title: Transcriptome profiling of Drosophila intestinal cells

city: Utrecht

first: Devanjali

last: Dutta

state: Netherlands

address: Uppsalalaan 8

institute: Hubrecht Institute

summary:
Purpose: We isolated Drosophila midgut cells : Delta+ intestinal stem cells (ISCs), Su(H)+enteroblasts (EBs), Esg+ cells (ISC+EB), Myo1A+Enterocytes (ECs), Pros+Enteroendocrine cells (EEs) and How+Visceral muscle cells (VM) from whole midguts to identify stem cell specific genes and study cell type specificities of midgut cells.
We also isolated all the cell types from the 5 major regions (R1-R5) of the Drosophila midgut to study differences in cells in different regions.
Methods: 3-7 day old female flies were dissected. Flies with GFP/YFP marking different cell types  (using the GAL4-UAS system) were used to separate cells of the midgut.The midguts were dissociated with Elastase and FACS sorted using FACS AriaIII. RNA was extracted, amplified and sequenced. Whole midgut samples were sequenced on Illumina GAIIX and regional cell populations were sequenced on HiSeq2000.
Methods:Raw fastqc reads were mapped to the Drosophila genome (Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa) using Tophat 2.0.9 at default (using boost_1_54_0, bowtie2-2.1.0, samtools-0.1.19).
Methods: For differential expression analysis, DESeq (p-value adjustment 0.05 by method Benjamini-Hochberg) was used. The reads were normalized also to Reads per kilobase of transcript per million mapped reads (RPKM).
Results: More than 50% of the genome is expressed in the adult midgut (FlyAtlas- Chintapalli et al., 2007), of these genes about 50% (2457) were differentially expressed (DE) between all 4 cell types (ISCs, EBs, ECs and EEs) atleast 2 folds with 95% confidence
Results: 159 genes that were specifically enriched in ISCs, 509 genes were specifically repressed in ISCs
Conclusions: Our study represents the first detailed analysis of Drosophila intestinal cell transcriptomes, with biologic replicates, generated by RNA-seq technology.Our data facilitates comparative investigations of expression profiles of cells and reveals novel stem cell genes. Further region specific profiling adds precision to the analysis of variances in the midgut regions. We identify transcriptional regulators and regional transcription factors which modulate the midgut physiology. The dataset will be a great resource for hypothesis generation, tool building and fine tuned studies on the Drosophila midgut.

overall_design: mRNA profiles of Drosophila intestinal cells from whole midguts and midgut regions were generated by Deep Sequencing. Whole midgut profiles were generated in triplicates (Illumina GAIIx, 72 bp read length) and regional cell type profiles were genrated in duplicates (HiSeq 2000, 50bp read length).

first: Bruce

middle: A

last: Edgar

first: Nicolas

last: Buchon


title: Progesterone receptor directs a distinct estrogen receptor-alpha chromatin binding profile in breast cancer to elicit good clinical outcome

status: Public on May 22 2015

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ChIP-seq of ERa and PR in two ER+ breast cancer cell lines treated with and without estrogen and with and without progestins

summary: Exploring effect of estrogen and progesterone/progestin treatment on ER and PR binding.

overall_design: Two cell lines, four conditions (Vehicle, E2, Progesterone, E2+Progesterone), two factors (ERa, PR), all with three replicates.

first: Hisham

last: Mohammed

first: Rory

last: Stark


title: The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [RNA-Seq]

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

summary: Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts.

overall_design: RNA sequencing of WT and mutant S.pombe strains, processed data is normalized to median non-intron containing gene-expression, no replicates

first: Yang

last: Zhou

first: Jianguo

last: Zhu

first: Géza

last: Schermann

first: Corina

last: Ohle

first: Katja

last: Bendrin

first: Rie

last: Sugioka-Sugiyama

first: Tomoyasu

last: Sugiyama

first: Tamás


title: Leo1 is a Global Regulator of Heterochromatin Cis-spreading

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: Domains of heterochromatin play important roles in the maintenance and regulation of eukaryotic genomes. However, the repressive nature of heterochromatin combined with its propensity to self-propagate necessitates the existence of robust mechanisms that limit heterochromatin spreading and thereby avoid silencing of expressed genes. A number of specific sequence elements have been found to serve as barriers to heterochromatin spreading; however, the mechanisms by which spreading is curtailed are generally not well understood. Here we uncover a role for PAF complex component Leo1 in regulating heterochromatin cis-spreading. A genetic screen revealed that loss of Leo1 results in spreading of heterochromatin across a centromeric (IRC) boundary element in fission yeast. Similar heterochromatin spreading was seen upon deletion of other components of the PAF complex, but not other factors involved in transcription-coupled chromatin modification, indicating a specific role for the PAF complex in heterochromatin regulation. Loss of Leo1 is associated with reduced levels of H4K16 acetylation at the boundary, while tethering of the H4K16 acetyltransferase Mst1 to boundary chromatin suppresses heterochromatin spreading in leo1Δ cells, suggesting that Leo1 antagonises heterochromatin spreading by facilitating H4K16 acetylation. Interestingly, Leo1 also regulates heterochromatin spreading independently of boundaries, and loss of Leo1 causes redistribution of heterochromatin, in particular resulting in substantial expansion of telomeric heterochromatin domains. The PAF complex is known to be an important regulator of transcription-related chromatin modifications; our findings reveal a previously undescribed role for this complex in global regulation of heterochromatin spreading in cis.

overall_design: 8 samples: input (whole cell extract) and IP from H3K9me2 ChIP in wild-type and leo1Δ cells, in duplicate

first: Laure

last: Verrier

first: Elizabeth

middle: H

last: Bayne


title: Small RNA profiling of the allelic series of miR-17~92 mutant embryos

city: New York

first: Doron

last: Betel

state: NY

address: 1305 York Avenue (Box 140)

department: Medicine

country: USA

institute: Weill Cornell Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: The study sought to determine whether deletion of individual seed families within the miR-17~92 cluster affected the expression of the remaining microRNAs of the cluster.

overall_design: There were 8 samples analyzed. The reference is the wild-type embryo.

first: Carla

middle: P

last: Concepcion

first: Yoon-Chi

last: Han

first: Joana

last: Vidigal

first: Andrea

last: Ventura


title: ChIP-seq of ER, PR, p300 in two ER+ breast cancer cell lines treated with estrogen and with and without progestins

first: Chandra

last: Chilamakuri

summary: Exploring effect of progesterone/progestin treatment on ER and PR binding.

overall_design: Two cell lines, three conditions (Full Media with E2, E2+ Progesterone, Full Media + R5020 Progestin), three factors (ER, PR, p300), all with three replicates, each with a matched Input control.

first: Hisham

last: Mohammed

first: Rory

last: Stark


title: Pachytene piRNAs target endogenous mRNAs for silencing during meiosis

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

country: China

institute: Shenzhen Bay Laboratory

summary: During embryonic germ cell development in mice, transposon-enriched, piwi-interacting RNAs (piRNAs) guide MILI and MIWI2 to direct silencing of potentially active mobile element families. In contrast, we know much less about the function of the highly abundant and extremely diverse class of piRNAs, which partner with MIWI and MILI during meiosis. Both MIWI and its catalytic activity are required for successful spermatogenesis, strongly indicating that piRNA-guided cleavage is critical for germ cell development. To gain an understanding of meiotic piRNA targets, we augmented the mouse piRNA repertoire by introducing an entire human meiotic piRNA cluster. This triggered a spermatogenesis defect, presumably by inappropriately targeting the piRNA machinery to mouse RNAs essential for germ cell development. Through an analysis of such de novo targets, we derived a signature for pachytene piRNA target recognition. This enabled identification of both transposable elements and meiotically expressed protein coding genes as targets of native piRNAs. Cleavage of genic targets begins at the pachytene stage when meiotic piRNAs first appear. As such, target mRNA levels attenuate starting from the pachytene stage and are further repressed throughout meiosis. Target mRNA-piRNA pairs also show evidence of an ongoing cleavage-dependent amplification cycle, which is not normally a strong feature of meiotic piRNAs. Our data support the idea that meiotic piRNA populations must be strongly selected to enable successful spermatogenesis, both driving the response away from essential genes and directing the pathway toward mRNA targets that are regulated by small RNAs in meiotic cells.

overall_design: 48 samples

first: W

middle: S

last: Sho Goh

first: Oliver

last: Tam

first: Gregory

middle: J

last: Hannon


title: Transcriptome comparison of pancreatic islets of Urocortin3 null islets and wild type controls.

city: Davis

first: Mark

middle: O.

last: Huising

state: CA

address: One Shields Avenue

department: Neurobiology, Physiology and Behavior

institute: University of California, Davis

summary: The peptide hormone Urocortin3 (Ucn3) is abundantly expressed by mature beta cells, yet its physiological role is unknown. Transcriptome data from Ucn3 null islets compared to wild type controls reveals selective depletion for delta cell markers and supports a role for Ucn3 as a trigger for somatostatin-mediated negative feedback.

overall_design: Isolated islets from Ucn3 knockout animals compared to wild type littermate controls. Islets from three indivual males were used for each genotype, lysed in Trizol for RNA isolation and library construction.

middle: O


title: New non-coding lytic transcripts derived from the Epstein Barr virus latency origin of replication oriP are hyper-edited, bind the paraspeckle protein, NONO/p54nrb, and support lytic viral transcription

status: Public on May 21 2015

city: New Orleans

first: Erik

middle: K

last: Flemington

state: Louisiana

address: 1430 Tulane Avenue, SL-79

department: Tulane Cancer Center/Pathology and Laboratory Medicine

institute: Tulane University

summary: We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long non-coding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward transcripts (oriPtRs) are largely localized in the nucleus. While the oriPtLs are most likely non-coding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5’UTRs may partially serve non-coding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics and their expression is inhibited by phosphonoacetic acid. RNA-seq analysis showed that oriPtLs and oriPtRs exhibited extensive “hyper-editing” at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The double-stranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts suggesting that oriPts interacts with the paraspeckle-based innate anti-viral immune pathway. Knock-down and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade.

overall_design: RNA-seq analysis for oriPtL knockdown and overexpression experiments

first: Subing

last: Cao

first: Walter

last: Moss

first: Tina

last: O’Grady

first: Monica

last: Concha

first: Michael

last: Strong

first: Xia

last: Wang

first: Yi

last: Yu

first: Melody

last: Baddoo

first: Kun

last: Zhang

first: Claire

last: Fewell

first: Zhen

last: Lin

first: Yan

last: Dong


title: DALIA-1 Whole Blood Longitudinal Gene Expression

city: Dallas

first: Jason

last: Skinner

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: The DALIA-1 trial was designed to evaluate the safety and immunogenicity of a DC-based vaccine generated by culturing blood monocytes with GM-CSF and IFN-a. DCs were pulsed for 24 hrs with the ANRS LIPO5 peptide pool and activated for the last 6 hrs with LPS. In total, 19 asymptomatic HAART-treated patients were included in the study. Microarray samples were collected in both the treatment phase and follow-up phase of the study.

overall_design:
Whole blood RNA samples were collected at two time points prior to the first vaccination (Weeks -8 and -4) and served as a pre-vaccination baseline. Additional whole blood RNA samples were collected at the time of vaccination (Weeks 0, 4, 8, 12) and post-vaccination at weeks 16, 22, and 24. At week 24, an analytical treatment interruption (ATI) was initiated during which HAART was suspended. During this post-ATI follow-up phase, whole blood RNA samples were collected at weeks 25, 26, 27, 28, 32, 36, 40, , 44, and 48). Additionally, at weeks -4, 16, and 48 patients were apheresed.  18 samples are constituents of both the pre-ATI and post-ATI datasets, which were normalized separately.

The normalised data underwent the following preprocessing:
First a normal-exponential convolution model was applied (Xie et al, Bioinformatics, 2009; Shi et al, Nucleid Acids Research, 2010) to correct for the background noise.  An offset of 16 (default value) was then added to the data (to improve precision and avoid a compression of the fold changes) before a quantile-quantile normalization was performed. Finally, data were log2 transformed. Only probes whose pval-detection (provided by Illumina Genome-Studio software) was below 0.01 in at least one sample were kept further on. At last, the ComBat method (Johnson et al, Biostatistics, 2007) was applied to those data in order to correct for batch effects (namely a small hybridization chamber effect, that was identified through Principal Variance Component Analysis - Li et al, chap. 12, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Wiley, 2009).

first: Boris

last: Hejblum

first: Rodolphe

last: Thiébaut


title: CDK7-dependent Transcriptional Addiction in Basal-like Breast Cancer

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research


title: ChIP-seq of ER and PR in xenografted MCF7 tumors grown in mice [xenograft]

first: Chandra

last: Chilamakuri

summary: Exploring effect of estrogen and/or progesterone treatment on xenografts tumors in vivo

overall_design: MCF7 cells implanted in mice (two each), subjected to different treatment. Six replicates of each condition we ChIPed.

first: Hisham

last: Mohammed

first: Rory

last: Stark


title: Transcriptome analysis of Liangshan pig muscle development at the growth curve inflection point and asymptotic stages using digital gene expression profiling

status: Public on May 25 2015

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds.

overall_design: The aim of our study is to identify different expression genes that are linked to phenotypic differentiation (eg: grow rate, meat quality) between inflection point and asymptote stages.

first: Jia

last: Luo

first: Jingjing

last: Du

first: Chendong

last: Liu

first: Xiaoqian

last: Wu

first: Qiang

last: Pu

first: Yuhua

last: Fu

first: Qianzi

last: Tang

first: Yuanrui

first: Runlin

last: Yang

first: Xuewei

last: Li

first: Guoqing

first: Yanzhi

last: Jiang

first: Mingzhou

first: Shunhua

first: Li

last: Zhu


title: Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [CAGE-seq]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate.
Investiagtion of promoters usage changes during ESCs neural induction

overall_design: ESCs and NESCs promoter usage profiling by CAGE-seq

first: Valentina

last: Poletti

first: Alessia

middle: D

last: Carri

first: Guidantonio

middle: M

last: Tagliazucchi

first: Luca

last: Petiti

first: Emilia

last: Mazza

first: Clelia

last: Peano

first: Gianluca

last: De Bellis

first: Annarita

last: Miccio

first: Elena

last: Cattaneo

first: Fulvio

last: Mavilio


title: Single-cell transcriptome analyses reveal signals to activate dormant neural stem cells.

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: Through single cell transcriptome analysis, we uncovered molecular signatures of CD133+/GFAP- ependymal (E) cells, CD133+/GFAP+ neural stem (B) cells, Dlx2+ neuroblasts (A cells), and Sox10+ oligodendrocyte progenitors (O cells) in the adult mouse forebrain neurogenic zone. prominent hub genes of the gene network unique to ependymal CD133+/GFAP- quiescent cells are enriched for receptors of angiogenic factors and immune-responsive genes. Administration of VEGF activated CD133+ ependymal stem cells lining not only the lateral, but also the 4th ventricles, and together with bFGF, elicited subsequent neural lineage differentiation and migration.

overall_design: Examination of 28 single cells and 4 populations of 10 cells from adult mouse forebrain neurogenic zone.

first: Yuping

last: Luo

first: Yi

middle: E

last: Sun

first: Siguang


title: Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [ChIP-seq]

summary:
Genome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate.
Genome-wide mapping of H3K4me1 and H3K4me3 in NESCs

overall_design: ChIP-seq for H3K4me1 and H3K4me3 in NESCs


title: 8p Loss of Heterozygosity triggers metastasis and drug resistance

city: Leuven

first: Anna

last: Sablina

state: Vlaams Brabant

address: O&N4, Herestraat 49, bus 602

department: Center for the Biology of Disease

country: Belgium

institute: VIB/KU Leuven

summary: Chromosome arm deletions are frequently observed in human cancers. Such large-scale aberrations may trigger phenotypes distinct from those that arise by loss of single genes. Using TALEN-based genomic engineering, we generated cell models with targeted 8p loss-of-heterozygosity (LOH) that mimics an 8p deletion commonly found in breast cancer patients. 8p LOH triggered up-regulation of the mevalonate pathway. The alterations in lipid metabolism led to increased metastatic potential and drug resistance of 8p-deleted cells that are in agreement with poorer survival rates of breast cancer patients harbouting 8p LOH. Our findings also suggest novel therapeutic strategies for treatment of 8p LOH tumors.

overall_design: RNASeq Analysis of two Wt 8p Cell clones vs two 8p LOH cell clones generated via TALEN Approach

first: YanYan

last: Cai

first: Jonathan

last: Crowther

first: Tibor

last: Pastor

first: Layka

last: Abbasi Asbagh

first: Iria

last: Vazquez

first: Ali

last: Talebi

first: Fabrizio

last: Renzi

first: Johan

last: Swinnen


title: The impact of pregnancy experience on uterine gene expression and decidualization

status: Public on May 20 2015

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: To capture the global gene changes associated with pregnancy experience, uterine tissues were collected on day 8 of pregnancy from mice during the first pregnancy and second pregnancy, respectively. Transcriptomes were determined by RNA-seq.

overall_design: Identifying global gene changes associated with pregnancy experience


title: Genome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells

first: Silvio

last: Bicciato

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

overall_design: Refer to individual Series


title: Skin transcriptome profiles associated with skin color in chickens

city: yangling

first: jianqin

last: zhang

state: shaanxi

address: xinong street No. 22

department: college of animal science and technology

institute: Northwest A&F university

summary: This work was to study the transcriptome profiles in the skin of chickens with black versus white skin using high-throughput RNA deep-sequencing technology, to investigate the different expression profiles of the genes involved in skin pigmentation, then look for the main differences between black and white skin colors in Lueyang chickens.

overall_design: 16-week-old white and black female Lueyang chickens (5 birds per color) were selected for the sample collection. A piece of skin (8 mm in diameter) from the left back was collected . Total RNA was extracted from the sample using Trizol reagent . Three RNA samples from either the black or white skin samples were pooled following mRNA isolation. The sequencing of the library was performed using an Illumina HiSeq 2000 (LianChuan Sciences, Hangzhou, China). According the result of sequencing, some colored gene expressions were validated using Real time quantitative polymerase chain reaction (qPCR).

first: Jianqin


title: Gene target specificity of the Super Elongation Complex (SEC) family: How HIV-1 Tat employs selected SEC members to activate viral transcription

city: Berkeley

first: Qiang

last: Zhou

address: 575 LKS, UC Berkeley

department: MCB

institute: UC Berkeley

summary: The AF4/FMR2 proteins AFF1 and AFF4 act as a scaffold to assemble the Super Elongation Complex (SEC) that strongly activates transcriptional elongation of HIV-1 and cellular genes. Although they can dimerize, it is unclear whether the dimers exist and function within a SEC in vivo. Furthermore, it is unknown whether AFF1 and AFF4 function similarly in mediating SEC-dependent activation of diverse genes. Providing answers to these questions, our current study shows that AFF1 and AFF4 reside in separate SECs that display largely distinct gene target specificities. While the AFF1-SEC is more potent in supporting HIV-1 transactivation by the viral Tat protein, the AFF4-SEC is more important for HSP70 induction upon heat shock. The functional difference between AFF1 and AFF4 in Tat-transactivation has been traced to a single amino acid variation between the two proteins, which causes them to enhance the affinity of Tat for P-TEFb, a key SEC component, with different efficiency. Finally, genome-wide analysis confirms that the genes regulated by AFF1- and AFF4-SEC are largely non-overlapping and perform distinct functions. Thus, the SEC represents a family of related complexes that exist to increase the regulatory diversity and gene control options during transactivation of diverse cellular and viral genes.

overall_design: RNA-seq in HeLa cells of wild-type and after RNAi of AFF1 or AFF4.

first: Huasong

last: Lu

first: Wei


title: CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

city: Salisbury Cove

first: Dustin

middle: Lynn

last: Updike

state: ME

address: 159 Old Bar Harbor Rd.

institute: Mount Desert Island Biological Laboratory

summary: P granules in C. elegans are required for fertility and function to maintain germ cell identity and pluripotency.  Sterility in the absence of P granules is often accompanied by the mis-expression of soma-specific proteins and the initiation of somatic differentiation in germ cells.  To investigate whether this is caused by the accumulation of somatic transcripts, we performed mRNA-seq on dissected germlines with and without P granules.  Strikingly, we found that somatic transcripts do not increase in the young adult germline when P granules are impaired.  Instead, we found that impairing P granules causes sperm-specific mRNAs to become highly overexpressed.  This includes the accumulation of major sperm protein (MSP) transcripts in germ cells, a phenotype that is suppressed by feminization of the germline.  A core component of P granules, the endo-siRNA-binding Argonaute protein CSR-1, has recently been ascribed with the ability to license transcripts for germline expression.  However, impairing CSR-1 has very little effect on the accumulation of its mRNA targets.  Instead, we found that CSR-1 functions with P granules to prevent MSP and sperm-specific mRNAs from being transcribed in the hermaphrodite germline.  These findings suggest that P granules protect germline integrity through two different mechanisms, by 1) preventing the inappropriate expression of somatic proteins at the level of translational regulation, and by 2) functioning with CSR-1 to limit the domain of sperm-specific expression at the level of transcription.

overall_design: Four biological replicates of each condition (empty vector control, P granule RNAi, and CSR-1 RNAi germlines) were collected for total RNA.

first: Anne

middle: C

last: Campbell

middle: L


title: Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

city: Boston

first: Allon

last: Klein

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

summary: Recently, RNA sequencing has achieved single cell resolution, but what is limiting is an effective way to routinely isolate and process large numbers of individual cells for in-depth sequencing, and to do so quantitatively. We have developed a droplet-microfluidic approach for parallel barcoding thousands of individual cells for subsequent RNA profiling by next-generation sequencing. This high-throughput method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. Using this technique, we analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after LIF withdrawal. The reproducibility and low noise of this high-throughput single cell data allowed us to deconstruct cell populations and infer gene expression relationships.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A total of 8 single cell data sets are submitted: 3 for mouse embryonic stem (ES) cells (1 biological replicate, 2 technical replicates); 3 samples following LIF withdrawal (days 2,4, 7); one pure RNA data set (from human lymphoblast K562 cells); and one sample of single K562 cells.

first: Linas

last: Mazutis

first: Ilke

last: Akartuna

first: Naren

last: Tallapragada

first: Adrian

last: Veres

first: Victor

last: Li

first: Leonid

last: Peshkin

first: David

last: Weitz

first: Marc

middle: W

last: Kirschner


title: Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein

city: Haifa

first: Naftalie

last: Senderovich

state: International

address: Technion city, Faculty of biology

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

summary: How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment, the nature of which is far from being clear. In the case of the lymphatic system, venous endothelial cells are thought to give rise to lymphatic vessels, through a process of trans-differentiation. Upon expression of a set of transcription factors, venous cells acquire a lymphatic fate, and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells (LECs) do arise in the Cardinal Vein (CV), they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic-specific transgenic zebrafish, in combination with endothelial photoconvertible reporters, and long-term live imaging, we demonstrate that these multipotent angioblasts can generate not only lymphatic, but also arterious, and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b, which acts as a lymphatic inductive signal, promoting the angioblast-to-lymphatic transition. Moreover, Wnt5b induced lymphatic specification in human embryonic stem cells- derived vascular progenitors, suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation, whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium, and provide the first characterization of their inductive niche. More broadly, our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations, analogous to the hematopoietic niche in the aortic floor.

overall_design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tg(fli1:gal4;uasKaede) embryos at 24 hpf, 6 embryos per group were used for FACS isolation of Kaede photconverted (red) ECs.

first: Julian

last: Nicenboim

first: Karina

last: Yaniv


title: MEIS1-HLF axis regulates oxidative metabolism and is essential for MLL-fusion gene leukemia

city: Cincinnati

first: Ashish

last: Kumar

state: Ohio

address: 3333 Burnet Avenue. Cincinnati. Ohio 45229

department: Bone Marrow Transplanation

summary: The pathogenesis of MLL-fusion gene leukemias has been linked to upregulated expression of HOX genes and of the HOX-cofactor Meis1.The functions of the HOX/MEIS1 complex in leukemia however remain unclear. Here, we used inducible MEIS1-knockout mice coupled with MLL-AF9 knockin mice to decipher the role of MEIS1 in leukemia. We found that MEIS1 was critically required for established leukemia. Further, MEIS1 loss led to increased oxygen flux and apoptosis, while hypoxia reversed these effects. Finally, we identify HLF as a downstream mediator of MEIS1 in leukemia. Overexpression of HLF prevents oxygen flux and rescues the leukemia phenotype in MEIS1-deficient cells. Thus, the oncogenic effects of MEIS1 are at least partly mediated by an HLF-driven hypoxic state.

overall_design: Mouse bone marrow MLL-AF9 knockin cells of conditional Meis1f/f or control genotypes were treated with vehicle or 1000 nM of 4-hydroxy tamoxifen for 24 hours in IMDM with 10% FBA and 10 ng/ml of murine GM-CSF, IL-3, IL-6, SCF.  RNA was isolated from treated cells and submitted to gene expression and sequencing core of Cincinnati  Children's Hospital & Medical Center. A total of four samples were included, and two groups were assisgned. Comparison comprises mRNA expression profile of vehicle and 4-OHT treatment in control cells versus Meis1-deleted cells.

first: Jayeeta

last: Roychoudhury


title: Purification and transcriptomic analysis of mouse fetal Leydig cells reveals candidate genes for disorders of sex development

city: Melbourne

first: Katrina

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

institute: MCRI

summary: To examine the transcriptome of early testicular somatic cells during gonadogenesis at 12.5dpc RNA sequencing (RNA-Seq) was performed on murine primary testicular cell lineages isolated from the Sf1-eGFP line by FACS. The three main somatic cell lineages of the testis were isolated: the Sertoli cells which direct male development; the fetal Leydig cells (FLCs) that produce steroid hormones and virilise the XY individual and a heterogenous population of interstitial cells, some of which give rise to the adult Leydig cells (ALCs). This dataset provides a platform for exploring the biology of FLCs and understanding the role of these cells in testicular development and masculinization of the embryo, and a basis for targeted studies designed to identify causes of idiopathic XY DSD.

overall_design: RNA-Seq of 3 enriched cell populations from 12.5dpc mouse gonad (Sertoli cells, Leydig cells and Interstitial cells isolated by FACS-sorting) on an Illumina HiSeq 1500, in triplicate.

first: Kathryn

last: McClelland

first: Christian

last: Larney

first: Peter

last: Koopman

first: Josephine

last: Bowles

first: Alicia

last: Oshlack


title: The carbonic anhydrase inhibitor ethoxzolamide inhibits the Mycobacterium tuberculosis PhoPR regulon and Esx-1 secretion and attenuates virulence

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: The purpose of this study was to examine how ethoxzolamide modulates gene M. tuberculosis gene expression at acidic pH. We observed that ethoxzolamide downregulates genes of the PhoPR regulon.

overall_design: Mtb strain CDC1551 was grown at 37C in T-25 vented, standing tissue culture flasks in 8 ml of buffered 7H9 medium seeded an initial OD of 0.2. Three conditions were examined with two biological replicates: 1) DMSO treated, pH 7.0, 2) DMSO treated, pH 5.7, 3) 40 µM ethoxzolamide treated, pH 5.7. The CDC1551(phoP::Tn) mutant was grown in a similar manner and treated with DMSO at pH 7.0 and 5.7. Following six days incubation, total bacterial RNA was extracted and analyzed as previously described.

first: Benjamin

last: Johnson

first: Christopher

last: Colvin

middle: B


title: RNA-seq transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

city: Houston

first: Horatiu

last: Voicu

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: The biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and epithelioid (E-) and rhabdoid (R-) components of rhabdoid RCC shared a similar transcriptomic signature, despite morphologic differences; by contrast, the transcriptome of sarcomatoid and rhabdoid RCC was sharply distinct from non-sarcomatoid RCC.

overall_design: Total RNA was processed for RNA-seq from the following patient samples:  7 sarcomatoid RCC (E- and S- pairs), 4 rhabdoid RCC (E- and R- pairs) and 15 non-sarcomatoid RCC.

first: Kanishka

last: Sircar


title: Genome-wide changes in DNase-hypersensitivity during osteoblastogenesis reveal differential usage of DNA motifs and define novel cis-regulatory regions that control gene expression during differentiation

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont


title: Allele-Specific Analysis of DNA Replication Origins in Mammalian Cells

status: Public on May 19 2015

city: Bronx

first: Eric

last: Bouhassira

address: 1300 Morris PArk Ave

department: Cell Biology

institute: Albert Einstein College Of Medicine

summary: Nascent strand were purified with the BrdU methods from culture human basophilic erythroblasts and sequenced.

overall_design: An allele-specific analysis of origin of replication efficiency was performed by taking advantage of the phased genome sequence of an individual

first: Boris

last: Bartholdy

first: Rituparna

last: Mukhopadhyay

first: Julien

last: Lajugie

first: Mirit

middle: I

last: Aladjem


title: De novo assembly and transcriptome analysis of Ocimum americanum var. pilosum under low temperature

first: Lan

last: Yang

address: 300 Fenglin Road

institute: Institute of Plant Physiol & Ecology, Chinese Academy of Sciences

summary: One-month-old Ocimum americanum var. pilosum plants were treated with 4 ºC for 12 hours. Total RNAs were extracted from these chilling-treated plant leaves and untreated ones. Two seperate replicates of total RNA samples are from different individuals. The genomic DNA residual in each sample was removed by DNase I digestion.

overall_design: Our goal is to get a more particlular knowledge of transcriptional regulation after chilling treatment in such a chilling-hypersensitive herb.

first: Zhaobo

last: Lang

first: Xiangqiang

last: Zhan


title: The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome

city: Canberra

first: Tamas

last: Fischer

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

institute: The Australian National University


title: A survey of human brain transcriptome diversity at the single cell level

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained from epileptic patients during temporal lobectomy for medically refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain.

overall_design: Examination of cell types in healthy human brain samples.

first: Spyros

last: Darmanis

first: Stephen

middle: R

last: Quake

first: Steven

middle: A

last: Sloan

first: Ben

last: Barres

first: Ye

last: Zhang

first: Christine

last: Caneda

first: Melanie

middle: G

last: Hayden Gephart

first: Lawrence

last: Shuer


title: Deep sequencing reveals cell-type specific patterns of single cell transcriptome variation

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

institute: University of Pennsylvania

summary: We present high quality deep read-depth single cell RNA sequencing for 91 cells from five mouse tissues and 18 cells from two rat tissues, along with 30 control samples of bulk RNA diluted to single-cell levels. We find that transcriptomes differ globally across tissues with regard to the number of genes expressed, the average expression patterns, and within cell-type variation patterns. We develop methods to filter genes for reliable quantification and to calibrate biological variation. All cell types include genes with high variability in expression, in a tissue-specific manner. We also find evidence that single cell variability of neuronal genes in mice is correlated with that in rats consistent with the hypothesis that levels of variation may be conserved.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: From an initial 143 cells we identified 107 high quality samples with deep genic coverage, including 13 brown adipocytes, 19 cardiomyocytes, 19 cortical pyramidal neurons and 18 hippocampal pyramidal neurons from embryonic mouse, 8 cortical pyramidal neurons and 8 hippocampal pyramidal neurons from embryonic rat, and 22 serotonergic neurons from adult mouse. While mouse data is collected from three strains of mice at different ages, each cell type dataset is internally consistent. There are no technical replicates of single-cell samples. We additionally prepared 30 control samples, amplifications of bulk total cardiomyocyte RNA diluted to single cell quantities.

first: Hannah

last: Dueck

first: Mugdha

last: Khaladkar

first: Tae

first: Jennifer

last: Spaethling

first: Chantal

last: Francis

first: Sangita

last: Suresh

last: Fisher

first: Patrick

last: Seale

first: Sheryl

last: Beck

last: Bartfai

first: Bernhard

last: Kuhn

first: Jim

last: Eberwine


title: Scalable Microfluidics for Single Cell RNA Printing and Sequencing

city: New York

first: Peter

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Single cell transcriptomics has emerged as a powerful approach to dissecting phenotypic heterogeneity in complex, unsynchronized cellular populations.  However, many important biological questions demand quantitative analysis of large numbers of individual cells. Hence, new tools are urgently needed for efficient, inexpensive, and parallel manipulation of RNA from individual cells. We report a simple microfluidic platform for trapping single cell lysates in sealed, picoliter microwells capable of “printing” RNA on glass or capturing RNA on polymer beads. To demonstrate the utility of our system for single cell transcriptomics, we developed a highly scalable technology for genome-wide, single cell RNA-Seq. The current implementation of our device is pipette-operated, profiles hundreds of individual cells in parallel with library preparation costs of ~$0.10-$0.20/cell, and includes five lanes for simultaneous experiments. We anticipate that this system will ultimately serve as a general platform for large-scale single cell transcriptomics, compatible with both imaging and sequencing readouts.!Series_type = Expression profiling by high throughput sequencing

overall_design: A microfluidic device that pairs sequence-barcoded mRNA capture beads with individual cells was used to barcode cDNA from individual cells which was then pre-amplified by in vitro transcription in a pool and converted into an Illumina RNA-Seq library. Libraries were generated from ~600 individual cells in parallel and extensive analysis was done on 396 cells from the U87 and MCF10a cell lines and from ~500 individual cells with extensive analysis on 247 cells from the U87 and WI-38 cell lines. Sequencing was done on the 3'-end of the transcript molecules.  The first read contains cell-identifying barcodes that were present on the capture bead and the second read contains a unique molecular identifier (UMI) barcode, a lane-identifying barcode, and then the sequence of the transcript.


title: Integrator complex regulates NELF-mediated RNA Polymerase II pause/release and processivity at coding genes [RNA-seq]

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

summary: RNAPII pausing/termination shortly after initiation is a hallmark of gene regulation. However, the molecular mechanisms involved are still to be uncovered. Here, we show that NELF interacts with Integrator complex subunits (INTScom) forming a stable complex with RNPII and Spt5. The interaction between NELF and INTScom subunits is RNA and DNA independent. Using both HIV-1 promoter and genome wide analyses, we demonstrate that Integrator subunits specifically control NELF-mediated RNAPII pause/release at coding genes. The strength of RNAPII pausing is determined by the nature of the NELF-associated complex. Interestingly, in addition to controlling RNAPII pause release INTS11 catalytic subunit of the INTScom is required for the synthesis of full length mRNA. Finally, INTScom-target genes are enriched in HIV-1 TAR/ NELF-binding element and in a 3’box sequence required for snRNA biogenesis. Revealing these unexpected functions of INTScom in regulating RNAPII pausing/release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle.

overall_design: Genome-wide expression in HeLa cells in the absence of Integrator 11, or NELF or mock (control) depleted by strand-specific RNASeq (Illumina)

first: Bernd

last: Stadelmayer

first: Gaël

last: Micas

first: Pascal

last: Martin

first: Dany

last: Severac

first: Stéphanie

last: Rialle

first: Hugues

last: Parrinello

first: Monsef

last: Benkirane


title: Integrator complex regulates NELF-mediated RNA Polymerase II pause/release and processivity at coding genes.


title: Role of cervicovaginal microbiota in genital inflammation

city: Cambridge

first: Melis

last: Anahtar

address: 400 Technology Sq

department: Ragon Institute of MGH, MIT, Harvard

institute: Massachusetts General Hospital

summary: We performed gene expression analysis using the SCRB-Seq method from cervical and peripheral blood antigen presenting cells that were collected from women with different cervicovaginal bacterial community types.

overall_design: Cervical and peripheral blood antigen presenting cells were FACS sorted using the gating strategy: FSC vs. SSC  -> Singlets -> Live CD45+ -> HLA-DR+ -> CD11c+ or CD14+. The genital bacterial microbiomes were characterized in the same women and categorized into Lactobacillus dominance, Gardnerella dominance, or Prevotella dominance.

middle: N

first: Magali

last: Soumillon


title: An ancient protein-DNA interaction underlying metazoan sex determination

status: Public on May 18 2015

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

summary: Sexual reproduction is nearly universal among multicellular animals, but sex can be determined by cues including sex chromosomes, temperature, social status, and photoperiod. DMRT transcription factors are key regulators of sex in animals that use diverse sex-determining strategies. These proteins are related to the sexual regulators Doublesex (Dsx) and Male abnormal-3 (MAB-3) of insects and nematodes, respectively.  DMRT proteins share the DM DNA binding domain, comprised of a unique intertwined double zinc-binding module flanked by a C-terminal recognition helix that binds to a pseudopalindromic target DNA. Despite the central role of DMRT proteins in metazoan sexual development, how they recognize target DNA sequences is poorly understood. Here we find that DMRT proteins employ multiple DNA binding modes due to surprising versatility in how specific base contacts are made. Human DMRT1 can bind as a dimer, trimer or tetramer, in each case using paired antiparallel recognition helices that together insert into a widened DNA major groove to make base-specific contacts. Insertion of two helices in a single major groove is, to our knowledge, a DNA binding interaction unique to DMRT proteins. High resolution in vivo DNA binding analysis (ChIP-Exo) indicates that multiple DNA binding modes also are used in the mouse testis. Finally, we show that mutations affecting amino acid residues crucial for DNA recognition are associated with sex reversal in flies and also, for the first time, with male-to-female sex reversal in humans. Our results illuminate an ancient molecular interaction that underlies much of metazoan sexual development.

overall_design: ChIP-Seq (2 samples) and Chip-Exo (1 sample) in 8 week mouse Testis, ChIP-Seq in adult Human Testis (1 sample).

first: Vivian

middle: J

last: Bardwell


title: Different molecular pathways along with pathogenesis of three subtypes of Leiomyosarcoma

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

summary: Leiomyosarcoma (LMS) is a malignant neoplasm of smooth muscle and is an aggressive soft tissue tumor, have complex genetic abnormalities and could be defined as three molecular subtypes. Since that the molecular heterogeneity of LMS, the pathogenesis analysis per subtype will be highly necessary and helpful to understand the etiology of this more common sarcoma.

overall_design: Within this study, we collected four Myometrium, three Leiomyoma, three LMS cell lines and 99 LMSs (GSE45510), performed the system-wide gene expression profiling by 3'end RNA Sequencing, and found that there are significant different molecular pathways along the pathogenesis for those three molecular subtypes.

first: Shirley

middle: X

last: Zhu

first: Sushama

last: Varma

first: Robert

last: West

first: Matt

last: van de Rijn


title: Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Polyploidy provides evolutionary and morphological novelties in many plants and some animals. However, the role of genome dosage and composition in gene expression changes remains poorly understood. Here, we generated a series of resynthesized Arabidopsis tetraploids that contain 0-4 copies of Arabidopsis thaliana and Arabidopsis arenosa genomes and investigated ploidy and hybridity effects on gene expression. Allelic expression can be defined as dosage dependent (expression levels correlate with genome dosages) or otherwise as dosage independent. Here, we show that many dosage-dependent genes contribute to cell cycle, photosynthesis, and metabolism, whereas dosage-independent genes are enriched in biotic and abiotic stress responses. Interestingly, dosage-dependent genes tend to be preserved in ancient biochemical pathways present in both plant and nonplant species, whereas many dosage-independent genes belong to plant-specific pathways. This is confirmed by an independent analysis using Arabidopsis phylostratigraphic map. For A. thaliana loci, the dosage-dependent alleles are devoid of TEs and tend to correlate with H3K9ac, H3K4me3, and CG methylation, whereas the majority of dosage-independent alleles are enriched with TEs and correspond to H3K27me1, H3K27me3, and CHG (H = A, T, or C) methylation. Furthermore, there is a parent-of-origin effect on nonadditively expressed genes in the reciprocal allotetraploids especially when A. arenosa is used as the pollen donor, leading to metabolic and morphological changes. Thus, ploidy, epigenetic modifications, and cytoplasmic-nuclear interactions shape gene expression diversity in polyploids. Dosage-dependent expression can maintain growth and developmental stability, whereas dosage-independent expression can facilitate functional divergence between homeologs (subfunctionalization and/or neofunctionalization) during polyploid evolution.

sample_organism: Arabidopsis thaliana x Arabidopsis arenosa

overall_design: Examination of gene expression in 5 tetraploid Arabidopsis using mRNA-seq

first: Xiaoli

last: Shi

first: Changqing

last: Zhang

first: Dae

middle: K

last: Ko

first: Jeffrey

middle: Z


title: BRACHYURY orchestrates distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: The transcription factor BRACHYURY (T, BRA) is one of the first markers of gastrulation and lineage specification in mammals. Despite its wide use and importance in stem cell and developmental biology, its genomic targets are largely unknown. Here, we used differentiated human embryonic stem cells to study the role of BRA in Bmp4-induced mesoderm and Activin-induced endoderm progenitors by ChIP-seq. We show that BRA has distinct genome-wide binding landscapes in these two populations. Our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context-dependent.

overall_design: ChIP-seq of BRACHYURY (T, BRA) in two cell types: endoderm and mesoderm progenitors derived from human embryonic stem cells after 36 hours of growth in chemically-defined media (described in Bernardo et al., Cell Stem Cell, 2011, 9:144-155). Input DNA samples are included as a control.

first: Tiago

last: Faial


title: Integrator complex regulates NELF-mediated RNA Polymerase II pause/release and processivity at coding genes [ChIP-seq]

first: Olivier

last: Cuvier

overall_design:
Binding profiles of Integrator subunits in HeLa cells by ChIP-Seq (Illumina)
Please note that the MACS14*.tar.gz contains MACS output bed and xls files and the 'readme.txt' contains a detailed description of each file.

first: Bernd

last: Stadelmayer

first: Gaël

last: Micas

first: Pascal

last: Martin

first: Dany

last: Severac

first: Stéphanie

last: Rialle

first: Hugues

last: Parrinello

first: Monsef


title: Comparative transcriptomic analysis of self-organized, in vitro generated optic tissues

city: Chuo-ku

first: Munazah

last: Andrabi

state: Kobe

address: 2-2-3 Minatojima-minamimachi

country: Japan

institute: RIKEN:Center for Developmental Biology

summary: Embryonic stem (ES) cells have a remarkable capacity to self-organize complex, multi-layered optic cups in vitro via a culture technique called SFEBq. During both SFEBq and in vivo optic cup development, Rax (Rx) expressing neural retina epithelial (NRE) tissues utilize Fgf and Wnt/β-catenin signalling pathways to differentiate into neural retina (NR) and retinal-pigmented epithelial (RPE) tissues, respectively. How these signaling pathways affect gene expression during optic tissue formation has remained largely unknown, especially at the transcriptome scale.

overall_design: We generated Day 10 Rx+ optic tissue using SFEBq, exposed these tissues to either Fgf or Wnt/β-catenin stimulation, and assayed their gene expression at Days 12 and 15 using RNA-Seq. We measured gene expression in these 5 sample groups in biological triplicate using RNA-seq (Illumina HiSeq) .

first: Shigehiro

last: Kuraku

first: Nozomu

last: Takata

first: Yoshiki

last: Sasai

first: Nick

last: Love


title: The forkhead transcription factor FOXP1 profile in B-cells and B-cell lymphoma cell lines

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

summary: Expression of the forkhead transcription factor FOXP1 is essential for early B cell development, whereas downregulation of FOXP1 at the germinal center (GC) stage is required for GC B cell function. Aberrantly high FOXP1 expression is frequently observed in diffuse large B cell lymphoma (DLBCL) and mucosa-associated lymphoid tissue (MALT) lymphoma, being associated with poor prognosis. Here, by gene expression microarray [GSE51382] and quantitative RT-PCR analysis upon ectopic overexpression of FOXP1 in primary human memory B cells (MBCs) and B-cell lines, combined with chromatin immunoprecipitation-sequencing (ChIP-seq), we established that FOXP1 directly represses expression of PRDM1, IRF4, and XBP1, transcriptional master regulators of plasma cell (PC) differentiation. In accordance, FOXP1 is prominently expressed in primary human naive and MBCs but expression strongly decreases during plasma PC differentiation. Moreover, as compared to IgM+ MBCs, IgG+ MBCs combine lower expression of FOXP1 with an enhanced intrinsic PC differentiation propensity, and constitutive (over)expression of FOXP1 in B cell lines and primary human MBCs represses their ability to differentiate into PCs. Taken together, our data indicate that proper control of FOXP1 expression plays a critical role in PC differentiation, whereas aberrant overexpression of FOXP1 might contribute to lymphomagenesis by blocking terminal B cell differentiation.

overall_design: OXP1 ChIP-seq profile in primary human memory B cells (MBCs) and B-cell lines


title: Genome-wide changes in DNase-hypersensitivity during osteoblastogenesis reveal differential usage of DNA motifs and define novel cis-regulatory regions that control gene expression during differentiation [DNase-Seq]

first: Jonathan

last: Gordon

summary: Gene regulation during the process of osteoblastogenesis has been well-described, yet the discovery of novel regulatory regions has been limited by how we currently predict the locations of functional cis-regulatory modules.  Historically, the de novo identification of sequences critical for the control of gene expression relied primarily on sequence conservation in promoters.  Queries for binding motifs were based on position weight matrices of known transcription factors and the identification of disease-causing, non-coding mutations near critical genes.  However, we now must consider that regulatory elements also rely on 3-dimensional chromosomal interactions between far-distal regions, epigenetic chromosomal modifications, and RNA:DNA interactions.  Traditionally, DNaseI-hypersensitivity assays have been used for the identification of regulatory regions via preferential digestion at chromatin depleted or displaced of nucleosomes, as a result of transcription factor occupancy.  We probed DNase hypersensitivity on a genome-wide scale to determine whether osteogenic differentiation and/or bone-related gene regulation is marked by the presence of commonly utilized DNA motifs within active cis-regulatory modules.  We thus sought to evaluate the gain or loss of motif representation within hypersensitive regions during osteoblastogenesis, from day-0 (growth-phase) to day-28 (mineralizing) MC3T3 cultures.  We find that differentiation is marked by an increased enrichment of NFkB-p65, MEF2, and bHLH/E-box motifs within hypersensitive regions, while CTCF, NF1, TEAD, and AP1 motifs decrease.  Furthermore, grouping hypersensitive regions based on genomic positioning (promoters, introns, exons, and far-distal regions) reveals significant differences in motif abundance in first introns versus other genomic positions.  This finding suggests that the regulation conferred within first intron sequences may be somewhat distinct.  Interestingly, the majority of motifs that were enriched, regardless of genomic position or differentiation time-point, were not completely matched to currently known transcription factor motifs (curated in the JASPAR database).  Taken together, the changes in DNase-hypersensitive regions during osteoblastogenesis and the enrichment of distinct motifs within these regions indicate that osteoblasts utilize unique sets of motif rules for transcription factor binding or that regulatory control operates through undiscovered factors.

overall_design: Genome-wide DNase hypersensitivity mapping of osteoblast cultures was performed by adapting the DNase-seq protocol from Song et al. (Song and Crawford, 2010) with slight modifications.  Growth-phase (day 0), matrix-deposition stage (day 9), or mineralization stage (day 28) MC3T3-E1 clone-4 cultures were subjected to DNase-seq library preparation.  Libraries of purified DNA were generated using custom adapters described in Song et al.  High-throughput sequencing was performed by Illumina Genome Analyzer II with 36 base reads and on an Illumina Hiseq-1000  with 100 base reads.  Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina). Two independent biological repeats of DNase-seq libraries were prepared for each time point.  Each biological repeat is represented by two technical repeats.

first: Phillip

last: Tai

first: Hai

last: Wu

first: Troy

last: Whitfield

first: Andre

last: van Wijnen

first: Jane

last: Lian

first: Gary

middle: S

last: Stein

first: Janet


title: Human germ cell formation in xenotransplants of induced pluripotent stem cells carrying X chromosome aneuploidies

first: HyoJin

middle: Rosaria

last: Chiang

address: 265 Campus Dr.

institute: Stanford

summary: Induced pluripotent stem cells (iPSCs) offer opportunity for insight into the genetic requirements of the X chromosome for somatic and germline development. Turner syndrome is caused by complete or partial loss of the second sex chromosome; while more than 90% of Turner cases result in spontaneous fetal loss, survivors display an array of somatic and germline clinical characteristics. Here, we derived iPSCs from Turner syndrome and control individuals and examined germ cell development as a function of X chromosome composition. We analyzed gene expression profiles of derived iPSCs and in vitro differentiated cells by single cell qRT-PCR and RNA-seq. We whoed that two X chromosomes are not necessary for reprogramming or pluripotency maintenance. Genes that escape X chromosome inactivation (XCI) between control iPSCs and those with X chromosome aneuploidies revealed minimal expression differences relative to a female hESC line. Moreover, when we induced germ cell differentiation via murine xenotransplantation of iPSC lines into the seminiferous tubules of busulfan-treated mice, we observed that undifferentiated iPSCs, independent of X chromosome composition, when placed within the correct somatic environment, are capable of forming early germ cells in vivo. Results indicate that two intact X chromosomes are not required for germ cell formation; however, clinical data suggest that two sex chromosomes are required for maintenance of human germ cells.

overall_design: RNA-seq of  H9 cells, iPSCs from Turner syndrome and control individuals and in vitro differentiated cells

first: Antonia

middle: H

last: Dominguez

first: H

first: Meena

last: Sukhwani

first: Kyle

middle: E

last: Orwig

first: Renee

last: Reijo Pera


title: Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

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

overall_design: Refer to individual Series


title: Regulation of the core pre-mRNA splicing machinery by MYC and PRMT5 is essential to sustain lymphomagenesis [B-cells]

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Over-expressed MYC binds to virtually all active promoters within a cell, although with different binding affinities, and modulates gene expression, both positively and negatively. Here, we show that during lymphomagenesis in Eµ-myc transgenic mice, MYC directly up-regulates the transcription of the core snRNP assembly genes, including PRMT5, an arginine methyltransferase, that methylates Sm proteins as an early step in lymphomagenesis. This coordinated regulatory effect is direct and is critical for snRNP biogenesis, the maintenance of effective mRNA splicing and cellular viability in cycling cells, in either fibroblasts or B-cells.

overall_design: mRNA profiles of wild type and pre-tumoral eu-myc mice by deep sequencing, in triplicate, using Illumina NextSeq 500


title: Undifferentiated pleomorphic sarcoma recapitulates the expressional profile of Subtype II Leiomyosarcoma

first: Xiangqian

last: Guo

summary: Background: Undifferentiated pleomorphic sarcoma (UPS), used to be called malignant fibrous histiocytoma (MFH), is a malignant soft tissue tumor of uncertain origin, and is characterized by morphology. UPS often share similar morphological characters with other sarcomas, especially Leiomyosarcoma.  Leiomyosarcoma (LMS) is another malignant soft tissue sarcoma with complex genomic abnormalities, origin from smooth muscle.  As a result, development of gene signature and/or biomarkers distinguishing UPS and LMS will definitely help the pathologist to precisely diagnose those patients. However, in the past, UPS was reported to be indistinguishable with LMS by genomic profiles.  Methods and Results: In this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile 6 UPS and 99 LMS cases.  Overall, UPS was undistinguished with LMS by 3SEQ data, however, when we stratified LMS into three subtypes, UPS was shown to share similar expression pattern with Subtype II LMS, but had distinct molecular expression patterns with Subtype I and Subtype III LMS.  Additional Immunohistochemistry staining by using LMS Subtype I and Subtype II markers validated that UPSs were positive for Subtype II marker ARL4C, but negative for Subtype I marker LMOD1. Furthermore, CD4 was shown to be significantly more highly expressed in UPS than LMS in both mRNA and protein levels.  Conclusion: This study first reported that UPS shared similar gene expression pattern with subtype II LMS and UPS recapitulated the expression profiles of subtype II LMS.

overall_design: In this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile 6 UPS and 99 LMS cases. In order to explore the molecular differences between UPS and LMS, We analyzed the expression data by SAMseq  to identify the genes which were significantly differently expressed between UPS and LMS, between UPS and each LMS subtype.

first: Shirley

last: Zhu

first: Sushama

last: Varma

last: Kwok

first: Robert

middle: B

last: West

first: Matt

last: van de Rijn


title: Host genomic regions susceptible to damage during H. pylori infection

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

summary: We identify here host genomic regions that are more likely to be damaged during an infection with the human gastirc pathogen Helicobacter pylori and characterize underlying features of them. By ChIP-seq we obtained global information about the localization of the DNA-damage marker H2AXpS139. We used 20 ng of immunoprecipitated DNA of the human gastric cell line AGS to produce 240 mio sequence reads in total and compared the damage-pattern of 6 h and 19 h infected cells with that of 10 Gy irradiated ones. While the overall levesl of DNA damage wetre similar in terms of broken DNA and accumulation of H2AXpS139, infection-induced damage clearly accumulates towards the ends of chromosomal arms, namely telomere-proximal and close to centromeres, it also enriches mainly in genic and especially in transcribed regions. We show, taht this damage pattern is unique to the infection, occurs also in human non-transformed gastric epithelial cells and shows some correlation with previously identified cancer-related genes.

overall_design: Examination of a DNA-damage induced histone modification from four different conditions.

first: Max

last: Koeppel


title: RNA sequencing analysis of miR-603 overexpression

city: shanghai

first: jin

last: fan

address: dongchuan Road

institute: novelbio informatics company

summary:
Alzheimer’s disease (AD) is a serious neurodegenerative disease in which miRNAs have been linked to its pathogenesis.
miR-603 is a primate-specific miRNA. Through ADNI data analysis, we found a SNP rs11014002 in pre-miR-603 which promotes the biogenesis of mature miR-603 is associated with AD risk.
We further identified that LRPAP1, a protein which antagonizes the function of LRP1 in Aβ clearance and AD susceptibility, is a target gene of miR-603.
Moreover, overexpression of miR-603 increased the protein level of LRP1, suggesting the protective role of miR-603 in AD.
Both significant increase and loss of regulatory function of miR-603 hint the existence of a compensatory mechanism in hippocampus of AD subjects. Furthermore, we found that miR-603 could directly downregulate E2F1 and prevent cells from H2O2 induced-apoptosis.
This work provides the first evidence that miR-603 may modulate AD susceptibility and the SNP rs11014002 (T-carrier genotype) might be a protective factor for AD.

overall_design: There are two groups: Negative Control and miR-603 overexpression. We performed experiments on HEK293 cell and Hela cell.

first: Chi

last: Zhang

first: Jie

last: Lu


title: Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency (miRNA-Seq)

summary: In this study, we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA-seq and miRNA-seq technique, several deregulated genes and miRNAs were found to be related with hematopoiesis, vascular development and apoptosis process in RPS24-deficient zebrafish. Meanwhile, a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond-Blackfan Anemia. Interestingly, we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs, with partial verification from previous studies, revealing that our network-based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24-deficient zebrafish embryos as a model of DBA, which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24-mediated human diseases.

overall_design: Determine the differences of miRNome between RPS24-deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24-mediated human diseases

first: Xiangdong

last: Fang


title: Regulation of Transcription Termination by Glucosylated Hydroxymethyluracil, Base J, in L. major and T. brucei

city: athens

first: robert

last: sabatini

state: GA

address: 120 Green street

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Base J, β-D-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA Polymerase (RNAP) II initiation and termination. We have previously demonstrated a role of J in regulating RNAP II initiation in Trypanosoma cruzi. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in L. major and T. brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription elongation and increased expression of downstream genes. Thus, J regulation of transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates RNAP II elongation and gene expression at specific genomic loci.

sample_organism:
Leishmania major
Trypanosoma brucei

platform_organism:
Leishmania major
Trypanosoma brucei

overall_design: We studied the effect of loss of base J on transcription using WT and WT cells grown in DMOG-containing medium. We used 2 RNA-seq libraries containing processed RNA products and 4 small RNA libraries representing the entire transcriptome.

last: Sabatini

first: David

last: Reynolds

first: Laura

last: Cliffe

first: Nicolai

last: Siegel

first: Konrad

last: Förstner

first: Chung

middle: C

last: Hon


title: Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency (mRNA-Seq)

first: yadong

last: yang

overall_design: Determine the differences of transcriptome between RPS24-deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24-mediated human diseases


title: BIM is the primary mediator of MYC-induced apoptosis in multiple solid tissues

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: C-MYC (henceforth MYC) is one of the most frequently overexpressed oncogenes in human cancer and even modestly deregulated MYC expression can initiate ectopic proliferation in many post-mitotic, terminally differentiated cell types in vivo. Metazoan organisms have consequently evolved a number of mechanisms to counteract MYC's oncogenic potential, of which apoptosis is arguably the best understood. However, the mechanisms through which MYC induces apoptosis remains controversial, with some studies implicating p19ARF-mediated stabilization of p53, followed by induction of pro-apoptotic BH3 family member NOXA and PUMA, while others argue for more direct regulation of BH3 proteins, especially BIM. The debate likely stems from the use of different experimental systems, modes of perturbation, and quite possibly different levels of MYC expression. Here, we use a single experimental system to systematically evaluate the roles of p19ARF and BIM during MYC-induced apoptosis, in vitro, in vivo, and in combination with a widely used tumoricidal chemotherapeutic, Doxorubicin. We find a common specific requirement for BIM during MYC-induced apoptosis in multiple settings, which does not extend to the p53-responsive BH3 family member PUMA, and find no evidence of a role for p19ARF during MYC-induced apoptosis in the tissues examined.

overall_design: MYC-ER ChIP-Seq with HC20 anti-ER antibody in MCF10A cells performed on an Illumina IIx Genome Analyzer.

first: Nathiya

last: Muthalagu

first: Melissa

last: Juntilla

first: Katrin

last: Wiese

first: Elmar

last: Wolf

first: Barbara

last: Bauer

first: Jennifer

last: Morton

first: Gerard

middle: I

last: Evan

first: Daniel

last: Murphy


title: The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis

first: Xiaopeng

last: Ma

state: Outside US and Canada

address: HaiDian district

institute: Tsinghua Univeristy

summary: To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastomeres at 8-cell stage, extracted the maternal mRNA respectively and analyzed them by RNA-seq technology. We identified 43 maternal transcripts significantly enriched in the vegetal region (FDR<0.05) by R/Bioconductor package DESeq

overall_design: RNAseq of animal and vegetal blastomeres with 2 biological replicates

first: Guanni

last: Sun

first: Zhirui

last: Hu

first: Zheying

last: Min

first: Xiaohua

last: Yan

first: Zhenpo

last: Guan

first: Hanxia

last: Su

first: Yu

last: Fu

first: YeGuang

last: Chen

first: Michael

middle: Q

last: Zhang

first: Qinghua

last: Tao

first: Wei

last: Wu


title: Regulation of the core pre-mRNA splicing machinery by MYC and PRMT5 is essential to sustain lymphomagenesis

first: Diana

last: Low


title: Systemic suppression of the rice shoot metabolism upon root rot nematode infection

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

institute: VUB/ULB

summary: Rice (Oryza sativa L.) is one of the most important staple foods in the world, feeding more than 50% of the human population. One of its most damaging pathogens, with major impact on rice yield, is the migratory root rot nematode Hirschmanniella oryzae. In comparison with the existing knowledge on the infection process of dicots by sedentary nematodes, far less is known about the interaction between monocot plants and nematodes or plant interactions with migratory nematode species. Therefore, to gain deeper insight into the systemic transcriptional changes in rice after migratory root rot nematode infection we have performed mRNA-Seq on the shoots of root rot nematode infected rice plants. The observations were independently validated using qRT-PCR and biochemical analyses. This research reveals significant modifications in the metabolism of the plant, with a general suppression of chlorophyll biosynthesis, and primary metabolic processes involved in plant growth .

overall_design: Differential expression analysis between controls rice shoots and shoots from root rot nematode (H. oryzae) infected rice at two time points.

first: Tina

last: Kyndt

middle: L

first: Lander

last: Bauters

first: Wim

last: Van Criekinge

first: Tim

last: De Meyer


title: A microfluidic device for label-free, physical capture of circulating tumor cell-clusters

status: Public on May 17 2015

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

summary: Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC-clusters). Existing technologies for CTC enrichment are designed primarily to isolate single CTCs, and while CTC-clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here, we developed a microchip technology (Cluster-Chip) specifically designed to capture CTC-clusters independent of tumor-specific markers from unprocessed blood. CTC-clusters are isolated through specialized bifurcating traps under low shear-stress conditions that preserve their integrity and even two-cell clusters are captured efficiently. Highly parallel architecture of the chip allows deterministic screening of clinically relevant volumes of blood samples at slow, and hence, non-damaging flow rates. Using the Cluster-Chip, we identify CTC-clusters in 30-40% of patients with metastatic cancers of the breast, prostate and melanoma. RNA sequencing of CTC-clusters confirms their tumor origin and identifies leukocytes within the clusters as being tissue-derived macrophages. Together, the development of a device for efficient capture of CTC-clusters will enable detailed characterization of their biological properties and role in cancer metastasis.

overall_design: We used the Cluster-Chip to capture CTC-clusters from the blood of a breast cancer patient with high CTC counts, released CTC-clusters in solution, stained them with TexasRed-conjugated antibodies against the leukocyte cell surface markers CD45, CD14 and CD16, and then isolated intact CTC-clusters individually using a micromanipulator. From a single time point, we retrieved 15 CTC-clusters, and each of those clusters was individually subjected to RNA-sequencing analysis using a next generation platform (SOLiD 5500). In addition, two leukocytes were isolated from the blood of a healthy donor were individually subjected to RNA-sequencing analysis using the same platform.

first: A

last: Sarioglu

first: Nicola

last: Aceto

first: Nikola

last: Kojic

first: Maria

last: Donaldson

first: Mahnaz

last: Zeinali

first: Bashar

last: Hamza

first: Amanda

last: Engstrom

first: Huili

last: Zhu

first: Tilak

last: Sundaresan

first: David

middle: T

last: Miyamoto

first: Xi

last: Luo

first: Aditya

last: Bardia

first: Sridhar

last: Ramaswamy

first: Toshi

last: Shioda

last: Ting

first: Shannon

last: Stott

first: Ravi

last: Kapur

first: Shyamala

last: Maheswaran

first: Daniel

middle: A

last: Haber

first: Mehmet

last: Toner


title: UTX and JMDJ3 regulate NKT development

city: Bethesda

last: Northrup

state: MD

address: 9000 Rockville Pike Building 10 7B04

institute: NIH

summary: The goal of this study was to understand the transcriptional differences between UTX/JMJD3 DKO NKT precursors (P1) and WT litter mater controls.  Two female and one male sample for each is included.

overall_design: 6 samples, 3 WT(2F, 1M), 3 DKO (2F, 1M)

first: Dan

first: Gangqing

last: Hu


title: RNAi profiling of primary human AML cells identifies ROCK1 as a therapeutic target and nominates Fasudil as an anti-leukemic drug.

status: Public on May 16 2015

city: Dresden

first: Maciej

last: Paszkowski-Rogacz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

type: Genome variation profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) is characterized by a marked genetic heterogeneity, which complicates the development of novel therapeutics. The delineation of pathways essential within the patient-individual mutational background might overcome this limitation and facilitate personalized treatment. We report the results of a large-scale lentiviral loss-offunction RNA-interference-(RNAi)-screen in primary leukemic cells. Stringent validation identified six genes (BNIPL1, ROCK1, RPS13, STK3, SNX27, WDHD1) whose knockdown impaired growth and viability of the cells. Dependence on these genes was not caused by mutation or overexpression and while some of the candidates seemed to be rather patientspecific, others were essential in cells isolated from other AML patients. In addition to the phenotype observed after ROCK1 knockdown, treatment with the approved ROCK-inhibitor fasudil resulted in increased apoptosis and decreased viability of primary AML cells. In contrast to observations in some other malignancies, ROCK1-inhibition did not foster growth of immature malignant progenitors; but was also toxic to this cell fraction in feeder-co-culture and xenotransplantion experiments, indicating a distinct effect of ROCK1 inhibition on leukemic progenitors. We conclude that large scale RNAi screens in primary patient-derived cells are feasible and can complement other methods for personalized cancer therapies, such as expression and mutation profiling.

overall_design: Large-scale lentiviral loss-of-function shRNA screen in primary leukemic cells with two time points, exome sequencing of primary leukemic cells, and a gene expression profiling of primary cells from four leukemic and three healthy samples.

first: Martin

last: Wermke

first: Aylin

last: Camgoz

first: Sebastian

last: Thieme

first: Andreas

last: Dahl

first: Uwe

last: Platzbecker

first: Mirko

last: Theis

first: Gerhard

last: Ehninger

last: Brenner

last: Bornhaeuser

first: Frank

last: Buchholz


title: Transcriptional response to hypoxia in the rice blast fungus, M. oryzae

city: Seoul

first: Gir Won

last: Lee

address: Sangdo-dong

country: South Korea

institute: Soongsil University

summary: Transcriptional analysis using RNA-Seq to low oxygen

overall_design: Samples from wild type mycelia with and without oxygen (21% and 1% Oxygen)

first: Jaehyuk

last: Choi

first: Gir-Won

first: Sun-Ki

last: Koh

first: Suhn-Kee

last: Chae

first: Yong-Hwan


title: Shear Stress and NOTCH1 Regulate Calcification Related Genes in Human Aortic Valve Endothelium (ChIP-Seq)

city: San Francisco

first: Deepak

last: Srivastava

state: CA

address: 1650 Owens St.

department: Gladstone Institute of Cardiovascular Disease

institute: J. David Gladstone Institutes

summary: We are interested in the role of NOTCH1 and Shear Stress in Aortic Valve Endothelium.

overall_design: Primary aortic valve endothelial cells were infected with NOTCH1 intracellular domain fused with a myc tag in order to perform ChIP-seq.

first: Mark

middle: P

last: White


title: Shear Stress and NOTCH1 Regulate Calcification Related Genes in Human Aortic Valve Endothelium


title: GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of histone H3, lysine 27.

first: Boaz

middle: Eliezer

last: Aronson

state: Massachusetts

address: 300 Longwood Avenue

department: GI/Nutrition

institute: Children's Hospital Boston

summary: GATA4 is expressed in the proximal 85% of small intestine where it promotes a proximal intestinal ('jejunal') identity while repressing a distal intestinal ('ileal') identity, but its molecular mechanisms are unclear. Here, we tested the hypothesis that GATA4 promotes a jejunal versus ileal identity in mouse intestine by directly activating and repressing specific subsets of absorptive enterocyte genes by modulating the acetylation of histone H3, lysine 27 (H3K27), a mark of active chromatin, at sites of GATA4 occupancy. Global analysis of mouse jejunal epithelium showed a statistically significant association of GATA4 occupancy with GATA4-regulated genes. Occupancy was equally distributed between down- and up-regulated targets, and occupancy sites showed a dichotomy of unique motif over-representation at down- versus up-regulated genes. H3K27ac enrichment at GATA4-binding loci that mapped to down-regulated genes (activation targets) was elevated, changed little upon conditional Gata4 deletion, and was similar to control ileum, whereas H3K27ac enrichment at GATA4-binding loci that mapped to up-regulated genes (repression targets) was depleted, increased upon conditional Gata4 deletion, and approached H3K27ac enrichment in wild-type control ileum. These data support the hypothesis that GATA4 both activates and represses intestinal genes, and show that GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of H3K27.

overall_design: 2 samples were analyzed (1 ChIPseq, 1 input sample), control was done by confirming ChIP-qPCR on specific targets


title: An epigenetic memory of pregnancy in the mouse mammary gland

status: Public on May 15 2015

city: Cold Spring Harbor

first: Camila

last: dos Santos

state: NY

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

type: Methylation profiling by high throughput sequencing

summary: Pregnancy is the major modulator of mammary gland activity. It induces a tremendous expansion of the mammary epithelium and the generation of alveolar structures for milk production. Anecdotal evidence from multiparous humans indicates that the mammary gland may react less strongly to the first pregnancy than it does to subsequent pregnancies. Here we verify that the mouse mammary gland responds more robustly to a second pregnancy, indicating that the gland retains a long-term memory of pregnancy. A comparison of genome-wide profiles of DNA methylation in isolated mammary cell types revealed substantial and long lasting alterations.  The majority of these alterations affect sites occupied by the Stat5a transcription factor and mark specific genes that are upregulated during pregnancy.  We postulate that the epigenetic memory of a first pregnancy primes the activation of gene expression networks that promote mammary gland function in subsequent reproductive cycles.  More broadly, our data indicate that physiological experience can broadly alter epigenetic states, functionally modifying the capacity of the affected cells to respond to later stimulatory events.

overall_design:
Mammary gland cells (six distinct cell types) from nulliparous and parous female mice were FACS-sorted using a combination of cell surface markers. Genomic DNA was bisulfite converted and used to obtain genome-wide DNA methylation profiles.

The current work focuses on the analysis of the first 12 samples (GSM1646785-96) and uses the other two samples to confirm some properties of the analysis results based on samples 1-12.
Consequently, samples GSM1646797, GSM1646798 were analyzed in a much more limited manner compared to the other 12 samples, generating two plots included in the associated manucript.

first: Egor

last: Dolzhenko


title: Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure

city: Ipswich

first: Ryan

middle: Timothy

last: Fuchs

state: MA

address: 240 County Road

department: RNA Biology

institute: New England Biolabs

summary: High-throughput sequencing (HTS) has become a powerful tool for the detection of and sequence characterization of microRNAs (miRNA) and other small RNAs (sRNA).  Unfortunately, the use of HTS data to determine the relative quantity of different miRNAs in a sample has been shown to be inconsistent with quantitative PCR and Northern Blot results.  Several recent studies have concluded that the major contributor to this inconsistency is bias introduced during the construction of sRNA libraries for HTS and that the bias is primarily derived from the adaptor ligation steps; specifically where single stranded adaptors are sequentially ligated to the 3' and 5'-end of sRNAs using T4 RNA ligases.  In this study we investigated the effects of ligation bias by using a pool of randomized ligation substrates, defined mixtures of miRNA sequences and several combinations of adaptors in HTS library construction.  We show that like the 3' adaptor ligation step, the 5' adaptor ligation is also biased, not because of primary sequence, but instead due to secondary structures of the two ligation substrates.  We find that multiple secondary structural factors influence final representation in HTS results.  Our results provide insight about the nature of ligation bias and allowed us to design adaptors that reduce ligation bias and produce HTS results that more accurately reflect the actual concentrations of miRNAs in the defined starting material.

overall_design: 28 samples were sequenced and the libraries were made using various synthetic oligo mixtures and adaptor combinations

first: Zhiyi

last: Sun

first: Fanglei

last: Zhuang

first: G

last: Robb