title: TFE3 Xp11.2 translocation renal cell carcinoma mouse model

status: Public on Apr 20 2019

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

summary: Renal Cell Carcinoma (RCC) associated with Xp11.2 translocation (TFE3-RCC) has been recently defined as a distinct subset of RCC. The Xp11 translocations involve the TFE3 transcription factor and produce chimeric TFE3 proteins retaining the basic helix-loop-helix leucine zipper structure for dimerization. To facilitate the development of molecular-based diagnostic tools and targeted therapies for TFE3-RCC, we generated a translocation RCC mouse model and performed DNA microarray analysis.

overall_design: A Rosa26-LSL-PRCC-TFE3 knockin (KI) mouse (PRCC-TFE3) was generated and crossed with KSP-Cre+ mouse. Kidneys were dissected out from 4 month old PRCC-TFE3; KSP-Cre(+) mice (n=4) , 4 month old PRCC-TFE3; KSP-Cre(-) mice (n=4), 7 month old PRCC-TFE3; KSP-Cre(+) mice (n=4) and 7 month old PRCC-TFE3; KSP-Cre(-) mice (n=3). Total RNA was isolated from flash frozen mouse kidneys using TRIzol reagent. cDNA preparation and hybridization of the probe arrays were performed according to the manufacturer's instructions (Affymetrix). Affymetrix GeneChip Mouse Gene 2.0 ST Arrays were applied. Partek Genomics Suite 6.6 was used for RMA-based data normalization and the subsequent data analysis, including PCA and ANOVA.

first: Mitsuko

last: Furuya

first: Takanobu

last: Motoshima

first: Martin

last: Lang

first: Shintaro

last: Funasaki

first: Wenjuan

last: Ma

first: Hong-Wei

last: Sun

first: Hisashi

last: Hasumi

first: Ying

last: Huang

first: Ikuma

last: Kato

first: Tsuyoshi

last: Kadomatsu

first: Yorifumi

last: Satou

first: Nicole

last: Morris

first: Baktiar

middle: O

last: Karim

first: Lilia

last: Ileva

last: Kalen

first: Luh

last: Ade Wilan Krisna

first: Yukiko

first: Aiko

last: Sugiyama

first: Ryoma

last: Kurahashi

first: Koshiro

last: Nishimoto

first: Masafumi

last: Oyama

first: Yoji

last: Nagashima

first: Naoto

last: Kuroda

first: Kimi

last: Araki

first: Masatoshi

last: Eto

first: Masahiro

last: Yao

first: Tomomi

last: Kamba

first: Toshio

last: Suda

first: Yuichi

last: Oike

first: Laura

middle: S

last: Schmidt

first: W

middle: M

last: Linehan


title: Transcriptome analysis of Psoriasis

status: Public on Mar 18 2019

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Louisville

type: Expression profiling by high throughput sequencing

summary: Newly diagnosed psoriatic patients were recruited into this study (total 12 patients. Initially 16 patients were enrolled but only 12 of these patients had complied IRB protocol). These patients were all treated with glucocorticoid (GC) for 2 months and then stopped treatment. Among these patients, patients #2, 4, 6, 7, 10, 11, 12 were considered as effective response to treatment. However, all these patients recurred. In addition, patients #6 and 12 developed more severed disease than pre-treatment. For patient #3, treatment had effect but this patient did not have recurrence. For patients 5, 8, 15, and 16, these patients did not respond to treatment. Thus disease persisted. The purpose of this study is to determine the molecular signatures which can differentiate patients who responded to treatment from those who did not. Secondly we want to understand why some patients developed even more severe disease.

overall_design: The study samples are from 12 of 16 patients with IRB compliance. The samples consist of pre-treatment, post-treatment, and recurrent for each patient, resulting in a total of 36 samples (12 patients x 3 conditions). Seven patients (2, 4, 6, 7, 10, 11, and 12) all had effective response to treatment with recurrence. Of these, two (6 and 12) developed more severe disease than pre-treatment. One patient (3) had no recurrence, and four (5, 8, 15 and 16) did not respond to treatment.

first: Jun

last: Yan

first: David

last: Tieri

middle: C


title: Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer [RNA-seq]

status: Public on Mar 05 2019

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Increasingly effective therapies targeting the androgen receptor have paradoxically promoted the incidence of neuroendocrine prostate cancer (NEPC), the most lethal subtype of castration-resistant prostate cancer (PCa), for which there is no effective therapy. Here we report that protein kinase C (PKC)l/i is downregulated in de novo and during therapy-induced NEPC, which results in the upregulation of serine biosynthesis through an mTORC1/ATF4-driven pathway. This metabolic reprogramming increases intracellular SAM levels to support cell proliferation and epigenetic changes that favor the development of NEPC characteristics. Altogether, we have uncovered a metabolic vulnerability triggered by PKCl/i deficiency in NEPC, which offers potentially actionable targets to prevent therapy resistance in PCa.

overall_design: sgC (WT), PKCl/i KO (sgPKCl/i), and PKCl/i KO rescued with WT-PKCi (sgPKCl/i-R) C42B cells were profiled in three biological replicates under normal conditions.

first: Miguel

last: Reina-Campos

first: Juan

middle: F

last: Linares

first: Angeles

last: Duran

first: Thekla

last: Cordes

first: Antoine

last: L'Hermitte

first: Mehmet

middle: G

last: Badur

first: Munveer

last: Bhangoo

first: Phataraporn

middle: K

last: Thorson

first: Alicia

last: Richards

first: Tarmo

last: Rooslid

first: Dolores

last: Garcia-Olmo

first: Syongh

middle: Y

last: Nam-Cha

first: Antonio

last: Salinas-Sanchez

first: Ken

last: Eng

first: Himisha

last: Beltran

middle: A

last: Scott

first: Christian

last: Metallo

first: Maria

middle: T

last: Diaz-Meco


title: Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia

status: Public on Jan 30 2019

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

institute: University of Colorado School of Medicine

summary: Acute myeloid leukemia (AML) is the most common acute leukemia in adults. Leukemia stem cells (LSCs) drive the initiation and perpetuation of AML, are quantifiably associated with worse clinical outcomes, and often persist after conventional chemotherapy resulting in relapse1-5. In this report, we show that treatment of older patients with AML with the B cell lymphoma 2 (BCL-2) inhibitor venetoclax in combination with azacitidine results in deep and durable remissions and is superior to conventional treatments. We hypothesized that these promising clinical results were due to targeting LSCs. Analysis of LSCs from patients undergoing treatment with venetoclax + azacitidine showed disruption of the tricarboxylic acid (TCA) cycle manifested by decreased α-ketoglutarate and increased succinate levels, suggesting inhibition of electron transport chain complex II. In vitro modeling confirmed inhibition of complex II via reduced glutathionylation of succinate dehydrogenase. These metabolic perturbations suppress oxidative phosphorylation (OXPHOS), which efficiently and selectively targets LSCs. Our findings show for the first time that a therapeutic intervention can eradicate LSCs in patients with AML by disrupting the metabolic machinery driving energy metabolism, resulting in promising clinical activity in a patient population with historically poor outcomes.

overall_design: Single-cell RNA-seq of PBMCs to monitor an AML response to chemotherapy treatment.

first: Jay

middle: R

last: Hesselberth

first: Brett

last: Stevens


title: Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer [MicroArray]

first: Jorge

last: Moscat

overall_design: shNT and shPKCl/I PrEC cells were profiled in three biological replicates under normal conditions.

first: Miguel

last: Reina-Campos

first: Juan

last: Linares

first: Angeles

last: Duran

first: Thekla

last: Cordes

last: L'Hermitte

first: David


title: Transcriptomic analysis of active form of Srebf1-overexpressed fibroblasts in bleomycin-induced lung fibrosis

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

summary: Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although lung fibroblasts play central roles in PF, their key regulatory molecules remain unclear. We performed transcriptome analysis of lung fibroblasts from bleomycin- and silica-treated murine lungs and identified 55 hub transcription factors highly connected to gene modules differentially expressed in PF. To elucidate whether fibroblast-specific intervention against the hub transcription factor Srebf1 modulates pathogenic activation of lung fibroblasts in vivo, we intratracheally-transferred active form of Srebf1-overexpressed fibroblasts into bleomycin-treated lungs and performed global transcriptome analysis.

overall_design: Active form of Srebf1-overexpressed fibroblasts and mock-expressed fibroblasts were intratracheally-transferred to B6 mice at day 5 post-administration of 2 mg/kg of bleomycin. Expression of active form of Srebf1 was induced by doxycycline administration at day 7 post-administration of 2 mg/kg of bleomycin. Donor cells were recovered at day 10 post--administration of 2 mg/kg of bleomycin by cell sorting. Global transcriptome of transferred fibroblasts was generated by 3'SAGE-seq using Ion Proton sequencer.

first: Shin-ichi

last: Hashimoto

first: Mikiya

last: Otsuji

first: Shungo

last: Deshimaru

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: Time-series transcriptomic analysis of lung fibroblasts in bleomycin- and silica-induced pulmonary fibrosis

summary: Pulmonary fibrosis (PF) is an intractable disorder with a poor prognosis. Although lung fibroblasts play central roles in PF, their key regulatory molecules remain unclear. To identify PF pathology-associated gene modules and their hub TFs in activated lung fibroblasts, we performed time-course transcriptome analysis of the fibroblasts purified from the lungs of bleomycin- and silica-treated Col1a2-GFP reporter mice.

overall_design: To clarify transcriptomic landscape of lung fibroblasts throughout PF initiation, progression, and resolution, we induced reversible or progressive PF in Col1a2-GFP transgenic mice by bleomycin or silica aspiration, respectively. We purified lineage (CD45, CD31, EpCAM, CD146, and Ter119)– Col-GFP+ lung fibroblasts by flow-cytometry at 0, 7, 14, and 63 days post-induction in both models and performed transcriptome analysis by 3′SAGE-seq using Ion Proton sequencer.


title: Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA

status: Public on Feb 21 2019

city: Sherbrooke

first: Michelle

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

summary: The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 115 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new tRNA and snoRNA genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distort the perceived architecture of the human transcriptome.

overall_design: RNA was isolated from SKOV3ip1 human cell lines and various normal human tissues from which fragmented ribo-depleted TGIRT-Seq libraries were made. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.

first: Vincent

last: Boivin

first: Étienne

last: Fafard-Couture


title: Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer [MeDIP-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: sgC (WT) and PKCl/i KO (sgPKCl/i) C42B cells were profiled under normal conditions.

first: Antoine

first: Mehmet

last: Badur

first: Munveer

last: Bhangoo

first: Phataraporn

last: Thorson

first: Alicia

last: Richards

first: Tarmo

last: Rooslid

first: Dolores

last: Garcia-Olmo

first: Syongh

last: Nam-Cha

first: Antonio

last: Salinas-Sanchez

first: Ken

last: Eng

first: Himisha

last: Beltran

first: Christian

last: Metallo

first: Maria

last: Diaz-Meco


title: Effects of MIR205HG silencing or overexpression

status: Public on Jan 23 2019

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale Tumori

summary: We aimed at analyzing the transcriptome changes associated with MIR205HG knock-down in RWPE-1 cells or overexpression in DU145 cells

overall_design: MIR205HG was targeted in RWPE-1 cells by using either a siRNA directed against its RefSeq transcript or a gapmer antisense directed against an intron within its primary transcript (experiments conducted in triplicate). MIR205HG expression was reconstituted in DU145 cells by stably transfecting vectors containing either the full length or the RefSeq sequence (experiments conducted in quadruplicate).

first: Stefano

last: Percio


title: Transcriptome network analysis reveals the LXR-Srebf1 axis as  protective hub of fibroblast activation in murine pulmonary fibrosis

first: Shigeyuki

last: Shichino

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

overall_design: Refer to individual Series


title: Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism

status: Public on Jan 21 2019

city: Lausanne

first: Benjamin

middle: D

last: Weger

state: VD

address: Station 15

department: SV

country: Germany

institute: EPFL

summary:
Background
Deficient glucocorticoid biosynthesis leading to adrenal insufficiency is life-threatening and is associated with significant co-morbidities. The affected pathways underlying the pathophysiology of co-morbidities due to glucocorticoid deficiency remain poorly understood and require further investigation.
Methods
To explore the pathophysiological processes related to glucocorticoid deficiency, we have performed global transcriptional, post-transcriptional and metabolic profiling of a cortisol-deficient zebrafish mutant with a disrupted ferredoxin (fdx1b) system.
Findings
fdx1b−/− mutants show pervasive reprogramming of metabolism, in particular of glutamine-dependent pathways such as glutathione metabolism, and exhibit changes of oxidative stress markers. The glucocorticoid-dependent post-transcriptional regulation of key enzymes involved in de novo purine synthesis was also affected in this mutant. Moreover, fdx1b−/− mutants exhibit crucial features of primary adrenal insufficiency, and mirror metabolic changes detected in primary adrenal insufficiency patients.
Interpretation
Our study provides a detailed map of metabolic changes induced by glucocorticoid deficiency as a consequence of a disrupted ferredoxin system in an animal model of adrenal insufficiency. This improved pathophysiological understanding of global glucocorticoid deficiency informs on more targeted translational studies in humans suffering from conditions associated with glucocorticoid deficiency.fdx1b-/- mutants show a pervasive reprogramming of metabolism, in particular of glutamine-dependent pathways such as glutathione metabolism, and exhibit changes of oxidative stress markers. The glucocorticoid-dependent post-transcriptional regulation of key enzymes involved in de novo purine synthesis was also affected in this mutant. Moreover, fdx1b-/- mutants exhibit crucial features of primary adrenal insufficiency, and mirror metabolic changes detected in primary adrenal insufficiency patients. Our study provides a detailed map of metabolic changes induced by glucocorticoid-deficiency as a consequence of a disrupted ferredoxin system in an animal model of adrenal insufficiency. This improved pathophysiological understanding of global glucocorticoid deficiency informs on more targeted translational studies in humans suffering from conditions associated with glucocorticoid deficiency.

overall_design: Whole larvae samples at 5 days post fertilization of siblings and fdx1b mutants were collected and subjected to Total RNAseq (n=3 per phenotype), corresponding to a total of 6 samples.

first: Meltem

last: Görling

first: Gernot

last: Poschet

first: Melek

last: Yildiz

first: Rüdiger

last: Hell

first: Burkhard

last: Luy

first: Teoman

last: Akcay

first: Tülay

last: Güran

first: Thomas

last: Dickmeis

first: Ferenc

last: Müller

first: Nils

last: Krone


title: Gene expression in WT and Thpok-deficient LCMV-specific memory T cells

status: Public on Jan 08 2019

last: Ciucci

summary: Gene expression of memory CD4+ and CD8+ T cells determined by RNAseq 30 days after LCMV Armstrong infection

overall_design: 30 days post-infection with LCMV Arm spleen GP66:I-Ab+  T cells from Zbtb7bAD (CD4 Zbtb7bAD) or Tnfrsf4-Cre– (CD4 Ctrl) mice and of spleen GP33:H-2Db+  T cells from Tnfrsf4-Cre–  animals (CD8 Ctrl) were sorted and gene expression was determined by RNAseq

first: Remy

last: Bosselut


title: Analysis of transcriptome changes arising from MIR205HG modulation in prostate cells


title: Single-cell gene expression of anti-viral  WT and Thpok-deficient effector and memory T cells

summary: Single-cell gene expression of effector and memory  CD4+ and CD8+ T cells from WT or Thppok-deficient animals was determined by sRNAseq after LCMV Armstrong infection

overall_design: 7 and 30 days post-infection with LCMV Arm spleen T cells were sorted and gene expression was determined by scRNAseq


title: Effects of deletion of a portion of the Alu element from MIR205HG transcript

summary: We aimed at analyzing the transcriptome changes associated with the deletion of a portion of the Alu element from MIR205HG transcript

overall_design: MIR205HG expression was reconstituted in DU145 cells by stably transfecting a vector containing the RefSeq sequence deleted for a portion of the Alu element from MIR205HG transcript (experiments conducted in triplicate).


title: Enduring and sex-specific changes in hippocampal gene expression after subchronic immune challenge

status: Public on Feb 18 2019

city: Ann Arbor

first: Natalie

middle: Celia

last: Tronson

state: MI

address: 530 Church st

department: Psychology

institute: University of Michigan

summary: The goals of this study include examining long-lasting changes in hippocampal gene expression in males and in females after a systemic, subchronic immune challenge and transcriptional response to a subsequent, acute immune insult

overall_design:
6 experimental conditions, 3 replicates/condition:
Long-Term (3 months after subchronic immune challenge), Long-term + acute (subchronic immune challenge + acute immune challenge 3 months later), Acute (6 hrs after single immune challenge);
Control samples include Vehicle treated males (VVM) and Vehicle treated females (VVF)

LPS.vehicle (LV) = the Long-Term condition
LPS.LPS (LL) = the Long-term + acute condition
vehicle.LPS (VL) = the Acute condition
vehicle.vehicle (VV) = the Control condition

first: Daria

last: Tchessalova


title: Effects of MIR205HG silencing

first: Paolo

last: Gandellini

summary: We aimed at analyzing the transcriptome changes associated with MIR205HG knock-down in RWPE-1 cells

overall_design: Trascriptome of RWPE-1 cells knocked-down for MIR205HG using an antisense gapmer directed against an exon-exon junction of the transcript were compared to those of RWPE-1 cells transfected with a scrambled oligomer. Experiments were conducted in triplicate

last: Percio


title: The Human Testis Cell Atlas via Single-cell RNA-seq (Infant scRNA-seq data set)

status: Public on Oct 15 2018

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

summary: Human adult spermatogenesis involves a balance of spermatogonial stem cell self renewal and differentiation, alongside complex germline-niche interactions. To better understand, we performed single cell RNA sequencing of ~7000 testis cells from three healthy men of peak reproductive age. Our analyses revealed multiple distinctive transcriptional ‘states’ of self-renewing and differentiating spermatogonia, the cellular stages of gametogenesis, five niche cells (Leydig, Myoid, Sertoli, Endothelial, macrophage) and insights into germline-niche communication. Spermatogenesis was reconstructed computationally, which identified sequential coding, noncoding, and repeat-element transcriptional signatures. A new, developmentally early and likely quiescent spermatogonial state is identified (GFRA1-/ETV5-/ID4+/UTF1+/FGFR3+). Notably, certain epigenetic features combined with nascent transcription analyses suggest considerable plasticity within certain spermatogonial populations/states. Key findings were validated via RNA and protein staining. Taken together, we provided the first “Cell Atlas” of the adult human testis, and provide multiple new insights into germ cell development and germ cell – niche interaction.

overall_design: We isolated single testicular cell from two infant (13 months old). Two technical replicates were performed for each individual.

first: Bradley

last: Cairns


title: The Human Testis Cell Atlas via Single-cell RNA-seq (KIT+ spermatogonia ATAC-seq data set)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We isolated KIT-enriched spermatogonia from adult testis via magnetic-activated cell sorting (MACS). Two technical replicates were performed.


title: Thpok genome-wide occupancy in CD4+ T cells

summary: Genome-wide occupancy of the transcription factor Thpok in activated CD4+ T cells

overall_design: Streptavidin immunoprecipitation from the chromatin of  CD4+ T cells isolated from ThpokBio/+ Rosa26BirA or Rosa26BirA animals


title: Variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among three Taxus species

status: Public on Oct 20 2018

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

country: China

institute: Hangzhou Normal University

summary:
Background：Taxol is an efficient anticancer drug; however, the accumulation of taxoids can vary hugely among Taxus species. The mechanism underlying differential accumulation of taxoids are largely unknown. Thus, the comparative analysis of the transcriptomes in three Taxus species, including T. media, T. mairei and T. cuspidata, was performed.
Results:KEGG enrichment analysis revealed that the diterpenoid biosynthesis and cytochrome P450 pathways were significantly enriched in the differential expressed genes. Dynamic expressions of the taxol biosynthesis related genes might be a potential explanation for the interspecific differential accumulation of taxol and its derivatives. Besides, the sequences of several key enzymes were re-assembled based on independent transcriptomes from different Taxus species. Our data showed that sequence diversity may be another factor that determines the variations in taxoids. Furthermore, five jasmonic acid (JA) metabolism-related GO terms were analyzed. The differential expression of these JA-related transcription factors suggested distinct responses to exogenous MeJA applications in the three Taxus species.
Conclusions:Our results revealed the comprehensive variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among different Taxus species. The data give us an opportunity to reveal the mechanism underlying the variations in the taxoid contents and to select the highest-yielding Taxus species.

sample_organism:
Taxus x media
Taxus cuspidata
Taxus mairei

overall_design: Examination of three different Taxus species  in sequence

first: Chenjia

last: Shen


title: nanoPARE: Parallel analysis of RNA 5' ends from low input RNA

status: Public on Oct 08 2018

city: Wageningen

first: Michael

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

summary: A diversity of RNA molecule 5' ends are generated during transcriptional and post-transcriptional processes. Different RNA ends can confer or represent different functional activities and thus the identification of RNA end usage dynamics contributes to the functional characterization of RNA molecules. Here we present a method that enables the accurate identification of RNA 5' ends from samples with low amounts of total RNAs, and thus allow characterization of RNA regulatory mechanisms in specific cell-types.

overall_design: NanoPARE, or RNA 5' end enrichment, libraries were constructed for three biological replicates of ten conditions/genotypes. mRNA-Seq libraries were generated were constructed for three biological replicates of two conditions/genotypes.

last: Schon

first: Max

last: Kellner


title: Gene expression in adult sciatic nerves upon miRNA ablation and crush injury

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

institute: UCSF

summary: We report RNA sequencing data from induced Schwann cell specific knockouts for DICER and DGCR8 as well as crush injured wild type animals. Induced deletion of DICER and DGCR8 results in expression of numerous injury response genes suggesting a requirement of those proteins in maintaining the myelinated Schwann cell fate.

overall_design: Sciatic nerve RNA expression profiles of adult 3 months post tamoxifen induced P0-CreERT2-Dicer and P0-CreERT2-Dgcr8 mice (in triplicate) and C57BL6 3 days post crush injury (in quadruplicate) in comparison to contralateral (in quadruplicate) and uncrushed controls (in triplicate) were generated by deep sequencing, using Illumina HiSeq.

first: Deniz

last: Goekbuget

first: Jorge

last: Pereira

first: Lennart

last: Opitz

first: Ueli

last: Suter


title: Identification of novel immune and barrier genes in atopic dermatitis by means of laser capture microdissection

status: Public on Oct 02 2018

first: James

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: This is the first report that establishes robust epidermal and dermal genomic signatures of lesional and nonlesional AD skin and normal skin compared with whole tissues. These data establish the utility of laser capture microdissection to separate different compartments and cellular subsets in patients with AD, allowing localization of key barrier or immune molecules and enabling detection of gene products usually not detected on arrays.

overall_design: Laser capture microdissection was performed to separate the epidermis and dermis of lesional and nonlesional skin from patients with AD and normal skin from healthy volunteers, followed by gene expression (microarrays and real-time PCR) and immunostaining studies.

first: Emma

last: Guttman-Yatski

first: Mayte

last: Suárez-Fariñas

first: David

last: Ewald


title: Transcriptome analyses of miRNA pathway mutants and injury response in developing and adult sciatic nerves

summary: We addressed the requirement of DGCR8, DROSHA and DICER functions in developing and adult Schwann cells (SCs) using mouse mutants. We found that the microprocessor components DGCR8 and DROSHA are crucial for axonal radial sorting and to establish correct SC numbers upon myelination. Transcriptome analysis revealed that the microprocessor is essential to prevent aberrant accumulation and de novo expression of injury-response genes. Those genes are predicted targets of stage-specifically enriched miRNAs. In agreement, DGCR8 and DICER are required for proper maintenance of the myelinated SC state. We conclude that the miRNA pathway is crucial for preventing inappropriate activity of injury response genes in developing and adult SCs.

overall_design:
At post natal day 1, sciatic nerves of Schwann cell specific conditional mutants for DICER, DGCR8, DROSHA and respective controls were analyzed by RNA sequencing in triplicate.

Sciatic nerves of induced Schwann cell specific mutants for DICER and DGCR8 were analyzed 3 months after administration of tamoxifen and compared to P0-CreERT2-negative controls in triplicate. In addition, wild-type adult sciatic nerves were analyzed 3 days post crush injury (in quadruplicate) in comparison to contralateral (in quadruplicate) and uncrushed sciatic nerve controls (in triplicate).


title: Cyclin D1 levels induces global transcriptional downregulation in malignant lymphoid cells and correlate with total RNA levels in mantle cell lymphoma cell lines

status: Public on Aug 09 2018

last: Albero

address: 1130 St Nicholas Ave

institute: Columbia University

summary: Study of the transcriptional role of cyclin D1 in lymphoid tumor cells with cyclin D1 oncogenic overexpression. We perform global transcriptional analysis of four mantle cell lymphoma cell lines and we observed a correlation between the cyclin D1 levels and the transcriptional output. We confirmed our hypothesis using a lymphoblastic cell lines (JVM-13) cyclin D1 negative, where the overexpression of a mutant, more stable, form of cyclin D1 downregulated the transcriptome globally.

overall_design: mRNA profiles of 4 mantle cell lymphoma and two transduced lymphoblastic cell lines (mutant cyclin D1  or empty vector) by deep sequencing, using Illumina MiSeq instrument.

first: Giancarlo

last: Castellano

first: Anna

last: Enjuanes

first: Pedro

last: Jares


title: RNA expression in mutants of the miRNA pathway during myelination

summary: RNA sequencing was performed comparing sciatic nerves of Schwann cell specific DICER mutants with SC-specific DGCR8 and DROSHA mutants.

overall_design: Total RNA from sciatic nerves of P1 DICER mutants, DGCR8 mutants, DROSHA mutants and controls was used to perform RNA sequencing analysis.


title: Expression data from patients with Essential Thrombocythemia (ET), Polycythemia Vera (PV), Primary Myelofibrosis (PMF)

status: Public on Jun 15 2018

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

summary: Microarrays were used to assess gene expression in patients with ET, PV, and PMF before and after treatment with IFNalpha2 in a paired design.

overall_design: Total RNA was purified from whole blood and amplified to biotin-labeled aRNA and hybridized to microarray chips. Background correction, normalization, and gene expression index calculation were performed with the robust multi-array (rma) method. The regularized t-test limma for pairwise data was used to calculate differences in gene expression between patients before and after treatment with IFN-alpha2.

first: Hans

last: Hasselbalch


title: A multi-tissue full lifespan epigenetic clock for mice [I]

status: Public on Nov 29 2018

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary: Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs.  However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.

overall_design: Reduced representation bisulfite-sequencing (RRBS) data from public and in-house sources were processed consistently and merged to form a set of over 1000 mouse samples from various tissues and chronological ages.  These data were used to investigate the relationship between chronologic age and epigenetic age.

middle: J

last: Thompson


title: RNA-seq of head and neck cancer cell lines

status: Public on May 10 2018

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: Transcriptome analysis in head and neck cancer cell lines, FaDu and UMSCC47  with and without 5-aza'2-deoxycytidine(Aza)/trichostatin A(TSA) treatment.

overall_design: FaDu and UMSCC47 with and without 5-aza'2-deoxycytidine(Aza)/trichostatin A(TSA) treatment transcriptomes were analyzed by RNA-sequencing.

first: Takuya

last: Nakagawa

first: Atsushi

last: Kaneda


title: MicroRNAs-wide analysis of primordial germ and somatic cells reveals sexual and developmental differential functional regulation in mouse embryonic gonads

status: Public on Feb 28 2018

city: Madrid

first: Jesus

last: del Mazo Martinez

address: C/ Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biologicas (CIB) - CSIC

type: Non-coding RNA profiling by high throughput sequencing

summary: We have characterized by small-RNAseq the miRNA expression pattern of mouse male and female Primordial Germ Cells (PGCs) and somatic stromal cells from gonads at E11.5, E12.5 and E13.5. MiRNA accumulation was higher in somatic cells than in PGCs and more stable across the different developmental stages analyzed. Differential expression analyses showed differences in the regulation of key miRNA clusters such as miR-199-214, miR-182-183-96 and miR-34c-5p whose targets have defined roles in both germ and somatic cells in gonadal sexual determination. Extensive analyses of miRNA sequences revealed an increase in non-canonical isoforms in PGCs at E12.5 compared to E11.5 and E13.5 and a dramatic change in isomiR expression and non-template 3' nucleotide additions in female PGCs at E13.5 respect to the other samples.

overall_design: miRNA profiles of 12 different mice samples, corresponding to PGCs and gonadal somatic cells from E11.5, E12.5 and E13.5 male and female gonads, generated by deep sequencing using MiSeq Sequencing System (Illumina).

first: Daniel

last: Fernandez-Perez

first: Miguel

last: Brieño-Enríquez

first: Javier

last: Isoler-Alcaraz

first: Eduardo

last: Larriba

first: Jesús

last: del Mazo


title: Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [WGBS]

status: Public on Apr 13 2018

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

summary: H3K9me3-dependent heterochromatin is considered as one of the major barriers for cell fate changes, and must be reprogrammed during fertilization to reactivate highly specialized paternal and maternal genome to establish totipotency. However, the molecular details are lacked for early embryos due to the limited materials. Here we map the genome-wide distribution of H3K9me3 modification in the early embryo as well as in the cell fate determined embryonic tissues after implantation. We find that H3K9me3 exhibits distinct dynamic features in promoters and retro-transposons. Both maternal and paternal genome undergo large scale of H3K9me3 reestablishment after fertilization, and the imbalance of maternal H3K9me3 signal over paternal last until the blastocyst stage. The rebuilding of H3K9me3 on LTR retro-transposons maintains its repression state after the global DNA demethylation, and we further discover that Chaf1a is essential for the establishment of H3K9me3 on LTRs and the loss function of Chaf1a leads to embryo development failure. Finally, we find that lineage specific H3K9me3 is established after lineage commitment in post-implantation embryos. Thus, our data demonstrate that H3K9me3-dependent heterochromatin undergoes dramatic reprogramming during early embryo development and the establishment of H3K9me3 on LTRs is essential for proper embryo development.

overall_design:
We mapped the H3K9me3 modifications on embryos from zygote to 8.5 day stage (with separated ICM and TE, Epi and Exe). The mouse metaphase II (MII) oocytes, sperm, as well as mouse embryonic stem cells (mESCs) and mouse trophoblast stem cells (mTSCs) were also analyzed. In the ChIP-seq analysis on pre-implantation embryos, 500 cells were used for per reaction and two or three replicates were performed for each stage.

This series contains the Whole Genome Bisulfite-seq data on embryos from zygote to 7.5 day stage (with separated ICM and TE, Epi and Exe).

first: Chenfei

last: Wang

first: Xiaoyu

last: Liu

first: Yawei

first: Lei

last: Yang

first: Chong

last: Li

first: Wenqiang

first: Chuan

last: Chen

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Hong

first: Yong

last: Zhang


title: ATF4 inhibition by p62 represses stromal metabolic reprogramming and tumorigenesis

status: Public on Feb 14 2018

first: Jorge

last: Moscat

address: 1188 York Avenue

institute: WEILL CORNELL MEDICINE

summary: Tumors often undergo stress and need to reprogram their metabolism to survive and grow under nutrient challenging conditions. The stroma could play a critical role in this process by providing nutrients or signals to support the epithelial compartment of the tumor. Autophagy has been shown to play key roles both in the stroma and in the epithelium. However, how autophagy adaptors, such as p62, participate in the mechanisms whereby the stroma supports tumor progression is not yet fully understood. Here we show that p62 deficiency in stromal fibroblasts promotes resistance to glutamine deprivation through a metabolic reprogramming orchestrated by the direct control of ATF4 stability by p62-mediated polyubiquitination. This, in turn, activates the flux of glucose carbons through a pyruvate carboxylase-asparagine synthase cascade that results in asparagine-mediated stromal cell growth and tumor epithelial proliferation, independent of autophagy. This supports a new model in which p62 directly targets nuclear transcription factors to control metabolic reprograming in the microenvironment to repress tumorigenesis, and emerges as global tumor suppressor.

overall_design: 52 weeks old p62f/f and p62fspKO prostates were harvested and snap-frozen in dry ice.

first: Juan

last: Linares

first: Thekla

last: Cordes

first: Angeles

last: Duran

last: Reina-Campos

first: Elias

last: Castilla

first: Christian

last: Metallo

first: Maria

last: Diaz-Meco


title: Dynamic Changes in the Expressions of Elastogenesis- and Elastinolysis-Associated Genes and Remodeling of the Elastin Network in Volume-Overloaded Heart

status: Public on Mar 31 2018

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Background: In the remodeling process of the volume-overloaded heart, the extracellular matrix (ECM) may be dynamically modified to adapt to hemodynamic stress. We investigated the expression of ECM-related genes and modification of the elastin network in the remodeling process of the left ventricles (LVs) of rats with aortocaval fistulae.  Methods and Findings: Gene array analysis identified 36 upregulated and 11 downregulated ECM-related genes during evolution from the compensated to the late decompensated phase. Ingenuity Pathway Analysis identified the formation of elastic fibers as an important biological function. Real-time PCR confirmed persistent upregulation of elastogenesis-associated genes, including elastin, lysyl oxidase, lysyl oxidase like-1, fibrillin 1, fibulin 2, versican and latent transforming growth factor beta binding protein 2 at various intervals. The expression levels and enzymatic activities of potent elastases, cathepsin S and cathepsin K increased during the early phase. Immunofluorescence confocal microscopy showed that the microstructure of the elastin network was preserved during the early phase, degraded during the compensated phase, partially repaired during the early decompensated phase, and reinforced during the late decompensated phase. Assessment of elastin concentrations in the LVs showed a consistent temporal pattern throughout the course.
Conclusions: In the volume-overloaded heart, upregulation of potent elastases during the early phase and persistent upregulation of elastogenesis-related genes result in early degradation followed by repair and reinforcement of the elastin network of the LV. Remodeling of the elastin network may contribute to changes in the mechanical property of the volume-overloaded heart.

overall_design: Left ventricles of rats with creation of aortocaval fistulae for 8, 16 and 24 weeks were compared with the sham. LV tissue were tested for RNA extraction and hybridization on Affymetrix microarrays. The experiments have been biological replicated three times. The differential expression genes were selected and validated with qPCR method.

first: Chi-Jen

last: Chang

first: Lung-Sheng

last: Wu

first: Lung-An

last: Hsu

first: Jang-Hau

last: Lian

first: Yu-Shein

last: Ko


title: Chemical Screening Identifies Enhancers of Mutant Oligodendrocyte Survival and Unmasks a Distinct Pathological Phase in Pelizaeus-Merzbacher Disease

status: Public on Aug 22 2018

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

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

overall_design: Refer to individual Series


title: Circular RNA in Stage III Gastric cancer: Tumour vs. Normal mucosa tissue

status: Public on Dec 14 2017

city: Guangzhou

first: Yan

state: Guangdong

address: 1838 north guangzhou avenue

institute: southern medical university, nanfang hospital

summary: Transcriptional profiling of  circular RNA in stage III gastric cancer patient: Tumour vs. Normal mucosa tissue

overall_design: T vs. N. Biological replicates: 6 tumour and 6 adjanct normal mucosa tissue


title: ATF4 inhibition by p62 represses stromal metabolic reprogramming and tumorigenesis II

city: New York

overall_design: WPMY sgC and sgp62 were cultured in No Glutamine, 10% dyalized FBS DMEM during 24h.

first: Miguel


title: Analysis of gene expression in the rel- relA+ and the rel- relAE335Q strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

status: Public on Dec 12 2017

city: Cambridge

first: Anna

last: Puszynska

state: MA

address: 455 Main street

institute: Whitehead Institute for Biomedical Research

summary: We investigated the role of basal ppGpp levels in Synechococcus elongatus PCC7942 in adaptation to darkness. We performed RNA-seq experiments using the rel- relA+ and the rel- relAE335Q strain at dusk and during exposure to 12 h of darkness. We show that basal ppGpp levels is not sufficient for restoration of appropriate transcriptional shutdown in response to darkness.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Enriched mRNA was prepared from synchronized S. elongatus cells at indicated time points using the Illumina TruSeq Stranded mRNA Sample Prep Kit and Illumina HiSeq technology.

first: Erin

last: O'Shea


title: Analysis of RNA polymerase stalling index in wild type and the rel- strain of Synechococcus elongatus PCC7942 - chromatin immunoprecipitation followed by sequencing during exposure to darkness (cells grown in light/dark conditions)

summary: We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed ChIP-seq experiments using wild type and the rel- strain at dusk, during exposure to 12 h of darkness and at dawn. We show that the RNA polymerase pausing index is globally lower in the rel- strain.

platform_organism: Synechococcus elongatus PCC 7942 = FACHB-805


title: Analysis of gene expression in the rel- + relA+ and  rel- + relAE335Q strains of Synechococcus elongatus PCC7942 with RNA sequencing during constant light conditions

summary: We investigated the role of the basal levels of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using the rel- + relA+ and  rel- + relAE335Q strains and show that basal levels of ppGpp are required for regulation of global transcription in light.


title: Gene expression in the wild type + relA+ and  wild type + relAE335Q strains of Synechococcus elongatus PCC7942 after induction of expression of RelA+ or RelAE335Q with theophylline at subjective dusk - RNA sequencing during constant light conditions

summary: We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using  wild type + relA+ and  wild type + relAE335Q strains after induction with theophylline starting at subjective dusk. We show that ppGpp induction inhibits global transcription in light.


title: Analysis of gene expression in the wild type and rel- strains of Synechococcus elongatus PCC7942 with RNA sequencing during constant light conditions

summary: Rel is an enzyme involved in the metabolism of ppGpp. We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light and after exposure to darkness. We performed RNA-seq experiments using the rel- strain and wild type and show that ppGpp is required for regulation of global transcription in light and in darkness.

overall_design: Enriched mRNA was prepared from synchronized S. elongatus cells at indicated time points using the Illumina TruSeq Stranded mRNA Sample Prep Kit and Illumina HiSeq technology. Gene expression in the rel- strain was compared at each time point to the control wild type strain.


title: Analysis of gene expression in wild type and the rel- strain of Synechococcus elongatus PCC7942 - RNA sequencing during exposure to darkness (cells grown in light/dark conditions)

summary: We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed RNA-seq experiments using wild type and the rel- strain at dusk and during exposure to 12 h of darkness. We show that ppGpp is required for correct response to darkness.


title: Gene expression profiling of WT and STAT3-/- Tc17 CD8+ T cells

status: Public on Nov 27 2017

first: Thomas

last: Ciucci

summary: CD8+ T cells are pre-programmed for cytotoxic differentiation. However, a subset of effector CD8+ T cells (‘Tc17’) produce IL-17 and fail to express cytotoxic genes. Here, we show that the transcription factors directing IL-17 production inhibit cytotoxicity despite persistent Runx3 expression. Cytotoxic gene repression did not require the transcription factor Thpok. We further show that STAT3 restrained cytotoxic gene expression in CD8+ T cells and that RORgt represses cytotoxic genes by inhibiting the functions but not the expression of the ‘cytotoxic’ transcription factors T-bet and Eomesodermin. Thus, the transcriptional circuitry directing IL-17 expression inhibits cytotoxic functions.

overall_design: Naïve WT and Cd4cre+ STAT3fl/fl (STAT3-/-) CD8+ T cells were sorted and mix at 1:1 ratio before activation in the presence of IL-12 (Tc1) or IL-6 and TGFb (Tc17). After 4 days WT and STAT3-/- cells were sorted separetly based on the expression of allelic markers

first: Remy

last: Bosselut


title: Gene expression profiling of Tc1 and Tc17 CD8+ T cells

overall_design: Naïve CD8+ T cells were sorted and activated for 4 days in the presence of IL-12 (Tc1) or IL-6 and TGFb (Tc17)


title: ppGpp controls global gene expression in light and in darkness in S. elongatus


title: NGS analysis of RNAs associated with the betaNACtes-containing ribosomes in Drosophila melanogaster testes

status: Public on Oct 12 2017

city: Moscow

first: Sergey

last: Lavrov

address: Kurchatov sq. 2

department: DMBC

country: Russia

institute: IMG

summary: NAC (nascent polypeptide-associated complex) post-meiotic heterodimeric αβ-complex promoting chaperone-like cotranslational protein folding on the ribosome and its early role in the birth of nascent proteins is suggested. Here, we demonstrate the presence of specific NAC complex (NACtes) associated with ribosomes in spermatocytes. The RNAseq analysis of mRNAs associated with testis-specific and immunoprecipitated NACtes-carrying ribosomes revealed a preferential association of the latter with mRNAs encoding meiotic and post meiotic proteins. The NACtes ribosomes are also shown to be enriched in mRNAs encoding proteins of central metabolism pathways that have been reported as overexpressed in testes. The specificity of association of NACtes ribosomes with particular mRNA sets was also demonstrated by the observation of significant underrepresentation of abundant mRNAs encoding ubiquitously expressed ribosomal proteins in NACtes-associated ribosomes. At the same time, NACtes ribosomes are enriched in mRNA encoding a testis specific ribosomal protein. These results bring new arguments in favor of “specialized ribosomes hypothesis” proposing a special composition of ribosomes necessary for the control of selected gene expression.

overall_design: RNA profiles from the fraction of testes ribosomes immunoprecipitated with βNACtes antibodies (three replicas) and from total testes ribosomes (two replicas)

first: Galina

middle: L

last: Kogan


title: Control of Paneth cell fate, intestinal inflammation and tumorigenesis by PKCλ/ι

status: Public on Aug 23 2017

first: Jorge

last: Moscat

summary: Paneth cells are a highly specialized population of intestinal epithelial cells located in the crypt adjacent to Lgr5+ stem cells, from which they differentiate through a process that requires downregulation of the Notch pathway. Their ability to store and release antimicrobial peptides protects the host from intestinal pathogens and controls intestinal inflammation. Here we show that PKCλ/ι is required for Paneth cell differentiation at the level of Atoh1 and Gfi1, through the control of EZH2 stability by direct phosphorylation. The selective inactivation of PKCλ/ι in epithelial cells results in the loss of mature Paneth cells, increased apoptosis and inflammation, and enhanced tumorigenesis. Importantly, PKCλ/ι expression in human Paneth cells decreases with progression of Crohn's disease. Kaplan-Meier survival analysis of CRC patients revealed that low PRKCI levels correlated with significantly worse patient survival. Therefore, PKCλ/ι is a negative regulator of intestinal inflammation and cancer through its role in Paneth cell homeostasis.

overall_design: Intestinal crypts of PrkciIEC-KO mice compared to WT mice. Three biological replicates.

first: Yuki

last: Nakanishi

last: Reina-Campos

first: Naoko

first: Victoria

last: Llado

first: Lisa

last: Elmen

first: Scott

last: Peterson

first: Alex

last: Campos

first: Surya

last: De

first: Hiroki

last: Ikeuchi

first: Maurizio

last: Pellecchia

first: Richard

last: Blumberg


title: Multi-dimensional histone modifications for coordinated regulation of gene expression under hypoxia  [array]

status: Public on Aug 17 2017

city: Daegue

first: Jieon

last: Lee

address: 333. Techno Jungang-daero Hyeongpung-myeon, Dalseong-gun

department: Chemical Engineering

country: South Korea

institute: POSTECH

summary: Analysis of epigenetic changes at hypoxia at gene level. The hypothesis was that different types of methylation affect gene expression coordinately regulate specific induction or repression of hypoxia-responsive genes.

overall_design: Total RNA obtained from adipocyte-derived stem cell subjected to 48 hours in hypoxic condition compared to normoxia condition.

first: Ho-Youl

first: Sehyun

last: Chae

first: SeongYoul

first: Daehee

last: Hwang

first: Hyunsung

last: Park


title: Multi-dimensional histone modifications for coordinated regulation of gene expression under hypoxia


title: Multi-dimensional histone modifications for coordinated regulation of gene expression under hypoxia  [ChIP-Seq]

overall_design: genomic DNA obtained from adipocyte-derived stem cell subjected to 48 hours in hypoxic condition compared to normoxia condition.


title: Gene expression analysis of WT and Keap1–/– MEFs in vitro culture condition (2D) and in allograft condition (3D)

status: Public on May 06 2017

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University

summary: WT TR MEFs and Keap1–/– TR MEFs were established according to the following method.  Keap1+/– mice were mated, and WT and Keap1–/– embryos were collected at embryonic day 13.5.  Primary MEFs were immortalized by expression of SV40 T antigen.  The immortalized MEFs were transformed by expression of HRAS G12V to generate WT TR MEFs and Keap1–/– TR MEFs.

overall_design: Total RNA from WT-TR MEFs and Keap1–/–-TR MEFs was prepared for in vitro culture conditions (2D) and allograft conditions (3D).  To prepare the total RNA from the 3D conditions, 1 x 10^7 WT-TR MEFs and 3 x 10^6 Keap1–/–-TR MEFs were injected into nude mice, and the tumors were harvested for extraction of total RNA when their volumes reached 100-150 mm^3.

first: Hiroshi

last: Kitamura


title: Using DNA methylation profiling to evaluate biological age and longevity interventions.

status: Public on Apr 05 2017

city: Boston

first: Daniel

middle: Adam

last: Petkovich

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Genetics

institute: Brigham and Women's Hospital

summary: We utilized Reduced Representation Bisulfite Sequencing to profile DNA methylomes from whole blood of mice to develop a robust predictor of mouse biological aging. Based on DNA methylation profiles of mice from various ages, strains, genetic backgrounds, and diets, an aging methylation signature was observed and an epigenetic clock was created with elastic net linear regression. Profiles from fibroblasts and iPSCs showed that the aging clock can be reset.

overall_design: Profile methylomes from whole blood of mice from various ages, strains, genetic treatments and diets as well as methylomes from fibroblasts and iPSCs.

first: Dmitriy

middle: I

last: Podolskiy

first: Alexei

middle: V

last: Lobanov

first: Vadim

middle: N

last: Gladyshev


title: RNA-Seq Study Reveals Genetic Responses of Diverse Wild Soybean Accessions to Increased Ozone Levels

status: Public on Jul 21 2017

city: Chicago

first: Nathan

last: Waldeck

state: IL

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

summary: Analysis of gene expression data from four genetically diverse wild soybean accessions helps reveal both sensitive and resistant responses of the plants to increased ozone levels. Results help characterize genetic response of wild soybean to ozone stress and could help provide information on genetic resources for creating ozone-tolerant soybean breeding lines.

overall_design: 2 sensitive genotypes (PI 407179 and PI 424007) and 2 resistant genotypes (PI 424123 and PI 507656) were replicated in 4 complete block designs and subjected to either 75 parts per billion (ppb) ozone or a control of charcoal-filtered conditions (< 10 ppb ozone). Total RNA was isolated from the first three trifoliate of each plant and deep sequenced using Illumina HiSeq 2500.

first: Earl

middle: W

last: Taliercio

first: Thomas

middle: E

last: Carter

first: Kent

middle: O

last: Burkey

first: David

last: Dickey

first: Qiajin

last: Song


title: DNA methylation in blood from neonatal screening cards and the association with BMI and insulin sensitivity in early childhood

status: Public on Sep 09 2017

city: Darlinghurst

first: Timothy

middle: John

last: Peters

state: NSW

address: 384 Victoria St

department: Immunology

country: Australia

institute: Garvan Institute of Medical Research

type: Methylation profiling by genome tiling array

summary:
There is increasing evidence that metabolic diseases originate in early life, and epigenetic changes have been implicated as key drivers of this early life programming. This led to the hypothesis that epigenetic marks present at birth may predict an individual’s future risk of obesity and type 2 diabetes. In this study, we assessed whether epigenetic marks in blood of newborn children were associated with BMI and insulin sensitivity later in childhood.
DNA methylation was measured in neonatal blood spot samples of 439 children using the Illumina Infinium 450k BeadChip. Associations were assessed between DNA methylation at birth and BMI z-scores, body fat mass, fasting plasma glucose, insulin and HOMA-IR at age 5 years, as well as birthweight, maternal BMI and smoking status.
No individual methylation sites at birth were associated with obesity or insulin sensitivity measures at 5 years. DNA methylation in 69 genomic regions at birth was associated with BMI z-scores at age 5 years, and in 63 regions with HOMA-IR. The methylation changes were generally small (<5%), except for a region near the non-coding RNA nc886 (VTRNA2-1) where a clear link between methylation status at birth and BMI in childhood was observed (P=0.001). Associations were also found between DNA methylation, maternal smoking, and birth weight.
We identified a number of DNA methylation regions at birth that were associated with obesity or insulin sensitivity measurements in childhood. These findings support the mounting evidence on the role of epigenetics in programming of metabolic health. Whether many of these small changes in DNA methylation are causally related to the health outcomes, and of clinical relevance, remains to be determined, but the nc886 region represents a promising obesity risk marker that warrants further investigation.

overall_design: Illumina HumanMethylation450K BeadChip arrays were used for genome-wide methylation profiling of blood DNA samples of 438 children at birth and 148 children at age 5 years.

first: Susan

last: van Dijk

first: Michael

last: Buckley

first: Jing

last: Zhou

first: Peter

last: Jones

first: Robert

last: Gibson

first: Maria

last: Makrides

first: Beverly

middle: S

last: Muhlhausler

last: Molloy


title: DNA demethylation by Tet dioxygenases controls gastrula patterning by regulating Lefty-Nodal signaling

status: Public on Oct 27 2016

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

summary: Mammalian genomes are subjected to epigenetic modifications, including cytosine methylation by DNA methyltransferases (Dnmt) and further oxidation by Ten-eleven-translocation (Tet) family of dioxygenases. Cytosine methylation plays key roles in multiple processes such as genomic imprinting and X-chromosome inactivation. However, the functional significance of cytosine methylation and the further oxidation has remained undetermined in mouse embryogenesis. Here we show that global inactivation of all three Tet genes in mice led to consistent defects in gastrulation. The defects include reduced specification of the axial mesoderm and paraxial mesoderm, mimicking phenotypes in embryos with gain-of-function Nodal signaling, a cardinal cue for gastrulation. Introduction of a single mutant allele of Nodal in the Tet mutant background partially restored patterning, suggesting that hyperactive Nodal signaling is a leading cause for the gastrulation failure of Tet mutants. Increased Nodal signaling is likely due to diminished expression of the Lefty1 and Lefty2 genes, inhibitors of Nodal signaling. Moreover, reduction in the Lefty gene expression can be ascribed to elevated DNA methylation as both Lefty-Nodal signaling and normal morphogenesis are largely restored in Tet-deficient embryos when the Dnmt3a and Dnmt3b genes are disrupted. Additionally, specific inactivation of Tet by point mutations abolishing the dioxygenase activity causes similar molecular and gastrulation abnormalities. Taken together, our results show that Tet-mediated DNA oxidation modulates the Lefty-Nodal signaling by promoting demethylation of the shared target genes with Dnmt3a and Dnmt3b. These findings reveal a fundamental epigenetic mechanism featuring dynamic DNA methylation and demethylation and their role in the regulation of key signaling in body plan formation during early embryogenesis.

overall_design: Examine RNA expression and DNA methylation differences between Tet-null and wild type samples of mouse epiblast in E6.5.


title: Comparison of transcriptomic profile of the murine B16F1-GFP-M melanoma cells with the derived dormant B16F1-GFP-D cells

status: Public on Feb 14 2017

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary:
Cancer patients after successful therapy contain nested in their organs and/or circulating in the systemic fluids tumor cells that remain asymptomatic for an extended period of time. They stay dormant with no apparent immediate potential to develop into a clinically manifested tumor until activated by yet not well defined mechanisms. In the present study, we developed tumor dormancy model of murine melanoma, a cancer with a high potential of phenotype plasticity to adapt to micro-environmental changes, in which to investigate cellular quiescence and related factors as a potential mechanism of tumour dormancy. To explore molecular mechanism responsible for cellular dormancy, we performed a comparative transcriptome analysis of dormant B16F1-GFP-D and maternal B16F1-GFP-M cells.
Peroxisome proliferator-activated receptor-gamma (PPARgamma) is a nuclear receptor highly expressed by colonic epithelial cells. It plays a key role in gut homeostasis and metabolism regulation. We previously showed that PPARgamma has a role in the action of aminosalycilates (5-ASA), one of the oldest anti-inflammatory agents used in the treatment of inflammatory bowel disease. These data have prompted us to develop novel analogues of 5-ASA with greater PPARgamma-activating properties (GED).
The various PPARgamma ligands appear to have some markedly different effects, some of which can induce adverse effects. The transcriptomic profiles induced by various families of PPARgamma ligands are very poorly known and especially in intestinal epithelial cells. Hence, the objectives of the present project are to compare the gene expression profile induced by GED, 5-ASA, and pioglitazone in Caco-2 cells, in order to better understand these compounds’ modes of action, to discover potential new PPARgamma target genes in intestinal epithelial cells and to explain the efficacy difference between GED and 5-ASA.

overall_design: 1 million of B16F1-GFP-M and B16F1-GFP-D melanoma cells were cultured in DMEM 10% FBS medium. The cells were rinsed twice with sterile PBS. Total RNA extraction was performed following the manufacturer's protocol (RNeasy Kit, Qiagen, Courtaboeuf, France) with optional DNase treatment.

first: Yasmine

last: Touil


title: Arabidopsis: 3OC6-HSL-treated  vs Control

status: Public on Sep 21 2016

city: Shijiazhuang

first: Qian

last: Zhao

address: 46th South Street of Friendship

institute: Biology Institute, Hebei Academy of Sciences

summary:
Transcriptional profiling of Arabidopsis comparing 1μM 3OC6-HSL-treated Arabidopsis wild-type Col-0 with control untreated Col-0.
A transcriptomic analysis for Arabidopsis responses to bacterial quorum sensing molecule N-3oxo-hexanoyl-homoserine lactone (3OC6-HSL).

overall_design: Two-condition experiment, 3OC6-HSL-treated Arabidopsis vs untreated Arabisopsis. One replicate per array

first: Shuishan

first: Fang

last: Liu


title: Integrative Epigenome-Wide Analysis Shows That DNA Methylation May Mediate Genetic Risk In Inflammatory Bowel Disease [Whole blood, Methylation profiling]

status: Public on Nov 13 2016

city: Edinburgh

first: Nichols

last: Ventham

address: Western General Hospital

department: CGEM

country: United Kingdom

institute: Univerisity of Edinburgh

summary:
Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe  epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2, TXK) in an independent cohort.
Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two genetic polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data highlight the cell type of origin of epigenetic signals seen in whole blood; IBD-associated hypermethylation within the TXK gene transcription start-sitepromoter region negatively correlates with gene expression in whole blood and CD8+ T-cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD are relatedrelate to underlying genotype and associate with cell-specific alteration in gene expression.

overall_design:
DNA methylation analysis of whole blood samples derived from patients with Inflammatory bowel disease (IBD) and controls. This is the unprocessed dataset containing 384 samples. During processing additional whole blood DNA samples were added from a separate dataset. This explains the discrepancy between the number of samples in the unprocessed and processed datasets. A separate metadata file is supplied for each.
The unprocessed dataset containing 384 samples. The processed dataset contains 382 samples. Several samples were excluded during sample processing (e.g. sex mismatches, mislabelled samples, technical replicates).  The following samples were excluded from the processed dataset (0068H, 0057HC). Patients can be linked across datasets using Patient_Number.
Full_Diagnosis: CD=Crohn's disease, UC=Ulcerative colitis, HL=Healthy Lab Control, IB = Symptomatic Control

first: Nicholas

first: Jack

last: Satsangi


title: DNA methylation profiles of human blood samples from Hispanics and Caucasians

status: Public on Jul 13 2016

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles

summary:
Human DNA methylation Beadchip v1.2 was used to profile n=335 whole blood samples.
The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of Hispanics and Caucasians from the USA. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.

overall_design: We analyzed whole blood samples from 289 Caucasians and 46 Hispanics.

first: Beate

last: Ritz


title: Plasticity between Epithelial and Mesenchymal States Unlinks EMT from Metastasis-Enhancing Stem Cell Capacity

status: Public on Mar 09 2016

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: In this study we studied the presence of tumor cells that underwent epithelial-to-mesenchymal transition within polyoma middle T antigen (PyMT) breast tumors. For this we dissociated tumors and isolated Ecad positive tumor cells by FACS sorting. We confirmed that PyMT tumors contain a small set of tumor cells that have undergone EMT in the primary tumor and that E-cadherin can be used as a marker on single cell level for mesenchymal status in this model.

overall_design:
(i) We isolated primary tumors from mice, dissociated the tumors and FACS-sorted for single Ecad positive tumor cells, after this we performed single cell sequencing of the cells.
(ii) We isolated CTCs and solid tumor cells from mice, dissociated the tumors and FACS-sorted for single Ecad positive and negative cells, after this we performed single cell sequencing of the cells.

first: Lennart

last: Kester

first: Danielle

last: Seinstra

first: Jacco

last: van Rheenen

first: Alexander

last: van Oudenaarden


title: Gene expression differences between Gata2cko and wt mouse rhombomere 1

status: Public on Nov 01 2016

city: Heidelberg

first: Kaia

last: Achim

address: Meyerhofstr. 1

department: Developmental Biology Unit

institute: EMBL

summary: During development, rhombomere 1 gives rise to a multitude of cell types, including serotonergic as well as glutamatergic neurons that populate the raphe nuclei. Transcription factor Gata2 has been shown to regulate the development of the serotonergic neurons in the rhombomere 1. To further understand the role and targets of Gata2 in the rhombomere 1 during development, we used cDNA microarrays to compare gene expression in the embryonic day 12.5 (E12.5) rhombomere 1 tissues extracted from wild-type and Gata2 mutant embryos.

overall_design: Rhombomere 1 region was dissected from the E12.5 mouse embryos from the En1-cre, Gata2 flox/+ x Gata2 flox/flox crosses, and frozen in liquid nitrogen. After genotyping, dissected rhombomere 1 pieces were pooled according to genotype, combining 6 En1-cre, Gata2 flox/+ samples into one control pool, and 6 En1-cre, Gata2 flox/flox samples as one mutant pool. RNA was extracted from 3 sample pools (biological replicates) per genotype, reverse transcribed and labelled according to standard Illumina protocols and hybridized on Illumina Mouse WG-6 Expression BeadChip arrays. For the comparison of gene expression, samples were grouped according to genotype (control vs mutant).


title: p62, upregulated during preneoplasia, induces hepatocellular carcinogenesis by maintaining survival of stressed HCC-initiating cells

status: Public on Nov 23 2016

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: p62/SQSTM1 is a ubiquitin-binding autophagy receptor and signaling protein that  accumulates in premalignant liver diseases and most hepatocellular carcinomas  (HCC). Although p62 was proposed to participate in formation of benign adenomas in  autophagy-deficient livers, its role in HCC initiation was not explored. Here we show  that p62 is necessary and sufficient for HCC induction in mice and that its high  expression level in non-tumor human liver predicts rapid HCC recurrence after curative  ablation. High p62 expression is needed for activation of NRF2 and mTORC1, c-Myc  induction and protection of HCC-initiating cells from oxidative stress-induced death.

overall_design: p62F/F and Tsc1 F/F mice (Mori et al., 2009; Muller et al., 2013) were backcrossed to C57BL/6  mice for at least 7 generations, and then bred with Alb-Cre transgenic mice (also on C57BL/6  background) to generate p62F/F; Alb-Cre (p62Δhep) and Tsc1F/F; Alb-Cre (Tsc1Δhep)mice, respectively.  p62Δhep mice were crossed to Tsc1Δhep and MUP-uPA mice to generate p62F/F; Tsc1F/F; Alb-Cre  (Tsc1/p62Δhep) mice and p62Δhep/MUP-uPA transgenic mice, respectively. Genotyping was performed as  described (Muller et al., 2013). All animal studies were in accordance with NIH guidelines for use and  care of live animals and were approved by the UCSD Institutional Animal Care and Use Committee.  Mice were maintained in filter-topped cages on autoclaved chow diet (low-fat diet; LFD, composed of  12% fat, 23% protein, 65% carbohydrates based on caloric content) or high-fat diet (HFD, composed of  59% fat, 15% protein, 26% carbohydrates based on caloric content; Bio-Serv) and water at UCSD  according to NIH Guidelines.

first: Atsushi

last: Umemura

first: Feng

last: He

first: Hayato

last: Nakagawa

first: Shinichiro

last: Yamachika

first: Koji

last: Taniguchi

first: Joan

last: Font-Burgada

first: Zhenyu

last: Zhong

first: Shankar

last: Subramaniam

first: Sindhu

last: Raghunandan

first: Angeles

last: Duran

first: Juan

middle: F

last: Linares

first: Miguel

last: Reina-Campos

first: Shiori

first: Mark

middle: A

last: Valasek

first: Ekihiro

last: Seki

first: Kanji

last: Yamaguchi

first: Kazuhiko

last: Koike

first: Yoshito

last: Itoh

first: Maria

last: Diaz-Meco

first: Michael

last: Karin


title: Expression data from human cell line infected by human cytomegalovirus with over-expression lncRNA

status: Public on Mar 01 2016

city: ShiJiaZhuang

first: Qi

last: Wang

address: DuJuan Road

institute: EpiGenoMine

summary:
RNA2.7 is a long non-coding RNA encoded by HCMV, which has be reported related with apoptosis. We have found RNA2.7 can also affect virus replication.
We used the microarrays to look for HCMV RNA2.7 related host transcripts.

overall_design: We infected HELF cells by HCMV BAC HAN which was contructed from a HCMV clinical isolate, and BAC HAN^RNA2.7 which was a mutant of BAC HAN by deletion of RNA2.7. By running microarray and bioanalysis, we aimed to find RNA2.7 involvement in host and virus replication and transcription.

first: Yujing

last: Huang

first: Qiang

last: Ruan


title: NusA-dependent Transcription Termination Prevents Global Misregulation of Gene Expression

status: Public on Jan 01 2016

city: University Park

first: Paul

last: Babitzke

state: PA

address: 203 Althouse Laboratory

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Canonical bacterial intrinsic terminators do not require additional factors for efficient transcription termination, although the general transcription elongation factor NusA was known to increase the termination efficiency slightly in vitro. We found that the effect of NusA varies widely among different terminators and identified a subclass of weak non-canonical terminators that largely depend on NusA for recognition by RNA polymerase. Using genome-wide 3’ end-mapping on an engineered Bacillus subtilis NusA depletion strain, we identified >2000 intrinsic terminators, hundreds of which are NusA-dependent. Our in vitro and in vivo characterization showed that terminators with weak RNA hairpins and distal U-tract interruptions tend to be NusA-dependent. Our observations indicate that the lethality associated with deletion of nusA is caused by global readthrough of NusA-dependent terminators, resulting in misregulation of physiologically important downstream genes. We also show that nusA expression is autoregulated by a transcription attenuation mechanism that is mediated by NusA-dependent termination.

overall_design: 3' end-mapping and mRNA profiling of stationary phase B. subtilis NusA-depletion (PLBS802) strain in NusA expressing and depleted conditions, 6 replicates each.

first: Smarajit

last: Mondal

first: Alexander

last: Yakhnin

first: Aswathy

last: Sebastian

first: Istvan

last: Albert


title: p62/SQSTM1 by binding to vitamin D receptor inhibits hepatic stellate cell activity, fibrosis and liver cancer

city: New York

first: Jorge

last: Moscat

summary: Hepatic stellate cells (HSC) play critical roles in liver fibrosis and hepatocellular carcinoma (HCC). Vitamin D receptor (VDR) activation in HSC inhibits liver inflammation and fibrosis. Here we show that p62/SQSTM1, a protein that is upregulated in liver parenchymal cells but downregulated in HCC-associated HSC, negatively regulates HSC activation. Total body or HSC-specific p62 ablation potentiates HSC activation and enhances inflammation, fibrosis and HCC progression. We demonstrate that p62 directly interacts with VDR and RXR promoting their heterodimerization, which is critical for VDR:RXR target genes recruitment. Loss of p62 in HSC impairs the repression of fibrosis and inflammation by VDR agonists. This demonstrates that p62 is a negative regulator of liver inflammation and fibrosis through its ability to promote VDR signaling in HSC, whose activation supports HCC development.

overall_design: RNA was extracted from liver tissue from WT or p62KO mice previously injected with DEN and fed with HFD. Mouse Hepatic Stellate Cells (HSC) from WT or p62KO livers were extracted, immortalized with SV40 Ag (LVP016-Bsd, Genetarget) and cultured in-vitro with or without Calcipotriol for the indicated time points.

first: Angeles

last: Duran

first: Eloy

last: Hernandez

first: Miguel

first: Elias

last: Castilla

first: Shankar

last: Subramanian

first: Sindhu

last: Raghunandan

first: Lewis

last: Roberts

first: Tatiana

last: Kisseleva

middle: T


title: Gene expression of 7 day combinatorial yohimbine and imipramine treated rat hippocampi

status: Public on Dec 31 2015

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Rats treated on 7 consecutive days with either 2 injections of vehicle (Ctl) (DMSO for yohimbine, saline for imipramine) or Y+I (2mg/kg Yohimbine + 20mg/kg Imipramine) were sacrificed 2 hours post the last injection and their hippocampi used for gene expression analysis.

overall_design: Agilent one-color experiment,Organism: Rat, Agilent-Rat  8x60k Microarray Gene expression (AMADID: 028279), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Vidita

last: Vaidya

first: Ishira

last: Nanavaty

first: Basma

last: Husain


title: Aging-associated DNA methylation changes in middle-aged individuals: The Young Finns Study

status: Public on Apr 21 2016

city: University of Tampere

first: Laura

middle: Eeva Marketta

last: Kananen

state: Pirkanmaa

address: Biokatu 6

department: Department of Microbiology and immunology

country: Finland

institute: University of Tampere/School of Medicine

summary: Background  Chronological aging-associated changes in the human DNA methylome are studied by multiple epigenome-wide association studies (EWAS); however, the aging-associated DNAmet changes identified among different age groups and tissues vary and especially the rates of aging-associated alterations in the epigenome during adulthood remain unclear. Here, we further explore and characterize CpG-sites where DNA methylation levels alter at a constant rate during adulthood and are also independent of blood cell type heterogeneity.   Results  In the study, we observed 1,202 aging-associated CpG-sites (a-CpGs), of which 48% were hypermethylated with advancing age in whole blood with an especially narrow age range (40 - 49 years). Repeatedly reported a-CpGs in ELOVL2, FHL2, PENK and KLF14 were also identified. Regions with aging-associated hypermethylation were enriched to several gene ontology terms (especially on the cluster of developmental processes), while hypomethylated sites showed no enrichment. The genes with a higher number of a-CpG hits were more often hypermethylated. Of the 1,202 aging-associated CpG-sites in the present study, 987 were identified in previous study (Vitality 90+) as differentially methylated also between nonagenarians and young adults in a previous study, and importantly, the directions of changes were identical in the previous and in the present study.   Conclusions  The set of 987 replicated a-CpGs presented here are altered in strong association with chronological aging in the whole range of adulthood. Consequently, future studies should note the variability of the types of a-CpGs, and the a-CpGs presented here should be dissociated from the environmental-sensitive CpG-sites or from regions that are associated with aging in a non-linear manner due to the accumulation of senescence-related features. This report offers detailed and verified pool of a-CpGs in which DNAmet levels associate linearly with chronological age and of which are different from the non-linearly changing ones.

overall_design: Bisulphite converted DNA from 184 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Saara

last: Marttila

first: Tapio

last: Nevalainen

first: Juulia

last: Jylhava

first: Nina

last: Mononen

first: Mika

last: Kähönen

first: Olli

last: Raitakari

first: Terho

last: Lehtimäki

first: Mikko

last: Hurme


title: Survey of cryptic unstable transcripts in yeast

status: Public on May 23 2016

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

country: USA

institute: University of Colorado Boulder

summary: We sequenced both the stable (WT) and unstable (rrp6delta) transcriptomes of three S.cerevisiae strains: S288c, Σ1278b, JAY291 and the S.paradoxus strain N17 for de novo annotation of cryptic unstable transcripts (CUTs).  Doing so we have greatly expanded on previous CUTs which were limited to the S.cerevisiae strain S288c and have provided the first assessment of CUT expression conservation in yeast

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: Examination of polyadenylated RNA populations between wildtype and nuclear exosome mutant rrp6delta yeast cells in biological replicates

first: Jessica

middle: M

last: Vera

middle: D


title: Peri-adolescent high-fructose diet effects on hypothalamic transcriptome

status: Public on Mar 25 2015

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Fructose consumption has increased by over 25% since 1970, and excess consumption has deleterious metabolic effects. Additionally, fructose can alter hypothalamic pituitary adrenal axis function, potentially resulting in increased vulnerability to mood disorders. Adolescents are the greatest consumers of fructose and also at a critical period of development.  Here, we examine the effects of consumption of a 55% fructose diet from weaning until adulthood on the hypothalamic transcriptome.

overall_design: RNA from whole hypothalamus of standard-chow and fructose-fed rats

first: Gretchen

last: Neigh

first: Constance

last: Harrell

first: Jillybeth

last: Burgado

first: Sean

last: Kelly

first: Nirav

last: Patel

first: Zachary

middle: P

last: Johnson


title: Gene expression profiling of diffuse large B-cell lymphomas supervised by CD5 expression

status: Public on May 19 2015

city: Tsu

first: Kana

last: Miyazaki

state: Mie

address: 2-174 Edobashi

department: Department of Hematology and Oncology

country: Japan

institute: Mie University

summary: CD5-positive (CD5+) diffuse large B-cell lymphoma (DLBCL) has a poor prognosis and high incidence of central nervous system (CNS) relapse, even in the rituximab era. To determine the gene expression profile of CD5+ DLBCL, total RNA from 90 patients with DLBCL, including 33 CD5+ DLBCL and 57 CD5-negative (CD5-) DLBCL patients, was examined using Agilent human oligo microarrays. These cases were separated into 78 activated B-cell-like (ABC) DLBCLs and 12 germinal center B-cell-like (GCB) DLBCLs. All cases of CD5+ DLBCL were classified as ABC DLBCLs. The classifier based on gene expression used in a supervised analysis correctly identified CD5 expression in the DLBCL and ABC DLBCL samples. The gene most relevant to CD5 expression was SH3BP5. The enriched GO categories in the CD5+ ABC DLBCL signature gene set were multicellular organismal signaling, transmission of nerve impulse, and synaptic transmission. This present study, which includes the largest reported number of patients with CD5+ DLBCL, confirmed that most CD5+ DLBCLs are ABC DLBCLs, suggesting that therapeutic strategies for ABC DLBCL may be effective for the treatment of CD5+ DLBCL. Our CD5+ ABC DLBCL signature gene set may provide insights into the cause of the high frequency of CNS relapse in CD5+ DLBCL.

overall_design: This present study involved 90 cases (33 patients with CD5+ DLBCL and 57 with CD5- DLBCL) of de novo consecutive DLBCL diagnosed at Mie University Hospital with available frozen biopsy specimens and total RNA samples. Lymphoma tissue RNA from 90 patients was extracted for target preparation and hybridization onto Agilent microarrays. The expression of CD5 in tumor cells was confirmed by means of immunohistochemistry using frozen sections.

first: Motoko

last: Yamaguchi


title: Small RNA expression in wild-type sciatic nerves during myelination

status: Public on Oct 12 2015

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

institute: UCSF

summary: miRNAs are critical for myelination in the peripheral nervous system. We report the differential expression of miRNAs during myelination in sciatic nerves of wild-type mice. This data serves as a starting point to identify physiologically relevant regulatory miRNAs in the peripheral nervous system.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: total RNA from sciatic nerves of wild-type C57BL6 from embryonal day 17.5, postnatal (P) day 1, P4, P10, P30, P60 each in 2 biological replicates was used to perform the study. Additionally total RNA from differentiated primary rat Schwann cells has been included.

first: Deniz

last: Goekbuget

first: Jorge

last: Pereira

first: Antonin

last: Marchais

last: Ciaudo

first: Ueli

last: Suter


title: RNA expression in P1 sciatic nerves

summary: RNA seq was performed comparing SC-specific Dicer mutants with SC-specific Lin28B transgenics to obtain an unbiased list of potentially de-regulated miRNA target candidates.

overall_design: total RNA from sciatic nerves of P1 Dicer mutants, P1 Lin28 transgenics and their respective controls was used to perform RNA sequencing analysis.


title: Generation of Patient-Matched Malignant and Normal Primary Cell Cultures from Clear Cell Renal Cell Carcinoma Patients

status: Public on Jun 01 2016

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: Transcriptome profiling of de novo-derived ccRCC cell cultures and their matching parental tumours.  VHL-mutant and VHL wild-type cultures were established by isolating CA9+ and CA9- cells from tumor samples using FACS.

overall_design: RNASeq expression profiling of 18 renal cell carcinoma samples, including 6 patient tumours, 6 VHL mutant and 6 VHL WT derivative cell cultures

first: Kevin

middle: R

last: Brown


title: Sequencing analysis of sciatic nerves during myelination

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

overall_design: Refer to individual Series


title: Age-associated Changes in Basal NF-κB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 4)

status: Public on Jan 08 2015

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Immune impairment and high circulating level of pro-inflammatory cytokines are landmarks of human aging. However, the molecular basis of immune dysregulation and the source of inflammatory markers remain unclear. Here we demonstrate that in the absence of overt cell stimulation, gene expression mediated by the transcription factor NF-κB is higher in purified and rested human CD4+ T lymphocytes from older compared to younger individuals. This increase of NF-κB -associated transcription includes transcripts for pro-inflammatory cytokines such as IL-1 and chemokines such as CCL2 and CXCL10. We demonstrate that NF-κB up-regulation is cell-intrinsic and mediated in part by phosphatidylinositol 3-kinase (PI3K) activity induced in response to metabolic activity, which can be moderated by rapamycin treatment. Our observations provide direct evidence that dysregulated basal NF-κB activity may contribute to the mild pro-inflammatory state of aging.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. To test the effects of serum, 5x10^6 CD4+ T cells in 3 ml of RPMI 1640 with serum or AIM V (Life Technologies, Carlsbad, CA, USA) serum-free medium were held at 4°C or incubated for 4h at 37ºC (5% CO2 incubator). After incubation, cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol and the biotin-labeled cRNA was hybridized to Illumina's HumanHT-12 V4.0 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

first: Arsun

last: Bektas

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: William

middle: H

last: Wood III

middle: G

last: Becker

first: Karen

last: Madara

first: Luigi

last: Ferrucci

first: Ranjan

last: Sen


title: Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers

status: Public on Sep 17 2015

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

institute: Victoria University

summary: Background: The mechanisms of how genetic variants (SNPs) identified in genome-wide association studies act to influence body mass remain unknown for most of these SNPs, which continue to puzzle the scientific community. Recent evidence points to epigenetic and chromatin state of the genome to have an important role.  Methods: 355 healthy young individuals were genotyped for 52 known obesity-associated SNPs and we obtained DNA methylation levels in their blood using the Illumina 450K BeadChip. Associations between alleles and methylation at proximal cytosine residues were tested using a linear model adjusted for age, sex, weight category and a proxy for blood cell type counts. For replication in other tissues, we used two open-access datasets (skin fibroblasts, n=62; four brain regions, n=121-133) and an additional dataset in subcutaneous and visceral fat (n=149).  Results: We found that alleles at 28 of these obesity-associated SNPs associate with methylation levels at 107 proximal CpG sites. Out of 107 CpG sites, 38 are located in gene promoters, including genes strongly implicated in obesity (MIR148A, BDNF, PTPMT1, NR1H3, MGAT1, SCGB3A1, HOXC12, PMAIP1, PSIP1, RPS10-NUDT3, RPS10, SKOR1, MAP2K5, SIX5, AGRN, IMMP1L, ELP4, ITIH4, SEMA3G, POMC, ADCY3, SSPN, LGR4, TUFM, MIR4721, SULT1A1, SULT1A2, APOBR, CLN3, SPNS1,SH2B1, ATXN2L, and IL27). Interestingly, the associated SNPs are in known eQTLs for some of these genes. We also found that the 107 CpGs are enriched in enhancers in peripheral blood mononuclear cells. Finally, our results indicate that some of these associations are not blood-specific as we successfully replicated four associations in skin fibroblasts.  Conclusions: Our results strongly suggest that many obesity-associated SNPs are associated with proximal gene regulation, which was reflected by association of obesity risk allele genotypes with differential DNA methylation. This study highlights the importance of DNA methylation and other chromatin marks as a way to understand the molecular basis of genetic variants associated to human diseases and traits.

overall_design: Bisulphite converted DNA from 355 individuals aged 14-34 were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Markus

last: Almén

first: Galina

middle: Y

last: Zheleznyakova

first: Lina

last: Lundberg

first: Sanaz

last: Zarei

first: Sandra

last: Castillo

first: Fia

last: Eriksson

first: Emil

last: Nilsson

first: Yvonne

last: Böttcher

first: Peter

last: Kovacs

first: Janis

last: Klovins

first: Mathias

last: Rask-Andersen

first: Helgi

middle: B

last: Schiöth


title: Age-associated Changes in Basal NF-κB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase

first: Supriyo

last: De


title: Age-associated Changes in Basal NF-κB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 1)

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. After a 4h incubation at 37ºC (5% CO2 incubator), cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol, and the biotin-labeled cRNA was hybridized to Illumina's HumanRef-8 v2.0 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3. Samples were divided into 2 age groups, young and old, with the cut off at 65 years and above as old.

first: Arsun

last: Bektas

first: Yongqing

last: Zhang

first: Elin

last: Lehrmann

first: William

last: Wood III

first: Kevin

last: Becker

first: Karen

last: Madara


title: Age-associated Changes in Basal NF-κB Function in Human CD4+ T Lymphocytes via Dysregulation of PI3 Kinase (dataset 2)

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque Plus density gradient centrifugation. CD4+ T cells were obtained by positive selection using anti-human CD4 microbeads. After a 4h incubation at 37ºC (5% CO2 incubator), cells were harvested and collected by centrifugation. Total cellular RNA was prepared using Qiagen RNeasy protocols. Labeling and amplification were done with the standard Illumina protocol, and the biotin-labeled cRNA was hybridized to Illumina's HumanHT-12 v4 Expression BeadChip. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3. Samples were divided into 2 age groups, young and old, with the cut off at 65 years and above as old.

first: Luigi

last: Ferrucci

first: Ranjan

last: Sen


title: DNA methylation profiles of human blood samples from a severe developmental disorder and controls

status: Public on May 28 2015

first: Steve

last: Horvath

state: CA

department: Human Genetics

summary:
Human DNA methylation Beadchip v1.2 was used to obtain n=113 Illumina DNA methylation array from whole blood samples.
The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of subjects with a severe developmental disorder (known as syndrome X) and controls. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.

overall_design: The data set contains 5 affected female subjects who exhibit a pure form of syndrome X. Further, the study includes two syndrome X-like subjects who also have Down syndrome and Ring- X Turner syndrome, respectively. For the diseased subjects, we collected several family members (parents and possibly siblings). We also collected several control families who do not have an affected child. Apart from family data, we also analyzed 62 blood samples from healthy controls.

first: Richard

last: Walker