title: dCas9-based Scn1a gene activation restores inhibitory interneuron excitability and restrains epileptic crises in Dravet syndrome mice

status: Public on Mar 05 2019

city: Milano

first: Luca

last: Massimino

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: Dravet syndrome (DS) is a severe epileptic encephalopathy caused by heterozygous loss-of-function mutations in the SCN1A gene, indicating a haploinsufficient genetic mechanism underlining this pathology. Here, we tested whether dCas9-mediated Scn1a gene activation could rescue Scn1a haploinsufficiency and restore physiological levels of its gene product, the Nav1.1 voltage-gated sodium channel. We screeened sgRNAs for their ability to stimulate Scn1a gene transcription in association with the dCas9 activation system. Interestingly, we identified one single sgRNA able to significantly increase Scn1a gene expression levels in cell lines as well as in primary neurons, with high specificity. Accordingly, levels of Nav1.1 protein were sufficiently augmented to potentiate firing ability of wild-type immature GABAergic interneurons. A similar effect in activating the Scn1a transcription was elicited in Dravet GABAergic interneurons rescuing their dysfunctional properties. To determine whether this approach could have therapeutic effect, we packaged adeno-associated viruses with the Scn1a-dCas9 activation system and showed their ability to ameliorate the febrile epileptic crises in DS mice. Our results pave the way for exploiting the dCas9-based gene activation as an effective and targeted approach to DS and other similar disorders resulting from altered gene dosage.

overall_design: 3 neuronal cultures overexpressing Scn1a sgRNA, and 3 control cultures

first: Gaia

last: Colasante

first: Vania

last: Broccoli


title: TNF-alpha-stimulated human umblical vein endothelial cells (HUVECs)

status: Public on Apr 11 2019

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome-wide effect profile of HuR inhibitor KH-3

status: Public on Apr 05 2019

city: Lawrence

first: Liang

last: Xu

state: KS

address: 1567 Irving Hill Rd 3177 ISB

country: USA

institute: University of Kansas

summary: The purpose of this study is to generate mRNA effect profle of KH-3, an inhibitor of RNA-binding protein HuR, in human breast cancer cell line MDA-MB-231 cells by RNA sequencing. Total RNA from cells treated with DMSO or KH-3 was collected for library prepareation and deep sequencing, in duplicate, using Illumina Hiseq 2500 system.  About 30 million sequence reads per sample were mapped against the transcript databases annotated in GENCODE v24 using STAR default parameters. The read counts for each transcript were calculated using eXpress. The differentially expressed transcripts were detected using DESeq2 with a q-value cutoff of 0.05.

overall_design: mRNA effect profile of KH-3 in MDA-MB-231 cells was generated by RNA-seq, in duplicate, using Illumina Hiseq 2500 system.

first: Xiaoqing

last: Wu


title: H2A.Z is dispensable for both basal and activated transcription in post-mitotic mouse muscles

status: Public on Mar 08 2019

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: While the histone variant H2A.Z is known to be required for mitosis, it is also enriched in nucleosomes surrounding the transcription start site of active promoters, implicating H2A.Z in transcription. However, evidence obtained so far mainly rely on correlational data generated in actively dividing cells. We have exploited a paradigm in which transcription is uncoupled from the cell cycle by developing an in vivo system to inactivate H2A.Z in terminally differentiated post-mitotic muscle cells. ChIP-seq, RNA-seq and ATAC-seq experiments performed on H2A.Z KO post-mitotic muscle cells show that this histone variant is neither required to maintain nor to activate transcription. Altogether, this study provides in vivo evidence that in the absence of mitosis H2A.Z is dispensable for transcription and that the enrichment of H2A.Z on active promoters is a marker but not an active driver of transcription.


title: Dynamics of gene expression in single root cells of A. thaliana

status: Public on Mar 29 2019

city: Seattle

first: Christine

last: Queitsch

state: WA

address: 3720 15th Ave NE, Foege Hall

department: Genome Sciences

institute: University of Washington

summary: Here, we apply this approach to A. thaliana root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single-cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution

overall_design:
Single-cell RNA-seq experiments were performed on protoplast cells extracted from the whole roots of 7-8 day old Arabidopsis thanliana seedlings. Plants were grown under control conditions at 22C. Plants were moved from 22C to 38C for 45 min to be heatshocked.
Please note that the 'whole_root_Control_2' data was aggregated with the 'whole_root_Heatshock data' for comparative analysis.

first: Joshua

last: Cuperus


title: RNA immunoprecipitation (RIP) followed by microarray for identification of miRNA-target genes in human umblical vein endothelial cells (HUVECs).

summary: Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are mostly linked to gene repression. However, functions of repressive histone methylation dynamics during inflammatory responses remain poorly understood. Here, we show that lysine demethylase 7A (KDM7A) and 6A (UTX) are rapidly transported to nuclear factor kappa-B (NF-κB) related elements in human endothelial cells in response to tumor necrosis factor (TNF)-α. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and cooperatively activate NF-κB dependent inflammatory genes. Furthermore, using both in situ Hi-C and other 3C based technology, loops between super enhancers (SEs) are newly formed following TNF-α-stimuli at NF-κB-dependent inflammatory loci where KDM7A- and UTX-recruitment coincide. Collectively, these findings suggest that erasing of repressive histone marks by KDM7A and UTX within NF-κB-related elements might functionally associate with formation of SE-SE three-dimensional interactions and could be a cue signal during inflammatory responses in human endothelial cells.

overall_design: Total 4 samples were derived from HUVECs in the presence of TNF-alpha (4 hrs) with or without miRNA mimics to identify miRNA-target genes.

first: Yasuharu

last: Kanki


title: Gene knockdown in malaria parasites via non-canonical RNAi

status: Public on Feb 22 2019

city: Nijmegen

first: Sabine

last: Fraschka

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen

summary: To introduce a non-canonical RNA interference pathway into Plasmodium berghei (P. berghei), we generated a P. berghei line constitutively expressing the human protein Argonaute 2 (Ago2) and episomally expressed Ago2-dependent short hairpin RNAs (AgoshRNAs) against GFP. Using RNA sequencing (RNA-Seq), we analyzed transcriptomes of wild type parasites (PbGFPcon), Ago2-expressing parasites (PbAgo2) and PbAgo2 parasites expressing a scrambled AgoshRNA (scr) or anti-GFP-AgoshRNA (aGFP). We compared PbAgo2 to wildtype PbGFPcon parasites and find that Ago2 expression interferes with the expression of development-of-zygote-inhibited (DOZI)-dependent transcripts. When comparing PbAgo2 plus scr with PbAgo2 expressing aGFP, we find a clear knockdown of GFP; Other than that, we do not observe a significant off-targeting in these samples besides differential expression of genes belonging to multi-gene families.

overall_design: For PbGFPcon, two independently prepared technical replicates were analyzed. For all other samples (PbAgo2, PbAgo2 + scr, PbAgo2 + aGFP) two biological replicates resulting from independent transfections were analyzed.

first: Franziska

last: Hentzschel

first: Richard

last: Bartfái

first: Ann-Kristin

last: Mueller

first: Dirk

last: Grimm


title: Mutations in RABL3 Alter KRAS Prenylation and are Associated with Hereditary Pancreatic Cancer

status: Public on Mar 30 2019

city: Boston

first: Sahar

last: Nissim

state: MA

address: 77 Ave Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with limited treatment options. Familial predisposition to PDAC occurs in ~10% of cases, but causative genes have not been identified in most families. Uncovering the genetic basis for PDAC susceptibility has immediate prognostic implications for families and can provide mechanistic clues to PDAC pathogenesis. Here, we perform whole-genome sequence analysis in a family with multiple cases of PDAC and identify a germline nonsense mutation in the member of RAS oncogene family-like 3 (RABL3) gene never before directly associated with hereditary cancer. The truncated mutant allele (RABL3_p.S36*) co-segregates with cancer occurrence. To evaluate the contribution of the RABL3 mutant allele in hereditary cancer, we generated rabl3 heterozygous mutant zebrafish and found increased susceptibility to cancer formation in two independent cancer models. Unbiased approaches implicate RABL3 in RAS pathway regulation: the transcriptome of juvenile rabl3 mutants reveals a KRAS upregulation signature, and affinity-purification mass spectrometry for proteins associated with RABL3 or RABL3_p.S36* identifies Rap1 GTPase-GDP Dissociation Stimulator 1 (RAP1GDS1, SmgGDS), a chaperone that regulates prenylation of RAS GTPases. Indeed, we find that RABL3_p.S36* accelerates KRAS prenylation and requires RAS proteins to promote cell proliferation. Furthermore, rabl3 homozygous mutant zebrafish develop severe craniofacial, skeletal, and growth defects consistent with human RASopathies, and these defects are partially rescued with the MEK inhibitor trametinib. Finally, we identify additional germline mutations in RABL3 that impact RAS activity in vivo and have a significant burden in a cohort of patients with developmental disorders, suggesting a role in undiagnosed RASopathies. Moreover, RABL3 is upregulated in multiple human PDAC cell lines and knockdown abrogates proliferation, consistent with a broader role for RABL3 in PDAC. Our studies identify the RABL3 mutation as a new target for genetic testing in cancer families and uncover a novel mechanism for dysregulated RAS activity in development and cancer.

overall_design: WT (4 replicates) and homozygous rabl3-TR41 mutant (3 replicates) larval zebrafish at 21 days of age.

first: Yariv

last: Houvras

first: Wolfram

last: Goessling


title: Differential gene expression in postnatal day 10 Scn1b+/+ vs. Scn1b -/- cortical layer VI

status: Public on Mar 21 2019

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Scn1b null mice are a model of a severe developmental and epileptic encephalopathy called Dravet Syndrome (DS). The goal of this study was to identify changes in gene expression between Scn1b wild-type and Scn1b null mice before seizure onset (postnatal day 10) in cortical layer VI, a region known to have differences in excitability in Scn1b null mice. RNA-Seq identified 21 genes, primarily extracellular matrix genes, which were differentially expressed between the two genotypes.

overall_design: RNA-Seq in postnatal day 10 Scn1b+/+ vs. Scn1b -/- cortical layer 6

first: Lori

last: Isom

first: Alexandra

last: Bouza

first: Rebecca

last: Tagett


title: Nitro-fatty acids protect against steatosis and fibrosis during development of nonalcoholic fatty liver disease in mice

status: Public on Feb 08 2019

summary: Lack of non-invasive diagnostic tools and effective therapies constitute two of the major hurdles for a bona fide treatment against non-alcoholic steatohepatitis (NASH) progression and/or regression of nonalcoholic fatty liver disease (NAFLD). Nitro-oleic acid (OA-NO2) has been proven effective in multiple experimental models of inflammation and fibrosis. Thus, the potential benefit of in vivo administration of OA-NO2 to treat advanced NAFLD was studied in a model of long-term NASH diet-induced liver damage. Non-invasive imaging (e.g. photoacustic-ultrasound (PA-US)) was pursued to establish advanced experimental NASH in mice in which both steatosis and fibrosis were diagnosed prior experimental OA-NO2 therapy. CLAMS and NMR-based analysis demonstrates that OA-NO2 improves body composition and energy metabolism and inhibits hepatic triglyceride accumulation. PA-US imaging revealed a robust inhibition of liver steatosis and fibrosis by OA-NO2. RNA-sequencing analysis uncovered inflammation and fibrosis as major pathways suppressed by OA-NO2 administration, as well as regulation of lipogenesis and lipolysis pathways, with a robust inhibition of SREBP1-dependent lipogenic gene expression by OA-NO2. Global liver transcriptome in response to OA-NO2 was confirmed in vivo and in isolated hepatocytes. These results were further supported by histological analysis and quantification of lipid accumulation, lobular inflammation (F4/80 staining) and fibrosis (collagen deposition, αSMA staining) as well as established parameters of liver damage (ALT). In vitro studies indicate that OA-NO2 inhibits TG biosynthesis and accumulation in hepatocytes and inhibits fibrogenesis in human stellate cells. Taken together, OA-NO2 improve steatohepatitis and fibrosis and may constitute an effective therapeutic approach against advanced NAFLD that warrants further clinical evaluation.

overall_design: C57BL/6J mice were fed standard chow diet (CD) or NASH-diet rich in saturated fat, trans-fat, fructose and cholesterol (40% of calories from fat, Research Diets D17010103) for 24 weeks. All mice were maintained on a 12-hour light/dark cycle and had ad libitum access to food and water. Mice were subjected to subcutaneous implantation of osmotic minipumps for delivery of polyethylenglycol (PEG), PEG-solvated oleic acid (OA),  or PEG-solvated OA-NO2 at an infusion rate of 5 mg/kg/day.

first: Luis

last: Villacorta

first: Oren

last: Rom

first: Eugene

last: Chen

first: Seongho

last: Kim

first: Zhipeng

last: Liu

first: Wanqing


title: A familial Alzheimer’s disease-like mutation in the zebrafish presenilin 1 gene affects brain energy production

status: Public on Feb 06 2019

city: Adelaide

first: Nhi

last: Hin

address: North Terrace

country: Australia

institute: University of Adelaide

summary:
To prevent or ameliorate Alzheimer’s disease (AD) requires that we understand its molecular basis. AD develops over decades but detailed molecular analysis of AD brains is limited to postmortem tissue where the stresses initiating the disease may be obscured by compensatory responses and neurodegenerative processes. Rare, dominant mutations in a small number of genes drive early onset of familial AD (EOfAD). Numerous transgenic models of AD have been constructed in mouse and other organisms based on these mutant genes, but transcriptomic analysis of these models has raised serious doubts regarding their representation of the disease state. Objective: In the absence of an understanding of the molecular mechanism(s) underlying AD, we posit that the most valid approach is to model the human genetic state as closely as possible – i.e. to analyse single, heterozygous EOfAD-like mutations of endogenous genes in intact brains.
We used genome editing to introduce an EOfAD-like mutation (Q96_K97del) into the endogenous presenilin 1 (psen1) gene of zebrafish. We analysed transcriptomes of young adult (6-month-old) entire brains from a family of heterozygous mutant and wild type sibling fish. Gene ontology (GO) analysis revealed effects on mitochondria, particularly ATP synthesis, and on ATP-dependent processes including vacuolar acidification.

overall_design:
We generated a family of heterozygous mutant (Q96K97/+ at psen1) and wild type (+/+) sibling zebrafish by mating a psen1Q96K97del/+ individual with a +/+ individual and raising the progeny from a single spawning event together in one tank. Since AD is more prevalent in human females than males, and to further reduce gene expression “noise” in our analyses, we obtained brain transcriptome data from four female wild type fish and four female heterozygous mutant fish.

Note: While the results in the associated publication are based on these 6-month-old samples only, the differential gene expression analyses also used additional samples from the same batch (see GSE149149) to obtain more accurate variance estimates.

first: Morgan

last: Newman

first: Stephen

last: Pederson

first: Michael

last: Lardelli


title: small RNA profiling of human blood derived macrophages upon infection with Legionella Pneumophila

status: Public on Jan 25 2019

city: Berlin

first: Brian

last: Caffrey

state: Germany

address: Ihnestrasse 63-73

department: Computational Molecular Biology

country: Germany

institute: Max Planck Institute for Molecular Genetics

type: Non-coding RNA profiling by high throughput sequencing

summary: Legionella pneumophila (corby) infected blood derived macrophages are infected in a time course experiment (24& 48hours)

overall_design: Infection of BDMs with L.p. over two time points

first: Annalisa

last: Marsico

middle: E


title: Colistin resistant A. baumannii: genomic and transcriptomic traits acquired under colistin therapy

status: Public on Jan 23 2019

city: Catania

first: Viviana

last: Cafiso

state: Italy

address: Via Santa Sofia,97

department: Biometec

institute: University of Catania

summary: Comparative Genomic and Transcriptomic Characterization of Colistin-Resistant Acinetobacter baumannii

overall_design: Two Italian XDR colistin-susceptible/resistant (COL-S/R) strain pairs were investigated. The genomic and transcriptomic characterization of colistin resistance mechanism were carried out using high-throughput-sequence-technologies (Illumina Mi-seq) and transcript analysis.

first: Stefano

last: Stracquadanio

first: Flavia

last: Lo Verde

first: Giacoma

last: Gabriele

first: Maria-Lina

last: Mezzatesta

first: Carla

last: Caio

first: Giuseppe

last: Pigola

first: Alfredo

last: Ferro

first: Stefania

last: Stefani


title: Modeling germline mutations in pineoblastoma uncovers lysosome disruption-based therapy

status: Public on Jan 31 2019

city: TORONTO

first: Eldad

last: Zacksenhaus

state: ON

address: 67 College St.

country: Canada

institute: University of Toronto

summary: Transcriptome analysis of mRNA samples from Rb/p53-deficient mouse pineoblastomas

overall_design: We anlayzed 12 Rb/p53-deleted mouse pineoblastoma, 5 Rb/p53-mutated pineoblastoam, 3 Dicer1/p53-deleted pineoblastoma, 3 Rb/Dicer1/p53-deleted pineoblastoma and 3 normal mouse cerebellum using Affymetrix Mouse Gene 1.0 ST Array and Affymetrix Mouse Gene 2.0 ST Array

first: Philip

last: Chung


title: Transcriptomic de novo analysis of pitaya (Hylocereus polyrhizus) canker disease caused by Neoscytalidium dimidiatum

status: Public on Jan 17 2019

city: Haikou

first: Min

last: Xu

address: No.58 Renmin Avenue,Haikou, Hainan, China

country: China

institute: Hainan University

summary: Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8, was isolated from the wild-type red-fleshed pitaya (Hylocereus polyrhizus) of Hainan Province. Here, we studied mainly the host responses of red-fleshed pitaya (H. polyrhizus) cultivars against N. dimidiatum using Illumina RNA-Seq technology.

overall_design: Healthy and diseased stem tissues of red-fleshed pitaya (H. polyrhizus) were collected in the orchard of Ledong County, Hainan Province. They had been growing for about five years in a plantation under natural conditions. The collected stem tissues were divided into two groups with similar characteristics in triplicate within each group. The stems were cut into pieces and immediately frozen in liquid nitrogen. The three replicates of the normal group were named N1, N2, and N3, whereas the three replicates of the diseased group were named D1, D2, and D3. Three biological replicates, each consisting of four stem cutting bases, were frozen in liquid nitrogen and stored at -80 °C until further analysis. Sample tissues were entrusted to Shenzhen BGI Tech Company (Shenzhen, China) for transcriptome de novo assembly and sequencing using an Illumina HiSeq system. This represents D1, D3, N2, and N3 only.

first: Cheng-Li

last: Liu

first: Juan

last: Luo

first: Zhao

last: Qi

first: Zhen

last: Yan

first: Yu

last: Fu

first: Shuang-Shuang

last: Wei

first: Hua

last: Tang


title: FET fusion oncoprotein-regulated genes in HT1080 cell line

status: Public on Mar 12 2019

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

summary: Some specific sarcomas and leukemias are defined by characteristic FET (FUS, EWSR1, TAF15) fusion oncogenes. Myxoid liposarcoma and Ewing sarcoma are the most common entities characterized by FUS-DDIT3 and EWSR1-FLI1, respectively. Here, we performed whole transcriptome analysis of HT1080 cells with either ectopic FUS-DDIT3 or ectopic EWSR1-FLI1 expression.

overall_design: Four different variants of HT1080 fibrosarcoma cells were analyzed using RNA sequencing: native HT1080 cells, HT1080 cells expressing EGFP, HT1080 cells expressing FUS-DDIT3-EGFP and HT1080 cells expressing EWSR1-FLI1-EGPF were analyzed (n = 3 -4).

first: Pierre

last: Åman

first: Anders

last: Ståhlberg


title: Lipopolysaccharide inhalation recruits monocytes and dendritic cell subsets DC2,3 and DC5 to the alveolar airspace

status: Public on Feb 23 2019

city: Newcastle

first: Laura

last: Jardine

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

summary:
Using lipopolysaccharide inhalation to induce acute inflammation in healthy volunteers and examine the impact on bronchoalveolar lavage (BAL) fluid and blood MP repertoire.
This study defines the characteristics of human DCs and monocytes recruited into bronchoalveolar space immediately following localised acute inflammatory stimulus in vivo.

overall_design: 54 samples were analyzed in total, including 23 LPS BAL samples across 6 cell types, 14 Saline solution controls across 4 cell types and 17 healthy control blood samples across 6 cell types.

first: Sarah

last: Wiscombe

first: Gary

last: Reynolds

first: David

last: McDonald

first: Andrew

last: Fuller

first: Kile

last: Green

last: Filby

first: Ian

last: Forrest

first: Marie

middle: H

last: Ruchaud-Sparagano

first: Jonathan

last: Scott

first: Matthew

last: Collin

first: Muzlifah

last: Haniffa

first: John

middle: A

last: Simpson


title: PAX5-KIDINS220 gene expression array in Ba/F3 cells

status: Public on Mar 01 2019

city: Kyoto

first: Takuyo

last: Kanayama

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Pediatrics

institute: Kyoto Prefectural University of Medicine

summary: PAX5-KIDINS220 (PAX5-K220) is a novel chimeric fusion gene identified in a pediatric Philadelphia chromosome (Ph)-like acute lymphoblastic leukemia (ALL) patient, but the function of the encoded fusion protein has not yet been analyzed.We successfully generated PAX5-K220 expressing cells and demonstrate that PAX5-K220 is a nuclear protein. In addition, PAX5-K220 activates JAK2-STAT5 pathway through the repression of Socs5, a known negative regulator of JAK-STAT pathway. However, although identified in Ph-like ALL, PAX5-K220 does not induce IL-3-independent proliferation when transduced in the IL-3-dependent Ba/F3 murine leukemia cells, but rather attenuates growth. Luciferase reporter assay reveals that PAX5-K220 inhibits wild type PAX5 transcriptional activity in a dominant-negative fashion like other PAX5-related fusion proteins, and may contribute to lymphocyte differentiation block. These results reveal that PAX5-K220 certainly shares the character with other PAX5-related fusion proteins rather than other fusion proteins with tyrosine kinase activity identified in Ph-like ALL, and did not contribute to proliferation activity.

overall_design: To reveal which pathways were affected by PAX5-KISINS220 (P-K220), Ba/F3 cells transduced with P-K220 fusion protein by the Retro-X Tet-on Advanced Inducible System (Clontech) were cultured with or without 500 ng/mL doxycycline (in other words, with or without expression of P-K220), and 24 hours later, total RNA were extracted from Ba/F3 with or without expression of P-K220.

first: Toshihiko

last: Imamura

first: Azusa

last: Mayumi

first: Emi

last: Soma

first: Kenichi

last: Sakamoto

first: Fumihiko

last: Hayakawa

first: Akihiko

last: Tanizawa

first: Nobutaka

last: Kiyokawa

first: Hajime

last: Hosoi


title: CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [ChIP-Seq]

status: Public on Mar 18 2019

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

summary: Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here we mapped active chromatin landscapes with gene expression, whole-exomes, copy number profiles, and DNA methylomes across 44 glioblastoma stem cell (GSCs) models, 50 primary glioblastomas, and 10 neural stem cells (NSCs) with the goal of identifying essential super enhancer (SE)-associated genes and the core transcription factors that establish them and glioblastoma identity. Glioblastomas segregate with two dominant enhancer profiles that coopt unique developmental transcription factor regulatory programs to enforce tumor identity. From group specific enhancer profiles, we inferred core transcription factors that define subgroup identity. These transcription factors show higher activity in glioblastomas versus normal neural stem cells, are associated with poor clinical outcomes, and are required for glioblastoma growth in vitro and in vivo. Given challenges with genetically-defined targeted therapies for glioblastoma, we propose targeting underlying transcriptional identity may serve as an important therapeutic strategy.

overall_design:
Dataset consists of active chromatin profiles as measured by H3K27 acetylation ChIP-seq analysis on glioblastoma primary tissue and chromatin derived from glioblastoma stem cells
For primary GBM samples, we have 50 GBM samples in total, 46 of which have H3k27ac ChIPseq data, 45 of which have RNAseq data, and 39 of which have methylation data (GBM74 has replicate data).

For glioblastoma stem cell samples, we have 44 GSC samples in total, 43 of which have H3k27ac ChIPseq data, 44 of which have RNAseq data, and 41 of which have methylation data.

For neural stem cell samples, we have 10 NSC samples in total, 9 of which have H3k27ac ChIPseq data, 9 of which have RNAseq data, and 9 of which have methylation data.

middle: C

last: Mack

first: Irtisha

last: Singh

first: Xiuxing

last: Wang

first: Rachel

last: Hirsch

first: Charles

middle: Y

last: Lin

first: Jeremy

middle: N

last: Rich


title: A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe

status: Public on Dec 12 2018

city: Melbourne

first: Dane

middle: Aaron McKay

last: Vassiliadis

address: Parkville VIC 3000

institute: Peter MacCallum Cancer Centre

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

overall_design: Refer to individual Series


title: A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe [RNA-seq]

summary: Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. The transcriptional response of S. pombe to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities which govern this system.

overall_design: RNA-sequencng for wild type S. pombe cells cultured in rich (YES) medium containing 3% glucose, 3% sucrose 3% glycerol + 0.1% glucose (glucose-deficient) or 3% glycerol (glucose-starved). RNA-seq from scr1 disruption and scr1 deletion strains was performed in glucose and sucrose conditions only.

first: Brendon

last: Monahan


title: Single-cell transcriptional analysis of disseminated tumor cell clusters acquired from epithelial ovarian cancer ascites [DTCC]

status: Public on Feb 07 2019

city: Hong Kong

first: Tongtong

last: Kan

address: 83 Tat Chee Avenue

institute: City University of Hong Kong

summary: We used single-cell RT-PCR to analyze the cellular components and the EMT program of  disseminated tumor cell clusters acquired from epithelial ovarian cancer (EOC) ascites.

overall_design: The disseminated tumor cell clusters of each ascites sample were isolated through 2 approaches: randomly picked up after size-based selection and picked up after classified into 3 biological subpopulations using EpCAM and CD45 antibodies. The  disseminated tumor cell clusters were further dissociated into single cells. We used single cell RT-PCR to compare the expression levels of 53-EMT signature genes in different cell types. The data contain 195 intra-cluster single cells from 27 disseminated tumor cell clusters from 4 EOC ascites samples.

first: Mengsu

last: Yang


title: Differentially expressed genes after siRNA transfection in human cancer cell lines (TE1, TE8, 786-O and A498)

status: Public on Dec 05 2018

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: To identify differentially expressed genes by anti cancer treatments (miRNA and siRNAs) in human cancer, several cell lines (esophagus cancer and renal cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (TE1, TE8, 786-O and A498) were treated with miRNA (miR-143-5p and miR-143-3p) and siRNAs (si-DONSON and si-AQP9).

first: Yasutaka

last: Yamada


title: Single-cell transcriptional analysis of disseminated single cells and disseminated tumor cell clusters acquired from epithelial ovarian cancer ascites


title: Transcriptional profiling of pig striatum after deep hypothermic cardiac arrest

status: Public on Jan 15 2019

first: Vishal

last: Nigam

address: 1900 9th Ave

institute: Seattle Childrens Research Institute

summary: The goal of the study was to identify the gene changes that occur in the striatum of neonatal piglets exposed to cardiopulmonary bypass (CPB) with deep hypothermic cardiac arrest (DHCA) then recovered for 6h. To accomplish our goal, mRNA-seq was performed on RNA isolated from neonatal pigs exposed to either DHCA or sham conditions.

overall_design: RNA samples were isolated from the striatum from the brains of 6 neonatal piglets exposed to sham conditions were used as the controls; while samples from 6 piglets exposed to DHCA of 18o for 30 min then recovered for 6h were the experimental group.


title: Single-cell transcriptional analysis of disseminated single cells acquired from epithelial ovarian cancer ascites [DSC]

summary: We used single-cell RT-PCR to analyze the EMT program of disseminated single cells acquired from epithelial ovarian cancer (EOC) ascites.

overall_design: The disseminated single cells of each ascites sample were classified into 3 biological subpopulations using EpCAM and CD45 antibodies. We used single cell RT-PCR to compare the expression levels of 53-EMT signature genes in different cell types. The data contain 120 disseminated single cells from 4 EOC ascites samples.


title: A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage

status: Public on Nov 16 2018

city: Baltimore

first: Charlotte

middle: Park

last: Choi

state: MD

address: 3400 North Charles Street

department: Department of Biology

institute: Johns Hopkins University

summary: The piRNA pathway, which protects germline genomes from selfish elements such as transposons, operates in two modes: 1) cleavage of transcripts of selfish elements in the cytoplasm, and 2) their transcriptional silencing in the nucleus. Here we describe a novel mechanism by which these two modes exchange the information. We show that the nuclear subpathway component Piwi interacts with the nuage, the compartment that mediates the cytoplasmic subpathway, during mitosis of Drosophila spermatogonia. At the end of mitosis, Piwi leaves nuage to return to the nucleus. We found that dissociation of Piwi from nuage occurs at the depolymerizing microtubules of the central spindle, mediated by a microtubule-depolymerizing kinesin Klp10A. When Piwi’s return to the nucleus is delayed upon klp10A depletion, piRNA production is impacted, suggesting the importance of nuclear-cytoplasmic communication in piRNA biogenesis. We propose that cell cycle-dependent communication of piRNA subpathways plays important roles in coordinated piRNA production.

overall_design: We performed biological triplicate small RNA-seq and mRNA-seq in  wild-type and klp10A-knockdown germ cells (nos-gal4>UAS-klp10ARNAi).

middle: P

first: Zsolt

middle: G

last: Venkei

first: Suhua

last: Feng

first: Steve

last: Jacobson

first: John

middle: K

last: Kim

first: Yukiko

middle: M

last: Yamashita


title: Transcriptome Landscape of Human Folliculogenesis Reveals Oocytes and Granulosa Cells Interactions

status: Public on Nov 20 2018

city: Beijing

first: Zhiqiang

last: Yan

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: The dynamic transcriptional regulation and interactions of human germlines and surrounding somatic cells during folliculogenesis remains unknown. Using RNA-Seq analysis of human oocytes and corresponding granulosa cells (GCs) spanning five follicular stages, we revealed unique features in transcriptional machinery, transcription factor networks and reciprocal interactions in human oocytes and GCs that displayed developmental-stage-specific expression patterns. Notably, we identified specific gene signatures of two cell types in particular developmental stage that may reflect developmental competency and ovarian reserve. Additionally, we uncovered key pathways that may concert germline-somatic interactions and drive the transition of primordial-to-primary follicle which represents follicle activation. Thus, our work provides key insights into the crucial features of the transcriptional regulation in the stepwise folliculogenesis and offers important clues for improving follicle recruitment in-vivo and restoring fully competent oocytes in-vitro.

overall_design: Transcriptome profiles of oocytes and granulosa cells from five  follicle development stages were generated by deep sequencing using illumina Hiseq X10.

first: Yaoyao

last: Zhang

first: Jie

last: Qiao


title: Activating Transcription Factor 4 modulated TGFb-induced aggresiveness in triple negative breast cancer vis SMAD2/3/4 and mTORC2 signaling

status: Public on Jan 10 2019

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Based on the identified stress-independent cellular functions of activating transcription factor 4 (ATF4), we reported enhanced ATF4 levels in MCF10A cells treated with TGFβ1. ATF4 is overexpressed in triple negative breast cancer (TNBC) patients, but its impact on patient survival and the underlying mechanisms remain unknown. We aimed to determine ATF4 effects on breast cancer patient survival and TNBC aggressiveness, and the relationships between TGFβ and ATF4.

overall_design: RNA seq analysis was carried out on 20 Triple Negative Breast Cancer Patient Derived Xenograft models

first: Sergio

last: Granados

first: Olivier

last: Elemento


title: A monocyte gene expression signature in the early clinical course of Parkinson’s disease

status: Public on Oct 08 2018

city: La Jolla

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

summary: Recent studies suggest that the activation of the innate immune system is an integral part of Parkinson’s disease (PD) pathology. Monocytes have a critical role as effectors and regulators of the innate immune system, and a recent expression quantitative trait locus (eQTL) study links monocytes to PD. Patients diagnosed with PD according to the National Institute of Neurological Disorders and Stroke  diagnostic criteria for PD were included. We applied a standardized procedure with blood drawing from fasting participants. PD patients with Hoehn and Yahr > 2 and/or cognitive impairment were not recruited. Participants with a history of cancer, infectious diseases within the past three months, or taking anti-inflammatory drugs were excluded. Altogether, we analyzed the monocytic transcriptome profiles of 10 PD patients and 9 age- and sex-matched controls using mRNA sequencing.

overall_design: Monocyte mRNA profiles of 10 early stage Parkinson's disease patients and 9 age-and-sex-matched controls

first: Johannes

last: Schlachetzki

first: Iryna

last: Prots

first: Christian

last: Büttner

first: Arif

middle: B

last: Ekici

first: André

last: Reis

first: Kaoru

last: Saijo

first: Hyun

last: Chun

first: Beate

last: Winner

first: Christopher

last: Glass

first: Jürgen

last: Winkler


title: Hypothalamus of lean mice treated with celastrol or DMSO

status: Public on Dec 27 2018

city: Boston

first: Umut

last: Ozcan

address: 3 Blackfan Circle, CLS 16

department: Endocrinology

institute: Boston Children's Hospital

summary: Given that celastrol?s leptin-sensitizing effect requires high levels of circulating leptin, but lean mice have low levels of circulating leptin so that celastrol has no effect on lean mice. Analysis celastrol-induced hypothalamic gene expression profile change in lean mice will also be serving as negative control for DIO mice analysis.

overall_design: lean mice were injected with celastrol or DMSO as vehicle control for 6h, 1day or 4 days and then the RNA was extracted from hypothalamus for microarray


title: Gene expression changes in THP1 cells at day 2 and 4 following shRNA knock-down of RUVBL2

status: Public on Jan 01 2019

city: London

first: Owen

last: Williams

address: 30 Guilford Street

department: Cancer section

institute: UCL GOS ICH

summary: We used an inducible shRNA system and RNA-Seq to examine gene expression changes in acute myeloid leukemia THP1 cells following silencing of RUVBL2. RUVBL2 is a AAA+ ATPase that functions in a number of cellular processes, including chromatin remodeling and transcriptional control, and is critical for survival of acute myeloid leukemia cells and in vivo disease progression.

overall_design: Total cellular RNA was extracted using the RNeasy Plus Mini Kit from THP1 cells transduced with RUVBL2-specific inducible shRNA, following 2 and 4 days exposure to doxycycline or medium controls. In total, 6 pairs of control and doxycycline-treated samples were analysed (3 control and 3 doxycycline-treated for each time-point).

first: Elena

last: Armenteros-Monterroso

first: Jasper

last: de Boer


title: Hypothalamus of db/db mice treated with celastrol and DMSO

summary: Given that celastrol?s leptin-sensitizing effect requires both high levels of circulating leptin and intact leptin receptor signaling, we analyzed the effect of celastrol on hypothalamic gene expression profile of db/db mice, which have high circulating levels of leptin, but lack intact leptin receptor signaling. This analysis will be serving as negative control for DIO mice analysis.

overall_design: db/db mice were injected with celastrol or DMSO as vehicle control for 6h, 1day or 4 days and then the RNA was extreacted from hypothalamus for microarray


title: Hypothalamus of diet-induced obese (DIO) mice treated with celastrol or DMSO

summary: Since leptin signaling in the hypothalamus is critical to regulate food intake and body weight, we investigated how celastrol alters the hypothalamic transcriptome of DIO mice. By doing this analysis, genes with potential relevance for celastrol-mediated leptin sensitization could be identified.

overall_design: DIO mice were injected with celastrol or DMSO as vehicle control for 6h, 1day or 4 days and then the RNA was extracted from hypothalamus for microarray


title: Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin (RNA-seq)

status: Public on Oct 06 2018

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Hypoxia inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF-a isoforms, HIF-1a and HIF-2a, are progressively stabilized in response to hypoxia and form heterodimers with HIF-1b to activate a broad range of transcriptional responses. Here we report on the pan-genomic distribution of isoform-specific HIF binding in response to hypoxia of varying severity and duration, and in response to genetic ablation of each HIF-a isoform. Our findings reveal that, despite an identical consensus recognition sequence in DNA, each HIF heterodimer loads progressively at a distinct repertoire of cell-type specific sites across the genome, with little evidence of redistribution under any of the conditions examined. Marked biases towards promoter proximal binding of HIF-1 and promoter distant binding of HIF-2 were observed under all conditions and were consistent in multiple cell type. The findings imply that each HIF isoform has an inherent property that determines its binding distribution across the genome, which might be exploited to therapeutically target the specific transcriptional output of each isoform independently.

overall_design: RNA_seq analysis of hypoxic gene regulation in HKC8 and HepG2 cell lines and in RCC4 cell lines stably transfected with wtVHL

middle: R


title: Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin (ChIP-seq)

overall_design: ChIP_seq analysis of HIF-1alpha, HIF-2alpha and HIF-1beta binding under varying conditions of hypoxia and in multiple cell lines


title: Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin


title: DNA methylation data from 58 primary neuroblastomas

status: Public on Dec 19 2018

city: Heidelberg

first: Kai-Oliver

last: Henrich

address: INF 280

institute: German Cancer Research Center DKFZ

summary: Genome wide DNA methylation profiling of primary neuroblastomas. The Illumina 450k methylation array was used to obtain DNA methylation profiles across approximately 485,000 CpGs in 58 neuroblastomas. Data were analyzed with regard to differential methylation at ATRX and DAXX loci in relation to genomic MYCN, TERT and ATRX status, presence of alternative lengthening of telomeres (ALT) and TERT expression. The analysis is part of the study: A mechanistic classification of clinical phenotypes in neuroblastoma (Ackermann et al., 2018)

overall_design: Bisulphite converted DNA from the 58 samples were hybridized to the llumina HumanMethylation450 BeadChip

first: Konstantin

last: Okonechnikov

first: Frank

last: Westermann

first: Sandra

last: Ackermann

first: Matthias

last: Fischer


title: Differential analysis of gene expression profiles in peripheral blood cells of patients with cervical lesions

status: Public on Oct 02 2018

first: Yong

last: Shao

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine

summary: Using RNA-sequencing analysis of peripheral blood cells from 11 cervical cancer patients, 21 cervical intraepithelial neoplasia patients and 19 healthy controls, we identified a group of differentially expressed genes. A real time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was applied to the validation of candidate markers in the blood of 115 patients and 46 healthy controls. The results suggest that a six-gene predictor set (GZMB, NDUFA1, GPR84, NUAK1, AGAP1 and CIR1) can be used as candidate genes for the detection of cervical cancer.

overall_design: The mRNA profiles of peripheral blood cells from 11 cervical cancer patients, 21 cervical intraepithelial neoplasia patients and 19 healthy control participants were sequenced using Illumina 2500.

first: Quiling

last: Ma

first: Zhe

last: Zhou

first: Shengqi

last: Wang


title: RNA Polymerase II CTD phosphatase Rtr1 restricts noncoding transcript termination by Nrd1

status: Public on Sep 25 2018

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

summary: RNA Seq and ChIP-exo experiments related to this project

overall_design: Four RNA-Seq biological replicates each for deletion mutant (RTR1, RRP6, RTR1 RRP6) and reference cells (WT). Rpb3 and Nrd1 ChIP-exo on wildtype and RTR1-deletion cells.

first: Melanie

middle: J

last: Fox

first: Jose

middle: F

last: Victorinio

first: Whitney

last: Smith-Kinnaman

first: Hongyu

last: Gao

first: Asha

last: Boyd

first: Megan

last: Zimmerly

first: Rachel

last: Chan

first: Amber

middle: L

last: Mosley


title: Composition of the Colonic Mesenchyme and the Nature of its Plasticity in Inflammatory Bowel Disease

status: Public on Sep 27 2018

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

summary: 10x Chromium single cell RNA-Seq of colonic mesenchyme cell populations in health and Ulcerative Colitis in human patients and health in DSS-induced colitis in murine colon

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cells from colon of three healthy mice and 3 DSS-treated mice were sequenced on 10x Chromium /hiSeq4000 instruments. Cells from 2 healthy and 2 UC human patients were isolated and sequenced using 10x Chromium /hiSeq4000 instruments.

first: James

last: Kinchen

first: Hannah

last: Chen

first: Kaushal

last: Parikh

first: Agne

last: Antanaviciute

first: Marta

last: Jagielowicz

first: David

last: Fawkner-Corbett

first: Neil

last: Ashley

first: Esther

last: Mellado-Gomez

first: Moustafa

last: Attar

first: Eshita

last: Sharma

first: Quin

last: Wills

first: Rory

last: Bowden

first: Felix

last: Richter

last: Ahern

first: Jill

last: Henault

first: Francois

last: Gervais

first: Kamal

last: Puri

first: Hashem

last: Koohy


title: APOL1 renal-risk variants induce mitochondrial fission

status: Public on Sep 15 2018

city: Winston Salem

first: Lijun

last: Ma

state: NC

address: 1 Medical Center Blvd

department: Nephrology

institute: Wake Forest School of Medicine

summary: To assess gene expression by APOL1 genotypes in primary proximal tubule cells (PTCs), global gene expression (mRNA) levels were examined on Affymetrix HTA 2.0 arrays in primary PTCs cultured from non-diseased kidney in African Americans without CKD who underwent nephrectomy for localized renal cell carcinoma.

overall_design: To detect gene profiles attributable to APOL1 renal-risk genotypes, African American primary proximal tubule cells with two APOL1 renal-risk alleles (N=5), one risk allele (N=23),  and lacking renal-risk alleles (N=22) were compared for  global gene expression when poly IC stimulation was absent (pre-) or present (post-) .

last: Ainsworth

first: James

middle: A

last: Snipes

first: Mariana

last: Murea

first: Young

last: Choi

first: Carl

middle: D

last: Langefeld

first: John

middle: S

last: Parks

first: Manish

last: Bharadwaj

first: Jeff

middle: W

last: Chou

first: Ashok

last: Hemal

first: Snezana

last: Petrovic

first: Ann

last: Craddock

first: Dongmei

last: Cheng

first: Gregory

last: Hawkins

first: Lance

last: Miller

first: Pamela

last: Hicks

first: Moin

last: Saleem

first: Jasmin

last: Divers

first: Anthony

last: Molina

first: Barry

middle: I

last: Freedman


title: A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe [ChIP-seq]

first: Dane

middle: Aaron McKay

last: Vassiliadis

summary: Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. The transcriptional response of S. pombe to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities which govern this system.

overall_design: ChIP-sequencing of Scr1, Tup11, Rst2 for cells expressing TAP tags fused to the C-terminus of the respective proteins in rich (YES) medium containing 3% glucose, 3% sucrose or 3% glycerol (glucose-starved). Additionally, RNA Pol II Ser5 ChIP-seq for wild type or Scr1-TAP cells in the same growth conditions as the other ChIP-seq samples.

first: Brendon

last: Monahan


title: Gene expression of murine hematopoietic stem and progenitor cells transduced with integrating vectors

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

summary: Gene therapy has emerged as a promising therapeutic strategy, but efficient in vitro assessment of vector safety remains challenging. To create a predictor of vector induced genotoxicity, we developed the Surrogate Assay for Genotoxicity Assessment (SAGA), which uses genetic algorithm-enhanced machine learning to detect the deregulation of a specific gene expression signature in murine hematopoietic stem and progenitor cells (HSPC) transduced with potentially genotoxic vectors. For the SAGA assay, murine lineage negative (Lin-) HSPC are isolated and transduced with high multiplicities of infection (MOI) to reach at least 3 vector copies per cell. Post-transduction, bulk cultures are expanded for a total of 15 days in medium supplemented with cytokines promoting myeloid differentiation. Total RNA is prepared from the bulk cultures on day 15 and gene expression profiles are analyzed on microarrays.SAGA classifies samples based on their gene expression profile by using a support vector machine with a radial kernel on 9 features deduced by a genetic algorithm. SAGA is more robust, sensitive and faster than previous assays and reliably predicts a mutagenic risk for vectors that led to leukemia in clinical trials.

overall_design:
Murine Lineage-negative bone marrow cells were isolated and transduced with integrating vectors followed by ex vivo culture for 15 days. RNA was hybridized to a custom versions of the Agilent Whole Mouse Genome Oligo Microarray 4x44K v2.

All arrays used in this study represent refined versions of the Agilent Whole Mouse Genome Oligo Microarray 4x44K v2 (Design ID 026655) comprised of all probes of this array in quadruplicates, but a different number of custom control probes. For the Gene expression matrix only the original Agilent Probes (A_XX_XXXXX) were used, which are the same on all arrays. ID-048306 (GPL19795) was developed by the Research Core Unit Genomics (RCUG) of Hannover Medical School. All non-control probes of design ID 026655 were printed four times within one 180K region. Design ID 066423 (048306On1M) and ID-084107 (048306On1M_V3 /GPL24228) were also developed by RCUG, using a 1x1M design format. All non-control probes of design ID 026655 were printed four times within a region comprising a total of 181560 Features. Four of such regions were placed within one 1M region.

We have assigned all of these samples to GPL24228, a platform which contains the probe data consistent across all revised versions of Design ID 026655.  The Agilent Design ID for each sample is available in the 'description' field and in the header of the raw data file.

first: Michael

last: Rothe


title: Effect of HFD exposure on hepatic transcriptome on Wild Type mice (WT), hepatocyte-specific PPARα knockout mice (LKO) and whole body PPARα knockout mice (KO).

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: Adult (12 weeks old) WT, LKO and KO male mice from C57Bl6J were either treated with a control diet (CTRL) or an High Fat Diet (HFD) during 12 weeks prior to liver gene expression analysis

overall_design: 8 mice per group (CTRL and HFD) and per genotype (WT, LKO, KO).

first: Marion

last: Régnier

first: Arnaud

last: Polizzi

first: Sarra

last: Smati

first: Claire

last: Naylies

first: Nicolas

last: Loiseau

first: Alexandra

last: Montagner

first: Yannick

last: Lippi


title: Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

status: Public on Oct 29 2018

first: zemin

last: zhang

address: Yiheyuan Road

department: BIOPIC

summary: T cells are central players in cancer immunotherapy1, yet some of their fundamental properties such as development and migration within tumours remain elusive. The enormous T cell receptor (TCR) repertoire, required for recognising foreign and self-antigens2,3, could serve as lineage tags to track these T cells in tumours4. Here, we obtained transcriptomes of 11,138 single T cells from 12 colorectal cancer (CRC) patients and developed STARTRAC (Single T-cell Analysis by Rna-seq and Tcr TRACking) indices to quantitatively analyse dynamic relationships among 20 identified T cell subsets with distinct functions and clonalities. While both CD8+ effector and ?exhausted? T cells exhibited high clonal expansion, they were independently connected with tumour-resident CD8+ effector memory cells, implicating a TCR-based fate decision. Of the CD4+ T cells, the majority of tumour-infiltrating Tregs showed clonal exclusivity, whereas certain Treg clones were developmentally linked to multiple TH clones. Notably, we identified two IFNG+ TH1-like clusters in tumours, the GZMK+ TEM and CXCL13+ TH1-like clusters, which were associated with distinct IFN-?-regulating transcription factors, EOMES/RUNX3 and BHLHE40, respectively. Only BHLHE40+ CXCL13+ TH1-like cells were preferentially enriched in tumours of microsatellite-instable (MSI) patients, which might explain their favourable response rates to immune-checkpoint blockade. Furthermore, we found IGFLR1 to be highly expressed in both BHLHE40+CXCL13+ TH1-like and CD8+ exhausted T cells and possessed co-stimulatory functions. Our integrated STARTRAC analyses provided a powerful avenue to comprehensively dissect the T cell properties in CRC, which could shed new insights into the dynamic relationships of T cells in other cancers.

overall_design:
T cells from CRC patients were sorted, profiled by Smart-seq2 and sequenced on HiSeq4000. Based on FACS analysis, single cells of different subtypes, including CD8+ T cells (CD3+ and CD8+), T helper cells (CD3+, CD4+ and CD25-), and regulatory T cells (CD3+, CD4+ and CD25high) were sorted to perform RNA sequencing. The categories ?""sampleType"" column in the SAMPLES section? contain PTC(CD8+ T cells from peripheral blood), NTC(CD8+ T cells from adjacent normal colonrectal tissues) ,TTC (CD8+ T cells from tumor), PTH(CD3+, CD4+ and CD25- T cells from peripheral blood), NTH(CD3+, CD4+ and CD25- T cells from adjacent normal colonrectal tissues), TTH(CD3+, CD4+ and CD25- T cells from tumor), PTR(CD3+, CD4+ and CD25high T cells from peripheral blood), NTR(CD3+, CD4+ and CD25high T cells from adjacent normal colonrectal tissues), TTR(CD3+, CD4+ and CD25high T cells from tumor), PTY(CD3+, CD4+ and CD25mediate T cells from peripheral blood), NTY(CD3+, CD4+ and CD25mediate T cells from adjacent normal colonrectal tissues), TTY(CD3+, CD4+ and CD25medate T cells from tumor), PP7(CD3+, CD4+ T cells from peripheral blood), NP7(CD3+, CD4+ T cells from adjacent normal colonrectal tissues), TP7(CD3+, CD4+ T cells from tumor).

Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001002791

first: Lei

last: Zhang

first: Xin

last: Yu

first: Liangtao

last: Zheng

first: Yuanyuan

first: Yansen

last: Li

first: Qiao

last: Fang

first: Ranran

last: Gao

first: Boxi

last: Kang

first: Qiming

first: Julie

middle: Y

last: Huang

first: Hiroyasu

last: Konno

first: Xinyi

last: Guo

first: Yingjiang

last: Ye

first: Songyuan

first: Shan

last: Wang

first: Xueda

last: Hu

first: Xianwen

last: Ren

first: Zhanlong

last: Shen

first: Wenjun

last: Ouyang

first: Zemin


title: ERK1/2-dependent gene expression in the bovine ovulating follicle

status: Public on Oct 23 2018

city: Ste Anne de Beelvue

first: Yasmin

last: Schuermann

state: Quebec

address: 21 111 lakeshore Road

department: Animal Science

institute: McGill University

summary:
Purpose: establishing a role for ERK1/2 in bovine ovulation by using RNA-Seq to compare granulosa cells collected from the dominant follicle at different times post GnRH treated with PD0325901 (ERK1/2 signaling inhibitor)
Methods: The dominant follicle of cattle was subject to ultrasound-guided intrafollicular injection of either a Vehicle treatment or PD0325901 inhibitor treatment. Thirty minutes later we collected granulosa cells from Vehicle treated cows (Vehicle_0h_GnRH), while other cows were administered with an intramuscular injection of goonadotropin releasing hormone (GnRH) to simulate an LH surge. Six hours later granulosa cells were collected from Vehicle treated and PD0325901 treated cows (Vehicle_6h_GnRH & PD0325901_6h_GnRH).  All granulosa cell RNA was subject to the Illumina HiSeqq 2500 PE 125. Quality check for reads was performed using FastQC v0.11.5 and adapters were removed by Trimmomatic v0.36. The data was aligned to the bovine Genome (Btau4.6.1) using Bowtie v2.2.1.0 and TopHatv2.0.11. Next, the rnumber of reads mapped to each gene were counted using HTSeq v0.6.1
Results: The counts from our 8 samples (Vehicle_0h_GnRH; n=2 , Vehicle_6h_GnRH; n=3, PD0325901_6h_GnRH; n=3) were subject to analysis to determine differentially expressed genes (DEGs) between our groups. Using The DESeq2 R package we observed 2 121 DEGs between Vehicle_0h_GnRH & Vehicle_6h_GnRH and 285 DEGs between Vehicle_6h_GnRH and PD0325901_6h_GnRH. We confirmed our RNA-seq analysis for a number of known genes in ovulation (ADAMTS1, TNFAIPs, EGR1, etc..) by qPCR.
Conclusions: ERK1/2 is essential for ovulation in cattle as observed by the DEGs in granulosa cells in the pre-ovulatory follicle. To our knoweldge, we are the firs tto iinhbiti ERK1/2 signaling in vivo in cattle.

overall_design: bovine granulosa cell mRNA profiles from the dominant follicle/pre-ovulatory follicle treated with PD0325901 (in vivo) were generated by deep sequencing using Illumina HiSeq 2500 PE125

first: Raj

last: Duggavathi


title: Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo

status: Public on Dec 04 2018

city: Davis

first: Susan

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

summary: The earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. To characterize the evolutionary dynamics and functional constraints on the timing of early embryonic expression, we created a transcriptomic dataset for 14 Drosophila species spanning over 50 million years of evolution, at developmental stages before and after the MZT, and compared our results with a previously published Aedes aegypti developmental time course. We found deep conservation over 250 million years of a core set of genes transcribed only by the zygote. This select group is highly enriched in transcription factors that play critical roles in early development. However, we also identify a surprisingly high level of turnover of transcripts represented at both stages over the phylogeny. While mRNA levels of genes with maternally deposited transcripts are more highly conserved than zygotic genes, those maternal transcripts that are completely degraded at the MZT vary dramatically between species. We also show that hundreds of genes have different isoform usage between the maternal and zygotic genomes. Our work suggests that maternal transcript deposition and early zygotic transcription are surprisingly dynamic over evolutionary time, despite the widespread conservation of early developmental processes.

sample_organism:
Drosophila ananassae
Drosophila erecta
Drosophila mauritiana
Drosophila melanogaster
Drosophila miranda
Drosophila mojavensis
Drosophila persimilis
Drosophila pseudoobscura
Drosophila sechellia
Drosophila simulans
Drosophila virilis
Drosophila yakuba
Drosophila willistoni
Drosophila santomea

overall_design: We sequenced mRNAs from individual stage 2 and stage 5 embryos (at least 3 replicates each) from 14 species. Some of the samples and species were sequenced as carrier mRNA for SliceSeq with D. melanogaster embryos (see Combs & Eisen,2013,PLOS ONE), so raw data is a mix of a small amount of D. melanogaster mRNA and mRNA from another distantly related species, as noted under samples "characteristics: raw data mixed with D. melanogaster". Other data used in the paper can be found at GSE68062 and GSE53483-renalyzed Samples, which includes stage 5 samples for D melanogaster, D. yakuba, D. virilis, and all samples from D. pseudoobscura and D. miranda.

first: Joel

last: Atallah

middle: E


title: An unbiased Boolean analysis of public gene expression data for core cell cycle gene classification

status: Public on Aug 29 2018

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

institute: UCSD

type:
Expression profiling by array
Third-party reanalysis

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

sample_organism:
Arabidopsis thaliana
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of estrogen (E2) treatment on the C4-12 relative to the MCF7 cells

status: Public on Aug 30 2018

city: Duarte

first: Karineh

last: Petrossian

address: 1500 E. Duarte Road

department: Cancer Biology

institute: Beckman Research Institute at City of Hope

summary: To confirm the effect of estrogen, through the estrogen receptor, on cell cycle progression and to identify the key molecules that play an important role in this regulation, MCF-7aro (ER+ cell line) and C4-12ERaERE (ER lacking cell line stably transfected with ERaERE) were used for RNAseq analysis.  Processed data includes new data for C4-12 samples as well as re-processed data from SRP035276.

overall_design: 6 new C4-12 samples were analyzed (3 control and 3 E2 treated). Same design as for subset of MCF7aro SRP035276 re-processed samples, in addition to Paroxetine and Paroxetine+E2 treatments.

first: Noriko

last: Kanaya

first: Shiuan

last: Chen


title: Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

status: Public on Jul 26 2018

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

summary: We performed ChIP-seq of Hsf1 under non heat shock, 5-minute heat shock and 120 minute heat shock conditions. We used the conditional chemical genetics approach known as “anchor away” (AA) to rapidly inactivate Hsf1. We coupled Hsf1-AA to and nascent RNA seq (NAC)-seq to define the genes whose expression depends on Hsf1 during heat shock.

overall_design: 3 yeast Hsf1 ChIP-seq samples, 4 yeast NET-seq samples


title: Gene expression profiling allows the identification of pathways involved in seeds development of Jatropha curcas

status: Public on May 31 2018

city: Vienna

first: Klemens

last: Vierlinger

address: Giefinggasse 4

department: HMD

country: Austria

institute: AIT

summary:
Jatropha curcas, a tropical shrub, is an attractive biofuel crop, which produces seeds with a high content of oil and protein. Most J. curcas accessions contain a range of toxins and anti-nutritional compounds, which are unfavorable for human consumption and animal feed. With the goal of better understanding the development of its seeds and to improve Jatropha`s agronomic performance, a two-step approach was performed: 1) generation of the entire transcriptome of six different developmental stages of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels in six different developmental stages of seeds using a custom Agilent 8x60K oligonucleotide gene expression microarray.
A total of 793,875 high quality reads with an average length of 358 bp were generated and assembled into 19,841 unique full-length contigs, of which 13,705 could be annotated with GO terms. Microarray data analysis identified a total of 9,111 contigs which were differentially expressed between the six developmental stages (based on P-value of < 1e-8). The microarray-based differential expression results were validated for 192 putative genes using high-throughput quantitative real-time PCR.
Results from Gene Ontology (GO) and pathway enrichment analysis showed that the upstream biosynthesis pathways were relatively active among differentially expressed sequences (DESs) during seed development, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, glycerophospholipid metabolism, amino sugar and nucleotide sugar metabolism. Further, DESs related to hormone and seed development, flavonoid biosynthesis-related pathways were over-represented. A pairwise comparison was used to discover particular seed maturation dependent patterns of gene expression. Genes related to fatty acid biosynthesis were over represented in early stage, while flavonoid biosynthesis in the late stage.
The data provide a useful resources and references for the seed transcriptome of J. curcas and other related species with oil producing seeds. The identified transcripts related to seed development provide a starting point for further investigation into the molecular mechanisms underlying this process.

overall_design: whole transcriptomes of leaves and seeds of toxic and non-toxic plants (n=32) at six different developmental stage were characterised on custom designed Agilent microarrays

first: Fatemeh

last: Maghuly


title: Mouse Boolean Implication Network

department: Pediatrics

summary: Numerous gene expression datasets from diverse mouse tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions.  We propose here a new large scale meta-analysis of all of the publicly available mouse datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

overall_design: 11,758 published mouse microarray samples assayed on the GPL1261 were re-analyzed. RMA was used to normalize the RAW CEL files all together.


title: Podocyte-specific induction of Krüppel-like factor 15 restores differentiation markers and attenuates kidney injury in proteinuric kidney disease

status: Public on Aug 02 2018

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: HSC-T16 Room 80E

department: Division of Nephrology and Hypertension

institute: Stony Brook University School of Medicine

summary: Podocyte injury is the hallmark of proteinuric kidney diseases, such as Focal Segmental Glomerulosclerosis and Minimal Change Disease. Therapeutic strategies in the management of proteinuric diseases are limited. Although agents such as glucocorticoids, cyclosporine, and rituximab have direct effects on the podocyte by stabilizing its actin cytoskeleton, these drugs are riddled with systemic toxicity and off-target effects that hinder their chronic use. We previously demonstrated that the loss of the kidney-enriched zinc finger transcription factor, Krüppel-like factor 15 (KLF15), increases susceptibility to proteinuric kidney disease as well as attenuates the salutary effects of retinoic acid and glucocorticoids in the podocyte. Here, we show that podocyte-specific induction of KLF15, using the tetracycline-inducible system, attenuated podocyte injury, glomerulosclerosis, tubulointerstitial fibrosis and inflammation, while improving renal function and overall survival in HIV-1 transgenic mice. Enrichment analysis of mRNA sequencing of isolated glomerular extracts from this model shows that podocyte-specific induction of KLF15 activates pathways involved in stabilization of actin cytoskeleton, focal adhesion, and podocyte differentiation. Transcription factor enrichment analysis, with further experimental validation, suggests that KLF15 activity is in part mediated by Wilms Tumor 1 (WT1), a transcription factor known to be critical for podocyte differentiation. Further, we confirmed the benefits of podocyte-specific induction of KLF15 in the adriamycin-induced proteinuric murine model. Collectively, these observations suggest that induction of KLF15 might be a potential therapeutic target in the treatment of proteinuric kidney disease.

overall_design: Transcriptome analysis of Tg26 and Tg26 KLF15OE

first: Yiqing

last: Guo

first: Jesse

last: Pace

first: Zhengzhe

last: Li

first: Avi

last: Ma'ayan

first: Zichen

first: Monica

last: Revelo

first: Edward

first: Xiangchen

last: Gu

first: Yaqi

last: Yang

first: Chelsea

last: Estrada

first: Vincent

first: John

last: He


title: Single cell and pooled embryo RNA-seq of of early Ciona embryos

status: Public on Jul 06 2018

city: Princeton

first: Nicholas

last: Treen

state: NJ

address: Carl Icahn Laboratory,, Princeton University, Washington Rd

institute: Princeton University

summary: This dataset provides gene expression levels of single cell and pooled embryos as part of a study on zygotic genome activation in Ciona embryogenesis. The single cell RNA-seq data suggested that Cyclin B3 was a key mediator of this process. This was confirmed by performing RNA-seq on pooled RNA isolated from embryos where Cyclin B3 was knocked down (using morpholinos) or overexpressed (using mRNA injections).

overall_design: 93 single cell transcriptomes consisting of cells from 4-, 8-, and 16-cell stage embryos. Each stage was performed in triplicate. 21 pooled embryo transcriptomes from total RNA of pooled embryos from 4- 8- and 16-cell stages for controls and embryos where Cyclin B3 has been knocked down (using morpholinos) as well as 16-cell embryos where Cyclin B3 has been overexpressed. All samples were performed in triplicate.

first: Michael

last: Levine


title: RNA-seq of circulating human eosinophils before and after oral prednisone administration

status: Public on Jul 19 2018

city: Bethesda

first: Luis

last: Franco

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Glucocorticoids are first-line agents for the treatment of many eosinophil-associated disorders. However, their mechanism of action in this group of disorders remains poorly understood, including the well-known clinical observation that glucocorticoids at therapeutic doses lead to profound, transient eosinopenia within hours of administration. To gain an unbiased, genome-wide view of the early transcriptional effects of glucocorticoids on human eosinophils in vivo, and torelate them to the kinetics of glucocorticoid-induced eosinopenia, RNA sequencing was performed on purified blood eosinophils obtained before and 30, 60, and 120 minutes after administration of a single dose of oral prednisone (1 mg/kg) to healthy subjects with hypereosinophilia (hypereosinophilia of unknown significance).

overall_design: Three subjects with hypereosinophilia of unknown significance were each given a single dose of oral prednisone, 1 mg/kg. Whole blood was collected before and 30 minutes, 1 hour, and 2 hours after prednisone administration. Eosinophils were purified from each peripheral blood sample. Total RNA was obtained from purified eosinophils and subject to library preparation and high-throughput sequencing.

first: Manasi

last: Gadkari

first: Michelle

last: Makiya

first: Paneez

last: Khoury

first: Amy

last: Klion


title: Differential circular RNAs expression in ovary during oviposition in honey bees

status: Public on Jun 07 2018

city: Beijing

first: Xiao

last: Chen

state: Beijing

address: Haidian Xiangshan Beigou No.1

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

summary: The present study is the first study to identify the involvement of circRNAs in the ovary activation and oviposition regulation processes in honey-bee queens.CircRNAs expresion profiles were examined in ovaries of virgin queens, egg-laying queens, egg-laying inhibited queens and egg-laying recovery queens.

overall_design: To identify the involvement of circRNAs in the ovary activation and oviposition regulation processes in honey-bee queens, a total of four different ovaries samples were used in this study: (1) ovaries of virgin queens (n=3); (2) ovaries of egg-laying queens (n=3); (3) ovaries of egg-laying inhibited queens (n=3) (4) ovaries of egg-laying recovered queens (n=3). To sample the caged queens' ovaries, the queens were caged and placed in the original colony respectively for seven days. And at the end of the seventh day, ovaries samples were collected. To sample the recovered queens' ovaries, the queen was released after caged for seven days. And then, on the eighth day, the queen recovered to normal condition and laid eggs, and ovaries samples were collected. All the samples were collected immediately, snap frozen in liquid nitrogen and stored at -80C.


title: Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture

status: Public on Feb 27 2018

city: Wuhan

first: Ping

last: Hong

state: Hubei

address: No.1,Shizishan Street

department: college of informatics

institute: Huazhong Agricultural University

summary: we developed a simple Digestion-Ligation-Only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome

overall_design: The DLO Hi-C library of K562 and THP-1

first: Da

last: Lin

first: Guoliang

first: Gang

last: Cao


title: Expression profiling of Cellvibrio japonicus using either glucose or chitin

status: Public on Jan 24 2018

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

summary: Understanding the strategies used by bacteria to degrade polysaccharides constitutes an invaluable tool for biotechnological applications Bacteria are major mediators of polysaccharide degradation in nature, however the complex mechanisms used to detect, degrade, and consume these substrates are not well understood, especially for recalcitrant polysaccharides such as chitin It has been previously shown that the model bacterial saprophyte Cellvibrio japonicus is able to catabolize chitin, but little is known about the enzymatic machinery underlying this capability Previous analyses of the C japonicus genome and proteome indicated the presence of four family 18 Glycoside Hydrolase (GH18) enzymes, and studies of the proteome indicated that all are involved in chitin utilization Using a combination of in vitro and in vivo approaches, we have studied the roles of these four chitinases in chitin bioconversion Genetic analyses showed that only the chi18D gene product is essential for the degradation of chitin substrates Biochemical characterization of the four enzymes showed functional differences and synergistic effects during chitin degradation, indicating non-redundant roles in the cell Transcriptomic studies revealed complex regulation of the chitin degradation machinery of C japonicus and confirmed the importance of CjChi18D and CjLPMO10A, a previously characterized chitin-active enzyme With this systems biology approach, we deciphered the physiological relevance of the GH18 enzymes for chitin degradation in C japonicus, and the combination of in vitro and in vivo approaches provided a comprehensive understanding of the initial stages of chitin degradation by this bacterium

overall_design:
One carbon condition (chitin); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples
Please note that glucose-grown sample data is published and thus, available in the previous GEO records [GSE90955; GSM2418311-GSM2418316].

middle: G


title: Airn isoforms are important for the functions of cardiomyocytes (Gene_Array-Airn)

status: Public on Feb 28 2018

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary: To elucidate the function of Airn isoforms in the heart, we conducted loss-of-function experiments in murine cardiomoycyte cell line HL-1.

overall_design: Using HL-1 cells, we performed microarray experiments.

first: Mohammed

last: Hosen


title: The rate of ageing-associated DNA methylation dynamics is a molecular readout of lifespan variation amongst mammalian species [Bis-PCR: dog]

status: Public on Jan 17 2018

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

type: Methylation profiling by high throughput sequencing

summary: We used buccal samples from two different dog breeds with well established differences in average lifespan to perform genome-scale identification of ageing-associated differentially methylated positions (aDMPs) in a total of 48 different dogs. A significant proportion of aDMPs that gained methylation with age replicated in an independent cohort. Furthermore, we also show that human aDMPs show similar ageing-associated dynamics at the homologous genomic regions in the dog. The replicated aDMPs show a faster rate of change with age in the shorter lived dog species. Strikingly, these aDMPs also show a faster rate of change with age in dogs overall compared with humans.

overall_design: Bis-PCR profiling of dogs of various age from two different breeds.


title: Reprogrammed marrow adipocytes: an unexpected role in the genesis of myeloma-induced bone disease (ChIP-Seq)

status: Public on Apr 26 2018

city: Houston

first: Jing

last: Yang

state: Texas

address: 7455 Fannin

institute: MD Anderson Cancer Center

summary: Multiple myeloma is characterized by osteolytic lesions caused by osteoclast-mediated bone resorption and reduced bone formation. A unique feature of myeloma is a failure of bone healing following successful treatment. Identification of increased adipocyte numbers in marrow of successfully treated patients led us to demonstrate that normal marrow adipocytes, when co-cultured with myeloma cells, are reprogrammed and produce adipokines that activate osteoclastogenesis and suppress osteoblastogenesis. These adipocytes have reduced expression of peroxisome proliferator-activated receptor  (PPAR) mediated by recruitment of polycomb-repressive complex 2 (PRC2) via specificity protein 1, which modifies PPAR promoter methylation at trimethyl lysine-27 histone H3. We confirmed the importance of PPAR methylation by demonstrating that adipocyte-specific knockout of EZH2, a member of the PRC2, prevents adipocyte reprogramming and reverses bone changes in vivo. These results define a heretofore unrecognized role for adipocytes in genesis of myeloma-associated bone disease and that reversal of adipocyte reprogramming has therapeutic implications.

overall_design: Define a heretofore unrecognized role for adipocytes in genesis of myeloma-associated bone disease

first: Huan

last: Liu

first: Jin

first: Su

middle: P

last: Koh

first: Yuping

last: Zhong

first: Zhiqiang

last: Wang

first: Yujin

last: Zhang

first: Zongwei

last: Li

first: Bjorn

middle: T

last: Tam

first: Pei

first: Min

last: Xiao

first: Ken

middle: H

last: Young

first: Behrang

last: Amini

last: Starbuck

first: Hans

middle: C

last: Lee

first: Nora

middle: M

last: Navone

first: Richard

last: Davis

first: Qiang

last: Tong

first: P

last: Bergsagel

first: Jian

last: Hou

first: Qing

last: Yi

middle: Z

last: Orlowski

last: Gagel


title: Gene expression profile of CRC-derived HILEC

status: Public on Jan 01 2018

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: HILEC from CRC tissues isolated from human patients underwent RNA sequencing to define their expression profile by comparison with healthy cells.

overall_design: Human Intestinal Lymphatic Endothelial cells (HILEC) were isolated from colorectal cancers. HILEC were sorted for lymphatic-specific markers (podoplanin) and then were expanded to collect at least 1*10^6 cells. RNA was extracted for sequencing.

first: Ungaro

last: Federica

first: Silvio

last: Danese

first: Silvia

last: D'Alessio


title: Mapping human pluripotent stem cell differentiation pathways via high throughput single-cell RNA-sequencing

status: Public on Mar 06 2018

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

summary: Human pluripotent stem cells (hPSCs) provide both powerful models for studying cellular differentiations, and unlimited sources of cells for regenerative medicine. However, a comprehensive single cell level differentiation roadmap for hPSCs has not been achieved yet. Here, we used high throughput single-cell RNA-sequencing (scRNA-seq) method, based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body (EB) system. We presented a cellular landscape for hPSC early differentiations covering different cellular lineages, including neural cell, muscle cell, endothelial cell, stromal cell, liver cell, and epithelial cell. Through pseudotemporal analysis, we constructed the differentiation trajectories of these progenitor cells and revealed the gene expression dynamics in the process of differentiation. We reset Primed H9 into Naïve-like H9 and studied cell state transition process via scRNA-seq. We found that mesendoderm genes are enriched in Naïve-like H9. Functionally, Naïve-like H9 showed better potency for differentiation into the hematopoietic lineages. We constructed the differentiation landscape of hPSC early differentiation by scRNA-seq analysis. We offer new insights into molecular pathways of early embryonic lineages that can be harnessed for optimization of differentiation protocols. (Pipeline for C1 data demultiplex : https://github.com/bioeauty/sccpipe)

overall_design: scRNA-seq analysis of naïve and primed human pluripotent stem cells and embryoid bodys

first: Xiaoping

last: Han

first: Daosheng

last: Huang


title: Transcriptome profiling of embryonic cortex E18 and primary cortical neuron cultures deficient for the Amyloid Precursor Protein (APP)

status: Public on Sep 01 2018

city: Brussels

first: Pascal

last: Kienlen-Campard

address: Avenue E. Mounier 53

department: Institute of NeuroScience

country: Belgium

institute: Université Catholique de Louvain

summary: The amyloid precursor protein (APP), an important player in the Alzheimer’s disease, regulates neurites formation and synaptic function by mechanisms still not fully understood. Its ability to control gene expression via its intracellular domain (AICD) was proposed to mediate several of these physiological functions. Here, we tested whether putative AICD target genes could be transcriptionally modified by the absence of APP in embryonic cortex (E18) and in primary cortical neurons during maturation after 3 or 7 days in vitro. Moreover, we aimed to identified novel APP dependent target genes that could be related to particular biological functions in the context of neuronal physiology.

overall_design: Primary neuronal culture from embryonic cortices were carried out using APP+/+ and APP-/- embryos at developmental stage E18. Primary neuronal cultures were kept in vitro for 3 (DIV3) or 7 (DIV7) days and subjected to RNA extraction and hybridization on Affymetrix microarrays. In addition, embryonic cortices at E18 (E18) were subjected RNA extraction and hybrization on Affymetrix microarrays. In all our experimental conditions (E18, DIV3 and DIV7), 3 biologicals replicates for each genotype (APP+/+ and APP-/-) were used.

first: Rémi

last: Opsomer


title: Blood Transcriptional Endotypes in Women with Pelvic Inflammatory Disease

status: Public on Feb 06 2018

city: Chapel Hill

first: xiaojing

last: zheng

address: 111 Mason Farm Road

institute: UNC-CH

summary: By comparing blood mRNA responses of women with biopsy confimed Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (GC) induced pelvic inflammatory disease (PID) to those from women with CT and/or GC infection limited to their cervix and asymptomatic uninfected women determined via microarray, we discovered important pathogenic mechanisms in PID and response differences that provide a pathway to biomarker discovery. Women with GC and/or CT-induced PID exhibit overexpression of myeloid cell genes and suppression of protein synthesis, mitochondrial oxidative phosphorylation, and T-cell specific genes. Coinfected women exhibited the greatest activation of cell death pathways and suppression of responses essential for adaptive immunity. Blood microarrays reveal discrete pathobiological endotypes in women with PID that are driven by pathogen invasion of the upper genital tract.

overall_design: Total RNA was extracted from whole blood collected in Tempus™ Blood RNA tubes of participants in this study at enrollment.

first: Xiaojing

last: Zheng

first: Catherine

last: O’Connell

first: Wujuan

last: Zhong

first: Toni

last: Darville


title: Neuro-glial crosstalk regulates microglia activation and control of viral encephalitis

status: Public on Feb 07 2018

city: Freiburg

first: Marta

middle: Joana Costa

last: Jordão

address: Breisacher strasse 64

department: Neuropathology

institute: Uniklinikum Freiburg

summary: In this study it was possible to compare the behaviour of different myeloid cell populations upon VSV infection.

overall_design: Non-activated microglia (Ly6G-CD45lowCD11b+Tomato+ cells) and activated microglia (Ly6G-CD45highCD11b+Tomato+ cells) from olfactory bulb and infiltrating monocytes (Ly6G-CD45highCD11bhigh-Tomato-) were FACS-sorted from Cx3cr1CreER:R26-Tomato mice in which all resident macrophages express the endogenous tomato signal while peripheral immune cells do not. The mRNA from the different populations was extracted and sequenced on Illumina HiSeq RNA-Seq. Three replicates per condition were used. As a control (reference samples) were used three replicates from non-activated microglia from non-infected mice (CCE9701-CCE9703). All the other samples are coming from VSV-infected mice.

first: C

last: Chhatbar

first: M

last: Jordao

last: Prinz

first: U

last: Kalinke


title: Transcriptomic responses to MCHM in Saccharomyces cerevisiae

status: Public on Jan 10 2018

city: Morgantown

first: Xiaoqing

last: Rong-Mullins

state: West Virginia

address: 53 Campus Dr

institute: West Virginia University

summary: This study investigates the transcriptomic responses of Saccharomyces cerevisiae S96 normal and petite cells to 4-Methylcyclohexanemethanol (MCHM), a coal cleaning chemical spilled in the water supply of central West Virginia in 2014.

overall_design: Examination of two cell types - normal and petite, in two growth media - YM and YPD, treated with MCHM or not treated; two replicates per cell type per growth medium per MCHM treatment

first: Michael

last: Ayers

first: Jennifer

last: Gallagher


title: The Arabidopsis SUMO E3 ligase SIZ1 mediates the temperature dependent trade-off between plant immunity and growth

status: Public on Jan 02 2018

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

summary:
Increased ambient temperature is widely considered to be inhibitory to basal and effector-triggered plant immunity. For example, SNC1-dependent auto-immunity in Arabidopsis results in enhanced basal resistance at 22ºC, which is fully suppressed at 28ºC. The sumoylation mutant siz1 also displays auto-immunity at 22ºC. We find that its auto-immunity is sustained at 28ºC while still requiring PAD4/EDS1 and SNC1 function. Moreover, its rosette size does not fully recover at 28ºC, which is normally seen for SNC1 gain-of-function mutants. Related, thermomorphogenesis is also compromised in the SUMO mutants. This role of SIZ1 in growth regulation does not depend on PAD4 or SNC1. In corroboration, SUMO mutants show a global delay in their transcriptional profile for thermosensitive growth regulators and these differentially expressed genes show an overrepresentation for PIF4 genomic targets. This transcription factor (TF) PIF4 is the central regulator of thermomorphogenesis, while also inhibiting plant immunity at 28ºC. Our findings thus reveal that SUMO conjugation has a central role in PIF4 regulation prioritizing growth over immunity at elevated temperatures. Such molecular understanding of how temperature affects growth over immunity is important to mitigate the effects of climate change on agriculture
This experiment we have examined how gene expression is affected in two SUMO mutants (siz1-2; sumo1 amiR-SUMO1 [aka. sumo1/2KD] ) when the plants are placed at 28C constant ambient temperature, which is a condition normally used to induce thermomorphogenesis. We used as control the pad1-4 background, as the siz1-2 and sumo1/2KD mutants normailly suffer from constitutive defence signalling due hyperaccumulation of SA, which is suppressed by introgression of pad4 in these backgrounds.

overall_design: Three biological replicates per samples; Arabidopsis plants were grown at 22C (t=0) and shifted to 28C (t=24hrs, and t=96 hrs post shift); In total three lines were compared: pad4-1 ('negative' control), siz1-2 pad4-1 double mutant, and sumo1-1 amiR-SUMO2 pad4-1  triple mutant

first: Valentin

last: Hammoudi

first: Bas

last: Beerens

first: Georgios

last: Vlachakis

first: Sayantani

last: Chatterjee

first: Like

last: Fokkens

first: Manuel

last: Arroyo-Mateos

first: Paul

middle: F

last: Wackers

middle: J

first: Harrold

middle: A

last: Van den Burg


title: Next-generation sequencing of human dermal fibroblasts transdifferentiated towards the otic lineage

status: Public on Jan 09 2018

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

country: Spain

institute: CSIC

summary: We report the RNAseq analysis of human dermal fibroblasts which have been treated by protocols to stimulate their differentiation towards the otic lineage. This was achieved by transfection with different transcription factors with the aim to induce an initial reprogramming of the cells and was followed by growth factor treatments known to promote otic differentiation. The results show that a partial differentiation towards the otic lineage is achieved by these protocols.

overall_design: RNAseq profiles were obtained from human dermal fibroblasts  with two different protocols. Prior to treatment with growth factors stimulating differentiation, the samples were either transfected with the transcription factors OCT4 or a combination of ATOH1, POU4F3 and GFI1.

first: Carlos

last: Prieto