title: Accelerated cartilage differentiation distinguishes the lower from the upper vertebrate face

city: Los Angeles

first: Gage

middle: DeKoeyer

last: Crump

address: 1425 San Pablo St, BCC403

department: Broad CIRM Center for Regenerative Medicine and Stem Cell Research

institute: University of Southern California

summary: Distinct shaping of the upper versus lower facial skeleton is essential for function of the vertebrate jaw and middle ear, yet the cellular mechanisms by which this occurs have remained unclear. Here, we show that Endothelin1 (Edn1) signaling accelerates mesenchymal condensation and subsequent cartilage formation in the lower face through antagonism of Jagged-Notch signaling and Prrx1 transcription factors. A genomic analysis of facial skeletal precursors in mutants and overexpression embryos reveals that Jagged-Notch signaling represses genes that are strongly induced as pharyngeal arch neural crest-derived cells begin skeletal differentiation. In wild types, initial Jagged-Notch repression dorsally ensures that barx1+ condensations and cartilage differentiation occur first in ventral-intermediate zones of the pharyngeal arches. Reduced Jagged-Notch signaling results in an expansion of pre-cartilage condensations in the upper face, with loss of barx1 partially restoring dorsal cartilage shapes in jag1b mutants. Further, by studying new mutants for zebrafish prrx1a and prrx1b, we find that Prrx1 genes function in parallel to Jagged-Notch signaling to restrict the formation of dorsal barx1+ pre-cartilage condensations. Consistently, combined losses of jag1b and prrx1a/b robustly rescue ventral barx1+ condensations and lower facial cartilage development in edn1 mutants. Together, our work suggests that Edn1 works through parallel inhibition of Jagged-Notch and Prrx1 pathways to promote an earlier and more extensive establishment of cartilage condensations in the lower face.

overall_design: We performed RNAseq on FACS-sorted neural crest-derived pharyngeal arch cells (fli1a:GFP; sox10:DsRed double positive) from wild-type embryos at 3 different stages (20, 28, and 36 hours post fertilization) and embryos with altered levels of Edn1 and Notch signaling (edn1 mutants and hsp70I:Gal4; UAS:Edn1 transgenics; jag1b mutants, dibenzazepine-treated embryos, and hsp70I:Gal4; UAS:NICD transgenics. We also sequenced RNA from heat-shocked UAS:Edn1+ and hsp70I:Gal4+ transgenics and jag1b+/+ controls.

first: Lindsey

last: Mork

first: Amjad

last: Askary

first: Elizabeth

last: Zuniga

first: Bartosz

last: Balczerski

first: Paul

last: Bump

first: James

last: Nichols


title: Characterization of MOL1 function by transcriptional profiling of Arabidopsis inflorescence stems

status: Public on Mar 23 2016

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

country: Germany

institute: Heidelberg University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Characterization of the ToxR Regulon Vibrio cholerae El Tor

city: Austin

first: Bryan

last: Davies

state: TX

address: 2506 Speedway

country: USA

institute: University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcriptional factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express critical host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands encoding the majority of V. cholerae’s major virulence factors. Our results suggest that ToxR has gained regulatory control over important acquired elements that not only drive V. cholerae pathogenesis but that also define the major transitions of V. cholerae pandemic lineages. We demonstrate that ToxR shares nearly half its regulon with the histone-like nucleoid structuring protein H-NS, and antagonizes H-NS for control of critical colonization functions. This regulatory interaction is the major role of ToxR in V. cholerae colonization since deletion of H-NS abrogates the need of ToxR in V. cholerae host colonization. By comparing the genome-wide binding profiles of ToxR and other critical virulence regulators, we show that despite similar predicted DNA binding requirements, ToxR is unique in its global control of progenitor-encoded and acquired genes. Our results suggest that, like H-NS, factors in addition to linear DNA sequence drive selection of ToxR binding sites.

overall_design: We used ChIP-seq to identify ToxR binding sites across the genome to determine the direct regulon of ToxR

first: Misha

middle: I

last: Kazi

middle: W


title: Genome wide mapping of NR4A binding reveals cooperativity with ETS factors to promote epigenetic activation of distal enhancers in acute myeloid leukemia cells [ChIP-Seq]

status: Public on Mar 22 2016

city: Houston

first: Orla

last: Conneely

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: NR4As are critical tumor suppressors of acute myeloid leukemia (AML) whose expression is broadly silenced in leukemia initiating cell enriched populations from human patients relative to normal hematopoietic stem/progenitor cells. Rescued NR4A expression in human AML cells inhibits proliferation and reprograms AML gene signatures via transcriptional mechanisms that remain to be elucidated. By intersecting an acutely regulated, NR4A1 dependent transcriptional profile with genome wide NR4A binding distribution, we now identify an NR4A targetome of 685 genes that are directly regulated by NR4A1. We show that NR4As regulate gene transcription primarily through interaction with distal enhancers that are co-enriched for both NR4A1 and ETS transcription factor motifs. Using a subset of NR4A activated genes, we demonstrate that the ETS factors ERG and FLI-1 are required for activation of NR4A bound enhancers and NR4A target gene induction. NR4A1 dependent recruitment of ERG and FLI-1 promotes binding of p300 histone acetyl transferase to activate NR4A bound enhancers. These findings disclose novel epigenetic mechanisms by which NR4As and ETS factors cooperate to drive NR4A dependent gene transcription in human AML cells.

overall_design: NR4A1 ChIP-seq after exogenous NR4A1 expression

first: Ryan

middle: P

last: Duren

first: Seth

last: Boudreaux

middle: M


title: The TfoY regulon of Vibrio cholerae.

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

summary: In this study, we determined the TfoY regulon of V. cholerae using RNA-seq to better uderstand the protein's function.

overall_design: mRNA profiles of a WT V. cholerae O1 El Tor strain (A1552) and of a TfoY-producing derivative of the WT strain (A1552-TntfoY). 3 independent biological replicates are provided for each bacterial strain. The bacteria were grown to high cell density and in the presence of arabinose (to induce TfoY in strain A1552-TntfoY).


title: Altered expression profile of long non-coding RNA and mRNA in mice cortex around bleeding areas after subarachnoid hemorrhage

city: Luzhou

first: Jianhua

last: Peng

state: Sichuan

address: NO.25 of Taiping Street, Jiangyang District

department: Neurosurgery

country: China

institute: The Affiliated Hospital of Southwest Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the altered expression profiles of lncRNA and mRNA in mice cortex after subarachnoid hemorrhage (SAH). Total of 617 lncRNAs transcripts and 444 mRNAs transcripts were aberrantly expressed at 24 hours after SAH.

overall_design: SAH was induced in C57BL/6 mice. The lncRNA and mRNA expression profiles in cortex of normal mice and SAH mice were examined by RNA-Seq.

first: Yong

last: Jiang

first: Xiaochuan

last: Sun

first: Yue

last: Wu

first: Jianjun

last: Zhong


title: Transcriptional profile of C. elegans fed E. coli (OP50) and B. subtilis (PY79)

city: Stanford

first: Stuart

last: Kim

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

summary:
We used RNA-seq to assay gene expression changes over time in response to OP50 and PY79
To understand the molecular processes underlying aging, we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C. elegans. The most significant hit was the GATA transcription factor encoded by elt-2, which is responsible for inducing expression of intestinal genes during embryogenesis. Expression of ELT-2 decreases during aging, beginning in middle age. We identified genes regulated by ELT-2 in the intestine during embryogenesis, and then showed that these developmental genes markedly decrease in expression as worms grow old. Overexpression of elt-2 extends lifespan and slows the rate of gene expression changes that occur during normal aging. Thus, our results identify the developmental regulator ELT-2 as a major driver of normal aging in C. elegans.

overall_design: Whole-worm mRNA was sequenced from E. coli- and B.subtilis-fed worms.  For each condidtion, one replicate was sequenced at Day 4 and Day 13

first: Frederick

middle: G

last: Mann

middle: K


title: Persistent chromatin modifications induced by high fat diet

city: Duarte

first: Amy

last: Leung

address: 1500 E. Duarte Rd

department: Diabetes/Cancer

institute: Beckman Research Institute, City of Hope

summary: Obesity is a highly heritable complex disease that results from the interaction of multiple genetic and environmental factors. Formerly obese individuals are susceptible to metabolic disorders later in life, even after lifestyle changes are made to mitigate the obese state. This is reminiscent of the metabolic memory phenomenon originally observed for persistent complications in diabetic patients, despite subsequent glycemic control. Epigenetic modifications represent a potential mediator of this observed memory. We previously demonstrated that a high fat (HF) diet leads to changes in chromatin accessibility in the mouse liver. The regions of greatest chromatin changes in accessibility are largely strain dependent, indicating a genetic component in diet-induced chromatin alterations. We have now examined the persistence of diet-induced chromatin accessibility changes upon diet reversal in two strains of mice. We find that a substantial fraction of loci that undergo chromatin accessibility changes with HF diet remain in the remodeled state after diet reversal in C57BL/6J mice. In contrast, the vast majority of diet-induced chromatin accessibility changes in A/J mice are transient. Our data also indicate that the persistent chromatin accessibility changes observed in C57BL/6J are associated with specific transcription factors and histone posttranslational modifications. The persistent loci identified here are likely to be contributing to the overall phenotype and are attractive targets for therapeutic intervention.

overall_design: Examination of chromatin remodeling with FAIRE-seq in livers of C57BL/6J and A/J mice on three diet regimen: 1) control diet for 16 weeks, 2) high fat diet for 16 weeks, or 3) high fat diet for 8 weeks with control diet for 8 weeks. These chromatin profiles were complemented with gene expression data (RNA-seq)

first: Candi

last: Trac

first: Juan

last: Du

first: Rama

last: Natarajan

first: Dustin

middle: E

last: Schones


title: Single-cell RNA-seq Reveals Unique Vascular Smooth Muscle Cell Phenotypes in Culture

city: Excelsior

first: Rod

middle: A.

last: Staggs

state: MN

address: 20040 Cottagewood Ave

institute: Minnesota Informatics

summary: Background.  Heterogeneity in vascular smooth muscle cells (VSMCs) has been classically defined with a small set of predefined markers.  Single cell genomics provides a unique unbiased approach to evaluate VSMC phenotypes. Objectives. The goal of this study was to define the heterogeneity of primary murine VSMCs grown in culture. VSMCs grown in culture are routinely used as a model of VSMCs in the vessel wall.  We wanted to better understand the assumptions of this model.

overall_design: RNA sequencing was performed on single aortic VSMCs from 3-4 month old male mice at passages 1 and 2 (P1 and P2). Single cell contractility measurements were performed using Traction Force microscopy.

first: Neeta

last: Adhikari

first: Rodney

first: Kadambari

middle: C

last: Shekar

first: Jennifer

middle: L

last: Hall


title: A Mammalian Enhancer trap Resource for Discovering and Manipulating Neuronal Cell Types

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: There is a continuing need for driver strains to enable cell type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (http://enhnacertrap.bio.brandeis.edu).

overall_design: Examination of 6 cortical mouse neuronal cell types. 5 of which are in layer 6 in 3 different cortical regions.

first: Yasuyuki

last: Shima

first: Sacha

last: Nelson


title: RNA-Sequencing of primary myoblasts from mice with a satellite cell specific knockout of the histone demthylase UTX/KDM6A

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

summary: The KDM6 histone demethylases (UTX/KDM6A and JMJD3/KDM6B) mediate removal of repressive histone H3K27me3 marks to establish transcriptionally permissive chromatin. Loss of UTX in female mice is embryonic lethal. Unexpectedly, male UTX-null mice escape embryonic lethality due to expression of UTY, a paralog lacking H3K27-demethylase activity. This suggests that UTX plays an enzyme-independent role in development, and challenges the need for active H3K27-demethylation in vivo. However, the requirement for active H3K27-demethylation in stem cell-mediated tissue regeneration remains untested. Using an inducible mouse knockout that ablates UTX in satellite cells, we show that active H3K27-demethylation is necessary for muscle regeneration. Indeed, loss of UTX in satellite cells blocks myofiber regeneration in both male and female mice. Furthermore, we demonstrate that UTX mediates muscle regeneration through its H3K27-demethylase activity using a chemical inhibitor, and a demethylase-dead UTX knock-in mouse. Mechanistically, dissection of the muscle regenerative process revealed that UTX is required for expression of the transcription factor Myogenin that drives differentiation of muscle progenitors. Thus, we have identified a critical role for the enzymatic activity of UTX in activating muscle-specific gene expression during myofiber regeneration, revealing for the first time that active H3K27-demethylation has a physiological role in vivo.

overall_design: Satellite cells were sorted based on Cre-dependent expression of TdT reporter gene. Sorted UTXmKO or UTX WT satellite cells were then induced to differentiate for 24 hrs. RNA was then isolated and subjected to RNA-Seq analysis.

first: Hervé

last: Faralli

first: Alphonse

last: Chu

first: Jeffrey

middle: F

last: Dilworth


title: Genome-wide mapping of Hif-1α binding sites in zebrafish

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore


title: Transcriptional profile of C. elegans following over-expression of elt-2 [L4 stage & Day 13]

first: Stuart

last: Kim

summary: We used RNA-seq to discover that gene expression changes during aging are attenuated in elt-2 overexpressors relative to controls

overall_design: Whole-worm mRNA was sequenced from worms over-expressing elt-2 and control worms.  Five biological replicates were collected for each condition.

first: Frederick

last: Mann


title: Transcriptional profile of C. elegans following RNAi of elt-2 [L1 stage]

summary: We used RNA-seq to identify 162 genes that are differentially-regulated following elt-2 RNAi

overall_design: Whole-worm mRNA was sequenced from elt-2 RNAi- and control-fed worms.  Biological triplicates were assay for each condition


title: Sperm is epigenetically programmed to regulate gene transcription in embryo

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

type: Methylation profiling by high throughput sequencing

summary: Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in embryos. We observe that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks, at fertilization, deregulates gene expression in the resulting embryos in a paternal chromatin dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits.

overall_design:
48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down.
14  samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos.
3 replicates of single-ended RNA-seq libraries for spermatid cells.
22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b
16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b
6 samples of single-ended MNase-seq from sperm and spermatid chromatin
12 samples of MBD-seq from sperm and spermatid chromatin

first: Marta

last: Teperek

first: Angela

last: Simeone

first: Vincent

last: Gaggioli

first: Kei

last: Miiyamoto

first: George

last: Allen

first: Serap

last: Erkek

first: Taejoon

last: Kwon

first: Edward

last: Marcotte

first: Philip

last: Zegermann

middle: R

first: Antoine

last: Peters

first: John

middle: B

last: Gurdon

first: Jerome

last: Jullien


title: An Inducible TGF-β2-TGFβR Pathway Modulates the Sensitivity of HNSCC Cells to Tyrosine Kinase Inhibitors Targeting Dominant Receptor Tyrosine Kinases

city: Cleveland

first: Jihye

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: The epidermal growth factor receptor (EGFR) is overexpressed in approximately 90% of head and neck squamous cell carcinomas (HNSCC), and molecularly targeted therapy against the EGFR with the monoclonal antibody cetuximab modestly increases overall survival in head and neck cancer patients. We hypothesize that co-signaling through additional pathways limits the efficacy of cetuximab and EGFR-specific tyrosine kinase inhibitors (TKIs) in the clinical treatment of HNSCC. Analysis of gene expression changes in HNSCC cell lines treated 4 days with TKIs targeting EGFR and/or fibroblast growth factor receptors (FGFRs) identified transforming growth factor beta 2 (TGF-β2) induction in the three cell lines tested. Measurement of TGF-β2 mRNA validated this observation and extended it to additional cell lines. Moreover, TGF-β2 mRNA was increased in primary patient HNSCC xenografts treated for 4 weeks with cetuximab, demonstrating in vivo relevance of these findings. Functional genomics analyses with shRNA libraries identified TGF-β2 and TGF-β receptors (TGFβRs) as synthetic lethal genes in the context of TKI treatment. Further, direct RNAi-mediated silencing of TGF-β2 inhibited cell growth, both alone and in combination with TKIs. Also, a pharmacological TGFβRI inhibitor similarly inhibited basal growth and enhanced TKI efficacy. In summary, the studies support a TGF-β2-TGFβR pathway as a TKI-inducible growth pathway in HNSCC that limits efficacy of EGFR-specific inhibitors.

first: Emily

last: Kleczko

first: Stephen

last: Keysar

first: Lydia

last: Heasley

last: Eagles

first: Matthew

last: Simon

first: Marianne

last: Marshall

first: Katherine

last: Singleton

first: Antonio

last: Jimeno

first: Aik-Choon

last: Tan

first: Lynn


title: Transcriptional profile of C. elegans following RNAi of elt-2

first: Stuart

last: Kim


title: Transcriptional profile of C. elegans following RNAi of elt-2 [L4 stage]

summary: We used RNA-seq to identify 292 genes that are differentially-regulated following elt-2 RNAi

first: Frederick

last: Mann


title: A blood RNA signature for tuberculosis disease risk: a prospective cohort study

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

summary:
Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis  infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to  assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective  signatures of risk of active tuberculosis disease.
RESULTS:Between July 6, 2005, and April 23, 2007, we enrolled 6363 from the ACS study and 4466 from independent  South African and Gambian cohorts. 46 progressors and 107 matched controls were identified in the ACS cohort. A  16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1%  (95% CI 63·2–68·9) and a specificity of 80·6% (79·2–82·0) in the 12 months preceding tuberculosis diagnosis. The  risk signature was validated in an untouched group of adolescents (p=0·018 for RNA sequencing and p=0·0095 for  qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a  sensitivity of 53·7% (42·6–64·3) and a specificity of 82·8% (76·7–86) in 12 months preceding tuberculosis.
Interpretation: The whole blood tuberculosis risk signature prospectively identified people at risk of developing active  tuberculosis, opening the possibility for targeted intervention to prevent the disease.

overall_design: In this prospective cohort study, we followed up healthy, South African adolescents aged 12–18 years from  the adolescent cohort study (ACS) who were infected with M tuberculosis for 2 years. We collected blood samples from  study participants every 6 months and monitored the adolescents for progression to tuberculosis disease. A prospective  signature of risk was derived from whole blood RNA sequencing data by comparing participants who developed  active tuberculosis disease (progressors) with those who remained healthy (matched controls). After adaptation to  multiplex qRT-PCR, the signature was used to predict tuberculosis disease in untouched adolescent samples and in  samples from independent cohorts of South African and Gambian adult progressors and controls. Participants of the  independent cohorts were household contacts of adults with active pulmonary tuberculosis disease.

first: D

first: A

last: Penn-Nicholson

first: T

middle: J

last: Scriba


title: Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node

city: New York City

first: Yong

last: Zhao

state: NY

address: 1470 Madison Ave

department: Mindich Child Health and Development Institute

institute: Icahn School of Medicine at Mount Sinai

summary: We specifically deleted Baf250a in the SAN by using Hcn4-CreERT2 mice. We performed mRNA-seq to identify dysregulated genes in the SAN after deletion of Baf250a. To identify direct targets of Baf250a and sequential transcriptional events after deletion of Baf250a in the SAN, we performed mRNA-seq at 6 time points. i.e. 0 hr (tamoxifen treatment), 16 hr after tamoxifen treatment, 20 hr, 24 hr, 48 hr, and 6 days after tamoxifen treatment.

overall_design: mRNA-seq were performed at 0 hr, 16 hr, 20 hr, 24 hr, 48 hr, and 6 days after tamoxifen treatment.


title: Integration of genome-wide DNA methylome and transcriptome of human intestinal fibroblasts reveals novel candidate gene signatures in Crohn’s disease-associated fibrosis

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Tissue fibrosis is a serious complication of Crohn’s disease (CD) as well as of a variety of other complex, chronic pathologies. Understanding the underlying pathophysiology of tissue fibrosis is crucial for the development of tissue-specific prevention and interventional treatment strategies. To identify molecular states specific to fibrotic disease, we employed deep sequencing to define the genome-wide DNA methylome and the whole transcriptome of purified human intestinal fibrotic fibroblasts (HIFs) isolated from the colon of patients with fibrotic CD. Integration of this information, via computational tools, identified candidate molecular interactions that could lead to fibrosis pathology. Our definition of a genome-wide fibrosis-specific DNA methylome provides a new paradigm for understanding mechanisms of pathological gene expression that lead to intestinal fibrosis and may have relevance to fibrogenesis in other organs.

overall_design: Human intestinal fibroblasts (HIFs) were extracted and cultured from colon specimens of two groups: Crohn’s disease with associated fibrosis (n=3) and normal fibroblasts from patients with Diverticulitis (n=3). Both RNA-seq and MBD-isolated genome sequencing (MiGS) were performed on every sample.

first: Tammy

last: Sadler

first: Jeffrey

last: Bhasin

first: Yaomin

last: Xu

first: Jil

last: Barnholz-Sloan

first: Yanwen

last: Chen

first: Eleni

last: Stylianou


title: Genome-wide mapping of Hif-1α binding sites in zebrafish [ChIP-seq]

first: Justin

last: Joseph Gnanakkan

summary: Analysis of the binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf by ChIP linked next generation sequencing. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the transcriptional response to genetically induced hypoxia in zebrafish.

overall_design: Analysis of the DNA binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the dependency of the transcriptional response on Hif-1α in conditions of  genetically induced hypoxia in zebrafish.

first: David

last: Greenald

last: Jeyakani

first: Bernd

last: Pelster

first: Ian

last: Sealy

first: Sinnakaruppan

last: Mathavan

first: Fredericus

last: van Eeden


title: REF6 recognizes specific DNA sequence to regulate H3K27me3 demethylation and organ boundary formation

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

summary: RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb mediated gene silencing through demethylating histone H3 lysine 27 trimethylation (H3K27me3) in Arabidopsis. Genome-wide analysis has demonstrated that REF6 dependent H3K37me3 demethylation occurs on hundreds of genes. However, how these genes are selectively subjected to H3K27me3 demethylation remains elusive. Here we show that a tandem array of four Cys2-His2 zinc finger domains (C2H2-ZF) at REF6 C-terminus are essential for REF6 function. Mechanistically, we find that C2H2-ZF cluster can directly recognize a specific DNA sequence motif, and is essential for binding of REF6 to its targets. In addition, we demonstrate that CUP-SHAPED COTYLEDON 1 (CUC1) and CUC3 harbor such sequence motif and are direct targets of REF6; while their close homolog, CUC2, without such binding motif is not bound by REF6. Furthermore, REF6 is essential for proper H3K27me3 level at CUC1 locus, CUC1 activation and cotyledon separation. Collectively, our study reveals not only a novel mechanism of H3K27me3 demethylase genome targeting to counteract Polycomb silencing, but also a new function of H3K27me3 demethylation in organ boundary formation.

overall_design: All seeds, except for H3K9me2 ChIP-seq, were grown on 1/2MS plate at 23°C under long day condition. 12 day after germination (12DAG), whole seedling were harvested for ChIP-seq. anti-HA ChIP-seq were performed with three samples: Col (WT,Negtive control), REF6-HA(REF6p::REF6-HA ref6-1),REF6-ZnF-HA(REF6p::REF6-ZnF-HA ref6-1). anti-H3K27me3 ChIP-seq were performed with four samples: Col (WT), ref6-1 (mutant), REF6-HA(REF6p::REF6-HA ref6-1),REF6-ZnF-HA(REF6p::REF6-ZnF-HA ref6-1).For H3K9me2 ChIP-seq, plants were grown in soil at 23°C under long day condition. Aerial part of plants were harvested for ChIP-seq 28d after germination.

first: Xia

last: Cui

first: Falong

last: Lu

first: Qi

last: Qiu

first: Bing

last: Zhou

first: Lianfeng

last: Gu

first: Shuaibin

last: Zhang

first: Yanyuan

last: Kang

first: Xiekui

first: Xuan

last: Ma

first: Qingqing

last: Yao

first: Jinbiao

first: Xiaoyu

first: Xiaofeng

last: Cao


title: Cajal bodies are linked to genome conformation [smallRNA-Seq]

status: Public on Mar 21 2016

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. We examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly, and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromatin conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear and nucleoar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. We observed a number of CB-dependent gene positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production resulted in increased splicing noise, even in CB-distal regions. We conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity.

overall_design: Examination of RNA expression following depletion of Cajal bodies using siRNAs targeting TCAB1 and USPL1

first: Qiuyan

last: Wang

first: Iain

middle: A

last: Sawyer

first: Myong-Hee

last: Sung

first: David

last: Sturgill

first: Sergei

last: Shevtsov

first: Gianluca

last: Pegoraro

first: Ofir

last: Hakim

first: Gordon

last: Hager

first: Miroslav

last: Dundr


title: The cohesin associated protein Wapal is required for proper polycomb-mediated gene silencing [Ring1b ChIP-seq]

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: The cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in offloading cohesin to facilitate sister chromatid separation, but its role in regulating mammalian gene expression is not understood.  We used embryonic stem cells (ESCs) as a model given the well-defined transcriptional regulatory circuits established through master transcription factors and epigenetic pathways that regulate their ability to maintain a pluripotent state. RNAi-mediated depletion of Wapal causes a loss of pluripotency, phenocopying loss of core cohesin subunits. Using chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) we determine that Wapal occupies genomic sites distal to genes in combination with CTCF and core cohesin subunits such as Rad21. Interestingly, genomic sites occupied by Wapal appear enriched for cohesin, implying Wapal does not offload cohesin at regions it occupies. Wapal depletion induces derepression of Polycomb Group (PcG) target genes without altering total levels of Polycomb-mediated histone modifications, implying that PcG enzymatic activity is preserved.  By integrating ChIP-seq and gene expression changes data we identify that Wapal binding is enriched at the promoters of PcG silenced genes and is required for proper Polycomb Repressive Complex 2 (PRC2) recruitment.  Lastly, we demonstrate that Wapal is required for the interaction of a distal cis-regulatory element (CRE) with the c-Fos promoter. Collectively, this work indicates that Wapal plays a critical role in silencing of PcG target genes through the interaction of distal CREs with promoters.

overall_design: ChIP-seq for Ring1b, before or after depletion of Wapal by RNAi


title: Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methyl-seq data for the identification of hap-ASM

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

summary: Haplotype-dependent allele-specific methylation (hap-ASM) can impact disease susceptibility, but maps of this phenomenon using stringent criteria in disease-relevant tissues remain sparse. Here we apply array-based and Methyl-seq approaches to multiple human tissues and cell types, including brain, purified neurons and glia, T lymphocytes, and placenta, and identify 795 hap-ASM differentially methylated regions (DMRs) and 3,082 strong methylation quantitative trait loci (mQTLs), most not previously reported. More than half of these DMRs have cell type-restricted ASM, and among them are 188 hap-ASM DMRs and 933 mQTLs located near GWAS signals for immune and neurological disorders. Targeted bis-seq confirmed hap-ASM in 12/13 loci tested, including CCDC155, CD69, FRMD1, IRF1, KBTBD11, and S100A*-ILF2, associated with immune phenotypes, MYT1L, PTPRN2,CMTM8 and CELF2, associated with neurological disorders, NGFR and HLA-DRB6, associated with both immunological and brain disorders, and ZFP57, a trans-acting regulator of genomic imprinting. Polymorphic CTCF and transcription factor (TF) binding sites are over-represented among hap-ASM DMRs and mQTLs, and analysis of the human data, supplemented by cross-species comparisons to Macaca mulattamacaques, indicates that CTCF and TF binding likelihood predicts the strength and direction of the allelic methylation asymmetry. These results show that hap-ASM is highly tissue-specific; an important trans-acting regulator of genomic imprinting is regulated by this phenomenon; variation in CTCF and TF binding sites is an underlying mechanism in primary tissues, and maps of hap-ASM and mQTLs reveal regulatory sequences underlying supera- and sub-threshold GWAS peaks in immunological and neurological disorders.

overall_design: We used the Agilent SureSelect Methyl-seq DNA hybrid capture kit, followed by deep Nextgen bis-seq. In this protocol, targeted regions (total of 3.7M CpGs) include RefGenes, promoter regions, CpG islands, CpG island shores, shelves, and DNAse I hypersensitive sites.  DNA was sheared to an average size of 250 bp and bisulfite converted with the EZ DNA methylation kit (Zymo). Paired-end reads (150 bp) were generated with an Illumina HiSeq2000 sequencer. One of the brain samples (5984) was relatively under-represented in the library, so additional sequences were generated on a MiSeq sequencer to improve the coverage for this sample. After trimming for low-quality bases (Phred score<30) and reads with a length <40 bp with TrimGalore, the reads were aligned to the human genome (GRCh37) using Bismark and duplicate reads were removed using Samtools. Methylation calling was performed using Bismark and and SNP calling was performed with BisSNP with  default settings and dbSNP137 as references. ASM calling was performed with Bismark, after separating the valid SNP-containing reads by allele.

first: Catherine

last: Do

first: Charles

last: Lang

first: John

last: Lin

first: Huferesh

last: Darbary

first: Izabela

last: Krupska

first: Aulona

last: Gaba

first: Lynn

last: Petukhova

first: Jean-Paul

last: Vonsattel

first: Mary

last: Gallagher

first: Robin

middle: S

last: Goland

first: Raphael

last: Clynes

first: Andrew

last: Dwork

last: Kral

last: Monk

first: Angela

last: Christiano


title: The cohesin associated factor Wapal is required for proper polycomb-mediated gene silencing

last: Rao

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq reveals activation of unique gene groups as a consequence of stem cell-parenchymal cell fusion

city: Minneapolis

first: Brenda

last: Ogle

state: Minnesota

address: 312 Church St SE

department: Biomedical Engineering

institute: University of Minnesota-Twin Cities

summary: Fusion of donor mesenchymal stem cells with parenchymal cells of the recipient can occur in the brain, liver, intestine and heart following transplantation.  The therapeutic benefit or detriment of resultant hybrids is unknown.  Here we sought a global view of phenotypic diversification of mesenchymal stem cell-cardiomyocyte hybrids and associated time course. Using single-cell RNA-seq, we found hybrids consistently increase ribosome components and decrease genes associated with the cell cycle suggesting an increase in protein production and decrease in proliferation to accommodate the fused state.  But in the case of most other gene groups, hybrids were individually distinct.  In fact, though hybrids can express a transcriptome similar to individual fusion partners, approximately one-third acquired distinct expression profiles in a single day.  Some hybrids underwent reprogramming, expressing pluripotency and cardiac precursor genes latent in parental cells and associated with developmental and morphogenic gene groups.  Other hybrids expressed genes associated with ontologic cancer sets and two hybrids of separate experimental replicates clustered with breast cancer cells, expressing critical oncogenes and lacking tumor suppressor genes. Rapid transcriptional diversification of this type garners consideration in the context of cellular transplantation to damaged tissues, those with viral infection or other microenvironmental conditions that might promote fusion.

overall_design: Examination was performed using single-cell RNA-seq of five fusion products (BiFC_D1_F1-5, 24 hours) identified using BiFC, twenty-three fusion products (DC_D1_F1-16, 24 hours; DC_D3_F1-7, 72 hours) identified using dual expression of GFP and mCherry, the parental controls, and the population controls (mMSC_PC and HL1cm_PC).  Parental controls included 15 cells of each parental type isolated prior to co-culture (mMSC_1-15 and HL1cm_1-15) and 5 cells of each parental cell type isolated 24 hours after co-culture (mMSC_D1_1-5 and HL1cm_D1_1-5).  In addition, a population containing a mixture of both parental cells and fusion products obtained 24 hours after co-culture was included (Mix_D1).

first: Brian

middle: T

last: Freeman

first: Philip

last: Jung


title: Identification of Sik3-targeting compound, pterosin B, for treatment of osteoarthritis

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Osteoarthritis is a common joint disorder that causes debilitating conditions among the elderly. Risk factors of osteoarthritis include age, which is often associated with the thinning of articular cartilage. We generated conditional knockout mice that lack salt-inducible kinase 3 (Sik3) specifically in chondrocytes after birth by tamoxifen administration. Deletion of Sik3 at 2 or 8 weeks after birth increased the thickness of articular cartilage by increasing the chondrocyte population. Additionally, Sik3 deletion protected cartilage against osteoarthritis development. We identified the edible Pteridium aquilinum ingredient, pterosin B, as a compound that inhibits the Sik3 pathway. Intraarticular injection of pterosin B protected cartilage against osteoarthritis development. Sik3 deletion or pterosin B treatment inhibited activation of the hypertrophic program through the histone deacetylase 4 (Hdac4) pathway, increased Prg4 expression in chondrocytes, and protected cartilage against osteoarthritic attack. Collectively, our results suggest Sik3 is a regulator that regulates homeostasis of articular cartilage thickness and a target for treatment of osteoarthritis, and that pterosin B can be the lead compound for relevant drugs.

overall_design: RNA-seq analysis for pellet culture of mouse primary chondrocytes in the presence or absence of 300 micromolar pterosin B (n = 3 each) and 13 mouse tissues (n = 1 each).

first: Noriyuki

last: Tsumaki

first: Yasuhito

last: Yahara

first: Masahiro

last: Nakamura


title: Ion Torrent RNA-sequencing of exosomes isolated from ovarian cancer cells, fibroblasts and adipocytes

city: Houston

first: Chi Lam

last: Au Yeung

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: We used next-generation sequencing to identify differential microRNA (miRNA) signatures in exosomes isolated from ovarian cancer cells and ovarian cancer-associated fibroblasts (CAFs) and adipocytes (CAAs). We found that a significantly higher levels of miR21 isomiRNAs in exosomes isolated from CAFs and CAAs than in those from ovarian cancer cells.

overall_design: Samples are exosomes isolated from four ovarian cancer cell lines (A2780, HeyA8, OVCA433 and SKOV3), two normal fibroblasts, three CAFs, two normal adipocytes and two CAAs

first: Ngai Na

last: Co

first: Tetsushi

last: Tsuruga

first: Tsz-Lun

last: Yeung


title: Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation

first: Benjamin

last: Tycko

type: Methylation profiling by genome tiling array


title: ER ChIP-seq of Androstenedione treated Letrozole Resistant Breast Cancer Cell line

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

summary: Acquired resistance to aromatase inhibitor (AI) therapy is a major clinical problem in the treatment of breast cancer. The detailed mechanisms of how tumour cells develop this resistance remain unclear. Here estrogen receptor ChIPseq analysis identifies adaptations of the ER in response to prolonged letrozole treatment.

overall_design: Let-R cells were treated with either Androstenedione or vehicle and immunoprecipitated with anti-ER

first: Ailis

last: Fagan

first: Jean

last: McBryan

first: Damir

last: Vareslija


title: Cajal bodies are linked to genome conformation [RNA-Seq]

first: Songjoon

last: Baek

first: Qiuyan

last: Wang

first: Iain

last: Sawyer

first: Myong-Hee

last: Sung

first: David

last: Sturgill

first: Sergei

middle: P

last: Shevtsov

first: Gianluca

last: Pegoraro

first: Ofir

last: Hakim

first: Gordon

last: Hager

first: Miroslav

last: Dundr


title: Comparing effects of perfusion and hydrostatic pressure on human chondrocytes using gene profiles

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: Hydrostatic pressure and perfusion have been shown to alter the chondrogenic potential of articular chondrocytes. In order to compare the effects of hydrostatic pressure plus perfusion (HPP) and perfusion (P) we investigated the complete gene expression profiles of human chondrocytes under HPP and P. A simplified bioreactor was constructed applying loading (0.1 MPa for 2 h) and perfusion (2ml) through the same piping by pressurizing the medium directly. High-density monolayer cultures of human chondrocytes were exposed to HPP or P for 4 days. Controls were maintained in static culture. Gene expression was evaluated by sequencing (RNAseq) and quantitative real-time PCR analysis. RNAseq identified similarities between the two treatments. Specifically, HPP and P increased COL2A1 expression and decreased COL1A1 and MMP-13 expression. Despite of the similarities, RNAseq revealed a list of cartilage genes including ACAN, ITGA10 and TNC, which were differentially expressed by HPP and P. Of these candidates adhesion related molecules were found to be upregulated in HPP. Both HPP and P treatment had beneficial effects on chondrocyte differentiation and decreased catabolic enzyme expression. The study provides new insight into how hydrostatic pressure and perfusion enhance cartilage differentiation and inhibit catabolic effects

overall_design: 9 samples

first: Ge

last: Zhu

first: Susanne

last: Meyer-Wagner

first: Christian

last: Schröder

first: Matthias

last: Woiczinski

first: Helmut

last: Blum

first: Ilaria

last: Lavagi

first: Julia

middle: I

last: Redeker

first: Andreas

last: Hölzer

first: Volkmar

last: Jansson

first: Oliver

last: Betz

first: Peter

last: Müller


title: The cohesin offloading factor Wapal is required for proper polycomb-mediated gene silencing [ChIP-Seq]

first: Sridhar

last: Rao

summary: The cohesin offloading protein Wapal also acts as a polycomb factor in flies.  We examined its role in transcriptional role in murine embryonic stem cells (ESCs)

overall_design: ChIP-seq was performed on a tagged version of Wapal.

first: Kirthi

last: Pulakanti


title: Cajal bodies are linked to genome conformation

first: Songjoon

last: Baek


title: Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in mud crab Scylla paramamosain during Vibrio parahaemolyticus infection

city: shantou

first: chuping

last: xie

state: Guangdong

address: Guangdong shantou university road 243

institute: Shantou University

summary:
Purpose:The mud crab Scylla paramamosain is an economically important marine crab in China suffering from severe outbreaks of infectious disease caused by marine bacteria such as Vibrio Parahaemolyticus, resulting in great economic losses. However, the mechanisms involved in the immune response of this crab to bacterial infection are not fully understood. To understand the molecular mechanisms underlying the immune response to such pathogenic bacteria, we used high-throughput deep sequencing technology to investigate the transcriptome and comparative expression profiles of the mud crab S.paramamosain infected with V.parahaemolyticus.
Methods: The hemocytes sampled at 0-24h after infection with V.parahaemolyticus were used for transcriptome analysis. The hemocytes sampled at 24 h after injections with V.parahaemolyticus and no injected 0h(as control) were used for gene expression profiling analysis.
Results: A total of 52,934,042 reads were obtained and assembled into 186,193 contigs in transcriptional responses of the V.parahaemolyticus-infected mud crab. Via annotation to the NCBI database and the Swissprot database, we obtained 48,934 identified unigenes. In total, 10,139(20.7%) unigenes were classified into Gene Ontology, and 25,349 unigenes were found in 20 KEGG categories. These genes included representatives from almost all functional categories. By using Solexa/Illumina's DeepSAGE, 1213 differentially expressed genes (P value < 0.05) were detected in comparative analysis of the expression profiles between V.parahaemolyticus-infected crabs and control crabs, including 538 remarkably upregulated genes and 675 remarkably downregulated genes.
Conclusions: Based on our results, we conclude that the inflammatory response may play an important role in the early stages of infection. The signaling cascades such as the chemokine, JAK-STAT, and MAPK pathways are regulated by V.parahaemolyticus infection. These results revealed changes of multiple signaling pathways involved in immunity during V.parahaemolyticus infection, which will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial infection in the mud crab.

overall_design: Transcriptome: hemocytes mRNA profiles of 0-24h Mixture (Mix). Gene expression profiling: 24 h after injections (24hVP) and no injected 0h (as control) (0hDZ) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Chuping

last: XIE

first: Shengkang

last: LI


title: Transcriptome analysis of rectal tissues of E. coli O157 super-shedding and E. coli O157 negative cattle

status: Public on Mar 20 2016

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

institute: University of Alberta

summary: Total RNA from rectal tissues of E. coli O157 super-shedders and non-shedders were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR. Fifteen of differentially expressed genes were related to innate and adaptive immune functions and were down-regulated in super-shedders, which could be one of reasons for super-shedding phenomenon.

overall_design: We performed a differential analysis of transcriptomes of rectal tissues collected from E. coli O157 super-shedders and non-shedders, to study molecular mechanisms of super-shedding phenomenon.

first: G

last: Leluo

first: W

last: Ou


title: Genome-wide profiling of gene expression under electro-acupuncture treatment on MI heart in rats

city: Nanjing

first: Bing-Mei

last: Zhu

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing university of Chinese Medicine

summary:
Purpose: Acupuncture exerts cardioprotective effects on several types of cardiac injuries, especially myocardial ischemia (MI). In order to  elucidate the potential mechanisms,  RNA-seq by next generation sequencing was used to identify the rat genome-wide alterations after MI and EA treatment  in this study
Methods: Adult male Sprague Dawley rats (250-300g)  were divided into three groups: Control, MI and electro-acupuncture (EA) groups, myocardium mRNA profiles of  rats in each group were generated by deep sequencing,using Illumina Hiseq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 25 million sequence reads per sample to the mouse genome (UCSC RN4) and identified 121,233, 178,242, 161,880 transcripts in the Control, MI and EA rats  with TopHat and Cufflinks workflow respectively.  Approximately 32% and 22% of the transcripts showed differential expression between the Control and MI, MI and EA respectively with a fold change ≥2.0.
Conclusions: Our results for the first time generated genome-wide gene expression profiles both in the rat MI model and in acupuncture treatment by high throughput sequencing. The optimized data analysis workflows reported here should provide a framework for acupuncture investigations of expression profiles.

overall_design: Myocardium mRNA profiles of  Control, MI and EA  rats were generated by Hiseq 2000, Control and MI+EA group there were three samples, MI group there were two samples.

first: Shu-Ping

last: Fu

first: Chen-Jun

last: Hu


title: Taf4 is required for preinitiation complex formation at genes associated with neuronal differentiation

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: Occupancies of promoters by TBP, PolII, TFIIB as well as chromatin marks H3K4Me3 and H3K27ac were compared in embryonic stem cells (ESC) and in embryoid bodies (EB) treated with retinoic acid (RA) derived from the WT and Taf4a-/- lineages. Reduced occupancies for these factors and decreased signals for H3K4Me3 and H3K27ac were observed for genes associated with neuronal differentiation in EB of Taf4a-/- line compared to EB of WT line.

overall_design: ChIP-seq experiment was performed for TFIIB, Pol II, H3K4me3, H3K27ac and TBP in wt and TAF4-/- mouse embryonic stem cells (ESC) and embryoid bodies (EB) treated with retinoic acid (RA).

first: Diana

last: Langer

first: Irwin

last: Davidson


title: Cajal bodies are linked to genome conformation [4C-Seq]

first: Qiuyan

last: Wang

first: Iain

last: Sawyer

first: Myong-Hee

last: Sung

first: David

last: Sturgill

first: Sergei

last: Shevtsov

first: Gianluca

last: Pegoraro

first: Ofir

last: Hakim

first: Gordon

last: Hager

first: Miroslav

last: Dundr


title: Transcriptome analysis of aging mouse meibomian glands

city: Irvine

first: Geraint

last: Parfitt

state: California

address: 843 Health Sciences Rd

department: Ophthalmology

institute: University of California, Irvine

summary: RNA-sequencing of young and old mouse eyelids identified a number of signaling pathways, including FGF and Wnt that were altered in meibomian glands and conjunctiva of aging mice.

overall_design: RNA isolated from frozen eyelid tissue excised from young and old mice was sequenced using an Illumina HiSeq 2500.

first: Donald

last: Brown

first: James

middle: V

last: Jester


title: Pasha: a versatile R package for piling chromatin HTS data

status: Public on Mar 18 2016

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

institute: CNRS

summary: We describe an R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha (preprocessing of aligned sequences from HTS analyses) allows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-Seq, FAIRE-seq, Mnase-Seq...) and offers innovative approaches to process and extract relevant information.

overall_design: ChIP-seq using antibodies directed against the N-terminal region of Human RNA Polymerase II. An extended range of DNA fragments size was selected using linear acrylamide before library preparation and paired-ends sequencing.

first: Nicolas

last: Descostes

first: Lionel

last: Spinelli

first: Frederic

last: Koch

first: Muhammad

last: Maqbool

first: Touati

last: Benoukraf

first: Pierre

last: Cauchy

first: Charlène

last: Innocenti

last: Ferrier

first: Jean-Christophe

last: Andrau


title: RNA sequencing of Taf4+/+ and Taf4-/- cells in their pluripotent state as well as 3 timepoints during the formation of neurons

first: diana

last: langer

address: 1 rue laurent fries

summary: We determined the Taf4 dependent differential expression of RNAs in WT as well as KO cells in their pluripotent state, before and after treatment with retinoic acid and immediately before plating to form neuronal precursors.

overall_design: Examination of RNA expression in 4 different cell lines (2 independent Taf4 WT and 2 independent Taf4 KO) in ES cells and at 3  timepoints during differentiation into neurons.

first: Diana

last: Langer


title: The Expansion of Thymopoiesis in Neonatal Mice is Dependent on Expression of High mobility group A 2 protein (Hmga2)

status: Public on Mar 19 2016

city: Los Angeles

first: Kenneth

last: Dorshkind

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

summary: The most immature progenitors in the murine thymus are early T lineage progenitors (ETP). These cells are the precursors of more mature thymocytes that ultimately leave the thymus and colonize peripheral lymphoid tissues. As part of our efforts to define age-related changes in ETP, we harvested them from mice of different ages and performed whole transcriptome profiling. This analysis revealed major differences in patterns of gene expression between young and old ETP, and we were particularly struck by the significantly reduced expression of the gene encoding high mobility group A 2 protein (Hmga2).

overall_design: The experiment compares gene expression in young adult (4-6 week old) and old (72 week old) mouse Early T Lineage Progenitors (ETP)

first: Beata

last: Berent-Maoz

first: Encarnacion

last: Montecino-Rodriguez

first: David

last: Casero

first: Christopher

last: Seet

first: Michael

last: Fice

first: Gay

middle: M

last: Crooks


title: MicroRNA-146a modulates B-cell oncogenesis by regulating EGR1

city: LOS ANGELES

first: Dinesh

last: Rao

state: CA

address: 750 CHARLES E YOUNG DRIVE, 12-272 FACTOR

department: PATHOLOGY AND LABORATORY MEDICINE

institute: UCLA

summary: miR-146a is a NF-κB induced microRNA that serves as a feedback regulator of this critical pathway.  In mice, deficiency of miR-146a results in hematolymphoid cancer at advanced ages as a consequence of constitutive NF-κB activity.  In this study, we queried whether the deficiency of miR-146a contributes to B-cell oncogenesis. Combining miR-146a deficiency with transgenic expression of c-Myc led to the development of highly aggressive B-cell malignancies.  Mice transgenic for c-Myc and deficient for miR-146a were characterized by significantly shortened survival, increased lymph node involvement, differential involvement of the spleen and a mature B-cell phenotype. High-throughput sequencing of the tumors revealed significant dysregulation of approximately 250 genes. Amongst these, the transcription factor Egr1 was consistently upregulated in mice deficient for miR-146a. Interestingly, transcriptional targets of Egr1 were enriched in both the high-throughput dataset and in a larger set of miR-146a-deficient tumors. miR-146a overexpression led to downregulation of Egr1 and downstream targets with concomitant decrease in cell growth. Direct targeting of the human EGR1 by miR-146a was seen by luciferase assay.  Together our findings illuminate a bona fide role for miR-146a in the modulation of B-cell oncogenesis and reveal the importance of understanding microRNA function in a cell- and disease-specific context.

overall_design: This experiment compares expression profiles between tumors that were derived from miR-146a +/+ and miR-146a-/- mice that are transgenic for c-Myc.

first: Jorge

last: Contreras

first: Jayanth

middle: K

last: Palanichamy

first: Tiffany

last: Tran

first: Thilini

last: Fernando

first: Norma

last: Rodriguez-Malave

first: Neha

last: Goswami

first: Valerie

last: Arboleda


title: CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

summary:
Background: The most common rearrangement in childhood precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the t(12;21)(p13;q22) translocation resulting in the ETV6-AML1 fusion gene. A frequent concomitant event is the loss of the residual ETV6 allele suggesting a critical role for the ETV6 transcriptional repressor in the etiology of pre-B ALL. However, the precise mechanism through which loss of functional ETV6 contributes to disease pathogenesis is still unclear
Results: To investigate the impact of ETV6 loss on the transcriptional network and identify new transcriptional targets of ETV6, we used whole transcriptome analysis of both pre-B leukemic cell lines and pre-B ALL patients combined with chromatin immunoprecipitation. Using this integrative approach, we identified 4 novel direct ETV6 target genes: CLIC5, BIRC7, ANGPTL2 and WBP1L. To further evaluate the role of chloride intracellular channel protein CLIC5 in leukemogenesis, we generated cell lines overexpressing CLIC5 and demonstrated an increased resistance to hydrogen peroxide-induced apoptosis. We further described the implications of CLIC5’s ion channel activity in lysosomal-mediated cell death, possibly by modulating the function of transferrin receptor with which it co-localizes intracellularly.
Conclusion: For the first time, we showed that loss of ETV6 leads to significant overexpression of CLIC5, which in turn leads to decreased lysosome-mediated apoptosis. Our data suggest that heightened CLIC5 activity could promote a permissive environment for oxidative-stress induced DNA damage accumulation and thereby contribute to leukemogenesis.

overall_design: To identify direct targets of ETV6, we first designed an in vitro RNA-seq experiment using ETV6-/- Reh-derived clones. Cells were transduced with lentiviral constructs to express ETV6-His and ETV6ΔETS_NLS-His. Total RNA was extracted from stable cell populations and RNA-seq libraries were sequenced. Expression profiles were analyzed using EdgeR. Gene expression profiles in ETV6-His cells were first compared with ETV6ΔETS_NLS-His and pLENTI cells to identify repressed genes (FDR ≤ 0.1). We then included data from the ETV6ΔETS_NLS-His vs. pLENTI comparison and further considered genes whose expression remains constant (p-value ≥ 0.05 or logFC ≥ -0.5) which are more likely to be direct ETV6 targets. Finally, only genes that showed a specific overexpression in t(12;21)-positive childhood pre-B ALL patients were considered.

first: Benjamin

last: Neveu

first: Jean-François

last: Spinella

first: Chantal

last: Richer

first: Karine

last: Lagacé

first: Pauline

last: Cassart

first: Mathieu

last: Lajoie

first: Silvana

last: Jananji

first: Jasmine

last: Healy

first: Gilles

last: Hickson


title: TFIID subunit TAF4 is essential at mid-gestation of murine embryogenesis and for embryonic stem cell differentiation

first: diana

last: langer

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

overall_design: Refer to individual Series


title: polyA depleted RNA-seq from neural cell (ENCSR995JXE)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
RNA-seq of H1-neuron cellular RNA greater than 200 bp depleted in polyadenlated mRNA

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HepG2 (ENCSR985KAT)

summary:
RNA Evaluation HepG2 Long Poly-A+ from Graveley

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Genome-wide profiling of gene expression under electro-acupuncture pretreatment on myocardial I/R injury in rats

first: Bing-Mei

last: Zhu

summary:
Purpose:Acupuncture exerts cardioprotective effect on myocardial I/R injury. In order to  elucidate the potential mechanisms,  RNA-seq by next generation sequencing was used to identify the rat genome-wide alterations by EA at Neiguan acupoint pretreatment  in this study
Methods: Adult male Sprague Dawley rats (250-300g)  were divided into four groups: Sham operation(SO), I/R, electro-acupuncture at Neiguan pretreatment (EA) and electro-acupuncture at non-acupoint (NA) groups and myocardium mRNA profiles of  rats in each group were generated by deep sequencing,using Illumina Hiseq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 20~43 million sequence reads per sample to the mouse genome (UCSC RN4) and identified 26190 22895 25160 22852 transcripts in the SO, I/R, EA and NA rats  with TopHat and Cufflinks workflow respectively.  Approximately 32% and 22% of the transcripts showed differential expression between the SO and I/R, I/R and EA , I/R and NA, respectively with a |log2 fold change |≥1.
Conclusions: Our results for the first time generated genome-wide gene expression profiles both in the rat I/R model and in acupuncture treatment by high throughput sequencing. The optimized data analysis workflows reported here should provide a framework for acupuncture investigations of expression profiles.

overall_design: Myocardium mRNA profiles of SO, I/R,  EA and NA  rats were generated by Hiseq 2000, Each group there were two samples.

first: Yan

last: Huang

first: Chen-Jun

last: Hu


title: The epigenetic impact of sampling procedures: Modulation of the clear cell renal cell cancer methylome following renal artery ligation

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

summary: Epigenetic changes, relative to sample collection

overall_design: 12 Biopsy and Nephrectomy Samples analysed by methylCap-seq DNA methylation

first: Christophe

last: Van Neste

first: Alexander

last: Laird

first: Fiach

last: O'Mahony

first: Wim

last: Van Criekinge

first: Dieter

last: Deforce

first: Filip

last: Van Nieuwerburgh

first: Thomas

last: Powles

first: David

last: Harrison

first: Grant

middle: D

last: Stewart

first: Tim

last: De Meyer

first: Geert

last: Trooskens


title: total RNA-seq from HT-29 (ENCSR971GPJ)

summary:
The libraries contained in this experiment come from independent growths of cell line HT-29, a colorectal adenocarcinoma from a 44 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RNA sequencing of Taf4+/+ and Taf4-/- cells in 1 timepoint during the differentiation into the cardiac lineage

first: diana

last: langer

summary: We determined the Taf4 dependent differential expression of RNAs in WT as well as KO cells at day 9 of the differentiation into the cardiac lineage.

overall_design: Examination of RNA expression in 4 different cell lines (2 independent Taf4 WT and 2 independent Taf4 KO) in 1 timepoint during cardiac differentiation.

first: Diana

last: Langer


title: total RNA-seq from hepatocyte (ENCSR908ZAS)

first: ENCODE

last: DCC

summary:
The libraries contained in this experiment come from stem cells that were differentiated down a hepatocytic pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from epithelial cell of alveolus of lung (ENCSR897KTO)

summary:
The libraries contained in this experiment come from independent isolates of epithelial cell of alveolus of lung primary of cell type (HPAE EpiC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from bipolar spindle neuron (ENCSR968WKR)

summary:
The libraries contained in this experiment come from independent growths of bipolar neurons that were differentiated from induced pluripotent stem cells. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients

city: Amsterdam

first: Monique

middle: C.

last: de Jong

address: Plesmanlaan 121

department: Dept of Biological Stress Response and Dept. of Radiation Oncology

country: Netherlands

institute: Netherlands Cancer Institute

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: total RNA-seq from SJSA1 (ENCSR880EGO)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line SJSA1. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from induced pluripotent stem cell (ENCSR938LSP)

summary:
The libraries contained in this experiment come from independent growths of cell line GM23338, an induced pluripotent stem cell (iPSC) line derived from cell line GM23248.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from endometrial microvascular endothelial cells (ENCSR919MZM)

summary:
The libraries contained in this experiment come from independent growths of endometrial microvascular endothelial primary cell line HEMEC.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from myotube (ENCSR828TEI)

summary:
The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myotubes.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from MG63 (ENCSR971KNW)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line MG63. They are stranded PE101 Illumina HiSeq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from GMP (ENCSR833HPM)

summary:
PSU mouse GMP RNA 100 cells RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mammary microvascular endothelial cell (ENCSR815UVL)

summary:
The libraries contained in this experiment come from independent isolates of mammary microvascular endothelial cell primary cell line (HMMEC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Splicing-independent loading of TREX on nascent RNA is required for efficient transcription of dual-strand piRNA clusters in Drosophila

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

summary: The conserved THO/TREX complex is critical for pre-mRNA processing and mRNA nuclear export. In Metazoa, TREX is loaded on nascent RNA transcribed by RNA polymerase II in a splicing-dependent fashion; however, how TREX functions is poorly understood. Here we show that Thoc5 and other TREX components are essential for the biogenesis of piRNA, a distinct class of small non-coding RNAs that control expression of transposable elements (TE) in the Drosophila germline. Mutations in TREX lead to defects in piRNA biogenesis resulting in derepression of multiple TE families, gametogenesis defects, and sterility. TREX components are enriched on piRNA precursors transcribed from dual-strand piRNA clusters and co-localize in distinct nuclear foci that overlap with sites of piRNA transcription. The localization of TREX in nuclear foci and its loading on piRNA precursor transcripts depends on Cutoff, a protein associated with chromatin of piRNA clusters. Finally, we show that TREX is required for accumulation of nascent piRNA precursors. Our study reveals a novel splicing-independent mechanism for TREX loading on nascent RNA and its importance in piRNA biogenesis.

overall_design: Examination of the effects of Thoc5 deficiency on the total and small RNA transcriptome, and characterization of the Thoc5-bound transcripts in the ovary of D. melanogaster.

first: Junho

last: Hur

first: Yicheng

last: Luo

first: Sungjin

last: Moon

first: Georgi

last: Marinov

first: Yun

last: Chung

first: Alexei

last: Aravin


title: total RNA-seq from airway epithelial cell (ENCSR822SUG)

summary:
The libraries contained in this experiment come from airway epithelial cells (HSA EpiC). They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from fibroblast of arm (ENCSR797BPP)

summary:
The libraries contained in this experiment come from independent growths of cell line GM23248, a fibroblast primary cell line derived from an arm skin punch of a 53 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: miRNA high-throughput sequencing of human prostate cancer cell lines P69, M12, M2182

city: Richmond

first: Sarah

last: Seashols-Williams

state: VA

address: 1015 Floyd Ave Box 843079

department: Forensic Science

institute: Virginia Commonwealth University

summary: Purpose: Next-generation sequencing (NGS) of miRNA expression in cancer cell lines provides a path for analysis of dysregulated pathways and potential treatment of dysregulation. The goals of this study are to compare NGS-derived miRNA expression data in a non-tumorigenic prostate cell line (P69) to its metastatic derivative cell lines M12 and M2182.

overall_design: small RNA sequencing of duplicate extractions of the benign human prostate cell line P69, its metastatic, tumorigenic derivative cell lines M2182 and M12, and a non-metastatic subline developed from M12 using microcell-mediated chromosomal transfer.

first: S

first: W

middle: E

last: Budd

first: Z

last: Zehner

first: G

middle: C

last: Clark

first: Q

last: Wu


title: total RNA-seq from H4 (ENCSR919QJT)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line H4. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from CMP (ENCSR767VHR)

summary:
PSU mouse CMP RNA 100 cells RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from hindbrain (ENCSR749BAG)

summary:
The libraries contained in this experiment come from independent isolates of hindbrain tissue.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from hair follicular keratinocyte (ENCSR680USE)

summary:
The libraries contained in this experiment come from hair follicular keratinocytes (HHFK). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from SK-MEL-5 (ENCSR669KQU)

summary:
The libraries contained in this experiment come from independent growths of cell line SK-MEL-5, a metastatic malignant melanoma from a 24 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from M059J (ENCSR696SMK)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line M059J. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from MCF-7 (ENCSR667JTA)

summary:
RNA Evaluation MCF7 Long Total from Graveley

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from forebrain (ENCSR723SZV)

summary:
The libraries contained in this experiment come from independent isolates of forebrain tissue.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from LHCN-M2 (ENCSR894WMQ)

summary:
The libraries contained in this experiment come from independent growths of immortalized cell line LHCN-M2 after 4 days of differentiation. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from G401 (ENCSR653DFZ)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line G401. They are stranded PE101 Illumina Hhi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from NCI-H460 (ENCSR625QJI)

summary:
The libraries contained in this experiment come from nuclear fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from bronchus fibroblast of lung (ENCSR620NSN)

summary:
The libraries contained in this experiment come from primary bronchial fibroblast cells (HBF).  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from NCI-H460 (ENCSR586SEE)

summary:
The libraries contained in this experiment come from cytoplasmic fractions of immortalized cell line NCI-H460 derived from a large cell lung carcinoma of a 37 year old male.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from A172 (ENCSR580GSX)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line A172. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-N-DZ (ENCSR569JKX)

summary:
The libraries contained in this experiment come from cytoplasmic fractions of a neuroblastoma immortalized cell line SK-N-DZ erived from a metastatic site in the bone marrow of a 2 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HT1080 (ENCSR535VTR)

summary:
The libraries contained in this experiment come from independent growths of cell line HT-1080, a connective tissue fibrosarcoma from a 35 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from Caki2 (ENCSR584JXD)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line Caki2. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from SJCRH30 (ENCSR568YRP)

summary:
The libraries contained in this experiment come from independent growths of cell line SJCRH30, a metastatic rhabdomyosarcoma from a 17 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from MEP (ENCSR549QME)

summary:
PSU mouse MEP RNA 100 cells RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from A375 (ENCSR504VXC)

summary:
The libraries contained in this experiment come from independent growths of cell line A375, a malignant melanoma from a 54 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from H7-hESC (ENCSR490SQH)

summary:
The libraries contained in this experiment come from independent growths of uninduced embryonic stem cell line H7-hESC.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from G1E (ENCSR826IXR)

summary:
PSU mouse G1E RNA 1ng RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from skeletal muscle myoblast (ENCSR444WHQ)

summary:
The libraries contained in this experiment come from independent growths of primary cell line HSMM that has been differentiated into myoblasts. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from myometrial cell (ENCSR371VGV)

summary:
The libraries contained in this experiment come from independent isolates of myometrial smooth muscle primary cell type (HMSMC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from kidney epithelial cell (ENCSR373BDG)

summary:
The libraries contained in this experiment come from independent isolates of kidney epithelial primary cell type (HREpiC).  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from HepG2 (ENCSR468ION)

summary:
RNA Evaluation HepG2 Long Total from Graveley

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from PC-3 (ENCSR420NLC)

summary:
The libraries contained in this experiment come from independent growths of cell line PC-3, a metastatic prostate grade IV adenocarcinoma from a 62 year old male.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from MCF-7 (ENCSR310FIS)

summary:
RNA Evaluation MCF7 Long Poly-A+ from Graveley

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from cardiac ventricle fibroblast (ENCSR369RVN)

summary:
The libraries contained in this experiment come from cardiac ventricle fibroblast cells (HCF-av). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from Karpas-422 (ENCSR314LXG)

summary:
The libraries contained in this experiment come from independent growths of cell line Karpas-422, a B cell from a 73 year old female with non-Hodgkins Lymphoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from LHCN-M2 (ENCSR332DBS)

summary:
The libraries contained in this experiment come from independent growths of immortalized cell line LHCN-M2. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from RPMI-7951 (ENCSR320BRR)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line RPMI-7951. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from neural cell (ENCSR292TAP)

summary:
RNA-seq H1-neuron cellular polyadenlated RNA greater than 200 bp

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-MEL-5 (ENCSR291DJH)

summary:
The libraries contained in this experiment come from cytoplasmic fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from neural progenitor cell (ENCSR244ISQ)

summary:
The libraries contained in this experiment come from independent growths of H9 embryonic stem cells that were differentiated down a neuronal pathway.  They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from astrocyte (ENCSR233IJT)

summary:
The libraries contained in this experiment come from independent growths of primary astrocytes.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-MEL-5 (ENCSR201WVA)

summary:
The libraries contained in this experiment come from nuclear fractions of a malignant melonoma immortalized cell line SK-MEL-5 derived from a metastatic axillary node of a 24 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from mesangial cell (ENCSR198TKA)

summary:
The libraries contained in this experiment come from primary mesangial cells (HRMC). They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from hematopoietic stem cell (ENCSR236ZIE)

summary:
PSU mouse HSC 100 cells RNA-seq

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from SK-N-DZ (ENCSR255NYQ)

summary:
The libraries contained in this experiment come from nuclear fractions of a neuroblastoma immortalized cell line SK-N-DZ derived from a metastatic site in the bone marrow of a 2 year old female. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from Daoy (ENCSR254JJM)

summary:
The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line Daoy. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HT1080 (ENCSR166QLP)

summary:
The libraries contained in this experiment come from cytoplasmic fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from SK-N-DZ (ENCSR136WGP)

summary:
The libraries contained in this experiment come from independent growths of cell line SK-N-DZ, a metastatic neuroblastoma from a 2 year old female.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from K562 (ENCSR109IQO)

summary:
RNA Evaluation K562 Long Total from Graveley

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from cardiac atrium fibroblast (ENCSR110BDY)

summary:
The libraries contained in this experiment come from independent isolates of cardiac atrium fibroblast primary cell type (HCF-aa).  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: polyA mRNA RNA-seq from HT1080 (ENCSR067UNX)

summary:
The libraries contained in this experiment come from nuclear fractions of a fibrosarcoma immortalized cell line HT1080 derived from the connective tissue from a 35 year old male. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: total RNA-seq from NCI-H460 (ENCSR164OCT)

summary:
The libraries contained in this experiment come from independent growths of cell line NCI-H460, a male large cell lung carcinoma.  They are stranded PE101 Illumina Hi-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf