title: Genome-wide binding pattern of β-catenin during Xenopus gastrulation

city: Berkeley

first: Richard

last: Harland

address: Life Sciences Addition #3200

institute: University of California, Berkeley

summary: The canonical Wnt/β-catenin signaling pathway plays multiple roles during Xenopus gastrulation, including posteriorization of the neural plate, patterning of the mesoderm, and induction of the neural crest. Wnt signaling stabilizes β-catenin, which then activates target genes. However, few targets of this signaling pathway that mediate early developmental processes are known. Here we sought to identify transcriptional targets of the Wnt/β-catenin signaling pathway using a genome-wide approach.

overall_design: Xenopus laevis emrbyos were injected with a triple FLAG tagged beta-catenin at levels that did not effect phenotype. Pools of about 500 embryos were fixed for ChIP processing. An input sample was taken prior to immunoprecipitation with a Flag antibody. Both input and ChIP material were used to make sequencing libraries.

first: Rachel

middle: S

last: Kjolby


title: Transcriptome analysis of Wnt knockdown embryos reveals candidate canonical Wnt/β-catenin target genes during Xenopus laevis gastrulation

status: Public on Apr 25 2016

state: CA

country: USA

type: Expression profiling by high throughput sequencing

overall_design: Total RNA was extracted from a single uninjected control and a single dkk injected embryo from the same mating and used to make sequencing libraries. There are three replicates, each pair from a different mating pair.

middle: M


title: Sequential regulatory loops as key gatekeepers for neuronal reprogramming in human cells [ChIP-seq]

city: La Jolla

first: Xiang-Dong

last: Fu

state: California

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Direct conversion of somatic cells into neurons holds great promise for regenerative medicine. However, neuronal conversion is relatively inefficient in human cells compared to mouse cells. It has been unclear what might be the key barriers to reprogramming in human cells. We recently elucidated an RNA program mediated by the polypyrimidine tract binding protein PTB to convert mouse embryonic fibroblasts (MEFs) into functional neurons. In human adult fibroblasts (HAFs), however, we unexpectedly found that invoking the documented PTB–REST–miR-124 loop generates only immature neurons. We now report that the functionality requires sequential inactivation of PTB and the PTB paralog nPTB in HAFs. Inactivation of nPTB triggers another self-enforcing loop essential for neuronal maturation, which comprises nPTB, the transcription factor BRN2, and miR-9. These findings suggest that two separate gatekeepers control neuronal conversion and maturation and consecutively overcoming these gatekeepers enables deterministic reprogramming of HAFs into functional neurons.

overall_design: Four Brn2 ChIP-seq libraries are analyzed. Brn2 genomic binding positions are revealed in human neural progenitor cells before and after two weeks of differentiation with two specific antibodies.

first: Yuanchao

last: Xue

first: Xihao

last: Hu

first: Bing

last: Zhou


title: Fixed tissue ChIP-Seq (FiT-Seq) of archived clinical samples reveals chromatin dynamics and tumor-specific enhancer profiles

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Analysis of cancer epigenomes has revealed important insights into key lineage determinants and oncogenic drivers. Chromatin immune-precipitation followed by next generation sequencing (ChIP-seq) has allowed the comprehensive mapping of transcription factor cistromes and histone modifications in fresh or frozen cells and tissues. It has not been possible, however, to apply ChIP-seq to the vast majority of clinical tissue samples, owing to the very extensive tissue fixation and cross-linking introduced during routine pathological processing. This severely limits the ability to study the most valuable, clinically annotated tissue resources. Here we describe Fixed-Tissue chromatin immune-precipitation sequencing (FiT-seq), which allows the epigenomic analysis of routine formalin-fixed paraffin-embedded (FFPE) tissue samples. FiT-seq enables reliable extraction of soluble chromatin from fixed tissues for accurate detection of histone marks and we verify high concordance between FiT-seq from FFPE and ChIP-seq from matched fresh frozen (FF) samples of the same tumors. We demonstrate the value of FiT-seq to investigate differences in chromatin states in normal and malignant colorectal epithelium and to identify robust correlations to methylated DNA, gene expression, and transcription factor activities. Using multiple histone marks we generate chromatin state maps and identify tissue- and tumor-specific cis-regulatory elements in clinical samples from various tumor types, readily distinguishing cancers by tissue of origin. Tumor specific enhancers and super-enhancers elucidated by FiT-seq are correlated with known biological drivers of cancer and can assist in understanding how chromatin state affects gene regulation.

overall_design: Histone marks analysis in FFPE samples to assess the performance of our newly designed method FiT-seq. The design comprises: 1) analysis of H3K4me2 in colorectal (CRC) FFPE vs matched FF tissues. 2) H3K4me2 comparison between CRC and corresponding colonic mucosas both for FF and FFPE samples. 3) analysis of enhancers by H3K4me2 across tumor types (CRC, breast cancer, seminoma, bladder cancer) in FFPE samples. 4) analysis of a series of histone marks that includes H3K36me3, H3K4me3, H3K4me2, H3K9ac, H3K27me3 in a FFPE bladder cancer (BlCa6) and includes H3K36me3, H3K4me3 and H3K4me2 in a FFPE (CRC8)

first: Paloma

last: Cejas

first: Lewyn

last: Li

first: Nicholas

middle: K

last: O’Neill

first: Melissa

last: Duarte

first: Prakash

last: Rao

first: Michaela

last: Bowden

first: Marta

last: Mendiola

first: Emilio

last: Burgos

first: Jaime

last: Feliu

first: Juan

last: Moreno-Rubio

first: Héctor

last: Guadalajara

first: Víctor

last: Moreno

first: Damián

last: García-Olmo

first: Joaquim

last: Bellmunt

first: Stephanie

last: Mullane

first: Michelle

last: Hirsh

first: Christopher

last: Sweeney

first: Andrea

last: Richardson

first: Shirley

last: Liu

first: Myles

last: Brown

middle: A

first: Henry

middle: W

last: Long


title: Wnt/β-catenin in Xenopus laevis gastrulation

first: Richard

last: Harland

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

overall_design: Refer to individual Series


title: Human milk cells and lipids conserve numerous known and novel miRNAs, some of which are differentially expressed during lactation

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

type: Non-coding RNA profiling by high throughput sequencing

summary: Human milk (HM) is rich in miRNAs, which are thought to contribute to infant protection and development. We used deep sequencing to profile miRNAs in the cell and lipid fractions of HM obtained post-feeding from 10 lactating women in month 2, 4, and 6 postpartum. In both HM fractions, 1,195 mature known miRNAs were identified, which were positively associated with the cell (p=0.048) and lipid (p=0.010) content of HM. An additional 5,167 novel miRNA species were predicted, of which 235 were high-confidence miRNAs expressed in ≥3 samples with total reads of >20. HM cells contained more known miRNAs than HM lipids (1,136 and 835 respectively, p<0.001), with 146 of the common species upregulated in HM cells and 133 in HM lipids (p<0.05). Further, the profile of the novel miRNAs was very different between the two HM fractions, with the majority conserved in the cell fraction and being mother-specific. However, out of the 776 known miRNA species commonly present in the two HM fractions, 63.9% were similarly expressed (p>0.05), with great similarities in the profile of top 20 known miRNAs. These were largely similar also between the three lactation stages examined, as were the total miRNA concentration, and the number and overall expression of the known miRNAs commonly present in the two HM fractions (p>0.05). Yet, approximately a third of known miRNAs were differentially expressed during the first 6 months of lactation (p<0.05), with more pronounced miRNA upregulation seen in month 4. These findings indicate that although the total miRNA concentration of HM cells and lipids provided to the infant does not change in the first 6 months of lactation, the miRNA composition is somewhat altered, particularly in month 4 compared to months 2 and 6. This may reflect the remodeling of the gland in response to infant feeding patterns, which usually change after exclusive breastfeeding, and thus adaptation to infant needs.

overall_design: Human milk samples were collected from 10 women longitudinally, at month 2, 4 and 6 postpartum. Total RNA and miRNA were extracted and quantified from cell and lipid fractions. Next-generation sequencing using Illumina HiSeq 2000 was performed on 45 samples (30 milk cells, and 15 lipid samples) to profile mature miRNAs in the breast milk cellular and lipid fractions longitudinally. Filtered (clean) reads were aligned to the latest version of miRBase 21.0. Also, mirdeep software was used to predict novel miRNAs. DESeq and Linear mixed effect models and ANOVA were used to compare miRNA expression levels between samples.

first: Foteini

last: Kakulas

first: Donna

middle: T

last: Geddes

first: Peter

middle: E

last: Hartmann

first: Chin

last: Tat-Lai


title: Hobit and Blimp1 instruct a universal transcriptional program of tissue-residency in lymphocytes

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: Tissue-resident memory T cells (Trm) are non-circulating memory T cells that localize to portals of pathogen entry such as the skin, gut and lung where they provide efficient early protection against reinfection. Trm are characterized by a molecular profile that actively prevents egress from peripheral sites including the constitutive expression of the lectin CD69 and down-regulation of the chemokine receptor (CCR)7 and sphingosine-1-phosphate receptor 1 (S1PR1). This program is partially mediated by down-regulation of the transcription factor KLF2; however, to date no transcriptional regulator specific to Trm has been identified. Here we show that the Blimp1 related transcription factor Hobit is specifically upregulated in Trm and together with Blimp1, mediates the development and maintenance of Trm in various tissues including skin, gut, liver and kidney. Importantly, we found that the Hobit/Blimp1 transcriptional module is also required for other tissue-resident lymphocytes including Natural Killer T (NKT) cells and liver tissue-resident NK cells (trNK). We show that these populations share a universal transcriptional program with Trm instructed by Hobit and Blimp1 that includes the repression of CCR7, S1PR1 and KLF2 thereby enforcing tissue retention. Our results identify Hobit and Blimp1 as major common regulators that drive the differentiation of distinct populations of tissue-resident lymphocytes.

overall_design: RNA-seq data were generated for multiple tissues in mice to investigate global expression difference between resident and circulating cells.

first: Yang

last: Liao

first: Axel

last: Kallies

first: Klaas

last: van Gisbergen


title: Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment

city: Aberdeen

first: Stefan

last: Hoppler

address: Foresterhill

department: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

summary: The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized the genomic loci bound by the Wnt signaling downstream component β-catenin in intact X. tropicalis gastrulae using ChIP-seq. We also determined the normal mRNA expression profile in control (uninjected and control-MO-injected) embryos and altered mRNA expression profiles in two experimental samples: embryos where endogenous wnt8a function was knocked down with wnt8a MO, and where we experimentally re-instated Wnt8a expression with a DNA construct (pCSKA-wnt8a) in the same wnt8a knock down.

overall_design: For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced.

first: Yukio

last: Nakamura

first: Eduardo

last: Alves


title: Cerebellar RNA-Seq from ATXN1 Transgenic Mice Reveals SCA1 Disease Progression and Protection Pathways

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

summary: SCA1, a fatal neurodegenerative disorder, is caused by a CAG expansion encoding a polyglutamine stretch in the protein ATXN1. We used RNA-seq to profile cerebellar RNA expression in ATXN1 mice, including lines with ataxia and progressive pathology and lines having ataxia in absence of Purkinje cell progressive pathology. Weighted Gene Coexpression Network Analysis of the cerebellar RNA-seq data revealed two gene networks that significantly correlated with disease, the Magenta (342 genes) and Light Yellow (35 genes) Modules. Features of the Magenta and Light Yellow Modules indicate they reflect distinctive pathways. The Magenta Module provides a description of suppressed transcriptional programs reflecting disease progression in Purkinje cells, while the Lt Yellow Module reflects other transcriptional programs activated in response to disease in Purkinje cells as well as other cerebellar cell types. We also found that up-regulation of cholecystokinin (Cck) blocked progression of Purkinje cell pathology and that loss of Cck function in mice lacking progressive disease enabled Purkinje cell pathology to progress to cell death.

overall_design:
Cerebellar mRNA expression profiles from ATXN1[82Q], ATXN1[30Q], and ATXN1[30Q]-D776 transgenic mice and wild type/FVB mice at 5 weeks, 12 weeks and 28 weeks of age
----------------------------
cuffnorm_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_genes.fpkm_tracking.txt: CuffNorm normalized values for all samples (snoRNAs and miRNAs removed)
cuffdiff_week5_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt: Cuffdiff comparison between samples at week 5; pairwise comparisons between  ATXN1[82Q], ATXN1[30Q]D776 and FVB
cuffdiff_week12_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt: Cuffdiff comparison between samples at week 12; pairwise comparisons between  ATXN1[82Q], ATXN1[30Q]D776 and FVB
cuffdiff_week28_ATXN1.82Q_ATXN1.30Q.D776_WTFVB_gene_exp.diff.txt: Cuffdiff comparison between samples at week 28; pairwise comparisons between  ATXN1[82Q], ATXN1[30Q]D776 and FVB
cuffdiff_week5_vs_week12_vs_week28_ATXN1.82Q_gene_exp.diff.txt: Cuffdiff comparison between ATXN1[82Q] at week 5, week 12 and week 28
cuffdiff_week5_vs_week12_vs_week28_ATXN1.30Q.D776_gene_exp.diff.txt: Cuffdiff comparison between ATXN1[30Q]D776 at week 5, week 12 and week 28
cuffdiff_week5_vs_week12_vs_week28_FVB_gene_exp.diff.txt: Cuffdiff comparison between wt/FVB at week 5, week 12 and week 28

first: Melissa

last: Ingram

first: Emily

last: Leathley

first: Lisa

last: Duvick

first: Rendong

last: Yang

first: Paul

last: Bergmann

first: Huda

middle: Y

last: Zoghbi

first: Harry

last: Orr


title: Global Regulatory Network Controlling Human Somatic Cell Reprogramming [RNA-seq]

status: Public on Apr 24 2016

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: This is the first study deciphering the global regulatory network that drives human somatic cells during epigenetic rewiring towards the pluripotent state.

overall_design: Examination of the Transcriptomic profiles of cells undergoing reprogramming.

first: Cheng-Xu

last: Delon Toh

last: EL Farran

first: Zheng-Shan

last: Chong

first: Julien

middle: J

last: Maury

first: James

last: Collins

first: George

middle: Q

last: Daley

first: Hu

last: Li

first: Yoon-Pin

last: Lim

first: Yuin-Han

last: Loh


title: The human placenta exhibits dichotomised DNA methylation pattern compared to homogenous somatic tissue

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: We sought to compare genome-wide methylation patterns of human placenta with blood neutrophils, a homogenous somatic tissue

overall_design: Here we generated single-nucleotide resolution DNA methylation maps of human placenta using Reduced Representation Bisulphite Sequencing (RRBS) and compared their methylation pattern with neutrophils.

first: Erin

middle: C

last: Macaulay

first: Euan

last: Rodger

first: Peter

last: Stockwell

first: Matthew

middle: F

last: Parry

first: Hester

last: Roberts

first: Tania

middle: L

last: Slatter

first: Noleyn

last: Hung

first: Celia

last: Devenish

first: Ian

last: Morison


title: Dnmt3a regulates myeloproliferation and liver-specific homing and expansion of hematopoietic stem and progenitor cells (Bisulfite-Seq)

city: New York

first: Barbara

last: Spitzer

state: NY

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

summary: DNMT3A mutations are observed in myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), and acute myeloid leukemia (AML).  Here we investigated the impact of conditional hematopoietic Dnmt3a loss on disease phenotype in primary mice.  Dnmt3a ablation led to a lethal, fully penetrant myeloproliferative neoplasm with myelodysplasia (MDS/MPN) characterized by marked, progressive hepatomegaly that was transplantable.  We detected expanded stem/progenitor populations in the liver of Dnmt3a-ablated mice.  Homing studies showed that Dnmt3a-deleted bone marrow cells preferentially migrated to the liver.  Hence, in addition to the established role of Dnmt3a in regulating self-renewal, Dnmt3a regulates tissue tropism and limits myeloid progenitor expansion in vivo.

overall_design: Dnmt3af/f mice (Nguyen et al) were crossed into hematopoietic-specific inducible Mx1-Cre deletor line; we examined transcriptomes from FACS-sorted LSK and GMP populations from Dnmt3af/f Mx1-Cre+ (KO) and Dnmt3af/f Mx1-Cre- (CTRL) animals at 12 months of age

first: Olga

last: Guryanova

first: Francine

last: Garrett-Bakelman

first: Ross

last: Levine


title: Dnmt3a regulates myeloproliferation and liver-specific homing and expansion of hematopoietic stem and progenitor cells (RNA-Seq)

first: Franck

last: Rapaport


title: Global Regulatory Network Controlling Human Somatic Cell Reprogramming [ChIP-seq]

first: Chadi

last: El Farran

overall_design: Examination of the Epigenetic rewiring in somatic cells undergoing reprogramming.

first: Cheng-Xu

last: Delon Toh

last: EL Farran

first: Zheng-Shan

last: Chong

first: Julien

last: Maury

first: James

last: Collins

first: George

last: Daley

first: Hu

last: Li

first: Yoon-Pin

last: Lim


title: Genome-wide analysis of histone modifications H3K27ac, H3K4me3, and H3K4me1 in differentiating primary human epidermal keratinocytes (NHEK)

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: The epidermis is a stratified squamous epithelium that serves to protect the body from dehydration, absorption of chemicals, and invasion of pathogens. In the epidermis, cells of the basal layer contain proliferative potential. As they divide and move upward in the tissue, they progressively differentiate, and activate the gene expression program required to create a barrier; eventually, cells in the uppermost layer are sloughed off from the surface of the epidermis. This system requires continual replacement of differentiating cells from the basal layer. Such a process requires very precise regulation of gene expression to balance proliferation and differentiation and maintain a functioning epithelium. Epigenetic mechanisms of gene regulation, including DNA methylation and histone modification have been shown to play a major role in tissue development and wound healing. To identify regulatory regions in differentiating epidermal cells, we performed ChIP-Seq with antibodies to H3K4me1, and H3K4me3 at 24 hours after induction of differentiation to complement publicly available ENCODE data for these marks in undifferentiated NHEK. With this data, we were able to identify enhancers, defined by the presence of high levels of H3K4me1 and H3K27ac, and low levels of H3K4me3. We identified approximately 20,000 of these regions each in undifferentiated and differentiated keratinocytes. Approximately 20 percent of these regions were shared between the two conditions, while about 30 and 43 percent were unique to differentiated and undifferentiated keratinocytes, respectively.

overall_design: ChIP experiments for histone modifications H3K4me1, H3K27ac, and H3K4me3 were performed on primary human epidermal keratinocyte cells that had been induced to differentiate through the addition of  calcium (1.8mM Calcium Chloride)  to the medium for 24 hours prior to collection. After ChIP, libraries were sequenced on the Illumina high-seq 2000.

first: Rachel

last: Herndon Klein


title: Global Regulatory Network Controlling Human Somatic Cell Reprogramming

first: Yuin-Han

last: Loh


title: RNA-Seq results of four Chinese cattle from longissimus muscles based on Illumina HiSeq 2000 platform

status: Public on Apr 23 2016

city: Nanchang

first: chenlong

last: liu

state: Jiangxi province

address: Lushanzhong street NO.888, Nanchang, China

department: Animal science and technology department

country: China

institute: Jiangxi Agricultural University

summary:
Purpose: The goals of this study are to identify the molecular mechanism by which NA improves meat quality and find differentially expressed genes in longissimus muscles between cattle treated with/without dietary NA.
Methods: gene expression profiles of longissimus muscle from 4 cattle mRNA pools including 6 control and 6 NA treated cattle were generated by single-end sequencing (50 bp), using Illumina HiSeq™ 2000. The sequence reads that passed quality control were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: Using SOAPaligner (V2.21) analysis, we mapped about 23,359,272-25,165,811 clean reads per sample to the bovine reference genome assembly (unmasked genomic DNA sequences: Bos_taurus.UMD3.1.75.dna.chromosome.1-29 and X) (ftp://ftp.ensembl.org/pub/release-75/fasta/bos_taurus/dna/). Our NOISeq analysis identified a list of 124 differentially expressed genes with a probability value ≥ 0.8 and an absolute value of log2 Ratio of NA to Control ≥ 1.
Conclusions: In our study, dietary NA increases the IMF content of longissimus muscle may through up-regulating the expressions of genes and pathways related to lipid metabolism.

overall_design: Four mRNA profiles of 6 control and 6 NA treated cattle were generated by single-end sequencing (50 bp), using Illumina HiSeq™ 2000.

first: Mingren

last: Qu

first: Zhuqing

last: Yang


title: Exploring pathogenic microRNAs of rice sheath blight pathogen

city: Wenjiang, Chengdu

first: Zheng

last: Aiping

state: Sichuan

address: Huimin Road 211 Hao

department: Rice Research Institute

institute: Sichuan Agricultural University

summary: We constructed seven small RNA libraries of Rhizoctonia solani AG1 IA and sequenced using Illumina GA II. The seven samples include  mycelium cultured on PDA without rice incubated, 6 different stages at 10 hours (10h), 18h, 24h, 32h, 48h and 72h spanning the Rhizoctonia solani AG1 strains infection rice. We identified miRNA-like small RNAs (milRNAs) using MIREAP and mirdeep2. The milRNAs were used for further analysis of interactions between milRNA and mRNA that may involve in plant-infection.

overall_design: Identification of milRNAs in R. solani AG1.

first: Liye

last: He

first: Runmao

last: Lin

first: Ping

first: Aiping

last: Zheng


title: Illumina sequencing of vaginal epithelial cells from women using depot medroxyprogesterone acetate or non-hormonal contraception

city: Birmingham

first: Zdenek

last: Hel

state: Alabama

address: 1825 University Blvd SHEL 677

institute: University of Alabama at Birmingham

summary: The use of the hormonal contraceptive DMPA has been associated with a moderate increase in sexually transmitted infections, including HIV-1. To better understand the biological mechanisms behind this phenomenon, we report here the use of mRNA-sequencing on the Illumina HiSeq2000 of vaginal epithelial cells from women using DMPA or controls. We found that women using DMPA demonstrate over 330-fold decrease in the anti-microbial peptide human beta defensin 3 (HBD3) and massive downregulation of genes involved in structural integrity, barrier function, and wound healing. CXCL6, CXCL1, and IL-1B among other inflammatory genes were up-regulated in the tissue of DMPA users compared to controls. Overall, these results demonstrate significant differences in basic epithelial functions following DMPA use.

overall_design: Vaginal epithelial cells from four women using DMPA or non-hormonal contraception were isolated using laser capture microdissection for subsequent Illumina analysis

first: Michel

last: Katherine

first: Hel

last: Zdenek


title: Deep Sequencing of Typha angustifolia Small RNAs

city: Nanjing

first: Yingchun

last: Xu

state: Jiangsu

address: College of Horticulture, Nanjing Agricultural University

department: College of Horticulture

institute: Nanjing Agricultural University

summary: We used high-throughput sequencing to identify conserved and nonconserved miRNAs and other short RNAs in Typha angustifolia under control and cadmium stressed condition. A total of 114 conserved miRNAs and 41 novel candidate miRNAs encoded by 66 hairpin precursors were identified in both small RNA libraries. 4 conserved and 6 novel miRNAs showed specific expression, which, combined with function of target genes, suggests that miRNAs may play a role in plant Cd stress response.These results provide a framework for further analysis of miRNAs and their role in regulating Typha angustifolia response to cadmium stress.

overall_design: Two small RNA libraries, with (Cd) and without (CK) cadmium-treatment, were sequenced by Illumina sequencing technology

first: Lingling

last: Chu


title: RNA-seq analysis of trait-associated genes (TAGs) in somatic cells from Holstein’s milk

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

country: South Korea

institute: Seoul National University

summary:
Background : Although the chemical, physical, and nutritional properties of bovine milk have been extensively studied, few studies have attempted to characterize the milk synthesizing genes associated with milk yielding traits. In addition, no previous attempts have been made to detect quantitative traits such as milk production related traits, associated genes on RNA-seq experiment with several biological replicates. Research in this field is necessary as bovine milk is a primary source of nutrition for humans.
Results : We investigated advantages of using linear models with continuous response variables over converted group variables in a Holsteins’ milk. Suggested methods were more suitable in detection of significant genes in our analysis; the proportion of false discoveries to total significant genes was observed to be much lower compared to the precedent approaches we employed. These were observed through mock comparison studies and quantitative real time PCR (qRT-PCR).
Conclusion : Several milk production related genes and pathways were identified from the suggested methods. Given the current trend in RNA-seq pricing, we expect our methods to be successfully applied in various RNA-seq studies with numerous biological replicates that handle continuous response traits.

overall_design: We generated 21 RNA-seq samples (biological replicates) from the RNA samples were extracted from the somatic cells of Holsteins’milk.

first: Jin

last: Jeong

first: Hyun-Jeong

last: Lee


title: Histone H3K4 methylation regulates deactivation of the Spindle Assembly Checkpoint through direct binding of Mad2

status: Public on Apr 22 2016

city: Smithville

first: Sharon

middle: Roth

last: Dent

state: Texas

address: 1808 Park Road 1C

institute: Univ Texas M.D. Anderson Cancer Center

summary: We report the genomic location of H3K4me2 and H3K4me3 in Saccharomyces cerevisiae by ChIP-Seq

overall_design: Examination of H3K4me2 and H3K4me3 across the Saccharomyces cerevisiae genome

first: Andria

last: Schibler

first: Yue

last: Lu


title: Deep sequencing of Paeonia ostii small RNAs in response to copper stress

summary: We used high-throughput sequencing to identify conserved and nonconserved miRNAs and other short RNAs in Paeonia ostii under control and copper stressed condition. 102 previously known plant miRNAs were identified and classified into 89 families according to their gene sequence identity. Some miRNAs were highly conserved in the plant kingdom suggesting that these miRNA play important and conserved roles. Combined our transcriptome sequencing data of Paeonia ostii under same conditions, 34 novel potential miRNAs were identified. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. Comparing the two libraries, it was observed that 12 conserved miRNAs and 18 novel miRNAs showed significantly changes in response to copper stress. Some of the new identified potential miRNAs might be involved in Paeonia ostii-specific regulating mechanisms under copper stress. These results provide a framework for further analysis of miRNAs and their role in regulating Paeonia ostii response to copper stress.

overall_design: Two small RNA libraries, with (TR) and without (CK) copper-treatment, were sequenced by Illumina sequencing technology

first: Qijiang

last: Jin

first: Zeyun

last: Xue


title: Combinatorial Control Logic of the Gene Expression Response to Endotoxin links Signal-Dependent Transcriptional Factors and Cytoplasmic Mechanisms

city: Los Angeles

first: Alexander

last: Hoffmann

address: 570 Boyer Hall

department: MIMG

institute: UCLA

summary: An iterative Systems Biology approach reveals how the pathogen-responsive transcriptome is specified by combinatorial codes of nuclear transcription factors, cytoplasmic mRNA halflife regulators, and autocrine mechanisms.

overall_design: RNASeq analysis of BMDMs stimulated with various stimuli for 0, 1, 3 and 8 hours


title: RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures

city: San Francisco

first: Maurizio

last: Pellegrino

address: 953 Indiana Street

institute: Mission Bio

summary:
Background: Rare cell subtypes can profoundly impact the course of human health and disease, yet their presence within a sample is often missed with bulk molecular analysis.  Single-cell analysis tools such as FACS, FISH-FC and single-cell barcode-based sequencing can investigate cellular heterogeneity; however, they have significant limitations that impede their ability to identify and transcriptionally characterize many rare cell subpopulations.
Results: PCR-activated cell sorting (PACS) is a novel cytometry method that uses single-cell TaqMan PCR reactions performed in microfluidic droplets to identify and isolate cell subtypes with high-throughput. Here, we extend this method and demonstrate that PACS enables high-dimensional molecular profiling on TaqMan-targeted cells. Using a random priming RNA-Seq strategy, we obtained high-fidelity transcriptome measurements following PACS-sorting of prostate cancer cells from a heterogeneous population.  The sequencing data revealed prostate cancer gene expression profiles that were obscured in the unsorted populations.  Single-cell expression analysis with PACS was subsequently used to confirm a number of the differentially expressed genes identified with RNA sequencing.
Conclusions: PACS requires minimal sample processing, uses readily available TaqMan assays and can isolate cell subtypes with high sensitivity.  We have now validated a method for performing next-generation sequencing on mRNA obtained from PACS isolated cells.  This capability makes PACS well suited for transcriptional profiling of rare cells from complex populations to obtain maximal biological insight into cell states and behaviors.

overall_design: The PACS workflow was used to isolate a spiked-in cell subpopulation and compare its RNA profile with the hegterogeneous starting population and the individual populations.

first: Adam

last: Sciambi

first: Jamie

last: Yates

first: Joshua

middle: D

last: Mast

first: Charles

last: Silver

first: Dennis

last: Eastburn


title: A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity

city: Milan

first: Alessio

last: Zippo

address: Via Francesco Sforza, 35

country: Italy

institute: National Institute of Molecular Genetics

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

overall_design: Refer to individual Series


title: The genomic context and co-recruitment of SP1 affect ERRα co-activation by PGC-1α in muscle cells

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel


title: The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs

city: Cambridge

first: Wendy

middle: V

last: Gilbert

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

summary: Translation is a core cellular process carried out by a highly conserved macromolecular machine, the ribosome. There has been remarkable evolutionary adaptation of this machine through the addition of eukaryote-specific ribosomal proteins whose individual effects on ribosome function are largely unknown. Here we show that eukaryote-specific Asc1/RACK1 is required for efficient translation of mRNAs with short open reading frames that show greater than average translational efficiency in diverse eukaryotes. ASC1 mutants in S. cerevisiae display compromised translation of specific functional groups, including cytoplasmic and mitochondrial ribosomal proteins, and display cellular phenotypes consistent with their gene-specific translation defects. Asc1-sensitive mRNAs are preferentially associated with the translational ‘closed loop’ complex comprised of eIF4E, eIF4G and Pab1, and depletion of eIF4G mimics the translational defects of ASC1 mutants. Together our results reveal a role for Asc1/RACK1 in a length-dependent initiation mechanism optimized for efficient translation of genes with important housekeeping functions.

overall_design:
Ribosome footprint profiling and matched RNA-Seq was performed on S. cerevisiae mutants with altered Asc1 function or expression. Data from additional ribosomal protein mutants, rpl23b∆, rpp1a∆, rps0b∆, and rps16b∆, was collected for comparison. Data was also collected from an ASC1 protein null mutant, asc1-M1X, in a stress condition (growth in glycerol-containing media). In each case, data was collected from two biological replicates.

Supplementary processed data files linked below:

abbreviations:
FP= ribosome footprint profiling
total= total RNA-Seq
TE= translation efficiency measurements
glycerol= yeast grown in rich media containing glycerol instead of glucose
rz= libraries made using Ribo-Zero rRNA subtraction rather than polyA selection
reprep= library made from the same biological replicate starting material, as noted, in order to obtain higher read coverage. For downstream analyses, the original and reprep libraries were pooled.

*counts.txt:
Counts per feature for each library. Unique-mapping reads only included.

*scaledcounts.txt
Counts scaled (per experiment, including replicates) using the DESeq R package.

*rpkms.txt:
Reads per kilobase per million mapped reads for each feature.

*foldchanges.csv:
log2 fold changes for all mutants (mutant vs. wild type, average values derived from two biological replicates).

*filtered_foldchanges.csv:
log2 fold changes of all mutants (mutant vs. wild type, average values derived from two biological replicates), filtered such that each comparison (i.e. mutant vs. WT total RNA-Seq) has a minimum of 128 reads. Features too lowly expressed to meet this cutoff were removed from the relevant comparison.

first: Mary

last: Thompson

first: Maria

last: Rojas-Duran

first: Paritosh

last: Gangaramani


title: Generation of Brain Region-specific Organoids using a Miniaturized Spinning Bioreactor and Modelling ZIKV Exposure

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

summary: Cerebral organoids, three-dimensional cultures that model organogenesis, provide a new platform to investigate human brain development. High cost, variability and tissue heterogeneity limit accessibility and broad applications of current organoid technologies. Here we developed a miniaturized spinning bioreactor (SpinΩ) to generate forebrain-specific organoids from human iPSCs. These organoids recapitulate key features of human cortical development, including progenitor zone organization, neurogenesis, gene expression, and importantly, a distinct human-specific outer radial glia cell layer. We have also developed protocols to generate midbrain and hypothalamic organoids. Finally, we employed this forebrain organoid platform to model Zika virus (ZIKV) exposure. Quantitative analyses revealed that preferential, productive ZIKA infection of cortical neural progenitors leads to increased cell death and reduced proliferation, resulting in decreased neuronal cell layer volume that resembles microcephaly. Together, our brain region-specific organoids and SpinΩ provide an accessible and versatile platform for modeling human brain development and diseases, and for compound testing.

overall_design: Time course of human cerebral organoid cultures.  No Zika virus infection is involved.


title: Genome-wide maps of human OEC innate immune responses to Burkholderia

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

institute: Griffith University

summary: We report a transcriptional response in human OECs that encompasses multiple innate immune networks not previously associated with these cells. Major pathways included immune cell trafficking, and differential cytokine production

overall_design: We used RNA-based sequencing technology for high-throughput profiling of innate immune responses in human OECs and the role of Burkholderia in triggering these responses

first: Deepak

middle: S

last: Ipe


title: Discovering miRNA regulatory networks in Holt-Oram Syndrome using a Zebrafish model [miRNA-seq]

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

institute: CNR

summary: To investigate the complex regulatory networks disrupted in Holt-Oram Syndrome, we characterized genome-widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points, 24 and 48 hpf.

overall_design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO-Tbx5a against the TSS of the gene. A MO-CT was used in CT samples. 1,5ng morpholinos were injected into the yolk of 1-cell stage embryos and total RNA extracted from 50 embryos collected at 24 and 48hpf.The Zebrafish  wild-type AB strain line was used.

first: Letizia

last: Pitto

first: Elena

last: Chiavacci

first: Mario

last: Baumgart

first: Marco

last: Groth


title: A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity (ChIP-Seq)

summary: Genome-wide mapping of H3K4me3, H3K27me3, SUZ12 in mESCs

overall_design: ChIP-seq for H3K4me3, H3K27me3, SUZ12 in mESCs

first: Luca

last: Fagnocchi

first: Hiroshi

last: Hatsuda


title: Discovering miRNA regulatory networks in Holt-Oram Syndrome using a Zebrafish model


title: FBXO10 deficiency and BTK activation upregulate BCL2 expression in mantle cell lymphoma

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify BTK targets by RNA-seq and high-throughput data analysis and verify these genes by quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods
Methods: mino/z138 sc4/shbtk stable cell lines were generated with tet-on system vector, small hairpins were induced for 48 hours after doxycycline addition, mRNA was exacted and used for RNA sequencing. After TopHat analysis followed by Cufflinks, down/up regulated genes list was generated. qRT–PCR validation was then performed using SYBR Green assays
Results: Using an optimized data analysis workflow and with a fold change ≥1.3 and p value <0.05, thousands of genes were changed. Altered expression of 6 genes was then confirmed with qRT–PCR, demonstrating the high qulity of the RNA-seq method.

overall_design: mino/z138 sc4/shbtk stable cell lines were generated with tet-on system vector, small hairpins were induced for 48 hours after doxycycline addition, total RNA from these cells was then used for RNA-seq analysis.

first: Lixin

last: Rui

first: Yangguang

last: Li

first: Li

last: Lu


title: The genomic context and co-recruitment of SP1 affect ERRα co-activation by PGC-1α in muscle cells [ChIP-Seq]

first: Christoph

last: Handschin

summary: The peroxisome proliferator-activated receptor γ co-activator 1α (PGC-1α) coordinates  the transcriptional network response to promote an improved endurance capacity in  skeletal muscle, e.g. by co-activating the estrogen-related receptor α (ERRα) in the  regulation of oxidative substrate metabolism. Despite a close functional relationship,  the interaction between these two proteins has not been studied on a genomic level.  We now mapped the genome-wide binding of ERRα to DNA in skeletal muscle cell line  with elevated PGC-1α and linked the DNA recruitment to global PGC-1α target gene  regulation. We found that, surprisingly, ERRα co-activation by PGC-1α is only  observed in the minority of all PGC-1α recruitment sites. Nevertheless, a majority of  PGC-1α target gene expression is dependent on ERRα. Intriguingly, the interaction  between these two proteins is controlled by the genomic context of response elements,  in particular the relative GC and CpG content, monomeric and dimeric repeat binding  site configuration for ERRα, and adjacent recruitment of the transcription factor SP1.  These findings thus not only reveal an unprecedented insight into the regulatory  network underlying muscle cell plasticity, but also strongly link the genomic context of  DNA response elements to control transcription factor - co-regulator interactions.

overall_design: We performed ChIP-Seq experiments to identify all DNA recruitment sites for ERRalpha in C2C12 cells, in presence of PGC-1alpha over-expression, on a genome-wide scale. The Whole Cell Extract (WCE; =input DNA) was used as background condition.

first: Silvia

last: Salatino

first: Barbara

last: Kupr

last: Baresic

first: Erik

last: van Nimwegen


title: Hipposeq: an RNA-seq based atlas of gene expression in excitatory hippocampal neurons

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome atlas of gene expression for every excitatory neuronal class in the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical neurons of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell class- and region-specific transcriptional atlas for these canonical populations.

overall_design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population

first: Nelson

last: Spruston


title: Epigenetic Profiles Signify Cell Fate Plasticity in Unipotent Spermatogonial Stem and Progenitor Cells (ChIP-Seq)

status: Public on Apr 21 2016

city: New York

first: Ying

last: Liu

address: 1300 York Ave

institute: Weill Cornell Medical College

summary: Mammalian spermatogonial stem cells (SSCs) spontaneously convert to multipotent adult spermatogonial-derived stem cells (MASCs) during in vitro expansion. Here, we examine the epigenetic signature of SSCs and MASCs, identifying bivalent histone H3-lysine4 and -lysine27 trimethylation at somatic gene promoters in SSCs and an ESC-like promoter chromatin state in MASCs.

overall_design: Examination of histone modifications K4me3, K27me3, and K27ac in different cell types.

first: Shahin

last: Rafii


title: Transcriptome profiling of banana in response to growth-promoting rhizobacteria

city: Bethesda

first: Leonardo

last: Mariño-Ramírez

state: MD

address: 8600 Rockville Pike

department: CBB

institute: NCBI/NLM/NIH

summary: We report the banana transcriptome profile in response to two distinct growth-promoting rhizobacteria, Bacillus amyloliquefaciens and Pseudomonas fluorescens. The goal of our study is to identify plant genes differentially regulated by rhizobacteria-plant interaction along time. At the same time, we show that despite these two rhizobacteria regulate distinct sets of genes, the same functional categories has been over-represented, such as transcription factor activity, response to stress and metabolic processes.

overall_design: Twenty-seven cDNA libraries were prepared from Musa acuminata Williams cultivar, including: root, pseudostems and leaves. Three biological replicates were collected for each treatment (control, inoculated with Bacillus amyloliquefaciens or Pseudomonas fluorescens) at three different times: 0, 48 and 96h post inoculation.

first: Newton

middle: M

last: Vidal

first: Rocío

last: Gamez

first: David

last: Landsman


title: Late pre-B cell tranLate pre-B cell transcriptomes from Zfp36l1 Zfp36l2 double knockout micescriptomes from Zfp36l1 Zfp36l2 double knockout mice

first: Martin

last: Turner

address: Babraham Hall

department: Lymphocyte Signalling and Development

institute: Babraham Institute


title: Epigenetic Profiles Signify Cell Fate Plasticity in Unipotent Spermatogonial Stem and Progenitor Cells (RNA-Seq)

overall_design: Examination of gene expression in different cell types.


title: Late pre-B cell transcriptomes from Zfp36l1 Zfp36l2 double knockout mice [RNA-Seq]

summary:
Purpose: Conditional knockout of Zfp36l1 Zfp36l2 in pro-B cells perturbs B cell development leading to reduced V(D)J recombination and diminished numbers of cells in successive stages of development.  This RNA seq experiment aimed to determine the molecular pathways affected by loss of Zfp36l1 and Zfp36l2, and to deduce direct targets of these RNA binding proteins.
Methods: RNAseq libraries were prepared from 0.1 µg of RNA from sorted control and DCKO late pre-B cells using TruSeq RNA sample preparation kit v2 modified to be strand specific using the dUTP method.  Libraries were sequenced by an Illumina genome analyzer II measuring 54bp single-end reads.  Over 30 million reads were measured from each sample.  The reads were trimmed to remove adapter sequences using Trim Galore then mapped using Tophat (version 1.1.4) to the NCBIm37 mouse assembly (April 2007, strain C57BL/6J); reads with an identical sequence to more than one genomic locus were not mapped.  Quality control analysis was carried out with FastQC.
Results: Read counts for each gene were generated in SeqMonk: transcripts from the same gene were collapsed into a single transcript containing all exons, so total reads were counted without considering alternative splice forms.  Since the libraries were strand-specific only reads on the opposing strand were counted.  Differences in the abundance of transcripts between DCKO and control late pre-B cells were calculated in the R/Bioconductor program DESeq (version 1.12.1).  Adjusted P values for differential expression were calculated in DESeq using a Benjamini-Hochberg correction: genes with an adjusted p-value of less than 5% were considered significant. Differentially expressed mouse transcripts identified using DESeq were analyzed for gene set enrichment using Toppfun.
Conclusions: We identified an enrichment of mRNAs involved in cell cycle progression within Zfp36l1 Zfp36l2 double conditional knockouts.

overall_design: RNAseq of late pre-B cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.

first: Alison

last: Galloway

first: Sebastian

last: Lukasiak

first: Helena

last: Ahlfors

first: Simon

last: Andrews


title: AF9/MLLT3 ChIP-Seq in LPS-stimulated RAW264.7 cells

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: We sought to characterize the genomic localization of the YEATS domain protein AF9 in the macrophage-like cell line RAW 264.7 +/- LPS stimulation and +/- sodium crotonate pretreatment. We performed chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) for endogenous AF9 or for a FLAG-tagged AF9 transgene in RAW264.7 or a RAW264.7 cell line engineered to express FLAG-AF9, respectively.

overall_design: ChIP-Seq for AF9 in RAW264.7 cells +/- LPS stimulation and +/- sodium crotonate pretreatment

middle: R


title: Co-regulation of splicing by Rbfox1 and hnRNP M [hnRNPM k-d+Rbfox1 RNA-Seq]

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

summary: hnRNP M and Rbfox proteins are subunits of the Large Assembly of Splicing Regulators (LASR). The purpose of this study is to investigate how these two splicing factors affect each others' role in regulating splice site choices in pre-mRNA. hnRNP M is knocked down by RNAi in Flp-In T-REx 293 cells (Invitrogen), whereas Rbfox1 is expressed inducibly under tetracycline control from construct integrated into the genome at the FRT site. Using this system, splicing and expression profiles of cells expressing and/or lacking these proteins are compared on a whole genome level by RNA-seq technology.

overall_design: The experiment was performed in Flp-In T-REx 293, Rbfox2 knockout cells (clone 7), in which the Rbfox2 ORF was disrupted in the first constitutive exon (exon 3), thus these cells do not produce endogenous Rbfox protein. In addition to this, cells expressing Flag-tagged Rbfox1 under tetracycline control from a pcDNA5/FRT/TO construct inserted into the FRT site were generated. hnRNP M was knocked down to 10% of the normal levels by transient expression of two RNA hairpins targeting separate 3' UTR regions. A non-targeting hairpin served as control. Four separate cell populations: not expressing Rbfox with normal levels fo hnRNP M; expressing Rbfox1 with normal hnRNP M levels; not expressing Rbfox, hnRNP M expression reduced by 90%; expressing Rbfox1, hnRNP M reduced by 90% were each grown independently in triplicates. Total RNA was collected from these cells and further treated with DNase I to avoid DNA contamination. Illumina TruSeq stranded mRNA kit was used to generate strand-specific libraries. These libraries were subjected to 50bp paired-end sequencing (Illumina HiSeq2000 platform). In parallel, a fraction of each cell population was lysed in RIPA buffer for protein analysis.

first: Andrey

last: Damainov

first: Chia-Ho

first: Yi

last: Ying

first: Douglas

last: Black


title: Conservation of parental genomic imprinting by cortex generated from embryonic stem cells [RRBS-seq]

city: Montpellier

first: Tristan

last: Bouschet

address: 141 rue de la cardonille

department: CNRS 5203, INSERM U661

country: France

institute: Institut de Génomique Fonctionnelle

summary: In vitro cortex generated from embryonic stem cells (ESCs) is a model system to investigate corticogenesis and a promising tool for cortical therapy. A fundamental question that has implications for understanding corticogenesis and for using stem cells therapeutically is to determine whether in vitro cortex reproduces some fine-tuned epigenetic modifications that are important for corticogenesis and function in vivo such as parent-of-origin dependent DNA methylation and expression of imprinted genes (IGs).  Here, we have compared at single-base resolution the parent-of-origin dependent DNA methylation and expression of IGs in hybrid cortices generated either in vivo or in vitro from ESCs using Reduced Representation Bisulfite Sequencing (RRBS) and RNA-seq. We report that in vitro cortex strictly reproduced the in vivo parental expression of 41 IGs, including those involved in corticogenesis such as Mest (paternal) and Cdkn1c (maternal). The expressed allele was set in ESCs and maintained during in vitro corticogenesis for most IGs but some switched from a biallelic expression in ESCs to the monoallelic expression observed in vivo. RRBS experiments revealed that parent-of-origin dependent methylation at imprinted loci were also largely similar in in vitro and in vivo cortices except at a few loci. The most discordant locus was Gpr1-Zdbf2: Zdbf2 RNA was paternal in vivo and biallelic in vitro, and this was concomitant with an aberrant gain of methylation on the maternal allele in vitro.  Thus, we conclude that the epigenetic mechanisms at imprinted loci are largely but not strictly preserved in vitro. We propose that in vitro corticogenesis, with its set of IGs displaying faithful parent-of-origin dependent expression and methylation, helps to define the poorly known mechanisms regulating imprinting in the brain and roles of IGs during corticogenesis.

overall_design: Global and parental allele specific genomic DNA methylation of in vivo cortex and ESC-derived in vitro cortex was determined by RRBS. Biological duplicates were used for the 13 analyzed conditions. In vitro samples were: E14 ESCs (d0) and E14 ESC-derived cortex (at d12 and d21), hybrid BJ1 (mother C57BL/6J x father JF1) and JB6 (mother JF1 x father C57BL/6J) at d0, d12, d21. In vivo samples were hybrid BJ1 and JB6 dorsal telencephalon (DT) at E13.5 and cortex (Ctx) at P0.

first: Emeric

last: Dubois

first: Christelle

last: Reynès

first: Satya

last: Kota

first: Stéphanie

last: Rialle

last: Maupetit-Méhouas

first: Mikael

last: Pezet

first: Anne

last: Le Digarcher

first: Sabine

last: Nidelet

first: Vincent

last: Demolombe

first: Patricia

last: Cavelier

first: Céline

last: Meusnier

first: Chloé

last: Maurizy

first: Robert

last: Sabatier

last: Feil

first: Philippe

last: Arnaud

first: Laurent

last: Journot

first: Annie

last: Varrault


title: Rbfox1, Rbfox2, and Rbfox3 iCLIP from mouse brain nuclear fractions

first: Chia-ho

last: Lin

summary: In this study we analyze the in vivo recruitment of mouse brain nuclear Rbfox proteins to RNA using individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP). Rbfox1, Rbfox, 2, and Rbfox3 iCLIP libraries were constructed from high molecular weight (HMW) nuclear fraction containing chromatin and the soluble nucleoplasm.

overall_design: This study includes six iCLIP libraries prepared from HMW nuclear fraction: Rbfox1_HMW_forebrain, Rbfox1_HMW_hindbrain, Rbfox2_HMW_forebrain, Rbfox2_HMW_hindbrain, Rbfox3_HMW_forebrain, and Rbfox3_HMW_hindbrain. Two libraries from the soluble nucleoplasm were prepared from the same biological sample: Rbfox1_soluble_forebrain and Rbfox1_soluble_hindbrain. Additionally, three other nucleoplasmic samples were prepared independently: Rbfox1_soluble_brain, Rbfox2_soluble_brain, and Rbfox3_soluble_brain.

first: Andrey

last: Damianov

first: Chia-Ho

first: Ji-Ann

last: Lee

first: Kelsey

last: Martin

first: Douglas

last: Black


title: Transcriptome of Colletotrichum graminicola during infection of Zea mays leaf sheaths

city: Lexington

first: Lisa

last: Vaillancourt

state: Kentucky

address: 201F Plant Science Building

department: Plant Pathology

institute: University of Kentucky

overall_design: Refer to individual Series


title: Co-regulation of splicing by Rbfox1 and hnRNP M

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Total RNA profiles associated with DDX3 wild-type (WT) or R534H variant expression with or without sodium arsenite treatment [RNA-seq]

city: Stanford

first: Sekyung

last: Oh

address: 1201 Welch Road, MSLS P224

department: Neurology and Neurological Sciences

institute: Stanford University School of Medicine

summary: RNA expression profiles are not significantly altered by DDX3 WT or R534H expression as well as by 45 minute exposure of cells to sodium arsenite.

overall_design: Cells expressing either DDX3 WT or R534H variant were treated with or without sodium arsenite and lysed in the presence of cyclohexime. Total cellular RNAs were extracted and sequenced.

first: Yoon-Jae

last: Cho


title: Dnmt3a regulates myeloproliferation and liver-specific homing and expansion of hematopoietic stem and progenitor cells

first: Barbara

last: Spitzer

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

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


title: Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment


title: Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [Ribo-Seq]

summary: By using ribosome profiling, we demonstrate that catalytic activity of the RNA helicase DDX3 is generally required for mediating translation repression under stress. Intriguingly, however, a cancer-related DDX3 variant DDX3 R534H selectively preserves translation of genes encoding core nucleosome components. Additionally, DDX3 variants also shift ORF usage on select genes, such as RPLP1 and stress-response factors as an added mechanism of translation regulation during stress. Thus, DDX3 through both extensive and selective interactions with RNA and the ribosomal machinery helps to remodel the translational landscape under stress and in cancer.

overall_design: Cells expressing either DDX3 WT or R534H variant were treated with or without sodium arsenite and lysed in the presence of cyclohexime. Ribosome-protected mRNA fragments after RNase I treatment were recovered and sequenced.


title: The transcriptome of Kawasaki Disease arteritis

city: London

first: Paul

last: Kelly

state: UK

address: Turner Street

department: Immunobiology

institute: Blizard Institute Barts & The London School of Medicine

summary:
Background: Kawasaki Disease (KD) is a childhood illness of suspected infectious etiology that causes medium-sized muscular arteritis, most critically affecting the coronary arteries. No single diagnostic test exists, hampering early diagnosis and treatment. Approximately 25% of untreated patients develop coronary artery disease, and children who are treated with intravenous gammaglobulin but do not respond are also at high risk. Subacute/chronic arteritis and luminal myofibroblastic proliferation are the pathologic processes occurring in KD CA after the second week of illness, when neutrophilic necrotizing arteritis has subsided. The specific dysregulated immune pathways contributing to subacute/chronic arteritis have been unknown, hampering the development of effective immunomodulatory therapies for patients not responding to intravenous gammaglobulin therapy.
Methods and Results: Deep RNA sequencing was performed on KD (n=8) and childhood control (n=7) coronary artery tissues, revealing 1074 differentially expressed mRNAs. Molecular pathways involving T helper cell, cytotoxic T lymphocyte, dendritic cells, and antigen presentation were the most significantly dysregulated. There was significant upregulation of immunoglobulin and type I interferon-stimulated genes.  80 upregulated extracellular genes encoding secreted proteins are candidate biomarkers of KD arteritis.
Conclusions: The immune transcriptional profile in KD coronary artery tissues is primarily T helper and cytotoxic lymphocyte-mediated, and has features of an antiviral immune response such as type I interferon-stimulated gene expression. This first report of the KD coronary artery transcriptome identifies specific dysregulated immune response pathways that can inform the development of new therapies for and biomarkers of KD arteritis, and provide direction for future etiologic studies.

overall_design: Primary analysis: 8 KD coronary arteries versus 7 childhood control coronary arteries. Subanalysis 1: 4 untreated KD coronary arteries versus 7 childhood control coronary arteries and subanalysis 2: 4 treated KD coronary arteries versus 7 childhood control coronary arteries

first: Anne

middle: H

last: Rowley

first: Kristine

last: Wylie

first: Kwang-Youn

middle: A

last: Kim

first: Adam

last: Pink

first: Amy

last: Yang

first: Rebecca

last: Reindel

first: Susan

last: Baker

first: Stanford

last: Shulman

first: Jan

last: Orenstein

first: Mark

middle: W

last: Lingen

first: George

last: Weinstock

first: Todd

middle: N


title: Profile of RNAs bound by wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [iCLIP-Seq]

summary: By iCLIP-seq, we demonstrated that DDX3 binds to specific sites on 18S ribosomal RNA and to messenger RNAs at 5’ leader and guanidine-rich sequences immediately upstream of ribosome-dense regions and that arsenite treatment redistributes DDX3 binding from 5'UTR to CDS, which is attenuated by DDX3 R534H.

overall_design: Cells were treated with or without sodium arsenite. RNAs crosslinked by UV to FLAG-tagged DDX3 WT or DDX3 R534H were immunoprecipitated sequentially, first with anti-FLAG antibody and second with anti-DDX3 antibody, then sequenced.

first: Ryan

last: Flynn

first: Howard

middle: Y

last: Chang


title: ChIP-seq and RNA-seq analysis of KMT2D-silenced metastatic melanoma cells

city: Milano

first: Luisa

last: Lanfrancone

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

summary:
Purpose: Study of the mechanism trough which KTM2D regulates chromatin modification and transcription in a xenograft model of human metatstatic melanoma
Methods: We generated patient derived xenografts (PDXs) from metastatic melanoma (MM) biopsies of three different patients.  The MMs carry NRASQ61L, NRASQ61Q or BRAFV600 mutations. Cells from secondary PDX (PDX2) were transduced with lentiviral vectors carrying Luciferase (shLuc) and KMT2D (shKMT2D) hairpins and mRNA profiles and genome-wide chromatin-state maps were generated by deep sequencing using Illumina HiSeq2000.
Results: we found that KMT2D regulates the activity of a subset of enhancers required for expression of specific genes.

overall_design: Examination of KMT2D gDNA binding sites, 3 different histone modifications and expression profiles (RNA-seq) in PDX cells from 3 human metatastatic melanomas after KMT2D silencing

first: Daniela

last: Bossi

first: Angelo

last: Cicalese

first: Gaetano

middle: I

last: Dellino

first: Lucilla

last: Luzi

first: Laura

last: Riva

first: Giulio

last: Draetta

first: Pier

middle: G

last: Pelicci


title: RNA-seq of zebrafish brain, liver and skin during perturbation with rotenone at young and old age

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Zebrafish of two different age groups (12 and 36 months) were treated with low amounts of rotenone (mild stress) and compared to untreated zebrafish. Two different durations were used (3 and 8 weeks). Illumina sequencing (HiSeq2000) was applied to generate 50bp single-end reads.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 68 sample: 3 tissues (brain, liver, skin); 2 age groups (12 and 36 months); controls and rotenone treated samples; 2-6 biological replicates for each group

first: Nils

last: Hartmann

first: Steffen

last: Priebe

first: Marco

last: Groth

first: Matthias

last: Platzer

first: Christoph

last: Englert


title: Late pre-B cell transcriptomes from Zfp36l1 Zfp36l2 double knockout mice [iCLIP]

first: Martin

last: Turner

summary:
Purpose: We aimed to identify the targets of the RNA binding protein ZFP36L1 in B cells.
Methods:  Mature B cells were stimulated with LPS, IL-4 and IL-5 for 48 hours to induce ZFP36L1 expression.  Cells were treated with UV light to crosslink RNA and proteins then RNA-protein complexes were pulled down with anti-ZFP36L1.  RNA was extracted and used to make cDNS libraries that were then sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing).
Results: Sample demultiplexing was performed by identification of the 3 known bases of the 7 bases barcode introduced in the 5’ end of the read by the RCLIP primer.  The remaining four random bases were used to remove PCR duplicate reads.  Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome mm10 using Bowtie.  After read mapping, the single-nucleotide at position -1 was annotated as unique ZFP36L1 crosslink site.  Identification of highly significant ZFP36L1 binding sites was performed using iCount to assign a FDR to each crosslink site
Conclusions: We identified ZFP36L1 binding sites in 1361 B cell mRNAs.

overall_design: Individual nucleotide resolution cross linking immunoprecipitation (iCLIP) of ZFP36L1-bound RNAs in LPS activated B cells from C57BL/6 mice.

first: Alexander

last: Saveliev


title: RNA sequencing of siSNRNP40 in breast cancer cells

status: Public on Apr 20 2016

last: Nguyen

state: New York

address: 1230 York Ave

institute: Rockefeller University

summary: To identify gene expression profile changes upon SNRNP40 depletion, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SNRNP40.

overall_design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina HiSeq 2500.

first: A

first: M

last: Yoshida

first: H

last: Goodarzi

first: S

last: Tavazoie


title: Expression of gallstone disease-associated genes in non-diseased and diseased gallbladder and liver samples

city: Framingham

first: Andrew

middle: Danner

last: Johnson

state: MASSACHUSETTS

address: The Framingham Heart Study

department: Cardiovascular Epidemiology and Human Genomics Branch

institute: National Heart, Lung and Blood Institute

summary: Following a large-scale genome-wide association study of gallstone disease, we performed RNA sequencing from tissues of four human gallbladders (3 healthy controls and 1 case with chronic gallstones) and one liver sample from the gallstone case. We aimed to determine the expression patterns of gallstone disease-associated genes in gallbladder and liver, two organs of interest in disease etiology.

overall_design: RNA-seq of four female human gallbladders (3 healthy controls and 1 case with chronic gallstones) and one liver sample from the gallstone case.

first: Yoshiyuki

last: Wakabayashi

first: John

last: Eicher

first: Yanqin

last: Yang

first: Jun

last: Zhu


title: FOXF1 inhibits endothelial barrier function in the lung and transcriptionally activates the gene for the S1PR1 receptor

city: Cincinnati

first: Vladimir

last: Kalinichenko

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Multiple signaling pathways, structural proteins and transcription factors are involved in regulation of endothelial barrier function.  The Forkhead protein FOXF1 is a key transcriptional regulator of lung embryonic development, and we use a conditional knockout approach to examine the role of FOXF1 in adult lung homeostasis and lung injury and repair.  Tamoxifen-regulated deletion of both Foxf1 alleles in endothelial cells of adult mice (Pdgfb-iCreER/Foxf1 caused lung inflammation and edema, leading to respiratory insuffency and uniform mortality.  Deletion of a single foxf1 allele was sufficient to increase susceptibility of heterozygous mice to acute lung injury.  FOXF1 abundance was decreased in pulmonary endothelial cells of human patients with acute lung injury.  Gene expression analysis of pulmonary endothelial cells of FOXF1 deletion indicated reduced expression for genes critical for maintance and regulation of adherens junctions.  FOXF1 knockdown in vitro and in vivo disrupted adherens junctions, increased lung endothelial permeability, and the abundance of mRNA and protein for sphingosine 1 phosphate receptor 1 (S1PR1), a key regulator of endothelial barrier function.  Chromatin immunoprecipitation and luciferase reporter assay demonstrated that FOXF1 directly bound to and induced the tanscriptional activity of the S1pr1 promoter.  Pharmacological administratiion of S1P to injured pdgfb-iCreER/Foxf1 mice restored endothelial barrier function, decreased lung edema and improved survival.  Thus, FOXF1 promotes normal lung homeostasis and lung repair, at least in part, by enhancing endothelial barrier function through transcriptional activation of the S1P/S1PR1/ signaling pathway.

overall_design: RNA was isolated and pooled from the lungs of multiple mice with either the Foxf1 floxed alleles alone or Pdgfb-iCreER Foxf1 floxed mice.

first: Yuqi

last: Cai

first: Craig

last: Blote

first: Tien

last: Le

first: Chinmyeee

last: Goda

first: Yan

last: Xu

first: Tanya

last: Kalin


title: Embryonic stem cell-derived cerebral cortex largely reproduces the in vivo epigenetic control of imprinted gene expression [RNA-seq]

first: Tristan

last: Bouschet

summary: In vitro differentiation of embryonic stem cells (ESC) provides models that reproduce in vivo development and cells for therapy. Whether the epigenetic signatures that are crucial for brain development and function and that are sensitive to in vitro culture are similar between native brain tissues and their artificial counterpart generated from ESC is largely unknown.  Here, using RNA-seq we have compared the parental origin-dependent expression of imprinted genes (IGs), a model of epigenetic regulation, in cerebral cortex generated either in vivo, or from ESCs using in vitro corticogenesis, a model that reproduces the landmarks of in vivo corticogenesis. For a majority of IGs, the expressed parental alleles were the same for in vivo and in vitro cortex. In most cases, this choice was already set in ESCs and faithfully maintained during the 3 weeks of in vitro corticogenesis. Confirming these findings, methylation, which selects the parental allele to be transcribed, was also largely equivalent between the 2 types of cortex and ESCs.   Our results thus indicate that the allele specific expression of imprinted transcripts, a model of epigenetic regulation resulting from a differential methylation of parental genomes, is mostly mimicked in cortical cells derived from ESC.

overall_design:
We have crossed two strains of mice (B6 and JF1) that display more than 12 million of SNPs (Takada et al., Genome Res. 2013 Aug;23(8):1329-38. doi: 10.1101/gr.156497.113). We have then analyzed allele specific expression transcriptome-wide using RNA-seq on hybrid F1 cortex generated either in vivo or in vitro from ESCs. In addition, we have used 2 different developmental stages of in vivo cortex (E13.5, P0) and three stages in vitro (undiffererentiated ESC, and differentiated into cortex for 12 and 21 days) to measure the dynamics of parental expression.

Please note that [1] the same raw data files were used to generate the '*allele-specific_sense_read_bases_by_gene_withoutContamination.txt' processed data files.
[2] The samples associated with each file are indicated in the file column header (as their GSM accession numbers).
[3] The readme.txt file contains the data processing steps, file description.

first: Emeric

last: Dubois

first: Christelle

last: Reynès

first: Satya

middle: K

last: Kota

first: Mikael

last: Pezet

first: Anne

last: Le Digarcher

first: Sabine

last: Nidelet

first: Vincent

last: Demolombe

first: Patricia

last: Cavelier

first: Céline

last: Meusnier

first: Claire

last: Prévost

first: Robert

last: Sabatier

first: Chloé

last: Maurizy

first: Philippe

last: Arnaud

last: Feil

first: Laurent

last: Journot

first: Annie

last: Varrault


title: Histone H1 limits DNA methylation in Neurospora

city: Athens

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Analysis of DNA methylation in wildtype and mutants lacking histone H1 revealed increased DNA methylation when H1 is absent.

overall_design: Replicates of each strain were grown in Vogel's minimal medium for 48 hours.


title: Exploiting single-cell expression to characterize co-expression replicability

city: Woodbury

first: Megan

last: Crow

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: We sequenced two types of interneurons from adult mouse frontal cortex across multiple library batches to assess the replicability of co-expression networks.

overall_design: Cells were harvested from four animals and processed in batches of 16 cells each. Two cells failed to amplify (ChC-49 and Pv-27) and were removed from our analysis.

first: Anirban

last: Paul

first: Sara

last: Ballouz

first: Z. Josh

last: Huang

first: Jesse

last: Gillis


title: Expansion of signal transduction pathways in fungi by extensive genome duplication

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

summary: Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the underlying mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide new insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides, and show that they have been shaped by an extensive genome duplication or, most likely, a whole genome duplication (WGD), which is rarely observed in fungi [3-6]. We show that the genome duplication has resulted in expansion of gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light indeed varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.

overall_design: For this experiment, three biological replicates were made for each condition, however during the differential expression analysis using the edgeR package, we determined that the WTMD3, WTSD3, WTSL2 and ΔL51SD2 libraries have greater dispersion compared to their respective biological replicas, so it was decided not to consider these data for the final analysis.

first: José

first: Luis

last: Corrochano

first: Igor

last: Grigoriev

first: Alexander

last: Idnurm

first: Toni

last: Gabaldon

first: Alfredo

last: Herrera-Estrella


title: Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [Retroviral scanning (MLV-Seq)]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. Cap Analysis of Gene Expression showed that the transcriptional state is largely maintained in the transition from early hematopoietic stem/progenitors to committed progenitor/precursors. A large fraction of differentially expressed active promoters in each cell type were classified as novel, possibly driving the expression of transcripts involved in HSPC commitment. Unannotated promoters harbored an enhancer chromatin signature, were enriched in cell-specific transcription factor binding sites, and were close to protein-coding cell-specific genes. To obtain a genome-wide description of regulatory regions, we performed ChIP-seq for histone modifications typical of promoters, enhancers and super-enhancers. ChIP-defined promoters were shared by HSPC and committed cells, whereas enhancer usage consistently changed upon commitment, thus indicating that the fine regulation of commitment is carried out by enhancer elements. The expression level of genes targeted by enhancers and super-enhancers was moderately higher in cells actively using these regulatory elements. However, functional annotation of targeted genes showed a low enrichment for cell-specific gene ontology categories. Finally, we used Moloney leukemia virus (MLV) to map functional regions of chromatin. Genomic regions targeted by MLV co-mapped with a fraction of epigenetically defined active regulatory elements, with two-third of MLV integrations falling in enhancers, and one-third in promoters. Most of MLV-targeted regulatory regions were differentially used between HSPC and their committed progeny. Analysis of the expression levels of promoters close to cell-specific MLV-targeted enhancers and functional assays indicated that MLV-defined regulatory regions are bona fide cell-specific enhancers. Finally, gene ontology analyses showed that MLV-targeted genes related to the peculiar cell identity. Overall, this study provided an overview of the differential transcriptional and epigenetic programs of HSPC and committed progenitors and represents a unique source of regulatory regions involved in HSPC commitment.

overall_design: Retroviral scanning: MLV transduction of human EPP and MPP and integration site analysis. SRA Study accession SRP051750. BioProject accession PRJNA271724. The data for HSPC_MLV was downloaded from SRA (SRX027104) and is therefore not included in SRP051750/PRJNA271724.

first: Oriana

last: Romano

first: Clelia

last: Peano

first: Guidantonio

last: Malagoli Tagliazucchi

first: Luca

last: Petiti

first: Valentina

last: Poletti

first: Fabienne

last: Cocchiarella

first: Ermanno

last: Rizzi

first: Marco

last: Severgnini

first: Alessia

last: Cavazza

first: Claudia

last: Rossi

first: Pasqualepaolo

last: Pagliaro

first: Alessandro

last: Ambrosi

first: Giuliana

last: Ferrari

first: Gianluca

last: De Bellis

first: Fulvio

last: Mavilio

first: Annarita

last: Miccio


title: Comparison of cortex generated either in vivo or in vitro from mouse ESC

first: Tristan

last: Bouschet


title: Genomic analysis of N. crassa histone H1

first: Zachary

last: Lewis

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

summary: Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-FLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stochiometery of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in wildtype and the ∆hH1 strain followed by sequencing (MNase-Seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation using methylC-sequencing (mC-Seq) revealed a modest but global increase in DNA methylation in the ∆hH1 mutant. Together, these data suggest that H1 acts as a non-specific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.

overall_design: Investigations used either wildtype, an H1 mutant strain, or an engineered strain containing a FLAG-tagged H1. In all cases, at least 2 biological replicate experiments were performed.


title: A threshold level of NFATc1 activity is critical for thymocyte differentiation and to prevent leukemia development

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

institute: University of Manchester

summary: NFATc1 plays a critical role in double-negative thymocyte survival and differentiation. However, the signals that regulate Nfatc1 expression are unknown. Here we show a developmental stage-specific differential expression pattern of Nfatc1 driven by the distal (P1) or proximal (P2) promoters in thymocytes. Whereas, preTCR-negative thymocytes exhibited only P2 promoter-derived Nfatc1b expression, preTCR-positive thymocytes expressed both Nfatc1b and P1 promoter-derived Nfatc1a transcripts. Inducing NFATc1a activity from P1 promoter in preTCR-negative thymocytes, in addition to the NFATc1a from P2 promoter impaired thymocyte development resulting in severe T cell lymphopenia. Additionally, we show that NFATc1 activity suppressed the B-lineage potential of immature thymocytes, and consolidated their differentiation to T cells. Further, in the pTCR-positive DN3 cells, a threshold level of NFATc1 activity was vital in facilitating T cell differentiation and to prevent T-acute lymphoblastic leukemia (T-ALL) development. Altogether, our results show NFATc1 activity is crucial in determining the T cell fate of thymocytes.

overall_design: ChIP-seq for H3K27ac was performed from DRag thymocytes

first: Stefan

last: Klein-Hessling

first: Ronald

last: Rudolf

first: Khalid

last: Muhammad

first: Klaus-Peter

last: Knobeloch

first: Pierre

last: Cauchy

first: Jean-Christophe

last: Andrau

first: Andris

last: Avots

first: Claudio

last: Talora

first: Volker

last: Ellenrieder

first: Isabella

last: Screpanti

first: Edgar

last: Serfling

first: Amiya

last: Patra


title: Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [ChIP-Seq]

first: Silvio

last: Bicciato

overall_design: ChIP-seq for histone modifications typical of regulatory elements (H3K4me3, H3K4me1, and H3K27ac) in HSPC and erythroid and myeloid progenitors/precursors. SRA Study accession SRP051209; BioProject accession PRJNA270485.

first: Oriana

last: Romano

first: Clelia

last: Peano

first: Guidantonio

last: Malagoli Tagliazucchi

first: Luca

last: Petiti

first: Valentina

last: Poletti

first: Fabienne

last: Cocchiarella

first: Ermanno

last: Rizzi

first: Marco

last: Severgnini

first: Alessia

last: Cavazza

first: Claudia

last: Rossi

first: Pasqualepaolo

last: Pagliaro

first: Alessandro

last: Ambrosi

first: Giuliana

last: Ferrari

first: Gianluca

last: De Bellis

first: Fulvio

last: Mavilio


title: Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [RNA-seq (CAGE)]

overall_design: Cap Analysis of Gene Expression (CAGE) was used to define the promoter usage in HSPC and their committed progeny. SRA Study accession SRP051234. BioProject accession PRJNA270570.

first: Annarita

last: Miccio


title: Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Genome-wide association studies (GWAS) have identified genomic loci associated with complex diseases but mechanistic insights are impeded by the lack of understanding of how specific risk variants functionally contribute to diseases. Here we describe an experimental strategy to robustly identify cis-acting effects of genetic variants in regulatory elements on gene expression by combining genome-wide epigenetic information with CRISPR/Cas genome editing in human pluripotent cells. Using this genetically controlled system, we identify a common Parkinson’s disease (PD)-associated risk variant in a non-coding distal enhancer element that regulates the expression of SNCA, a key gene implicated in the pathogenesis of PD. We provide data suggesting that the transcriptional deregulation of SNCA is associated with sequence-dependent binding of the brain-specific transcription factors EMX2 and NKX6-1. Our work provides a general experimental strategy to functionally connect genetic variation with disease relevant phenotypes.

overall_design: ChIP-Seq for H3K27ac and H3K4me1 in hES-derived neurons with and without modified SNCA enhancer alleles

first: Frank

last: Soldner

first: Yonatan

last: Stelzer

first: Chikdu

last: Shivalila

first: Brian

last: Abraham

first: M

last: Barrasa

first: Johanna

last: Goldmann

last: Myers

first: Rudolf

last: Jaenisch

first: Jeanne

middle: C

last: Latourelle


title: Efficient Generation of Cardiac Purkinje Fiber-like Cells from ESCs by Activating cAMP Signaling

city: New York

first: Todd

last: Evans

address: 1300 York Avenue, Box282

department: Surgery

institute: Weill Cornell Medical College

summary: Analysis of gene expression of mESC-derived cardiac purkinje fiber-like cells at mRNA level. Dysfunction of the cardiac conduction system (CCS) significantly impacts pathogenesis of arrhythmia, a major cause of morbidity and mortality. Strategies to derive cardiac conduction cells including Purkinje fiber cells (PC) would facilitate models for mechanistic studies and drug discovery, and also provide new cellular materials for regenerative therapies. A high-throughput chemical screen using CCS:lacZ and Contactin2:eGFP (Cntn2:eGFP) reporter embryonic stem cell (ESC) lines was used to discover a small molecule, sodium nitroprusside (SN), that efficiently promotes the generation of cardiac cells that express gene profiles and generate action potentials of PC-like cells. Imaging and mechanistic studies suggest that SN promotes the generation of PC from cardiac progenitors initially expressing cardiac myosin heavy chain, and that it does so by activating cAMP signaling. These findings provide a novel strategy to derive scalable PC, along with insight into the ontogeny of CCS development.

overall_design: Total RNA isolated from mESC-derived cardiac purkinje fiber-like cells. Mouse Contactin2:eGFP transduced with Lenti-viral aMHC: mCherry embryonic Stem Cells was used. Day 4 of differentiated cells were treated with Sodium Nitroprusside(SN).  After 25 days differentiation, by using FACS, we could separate SN-induced cells into three populations: negative, αMhc:mCherry+ (MHC) and Cntn2:eGFP+/dim αMhc:mCherry+(GFP). We then sequenced mRNA from these three populations and found that Cntn2:eGFP+ cells express cardiac purkinje-fiber gene profiles.

first: Su-Yi

last: Tsai

first: Glenn

last: Fishman

first: Shuibing

last: Chen


title: Small RNA sequencing of human prostate cancer samples

status: Public on Apr 19 2016

city: Rotterdam

first: Elena

last: Martens-Uzunova

address: Wytemaweg 80

department: Urology

country: Netherlands

institute: Erasmus MC

summary: We sequenced the small RNA transcriptome of prostate cancer at different stages and generated a quantified catalogue of 3927 small non-coding RNAs (sncRNAs) detected in normal and malignant prostate tissue. From these sncRNAs less than half are microRNAs. The remaining sncRNAs represent stable sncRNAs species that originate from snoRNA, tRNA and other sncRNAs.

overall_design: Small RNA seq of different grades (Gleason score) prostate tumors

first: Youri

last: Hoogstrate

first: Michael

last: Olvedy

first: Tapio

last: Visakorpi

first: Guido

last: Jenster


title: Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation

first: Silvio

last: Bicciato

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

overall_design: Refer to individual Series


title: Two components of the RNA-directed DNA methylation pathway associate with MORC6 and silence loci targeted by MORC6 in Arabidopsis

city: Beijing

first: Yongqiang

last: Li

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: DNA methylation is a conserved epigenetic mark that is required for the silencing of transposons and introduced transgenes in eukaryotes. An RNA-directed DNA methylation pathway mediates de novo DNA methylation and thereby leads to transcriptional silencing in Arabidopsis. In this study, we find that two RNA-directed DNA methylation components interact with the microrchidia (MORC) protein MORC6 and lead to transcriptional silencing through a mechanism that is distinct from the RNA-directed DNA methylation pathway. MORC6 was previously thought to mediate transcriptional silencing through heterochromatin condensation. Our study suggests that the interaction of the RNA-directed DNA methylation components with MORC6 may mediate a link between DNA methylation and heterochromatin condensation.

overall_design:
RNA-seq: Compare the mRNA profiles of 2-week-old seedlings materials of mutants (morc6 and suvh2suvh9) to wild type Col-0 by Illumina suquencing.
BS-seq: Whole genome methylation maps of 4 mutants (two replicates) were generated using BS-seq

first: Xin

last: He

first: Zhang

last: Liu

first: Yong


title: Next Generation Sequencing Facilitates Comparisons of Control and Schizophrenia-Patient derived hiPSC-derived neurons

first: Kristen

last: Brennand

state: NY

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary:
Cell-based models of many neurological and psychiatric diseases, established by reprogramming patient somatic cells into human induced pluripotent stem cells (hiPSCs), have now been reported.  While numerous reports have demonstrated that neuronal cells differentiated from hiPSCs are electrophysiologically active mature neurons, the “age” of these cells relative to cells in the human brain remains unresolved.  Comparisons of gene expression profiles of hiPSC-derived neural progenitor cells (NPCs) and neurons to the Allen BrainSpan Atlas indicate that hiPSC neural cells most resemble first trimester neural tissue.  Consequently, we posit that hiPSC-derived neural cells may most accurately be used to model the early developmental defects that contribute to disease predisposition rather than the late features of the disease. Though the characteristic symptoms of schizophrenia SZ generally appear late in adolescence, it is now thought to be a neurodevelopmental condition, often predated by a prodromal period that can appear in early childhood. Postmortem studies of SZ brain tissue typically describe defects in mature neurons, such as reduced neuronal size and spine density in the prefrontal cortex and hippocampus. We directly reprogrammed fibroblasts from SZ patients into hiPSCs and subsequently differentiated these disorder-specific hiPSCs into forebrain neurons.  SZ hiPSC differentiated into forebrain neurons have altered expression of a number of synaptic genes.
Methods: We compared global transcription of forebrain neurons from six control and four SZ patients by RNAseq.
Results:  Multi-dimensional scaling (MDS) resolved most SZ and control hiPSC neuron samples; 107 genes were significantly differentially expressed (FDR<0.01)

overall_design: 1-2 independent differentiations (biological replicates) for each of four control and four schizophrenia patients were analyzed; samples were generated in parallel to neuron RNAseq data.

first: Gang

last: Fang


title: Ribosome Profiling Reveals Translational Control During the Caulobacter crescentus cell cycle

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: The Caulobacter cell cycle includes sequential differentiation of the cell poles and an asymmetric cell division yielding distinct daughter cells.  RNA-seq and ribosome profiling were used to measure global messenger RNA (mRNA) abundance and translation levels throughout the Caulobacter cell cycle revealing translational control in 51% of cell cycle-regulated genes.   Ribosome profiling levels were temporally regulated for ten proteins encoding asymmetrically localized multi-protein assemblies that specify cell fate upon cell division, with five ORFs being regulated with a >2 fold contribution from the translation efficiency.  Individual ORFs within 198 operons undergo different cell cycle patterns of translation efficiency, allowing decoupling of the expression of these co-transcribed units.  This work reveals that, in addition to transcriptional control, there is prevalent translational control of cell cycle-regulated genes, providing a framework for a multi-level program of cell cycle control that generates daughter cells of different fates.

overall_design: Ribosome profiling and RNA-seq data were collected in sychronized Caulobacter crescentus NA1000 cells grown in M2G to measure changes in mRNA levels and translation levels during the asymmetric cell division cycle.

first: Gene-Wei

first: Weissman

last: Jonathan

first: Shapiro

last: Lucy


title: Loss of Ezh2 cooperates with Jak2V617F in the development of myelofibrosis in a mouse model of myeloproliferative neoplasm

city: Syracuse

first: Golam

last: Mohi

address: 766 Irving Avenue

department: Pharmacology

institute: SUNY Upstate Medical University


title: H3K27me3 ChIP-sequencing on LSK (Lin-Sca-1+c-kit+) cells isolated from control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- mice

summary: Inactivating EZH2 mutations have been associated with myelofibrosis (MF). Moreover, EZH2 mutations co-exist with the JAK2V617F mutation in a significant cases of MF. To determine the effects of concomitant loss of EZH2 and JAK2V617F mutation in hematopoiesis, we generated Ezh2-deficient Jak2V617F-expressing mice. To identify the Ezh2 target genes that are regulated by H3K27me3 in MF, we performed H3K27me3 ChIP-sequencing in sorted LSK cells from control, MxCre;Jak2VF/+ and MxCre;Jak2VF/+ EZH2-/- mice.

overall_design: 1500μg pI-pC was administrated to control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- at 4 weeks after birth in five times (300μg each time). Bone marrow cells were harvested from the mice at 12 weeks after pI-pC injections.ChIP-seq experiments were performed for LSK cells sorted from BM cells.

first: Yue

last: Yang


title: Effect of sphingosine kinase 1 deletion on HER/neu-induced mammary tumor development

city: Honolulu

first: Charles

last: Rosser

state: HI

address: 701 Ilalo Street

department: Clinical and Translational Research Program

institute: University of Hawaii Cancer Center

summary: Analysis of gene expression of mouse mammary tumors with different SphK1 expressions. The hypothesis tested in this study is that SphK1 deletion in mice influence the cancer promoting/inhibiting genes.

overall_design:
MMTV-neu Tg and SphK1 KO mice wre intercrossed and tumors from MMTV-neu Tg mice with homozygous KO, heterozygous KO and wild-type SphK1 were analyzed.
Please note that WT are SphK1 +/+  from the intercross and control MMTV-neu single Tg mice (SphK1+/+).

last: Rossr

first: Yoshiko

last: Shimizu


title: Analysis of gene-expression in normal, unmanipulated naïve (CD44lo/CD49dlo; CD5lo/CD5hi) and Virtual memory (CD44hi/CD49dlo) T cells

city: Aurora

first: Ross

middle: M.

last: Kedl

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: Splenocytes from lymphoreplete, unmanipulated mice were analyzed for basal mRNA levels. We hypothesized, based on previous data from our lab and others, that many cytokine/inflammatory response genes would show an increase from naïve CD5lo<CD5hi<Virtual memory.

overall_design: mRNA was analyzed from mouse splenocytes separated into naïve CD5lo, naïve CD5hi, and virtual memory cells. Mice were lymphoreplete and unmanipulated.

first: Jason

middle: T

last: White

first: Thomas

last: Danhorn