title: HNF4A intestinal epithelial conditional loss incidence on jejunum expression from mice fed a HFD.

status: Public on Mar 18 2020

city: Sherbrooke

first: François

last: Boudreau

address: 3201, rue Jean-Mignault

institute: Université de Sherbrooke

summary:
HNF4A encodes a nuclear receptor required for the development of the intestine and involved in the homeostasis maintenance of intestinal epithelial cells during the adulthood. Also strongly related to the hepatic lipid metabolism, little was known about its metabolic relevance from the intestine when challenged by a high fat diet.
We used microarrays to detail the global programme of jejunal gene expression depending on HNF4α and influenced by HFD.

overall_design: Adult mice conditionally deleted for HNF4α from intestinal epithelial cells and control mice were fed a high fat diet for 12 weeks.

first: Romain

last: Girard

first: Sarah

last: Tremblay

first: Christophe

last: Noll

first: Stéphanie

last: St-Jean

first: Yves

last: Gélinas

first: Mathieu

last: Laplante

first: André

last: Carpentier


title: Epigenomic and transcriptomic analyses of epithelial ovarian cancer

status: Public on Mar 10 2020

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 8700 Beverly Blvd

department: Women's Cancer Program

country: USA

institute: Cedars-Sinai Medical Center

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Profiling of active chromatin and gene expression in primary ovarian cancer specimens

overall_design: To catalogue the landscape of active chromatin in primary tissues representing the major histological subtypes of OC, we performed ChIP-seq for acetylated lysine 27 of histone H3 protein (H3K27ac), a mark of active promoters and enhancers, on 20 primary tissue specimens, specifically 5 CCOCs, 5 EnOCs, 5 HGSOCs, and 5 MOCs. We observed inter-histotype heterogeneity among the 20 epigenomic landscapes (union set = 295,349 peaks, encompassing 11.6% of the genome). As expected, the common peaks (n = 12,954) shared across all histologies were enriched in promoter regions when compared to the whole genome (odds ratio = 86, P < 0.001, Fisher’s exact test); in contrast, the histotype-specific regions defining CCOC (n = 5,401), EnOC (n = 20), HGSOC (n = 6,583) and MOC (n = 2,134) fall predominantly in enhancers. Using a matched RNA-sequence (RNA-Seq) dataset for 19 (out of 20) tumor specimens, we identified 1,214 differentially expressed genes (DEGs) specific for CCOC, just 16 DEGs for EnOC, 519 DEGs for HGSOC and 371 DEGs for MOC. Both analyses, H3K27ac ChIP-Seq and RNA-Seq, suggest a lack of specificity for EnOCs. Genes flanking histotype-specific peaks of active chromatin were consistently expressed at higher levels in the relevant histotype; conversely, genes flanking depleted regions were under-expressed in a histotype-specific manner, indicating that the different enhancer landscapes of OC histotypes regulate histotype-specific patterns of gene expression in cis.

first: Matthew

middle: L

last: Freedman


title: Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation

status: Public on Feb 18 2020

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells (OPCs). If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear, because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones, single cell RNA sequencing, in vivo calcium imaging and manipulation of neural activity, we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity, but infrequently differentiates, despite contact with permissive axons. Instead, these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs, which readily differentiates and which shows less elaborate, more dynamic processes, and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate, with implications for myelin development, plasticity, and repair.

overall_design: Single-cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations, and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tg(olig1:memEYFP) transgenic zebrafish at 5 days post fertilization were FACS sorted in 384-well plated containing cell lysis buffer and subsequently processed for SmartSeq2

first: Roberta

last: Marisca

first: Tobias

last: Hoche

first: Laura

last: Hoodless

first: Wenke

last: Barkey

first: Franziska

last: Auer

first: Gonçalo

last: Castelo-Branco

first: Tim

last: Czopka


title: Transcriptomic profiling of bat immune responses (P. alecto)

status: Public on Feb 12 2020

city: Singapore

first: Linfa

last: Wang

address: 8 college road

department: Programme in Emerging Infectious Diseases

country: Singapore

institute: Duke-NUS Medical School

summary: To examine the fundamental immunity in bats, particularly the status of their innate immune system in the basal healthy state, we profile Pteropus alecto bat tissue with Deep NGS coverage. This is coupled to a paired experiment where bats were stimulated in vivo with various PRR ligands to activate immune pathways.

overall_design: 5 bats as healthy control for lung, 4 bats x spleen/liver

first: Aaron

middle: T

last: Irving

first: Zhu

last: Feng


title: Enhanced deoxysphingobase production in HSN1 results in sensory nerve toxicity through deficits in both cell autonomous and axoglial signalling, ameliorated by serine treatment

status: Public on Mar 25 2020

city: Oxford

first: Georgios

last: Baskozos

address: Level 6, West Wing, John Radcliffe Hospital

department: NDCN

country: United Kingdom

institute: Oxford University

summary: Hereditary sensory neuropathy type 1 (HSN1) is caused by mutations in either the SPTLC1 or SPTLC2 sub-units of the enzyme Serine Palmitoyl Transferase resulting in the production of Deoxyshingobases (DSBs). Exogenous DSBs are toxic when acutely applied to neurons however it’s unknown whether endogenous DSBs are neurotoxic and the mechanism of such toxicity. Using induced pleuripotent stem cells (iPSC) from HSN1 patients we found increased DSB production from both hepatocytes and sensory neurons. Gene expression profiling in HSN1 iPSCd-sensory neurons showed dysregulation in axon outgrowth and lipid signalling pathways. We noted reduced lipid raft formation, impaired growth factor signalling and reduced neurite outgrowth in these neurons. Gangliosides which are essential for membrane dynamics and lipid raft formation and were globally reduced due to feedback inhibition of DSBs on the enzyme… In co-cultures between HSN1 iPSCd-sensory neurons and rat Schwann the nodal complex and myelin were disrupted.  HSN1 SPTLC mutations therefor impair cell autonomous and inter-cellular signalling due to altered lipid metabolism, changes which could largely be prevented by treatment with Serine (which reduces DSB production) supporting Serine as a rational therapy.

overall_design: RNA-seq Illumina HiSeq4000 of IPSC and IPS derived sensory neurons from healthy controls, patients with HSN1 in two time points, plus IPSDSN treated with serine

first: A

last: Clark

first: U

last: Kugathasan

first: G

first: I

last: Blesneac

first: T

last: Hornemann

first: F

last: Platt

first: M

last: Reilly

first: D

last: Bennett


title: DNA Methylation Potential Energy Landscape Analysis of MLL-rearranged Acute Myeloid Leukemia (AML) and Normal hematopoietic precursors [WGBS]

status: Public on Mar 02 2020

city: Baltimore

first: Michael

middle: A

last: Koldobskiy

state: MD

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

type: Methylation profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) carrying MLL rearrangements. We applied WGBS and the informME analysis pipeline to investigate the role of DNA methylation stochasticity in MLL-rearranged AML.

overall_design: WGBS was carried out on primary acute myeloid leukemia samples harboring KMT2A (MLL) rearrangements and on normal human myeloid progenitor cells.

first: Andrew

middle: P

last: Feinberg


title: Transcriptomic profiling of bat immune responses (e. spelaea)

summary: To examine the fundamental immunity in bats, particularly the status of their innate immune system in the basal healthy state, we profile Eonycteris spelaea bat tissue with Deep NGS coverage. This is coupled to a paired experiment where bats were stimulated in vivo with various PRR ligands to activate immune pathways.

overall_design: 2 bats as healthy control for lung, spleen and liver


title: Transcriptome and translatome of Streptomyces avermitilis MA-4680

status: Public on Mar 03 2020

city: Daejeon

first: Yongjae

last: Lee

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: The gram-positive bacterium, Streptomyces avermitilis holds industrial importance, which produces widely used anthelmintic agent, avermectin. Furthermore, S. avermitilis is generally considered as a prominent heterologous gene expression host for diverse secondary metabolites biosynthesis. However, despite of its industrial importance, it largely remains unknown how its genome is organized and regulated for timely gene expression. Here, we determined 1,601 transcription units (TU) encoded in its genome using the integrated analysis of high-throughput sequencing data including dRNA-Seq, Term-Seq, RNA-Seq, and Ribo-Seq. In addition to TU cataloguing, these information-rich results also revealed the presence of diverse regulatory elements for the transcriptional and translational control of individual TU, such as promoters, 5¢-UTRs, terminators, 3¢-UTRs, and riboswitches. The conserved promoter sequences for transcription initiation were identified from 2,361 transcription start sites as 5¢-TANNNT and 5¢-TGAC for -10 and -35 elements, respectively. Interestingly, the -35 element and spacer length between them were critical for transcriptional regulation of functionally distinct genes. Total 2,017 transcription termination sites were detected from Term-Seq analysis, revealing that stem structure formation is a prerequisite for transcription termination and that Rho-independent termination prevails in S. avermitilis. Lastly, the TU architecture suggests the presence of novel small RNAs and cis-regulatory elements in the genome. Our findings will serve as invaluable resources for comprehensive understanding on regulatory features of S. avermitilis. Moreover, it is anticipated the elevation of its potential as the heterologous expression host for diverse secondary metabolite biosynthesis.

overall_design: Profiles of 5' termini of primary transcripts, 3' termini of whole transcripts, whole transcripts and ribosome protected RNA fragements of Streptomyces avermitilis were generated by deep sequencing using Illumina Hi-Seq 2500

first: Yujin

last: Jeong

first: Namil

first: Soonkyu

last: Hwang

first: Woori

last: Kim

first: Suhyung

last: Cho

first: Bernhard

middle: O

last: Palsson

first: Byung-Kwan


title: The zinc-finger protein OEF-1 stabilizes patterns of activating and silencing modifications in the C. elegans germ line

status: Public on Mar 24 2020

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary: Sex-determining chromosomes exhibit complex global regulation in germ cells, in part due to the absence of dosage compensatory mechanisms found in the soma. In the XX hermaphrodite germ line of C. elegans, the X chromosome houses few germline-expressed genes [1] and is poorly expressed, though not completely silent, through most of germ cell development [2].  A chromatin-modifying pathway consisting of the histone methyltransferase (HMT) MES-4 and the Polycomb Repressive Complex 2 (PRC2) orthologs MES-2/3/6 contributes to X silencing in C. elegans germ cells [3-5]. MES-4 promotes H3K36me3 accumulation on autosomes, which leads to concentration of H3K27me3 on the X by MES-2/3/6 [5]. Loss of MES activity results in inappropriate activation of X-linked genes and second-generation sterility [5, 6]. The two marks occupy mutually exclusive domains of the genome [5, 7], leading to a model in which the presence of one modification prevents the accumulation of the other at specific loci. However, further details about how this repulsion mechanism between H3K27me3 and H3K36me3 is established remain mysterious. Here we implicate the zinc-finger protein OEF-1 in counterbalancing the accumulation of H3K27me3 throughout the genome, particularly on the X chromosome. Strikingly OEF-1, like MES-4, is localized to sites of active gene expression in the germ line, and promotes H3K36me3 levels in mes-4 mutants. Our data thus identify OEF-1 as a novel modulator of the fundamental relationship between gene activation and gene silencing in the C. elegans germ line.

overall_design: This data submission includes ChIP-seq samples in C. elegans performed in duplicate for two histone modifications on four genotypes, with one input sample per replicate. In addition, we are submitting a bigwig ile for each dataset.  We are also submitting six RNA-seq datasets representing triplicate analysis of wild type and mutant (oef-1(vr25)) dissected gonads from C. elegans.

first: Catherine

middle: E

last: McManus

first: Guifeng

last: Wei

first: Mei

last: Han


title: Heat-induced transcriptional memory profiled in human K562 erythroleukemia cells.

status: Public on Mar 04 2020

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH Royal Institute of Technology

summary: Precision run-on sequencing (PRO-seq) of nascent RNA synthesis across the human genome. The PRO-seq data was generated from human K562 erythroleukemia cells that were either unconditioned (unCond) or preconditioned with multiple heat shock exposures (preCond). After two day recovery from the preconditioning, during which the cells underwent two mitotic divisions, the cells were additionally subjected to a single heat shock to measure nascent transcription in response to heat shock in unconditioned versus preconditioned cells.

overall_design: Genome-wide nascent transcription profiles from human K562 cells that were either unconditioned or preconditioned with multiple heat shock exposures. The K562 cells' ability to mount transcriptional response to stress in unconditioned versus preconditioned cells was measured in the presence (scrambled sequence transfected) or absence (shHSF1) of the master transcriptional activator upon heat shock, HSF1.

first: Samu

middle: V

last: Himanen

first: Lea

last: Sistonen


title: RNA-sequencing of microglia from IL-5 or PBS treated aged (20mos) mice

status: Public on Jan 21 2020

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

summary: The role of IL-5 in brain neuroimmunity remains unknown. We investigated the role of IL-5 in cognitive function in aged mice. We examined the transcriptomes of sorted microglia and brain T cells from aged mice treated with PBS or IL-5.

overall_design: We used Single-end 75 bp high throughput sequencing to detail the global programme of different gene expression between the microglia and brain T cells of IL-5 or PBS treated aged mice.

first: Ivan

last: Fung


title: RNA-sequencing of cultured young (2-3mos) and aged (20-22mos) mouse brain ILC2

summary: We investigated how aging impacts the ILC2 population in the brain. Through RNA-sequencing of 2-week culture of sorted brain ILC2 from young and aged mice,we identified differential gene expressions regarding cellular exhaustion and self-renewal between young and aged brain ILC2.

overall_design: We used Single-end 75 bp high throughput sequencing to detail the global programme of different gene expression between the 2 weeks culture of young and aged mouse brain ILC2


title: Bulk and single cell transcriptomic data indicate that a dichotomy between inflammatory pathways in peripheral blood and arthritic joints complicates biomarker discovery

status: Public on Jan 10 2020

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

institute: Linköping University

summary:
Background: Unbiased studies using different genome-wide methods have identified several promising novel biomarkers for diagnosis and treatment response in Rheumatoid Arthritis (RA). However, clinical translation has proven difficult. Here, we hypothesized that one reason could be that inflammatory responses in peripheral blood are different from those in the arthritic joint.
Methods: We performed meta-analysis of gene expression microarray data from synovium, whole blood cells (WBC), peripheral blood mononuclear cells (PBMC), and CD4+ T cells from patients with RA and healthy control in order to identify overlapping pathways, predicted upstream regulators and potential biomarkers. We also analyzed single cell RNA-sequencing (scRNA-seq) data from peripheral blood and whole joints from a mouse model of antigen-induced arthritis.
Results: Analyses of two profiling data sets from synovium from RA patients and healthy controls all showed significant activation of pathways of known pathogenic relevance, such as Th1 pathway, role of NFAT in regulation of the immune response, dendritic cell maturation, iCOS-iCOSL signaling in T helper cells, Fc? receptor-mediated phagocytosis, interferon signaling, Cdc42 signaling, and cytotoxic T lymphocyte-mediated apoptosis. The most activated upstream regulators included TNF, an important drug target, as well as IFN-gamma and CD40LG, all of which are known to play important pathogenic roles in RA. The differentially expressed genes from synovium included several potential biomarkers, such as CCL5, CCL13, CCL18, CX3CL1, CXCL6, CXCL9, CXCL10, CXCL13, IL15, IL32, IL1RN, SPP1, and TNFSF11. By contrast, microarray studies of WBC, PBMC and CD4 + T cells showed variable pathways and limited pathway overlap with synovium. Similarly, scRNA-seq data from a mouse model of arthritis did not support that inflammatory responses in peripheral blood reflect those in the arthritic joints. These data showed pathway overlap between mouse joint cells and synovium from patients with RA, but not with cells in peripheral blood.
Conclusions: Our findings indicate a dichotomy between gene expression changes, pathways, upstream regulators and biomarkers in synovium and cell types in peripheral blood, which complicates identification of biomarkers in blood.

overall_design: Single-cell RNA sequencing of blood and joint samples from rheumatoid arthritis mouse model. The raw data from joint are previously published and can be found in the SRA  database  (https://www.ncbi.nlm.nih.gov/sra)  with  accession PRJNA504425, Gawel, Danuta R et al., Genome medicine vol. 11,1 47. 30 Jul. 2019.

first: Eun

first: Xinxiu

last: Li

first: Samuel

last: Schäfer

first: Huan

last: Zhang

first: Mikael

last: Benson


title: Regulatory T Cell depletion causes compensatory immune suppression and accelerated pancreatic carcinogenesis

status: Public on Jan 13 2020

city: Ann Arbor

first: Marina

last: Pasca Di Magliano

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

summary: In human patients and in mouse models, immunosuppressive regulatory T cells(Tregs)accumulate in Pancreatic Intraepithelial Neoplasia (PanIN), the precursor lesions to pancreatic cancer. Tregs are considered a potential therapeutic target with the goal to reverse immunosuppression in a number of malignancies, including pancreatic cancer. Here, using a genetically engineered mouse that allows at will depletion of Tregs during pancreatic carcinogenesis, we determined that Treg depletion failed to relieve immunosuppression. Contradicting the current paradigm, depletion of Tregs led to accelerated tumorprogression. We demonstratedthat Treg depletion resultsin changes in the fibroblast population, exemplified by loss of Smooth Muscle Actinexpression and an increase the myeloid recruiting chemokines Ccl3, Ccl6, and Ccl8. Treg depletion further resulted ina compensatoryinflux of suppressive myeloid cells, thereby preventing an anti-tumor immune response. Mechanistically, we show that themyeloid recruitment was driven through the CCR1 axis, with the receptor expressed on tumor associated myeloid cells and several ligands up-regulated in epithelial cells and fibroblasts upon Treg depletion. Finally,blockade of CCR1 signalingcombined with Treg-depletionsuccessfully inhibitedtumorigenesis, uncovering the immune-suppressive myeloid CCR1 axis as a potential therapeutic targetin pancreatic cancer.

overall_design: Single cell RNA sequencing of whole iKras-ON orthotopic tumor (2 replicates) and early 3 week iKras-ON lesions

first: Yaqing

first: Veerin

last: Sirihorachai

first: Katelyn

last: Donahue


title: Genome-wide microarray analysis on choroid plexus of young and aged mice

summary: Aging induces cognitive decline and Th2 cytokines have been found to promote neurogenesis and cognitive functions. ILC2 are potent producers of IL-5 and IL-13. The role of ILC2 in cognitive function in the context of aging has not been investigated. We report tissue resident ILC2 accumulate in the choroid plexus of the brain in aged mice. They are long-lived and can switch between cellular dormancy and proliferation in response to replication stress. ILC2 play a direct role in promoting the cognitive functions in aged mice, through producing IL-5. IL-5 has neuroprotective functions including neurogenesis and reducing pro-inflammatory functions of microglia in aged mice.

overall_design: We used microarrays to detail the global program of different gene expression between the choroid plexus of young (2-3 mos) and aged (20-22 mos) mice.


title: Targeting transcription-replication conflicts is an effective therapeutic principle for MYCN-driven neuroblastoma

status: Public on Nov 27 2020

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-sequencing of microglia, T cells and ILC2 from the brains of IL-33 treated aged (20-22mos) mice

summary: ILC2 are potent producers of IL-5 and IL-13 and Th2 cytokines have been found to promote neurogenesis and cognitive functions. We report microglia, brain T cells and ILC2 have a range of differentially expressed genes in IL-33 treated aged mice. Brain ILC2 upregulated a range of neuroprotective genes.

overall_design: We used Single-end 75 bp high throughput sequencing to detail the global programme of different gene expression between the microglia, T cells and ILC2 from the brains of IL-33 treated aged (20-22mos) mice.


status: Public on Dec 04 2019

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Neuronal expression of Alzheimer's disease-associated FAD mouse genotype at 3/6/12 months.

overall_design: Three month comparison of 5XFAD-TG (n = 2) vs WT (n = 2); six month comparison of 5XFAD-TG (n = 3) vs WT (n = 3); twelve month comparison of 5XFAD-TG (n = 3) vs WT (n = 2).

middle: I

first: Ping-Chung

last: Chen

first: Junmin

last: Peng


title: Prolonged generation of erythroid cells from human induced pluripotent stem cells in a  three-dimensional culture system with reduced cytokine support

status: Public on Dec 09 2019

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary:
Ex vivo red blood cell (RBC) differentiation from human induced pluripotent stem cells (hiPSCs) offers great potential
for developmental studies and innovative therapies.
However, ex vivo erythropoiesis from hiPSCs is currently limited by its complexity and the absence of a physiological niche,
which may impair cell growth and lineage-specific differentiation.
We describe a simplified culture system for RBC generation over 6 weeks from hiPSCs using
1) low cytokine support (SCF, EPO, and IL-3) and
2) maintenance of a three-dimensional organization during hematopoietic specification.
CD43+ hematopoietic cells containing high percentages of CD34+/CD45+ and CD36+/CD45+ progenitors were continuously released into the supernatant.
During further erythroid differentiation into >90% GPA+ cells, up to 60% of cells extruded their nuclei depending upon the hiPSC origin.
These advantages may be explained by the generation of an artificial niche within adherent spheroids that sufficiently mimics the spatiotemporal
signaling of the physiological microenvironment in which erythropoiesis occurs
RNA samples for microarray analysis were prepared using RNeasy columns (Qiagen, Germany)
with on-column DNA digestion.
300 ng of total RNA per sample were used as the input in the linear
amplification protocol (Ambion), which involved the synthesis of T7-linked double-stranded cDNAs and 12 hrs of in vitro transcription
incorporating biotin-labeled nucleotides.
Purified and labeled cRNA was then hybridized for 18 hrs onto HumanHT-12 v4
expression BeadChips (Illumina, USA) following the manufacturer’s instructions.
After the recommended washing,
the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.
The samples were exclusively hybridized as biological replicates.
The bead intensities were mapped to the corresponding gene information using BeadStudio 3.2 (Illumina) and background correction was performed
using the Affymetrix Robust Multi-array Analysis (RMA) background correction model (Irizarry et al., 2003).
Variance stabilization was performed using the log2 scaling,
and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.

overall_design:
3 samples were analyzed
H1-ESC, H1 humam Embryonics Stem Cells (ESCs), 2 replicates
PEB#1 iPS, Human Basophilic Erythroblasts (PEB) induced Pluripotent Stem Cells  (iPSCs), 1 replicate

first: Claudia

last: Bernecker

first: Mania

last: Ackermann

first: Nico

last: Lachmann

first: Lisa

last: Rohrhofer

first: Holm

last: Zaehres

middle: J

last: Araúuzo-Bravo

first: Emile

last: van den Akker

first: Peter

last: Schlenke

first: Isabel

last: Dorn


title: Influence of in vitro embryo culture in the epigenetic control of imprinted genes and transposable elements in children born via assisted reproduction technologies

status: Public on May 21 2020

city: DIJON

first: Yannis

last: Duffourd

address: Batiment B3, 15 boulevard Maréchal de Lattre de Tassigny

country: France

institute: Inserm U1231

summary:
Genome-wide DNA methylation profiling of buccal smears from children born via assisted reproductive technologies.
The Illumina 850k Human DNA methylation EPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Samples included 12 controls and 36 samples.

overall_design: Bisulphite-converted DNA from the 48 samples were hybridised to the Illumina 850k Human Methylation EPIC BeadChip.

first: Julie

last: Barberet

first: Christine

last: Binquet

first: Magali

last: Guilleman

first: Abiba

last: Doukani

first: Cécile

last: Choux

first: Céline

last: Bruno

first: Abderrahmane

last: Bourredjem

first: Caroline

last: Chapusot

first: Déborah

last: Bourc’his

first: Patricia

last: Fauque


title: Defining the influence of the A12 subunit on transcription elongation and termination by rna polymerase I

status: Public on Dec 21 2019

city: Birmingham

first: Andrew

middle: Martin

last: Clarke

state: Al

address: 720 20th street S

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: we performed Native Elongating Transcript Sequencing (NET-seq) on an rpa12Δ strain of S. cerevisiae and evaluated the resultant change in Pol I occupancy throughout the 35S gene and the IGS. Compared to WT, we observed template sequence-specific changes in Pol I occupancy throughout the 35S gene. We also observed rpa12Δ Pol I occupancy downstream of both termination sites and throughout most of the IGS, including the 5S gene. Occupancy of rpa12Δ Pol I increased just upstream of the promoter proximal Reb1 binding site and dropped significantly after, implicating this site as a third terminator for Pol I transcription.

overall_design: Native Elongating Transcript Sequencing (NET-seq) was performed in triplicate on WT and rpa12Δ S. cerevisiae strains.

first: David

last: Schneider

first: Chad

middle: M

last: Petit


title: Widespread roles for piRNAs and WAGO-class siRNAs in shaping the germline transcriptome of Caenorhabditis elegans

status: Public on Dec 03 2019

city: Fort Collins

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts.

overall_design: Small RNA and mRNA high-throughput sequencing was done using RNA isolated from whole animals and from the dissected distal gonads of wild type and prg-1 and mut-16 mutant animals. Differential expression analysis was done to identify mRNAs enriched in distal gonads relative to whole animals and in prg-1 and mut-16 mutants relative to wild type animals.

first: Kailee

last: Reed

first: Joshua

last: Svendsen


title: DNA methylation regulates nephron progenitor cell renewal and differentiation

status: Public on Nov 15 2019

city: Freiburg

first: Nicola

last: Wanner

address: Breisacherstraße 66

department: Renal Division

institute: University Medical Center Freiburg

summary: Nephron number is a major determinant of long-term renal function. We hypothesized a link between epigenetic regulation and nephron formation. In support of this hypothesis, expression analysis evidenced high levels of DNA methyltransferases Dnmt1 and Dnmt3a in the nephrogenic zone of the developing mouse kidney. Using targeted loss-of-function manipulations in mice, we show that deletion of Dnmt1 in nephron progenitor cells results in a marked hypoplasia and reduction of nephron number at birth. In contrast, deletion of Dnmt3a/3b in nephron progenitor cells or deletion of Dnmt1/3a/3b in differentiated renal cells did not lead to any overt kidney phenotype. Whole mount optical projection tomography and 3D-reconstructions uncovered a significant reduction of stem cell niches and progenitor cells in Dnmt1-deficient mice. Ultimately, RNA sequencing analysis revealed that Dnmt1 controls DNA transcription regulating progenitor renewal, identity and differentiation. In summary, this study establishes DNA methylation as key regulatory event of prenatal renal programming.

overall_design: RNA-seq of FACS-sorted cap mesenchyme of E18.5 Six2.Cre;Dnmt1 conditional heterozygous and homozygous knockout mice

first: Melanie

last: Boerries

first: Hauke

last: Busch

first: Wibke

last: Bechtel-Walz

first: Tobias

middle: B

last: Huber


title: Transcriptomic profiling reveals distinct modes of aging in the kidney

status: Public on Dec 31 2019

city: Bar Harbor

first: Yuka

last: Takemon

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

summary: The kidney is an excellent model for studying organ aging, but little is known about the molecular changes that take place during the aging process. In this article we measured mRNA expression and protein expression in a large cohort of Diversity Outbred mice at 6, 12, and 18 months of age, and studied the relationship between the changes we observe in mRNA and protein expression as a function of age. We observed enrichments of specific pathways including those that were previously observed to have significant changes with age at the mRNA level, and here we also identified enriched pathways at the protein level. Our analysis of the direction of change in mRNA and protein levels with age at the total population level revealed distinct functional groups that have either concordant or discordant changes in expression levels. The age-interactive quantitative trait loci (QTL) analysis of mRNA (eQTL) and protein (pQTL) revealed many distantly regulated loci as opposed to the many locally regulated eQTL and pQTL observed without age-interaction. From this, we found a locus on chromosome 12 and chromosome 15 to regulate many age-interactive eQTL and pQTL respectively. Overall, our findings demonstrate that the changes with age in the kidney at the protein level are distinctly different from the changes at the mRNA level and are not mediated by mRNA expression.

overall_design: Kidneys of 188 Diversity Outbred mice at 6-months, 12-months, and 18-months of age were sequenced using 100bp single-end HiSeq 2500 to understand transcriptional changes that occur in the aging kidney.

first: Gary

last: Churchill

first: Ron

last: Korstanje


title: Dysregulation of Placental Functions and Immune Pathways in Complete Hydatidiform Moles

status: Public on Oct 31 2019

city: Budapest

first: Gábor

middle: Nándor

last: Than

address: Magyar tudósok krt. 2

department: Institute of Enzymology

country: Hungary

institute: Research Centre for Natural Sciences

summary: We analyzed high-dimensional RNA data to characterize molecular features of complete hydatidiform moles (CHMs) and corresponding pathologic pathways. CHMs and first trimester placentas were collected, histopathologically examined, then flash-frozen. Frozen CHMs and control placentas were subjected to RNA-Seq, with resulting data and published placental RNA-Seq data subjected to bioinformatics analyses. Of the 14,022 protein-coding genes expressed in all samples, 3729 were differentially expressed (DE) in CHMs of which 72% were up-regulated. DE genes were enriched in placenta-specific genes (OR = 1.88, p = 0.0001) of which 79% were down-regulated, imprinted genes (OR = 2.38, p = 1.54 × 10−6), and immune genes (OR = 1.82, p = 7.34 × 10−18), of which 73% were up-regulated. DNA methylation enzymes and histone demethylases were dysregulated. “Cytokine–cytokine receptor interaction” was the most impacted of 38 dysregulated pathways, among which 17 were immune-related pathways.

overall_design: Frozen complete hydatidiform moles and control placentas were subjected to RNA-Seq, with resulting RNA-Seq data subjected to bioinformatics analyses.

first: Jennifer

middle: R

last: King

first: Melissa

last: Wilson

first: Szabolcs

last: Hetey

first: Peter

last: Kiraly

first: Andras

last: Szilagyi

first: Lynda

middle: D

last: Roman

first: Victoria

middle: K

last: Cortessis

first: Nandor

middle: G


title: Gene expression profiling in paired normal, apparently normal and breast tumour tissues

status: Public on Oct 18 2019

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

summary: The main objective of the study was to identify potential diagnostic and follow up markers along with therapeutic targets for breast cancer. We performed gene expression studies using the microarray technology on 65 samples including 41 breast tumours [24 early stage, 17 locally advanced, 18 adjacent normal tissue [paired normal] and 6 apparently normal from breasts which had been operated for non-malignant conditions. All the samples had frozen section done – tumours needed to have 70% or more tumour cells; paired normal and apparently normal had to be morphologically normal with no tumour cells.

overall_design:
Two-dye experiments using Universal Control RNA (Stratagene) and RNA from tissues.
Biological replicates - Apparently normal = 6, Paired normal = 18, Breast tumor tissues = 41

first: T

last: Rajkumar

first: Akhilesh

last: Rawat

first: Sabitha

last: Sridevi

first: S

last: Shirley


title: Expression profilling of C. glabrata response to fluconazole and the role of the transcription factor Rpn4 in such response

status: Public on Sep 27 2019

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

summary: The goals of this study are to compare C. glabrata transcriptome profiling (RNA-seq) upon exposure to the antifungal fluconazole in order to assess antifungal response. The role of the transcription factor Rpn4 is clarified through comparison of the transcrptome profiles of WT and Rpn4 mutant cells. mRNA profiles of WT and ∆rpn4 were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq. RNA-seq data allowed to identify genes whose expression is regulated by the Rpn4 transcription factor (80 positively regulated and 212 negatively regulated) with a log2fold change ≥0.5 and p value <0.05. The transcriptomics data was then used to guide further work to detail the function of Rpn4.

overall_design: Yeast mRNA profiles after 1h fluconazole exposure of WT and ∆cgrpn4 cells were generated by RNA-Seq, in duplicate (each duplicate made of triplicate samples pooled together) using Illumina HiSeq

first: Pedro

last: Pais

first: Raquel

last: Califórnia

first: Mónica

last: Galocha

first: Romeu

last: Viana

first: Mihaela

last: Ola

first: Azusa

last: Takahashi-Nakaguchi

first: Hiroji

last: Chibana

first: Geraldine

last: Butler

middle: C


title: Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics

status: Public on Sep 12 2019

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: We profile the transcriptomes of over 100,000 human single cells, yielding molecular definitions for non-parenchymal cell types present in healthy and cirrhotic human liver. We uncover a novel scar-associated TREM2+CD9+ macrophage subpopulation, which expands in liver fibrosis, differentiates from circulating monocytes, has a corollary population in mouse liver fibrosis and is pro-fibrogenic. We also define novel ACKR1+ and PLVAP+ endothelial cells which expand in cirrhosis, are topographically scar-restricted and enhance leucocyte transmigration. Multi-lineage ligand-receptor modelling of interactions between the novel scar-associated macrophages, endothelial cells and PDGFRα+ collagen-producing mesenchymal cells reveals intra-scar activity of several pro-fibrogenic pathways including TNFRSF12A, PDGFR and NOTCH signalling. Our work dissects unanticipated aspects of the cellular and molecular basis of human organ fibrosis at a single-cell level, and provides the conceptual framework required to discover rational therapeutic targets in liver cirrhosis.

overall_design: Single-cell transcriptomic data are presented from 5 healthy livers, 5 cirrhotic livers and 4 PBMC samples from cirrhotic patients. We also present single-cell transcriptomic data on hepatic macrophages from healthy mice or mice following chronic carbon tetrachloride administration.

first: Prakash

last: Ramachandran

first: Neil

last: Henderson


title: Next Generation Sequencing Analysis of miRNA profiling in fibroblast or myofibroblast

status: Public on Sep 18 2019

city: Omaha

first: Tu

last: Yaping

state: NE

address: 2500 California Plaza

department: Pharmacology

institute: Creighton University School of Medicine

summary: We reported the application of next generation sequencing technology for high-throughput profiling of miRNA expression in human primary lung fibroblast Cells with undifferentiated (fibroblast) or differentiated (myofibroblast) status. By comparation the expression aboundence of known miRNAs between undifferentiated and differentiated type human primary lung fibroblast cells, we found both upregulated and downregulated miRNAs in fibroblast cells during differentiation. This study provides a basic condition for further investigation of the roles of the regulated miRNAs during differentiation in fibroblast cells.

overall_design: Examination of miRNA profiling in fibroblast and myofibroblast subtypes of human primary lung fibroblast Cells

first: Yaping

last: Tu

first: Peng

last: Wei


title: Epigenetic modifications of gene promoters in the liver of Balb/c mice protected by vaccination against blood-stage malaria of Plasmodium chabaudi

status: Public on Sep 23 2019

first: Marcos

last: Araúzo-Bravo

type: Methylation profiling by genome tiling array

summary: Protective vaccination induces survival of more than 80% of female Balb/c mice otherwise succumbing to blood-stage malaria of Plasmodium chabaudi. This study investigates the effect of protective vaccination and P. chabaudi infections on DNA methylation of gene promoters in the liver of Balb/c mice. Using DNA methylation microarrays, protective vaccination is shown to affect per se the constitutive DNA methylation status of numerous gene promoters in the liver: Promoters of 256 genes are hyper(=up)- and 345 genes are hypo (=down)-methylated at a significance of p<0.05. Gene enrichment analysis reveals that genes with down-methylated promoters are most statistically significant enriched (p<0.01) with functions related to negative regulation of transcription, whereas genes with up-methylated promoters are related to positive regulation of transcription and immune system. Infections with P. chabaudi also induce changes in promoter DNA methylation. In vaccinated mice, these changes are observable already on day 1 p.i. and, in particular, at peak parasitemia on day 8 p.i., when 571 and 1013 gene promoters have become up- and down-methylated, respectively, in relation to constitutive DNA methylation at a signicance level of p<0.05. The corresponding gene promoters in non-vaccinated mice are also responsive to infection, but by far not as pronounced as in vaccinated mice. Our data demonstrate that vaccination modifies DNA methylation of gene promoters in the liver and augments promoter responsiveness to infection-induced DNA methylation alterations, which ultimately control expression of those genes in the liver required for survival of otherwise lethal blood-stage malaria of P. chabaudi.

overall_design:
18 samples were analyzed;
Nd0, Non-vaccinated day 0, 3 replicates
Vd0, Vaccinated day 0, 3 replicates
Nd1, Non-vaccinated day 1, 3 replicates
Vd1, Vaccinated day 1, 3 replicates
Nd8, Non-vaccinated day 8, 3 replicates
Vd8, Vaccinated day 8, 3 replicates

first: Saleh

last: Al-Quraishy

first: Mohamed

last: Dkhil

first: Abdel

middle: A

last: Abdel-Baki

first: Foued

last: Ghanjati

first: Lars

last: Erichsen

first: Simeon

last: Santourlidis

first: Frank

last: Wunderlich


title: Gene expression study in SF3B1-mutated, NOTCH1-mutated and WT CLL cells

status: Public on Sep 07 2019

city: Aviano

first: Federico

last: Pozzo

state: PN

address: via Franco Gallini 2

department: Department of Translational Research

country: Italy

institute: Centro di Riferimento Oncologico (CRO) di Aviano IRCCS

summary: Mutations of SF3B1 in CLL induce alternative splicing in multiple transcripts, including DVL2. DVL2 in turn can act as a negative regulator of NOTCH1 signaling. Gene Expression Profile (GEP) was used to investigate the activation of the NOTCH1 pathway in presence of alternatively spliced DVL2.

overall_design: Constitutive gene expression in CLL cells bearing either SF3B1 mutations, NOTCH1 mutation or none of them (WT). Bioinformatic analyses were performed by GenespringGX

first: Riccardo

last: Bomben

first: Valter

last: Gattei


title: Viral N6-methyladenosine upregulates replication and pathogenesis of human respiratory syncytial virus

status: Public on Sep 10 2019

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

summary: N6-methyladenosine (m6A) is the most prevalent internal modification of mRNAs in most eukaryotes. Likewise, viral RNAs may acquire m6A methylation during replication within these cells. Here we show that RNAs of human respiratory syncytial virus (RSV), a medically important non-segmented negative-sense (NNS) RNA virus, are modified by m6A within discreet regions and that these modifications enhance viral replication and pathogenesis. Overexpression of m6A binding proteins significantly enhanced RSV replication and gene expression. Knockdown of m6A methyltransferases decreased viral replication and gene expression whereas knockdown of m6A demethylases had the opposite effect. The G gene contained the most abundant m6A modifications. Recombinant RSV expressing a G gene lacking different m6A sites, resulted in RSVs with various degrees of defects in replication in A549 cells, primary well differentiated human airway epithelial (HAE) cultures, upper and lower respiratory tract of cotton rats, and were also less pathogenic to the lungs of cotton rats. One of the m6A-deficient rgRSVs, rgRSV-G12, was completely attenuated yet retained high immunogenicity in cotton rats. Moreover, a small molecule that inhibits S-adenosyl-L-homocysteine (SAH) hydrolase, thereby reducing the cellular SAH pool and viral RNA m6A, also inhibited RSV replication in HAE cells. Collectively, our results demonstrate viral m6A methylation upregulates RSV replication and pathogenesis and identify viral m6A methylation as a target for rational design of live attenuated vaccine candidates and for novel antiviral therapeutic agents for RSV.

overall_design: RSV virions were purified from supernatants of RSV-infected Hela and A549 cell lines. Virus derived mRNA as well as host mRNA were purified from total RNA, which were extracted from RSV infected cells.

first: Miaoge

last: Xue

first: Jianrong

last: Li


title: Pollution Effects on Metabolic Gene Expression During Late Organodifferenatiation of  Sensitive, Resistant and Hybrid Vertebrate Embryos

status: Public on Jul 19 2019

city: San Diego

first: Goran

last: Bozinovic

address: 3370 Dale Street

institute: Boz Institute

summary: The goal was to determine differences in gene expression of 384 metabolic genes during late organogenesis among embryos of parents from a clean site (Magotha Bay, VA) and polluted site (Elizabeth RIver, VA).  Hybrid gene expression was examined to explore parental effect.  Embryo morphology and heart rate during late organogenesis and pre-hatching was assessed in order to determine phenotypic differences between embryo groups.

overall_design: Labeled RNA samples were hybridized to slides according to the loop design, a randomized incomplete block design that involves constraints of different treatment types so that every comparison is represented by a direct contrast on a microarray.  Each sample was hybridized to 2 arrays using both Cy3 and Cy5 flourescent dyes, which is a simple and effective way for the direct comparison of two samples, and for reducing technical variation (Churchill, 2002).  The loop  consisted of Cy3 and Cy5 labeled individual embryo aRNA, resulting in total of 40 replicates (20 biological replicates x 2 dyes for each.  Since each array consisted of 4 replicates of metabolic genes, there were 8 total number of gene expression measurement for each embryo (embryo aRNA x 2 dyes x 4 gene replicates = 8 measurements / embryo).   The loop formed was CC5 -- PP41 --CP21--PC26--CC9--PP32--CP13--PC24--CC6_PP34--CP16--PC28--CC10--PP33-CP18-PC27-CC7-PP40-CP17-PC25-CC5, where each dash represents a separate hybridization (array) with the individual biological sample at the left of the dash labeled with Cy3 and the biological pool at the right of the dash labeled with Cy5.  C denotes clean site parent, P denotes polluted site parent; Hence, the CC, CP, PC, and PP represent treatments  (CC = embyo of a mother fomr the celan site and the fater from the clean site; CP = embryo of a mother from the clean site and fatehr from polluted site, etc...). A nuber after the treament (CC5, so #5) represents the individual embryo utilized (5th embryo in CC treamtent).

first: Marjorie

middle: F

last: Oleksiak


title: Estrogen deprivation triggers and immunosuppressive phenotype in breast cancer cells

status: Public on Jul 27 2019

city: Solna

first: Jordi

last: Carreras-Puigvert

state: Stockholm

address: Tomtebodavägen 23A, SciLifeLab, Alfa 4

department: Medical Biochemistry and Biophysics

institute: Karolinska Institutet

summary: Our study reveals that while antiestrogen therapies effectively limit tumor growth in ER-positive breast cancers, they also trigger a transcriptional program that favors immune evasion.

overall_design: Study of differential gene expression among MCF-7 breast cancer cells cultured in DMEM, SFM (steroid free medium) or Fulvestrant

first: Daniela

last: Hühn

first: Pablo

last: Marti-Rodrigo

first: Silvana

last: Mouron

first: Catherine

last: Hansel

first: Kirsten

last: Tschapalda

first: Maria

last: Häggblad

first: Louise

last: Lidemalm

first: Miguel

last: Quintela-Fandino

first: Oscar

last: Fernandez-Capetillo


title: Cytosolic Proteostatic Adaptation to Mitochondrial Stress Causes Progressive Muscle Wasting

status: Public on Aug 09 2019

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary:
Purpose: Muscle wasting (or atrophy) occurs in primary neuromuscular diseases and during aging, with sarcopenia affecting 35.4% and 75.5% of women and man over 60 years of age. Mitochondrial dysfunction is proposed to contribute to muscle wasting. Here, we show that chronic adaptation to mitochondrial Precursor Over-accumulation Stress (mPOS) causes muscle wasting. mPOS is a newly discovered cell stress mechanism caused by the saturation or damage of the mitochondrial protein import machinery, which consequently leads to the toxic accumulation of precursor proteins in the cytosol.
Methods: We generated transgenic mice with a two-fold increase of Ant1, an adenine nucleotide translocase involved in ATP/ADP exchange on the inner mitochondrial membrane (IMM). We found that these animals progressively lose muscle mass. At two years of age, the skeletal muscle becomes barely quantifiable, without affecting the overall lifespan. We then performed whole-transcriptome RNA-sequencing on skeletal muscle samples of male and female mice at 6 months of age.
Results: After alignment and quantification, we show that the ANT1-transgenic muscles have a drastically remodeled transcriptome that represses protein synthesis, and stimulates proteasomal function, autophagy, lysosomal amplification and Gadd45a-signaling. These four processes are all known to promote muscle wasting.
Conclusions: These results suggest that chronic proteostatic adaptation to mPOS is a robust mechanism of muscle wasting, and it leads to or depends in part on a robust set of transcriptional adaptations. This finding may help the understanding of how mitochondria contribute to muscle wasting during aging. It may also have implications for diseases that are associated with ANT1 overexpression.

overall_design: Skeletal muscle mRNA profiles of 6-month old wild type (WT) and Ant1 transgenic overexpressing mice were generated by stranded paired-end RNA sequencing, in quadruplicate, using Illumina NextSeq500.

first: XinJie

last: Chen


title: Oct4 and Hnf4alpha-induced hepatic stem cells attenuated hepatic function in liver injury model

status: Public on Aug 21 2019

first: Marcos

last: Araúzo-Bravo

summary: Generation of expandable induce hepatic stem cells (iHSCs) has a potential for cell-based therapy and drug screening in liver disease. Recently many groups reported reprogramming of somatic cells into hepatocyte-like cells by direct conversion. However, the induced hepatocytes have limitations in proliferation, function and viability for cell therapy and drug development.  We generated iHSCs which have properties including self-renewal and bipotency into hepatocytes and cholangiocytes. iHSCs-derived hepatocytes showed typical morphology and functions which include glycogen storage, low-density lipoprotein (LDL) uptake, Indocyanine green (ICG) metabolism, and Albumin secretion, and iHSCs-derived cholangiocytes also have functional characteristics of cholangiocytes, including cyst and tubules formation, cyst polarity, and the secretion of small substances by transmembrane channel protein. In addition, iHSCs attenuated liver injury, such as alcohol induced steatosis and carbon tetrachloride (CCl4) induced fibrosis models.  Taken together, generation of functional iHSCs would be used in therapeutic applications.

overall_design: 7 samples were analyzed: pHep, primary Hepatocytes, 1 replicate, MEF, Mouse Embryonic Fibroblast , 4 replicates, iHep, induced Hepatic Stem Cells , 2 replicates)

first: Myung

last: Park

first: Donggyu

last: Nam

first: Jeong

last: Kim


title: Elucidating the oncogenic role of Menin in prostate cancer progression

status: Public on Jun 18 2019

city: MARSEILLE

first: Chaima

last: cherif

address: 27 Bd lei Roure CS 30059

institute: crcm 1068 inserm

summary: Menin protein is encoded by the multiple endocrine neoplasia type 1 (MEN1) gene. It remains an enigmatic protein,  known as a tumor suppressor but its roles in cancer development have attracted significant attention in recent years. The goals of this study is to understand how the Menin tumor suppressor can be oncogenic in Prostate, we have profiled Menin chromatin occupancy by chromatin immunoprecipitation coupled to high-throughput DNA sequencing (ChIP-seq) in the normal prostate model (PNT1A) and in a different stage of prostate cancer CS model (LNCaP) and CR model (PC-3).

overall_design: Examination of the potential genetic changes in 3 differents cell line PNT1a, LNCaP and PC-3.

last: Cherif

first: Julien

last: Vernerey

first: Nadine

last: Carbuccia

first: Palma

last: Rocchi

first: Estelle

last: Duprez


title: Expression data from Saccharomyces cerevisiae F12 cells in the presence of insoluble solids at high concentration

status: Public on Aug 23 2019

city: Madrid

first: Antonio

middle: David

last: Moreno

address: Avda. Complutense 40

department: Department of Energy

country: Spain

institute: CIEMAT

summary: The implementation of a cost-effective lignocellulosic ethanol production requires developing efficient high gravity processes (i.e. working at high substrate concentrations). During the fermentation processes, the presence of high concentration of insoluble solids leads to lower glucose consumption rates, reduced ethanol volumetric productivities, and the accumulation of intracellular reactive oxygen species (ROS). Major repressed biological processes include cell cycle progression, trehalose and glycogen biosynthesis, DNA repair mechanisms, and certain genes involved in the general cell stress response. On the other hand, genes related to the glutathione, thioredoxin and methionine scavenging systems are induced.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: S. cerevisiae F12 cells were collected during fermentation in presence of insoluble solids for RNA extraction and hybridization on Affymetrix microarrays. Furthermore, cells collected during fermentation in absence of insoluble solids at the same time point were used as control.

first: Elia

last: Tomás-Pejó


title: Expression profiles of microRNAs in oxidized low-density lipoprotein-stimulated RAW 264.7 cells

status: Public on Jun 05 2019

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

country: China

institute: Sichuan Agricultural University

summary: Foam cells were one of the hallmarks of atherosclerosis, and microRNAs (miRNAs) played an important role in the formation of foam cells. In order to explore the roles of miRNA in the formation of foam cells, In the present study, to understand the molecular mechanisms of miRNAs involved in AS, we provide insights into the genome-wide dynamic profiles of miRNAs by using high-throughput sequencing technology.

overall_design: we investigated miRNA expression profiles from the control group (control-1, control-2, and control-3, n=3) and ox-48h group (ox-48h-1, ox-48h-2 and ox-48h-3, n=3) by using high-throughput sequencing technology.


title: Generation of induced oligodendrocyte progenitor cells from human somatic cells

status: Public on Apr 20 2019

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

institute: Korea University

summary: The goals of this study are to compare transcriptome of NGS-derived induced oligodendrocyte progenitor cells (RNA-seq)

overall_design: mRNA profiles of A2B5+ iOPCs, O4+ iOPCs, OLIG2+ iOPCs, SOX10+ iOPCs, and fibroblasts were generated by deep sequencing, in triplicate, using Illumina Hiseq2500.

first: Wonjin

last: Yun


title: The Caudate Nucleus Undergoes Dramatic and Unique Transcriptional Changes in Human Prodromal Huntington's Disease Brain

status: Public on Apr 09 2019

city: Boston

first: Adam

last: Labadorf

state: MA

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

summary: The mechanisms underlying degeneration of the specific neurons in the striatum of Huntingon's Disease (HD) brain are currently unknown. The striatum is massively degenerated in late stage HD, making examination of post-mortem brain tissue from symptomatic individuals problematic. In this study, caudate nucleus (CAU) tissue from two asymptomatic HD+ individuals was subjected for comparison with similar datasets with symptomatic HD individuals and healthy controls.

overall_design: 11 Huntington's Disease and 5 neurologically normal control samples from post-mortem human subjects

first: Richard

last: Myers

first: Agus

last: Filisia

first: Crespo

last: Diego


title: Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution

status: Public on Mar 20 2019

city: Beltsville

first: Lingzhao

last: Fang

address: 10300 Baltimore Avenue

department: ARS

institute: USDA

summary: Using whole-genome bisulfite sequencing (WGBS), we profiled 18  DNA methylomes of cattle sperms that were collected from 18 representative age-matched Holstein bulls with high reliable phenotypes on many complex traits, including  sire-conception rate (SCR), gestation length (GL),  sire calving ease (SCE), cow conception rate (CCR) and body depth (BDE).  Through comparison with human sperm methylome, we observed that genomic regions with differetial DNA methylation levels were enriched for GWAS signals and had important evolutionary impact. By comparing animals with extreme SCR, we showed that differentially methylated regions (DMR) associated with SCR and aging were significantly and selectively enriched for GWAS signals of male fertility traits in cattle. In addition, we detected ans compared DMRs assocaited with GL, CCR, SCE and BDE. We integrated GWAS signals of 37 complex traits with  DMRs associated with GL to provide insights into genetic basis of GL.

overall_design: Genomic DNA of sperm was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified sperm genomic DNA were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).

first: George

middle: E

last: Liu


title: Single cell RNA-sequencing of human fetal kidneys

status: Public on Feb 21 2019

city: Leiden

first: Stefan

last: Semrau

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

summary: 10X-based scRNA-seq data human fetal kidneys at 5 different ages

overall_design: w9, w11, w13, w16 and w18 human fetal kidneys

first: Mazène

last: Hochane

first: Patrick

last: van den Berg

first: Xueying

last: Fan

first: Noémie

last: Bérenger-Currias

first: Esmée

last: Adegeest

first: Monika

last: Bialenka

first: Maaike

last: Nieveen

first: Maarten

last: Menschaart

first: Susana

last: Chuva de Sousa Lopes


title: Generation of induced oligodendrocyte progenitor cells (OPCs) from human somatic cells by OCT4

status: Public on May 02 2019

first: Seungkwon

last: You

summary: The goal of this study is to identify the role of OCT4 in combination with small molecules as the critical cue governing the reprogramming of human somatic cells into OPCs using ChIP-seq

overall_design: DNA derived from Human A2B5+ iOPCs(H), Human A2B5+ iOPCs(M), and H9-hESCs subjected to ChIP with anti-OCT4 antibody were analyzed by deep sequencing, in tri- or duplicate, using NextSeq500 or Illumina Hiseq2500. A2B5+ iOPCs(H) were derived from human fibroblasts with high levels of OCT4 and A2B5+ iOPCs(M) were derived from human fibroblasts with medium levels of OCT4. H9-hESCs served as a sequencing control.

first: Wonjin

last: Yun


title: Development of a selective CDK7 covalent inhibitor reveals predominant cell cycle phenotype

status: Public on Jan 04 2019

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The relationship between promoter proximal transcription factor-associated gene expression and super-enhancer-driven transcriptional programs are not well-defined. Some level of their distinct genomic occupancy may suggest a mechanism with specific target gene control. We explored the transcriptional and functional interrelationship between E2F transcription factors and BET transcriptional co-activators in multiple myeloma. Global chromatin analysis reveals distinct regulatory axes for E2F and BETs, with E2F predominantly localized to active gene promoters of growth/proliferation genes and BETs disproportionately at enhancer- regulated tissue specific genes. Depletion of E2F selectively down-regulates its regulatory axis and is generally synergistic with BET inhibition. In vivo, combined inhibition of BETs and E2F strongly reduces tumor growth, implicating E2F as a myeloma dependency that is potently leveraged with BET inhibition.

overall_design: Cyclin-dependent kinase 7 (CDK7) regulates both cell cycle and transcription, but its precise role remains elusive. We previously described THZ1, a CDK7 inhibitor, which dramatically inhibits super-enhancer associated gene expression. However, potent CDK12/13 off-target activity obscured CDK7s contribution to this phenotype. Here, we describe the discovery of a highly selective, covalent CDK7 inhibitor.  YKL-5-124 causes arrest at the G1/S transition and inhibition of E2F-driven gene expression; these effects are rescued by a CDK7 mutant unable to covalently engage YKL-5-124, demonstrating on-target specificity. Unlike THZ1, treatment with YKL-5-124 resulted in no change to Pol II CTD phosphorylation; however, inhibition could be reconstituted by combining YKL-5-124 and THZ531, a selective CDK12/13 inhibitor, revealing potential redundancies in CDK control of gene transcription.  These findings highlight the importance of CDK7/12/13 polypharmacology for anti-cancer activity of THZ1 and posit that selective inhibition of CDK7 may be useful for treatment of cancers marked by E2F misregulation.

first: Calla

last: Olson

first: Yanke

last: Liang

first: Woojun

last: Park

first: Selma

middle: Z

last: Elsarrag

middle: Y

first: Nicholas

last: Kwiatkowski

first: Nathanael

middle: S

last: Gray


title: Identification of a novel lncRNA family that is required for efficient cellular transformation by Bcr-Abl oncogene

status: Public on Apr 17 2019

city: Beijing

first: Xuefei

last: Wang

state: Beijing

address: NO.1 West Beichen Road, Chaoyang District, Beijing 100101, China

institute: nstitute of Microbiology, Chinese Academy of Sciences (CAS)

summary:
Aberrantly expressed long noncoding RNAs (lncRNAs) have been described in diverse human diseases and cancer development. Chronic myeloid leukemia (CML) is a hematological malignancy induced by Bcr-Abl hybrid gene. Owing to the development of tyrosine kinase inhibitors (TKIs), especially the first-generation Imatinib, over 90% of CML patients can be cured in recent years. Here we attempt to identify Imatinib-inducible lncRNAs associated with CML by analyzing lncRNA expression profiles in K562 cells after Imatinib or control treatment. LncRNA microarray analysis revealed that numerous lncRNAs were differentially expressed in K562 cells after Imatinib treatment. In this study, we focus on a conserved, Imatinib-inducible lncRNA (IIR) family, named lncRNA-IIRX. Upregulation of lncRNA-IIRX has been detected in both human and mouse Abl-transformed cell lines after Imatinib treatment. Interestingly, lncRNA-IIRX levels were significantly lower in leukemic cells derived from Bcr-Abl-positive ALL patients than those in normal control group. Furthermore, altering lncRNA-IIRX expression remarkably affected survival of Abl-transformed leukemic cells, and tumorigensis induced by these leukemic cells in xenograft mouse model. Knockdown of lncRNA-IIRX in transgenic mice significantly promoted Bcr-Abl-mediated primary bone marrow transformation, and leukemia development in leukemia mouse model. These results indicate that lncRNA-IIRX functions as a suppressor gene in Bcr-Abl-induced tumorigenesis, and may provide novel insights into complicated mechanisms underlying cellular transformation by Bcr-Abl oncogene.
This microarray was performed to identify Imatinib-inducible lncRNAs associated with CML.

overall_design: Total RNAs were isolated from three independent groups of K562 cells treated with Imatinib or DMSO respectively. Then, total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

first: Jilong

last: Chen


title: Lhx2 controls changes in chromatin accessibility in retinal progenitor cells during developmental competence transitions.

status: Public on May 09 2019

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N. Broadway Avenue

department: Department of Neuroscience

institute: Johns Hopkins University School of Medicine

summary: We profiled retinal progenitor cells by integrating next generation sequencing methods and interrogating changes in chromatin accessibility at embryonic and post-natal murine stages. We identified putative factors involved in the developmental progression of the  retinal progenitors epigenome and we report Lhx2 role in the regulation of chromatin accessibility by coordinated action of developmentally regulated pioneer factors

overall_design: Next generation sequencing methods were performed on RPCs that express the neuro-retinal transgene Chx10-Cre:eGFP. Chx10 positive (Chx10+ve) RPCs were separated from the post-mitotic pool by fluorescence activated cell sorting, isolated at embryonic day (E) 14 and postnatal day (P) 2 and they have been hereafter referred to as GFP+, whereas the post-mitotic pool as GFP-.Flow sorted cells were profiled by RNA-Seq and ATAC-Seq, relying on direct in vitro transposition of sequencing adapters into native chromatin.   ChIP-Seq was then performed on the top transcription factor candidate, identified in the preliminary screening of the ATAC-Seq derived open chromatin regions.  ChIP-Seq binding sites for the candidate factor were ultimately integrated and compared with the age-matched  RNA-Seq and  ATAC-Seq profiles from control and knock-out retinas.

first: Cristina

last: Zibetti

first: Sheng

last: Liu

first: Jun

last: Wan

first: Jiang

last: Qian


title: Biotic stress-induced priming and de-priming of transcriptional memory in apple.

status: Public on Dec 04 2018

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary: In order to identify primed (and memorized) genes resulting from BTH and/ or flg22 application, we performed a series of microarray-based transcription profiles. 14 days after propagation plants were treated the first time with the indicated treatment and second time 17 days after propagation with the indicated treatment. Plants were harvested and RNA was extracted 31 days after propagation. BTH was applied as formulated compound Bion. The sample name reflects the treatment order. Samples with the name water_water are control treatments which were treated 14 and 17 days after propaghation with water. The sample with the name Bion_flg22 was treated 14 days after germination with BTH and 17 days after germination flg22.

overall_design: With this microarrays we investigate the long term memory effect of treatments with the SA analouge BTH (1mM) and with flg22 (1µM) with or after exposure with the SA analouge BTH, in two biological replicates for each comparison.

first: Kay

last: Gully

first: Jean-Marc

last: Celton

first: Alexandre

last: Degrave

first: Marie-Noelle

last: Brisset

first: Etienne

last: Bucher

first: Sandrine

last: Balzergue

first: Muriel

last: Bahut


title: Comparison between nitroglycerine and vehicle treatments in mouse trigeminal ganglia and nucleus accumbens

status: Public on Jan 02 2019

city: Urbana

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

summary: Chronic nitroglycerin treatment elicits hyperalgesia in mice that is significantly augmented by a human migraine trigger and reduced with migraine therapy. The purpose of this study was to  profile mRNA levels (transcriptome) to understand the differences between nitroglicerin and vehicle treatments in two nervous system regions, the trigeminal ganglia and the nucleus accumbens,

overall_design: RNA samples were obtained from 10 mice 24 hours after the last nitroglicerin injection (Intraperitoneal injections of nitroglycerin every second day for 9 days total) and were subjected to paired-end RNA sequencing


title: Biotic stress-induced priming and de-priming of transcriptional memory in Arabidopsis

summary: In order to identify primed (and memorized) genes resulting from BTH and/ or flg22 application, we performed a series of microarray-based transcription profiles. 7 days after germination Arabidopsis plants were treated the first time with the indicated treatment and second time 10 days after germination with the indicated treatment. Plants were harvested and RNA was extracted 21 days after germination. BTH was applied as formulated compound Bion. The sample name reflects the treatment order. Samples with the name water_water are control treatments which were treated 7 and 10 days after germination with water. The sample with the name Bion_flg22 was treated 7 days after germination with BTH and 10 days after germination flg22.

overall_design: With this microarrays we investigate the long term memory effect of treatments with the SA analouge BTH (1mM) and/ or flg22 (1µM) in two biological replicates


title: J_093015-circRNA-33 AS-CR-005 Human CircRNA V2 microarray 01272016

status: Public on Oct 31 2018

city: DUBLIN

first: JOHN

last: GREENE

address: ST JAMES'S HOSPITAL

country: Ireland

institute: TRINITY COLLEGE DUBLIN

summary:
Background: Most forms of castration-resistant prostate cancer (CRPC) are dependent on the androgen receptor (AR) for survival. While, enzalutamide provides a substantial survival benefit, it is not curative and many patients develop resistance to therapy. Although not yet fully understood, resistance can develop through a number of mechanisms, such as AR copy number gain, the generation of splice variants such as AR-V7 and mutations within the ligand binding domain (LBD) of the AR. Circular RNAs (circRNAs) are a novel type of non-coding RNA, which can regulate the function of miRNA, and may play a key role in the development of drug resistance. CircRNAs are highly resistant to degradation, are detectable in plasma and, therefore may serve a role as clinical biomarkers.

Methods: AR-V7 expression was assessed in an isogenic model of enzalutamide resistance. The model consisted of age matched control cells and two sub-lines displaying varied resistance to enzalutamide. circRNA profiling was performed on the panel using a high throughout microarray assay. Bioinformatic analysis identified a number of differentially expressed circRNAs and predicted five miRNA binding sites for each circRNA. miRNAs were stratified based on known associations with prostate cancer, and targets were validated using qPCR.

Results: Overall, circRNAs were more often down regulated in resistant cell lines compared with control (588 vs. 278). Of particular interest was hsa_circ_0004870 (Probe ID ASCRP3009662), which was down-regulated in enzalutamide resistant cells (p≤0.05, vs. sensitive cells), decreased in AR positive cells (p≤0.01, vs. AR negative), and in malignant cells (p≤0.01, vs. benign). The associated parental gene was identified as RBM39, a member of the U2AF65 family of proteins. Both genes were down-regulated in resistant cells (p<0.05, vs. sensitive cells).

Conclusion: This is one of the first studies to profile and demonstrate discrete circRNA expression patterns in an enzalutamide resistant cell line model of prostate cancer. Our data suggests that hsa_circ_0004870, through RBM39, may play a critical role in the development of enzalutamide resistance in CRPC.

overall_design: The isogenic enzalutamide resistance LNCaP model was gifted from Novartis (13). The panel consisted of an aged match control cell line (drug sensitive), and two sub-lines termed clone 1 and clone 9. Clone 1 was most resistance to the drug, with clone 9 displaying moderate resistance. Cells were cultured in RPMI-1640 media (Merck KGaA, Darmstadt, Germany) with 10% FBS (Merck KGaA) and 1% Penicillin Streptomycin (Merck KGaA). DU145 were cultured in ATCC-formulated Eagle's Minimum Essential Medium (Merck KGaA) with 10% FBS and 1% Penicillin Streptomycin and PC-3 were cultured in ATCC-formulated F-12K Medium containing 10% FBS and 1% Penicillin Streptomycin (Thermo Fisher Scientific, CA, US).

first: John

last: Greene


title: Epigenome analysis of depressed and control subjects.

status: Public on Jan 16 2019

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

summary: Genome wide DNA methylation profiling of depressed (n=489) and control subjects (n=210)  that were recruited at the Max Planck Institute of Psychiatry (MPIP). The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles based whole blood samples.

overall_design: Bisulphite converted DNA from the 699 samples were hybridised to the Illumina Infinium 450k Human methylation Beadchip .

first: Elisabeth

middle: B

last: Binder


title: Expression data from mouse lung from mice fed diets containing permethrin

status: Public on Dec 21 2018

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

country: Japan

institute: Sumitomo Chemical Co., Ltd.

summary:
Female Crlj:CD1(ICR) mice were fed diets containing 0 (control), 5000 and 10000 ppm permethrin and 2500 ppm isoniazid (positive control for tumor induction) for periods of 7 and 14 days.
We used microarrays to evaluate gene expression profiling in mouse lung at the early phase of treatment with permethrin and isoniazid.

overall_design: After treatment periods, lungs of 39 mice (4 or 5 mice in each group) were excised for RNA extraction and hybridization on Affymetrix microarrays.

first: Fumihiro

last: Yamada


title: BAF Complex Enhances Reprogramming of Adult Human Fibroblasts

status: Public on Nov 29 2018

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: Chromatin remodeling molecules of the BAF complex, Brg1 and Baf155, as well as other chromatin remodeling modeling molecules have been described to enhance Oct4, Sox2, Klf4 and c-Myc mediated reprogramming of mouse somatic cells into induced pluripotent stem cells (iPSCs). Brg1 maintains pluripotency of mouse embryonic stem cells (mESCs) by modulating the expression of pluripotency genes including Oct4 in synergism with LIF/STAT signaling. Interestingly, unlike mESCs, BAF complex in human embryonic stem cells (hESCs) is composed of both BAF155 and BAF170, where BAF170 plays a role in maintaining hESCs pluripotency. In this study, we describe that BRG1 and BAF155 enhance reprogramming of adult human fibroblasts. Overexpression of BAF155 does not affect pluripotency of hiPSCs as tested by global gene expression profiling as well as in vivo and in vitro assays. Additionally, these findings show that BRG1 and BAF155 expression can enhance reprogramming even in the absence of LIF/STAT signaling.

overall_design:
RNA samples for microarray analysis were prepared using RNeasy columns (Qiagen, Germany) with on-column DNA digestion. 300 ng of total RNA per sample were used as the input in the linear amplification protocol (Ambion), which involved the synthesis of T7-linked double-stranded cDNAs and 12hrs of in vitro transcription incorporating biotin-labeled nucleotides. Purified and labeled cRNA was then hybridized for 18 hrs onto HumanHT-12 v4 expression BeadChips (Illumina, USA) following the manufacturer's instructions. After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software. The samples were exclusively hybridized as biological replicates. The bead intensities were mapped to the corresponding gene information using BeadStudio 3.2 (Illumina) and background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model (Irizarry et al., 2003). Variance stabilization was performed using the log2 scaling, and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

19 samples were analyzed:
H1, H1 human Embryonic Stem Cells (ESCs), 3 replicates
H9, H9 human Embryonic Stem Cells (ESCs), 3 replicates
H4FiPS1, Human 4 factors (Oct4, Sox2, Klf4 and Myc) induced pluripotent stem (iPS) cells, clone 1, 3 replicates
H4FiPS2, Human 4 factors (Oct4, Sox2, Klf4 and Myc) induced pluripotent stem (iPS) cells, clone 2, 3 replicates
H6FiPS2, Human 6 factors (Oct4, Sox2, Klf4, Brg1 and Baf155) induced pluripotent stem (iPS) cells, clone 2, 3 replicates
H6FiPS3, Human 6 factors (Oct4, Sox2, Klf4, Brg1 and Baf155) induced pluripotent stem (iPS) cells, clone 3, 3 replicates
Fibro, F134 Human Fibroblast, 1 replicate

first: Nishant

last: Singhal

middle: J

first: Martina

last: Sinn

first: Holm

last: Zaehres


title: henn-1/HEN1 promotes germline immortality in Caenorhabditis elegans

status: Public on Sep 20 2019

city: Fort Collins

first: Taiowa

last: Montgomery

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

summary: Small RNA and mRNA high-throughput sequencing was done to explore the roles of henn-1 and small RNA methylation in regulating gene expression and small RNA stability in C. elegans. Our results point to a requirement for henn-1 in methylating piRNAs, primary siRNAs, and a subset of miRNAs. In the absence of henn-1, modest changes in gene expression were observed in animals grown under optimal condition.

overall_design: To explore the role of henn-1 on the various classes of small RNAs, RNA was isolated from various mutant animals and from Argonaute co-immunoprecipitates and subjected to small RNA and/or mRNA sequencing. Differential expression in mutants compared to wild type animals was done using a variety of methods, primary DESeq2 when doing genome-wide comparisons. Enrichment in Argonaute co-immunoprecipitates relative to cell lysates was used to assess Argonaute-small RNA interactions. RNA polyphosphatase treatment was used to assess 5' phosphorylation of small RNAs and to enable capture of 22G-RNAs. Sodium periodate treatment was used to asses 3'-2'-O-methylation of small RNAs.

first: Joshua

middle: M

last: Svendsen

first: Kailee

last: Reed


title: Single cell RNAseq analysis of PTHrP+ dental follicle cells

status: Public on Sep 19 2018

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: PTHrP is abundantly expressed by dental follicle cells. We set out to reveal single cell profiles of FACS-sorted PTHrP-mCherry+ cells isolated from the mandible.

overall_design: mCherry+ cells were FACS-isolated from postnatal day 6 (P6) dental follicles of PTHrP-mCherry+ mandibular molars. ~8,000 cells were loaded onto 10X Genomic Chromium platform. cDNA was sequenced by Illumina HiSeq4000.


title: Carcinogen-induced tumours arise from Lgr5+ intestinal stem cells in pp2a-/- mice

status: Public on Sep 27 2018

city: Taichung City

first: Yu-Ting

last: Yen

state: Taiwan

address: No. 2, Yude Road, North District,

country: Taiwan

institute: China Medical University

summary: Purpose: mRNA profiles of organoids from Lgr5-EGFP-CreERT2; Ppp2r1a flox/flox mice with DMBA or/and tamoxifen were generated by deep sequencing

overall_design: Examination of RNA expression in 5 treated organoid types.

first: Shih-Chieh

last: Hung


title: Epigenetic stabilization of DC and DC precursor classical activation by TNFalpha drives protective T-cell polarization

status: Public on Aug 15 2018

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

country: USA

institute: University of Iowa

summary: We report that TNFalpha mediated dendritic cell priming via alterations in histone 3 lysine 4 trimethylation (H3K4me3) sustains lasting protective Th1/Th17 responses during invasive Cryptococcus neoformans pulmonary infection. Cryptococcus neoformans pulmonary infection results in increased global lung dendritic cell H3K4me3 over naive lung dendritic cells. Blockage of TNFalpha during Cryptococcus neoformans pulmonary infection results in decreased H3K4me3 at sites crucial to protective Th1/Th17 responses.

overall_design: Examination of H3K4me3 in lung CD11c+ dendritic cells in 4 different conditions


title: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (ATAC-seq)

status: Public on Oct 05 2018

city: Los Angeles

first: Owen

middle: N

last: Witte

state: CA

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: MIMG

institute: UCLA

summary: Small cell carcinomas from different tissues exhibit transcriptional and epigenetic convergence and suggest common vulnerabilities for therapies

overall_design: Convergent neuroendocrine cancer from distinct epithelial tissues

first: Jung

middle: W

last: Park


title: Paternal exposure to Arctic contaminants alters the sperm epigenome and induces negative pregnancy outcomes transgenerationally

status: Public on Aug 30 2018

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

institute: UMR1078 - Université de Bretagne Occidentale

summary: Paternal exposure to environmentally-relevant Arctic contaminants induces adverse health outcomes and alters the sperm methylome over three generations.

overall_design: Genome-wide methylation profiles of rat epididymal sperm across F1, F2 and F3 generations spermatozoa profiles (6 organochlorines exposed and 6 controls per generation)

first: Janice

middle: L

last: Bailey


title: Comparative transcriptome analysis in induced neural stem cells reveals defined neural cell identities in vitro and after transplantation into the adult rodent brain

status: Public on Oct 04 2018

summary:
Reprogramming technology enables the production of large quantities of neural progenitor cells (NPCs) from somatic cells by direct transdifferentiation.
However, little is known on how neural programs in these neural stem cells (iNSCs) differ from those of alternative stem cell populations in vitro and in vivo.
Here, we performed transcriptome analyses on iNSCs in comparison to brain-derived neural stem cells (NSCs) and pluripotent stem cell-derived NPCs, which revealed distinct global, neural, metabolic and cell cycle-associated marks in these populations. iNSCs carried a hindbrain/spinal cord identity, which could be shifted towards caudal, partially to rostral but not towards ventral fates in vitro. iNSCs survived after transplantation into the rodent brain and exhibited in vivo-characteristics, neural and metabolic programs similar to those of transplanted NSCs. However, iNSCs vastly retained caudal identities demonstrating cell-autonomy of regional programs in vivo.
These data could have significant implications for a variety of biomedical applications using iNSCs.
For microarray analysis, total RNA was isolated using the RNeasy kit (QIAGEN) according to the manufacturer´s instructions and including an on-column DNA digestion. 300 µg of RNA were subsequently used in the linear amplification protocol (Ambion) including the synthesis of T7-linked double-stranded cDNA and 12 hr of in vitro transcription incorporating biotin-labeled nucleotides. cDNA samples were hybridized as biological replicates onto MouseRef-8 v2 expression BeadChips (Illumina) for 18 hr according to the manufacturer´s instructions. Chips were washed and subsequently stained with streptavidin-Cy3 (GE Healthcare), before being scanned using the iScan reader (Illumina) and the associated software. BeadStudio 3.2 software (Illumina) was used to map bead intensities to gene information. For background correction, the Affymetrix robust multi-array analysis (RMA) background correction model was applied.  Variance stabilization was performed using the log2 scaling and gene expression was normalized with the method utilized in the lumi package of R-Bioconductor.

overall_design: 13 samples were analyzed: NSC-In vivo, iNSC-In vivo, NSC, iNSC, ESC NPC, MEF, ESC

first: Anna-Lena

last: Hallmann

first: Christina

last: Zerfass

first: Volker

last: Senner

first: Marc

last: Ehrlich

first: Olympia

last: Psithaki

first: Don-Wok

last: Han

first: Natalia

last: Tapia

first: Hans

middle: R

last: Schöler

first: Tanja

last: Kuhlmann

first: Gunnar

last: Hargus


title: Stage-specific transcriptome analysis during differentiation from pluripotency to glial restricted progenitor stages

status: Public on Jul 26 2018

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

institute: Korea University

summary: The goals of this study are to compare NGS-derived neural transcriptome profiling (RNA-seq) and to investigate involving transcription factors at each stages

overall_design: mRNA profiles of BJ, iPSC, ESC, NSC, GPLC were generated by deep sequencing, in triplicate, using Illumina Hiseq2500.

first: Wonjin

last: Yun


title: Comparison of 5' UTR structures in Listeria monocytogenes

status: Public on Aug 11 2018

city: Berlin

first: Dmitriy

last: Ignatov

address: Charitéplatz 1

institute: Max Planck Unit for the Science of Pathogens

summary: To understand physiological processes in vivo, it is vital to disclose the conformation of biological molecules inside living cells and correlate their structure with their function. Here, we describe a method, FUSE (5’-UTR Structure Elucidation) that was used to characterize changes in the structures of 5’-UTRs at different conditions inside the human bacterial pathogen Listeria monocytogenes. Using FUSE, we discovered a novel RNA thermoswitch and calculated the ratio of two conformations that this thermoswitch assumes at different conditions. FUSE could also identify the site of base-pairing interaction between a small RNA and mRNA with a single-nucleotide resolution. Strikingly, FUSE discovered a functional mRNA-mRNA interaction, where the stability of mRNA encoding PrsA2 chaperone, was increased by the direct binding of an mRNA encoding its substrate, listeriolysin O, the main L. monocytogenes virulence factor. Owing to its focus on 5’-UTRs, FUSE can be applied to analyse these regulatory regions in any living organism.

overall_design: L. monocytogenes EGD-e cells or RNA isolated from these cells were treated with dimethyl sulphate (DMS). The modified RNA served as a template for cDNA library construction according to FUSE (5' UTR Structure Elucidation) or Structure-seq protocols. Both these methods employ TGIRTIII reverse transcriptase to encode methylated adenines and cytosines as mismatches in cDNA sequence. While Structure-seq protocol synthesizes cDNA from the total RNA, FUSE selectively enriches for the 5' UTR regions in the cDNA library. The resulting cDNA libraries were sequenced on Illumina MiSeq platform in 2 x 75 bp paired-end mode.

first: Jörgen

last: Johansson


title: Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin

status: Public on Jun 16 2018

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

summary: Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcriptomic analyses have previously been performed from bulk skin samples or from epithelial and immune cells expanded in cell culture. However, transcriptomic analysis of bulk skin tends to drown out expression signals from relatively rare cells while cell culture methods may significantly alter cellular phenotypes and gene expression profiles. To identify distinct transcriptomic profiles of multiple cell populations without substantially altering cell phenotypes, we employed a fluorescence activated cell sorting method to isolate keratinocytes, dendritic cells, CD4+ T effector cells, CD4+ Treg cells, and CD8+ T effector cells from healthy skin samples, followed by RNA-seq of each cell population. Principal components analysis revealed distinct clustering of cell types across samples, while differential expression and coexpression network analyses revealed transcriptional profiles of individual cell populations distinct from bulk skin, most strikingly in the least abundant CD8+ T effector population. Our work provides a high resolution view of cutaneous cellular gene expression and suggests that transcriptomic profiling of bulk skin may inadequately capture the contribution of less abundant cell types.

overall_design: Transcriptomic profiles from keratinocyte, dendritic cell, CD4+ T cell, CD4+ Treg cells, and CD8+ T cell populations were obtained from surgical skin discards from 11 healthy adults. Cell populations from whole skin were sorted via FACS and transcripts generated using an Illumina HiSeq 2500 platform. RNA-seq data for the bulk control samples were originally deposited in GEO study GSE74697.

first: Keyon

last: Taravati

first: Kevin

last: Lai

first: Kristina

last: Lee

first: Joanne

last: Nititham

first: Rashmi

last: Gupta

first: David

last: Chang

first: Sarah

middle: T

last: Arron

first: Michael

last: Rosenblum

first: Wilson

last: Liao


title: Differential Expression of miRNAs in control and NR_034085-silenced OSCCs under cisplatin treatment

status: Public on Jun 12 2018

city: Guangzhou

first: Guokai

last: Pan

address: 107 Yanjiang West Road

department: Department of Oral and Maxillofacial Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: chemoresistance frequently leads to therapeutic failure in oral squamous cell carcinoma (OSCC). Recently, studies have reported that lncRNAs play active roles in regulation biological properties of cancer and may regulate the expression of miRNA. We also found that miRNAs could regulate cisplatin sensitivity in TSCC previously. In this study, to explore the potential targets of lncRNAs in response to cisplatin, we performed microarray to detect miRNAs both in control and NR_034085–silenced CAL-27 and SCC-9 cells under cisplatin treatment.

overall_design: We investigated the differential expression profiles of miRNA in tongue squamous carcinoma cells between 6 groups: the CAL27 control group, the CAL27 stably transduced with shRNA1 targeted NR_034085  (CAL27 shRNA1 group), the CAL27 stably transduced with shRNA3 targeted NR_034085  (CAL27 shRNA3 group), the SCC9 control group and the SCC9 stably transduced with shRNA1 targeted NR_034085  (SCC9 shRNA1 group), the SCC9 stably transduced with shRNA3 targeted NR_034085  (SCC9 shRNA3 group).Sample labeling and array hybridization were performed by  Agilent_Human_miRNA_8x60k_70156_v21 (Agilent Technologies) according to the Agilent miRNA Microarray protocol. After quantile normalization of the raw data, the miRNAs detected were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through P value/FDR filtering.


title: Differential Expression of LncRNAs  after cisplatin treatment in tongue squamous carcinoma cells

summary: chemoresistance frequently leads to therapeutic failure in oral squamous cell carcinoma (OSCC). Recently, studies have reported that lncRNAs play active roles in regulation biological properties of cancer. To understand whether lncRNAs involve in regulating  cisplatin sensitivity in TSCC, in this study, we profiled the expression of lncRNAs in two TSCC cell lines(CAL-27 and SCC-9) under cisplatin treatment paired untreated cell lines by LncRNA Array (ArrayStar V3.0).

overall_design: We investigated the differential expression profiles of lncRNA in tongue squamous carcinoma cells between four groups: the CAL27 control group, the CAL27 treated with cisplatin group  (CAL27+ci24h group),  the SCC9 control group and the SCC9 treated with cisplatin group (SCC9+ci24h group). Sample labeling and array hybridization were performed by Arraystar Human lncRNA Microarray V3.0 according to the Arraystar microarray-based gene expression analysis protocol (Arraystar, Inc., Rockville, MD, USA). After quantile normalization of the raw data, the lncRNAs detected were chosen for further data analysis. Differentially expressed lncRNAs with statistical significance between the two groups were identified through P value/FDR filtering.