression data, and reverse transcription quantitative PCR (RT-qPCR). Phosphorylation quantification of AMPK-alpha (Thr172) and ribosomal protein S6 (RPS6) (Ser235/Ser236) were performed using western blotting, to infer the degree of activation of AMPK signalling and the rate of protein translation. Knockdowns were induced in hNPCs and Drosophila melanogaster using RNA interference (RNAi). Transcriptomic profiling of hNPCs was performed using microarrays, and motility behaviour was assessed in flies using the climbing assay.

Results
Expression of NT5C2 was higher during neurodevelopment, and was neuronally enriched in the adult human cortex. Knockdown in hNPCs affected AMPK signalling, a major nutrient sensing mechanism involved in energy homeostasis, and protein translation. Transcriptional changes implicated in protein translation were observed in knockdown hNPCs, and expression changes to genes related to AMPK signalling and protein translation were confirmed using RT-qPCR. The knockdown in Drosophila was associated with drastic climbing impairment.

Conclusions
We provide an extensive neurobiological characterisation of the psychiatric risk gene NT5C2, describing its previously unknown role on the regulation of AMPK signalling and protein translation in neural stem cells, and its association with Drosophila melanogaster motility behaviour.

overall_design: The transcriptomic effect of the knockdown of the psychiatric disease susceptibility gene NT5C2 was assessed in the human neural stem cell line CTX0E16. The Trilencer 27-mer NT5C2 siRNA kit (SR307908, Origene) was used to knockdown NT5C2 using the siRNA sequences A (n = 3) and B (n = 4), in parallel with a negative scramble control sequence (SR30004, n = 4). Cells were incubated with the siRNA sequences for 72 hours, followed by RNA/protein extraction. RT-qPCR analysis revealed a significant knockdown of NT5C2 in the samples analysed by microarray. For additional information, see Methods.

first: Rodrigo

last: Duarte

first: Nathaniel

last: Bachtel

first: Marie-Caroline

last: Côtel

first: Sang

middle: H

last: Lee

first: Sashika

last: Selvackadunco

first: Iain

middle: A

last: Watson

first: Gary

last: Hovsepian

first: Claire

last: Troakes

first: Gerome

last: Breen

first: Douglas

last: Nixon

first: Robin

last: Murray

first: Nicholas

last: Bray

first: Ioannis

last: Eleftherianos

first: Anthony

middle: C

last: Vernon

first: Timothy

last: Powell


title: The RFX transcription factor gene, daf-19, has dual funcitons in ciliated and non-ciliated neurons

city: Huddinge

first: Prasad

last: Phirke

address: Hälsovägen 7

summary: Cilia are required for many sensory and motility related functions and are involved in growing number of genetic disorders termed ciliopathies. DAF-19, RFX type transcription factor controls expression of many cilia structure and function related genes. To this end, transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using selectively staged larval stages where cilia mature and maintained, structurally as well as functionally.

overall_design: We used microarray based expression analysis to detail expression control exerted by DAF-19 at various stages of life cycle

first: Elizabeth

last: De Stasio

first: Peter

last: Swoboda


title: MRTF/SRF link the cytoskeleton and hedgehog pathway in drug-resistant basal cell carcinomas

status: Public on Jan 25 2018

city: Stanford

last: Oro

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

institute: Stanford University

summary: We use multi-dimensional genomic analysis using mouse resistant BCCs to identify a non-canonical hedgehog activation pathway driven by the transcription factor, serum response factor (SRF).

overall_design:
RNA and whole exome sequencing of mouse sensitive and resistant basal cell carcinoma tumors.
Additional samples include RNA-seq from ASZ001 resistant BCC cells treated with Vismodegib (Vismo), CCG-1423 (CCG), or vehicle control. Each treatmet contains triplicate samples sequenced using paired-end primers (2X75).

first: Gautam

last: Shankar


title: aCGH data from SCEC and corresponding normal samples

first: Juan

last: Wang

summary:
Primary SCEC is a rare malignancy without established treatment strategy. Although previous studies suggested that there were similarities between SCEC and SCLC in clinical manifestation and pathological morphology, genetic studies on this highly malignant tumour remains sparse.
This study was designed to investigate the copy number variations (CNVs) of SCEC.

overall_design: SCEC vs.corresponding normal samples. Biological replicates: 3 SCEC replicates, 3 control replicates.

first: Di

last: Liu

first: Jia-yan

last: Chen

first: Min

last: Fan


title: Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells

status: Public on Jan 17 2018

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

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

overall_design: Refer to individual Series


title: Expression data from human subsets of PBMC

status: Public on Jan 19 2018

city: Beijing

first: Ning

last: Lu

address: No. 15, Da Tun Road, Chaoyang District

department: Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

summary:
Human PBMC, there are major T, B, Dc, Basophil, Eosinophil and Neutrophil subsets with typical biological functions. The characteristic behavior of each subset was determined by its unique gene expression and regulation. Difference between each subset or different treatment to the same subset will induce huge amount different gene expression. This will provide the basic evidence of understanding why and how each subset cells functions properly.
We used microarrays to detail the global programme of gene expression in each subsets of human PBMC and identified distinctly up-regulated genes during this process.

overall_design:
Each subset of human PBMC was purified by cell sorting through its unique surface markers. After stimulation, total RNA were extracted and applied for hybridization on Affymetrix microarrays. We sought to obtain unique expression profiles of each subset cells. In the mean time, stimuli at each condition regulates the temporal resolution of expression profiles. We found many unique molecules relate to their major biological function of the subsets.
*** Raw data no longer available ***

first: Wei

last: Cao

first: Yui-His

middle: Y

first: Tomoki

middle: T

last: Ito

first: Hanabushi

last: Shino


title: Plant Elongator in light signaling

status: Public on Jan 23 2018

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Elongator is a histone acetyltransferase (HAT) complex associated with RNA polymerase II (RNAPII) to facilitate transcription elongation. It consists of subunits Elp1-6, with Elp3 conferring HAT activity. Elongator is conserved in yeast, plants and humans. In humans, mutations in Elp genes cause neuronal diseases. In plants, Elongator is a positive regulator of cell proliferation during leaf and root growth. Consequently, Arabidopsis Elongator mutants (elo) have narrow leaves and short roots; additionally, germination, vegetative growth and reproductive development are also affected. Mutants have altered auxin signaling, and a number of auxin-related genes are among those differentially expressed in the mutant. Only two genes have been confirmed as targeted by Elongator during RNAPII transcription elongation, including the light-regulated auxin response regulator IAA3/SHY2.

overall_design: Four-day-old darkness-grown Arabidopsis seedlings of the elo3-6 mutant and wild-type (reference sample) were illuminated for 1 hour with red or far-red light or kept in darkness (light treatment control). Each experiment consisted of six samples: two genotypes x three light conditions. Four biological replicates were performed resulting in 24 samples in total. Seedlings were grown on half-strength MS medium without sucrose. Total RNA was isolated using the Qiagen RNeasy Plant Mini Kit with on-column DNase digestion. The manufacturer protocol was followed, except four instead of two RPE washes were performed to improve the A260/A230 ratio in the resulting RNA samples. For microarrays, the Agilent-021169 Arabidopsis platform was used and the analysis was performed according to a loop design. Gene expression levels were compared between the mutant and wild-type seedlings exposed to the same light conditions or between seedlings of the same genotype non-illuminated and illuminated with red or far-red light.

first: Magdalena

last: Woloszynska

first: Steven

last: De Groeve

first: Filip

last: Vandenbussche

first: Dominique

last: Van Der Straeten

first: Mieke

last: Van Lijsebettens


title: High-throughput identification of RNA nuclear localization signals

status: Public on Jan 10 2018

city: Cambridge

first: John

last: Rinn

state: MA

address: 7 Divinity Avenue

department: SCRB

institute: Harvard University

summary: Since the sequencing of the human genome, one of the biggest surprises has been the annotation of thousands of long noncoding RNAs (lncRNAs). Although lncRNAs and mRNAs are similar in many ways, it has become clear they differ in localization properties with lncRNAs being more nuclear enriched and in several cases exclusively nuclear. Yet the RNA based sequences that determine nuclear localization remain poorly understood. Towards the goal of systematically dissecting the lncRNA sequences that impart nuclear enrichment, we developed a massively parallel reporter assay (MPRA). Unlike previous MPRAs that determine motifs important for transcriptional regulation, we have modified this approach to identify sequences sufficient for RNA nuclear enrichment for 38 lncRNAs. Using this approach, we identified 109 distinct, conserved nuclear enrichment regions, originating from 29 distinct lncRNAs. We also discovered two shorter motifs that are enriched in our nuclear enrichment regions—one specific to XIST, and a more general motif found in 21 different lncRNAs. We further validated the autonomous functionality of the XIST motif and three nuclear enrichment regions by single molecule RNA FISH. Taken together, these results give the first glimpse of sequence elements responsible for the nuclear enrichment of this critical class of RNA molecules.

overall_design: Comparison of nuclear localization of different fragments of lncRNA sequences relative to whole cell lysates.

first: Chinmay

last: Shukla

first: Alexandra

last: McCorkindale

first: Chiara

last: Gerhardinger

first: Keegan

last: Korthauer

first: Moran

last: Cabili

first: David

middle: M

last: Schechner

first: Rafael

last: Irizarry

first: Philipp

last: Maass


title: Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions

status: Public on Jan 08 2018

city: West Lafayette

first: Jie

last: Yin

state: Indiana

address: 170 S UNIVERSITY ST

department: Horticulture and Landscape Architecture

institute: Purdue University

summary: Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profil-ing and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome, and 65 of which were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long-chain fatty acid derivatives as compared to SH, whereas sugars are more abun-dant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F1 hybrids than the mid-parent averages and the accumulation of 17% of the metabo-lites in F1 plants transgressed the level in both parents. Concentrations of several metabolites in F1 hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the E. salsugineum genome and newly identified high-quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.

overall_design: Two transcriptomes with 1 replicate per transcriptome. Each transcriptome was obtained from pooled of 5 plant tissue.

first: Michael

last: Gosney

first: Brian

last: Dilkes

middle: V

last: Mickelbart