title: RNA-seq analyses of kdm5[A512P] and enzymatically inactive kdm5[JmjC*] in adult heads

status: Public on Dec 31 2018

city: Bronx

first: Julie

last: Secombe

address: 1300 Morris park ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: The goal of this study was to generate a Drosophila model of intellectual disability caused by mutations in kdm5. RNA-seq was used to define the transcriptional defects of a mutation in Drosophila that is analogous to a human intellectual disability-associated allele, kdm5[A512p]. These data revealed a total of 1609 dysregulated genes, 778 of which were upregulated and 831 were downregulated. To determine whether these transcriptional defects were due to the loss of KDM5-induced histone demethylation, we also carried out RNA-seq from a enzymatic inactive strain, kdm5[Jmjc*]. These data revealed a striking similarity between the two datasets and suggest that the primary defect of KDM5[A512P] is loss of histone demethylase activity.

overall_design: 3-5 day old adult heads from wildtype, kdm5[A512P] and kdm5[JmjC*] were used to generate RNA that was subsequently subjected to deep sequencing.


title: Conserved mRNA-granule component Scd6 targets Dhh1 to   repress translation initiation and activates Dcp2-mediated mRNA decay in vivo

status: Public on Feb 27 2019

city: Bethesda

first: Alan

last: Hinnebusch

state: MD

address: 6 Center Drive, Building 6, Room 233

department: NICHD

country: USA

institute: NIH

type: Expression profiling by high throughput sequencing

summary: We have identified mRNAs whose abundance or translational efficiency is regulated in nutrient-rich medium by the Scd6 or Dhh1 protein in either wild-type cells or dcp2∆ cells lacking the decapping enzyme

overall_design: Ribosome profiling and RNA-seq was conducted to determine changes in mRNA abundance, translation, or translational efficiecies in comparing scd6∆ or dhh1∆ mutants to an isogenic wild-type strain; or scd6∆dcp2∆ and dhh1∆dcp2∆ strains to a dcp2∆ mutant

first: Fan

last: Zhang

first: Quira

last: Zeidan

middle: G


title: A miRNA-mediated approach to dissect the complexity of tumor-initiating cell function and identify miRNA-targeting drugs

status: Public on Jan 21 2019

city: Ann Arbor

first: Analisa

last: DiFeo

state: Michigan

address: 1600 Huron Parkway

institute: UNIVERSITY OF MICHIGAN-ANN ARBOR

summary: Microarray analysis of miR-181a sensor sorted primary HGSOC cells to determine the ability of miRNA sensor to regulate various cancer related pathways.

overall_design: Total RNA was extracted from cell lysates of OCI-P5X miR-181a high and OCI-P5X miR-181a low cells in triplicate and Affymetrix Human Clariom S array and the WT Plus chemistry was performed


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats

status: Public on Dec 01 2018

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 1129 Farm Lane

department: Biochemistry and Molecular Biology

institute: Michigan State University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome–wide gene expression profile of adipocytes and infiltration macrophages obtained from abdominal (visceral and subcutaneous) and peripheral (thigh) adipose depots from Normal Glucose Tolerant and Type 2 Diabetics Asian Indians

city: Jaipur

first: Dr. Sandeep

middle: Kumar

last: Mathur

state: Rajasthan

address: Tonk Road

department: Department of Endocrinology

country: India

institute: SMS Medical College and Hospital

summary:
We have identified molecular-level alternations in different adipose depots (thigh, visceral and subcutaneous) of Asian Indians (both male and female) suffering from type-2 diabetes as compared to age and BMI matched normal glucose tolerant subjects by functional analysis of differentially expressed genes, and correlation of gene expression estimates with measured intermediate traits associated with T2D and its related co-morbidities (Hb1Ac, HOMA-B, HOMA-R, NEFA, Triglyceride, Total Cholesterol, HDL, LDL, VLDL, Leptin, Adiponectin, TNF-α,  Serum- Creatinine,  IL-6, High sensitivity - serum-creatinine (hs-CRP) and also size of adipocytes).

Funding:
Grant Id: 5/4/8/2012-RMC
Grant title: Clinical, Biochemical and Cellular Correlates of Transcriptome of  Adipose Tissue Among Type-2 Diabetics
Name of the funding source: Indian Council for Medical Research

overall_design: We have recruited 30 controls & 30 diabetic subjects undergoing femur bone surgery and 16 controls & 19 diabetic subjects undergoing abdominal surgery (two samples from each subject, one subcutaneous and one visceral fat biopsy were extracted). So total 130 samples were obtained and analyzed for genome –wide gene expression profile of Adipocytes and infiltration macrophages from three different depots of adipose tissue.

first: S

middle: K

first: Aditya

last: Saxena

first: Pradeep

last: Tiwari


title: Oligodendrocyte progenitor cells become regionally diverse and heterogeneous with age

status: Public on Jan 15 2019

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Oligodendrocyte progenitor cells (OPCs), which differentiate into myelinating oligodendrocytes during central nervous system (CNS) development, are the main proliferative cells in the adult brain. OPCs are conventionally considered a homogeneous population, particularly with respect to their electrophysiological properties, but this has been debated. We show, by using single-cell electrophysiological recordings, that OPCs start out as a homogeneous population, but become functionally heterogeneous, varying both within and between brain regions and with age. These electrophysiological changes in OPCs correlate with the differentiation potential of OPCs; thus, they may underlie the differentiational differences in OPCs between regions and likewise differentiation failure with age.

overall_design: Total RNA profiles of oligodendrocyte precursor cells isolated from 3 to 4 wild-type mice at different time points, using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian.

first: Kimberley

middle: A

last: Evans

first: Yasmine

last: Kamen

first: Ragnhildur

middle: T

last: Káradóttir


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats [ChIP-Seq]

summary: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist that elicits a broad spectrum of dose-dependent effects in the liver, including hepatic lipid accumulation coupled with inflammation. To determine the role of inflammatory lipid mediators in TCDD-mediated hepatotoxicity, eicosanoid metabolism was investigated in female Sprague-Dawley (SD) rats. Rats were gavaged with sesame oil vehicle or 0.01-10 µg/kg TCDD every 4 days for 28 days. Hepatic RNA-Seq data from female SD rats was compared with data from female C57BL/6 mice and functionally annotated to determine key toxicogenomic differences between the two species regarding TCDD exposure. Hepatic RNA-Seq data from female SD rats integrated with untargeted metabolomics of liver, serum, and urine identified dose-dependent changes in linoleic acid (LA) and arachidonic acid (AA) metabolism. TCDD also elicited dose-dependent differential gene expression associated with cyclooxygenase, lipoxygenase, and cytochrome P450 epoxidation/ hydroxylation pathways with corresponding changes in omega-6 (e.g. AA and LA) and omega-3 polyunsaturated fatty acids (PUFAs) as well as their eicosanoid metabolites. Overall, total omega-6 PUFAs increased, while total omega-3 PUFAs decreased. Phospholipase A2 (Pla2g12a) was induced 6-fold consistent with increased AA metabolism, while AA utilization by lipoxygenases Alox5 (2-fold) and Alox15 (10-fold) increased leukotrienes (LTs), important mediators signaling an inflammatory response. More specifically, TCDD increased pro-inflammatory eicosanoids, including leukotriene (LT) B4 (3-fold), and LTB3 (5-fold), known signals for the recruitment of neutrophils to areas of tissue damage. Dose-response modeling of metabolite and gene expression changes suggests the cytochrome P450 hydroxylase/epoxygenase and the lipoxygenase pathways are the most sensitive to TCDD. While several differentially expressed genes (DEGs) associated with eicosanoid biosynthesis contained putative dioxin response elements (pDRE) within their regulatory region, ChIP-Seq analysis showed little AhR enrichment, suggesting TCDD-elicited induction of eicosanoid biosynthesis is not a direct effect of AhR activation.

overall_design: 5 biological replicates

first: Claire

middle: M

last: Doskey

first: Rance

last: Nault

first: Kelly

last: Fader

first: Todd

last: Lydic

first: Jason

last: Matthews

first: Dave

last: Potter

first: Bonnie

last: Sharratt

middle: R


title: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) Alters Hepatic Polyunsaturated Fatty Acid Metabolism and Eicosanoid Biosynthesis in Female Sprague-Dawley Rats [RNA-Seq]

overall_design: Three biological replicates for rats given dose of sesame oil vehicle or 0.01, 0.03, 0.1, 0.3, 1, 3, or 10 μg/kg.


title: Microglial gene expression after TGFb1 treatment in vitro

status: Public on Sep 01 2018

city: Rostock

first: Björn

last: Spittau

address: Gertrudenstraße 9

department: Institute of Anaomy

country: Germany

institute: University of Rostock

summary: Primary microglia derived from P0/P1 pus of C57BL/6 mice were cultured under serum-free conditions and were treated with recombinant human TGFb1 (5 ng/ml) for 24 h. RNA was isolated using the TRIzol method.


title: Genome-wide analysis of gene expression in HTR8/SVneo cells treated with ZNF554 siRNA

status: Public on Dec 30 2018

city: Detroit

first: Adi

last: Tarca

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

summary: Analysis of the effect of ZNF554 knock-down on genome-wide gene expression in trophoblastic cells. The hypothesis tested in the present study was that ZNF554 regulates the expression of genes involved in trophoblastic cell migration and invasion. The results provide important information on the functions of ZNF554 in trophoblastic cells.

overall_design: Total RNA was obtained from HTR8/SVneo cells subjected to either ZNF554 (n=3) or scrambled (n=3) siRNA treatment.

first: Gaurav

last: Bhatti

first: Susan

last: Land

first: Roberto

last: Romero

middle: L

first: Nandor

last: Than

first: Yi

last: Xu


title: RNA-sequencing of WT and Asic3-null leukemia-initiating cells (LICs)

status: Public on Aug 03 2018

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

country: China

institute: Tongji hospital

summary: To tease apart the downstream signaling triggered by the Asic3-mediated ion current, RNA-sequencing analyses were conducted with WT and Asic3-null LICs. We found 199 genes were significantly up-regulated, while 587 were down-regulated in Asic3-null LICs. The gene ontology (GO) analysis showed that ASIC3 might mainly be involved in the pattern recognition receptor activity, protein complex binding and calcium ion binding. KEGG further indicated that ASIC3 was required for the glutathione metabolism and hematopoietic cell lineage.

overall_design: WT and Asic3-null YFP+Mac-1+c-Kit+ LICs were purified by flow cytometry for the extraction of total RNA and subjected to RNA-sequencing.

first: Jun-Ke

last: Zheng

first: Hao

last: Gu


title: Differentially expressed (DE) genes analysis in synovial fluid mesenchymal stem cells (SF-MSCs), SF-MSC derived iPSCs and iPSC derived MSCs (iPSC-MSCs)

status: Public on Oct 04 2018

city: Madison

first: Hongli

last: Jiao

state: WI

address: 1111 Highland Ave WIMR 5039

department: Department of Orthopedics and Rehabilitation

institute: University of Wisconsin-Madison

summary: We report the application of next-generation sequencing (NGS) to analysis the gene expression profile among three different cells:SF-MSCs, iPSCs and iPSC-MSCs. Our results shown that iPSC-MSCs were more similar to SF-MSCs than iPSCs.

overall_design: Human SF-MSCs were reprogrammed through the non-viral, integration-free episomal approach into induced pluripotent stem cells (iPSCs), which were then subsequently differentiated into MSCs to establish iPSC-MSC lines.

first: Wan-Ju

last: Li

first: Madeleine

last: Lemieux


title: PARP1 regulates VSMC phenotypic switch and neointima via Myocardin

status: Public on Sep 20 2018

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: We applied the transcriptome profiling (RNA-seq) for  high-throughput profiling of genes changes in VSMC dedifferentiation. Rat primary VSMCs were divided into 3 groups, control, PDGF-BB, PDGF-BB+PJ34,and mRNA sequence were performed. We found that PDGF-BB could upregualted the genes involved in cell proliferation and migration, and downregulated the VSMC contractile genes, all of which could be reversed by PARP inhibitor PJ34. Then we knockdowned the co-factor Myocardin in VSMCs, and found the above effects of PJ34 were nearly abolished.Our study  first provided the transcription changes by RNA-seq in VSMC dedifferentiation, and demonstrated the key roles of PARP1 and the PARylation process in VSMC phenotypic switch.

overall_design: Eximination of genes changes in VSMC dedifferentiation

first: Cheng

last: Wang

first: Wenjing

first: Kai

last: Huang


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

status: Public on Aug 01 2018

first: Andre

last: Nussenzweig

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

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

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

last: Wu

first: Xia

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela

first: Haiqing

last: Fu

first: Chrishtophe

last: Redon

first: Steven

last: Pruitt

first: Yan

last: Jaszczyszyn

first: Mirit

last: Aladjem

first: Peter

last: Aplan

first: Olivier

last: Hyrien


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

first: Andre

last: Nussenzweig

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan


title: Epigenome-wide analyis of neurobehavioral variation in preterm infants

status: Public on Mar 26 2019

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

type: Methylation profiling by genome tiling array

summary: Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in epigenomic measures from buccal cells were associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N=536). We tested whether epigenetic age, age acceleration, or DNA methylation (DNAm) levels at individual loci, measured via the Illumina EPIC microarray, differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications, ranging from most optimal to atypical. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations in buccal cells may be informative for infant neurobehavior.

overall_design:
DNA methylation was assessed for 542 samples using the Illumina MethylationEPIC Beadarray

**Additional samples (537-542) are added and the 'MatrixProcessed.txt.gz' is updated on Feb 18, 2021.

middle: J

first: Todd

last: Everson


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

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen

last: Stanlie

first: Wei

last: Wu

first: Xia


overall_design: Nascent RNA profile in B, and T cells untreated and upon HU treatment.

first: Amanda

last: Day

first: Nancy

last: Wong

first: Mianmian

last: Yin

first: Andres

last: Canela

first: Haiqing

last: Fu


title: Repli-seq profile from resting (G0) and cycling (S) phase untreated B cells

first: Chrishtophe

last: Redon

first: Steven

last: Pruitt

first: Yan

last: Jaszczyszyn

first: Mirit

last: Aladjem

first: Peter

last: Aplan


first: Andre

last: Nussenzweig

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

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

first: Anthony

last: Tubbs

first: Sriram

last: Sridharan

first: Olivier

last: Hyrien


title: Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse

first: Niek

last: van Wietmarschen

first: Yaakov

last: Maman

first: Elsa

last: Callen


title: RNA-sequencing of smpB-dependent gene expression in A. Veronii C4

status: Public on Sep 29 2018

city: Haikou

first: Hong

last: Li

address: NO. 58, Renmin Avenue

institute: Hainan Unversity

summary: We generated A. veronii strains that express SmpB(wt) or not(△smpB) in trans to evaluate the changes in gene expression upon SmpB expression. As SmpB participate in transtranslation sysytem, this allows us to explore the gene regulaton in A.veronii.

overall_design: wild type and △smpB of A.veronii were grown in M9 medium. mRNA profiles were generated by deep sequencing, in triplicate, using Illumina Hiseq xTen.

first: Zhu

last: Liu

first: Dan

last: Wang


title: miRNA changes induced by cyclic and chronic hypoxia in human Ecs

status: Public on Jul 12 2018

city: GDANSK

first: Rafal

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

type: Non-coding RNA profiling by high throughput sequencing

summary:
We report the results NGS based of miRNA profiling in human endothelial cells under chronic and cyclic hypoxia
Solid tumor microenvironments are often subjected to various levels of hypoxia. Although regulation of gene expression has been examined extensively, most studies have focused on chronic hypoxia. The tumor microenvironment, however, experience waves of hypoxia and reoxygenation that stimulates the expression of pro-angiogenic factors that promote blood vessel formation. In this study, we examined human umbilical vascular endothelial cells (HUVECs) under waves of intermittent (cyclic hypoxia) to determine how this process compares to chronic hypoxia, and more importantly, how this influences the microRNA profiles that potentially affect the posttranscriptional regulation of angiogenic genes. The rationale for these studies is that cancer cells subjected to cyclic hypoxia appear to have increased metastatic potential and endothelial cells exhibit a higher radiation resistance and greater migration potential. This indicates that the gene regulatory networks in cyclic hypoxia may be different from chronic hypoxia. Here we examined the consequences of cyclic hypoxia on miRNA gene expression and how these changes in miRNA expression could influence angiogenesis. Using Next Generation Sequencing, our results demonstrate that cyclic hypoxia has very different effects on the miRNA networks compared to chronic hypoxia, the in silico predicted effects on the certain mRNA target genes are more similar than might be expected. More importantly, these studies indicate that identifying potential miRNAs (including hsa-miR-19a-5p) as therapeutic targets for inhibiting angiogenesis and tumor progression will require this type of physiologically relevant analysis.

overall_design: mRNA profiles of HUVECs exposed to cyclic and chronic chypoxia were generated by deep sequencing.


title: Identifying Lsr2 binding sites in Streptomyces venezuelae

status: Public on Jun 09 2018

city: HAMILTON

first: Marie

last: Elliot

state: ON

address: 1280 Main Street West

country: Canada

institute: McMaster University

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

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

first: Emma

last: Gehrke


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


title: Cryptococcus neoformans sexual reproduction is controlled by a quorum sensing peptide

status: Public on May 15 2018

city: beijing

first: lei

last: chen

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

institute: the institute of microbiology chinese academy of sciences

summary: Mating pheromone is the best-known fungal paracrine signal whose essentiality in determining sexual reproduction has been recognized since six decades ago. We demonstrate that the pheromone cannot induce mating response during unisexual mating due to the lack of a compatible receptor from the same unisexual population. We identify a quorum sensing (QS) peptide Qsp1 in place of pheromone as a specific intercellular signal directing Cryptococcus unisexual reproduction.  A typical zinc finger regulator Cqs2 as the master regulator of QS signaling induces unisexual reproduction in response to Qsp1. Collectively, these data demonstrate that QS activation rather than pheromone induction as the pivotal social control mechanism underlies unisexual reproduction in C .neoformans.

overall_design: 64 samples contain wild type, cqs1delta ,opt1delta and cqs2delta, expression profiles of wild-type (WT) and the cqs1delta mutant in the presence of glucose or galactose of  two replicates.

first: Xiuyun

last: Tian

first: Guangjun

last: He

first: Pengjie

last: Hu

first: Lei

last: Chen

first: Changyu

last: Tao

first: Ying-Lu

last: Cui

first: Lan

last: Shen

first: Weixin

last: Ke

first: Haijiao

last: Xu

first: Youbao

last: Zhao

first: Qijiang

first: Fengyan

last: Bai

first: Bian

last: Wu

first: Ence

last: Yang

first: Xiaorong

last: Lin

first: Linqi


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

first: Marie

last: Elliot

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

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

first: Emma


status: Public on Jun 29 2018

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Expression and differential expression analysis of milk samples from healthy and diseased diary cows. Diseases were grouped by their occurrence in the mammary gland or extra-mammary. Furthermore, the diseases were classified by their severity. All cows were examined thoroughly by the dairy herd manager, trained staff, or a veterinarian. Expression and differential expression was assessed by using the Affymetrix Bovine Genome Array (GPL2112). Control animals (2-4 years old, 1st to 3th lactation, one animal 4th and one 8th lactation) showed no clinical signs of disease and had no abnormalities in the udder or milk. Their somatic cell count (SCC) was less than 100,000 cells/ml milk. Most of the control samples were taken during early lactation (10-100 days post-partum, dpp). Diseased cows were in their 1st to 8th lactation within 10-220 dpp.

overall_design: We analyzed 6 biological replicates each from milk samples from healthy diary cows, diary cows with mastitis and diary cows with endometritis.

first: K.

last: Zoldan

first: J.

last: Schneider

first: T.

last: Moellner

first: C.

last: Fueldner

last: Knauer

first: M.

last: Fuerll

first: A.

last: Starke

last: Specht

last: Hackermueller

first: S.

last: Kalkhof

last: von Bergen

first: U.

last: Bergfeld

first: R.

last: Fischer

last: Pache

last: Lehmann


title: Kir4.1-dependent astrocyte-fast motor neuron interactions are required for peak strength

status: Public on May 01 2018

city: Stanford

first: Kevin

last: Kelley

state: CA

address: 318 Campus Drive, W200

institute: Stanford University

summary: Diversified neurons are essential for sensorimotor function, but whether astrocytes become specialized to optimize circuit performance remains unclear. Large fast α-motor neurons (FαMNs) of spinal cord innervate fast-twitch muscles that generate peak strength. We report that ventral horn astrocytes express the inward rectifying K+ channel Kir4.1 (aka, Kcnj10) around MNs in a VGLUT1-dependent manner. Loss-of astrocyte-encoded Kir4.1 selectively altered FαMN size, function and led to reduced peak strength. Overexpression of Kir4.1 in astrocytes was sufficient to increase MN size through activation of the PI3K/mTOR/pS6 pathway. Kir4.1 was downregulated cell-autonomously in astrocytes derived from amyotrophic lateral sclerosis (ALS) patients with SOD1 mutation. However, astrocyte Kir4.1 was dispensable for FαMN survival even in the mutant SOD1 background. These findings show that astrocyte Kir4.1 is essential for maintenance of peak strength and suggest that Kir4.1 downregulation uncouples symptoms of muscle weakness from MN cell death in ALS.

overall_design: 8 samples total consisting of 4 biological replicates per group (Aldh1l1-cre:Kir4.1-floxed/floxed vs cre-negative) of flow sorted Aldh1l1-GFP+ astrocytes from spinal cord at P12-P14

middle: W

first: Lucile

last: Ben Haim

first: David

last: Rowitch


title: RNAseq profiling of FACS-sorted zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures

status: Public on Aug 11 2017

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

summary: We used different zebrafish transgenic lines to sort macrophages, neutrophils and immature lymphoid cells from 5-6 day old zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature.

overall_design: Embryos were grown into egg water refresh every day and incubated for 5 or 6 days at 28°C. 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) was added after 1 day to prevent melanisation. After the incubation period, embryos were dissociated into single cell suspension by Trypsin treatment and fluorescent cells were sorted by FACS. RNA extraction and library preparation were performed as previously described. (Rougeot et al., 2014, Methods Mol Biol 1197:41-66). For infection experiments, zebrafish embryos were manually dechorionated at 24 hours post fertilization (hpf) and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Infected larvae were collected for FACS sorting 5 day post infection.

first: Ania

last: Zakrzewska

first: Vincenzo

last: Torraca

first: Zakia

last: Kanwal

first: Hans

last: Jansen

first: Herman

middle: P

last: Spaink

first: Annemarie

middle: H

last: Meijer


title: Mistimed sleep disrupts circadian regulation of the human blood transcriptome - Heterozygotes

status: Public on Feb 08 2017

city: Guildford

first: Emma

last: Laing

address: Stag Hill

country: United Kingdom

institute: University of Surrey

summary: 4 healthy volunteers without sleep disorders were resident in an environmental scheduling facility and participated in a forced-desynchrony protocol, in which the sleep-wake cycle and the associated fasting-feeding cycle is scheduled to a 28-hour period, of which one third (i.e. 9h 20min) is scheduled for sleep. Under these conditions, during which light levels in the waking episode are kept low and sleep is scheduled in darkness, the phase of the melatonin rhythm occurred at approximately the same clock time during the first (D1) and fourth (D4) 28-h cycle and there were no major changes in either the amplitude or the waveform of this rhythm. During D1 and D4 7 blood samples were taken, RNA was extracted from leukocytes, labelled and hybridised to human whole-genome microarrays

overall_design: A total of 23 samples comprising 4 human subjects, for which 14 samples across multiple time-points/sleep condition were collected.

first: Carla

last: Moller-Levet

first: Simon

last: Archer

first: Giselda

last: Bucca

first: Ana

last: Slak

first: Renata

last: Kabiljo

first: June

last: Lo

first: Nayantara

last: Santhi

first: Malcolm

last: von Schantz

first: Colin

last: Smith

first: D

last: Dijk


title: Gene expression profiling of murine embryonic and epiblast stem cells under IQ1 treatment and Ctnnb1 K49 acetylation conditions

status: Public on Dec 12 2017

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

summary: Naïve pluripotency represents the ground state of mammalian development, but the molecular mechanisms controlling its establishment remain incompletely defined. To clarify the role of β-catenin (Ctnnb1) acetylation, we performed microarray-based transcriptome profiling of murine embryonic stem cells (ESCs, naïve) and epiblast stem cells (EpiSCs, primed) under different culture conditions. Particular focus was placed on the acetylation of Ctnnb1 at lysine 49 (K49) and its modulation by IQ1, a small molecule that inhibits Ep300 function and enhances K49 acetylation. This dataset enables comparison of gene expression signatures between naïve and primed states and provides insights into the induction of naïve-like characteristics in EpiSCs following IQ1 treatment.

overall_design: Naïve pluripotency is the developmental ground state. To define transcriptional programs associated with β-catenin (Ctnnb1) lysine-49 acetylation, we performed microarray profiling of mouse embryonic stem cells (ESCs; naïve), epiblast stem cells (EpiSCs; primed), and EpiSCs exposed to IQ1 to increase K49 acetylation. The dataset enables direct comparison of naïve versus primed states and assessment of IQ1-driven conversion toward a naïve-like transcriptome.

first: Takeshi

last: Teramura

first: Hirofumi

last: Suemori


title: The human blood transcriptome following sleep extension and sleep restriction: Heterozygote samples

summary: In a cross balanced design human subjects were given one week of sufficient sleep and insufficient sleep (6 h per day). Following each of these conditions they were then kept awake for a day, a night and the subsequent day. During each of these periods of extended wakefulness 10 blood samples were taken, RNA was extracted from leukocytes, labelled and hybridised to human whole-genome microarrays

overall_design: A total of 49 samples comprising 10 human subjects, for which three samples across multiple time-points/sleep conditions were collected.


title: CPD-seq map of UV damage formation in human fibroblasts

status: Public on Jun 21 2018

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary: UV light is an initiating factor in the etiology of human melanoma due to its production of mutagenic DNA photoproducts, primarily cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts. UV-induced mutations are heterogeneously distributed across melanoma genomes, being enriched, for example, in regions of compact heterochromatin and at active transcription factor binding sites (TFBS). Differential ability of nucleotide excision repair (NER) to remove UV-induced DNA lesions in these regions has been proposed as the primary factor establishing the observed regional differences in melanoma mutation density. However, it is not fully understood to what extent the binding of transcription factors and chromatin structure affect UV damage formation, nor how variations in initial damage levels contribute to mutagenesis. Here, we directly mapped sites of CPD formation across the genome in human cells, and show that variations in UV damage formation, due to primary chromatin structure and transcription factor binding, are strongly correlated with local differences in melanoma mutation density. Analysis of individual transcription factors revealed that the E26 transformation-specific (ETS) family is the major contributor to increased somatic mutation density at TFBS in melanoma, primarily because DNA binding by ETS family transcription factors stimulates the formation of CPD lesions, generating UV damage 'hotspots'. Moreover, many ETS binding sites, including those associated with known cancer genes, are recurrently mutated in human melanomas. These findings establish variable lesion formation as a key contributor to mutation heterogeneity in cancer.

overall_design: UV-induced cyclobutane pyrimidine dimers (CPDs) were mapped across the genome of NHF1 cells immediately following UV irradiation (0 hr time point) with doses of 100 J/m2 or 20 J/m2 of UVC light. As a control, isolated NHF1 genomic DNA (i.e., naked DNA) was irradiated in vitro with UV dose of 80 J/m2 of UVC light.

first: Peng

last: Mao


title: Genome-wide maps of KDM5 binding in drosophila adults

status: Public on Dec 22 2015

city: Bronx

first: Julie

last: Secombe

state: United states

address: 1300 Morris park ave. Ullmann 809

institute: Albert einstein college of medicne

summary: To determine which genes affected by loss of KDM5 in adults were direct targets, we carried out KDM5 ChIP-seq analyses. To valide  this data, we utilized a previously generated fly strain in which the sole source of KDM5 is from a transgene expressing an HA tagged form of KDM5 expressed under the control of its endogenous promoter. Comparing genome-wide gene expression and KDM5  binding analyses in Drosophila adults, we demonstrate the primary function of KDM5 in adults is to activate gene expression KDM5. To investigate the link between KDM5 and H3K4me3, we carried out anti-H3K4me3 ChIP-seq from wildtype adults . Genome-wide, KDM5 and H3K4me3 peaks showed a similar distribution, with both peaking at the transcription start site (TSS) showed a striking overlap with the presence of H3K4me3.

overall_design: Examination of KDM5 binding and histone H3K4me3 modifications in drosophila adults

first: Xingyin

last: Liu


title: A-to-I RNA editing promotes developmental-stage specific gene and lncRNA expression

status: Public on Dec 05 2016

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

summary: A-to-I RNA editing is a conserved and widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions. Although human RNAs contain millions of A-to-I editing sites, most of these occur in noncoding regions and their function is unknown. Knockdown of ADAR enzymes in C. elegans causes defects in normal development but is not lethal as it is in human and mouse, making C. elegans an ideal organism for studying the regulatory effects of RNA editing on the transcriptome. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, with the observation that lack of both mechanisms can suppress defects observed when only RNA editing is absent. To study the effects of RNA editing on gene expression and function, we established a novel screen that enabled to identify thousands of RNA editing sites in non-repetitive regions in the genome. These include dozens genes that are edited at their 3’UTR region. We found that these genes are mainly germline and neuronal genes and that they are downregulated in the absence of ADAR enzymes. Moreover, we discovered that almost half of these genes are edited in a developmental-specific manner. In addition, we found that many pseudogenes and other lncRNAs are also extensively downregulated in the absence of ADARs in embryo but not L4 larva developmental stage, while this downregulation is not observed in additional knockout of RNAi.  Taken together, our results suggest a role for RNA editing in normal growth and development by regulating silencing via RNAi.

overall_design: RNA-seq samples were generated from:  1. wildtype (N2) at embryo stage  2. wildtype (N2) at L4 stage  3. ADAR mutant (BB21 or BB4) worms at L4 stage   4. ADAR mutant (BB21 or BB4) worms at embryo stage   5. ADAR mutant and RNAi mutant (BB23, BB24) at embryo stage   RNA in high and low molecular weight fractions was extracted by mirVana kit (ambion).   mRNA was sequenced from the high molecular weight fraction by means of Illumina   TruSeq® RNA Sample Preparation kit automated by Agilent Bravo Automated Liquid Handling Platform. The resulting libraries were sequences with an Illumina HiSeq 2500.

first: Dean

last: Light


title: Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

status: Public on May 18 2016

city: Royal Parade

first: Andrew

last: Keniry

state: Victoria

department: Molecular Medicine

country: Australia

institute: The Waler and Eliza Hall Institute of Medical Research

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: KDM5 occupancy and expression profiling of kdm5 mutant flies and wt flies under normal condition and oxidative stress


title: Suckling lamb perirenal fat transcriptome

status: Public on Jul 18 2018

city: León

first: Beatriz

last: Gutierrez Gil

state: León

address: Faculty of Veterinary, Campus de Vegazana

department: Dpto Animal Production

country: Spain

institute: University of León

summary: The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf= 8, Churra= 6) was used for the RNA-Seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, while in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, while the Churra upregulated DEGs are linked to fat accumulation.

overall_design: The transcriptome analysis was performed with RNA extracted from perirenal adipose tissue from 14 suckling lambs from two different breeds (specifically, six Churra and eight Assaf lambs). All the lambs included in this study were males born between April and May 2016. After birth, lambs were maintained between 4-8 hours with their dams to suck the first colostrum. Then, in order to avoid the maternal effects, they were held in lamb pens and fed Ovilac 60 (Calfvet, Lleida, Cataluña, Spain) milk replacer powder using a milk replacer machine. Lambs were slaughtered when they reached an average live weight of (mean ± SD) 10.32 ± 0.73 kg, which is the common market weight range. Lambs ages at slaughter were from 19 to 35 days old, and carcass weight for Churra and Assaf lambs were 5.16 ± 0.44 and 5.34 ± 0.33 kg, respectively. The management, transport and sacrifice of the animals was in accordance with the Spanish and EU legislations (Spanish Laws 32/2007, 6/2013 and RD 37/2014; Council Regulation (EC) 199/2009). At slaughter, perirenal adipose tissue was collected from each lamb.

last: Gutiérrez-Gil

first: Juan

last: Arranz

first: Aroa

last: Suárez-Vega


title: The genetic control of left atrial gene expression determined by RNA sequencing

status: Public on Jun 16 2015

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

summary: Purpose: Genome wide association studies (GWAS) have identified 14 loci for atrial fibrillation, but the mechanisms responsible for these associations as well as the causal genetic variants remain enigmatic.  Genetic variants altering expression levels of nearby genes is one such plausible mechanism.

overall_design: Methods:  We performed polyA+ RNA sequencing of left atrial appendages from a biracial cohort of 265 subjects.  Approximately 50 million read fragments mapped to the transcriptome using TopHat aligner to hg19 and fragments counted against Ensembl 71 reference transcriptome with htseq.  We also obtained genotypes using Illumina Hap550v3 and Hap610-quad SNP microarrays.  Genotypes were then imputed to 1000 Genomes using IMPUTE.   Expression surrogate variables were calculated using the R package sva and used as covariates in a genome-wide eQTL scan.  Provision of raw data for this study, even to dbGaP, was not permitted per the study IRB. Therefore, raw data are not available for this study.

first: Jonathan


title: Allelic reprogramming of 3D chromatin architecture during early mammalian development

status: Public on Jul 12 2017

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

summary: In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genomewide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs) and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.

overall_design: Mouse preimplantation embryos were obtained from crosses of C57BL/6N and PWK/PhJ. Hi-C were performed on these embryos at various stages in preimplantation development.

first: Wei

last: Xie


title: Gene expression profiling of LCM captured breast cancer cells

status: Public on Sep 16 2014

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: The purpose of this study is to obtain comprehensive gene expression profiles in breast cancer. Mammary gland cells were specifically isolated from 433 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 417 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip.

overall_design: Mammary gland cells were captured from clinical tissues of breast cancer patient by LCM. Gene expression profilings for 417 tumor and 16 non-tumor samples were acquired using GeneChip Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA). Microarray datasets were normalized and transformed to log2 values using robust multi-array average (RMA) method with R statistical software and BioConductor package.

first: Yoshio

last: Miki

first: Masaaki

last: Matsuura

first: Tetsuo

last: Noda


title: Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration [left lobe only]

status: Public on Sep 11 2014

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

summary:
Scnn1b-Tg mice overexpress the beta subunit of the epithelial sodium channel (Scnn1b) in airway Club cells.  The general phenotype of these mice is described in three published manuscripts (Mall et al. 2004, Nature Medicine, 10(5):487-93;  Mall et al. 2008, Am J Respir Crit Care Med. 177(7):730-42; Livraghi-Butrico et al. 2012, Physiol. Genomics 44(8):470-84;  and Livraghi-Butrico et al. 2012, Mucosal Immunology 5(4):397-408). Briefly, overexpression of the Scnn1b transgene in airway Club cells leads to hyperabsorption of sodium from the airway surface liquid, which causes airway surface liquid and mucus dehydration, resulting in reduced mucus clearance and airway mucus obstruction.  The data provided here represents mRNA expression data from disseccted whole lung from male WT and Scnn1b-transgenic littermates (C57Bl/6NTac background) at 4 time points [postnatal days (PND) 0, 3, 10, and 42].  Histologically, PND 0 lungs are normal, at PND 3 the intrapulmonary airways exhibit transient and spotty Club cell necrosis, and by PND 10 airway mucus obstruction is evident in the proximal portion of the intrapulmonary main stem bronchus. At PND 42, Scnn1b-Tg lungs are charactyerized by chronic low level inflammation, with activated macrophages, neutrophilia, eosinophilia and increased incidence of bronchus-associated lymphoid tissue.  The data from the WT mice provides a global look at mRNA post-natal developmental changes, while the data from the Scnn1b-transgenic line allows differential gene expression due to airway surface liquid dehydration and mucus obstruction to be queried.
The data presented for the lung is part of a larger body of work evaluating gene expression in lung (left lobe only), trachea, and purified macrophages (from bronchoalveolar lavage fluid).

overall_design: 24 Total lung (left lobe only) samples were analyzed;  three from each timepoint for each genotype (wild type and Scnn1b-transgenic).  In our manuscript, we were most interested in changes between WT and Scnn1b-Tg mice, however, the data can also be used to evaluate changes in gene expression across time (PND 0, 3, 10, and 42).  We generated the following pairwise comparisons: Scnn1b-Tg vs WT mice for each PND time point; Intra-strain comparison between PND 3, or 10, or 42 vs PND 0.

first: Yogesh

last: Saini

first: Alessandra

last: Livraghi-Butrico

first: Wanda

last: O'Neal

first: Richard

middle: C

last: Boucher


title: Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans

status: Public on Feb 14 2015

first: Can

last: Cenik

address: 300 Pasteur Dr, Alway Building Rm M344

department: Genetics

summary: Elucidating the extent and consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding and chromatin have been explored, little is known about global variation in translation and its genetic determinants among humans. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA levels, translation, and protein abundance suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences.  Finally, we identify genetic differences that specifically modulate ribosome occupancy - many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation.

overall_design: Ribosome profiling and RNA sequencing experiments from human lymphoblastoid cells

first: Elif

last: Sarinay Cenik

first: Gun

last: Byeon

first: Fabian

last: Grubert

first: Sophie

middle: I

last: Candille

first: Damek

last: Spacek

first: Jason

last: Reuter

first: Bilal

last: Alsallakh

first: Hagen

last: Tilgner

first: Hua

last: Tang

first: Emiliano

last: Ricci

first: Carlos

last: Araya

first: Michael

last: Snyder


title: mRNA expression data from either wild-type mice or Scnn1b-transgenic mice at post-natal days 0, 3, 10, and 42

first: Hong

last: Dang


title: Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

status: Public on Dec 29 2016

city: Ithaca

first: Charles

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

summary: Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves.  Here we report the first comparative study of nascent transcription in primates.  We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups.  This approach allowed us to directly measure active transcription separately from post-transcriptional processes.  We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs.  Transcription factor binding sites are a primary determinant of transcriptional differences between species.  We found evidence for stabilizing selection on gene expression levels and adaptive substitutions associated with lineage-specific transcription.  Finally, rates of evolutionary change are strongly correlated with long-range chromatin interactions.  These observations clarify the role of primary transcription in regulatory evolution.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We analyzed collected PRO-seq data from CD4+ T-cells isolated from five mammalian species in two conditions.


title: mRNA expression data from whole trachea dissected from either wild-type mice or Scnn1b-Tg mice at post-natal days 0, 3, 10, and 42

summary:
Scnn1b-Tg mice overexpress the beta subunit of the epithelial sodium channel (Scnn1b) in airway Club cells.  The general phenotype of these mice is described in three published manuscripts (Mall et al. 2004, Nature Medicine, 10(5):487-93;  Mall et al. 2008, Am J Respir Crit Care Med. 177(7):730-42; Livraghi-Butrico et al. 2012, Physiol. Genomics 44(8):470-84; and Livraghi-Butrico et al. 2012, Mucosal Immunology 5(4):397-408). Briefly, overexpression of the Scnn1b transgene in airway Club cells leads to hyperabsorption of sodium from the airway surface liquid, which causes airway surface liquid and mucus dehydration, resulting in reduced mucus clearance and airway mucus obstruction.  The data provided here represents mRNA expression data from dissected whole trachea (distal and proximal ends were cut 3-4 cartilage rings below the larynx and just above the bifurcation, respectively) from male WT and Scnn1b-Tg littermates (C57Bl/6N Tac background) at 4 time points [postnatal days (PND) 0, 3, 10, and 42].  Histologically, PND 0 trachea are normal, a tracheal mucus plug/obstruction develops around PND 3 and typically recedes to the intrapulmonary airways after PND 10, and the trachea is again histologically normal by PND 42.  The data from the WT mice provides a global look at mRNA post-natal developmental changes, while the data from the Scnn1b-Tg line provides mRNA data that allows differential gene expression due to airway mucus obstruction to be queried.
The data presented for the trachea is part of a larger body of work evaluating gene expression in whole lung, trachea, and purified macrophages.

overall_design: 24 Total tracheal samples were analyzed;  three from each timepoint.  In our manuscript, we were most interested in changes between WT and Scnn1b-Tg mice, however, the data can also be used to evaluate changes in gene expression across time (PND 0, 3, 10, and 42).  It should be noted that a significant difference in RNA expression quality parameters was noted for the 10 day trachea data.

first: Yogesh

last: Saini

first: Alessandra

last: Livraghi-Butrico

first: Wanda

last: O'Neal


title: Whole genome characterisation of chemoresistant ovarian cancer

status: Public on May 19 2015

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

institute: QIMR Berghofer Medical Research Institute

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

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

overall_design:
Refer to individual Series

Contributor: The Australian Ovarian Cancer Study Group

first: Ann

first: Elizabeth

last: Christie

first: Dariush

last: Etemadmoghadam

first: Dale

last: Garsed

first: Joshy

last: George

first: Sian

last: Fereday

first: Katia

last: Nones

first: Prue

last: Cowin

first: Kathryn

last: Alsop

first: Peter

last: Bailey

first: Karin

middle: S

last: Kassahn

first: Felicity

last: Newell

last: Quinn

first: Stephen

last: Kazakoff

first: Kelly

last: Quek

first: Charlotte

last: Wilhelm-Benartzi

first: Ed

last: Curry

first: Huei

last: San

first: San

last: Leong

first: Anne

last: Hamilton

first: Linda

last: Mileshkin

first: George

last: Au-Yeung

first: Catherine

last: Kennedy

first: Jillian

last: Hung

first: Yoke

middle: E

last: Chiew

first: Paul

last: Harnett

last: Friedlander

first: Jan

last: Pyman

last: Cordner

first: Patricia

last: O'Brien

first: Jodie

last: Leditschke

first: Greg

last: Young

first: Kate

last: Strachan

last: Waring

first: Walid

last: Azar

first: Chris

last: Mitchell

first: Nadia

last: Traficante

first: Joy

last: Hendley

first: Heather

last: Thorne

first: Mark

last: Shackleton

first: David

last: Miller

first: Gisela


title: Single Cell RNA-sequencing of Pancreatic Circulating Tumor Cells

status: Public on Sep 22 2014

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. Using a pancreatic cancer mouse model, we applied a microfluidic device to isolate CTCs independently of tumor epitopes, subjecting these to single cell RNA-sequencing. This study was conducted to determine the heterogeneity of pancreatic CTCs and to compare these CTCs to matched primary tumors, cell line controls (NB508 cancer cell line and MEF non-cancer cell line), primary tumor single cells, and normal leukocytes/WBCs.

overall_design: We profiled RNA from 75 single cells circulating in mouse blood enriched for circulating tumor cells from 5 mice, 12 single cells from a mouse embryonic fibroblast cell line, 16 single cells from the nb508 mouse pancreatic cancer cell line, 12 single mouse white blood cells, 18 single GFP lineage-traced circulating tumor cells from two mice, 20 single GFP lineage-traced cancer cells from the primary pancreatic tumor of a mouse, and 34 dilutions to 10 or 100 picograms of total RNA from mouse primary pancreatic tumors from 4 mice.

last: Ting

first: Ajay

last: Shah

last: Miyamoto

first: Brian

last: Brannigan

first: Kristina

last: Xega

first: Jordan

last: Ciciliano

first: Huili

last: Zhu

first: Olivia

last: MacKenzie

first: Julie

last: Trautwein

first: Mohammad

last: Shahid

first: Haley

last: Ellis

last: Qu

first: Nabeel

last: Bardeesy

first: Miguel

middle: N

last: Rivera

first: Ravi

last: Kapur

first: Sridhar

last: Ramaswamy

first: Toshi

last: Shioda

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: Transcriptional response to interferon beta-1a treatment in patients with secondary progressive multiple sclerosis

status: Public on Oct 06 2015

city: Ramat-Gan

first: Michael

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

institute: Sheba Medical Center

summary:
Interferon (IFN) beta-1a is an approved treatment for relapsing remitting multiple sclerosis (RRMS) and has been examined for use in secondary progressive multiple sclerosis (SPMS). However, no information regarding blood transcriptional changes induced by IFN treatment in SPMS patients is available.
Our aim was to identify a subgroup of SPMS patients presenting a gene expression signature similar to that of RRMS patients who are clinical responders to IFN treatment.

overall_design: SPMS patients (n=50, 20 IFN treated and 30 untreated) were classified using unsupervised hierarchical clustering according to IFN inducible gene expression profile identified in RRMS clinical responders to treatment. IFN inducible gene expression profile was determined by finding differentially expressed genes (DEGs) between IFN treated (n=10) and untreated (n=25) RRMS patients.

first: Gadi

last: Miron

first: Rina

last: Falb

first: David

last: Magalashvili

first: Mark

last: Dolev

first: Yael

last: Stern

first: Anat

last: Achiron


title: Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation]

first: Ann-Marie

last: Patch

summary: Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

overall_design:
Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays. Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol. Arrays were scanned on Iscan (Illumina). Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007).

Contributor: The Australian Ovarian Cancer Study Group

first: Ann

first: Elizabeth

last: Christie

first: Dariush

last: Etemadmoghadam

first: Dale

last: Garsed

first: Joshy

last: George

first: Sian

last: Fereday

first: Katia

last: Nones

first: Prue

last: Cowin

first: Kathryn

last: Alsop

first: Peter

last: Bailey

first: Karin

last: Kassahn

first: Felicity

last: Newell

last: Quinn

first: Stephen

last: Kazakoff

first: Kelly

last: Quek

first: Charlotte

last: Wilhelm-Benartzi

first: Ed

last: Curry

first: Huei

last: San

first: San

last: Leong

first: Anne

last: Hamilton

first: Linda

last: Mileshkin

first: George

last: Au-Yeung

first: Catherine

last: Kennedy

first: Jillian

last: Hung

first: Yoke

last: Chiew

first: Paul

last: Harnett

last: Friedlander

first: Jan

last: Pyman

last: Cordner

first: Patricia

last: O'Brien

first: Jodie

last: Leditschke

first: Greg

last: Young

first: Kate

last: Strachan

last: Waring

first: Walid

last: Azar

first: Chris

last: Mitchell

first: Nadia

last: Traficante

first: Joy

last: Hendley

first: Heather

last: Thorne

last: Shackleton

middle: K

last: Miller

first: Gisela


title: Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration

first: Hong

last: Dang

summary:
Scnn1b-Tg mice overexpress the beta subunit of the epithelial sodium channel (Scnn1b) in airway Club cells.  The general phenotype of these mice is described in three published manuscripts (Mall et al. 2004, Nature Medicine, 10(5):487-93;  Mall et al. 2008, Am J Respir Crit Care Med. 177(7):730-42; and Livraghi-Butrico et al. 2012, Physiol. Genomics 44(8):470-84. Briefly, overexpression of the Scnn1b transgene in airway Club cells leads to hyperabsorption of sodium from the airway surface liquid, dehydrated airway surface liquid and mucus, and reduced mucus clearance associated with accumulation of mucus plugs/plaques.  The data provided here represents mRNA expression data from disseccted whole trachea (distal and proximal ends cut 3-4 cartliage rings below the larynx and just above the bifurcation, respectively) from male WT and Scnn1b-Tg littermates (C57Bl/6NTac background) at 4 time points [postnatal days (PND) 0, 3, 10, and 42].  PND 0 trachea are histologically normal, a tracheal mucus plug/obstruction develops around PND 3, the plug is receding to more distal airways by PND 10, and the trachea is again histologically normal by PND 42.  The data from the WT mice provides a global look at mRNA changes across time, while the data from the Scnn1b-Tg line provides mRNA data that allows differential gene expression due to mucus obstruction to be queried.
The data presented for the purified is part of a larger body of work evaluating gene expression in whole lung, trachea, and purified macrophages.

overall_design: 30 total macrophage samples were analyzed;  three from each timepoint (postnatal day 0, 3, 10, and 42) for both wildtype and Scnn1b-transgenic mice grown in specific-pathogen-free facilities and from postnatal day 42 wildtype and Scnn1b-transgenic mice maintained in a germ-free facility.  In our manuscript, we were most interested in changes between WT and Scnn1b-Tg mice, however, the data can also be used to evaluate changes in gene expression across time (postnatal day 0, 3, 10, and 42).  This data can also be used to evaluate the differences in macrophage biology at postnatal day 42 when mice are grown in specific-pathogen-free versus germ-free environments.

first: Yogesh

last: Saini

first: Alessandra

last: Livraghi-Butrico

first: Wanda

last: O'Neal

first: Richard

last: Boucher


title: Expression profiling by array of 44 adrenocortical carcinomas

status: Public on Apr 29 2014

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

country: France

institute: Ligue Nationale contre le Cancer

summary: Gene expression profiles of adrenocortical carcinomas were analyzed using Affymetrix Human Gene 2.0 ST Array to identify homogeneous molecular subgroups

overall_design: Gene expression profiles of 44 adrenocortical carcinomas were hybridized using Affymetrix Human Gene 2.0 ST Array

first: Eric

last: Letouzé

first: Aurélien

last: De Reynie

first: Windy

last: Luscap

first: Barreau

last: Olivia

first: Guillaume

last: Assié

first: Jérome

last: Bertherat


title: SNP data from 76 adrenocortical carcinomas

status: Public on Apr 07 2014

summary: SNP array data from 76 adrenocortical carcinomas were used to detect recurrent copy number alterations.

overall_design: 76 tumors were analyzed with Illumina HumanCore-12v1 BeadChip.

last: Letouze

first: Aurelien

last: de Reynies

last: Assie

first: Jerome


title: Genome-scale methylome profiling of adrenocortical carcinomas (ACC) and adenomas (ACA)

summary: Genome-scale DNA methylation was analyzed in a cohort of ACC and ACA to identify DNA methylation changes.

overall_design: Bisulfite converted DNA from 51 fresh frozen ACC and 30 ACA samples were hybridized to Illumina HumanMethylation27 BeadChips.

last: de Reyniès

first: Olivia

last: Barreau


title: Mistimed sleep disrupts circadian regulation of the human blood transcriptome

status: Public on Jan 23 2014

first: Emma

last: Laing

summary: 22 healthy volunteers without sleep disorders were resident in an environmental scheduling facility and participated in a forced-desynchrony protocol, in which the sleep-wake cycle and the associated fasting-feeding cycle is scheduled to a 28-hour period, of which one third (i.e. 9h 20min) is scheduled for sleep. Under these conditions, during which light levels in the waking episode are kept low and sleep is scheduled in darkness,  the phase of the melatonin rhythm occurred at approximately the same clock time during the first (D1) and fourth (D4) 28-h cycle and there were no major changes in either the amplitude or the waveform of this rhythm. During D1 and D4 7 blood samples were taken, RNA was extracted from leukocytes, labelled and hybridised to human whole-genome microarrays

overall_design: A total of 287 samples comprising 22 human subjects, for which 14 samples across multiple time-points/sleep condition were collected.

first: Carla

last: Moller-Levet

first: Simon

last: Archer

first: Giselda

last: Bucca

first: Ana

last: Slak

first: Renata

last: Kabiljo

first: Daan

last: van der Veen

first: Alpar

last: Lazar

first: John

last: Groeger

first: Nayantara

last: Santhi

first: Malcolm

last: von Schantz

first: Colin

last: Smith

first: D

last: Dijk


title: Identification of miR-181a target genes in Epithelial Ovarian Cancer

status: Public on Dec 01 2013

city: Ann Arbor

first: Analisa

last: DiFeo

state: Michigan

address: 1600 Huron Parkway

institute: UNIVERSITY OF MICHIGAN-ANN ARBOR

summary: We have identified a single miRNA, miR-181a, that can modulate TGF-β signaling to induce and maintain EMT, and effect further downstream events of tumour cell survival, altered response to chemotherapy, migration, invasion and dissemination in vivo. Our present study provides an understanding of how enhanced expression of miR-181a can confer malignant and invasive traits through the modulation of a canonical signaling pathway and a consequent maintenance of a mesenchymal state. Furthermore, inhibition of miR-181a led to a reversion of EMT and subsequent events through decreased TGF-β signaling. Our data confirmed Smad7 as a functional target through which TGF-β-mediated EMT occurs; re-expression of Smad7 lacking its 3'UTR was able to rescue miR-181a-mediated phenotypes, deeming Smad7 as a critical mediator of miR-181a-induced EMT. Other recent studies support the crucial role(s) that miRNAs play in mediating EMT and consequent aggressive disease traits. For example, the miR-106b-25 cluster has also been shown to target Smad7 and mediate TGF-β-induced EMT downstream to Six1 in breast cancer34. miR-9 directly targets E-cadherin and inhibition of miR-9 had led to an inhibition of metastasis35. Conversely, the miR-200 and -205 family was shown to target transcriptional repressors of E-cadherin, ZEB1 and SIP1, and re-expression of these miRNAs led to a mesenchymal-to-epithelial transition and prevented TGF-β -induced EMT36.

overall_design: A2780 ovarian cancer cell lines stably expressing either pBABE (control vector), p181a#1( clone 1 expressing miR-181a) or p181a#2( clone 2 expressing miR-181a)


title: Micro-RNA sequencing from 78 adrenocortical carcinomas

first: Nabila

last: Elarouci

summary: Micro-RNA sequencing of adrenocortical tumors and normal adrenal samples.

overall_design: miRNA sequencing of  45 adrenocortical carcinomas (ACC), 30 adrenocortical adenomas (ACA) and 3 normal adrenal samples.

first: Eric

last: Letouzé

first: Aurélien

first: Windy

last: Luscap

first: Guillaume

last: Assié

first: Jérome

last: Bertherat


title: Kinetics of progressive pulmonary cavitary TB disease in rabbits

status: Public on Dec 07 2011

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: Public Health Research Institute at UMDNJ

summary:
Every year, tuberculosis kills nearly 1.8 million people through out the world.  Though  outcome of M. tuberculosis infection into active disease is determined by the host and bacterial factors, a strong host immune response controls the growth of the bacilli effectively.  However, in a host with suboptimal immune response, the bacilli grows and mounts active disease.  Activation of immune response following M. tuberculosis infection affects the expression of many host genes that are involved in the production of immune system molecules such as cytokines, chemokines, surface receptors and transcriptional regulators that manifest in the change of subsequent cellular events, including activation, maturation, chemotaxis and proliferation of effector cells. However, the specific nature of the host-pathogen interactions and the outcome of Mtb infection are not fully understood.   In this study, we have analysed the systematic changes in the global host gene expression profile in the lungs of Mtb infected rabbits at various stages of infection.  Mtb infected rabbit lung tissues were isolated at T=0,2, 4 and 16 weeks post-infection.  Lung bacterial load, histologic changes and host and bacterial gene expression were determined  for each timepoint and compared . Our data suggests a strong correlation between the significant changes in the global transcriptome of infected rabbits and the progression of Mtb infection into a chronic, cavitary TB disease.
The microarray experiments involves comparison of: 1) Changes in rabbit gene expression between Mtb-HN878 infected and uninfected animals at 2,4 and 16 weeks post infection.

overall_design: New Zealand White rabbits were infected with Mtb HN878 at 3.2log10 (on day 0).   Lung tissue from Mtb-infected rabbits were isolated at Day0, 2, 4 and 16 weeks post infection and used for total RNA extraction.

first: Gilla

last: Kaplan


title: Spontaneous Latency in a Rabbit Model of Pulmonary Tuberculosis

status: Public on Jul 11 2012

summary:
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is an exquisitely adapted human pathogen capable of surviving for decades in the lungs of immune competent individuals in absence of disease. The World Health Organization estimates that 2 billion people have latent TB infection (LTBI), defined by positive immunologic response to Mtb antigens with no clinical signs of disease. A better understanding of host and pathogen determinants of LTBI and subsequent reactivation would benefit TB control efforts.  Animal models of LTBI have been hampered mainly by an inability to achieve complete bacillary clearance.  We have characterized a rabbit model of LTBI in which, similar to most humans, complete clearance of pulmonary Mtb infection and pathology occurs spontaneously. The evidence that Mtb-CDC1551-infected rabbits achieve LTBI, rather than sterilization, is based on the ability of the bacilli to be reactivated following immune suppression.
The microarray experiments involves comparison of: 1) Changes in rabbit gene expression between Mtb-CDC1551 infected and uninfected animals at 2,4,8 and 12 weeks post infection.

overall_design: New Zealand White rabbits were infected with Mtb CDC1551 at 3.5log10 (on day 0).   Lung tissue from Mtb-infected rabbits were isolated from uninfected (control) and at 2, 4, 8 and 16 weeks post infection and used for total RNA extraction. Total rabbit lung RNA was used for microarray analysis to determine infection induced changes in host gene expression.


title: SNP data from 45 adrenocortical carcinomas

summary: SNP array data from 45 adrenocortical carcinomas were used to detect recurrent copy number alterations.

overall_design: 7 tumors were analyzed with Illumina Human610-Quad v1.0 BeadChip. 38 tumors were analyzed with Illumina HumanOmniExpress BeadChip.

last: de Reyniès

first: Olivia

last: Barreau


title: Phenotype Enhancement Screen of a Regulatory spx Mutant Unveils a Role for the ytpQ Gene in the Control of Iron Homeostasis.

status: Public on Oct 25 2011

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: Spx is a global regulator of genes that are induced by disulfide stress in Bacillus subtilis. Most of the Spx-regulated genes (SRGs) are of unknown function, but many encode products conserved in low %GC Gram positive bacteria. Using a gene-disruption library of B. subtilis genomic mutations, the SRGs were screened for phenotypes related to Spx-controlled activities, such as growth in minimal medium and sensitivity to methylglyoxal, but nearly all of the SRG mutations showed little if any phenotype. To uncover SRG function, the mutations were rescreened in an spx mutant background to determine which mutant SRG allele would enhance the spx mutant phenotype. One of the SRGs, ytpQ, was the site of a mutation that, when combined with an spx null mutation, elevated the severity of the Spx mutant phenotype, as shown by reduced growth in a minimal medium and by hypersensitivity to methylglyoxal. Proteomic and transcriptomic data indicated that the ytpQ mutation caused the derepression of the Fur and PerR regulons, as well as heightened LexA-controlled gene expression. Our study suggests that the ytpQ gene, encoding a conserved DUF1444 protein, functions directly or indirectly in repairing or stabilizing Fe-bearing proteins, which are sensitive to thiol reactive agents and, therefore, likely influenced by Spx-controlled genes.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: The wild type parent, ytpQ and spx mutants were grown in a glucose minimal medium, with and without 2.8 mM methylglyoxal, to mid-log phase. Cells were harvested and RNA was extracted for microarray hybridization analysis to determine if any changes in the transcriptome could be detected that were attributable to the ytpQ mutation. Microarray hybridizations were performed with RNA from three biological replicates.

first: Shefali

last: Chauhan

first: Praseeda

last: Pilaka

first: Michiko

last: Nakano

first: Sairam

last: Gurumoorthy

first: Bui

last: Chi

first: Haike

last: Antelmann

first: Peter

last: Zuber


title: Super Elongation Complex (SEC) and global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals.

status: Public on Jul 19 2011

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we have performed global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. We have identified an essential role for the ELL/P-TEFbcontaining Super Elongation Complex (SEC) in the regulation of gene expression including several genes bearing paused RNA polymerase II (Pol II). Paused Pol II has been proposed to be associated with loci that respond rapidly to environmental stimuli. However, our studies in ES cells have also identified a requirement for SEC at genes without preloaded Pol II, which also respond dynamically to differentiation signals. Our findings suggest that SEC is a major class of active P-TEFb-containing complexes required for transcriptional activation in response to environmental cues such as differentiation signals.

overall_design: Examination of ELL2, AFF4, and Pol II before and after activation signals in two cell types.

first: Chengqi

last: Lin

last: Garrett

first: Ali

last: Shilatifard


title: Integrated genomic analyses of adrenocortical tumors (SNP array, DNA methylation, mRNA and miRNA expression).

first: Nabila

last: Elarouci

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Effect of sleep restriction on the human transcriptome during extended wakefulness

status: Public on Feb 27 2013

city: Guildford

first: Emma

last: Laing

address: Stag Hill

institute: University of Surrey

summary: In a cross balanced design human subjects were given one week of sufficient sleep and insufficient sleep (6 h per day). Following each of these conditions they were then kept awake for a day, a night and the subsequent day. During each of these periods of extended wakefulness 10 blood samples were taken, RNA was extracted from leukocytes, labelled and hybridised to human whole-genome microarrays

overall_design: A total of 438 samples comprising 26 human subjects, for which 20 samples across multiple time-points/sleep condition were collected.

first: Carla

last: Moller-Levet

first: Simon

last: Archer

first: Giselda

last: Bucca

first: Ana

last: Slak

first: Renata

last: Kabiljo

first: June

last: Lo

first: Nayantara

last: Santhi

first: Malcolm

last: von Schantz

first: Colin

last: Smith

first: D

last: Dijk


title: Serum stimulation of fibroblasts with cycloheximide

status: Public on Jun 27 2002

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
The transcriptional program in the response of human fibroblasts to serum. Serum was added to fibroblasts in the presence of cycloheximide.
This study is described more fully in Iyer VR, et al. 1999. Science 283:83-7
Keywords: time-course

first: V

last: Iyer

first: M

middle: B

last: Eisen

middle: T

last: Ross

first: G

last: Schuler

first: T

last: Moore

first: J

last: Lee

last: Trent

first: L

last: Staudt

last: Hudson

last: Boguski

last: Lashkari

last: Shalon

last: Botstein

first: P

middle: O

last: Brown


title: Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2 [Mnase-seq]

status: Public on Jun 07 2023

city: Philadelphia

first: Kenneth

last: Zaret

state: PA

address: 9-132, SCTR, 3400 Civic Center Boulevard

department: Cell and Developmental Biology

institute: University of Pennsylvania School of Medicine

summary:
Pioneer transcription factors, by interacting with nucleosomes, scan silent, compact chromatin to target regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity.  However, not all cognate motifs are targeted by pioneer factors and dynamic scanning parameters required to scan compact chromatin are unknown. A combined genomics and single-molecule tracking approach shows that to target DNase-resistant, low-histone turnover sites, pioneer factors FOXA1 and SOX2 display opposite dynamics of chromatin scanning: slow, with low nucleoplasmic diffusion and stable interactions, versus fast, with high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, the ability of FOXA1 and SOX2 to scan low-mobility chromatin, mediated by protein domains outside of the respective DNA binding domains, leads to targeting silent chromatin. By contrast, non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be performed through diverse dynamic processes.
Micrococcol nuclease digestion and sequencing (MNase-seq) of human BJ fibroblasts

overall_design: Andrew,Katznelson

first: Jonathan

last: Lerner