title: RAMPAGE from skeletal muscle tissue (ENCSR000AGT)

summary:
The libraries contained in this experiment come from human fetal skeletal muscle tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from spinal cord (ENCSR000AGV)

status: Public on Nov 08 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Expression profiling by high throughput sequencing

summary:
The libraries contained in this experiment come from human fetal spinal cord tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from temporal lobe (ENCSR000AGX)

summary:
The libraries contained in this experiment come from human fetal temporal lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from SK-MEL-5 (ENCSR007RIV)

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

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


title: RAMPAGE from camera-type eye (ENCSR000AHC)

summary:
The libraries contained in this experiment come from human fetal whole eye tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: small RNA-seq from stomach (ENCSR003SZJ)

type: Non-coding RNA profiling by high throughput sequencing

summary:
The libraries contained in this Experiment come from tissue sub-sections of a 53 year old female's stomach tissue section obtained from GTEx. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.

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


title: RAMPAGE from liver (ENCSR000AGP)

summary:
The libraries contained in this experiment come from human fetal liver tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from metanephros (ENCSR000AGO)

summary:
The libraries contained in this experiment come from human fetal kidney tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from lung (ENCSR000AGQ)

summary:
The libraries contained in this experiment come from human fetal lung tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from parietal lobe (ENCSR000AGS)

summary:
The libraries contained in this experiment come from human fetal parietal lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from heart (ENCSR000AGN)

summary:
The libraries contained in this experiment come from human fetal heart tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from occipital lobe (ENCSR000AGR)

summary:
The libraries contained in this experiment come from human fetal occipital lobe tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from urinary bladder (ENCSR000AGJ)

summary:
The libraries contained in this experiment come from human fetal urinary bladder tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from GM12878 (ENCSR000AEI)

summary:
The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.

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


title: RAMPAGE from frontal cortex (ENCSR000AGM)

summary:
The libraries contained in this experiment come from human fetal frontal cortex tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from cerebellum (ENCSR000AGK)

summary:
The libraries contained in this experiment come from human fetal cerebellum tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: RAMPAGE from diencephalon (ENCSR000AGL)

summary:
The libraries contained in this experiment come from human fetal diencephalon tissue from independent donors. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.

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


title: Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

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

country: Japan

institute: CyberomiX Inc

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

overall_design: Refer to individual Series


title: Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells [Single Cell RNA-Seq]

summary: Obtaining highly purified differentiated cells via directed differentiation from human pluripotent stem cells (hPSCs) is an essential step for the clinical application of hPSCs. Among the various conditions that should be optimized, the precise role and contribution of the extracellular matrix (ECM) during differentiation are relatively unclear. Here, using a short fragment of laminin 411 (LM411-E8), an ECM predominantly expressed in the vascular endothelial basement membrane, we demonstrated that the directed switching of defined ECMs robustly yields highly purified (>95%) endothelial progenitor cells (PSC-EPCs) from hPSCs in integrin-laminin axis and rho signaling pathway-dependent manner.

overall_design: Single cell RNA-sequencing was conducted to describe transcriptional dynamics from pluripotent stem cells toward the endothelial lineages.

first: Ryo

last: Ohta

last: Niwa

first: Megumu

last: Saito

first: Chihiro

last: Okada


title: Distinct Combinatorial Events Generated by ECM Degradation Dictate Cell Behavior

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: It is well established that the expression profiles of multiple and possibly redundant matrix remodeling proteases (e.g. collagenases) strongly differ in health, disease and development. Although enzymatic redundancy might be inferred from their close similarity in structure, their in-vivo activity can lead to extremely diverse tissue-remodeling outcomes. We observed that proteolysis of collagen-rich natural extracellular matrix (ECM), generated uniquely by individual homologous proteases, leads to specific combinatorial events, which eventually affects overall ECM topography, visco-elastic properties and composition. We reveal striking differences in the movement and signaling patterns, morphology, and gene expression profiles of cells interacting with natural collagen-rich ECM degraded by different collagenases. Thus, unlike envisioned before matrix-remodeling systems are not redundant and give rise to precise ECM-cell crosstalk. As ECM proteolysis is an abundant biochemical process critical to tissue homoeostasis, these results improve our fundamental understanding of combinatorial factors dictating cell behavior.

overall_design: We analyzed the transcriptional responses of fibroblasts interacting with MMP1 or MMP13-remodeled ECM 4 hours post seeding. Samples used: Fibroblasts interacting with MMP1-remodeled ECM; Fibroblasts  interacting with MMP13-remodeled ECM; Control samples- Fibroblasts interacting with natural ECM. All samples were run in duplicates.

first: I

last: Solomonov

first: E

last: Zehorai

first: D

last: Talmi-Frank

first: S

middle: G

last: Wolf

first: A

last: Shainskaya

last: Zuravlev

last: Kartvelishvily

first: R

last: Visse

first: Y

last: Levin

first: N

last: Kampf

middle: A

last: Jaitin

last: David

first: H

last: Nagase

last: Sagi


title: Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells [Bulk RNA-Seq]

last: Watanabe

overall_design: RNA-sequencing was conducted to identify the genes that were differentially expressed among differential conditions to induce the differentiation to the endothelial lineages.

last: Ohta

last: Niwa

last: Saito


title: FPS down-regulation alters chloroplast development and triggers an sterol-dependent induction of JA-related and Fe deficiency transcriptional responses

city: Cerdanyola del Vallés

first: David

last: Manzano

state: Barcelona

address: Edifici CRAG

department: PLANT METABOLISM AND METABOLIC ENGINEERING

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

summary: In order to study the role of Farnesyl diphosphate synthase (FPS) in post-embryonic plant development, we generated Arabidopsis conditional knockdown mutants expressing amiRNAs devised to simultaneously silence both FPS (FPS1 and FPS2) genes. The expression of the amiRNAs is regulated by using a methoxyfenozide (MFZ) inducible promoter. An RNAseq analysis was made to compare the differentially expressed genes between control (not induced)  and silenced (MFZ-induced) amiFPSa Arabidopsis seedlings. Differential gene expression analysis shows that a reduction in FPS activity levels triggers misregulation of genes involved in biotic and abiotic stress responses, the most prominent being the rapid induction of a set of genes related to the jasmonic acid (JA) pathway. Down-regulation of FPS also triggered a Fe-deficiency transcriptional response that is consistent with the Fe-deficient status observed in FPS silenced plants.

overall_design: To induce FPS gene silencing, seedlings were germinated and grown for three days on sterile filter papers that were first placed on MS plates and subsequently transferred onto new MS plates supplemented (treatment) or not (control) with 30 µM MFZ for five days more. Three independent pools of seedlings (100 mg of FW) were collected per each treatment. Seedlings were ground to a fine powder using TissueLyser equipment and used for extraction of RNA. The quality and quantity of total RNA samples were assessed using a Bionalyzer Expert 2100 Instrument (Agilent Technologies) and an equimolar mixture of RNA samples from each treatment was prepared. The RNA samples (3 μg) were fragmented and ligated with adaptors prior to cDNA synthesis and PCR amplification. The cDNA libraries were prepared according to the Illumina protocols and sequenced using an Illumina HiSeq2000 machine to perform 2x100 paired-end sequencing.


title: GATA1-deficient dendritic cells display impaired CCL21-dependent migration towards lymph nodes due to reduced levels of polysialic acid

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

summary: Dendritic cells (DCs) play a pivotal role in the regulation of the immune response. DC development and activation is finely orchestrated through transcriptional programs. GATA1 transcription factor is required for murine DC development and data suggests that it might be involved in the fine-tuning of the life span and function of activated DCs. We generated DC-specific Gata1 knockout mice (Gata1-KODC), which presented a 20% reduction of splenic DCs, partially explained by enhanced apoptosis. RNA-Seq analysis revealed a number of deregulated genes involved in cell survival, migration and function. DC migration towards peripheral lymph nodes was impaired in Gata1-KODC mice. Migration assays performed in vitro showed that this defect was selective for CCL21, but not CCL19. Interestingly, we show that Gata1-KODC DCs have reduced polysialic acid levels on their surface, which is a known determinant for the proper migration of DCs towards CCL21.

overall_design: Dendritic cells from Gata1 knock-out or wild-type mice were stimulated with LPS of unstimulated (under steady state), 2 biological replicates each

first: Maaike

middle: R

last: Scheenstra

first: Laura

last: Gutiérrez


title: Epigenomic-based identification of major cell identity regulators within heterogeneous cell populations [RNA-seq]

status: Public on Nov 07 2016

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

summary: Cellular heterogeneity within embryonic and adult tissues is involved in multiple biological and pathological processes. Here we present a simple and broadly applicable epigenomic strategy that allows the functional dissection of cellular heterogeneity. By integrating H3K27me3 Chip-seq and RNA-seq data, we demonstrate that the presence of broad H3K27me3 domains at transcriptionally active genes reflects the heterogeneous expression of major cell identity regulators. Using dorsoventral patterning of the spinal neural tube as a model, the proposed approach successfully identifies the majority (~90%) of previously known dorsoventral patterning transcription factors with high sensitivity and precision. Moreover, poorly characterized patterning regulators can be similarly predicted, as shown for ZNF488, which confers p1/p2 neural progenitor identity. Finally, we show that, as our strategy is based on universal chromatin features, it can be also used to functionally dissect cellular heterogeneity within various organisms and tissues, thus illustrating its potential applicability to a broad range of biological and pathological contexts.

overall_design: mRNA profiles were generated by RNA-seq from spinal neural tube sections isolated at the brachial levels of stage HH14 or HH19 chicken embryos. For each RNA-seq experiment, spinal neural tube sections of approximately 25 different embryos were pooled.

first: Rizwan

last: Rehimi

first: Alvaro

last: Rada-Iglesias


title: COSMIC-seq of bioactive N-methylpyrrole/N-methylimidazole polyamides

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

summary: Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to “read” specific DNA sequences.  However, the impact of different chromatin states on polyamide binding to its cognate sites across the genome is a crucial parameter that remains unresolved.  We applied COSMIC-seq (crosslinking of small molecules to isolate chromatin) to directly map, for the first time, the genome-wide binding profiles of two bioactive and structurally distinct polyamides in cells.

overall_design: To directly map polyamide binding sites across the genome in living cells, we developed COSMIC-seq. COSMIC consists of treating live cells with trifunctional derivatives of polyamides. These molecules were comprised of a DNA-binding polyamide, an affinity handle, and a photocrosslinker. The polyamide confers sequence specificity, while the affinity handle, biotin, is used to purify polyamide–DNA adducts with streptavidin-coated magnetic beads. The photocrosslinker, psoralen, enables the temporally-controlled formation of a covalent bond between the polyamide and DNA. Cells were first treated with the polyamide derivative, crosslinked with 365 nm UV light, lysed, sonicated to shear DNA, and streptavidin-coated magnetic beads were used to capture polyamide-DNA adducts. Because psoralen crosslinks are reversible, the captured genomic DNA can be separated from the polyamide, purified, and identified by massively parallel, next-generation sequencing (NGS). Sequencing reads are mapped to their location across the genome, and loci bound by polyamides show enrichment of sequencing reads relative to a reference input sample.

first: Graham

middle: S

last: Erwin

middle: Z


title: Gene expression profile of wt-, S473A- and S473D-KAP1-re-expression in KAP1-depleted MDA-MB-231 cell

city: Duarte

middle: Kong

last: Ann

address: 1500 E. Duarte Rd.

institute: City of Hope

summary: We study the gene regulation function of serine 473 phosphorylation of KAP1 (pS473-KAP1) in MDA-MB-231 cells. Wild type KAP1, S473A-KAP1 (phospho-acceptor site mutant) and S473D-KAP1 (phospho-mimetic mutant) are re-expressed in KAP1 knockdown cells. We analyze the gene expression profile in these three cells and find that many mitochondrial complex genes are up-regulated in S473D-KAP1 re-expressing cells. This study provides information about pS473-KAP1-regulated gene expression.

overall_design: mRNA profile of wt-, S473A- and S473D-KAP1-expressing MDA-MB-231 cells were generated by deep sequencing

first: Chun-Ting

last: Cheng

middle: K


title: Tumor-Specific Retrogene NANOGP8 Reprograms Prostate Cancer Cells to Castration Resistance by Engaging the FOXA1/AR Signaling Axis and MYC [RNA-seq]

city: Smithville

first: Collene

last: Jeter

state: TX

address: 1808 Park Rd 1C, Box 389

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Targeted disruption of the embryonic stem cell (ESC) self-renewal and pluripotency factor NANOG diminishes cancer cell clonogenic growth in vitro and tumor development in vivo. NANOG has also been shown to augment CSC properties and propel the emergence of castration-resistance prostate cancer (CRPC) phenotypes. Here, we investigate the molecular mechanisms underlying NANOG-mediated oncogenesis and prostate cancer progression to androgen independence.  ChIP-Seq analysis of LNCaP prostate cancer cells overexpressing doxycycline-inducible NANOG (either NANOG1 or NANOGP8 vs pLVX control) reveal that NANOG coordinately occupies regions of chromatin regulated by AR signaling steroid-receptor complex proteins AR, FOXA1 and NKX3.1. Taken together with the NANOG-induced changes in the prostate cancer transcriptome (RNA-Seq), NANOG appears to reprogram prostate cancer cells to castration resistance by converging on steroid-hormone receptor signaling.

overall_design: LNCaP empty vector (pLVX) vs NANOG overexpressing (NANOG1 or NANOGP8) cells cultured +doxycycline under androgen dependent (AD) or androgen independent (AI) conditions for the indicated period of time and subject to RNA extraction and Illumina sequencing

first: Yue

last: Lu

first: Dean

last: Tang


title: RAMPAGE from K562 (ENCSR000AER)

first: ENCODE

last: DCC

summary:
The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.

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


title: Tumor-Specific Retrogene NANOGP8 Reprograms Prostate Cancer Cells to Castration Resistance by Engaging the FOXA1/AR Signaling Axis and MYC

type: Genome binding/occupancy profiling by high throughput sequencing


title: Social status alters immune regulation and response to infection [LPS_RNAseq]

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

summary:
Social status is one of the strongest predictors of disease risk and mortality in humans, and often influences Darwinian fitness in social mammals more generally. To understand the biological basis of these effects, we combined a functional genomics approach with sequential social status manipulations in rhesus macaques to investigate how social status alters immune function. We demonstrate causal, but largely plastic, effects of social status on immune cell proportions, cell type-specific gene expression levels, and the gene expression and cytokine response to infection. Further, we identify specific transcription factor signaling pathways that explain these differences, particularly status-associated polarization of the TLR4 signaling pathway towards pro-inflammatory versus anti-viral responses. Our findings provide an unprecedented level of insight into the direct biological effects of social inequality on immune function, thus contributing to an improved understanding of social gradients in health and the evolution of social hierarchies.
For social status, please refer to table S1 in the manuscript.

overall_design: mRNA sequencing of LPS and control treated whole blood from female rhesus macaques

first: Jenny

last: Tung


title: Genome-wide analysis of SOX2 binding in asynchronous and mitotic mouse embryonic stem cells.

city: Lausanne

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

summary: SOX2 is part of the core network of transcription factors regulating embryonic stem cell pluripotency. We found that SOX2 has the ability to remain bound to mitotic chromosomes, in contrast to most transcription factors that are excluded from mitotic chromatin as transcription shuts down. We obtained a highly purified population of mitotic mouse embryonic stem cells and compared the genome-wide binding profile of SOX2 to that in asynchronous cells by Chromatin Immunoprecipitation followed by high throughput sequencing (ChIP-seq), and show that SOX2 remains bound to a small set of genes during mitosis.

overall_design: SOX2 ChIP-seq in asynchronous and mitotic mouse embryonic stem cells. The study includes three biological replicates for each of the two conditions, together with one input sample per replicate.

middle: M


title: RNA sequencing on uninjured and injured cardiac regions of B6 and C3H strains

city: Los Angeles

first: Larry

last: Lam

address: 610 Charles Young Drive East

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

summary:
Purpose: To analyze gene expression in calcific (C3H) and non-calcific (B6) hearts
Methods: B6 and C3H mice were induced cardiac injury by rapid freeze thaw of cardiac tissue (cryo-injury). A left thoracotomy was performed at the level of 2nd intercostal space and the exposed beating heart was frozen for 10 seconds by gently pressing a pre-cooled steel rod of 1mm diameter in dry ice. Freezing of cardiac tissue was confirmed by the rapid discoloration of the tissue. Seven days after injury, injured and uninjured regions from same heart were used for RNA sequence.
Results: In contrast to only 70 odd genes that were differentially upregulated following injury in non-calcified mouse hearts (B6) about 960 genes were upregulated in C3H hearts following injury induced calcification. Out of the 960 differentially upregulated genes, only 35 were found to be common or upregulated in both C3H and B6 hearts after injury illustrating of the overlapping but dramatically different magnitude of the injury response. Families of genes regulating diverse aspects of an injury response including inflammation, extracellular matrix proteins, cell proliferation and collagen production were differentially expressed between the calcific and non-calcific hearts after injury. The mean expression of osteogenic genes (osteogenic signature) was significantly higher in injured C3H hearts compared to uninjured C3H hearts. The osteogenic signature was not higher in injured B6 hearts compared to control uninjured B6 hearts.
Conclusions: Calcific hearts compared to non-calcific hearts responded to injury with a dramatically different transcriptional program.

overall_design: Gene expression were measured in uninjured and injured regions from each heart. N=3 animals for B6 uninjured and injured hearts; n=3 for C3H uninjured hearts and n=2 for C3H injured heart.

first: Shen

last: Li


title: RNA sequencing on cardiac fibroblasts harvested at different time points following induction of osteogenic differentiation

summary:
Purpose: To analyze cardiac fibroblasts gene expression at different time following induction of osteogenic differentiation
Methods: Freshly isolated cardiac fibroblasts (Passage 0 or passage 1) were plated at a density of 2.5 x 104 cells/cm2 in growth medium. After overnight incubation, osteogenesis was induced using differentiation medium (α-MEM supplemented with 10% FBS, 10 nM dexamethasone (Sigma, D4902), 20 mM β-glycerol phosphate (Sigma, G9422), and 50 μM L-ascorbic acid (Sigma, A4403). Cardiac fibroblasts harvested at Day0 (before differentiation medium treatment), Day7, Day14 and Day21 were used for RNA sequencing.
Results: Cardiac fibroblasts harvested at different time points following induction of differentiation revealed clusters of genes whose expression was significantly altered in a temporal specific manner. Genes regulating cell cycle that were highly expressed in undifferentiated cardiac fibroblasts were down-regulated at the onset of differentiation and remained at low expression levels throughout the duration of osteogenic differentiation, consistent with the principle that induction of differentiation is associated with reduced rates of proliferation. In contrast, genes that were minimally expressed in cardiac fibroblasts were induced in a specific temporal manner during the course of osteogenic differentiation and included sets of genes known to regulate inflammation, extracellular matrix proteins and cell metabolism.
Conclusions: Cardiac fibroblasts subjected to osteogenic differentiation progressively adopted an osteogenic signature.

overall_design: Cardiac fibroblasts harvested at Day0 (before differentiation medium treatment), Day7, Day14 and Day21 were used for RNA sequencing. 2 samples / each time point.


title: Epigenomic-based identification of major cell identity regulators within heterogeneous cell populations [ChIP-seq]

overall_design: Genome-wide binding profiles for various histone modifications  were generated by ChIP-seq using spinal neural tube sections isolated at the brachial levels of stage HH14 or HH19 chicken embryos. For each ChIP-seq experiment, spinal neural tube sections of approximately 25-30 different embryos were pooled.


title: New transgenic mouse lines for selectively targeting astrocytes and for studying calcium signals in astrocyte processes in situ and in vivo

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: The Khakh laboratory developed and characterized a new Aldh1l1-Cre/ERT2 transgenic mouse line to selectively target astrocytes in vivo. Crosses with RiboTag mice allowed sequencing of actively translated mRNAs and analyses of the cortical astrocyte transcriptome from adults.

overall_design: Cortices were extraced from 4 young adult (~P80) male and female Aldh1l1-Cre/ERT2 x Ribotag mice. After homogenization, RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

first: Tsai-Yi

first: Rahul

last: Srinivasan

first: Hua

last: Chai

first: Ji

last: Xu

first: Ben

last: Huang

first: Peyman

last: Golshani

first: Baljit

last: Khakh


title: SOX7 supresses the expression of RUNX1 target genes during EHT

city: Manchester

first: Andrew

middle: Joshua

last: Lilly

address: Wilmslow Road

department: Stem Cell Haematopoiesis

country: United Kingdom

institute: CRUK Manchester Institute

summary: The molecular mechanisms regulating endothelial to hematopoietic transition (EHT) of hemogenic endothelium (HE) are poorly understood.  Here we profile the transcriptional changes resulting from SOX7 overexpression during EHT

overall_design: FLK1+ cells were sorted from day 3.5 iSox7 EBs and cultured in liquid blast media for 48hours.  Dox was added for 6, 12 and 24 hours to induce SOX7 expression, before samples were harvested for RNAseq.

first: Muhammad

last: Fadlullah

first: Valerie

last: Kouskoff


title: Induction of antiviral RNA interference by influenza A virus in human cells

city: Riverside

first: Jinfeng

last: Lu

address: 900 University Ave

institute: UC Riverside

summary: We demonstrate that mature human somatic cells produce abundant virus-derived siRNAs co-immunoprecipitated with Argonaute proteins in response to IAV infection. We show that the biogenesis of viral siRNAs from IAV dsRNA precursors in infected cells is mediated by wild type human Dicer.

overall_design: Examination of 14 viral small RNA profiles sequenced from 2 human somatic cells infected by 2 different NS1-deficient influenza A virus strains, either with or without Argonautes co-immunoprecipitation

first: Yang

first: Shu-Wei

last: Dong

first: Yanhong

last: Han

first: Wan-Xiang

first: Shou-Wei

last: Ding


title: Excessive miR-27 expression impairs regulatory T cell-mediated immunological tolerance [Foxp3cre het miR-27Tg]

status: Public on Nov 05 2016

city: La Jolla

first: Li-Fan

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

summary: MicroRNAs (miRNAs) are tightly regulated in the immune system, as aberrant expression of miRNAs often results in hematopoietic malignancies and autoimmune diseases. Previously, elevated levels of miR-27 in T cells isolated from multiple sclerosis patients has been suggested to facilitate disease progression through inhibiting Th2 immunity and promoting pathogenic Th1 responses. Here we demonstrate that while mice with T cell-specific overexpression of miR-27 harbor dysregulated Th1 responses and develop autoimmune pathology, these disease phenotypes are not driven by miR-27 in effector T cells in a cell-autonomous manner but rather resulted from a perturbed regulatory T (Treg) cell compartment. Excessive miR-27 expression in T cells severely impairs Treg cell differentiation. Moreover, Treg cells with exaggerated miR-27-mediated gene regulation exhibit diminished homeostasis and suppressor function in vivo. Mechanistically, miR-27 represses several known as well as previously uncharacterized targets that play critical roles in controlling multiple aspects of Treg cell biology. Collectively, our data show miR-27 functions as a key regulator in Treg cell development and function and suggest that proper regulation of miR-27 is pivotal to safeguard Treg cell-mediated immunological tolerance.

overall_design: Treg cells isolated from healthy female mice with Treg cell-specific overexpression of miR-27a.

first: Leilani

middle: O

last: Cruz

first: Somaye

last: Hashemifar

first: Cheng

middle: J

last: Wu

first: Sunglim

last: Cho

first: Duc

middle: T

last: Nguyen

first: Ling

middle: L

last: Lin

first: Aly

last: Khan

first: Li

middle: F


title: Social status alters immune regulation and response to infection

first: Noah

last: Snyder-Mackler

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

overall_design: Refer to individual Series


title: shRNA TMEM258 knockdown in HeLa

city: Cambridge

first: Daniel

middle: Bartholomew

last: Graham

state: MA

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

summary: TMEM258 is associated with the OST complex. Loss of TMEM258 induces ER stress.

overall_design: TMEM258 was knocked down in HeLa cells using 4 distinct shRNA. 4 control shRNA were also used.

middle: B

first: Ramnik

last: Xavier


title: Excessive miR-27 expression impairs regulatory T cell-mediated immunological tolerance


title: The chromatin remodeler protein DDM1 regulates early seedling growth hybrid vigor by modulating gene expression in Arabidopsis

city: Boston

first: Yanqiang

last: Li

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

type: Methylation profiling by high throughput sequencing

summary: Despite of the paramount importance of heterosis in agriculture, the molecular mechanisms underlying heterosis remain elusive. Recent studies in Arabidopsis suggested possible involvement of DNA methylation in heterosis. We tested this hypothesis genetically by crossing homozygous mutants in DNA methylation-related genes in the Columbia (Col) ecotype with homozygous mutants in the same DNA methylation-related genes in the C24 ecotype. When genes in the RNA-directed DNA methylation (RdDM) pathway were mutated, the resultant F1 hybrids did not show appreciable loss of best parent heterosis (BPH) performances in early seedling growth. In contrast, mutations in the putative chromatin remodeling protein DECREASE OF DNA METHYLATION 1 (DDM1) caused ddm1-Col like growth pattern of ddm1-F1 hybrids, a mid-parent heterosis (MPH) performance. To understand the underlying molecular mechanisms, we compared the transcriptomes of the parental plants and reciprocal F1 hybrids in the wild type and ddm1 mutant backgrounds, and identified 183 non-additively expressed (NAE) genes, which were functionally enriched in defense response, a group of genes negatively associated with plant size. Interestingly, for the expression levels of the NAE genes, WT-F1 hybrids were enriched in the Golden Ration between mid-parent values (MPVs) and Col parents in WT, but ddm1-F1 hybrids were comparable to ddm1-Col parent in ddm1 mutant, which explained the MPH performance of ddm1-F1 hybrids. DNA methylation analyses revealed only one third of the NAE genes with highly methylated promoters whose expression is negatively associated with DNA methylation of promoters, strongly suggesting that DDM1 regulates heterosis by multiple epigenetic modifications.

overall_design: Whole genome bisulfite sequencing and RNA sequencing of the wild type and ddm1 mutant background of parent Col, C24, the hybrid ColXC24 and C24XCol to explore the role of the DDM1 in DNA hybrid vigor.

first: Qingzhu

last: Zhang

first: Tao

last: Xu

first: Dong

last: Wang

first: Liang

last: Zeng

first: Lan

last: Yang

last: He

first: Heng

first: Zhimin

last: Zheng

first: Dong-Lei

last: Zhao

first: Juan

first: Zhizhong

last: Gong

first: Renyi

last: Liu

first: Jian-Kang

last: Zhu


title: Epigenomic-based identification of major cell identity regulators within heterogeneous cell populations

first: Milos

last: Nikolic


title: RNA-Seq expression analysis of Entamoeba histolytica trophozoites adapted to grow in the presence of toxic amount of the Nitric Oxide donor S-Nitrosoglutathione (GSNO)

status: Public on Nov 06 2016

city: Haifa

first: Serge

last: Ankri

address: 1 Efron street

department: Microbiology

institute: Technion

summary: Entamoeba histolytica is a protozoan parasite responsible for amebiasis, a disease which is characterized by acute inflammation of the colon. Adaptation of the parasite to toxic level of nitric oxide (NO) produced by phagocytes may be essential for the establishment of chronic amebiasis and for the survival of parasite within the host. To obtain insight into the mechanism of adaptation to NO, E. histolytica trophozoites were selected in vitro by stepwise exposures to increasing amounts of NO donor S-Nitrosoglutathione (GSNO) up to a concentration of 110 µM. These NO adapted trophozoites (NAT) were more resistance to acute exposure of GSNO (350μM), to activated macrophages and have a better capability to invade porcine colon explants compared to wild-type trophozoites.  The transcriptome of NAT was investigated by RNA-sequencing (RNA-seq) and it showed only a weak overlapping with the transcriptome of trophozoites exposed to acute nitrosative stress (TEANS).

overall_design: RNA-Seq analysis of mRNA extracted from control trophozoites (two biological replicates) and from NAT (three biological replicates).

first: Preeti

last: Shahi

first: Meirav

last: Trebicz-Geffen


title: Reorganization of HoxD regulatory landscapes during the evolution of a snake-like body plan

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

institute: Hubrecht Institute

sample_organism:
Mus musculus
Pantherophis guttatus

platform_organism:
Mus musculus
Pantherophis guttatus


title: Reorganization of HoxD regulatory landscapes during the evolution of a snake-like body plan (ChIP-seq)

summary: While the vertebrate body plan is highly conserved amongst all species of this taxon, extreme variations thereof can be documented in snakes, which display both an absence of limbs and an unusually elongated trunk. As Hox genes are strong candidates both for the making and the evolution of this body plan, their comparative study in such a morphologically diverged group is informative regarding their potential causative importance in these processes. In this work we use an interspecies comparative approach where different aspects of regulation at the HoxD locus are investigated. We find that although spatial collinearity and associated epigenetic mark dynamics are conserved in the corn snake, other regulatory modalities have been largely restructured. A BAC transgenic approach indeed revealed that, while the majority of mesodermal enhancers in vertebrates appear to be mostly located outside of the cluster, the corn snake contains most mesodermal trunk enhancers within the HoxD cluster. We also find that, despite the absence of limbs and an altered Hoxd gene regulation in external genitalia, the bimodal chromatin structure at the corn snake HoxD locus is maintained. The analysis of particular enhancer sequences initially defined in the mouse and further isolated at the snake orthologous locus showed differences in their specificities for the limb and genital bud expression. Of particular interest, a snake counterpart of a mouse limb-only enhancer sequence evolved into a genital-only enhancer. Such a regulatory exaptation suggests that enhancer versatility may have been an important factor to accompany the transition towards the snake body plan. These results show that vertebrate morphological evolution is likely to have been associated with extensive reorganization at the HoxD regulatory landscapes while respecting a very conserved general regulatory framework.

overall_design: ChIP-seq analysis of H3K27me3 in corn snake brain and posterior trunk, H3K9me3 in corn snake  brain and H3K27ac in mouse and snake upper trunk


title: The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Promotes H2B Ubiquitylation Through a Direct Interaction with the Ubiquitin Conjugase Rad6

city: University Park

first: Alain

middle: Roger

last: Bataille

state: PA

address: 453 North Frear

department: BMB

institute: Penn State University

summary: Transcription by RNA polymerase II is regulated by epigenetic modifications to the chromatin template. The mono-ubiquitylation of H2B is established during transcription elongation and broadly impacts chromatin architecture and gene expression. The Polymerase Associated Factor 1 complex (Paf1C) is required for H2B ubiquitylation through an unknown mechanism. Here, we find that a 66-amino acid histone modification domain (HMD) within the Rtf1 subunit of Paf1C promotes H2B ubiquitylation in cells lacking all Paf1C members and present the crystal structure of this domain. Using site-specific in vivo crosslinking, we show that Rtf1 directly interacts with the ubiquitin conjugase Rad6 through a conserved surface on the HMD. Through ChIP-exo analysis, we observe that enrichment of Paf1C correlates with H2B ubiquitylation, and that the HMD, Rad6 and Bre1 localize to H2B. Finally, we demonstrate that the HMD directly stimulates H2B ubiquitylation in a reconstituted system, arguing that Paf1C functions as a cofactor for Rad6-Bre1 mediated catalysis.

overall_design: ChIP-exo of yeast Saccharomyces cerevisiae

first: S

last: Branden Van Os

first: Margaret

last: Shirra

first: Adam

middle: D

last: Wier

first: Kuangyu

last: Yen

first: Vinesh

last: Vinayachandran

first: In-Ja

last: Byeon

first: Annie

last: Heroux

first: Christine

middle: E

last: Cucinotta

first: Jongcheol

last: Jeon

first: Jaehoon

last: Kim

first: Angela

last: Gronenborn

first: Andrew

middle: P

last: VanDemark

first: B

last: Franklin Pugh

first: Karen

last: Arndt


title: Social status alters immune regulation and response to infection [cell_specific_RNAseq]

first: Noah

last: Snyder-Mackler

overall_design: mRNA sequencing of 5 purified cell types from 45 female rhesus macaques

first: Jenny

last: Tung


title: Comparative transcriptomic profiling at E3-E3.5, E5-E5.5 and E8-E8.5 stages of retina development in pigeon and chicken

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

summary: The macula and fovea located at the optical centre of the retina make primate visual perception unique among mammals. Pigeon retina and the human macula share a number of structural and functional properties that justify introducing the former as a new model system for retina development. Comparative transcriptome analysis of the pigeon and chicken retinas at different embryonic stages was undertaken to uncover how transcriptomic patterns translate into functional differences between the two bird species. The study showed that the pigeon’s genetic programs underlying cell differentiation are postponed until the end of the period of cell proliferation. This allows the pigeon to build a retina that displays the structural and functional traits typical of primate macula and fovea.

sample_organism:
Columba livia
Gallus gallus

platform_organism:
Columba livia
Gallus gallus

overall_design: Triplicate samples of RNA from E3-E3.5, E5-E5.5 and E8-E8.5 stages of pigeon and chicken developing retinas were profiled by RNAseq

first: Tania

last: Rodrigues

first: Dorota

last: Skowronska-Krawczyk

first: Lidia

last: Matter-Sadzinski

first: Jean-Marc

last: Matter


title: RNA-Seq data of CD4+ T cells from mice with Type-A vs Type-B EAE

city: Durham

first: Mari

last: Shinohara

state: NC

institute: Duke University School of Medicine

summary:
Purpose: To compare gene expression of CD4+ T cells between Type-A and Type-B EAE
Method: CD4+ T cells were FACS sorted from spleens 9-day post immunization.
Results: We found that Type-B EAE (NLRP3 inflammasome-dependent and IFNb treatment-resistant EAE) express high levels of CXCR2 and other chemokine receptors, which can be targeted to treat the Type-A EAE subtypes, instead of treating with IFNb.
Conclusions: Altering intensity of immunization significantly impacts on gene expression patterns in T cells.

overall_design: CD4+ T cells were FACS-sorted, then stranded mRNA libraries were made with the Illumina TruSeq Stranded mRNA kit (catalog number RS-122-2101). The quality of RNA libraries was checked by running them on a 2100 ioanalyzer instrument  (Agilent), pooled and sequenced on 2 lanes of Illumina HiSeq 50bp paired-end.

first: Makoto

last: Inoue


title: Ribosome profiling of dhh1∆ yeast

status: Public on Nov 04 2016

city: Münster

first: Danny

middle: D.

last: Nedialkova

address: Von-Esmarch-Str. 54

department: Max Planck Research Group for RNA Biology

institute: Max Planck Institute for Molecular Biomedicine

summary:
The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here
we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and
genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies
of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in
membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common
features. First, they contain long and highly structured CDSs, including a region located around 42 to
120 nucleotides after the translation initiation site, second, they are directly bound by Dhh1 with a
specific binding distribution and third, complementary experimental approaches suggest that they are
activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a conserved layer of translational control that involve
RNA helicases and RNA folding within CDS providing novel opportunities for regulation of
membrane and secretome proteins.

overall_design: Cells were grown in rich medium and sequencing was performed on ribosome-protected footprints and matched samples of randomly fragmented polyA-enriched RNA. Dataset contains three biological replicates.


title: An RNA-seq transcriptome analysis of floral buds of an interspecific Brassica hybrid between B. carinata and B. napus

city: Nanjing

first: Pu

last: Chu

address: No.1 Weigang street

country: China

institute: Nanjing Agriculture University

summary: Using the Illumina HiSeq 2000 platform, 39,598; 32,403and 42,208 genes were identified in flower buds of B. carinata cv.W29, B. napus cv. Zhongshuang 11 and their hybrids, respectively. The differentially expressed genes (DEGs) were significantly enriched in pollen wall assembly, pollen exine formation, pollen development, pollen tube growth, pollination, gene transcription, macromolecule methylation and translation, which might be associated with impaired fertility in the F1 hybrid. These results will shed light on the mechanisms underlying the low fertility of the interspecific hybrids and expand our knowledge of interspecific hybridization.

sample_organism:
Brassica napus
Brassica carinata
Brassica carinata x Brassica napus

overall_design: Transcriptome analysis of floral buds of the interspecific Brassica hybrid and its parents using the Illumina HiSeq 2000 platform,.

first: Rongzhan

last: Guan


title: Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii

city: Wuhan

first: Wei

last: Zhang

state: Hubei Province

address: Luoyu

institute: Central China Normal University

summary: The goal of this study is to compare NGS-derived transcriptome profiling (RNA-seq) from three tissues of  L. boringii between two critical periods of the spine growth cycle, and to identify potential genes regulating the seasonal development of nuptial spines in  L. boringii. We obtained 94,900 unigenes and 2,131 differentially expressed genes among three tissues between two different spine growh periods. In the upper jaw skin, DEGs were mainly enriched in cytosolic part, peptidase inhibitor activity and peptidase regulator activity. While in the other two tissues, DEGs were primarily involved in cell cycle, DNA replication and melatonin production. Specifically, insulin/insulin-like growth factor and sex steroid hormone related DEGs were identified in the upper jaw skin. The variation of IGF2 and estrogen related genes may be the main factors regulating the seasonal development of the spines.

overall_design: RNA profiles of three tissues from two different development periods, in triplicate, using Illumina sequencing. Compare the expression pattern between these two periods and identify differentially expressed genes.


title: Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [RNA-seq]

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

summary: Epithelial to mesenchymal transition (EMT) in cancer cells has been associated with metastasis, stemness and resistance to therapy. The reason why some tumors undergo EMT and other not might reflect intrinsic properties of their cell of origin, although this possibility is largely unexplored. By targeting the same oncogenic mutations to discrete skin compartments, we show cell type-specific chromatin and transcriptional states differentially prime tumors to EMT.  Squamous cell carcinomas (SCCs) derived from intrafollicular epidermis (IFE) are generally well-differentiated, while hair follicle (HF) stem cell-derived SCCs frequently exhibit EMT, efficiently form secondary tumors, and possess increased metastatic potential.  Transcriptional and epigenomic profiling revealed IFE and HF tumor-initiating cells possess distinct chromatin landscapes and gene regulatory networks associated with tumorigenesis and EMT that correlate with accessibility of key epithelial and EMT transcription factor binding sites.  These findings highlight the importance of chromatin states and transcriptional priming in dictating tumor phenotypes and EMT.

overall_design: Epcam+ cells were plated and treated or not with TGFb during 48 hours and then FACS sorted

first: M

last: Latil

last: Beck

first: S

last: Boumhadi

first: A

last: Brisebarre

first: C


title: Excessive miR-27 expression impairs regulatory T cell-mediated immunological tolerance [CD4cre miR-23 clusterTg Tr]

first: Li-Fan

last: Lu

overall_design: Treg cells isolated from mice with T cell-specific overexpression of the entire miR-23 cluster or individual miR-23 family members as well as from mice with T cell-specific deletion of both miR-23a/b clusters.

first: Leilani

last: Cruz

first: Somaye

middle: S

last: Hashemifar

first: Cheng

last: Wu

first: Sunglim

last: Cho

first: Duc

last: Nguyen

first: Ling

last: Lin

first: Aly

middle: A

last: Khan

first: Li


title: A new model for long-range chromatin reorganization linked to enhancer activation

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

type: Genome binding/occupancy profiling by genome tiling array

type: Expression profiling by genome tiling array


title: Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hotspots (sequencing)

city: Tampa

first: John

middle: Lamoine

last: Cleveland

state: FL

address: 12902 USF Magnolia Drive

institute: H. Lee Moffitt Cancer Center

summary: Meiotic recombination is initiated by the Spo11 endonuclease, which directs DNA DSBs. We report here that the recombinogenic cores of active hotspots in mice harbor several histone H3 and H4 acetylation and methylation marks that are typical of open, active chromatin. Further, deposition of these histone marks is dynamic and manifest at spermatogonia and/or pre-leptotene meiotic cells, which would facilitate the formation of DSBs at leptotene. Importantly, there was concordance in the overlap of the histone mark ChIP profiles with nucleosome occupancy maps, which were determined by real-time PCR and whole genome sequencing (WGS) analyses of micococcal-nuclease resistance regions across four mouse meiotic hotspots (HS22, HS59.4, HS59.5 and HS61.1). Our study reveals that there are instructive roles of histone acetylated marks at meiotic recombination hotspot cores and that they are necessary to promote hotspot activity and crossover resolution.

overall_design: Genome-wide sequencing of mono-nucleosomal mouse DNA using Illumina GAII Genome Analyzer.

first: Philippe

middle: R

last: Bois

first: Mohammad

last: Fallahi

first: Irina

middle: V

last: Getun


title: Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hotspots


title: Reorganization of HoxD regulatory landscapes during the evolution of a snake-like body plan (4C-seq)

first: Isabel

last: Guerreiro

overall_design: 4C-seq analysis of mouse and snake whole embryo and genital bud tissue using viewpoints contained within the cluster


title: Alternative splicing in tomato pollen in response to heat stress

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

summary: Alternative splicing caused by exposure of pollen to high temperatures leads to the generation of transcripts with pre-mature termination codon targeted for degradation or mRNAs putatively coding for truncated proteins with altered functions thereby controlling important cellular pathways including transport and localization, heat stress response, gene expression and various biosynthetic processes.

overall_design: 8 samples including 2 tomato cultivars und 2 conditions in two replicates each

first: Mario

last: Keller

first: Yangjie

last: Hu

first: Anida

last: Mesihovic

first: Sotirios

last: Fragkostefanakis

first: Enrico

last: Schleiff


title: Buffer composition affects ribosome footprint precision in Arabidopsis root and shoot

first: Polly

middle: Yingshan

last: Hsu

address: Duke University

department: Biology

institute: Duke University

summary: The goal of this study is to test ionic strength and buffering capacity in polysome extraction buffer on ribosome footprints in Arabidopsis root and shoot.

overall_design: Ribo-seq generated from Arabidopsis root and shoot prepared with four different polysome extraction buffers. All four buffers contain 2% polyoxyethylene 10 tridecyl ether, 1% deoxycholic acid, 1 mM DTT, 100 µg/mL cycloheximide, and 10 unit/mL DNase I, but with different ionic strength or buffering capacity listed below. Buffer A: 200 mM Tris-HCl (pH 8), 50 mM KCl, 25 mM MgCl2; buffer B: 200 mM Tris-HCl (pH 8), 40 mM KCl, 20 mM MgCl2; buffer C: 200 mM Tris-HCl (pH 8), 30 mM KCl, 15 mM MgCl2; buffer D: 100 mM Tris-HCl (pH 8), 40 mM KCl, 20 mM MgCl2. 8 libraries in total.

middle: Y

first: Philip

middle: N

last: Benfey


title: A novel translational control mechanism involving RNA structures within coding sequences

city: Goettingen

first: Markus

middle: T.

last: Bohnsack

address: Humboldtallee 23

department: Institute for Molecular Biology

institute: Goettingen University

summary: The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site, second, they are directly bound by Dhh1 with a specific binding distribution and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.

overall_design: Wild-type BY4741 yeast cells or cells expressing genomically His-Tev-ProtA-tagged Dhh1 were crosslinked using UV and analysed by CRAC.

first: Jennifer

last: Jungfleisch

first: Danny

last: Nedialkova

first: Ivan

last: Dotu

first: Katherine

last: Sloan

first: Neus

last: Martinez-Bosch

first: Lukas

last: Brüning

first: Emanuele

last: Raineri

first: Pilar

last: Navarro

middle: T

first: Sebastian

last: Leidel

first: Juana

last: Díez


title: Regulation of biofilm formation, twitching motility, and virulence in Galleria mellonella by AdeN protein of Acinetobacter baumannii

city: Winnipeg

first: Manu

middle: Kumar

last: Singh

state: Manitoba

address: 45 Chancellors circle, 412 Buller

country: Canada

institute: University of Manitoba

summary: AdeN deletion mutant AB141 was studied for its effects on biofilm formation, twitching motility, and virulence using phenotypic methods, and the further global role of AdeN was further studied using a multiomics approach

overall_design: A deletion mutant of the adeN gene in ATCC 17978 (AB141) was created by homologous recombination

first: Mark

last: Unger

first: Patrick

last: Chong

first: Garrett

last: Westmacott

first: Ayush

last: Kumar


title: Comparative small RNA analysis of pollen development in autotetraploid and diploid rice

city: Guangzhou

first: andyslee

last: Li

address: Wushan 483

institute: South China Agricultural University

summary: MicroRNAs (miRNAs) play key roles in plant reproduction. However, knowledge on microRNAome analysis in autotetraploid rice is rather limited. Here, high-throughput sequencing technology was employed to analyze miRNAomes during pollen development in autotetraploid rice. A total of 172 differentially expressed miRNAs (DEM) were detected in autotetraploid rice compared to its diploid counterpart, and 57 miRNAs were specifically expressed in autotetraploid rice. Of the 172 DEM, 115 and 61 miRNAs were found to be up-regulated and down-regulated, respectively. Gene Ontology analysis on the targets of up-regulated DEM showed that they were enriched in transport and membrane in pre-meiotic interphase, reproduction in meiosis, and nucleotide binding in single microspore stage. osa-miR5788 and osa-miR1432-5p_R+1 were up-regulated in meiosis and their targets revealed interaction with the meiosis-related genes, suggesting that they may involve in the genes regulation associated with the chromosome behavior. Abundant 24-nt siRNAs associated with transposable elements were found in autotetraploid rice during pollen development; however, they significantly declined in diploid rice, suggesting that 24-nt siRNAs may play a role in pollen development. These findings provide a foundation for understanding the effect of polyploidy on small RNA expression patterns during pollen development that lead to low pollen fertility in autotetraploid rice.

overall_design: To investigate the miRNAs associated with the pollen development of autotetraploid and diploid (CK) rice, three pollen development stages, including PMA (pre-meiotic interphase), MA (meiosis) and SCP (single microspore stage), were selected to construct six libraries and sequenced by Solexa high-throughput sequencing technology.

first: Xiangdong

last: Liu

first: Xiang


title: Ribosome profiling in Arabidopsis root and shoot

first: Polly

last: Hsu

summary: The goal of this study is to map genome-wide ribosome occupancy on mRNAs in Arabidopsis root and shoot to characterize translatome.

overall_design: RNAseq and ribo-seq generated from three biological replicates of root and shoot harvested from 4-day old wild-type plant (Col); 12 libraries in total.

first: Philip

last: Benfey


title: Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae HTA1-S121A strain upon thermo and osmotic stress.

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

institute: IRB Barcelona

summary: To study the relevance of the post-translational modification in the H2A histone residue S121, we assessed the genome-wide transcriptional response of the non-phosphorylatable histone mutant HTA1-S121A (H2AS121A) upon two different stress conditions; osmostress and heat shock. Results point out that the unphosphorylatable H2AS121A protein showed an impaired stress responsive gene expression indicating that this specific histone residue plays a relevant role in stress responsive transcriptional regulation.

overall_design: Total RNA obtained from the Saccharomyces cerevisiae HTA1 wild type and HTA1-S121A strains (Nakanishi, S. et al. (2008)  Nature structural & molecular biology, 15(8), 881-888) untreated or subjected to osmotic stress (15 min at 0,4M NaCl) or to heat stress (10 min at 39ºC). Experiment was done by triplicate.

first: Eulàlia

last: deNadal

first: Carme

last: Sole

first: René

last: Böttcher


title: Transcriptome sequencing of Macrobrachium nipponense hepatopancreas at different nitrite concentrations

city: Shanghai

first: Xu

last: Zhixin

address: 500 Dongchuan Rd.,Shanghai 200241

institute: East China Normal University

summary: Macrobrachium nipponense is one of the commonest species threatened by ambient superfluous nitrite. The mechanism of nitrite stress at the molecular level was studied using de novo RNA-Seq to explore the molecular pathways in M. nipponense exposed to the acute nitrite stress (26.05 mg/L nitrite-N) for 24h and the chronic nitrite stress (6.58 mg/L nitrite-N) for 21d. A total of 175.13 million reads were obtained and assembled into 58,871 unigenes with an average length of 1,028.7 bp and N50 of 1,294bp. 2,824 and 2,610 unigenes in the acute and chronic nitrite stress were significantly differentially expressed respectively. Based on the change in GO analysis and KEGG pathway analysis, pathways both in the acute and chronic nitrite stress were glycosphingolipid biosynthesis - ganglio series, alanine aspartate and glutamate metabolism, biotin metabolism and amino sugar and nucleotide sugar metabolism which revealed the commonly functional pathways in acute and chronic nitrite stress. The markedly altered pathways were divided into four sections of immunity, metabolism, cell and others. Immunity section contained the most pathways among the classifications as phagosome, folate biosynthesis, glycerolipid metabolism, glycine, serine and threonine metabolism, selenoamino acid metabolism, cysteine and methionine metabolism, amino sugar and nucleotide sugar metabolism and taurine and hypotaurine metabolism in the acute nitrite stress and lysosome, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, glycosaminoglycan degradation and amino sugar and nucleotide sugar metabolism in the chronic nitrite stress. This is the first report of whole molecular responses of M. nipponense under acute and chronic nitrite stress through de novo transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanisms of the nitrite stress for crustacean species.

overall_design: Examination of 4 different nitrite treated hepatopancreas in Macrobrachium nipponense

first: Tongyu

first: Zhixin

last: Xu


title: Integrative classification of human coding and non-coding genes based on RNA metabolism profiles

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

summary: The pervasive transcription of the human genome results in a heterogeneous mix of coding and long non-coding RNAs (lncRNAs). Only a small fraction of lncRNAs possess demonstrated regulatory functions, making it difficult to distinguish functional lncRNAs from non-functional transcriptional byproducts. This has resulted in numerous competing incoherent annotations of human lncRNA. To address these challenges, we quantitatively examined transcription, splicing, degradation, localization and translation for coding and non-coding human genes. Annotated lncRNAs had lower synthesis and higher degradation rates than mRNAs. We discovered mechanistic differences explaining the slower splicing of lncRNAs. We grouped genes into coherent classes by performing annotation-agnostic unsupervised classification of RNA metabolism profiles. These classes contained both mRNAs and lncRNAs to varying degrees; they exhibited distinct relationships between steps of RNA metabolism, evolutionary patterns, and sensitivity to cellular RNA regulatory pathways. Our classification provides a functionally coherent alternative to genomic context-driven annotations of lncRNAs.

overall_design:
HEK293 cells were labeled with 4-thiouridine for 0, 7.5, 15, 30, 45, and 60 minutes were collected in triplicate and strand-specifically paired-end sequenced on a HiSeq2500.

Please note that the 'readme.txt' contains detailed description of the 'ST*.txt' processed data file content and data processing steps.

first: Uwe

last: Ohler


title: Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

status: Public on Nov 03 2016

first: Michal

last: Mokry

address: Lundlaan 6

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

summary: Background: Genome wide association studies (GWASs) have revealed many susceptibility loci for complex genetic diseases. For most loci the causal genes have not been identified. The identification of candidate genes is currently mainly based genes that localize close to or within the identified loci. We have recently shown that 92 of the 163 Inflammatory Bowel Disease (IBD)-loci co-localize with noncoding DNA regulatory elements (DRE). Mutations in DRE can contribute to the pathogenesis of IBD through dysregulation of gene expression.  Consequently, genes that are regulated by these 92 DRE are to be considered as candidate genes. We developed a novel approach for candidate gene identification that is based on DNA regulatory mechanisms.Results: By using circular chromosome conformation capture-sequencing (4C-seq), we have identified genomic regions that physically interact with the 92 DRE that were found at IBD susceptibility loci. Since the activity of regulatory elements is cell type specific, 4C-seq was performed in monocytes, lymphocytes and intestinal epithelial cells. Altogether, we identified 902 novel IBD candidate genes. These genes include genes specific for one of the IBD subtypes and many noteworthy genes like ATG9A and IL10RA. We show that the expression of many novel candidate genes is genotype dependent and that these genes are upregulated during intestinal inflammation in IBD. Pathway analyses further identified HNF4α as a potential key upstream regulator of the IBD candidate genes.Conclusions: In this study, 4C-seq is used to systematically analyze chromatin interactions at IBD susceptibility loci that localize to regulatory DNA We reveal many novel and relevant IBD candidate genes, pathways and regulators.  Our approach complements classical candidate gene identification, links novel genes to IBD and can be applied to any existing GWAS data.

overall_design: 92 individual 4C-seq datasets in human monocytes, lymphocytes and DLD cell line. Lymphocyte dataset consists from two biological replicates.

first: M


title: chromatin changes upon short Hsp90 depletion and Sba1 ChIP-Seq

city: Urbana

first: Brian

middle: Christopher

last: Freeman

state: Illinois

address: 601 South Goodwin Avenue

department: Department of Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

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

overall_design: Refer to individual Series


title: Sba1 ChIP-Seq

summary: Chromatin immunoprecipitation of Sba1 (yeast p23 homolog) was performed as described (PMID: 10376605) using an antibody specific for Sba1 (PMID: 10691735) or normal rabbit serum (Control) and logarithmically growing yeast. We report 572 genomic locations associated with sba1.

overall_design: Genome wide sba1 occupancy on yeast genome were profiled using ChIP-seq

first: Yang

last: Zhang

middle: C


title: Yeast Hsp90-dependent chromatin changes as monitored using DNase-Seq

summary: We report the application of DNase-Seq (adapted from Hesselberth et al., 2009, as described in Zelin et al., 2012) to study the chromatin changes upon short Hsp90 depletion by exploiting temperature-sensitive allele G170D (Nathan and Lindquist, 1995). By generating ~43.6 million reads for wild type and 68.6 million reads for mutant, we were able to reconstitute the hypersensitivity maps under the regular conditions and under the conditions where Hsp90 was heat-inactivated. We find that there is a global reduction of open chromatin upon Hsp90 inactivation, as displayed by the decrease of total DHS size and the DHSs numbers. We also find that loss of Hsp90 leads to the increase of open chromatin at certain locations associated with chromatin remodelers such as RSC. Overall this study shows that short term improper functioning of Hsp90 results in genome-wide chromatin perturbations thereby demonstrating an Hsp90-dependence of chromatin architecture.

overall_design: DNase-Seq in WT and the Hsp90 temperature-sensitive strain with allele G170D at a non-permissive temperature

first: Zlata

last: Gvozdenov


title: RNA-seq of mouse embryonic stem cell states expressing Esrrb, Tbx3, and Zscan4

city: Pasadena

first: Michael

last: Elowitz

state: Ca

address: 1200 E California Blvd MC 114-96

department: Bioengineering

institute: Caltech

summary: We develop a theoretical-computational framework for inferring cell state transition dynamics, and apply it to mouse embryonic stem cells states defined by expression levels of Esrrb, Tbx3, and Zscan4. RNA-seq was performed to characterize the larger transcriptional differences between states expressing combinations of these three specific genes, and proceed to explore their dynamic interconversion.

overall_design: A double knock-in reporter for Esrrb and Tbx3 with distinct fluorescent proteins was constructed to enable purification of substates defined by their relative expression levels (Esrrb-/Tbx3-; Esrrb+/Tbx3-; Esrrb+/Tbx3+). A second line was constructed using a promoter-fragment reporter to isolate Zscan4+ from Zscan4- cells. Following FACS isolation, the subpopulations were sequenced on an Illumina HiSeq2500. Biological replicates were collected on different days.

middle: B

first: Zakary

last: Singer

first: Sahand

last: Hormoz


title: Identification of functional interactions through integration and systems analysis of matched gene and microRNA expression data across the Ludwig-Melbourne Melanoma (LM-MEL) Cell Line Panel

city: Houston

first: Miles

last: Andrews

address: 1881 East Road

department: Surgical Oncology

institute: MD Anderson Cancer Center

summary: MicroRNAs contribute to metastatic progression in many cancers by modulation of phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. However, it remains challenging to identify microRNA-mRNA interactions of functional significance at endogenous expression levels. The LM-MEL cell line panel comprises a large set of unique melanoma cell lines derived from largely metastatic melanoma tumours, as described in Behren et al, PCMR 2013 26(4):597-600 (PMID 23527996). For this study, 57 of the cell lines underwent matched gene expression (Illumina HT12v4 microarray) and small RNASeq (Illumina HiSeq) profiling in unperturbed conditions, generating a large dataset of matched gene and microRNA abundance data which was integrated with available phenotypic annotations covering several conditions of biological interest. We developed a novel systems analysis workflow to identify putative regulatory interactions suitable for subsequent validation.

overall_design: Small RNA profiling of 57 cell lines of the LM-MEL panel using the Illumina HiSeq platform, with miRNA profiling performed subsequently using the miRanalyzer webserver interface (http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php)

first: Andreas

last: Behren


title: Immunomodulatory induced by Cathepsin L1 vaccine in sheep infected with Fasciola hepatica.

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: Liver fluke (Fasciola hepatica) infection is both a welfare and productivity issue in sheep farming. Death can result from acute infection, and deaths are becoming more frequent as anthelmintic resistance increases. New control strategies are desirable, and vaccination is a good option. Previous studies have shown an experimental vaccine based on a F. hepatica protein, cathepsin L1, (rmFhCL1) may be a viable aid to control liver fluke in cattle/sheep, however efficacy is variable. A trial was conducted on sheep immunized with rmFhCL1 following infection with F. hepatica to understand the immune response changes induced by vaccinination at a molecular level . Peripheral blood mononuclear cells (PBMCs) were isolated at four different time points for RNA-Seq analysis. Genes differentially expressed between vaccinated and control animals were identified. Their functional roles were studied using in silico methods.

overall_design: Four vaccinated and five unvaccinated (control) lambs were used in this study. Blood was collected for all animals at pre-vaccination (Time point 0), pre-infection (Time point 1), one week post infection (Time point 2) and 14 weeks post infection (Time point 3). PBMCs were isolated and RNA extracted. A total of 36 libraries were constructed and sequenced using the Illumina Hiseq 2500 platform.

first: Yan

last: Fu

first: John

last: Browne

first: Mary

last: Sekiya

first: Grace

last: Mulcahy


title: The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem

city: Cologne

first: Peter

last: Frommolt

address: Joseph-Stelzmann-Str. 26

institute: CECAD

summary: Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. Within these founder-cells, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. In contrast to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, only subtle transcriptional reprogramming within the global auxin network was observed, suggesting that auxin response might play a minor role in the earliest stages of lateral floral initiation.

overall_design: Evaluation of the transcriptome of DRNL expressing and non-expressing protoplasts after Fluorescence-activated cell sorting in four biological replicates with additional comparison to the ap1 cal IM

first: Anneke

last: Frerichs

first: Rahere

last: Thoma

first: Ali

last: Abdallah

first: Wolfgang

last: Werr

middle: W

last: Chandler


title: SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis

status: Public on Nov 02 2016

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Epigenetic regulation is important for organismal development and response to the environment. Alteration in epigenetic status has been known mostly from the perspective of enzymatic actions of DNA methylation and/or histone modifications. In a genetic screen for cellular factors involved in preventing epigenetic silencing, we isolated an Arabidopsis mutant defective in SAC3B, a component of the conserved TREX-2 complex that couples mRNA transcription with nuleo-cytoplasmic export. Arabidopsis SAC3B dysfunction causes gene silencing at transgenic and endogenous loci, accompanied by elevation in the repressive histone mark H3K9me2 and by reduction in RNA polymerase Pol II occupancy. SAC3B dysfunction does not alter promoter DNA methylation level of the transgene d35S::LUC, although the DNA demethylase ROS1 is also required for d35S::LUC anti-silencing. THP1 and NUA were identified as SAC3B-associated proteins whose mutations also caused d35S::LUC silencing. RNA-DNA hybrid exists at the repressed loci but is unrelated to gene suppression by the sac3b mutation. Genomewide analyses demonstrated minor but clear involvement of SAC3B in regulating siRNAs and DNA methylation, particularly at a group of TAS and TAS-like loci. Together our results revealed not only a critical role of mRNA-export factors in transcriptional anti-silencing but also the contribution of SAC3B in shaping plant epigenetic landscapes.

overall_design: MethylC-Seq: 3 samples examined, Col-0, sac3b-7 (SALK 111245), and sac3b-3 (SALK 065672); mRNA-Seq: 2 samples examined and each sample has two replicates, Col-0 and sac3b-7 (SALK 111245); sRNA-Seq: 3 examples examined, Col-0, sac3b-7 (SALK 111245), and sac3b-3 (SALK 065672)

first: Yu

last: Yang

first: Honggui

last: La

first: Kai

last: Tang

first: Lan

first: Huiming

last: Zhang


title: Tyrosine Kinase Inhibitor Cardiotoxicity

city: Stanford

first: Jared

last: Churko

state: CA

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford


title: Genome-wide Gene Expression Profiling in DLBCL Cell Lines Treated with CUDC-907

city: Lexington

first: Kaiming

last: Sun

address: 4 Maguire Rd.

department: Translational Science

institute: Curis

summary: CUDC-907 is a small-molecule dual-acting inhibitor of HDACs and PI3Ks, which effectively suppresses the growth and survival of MYC-altered DLBCL. To evaluate the effect of CUDC-907 on MYC-associated genes, two DLBCL cell lines were treated with CUDC-907, a total of 948 differentially regulated genes were identified. 24 genes from the CUDC-907–regulated 948-gene set present either in the "HALLMARK_MYC_TARGETS_V1” 200-gene set or in the “HALLMARK_MYC_TARGETS_V2” 58-gene set in the Molecular Signatures Database (MSigDB). We then computed the correlation coefficients (r) between gene expression levels and MYC protein levels across all samples in the TCGA DLBCL dataset. We found that mRNA expression changes induced by CUDC-907 in the two DLBCL cell lines are negatively correlated with correlation coefficients between expression levels and MYC protein level in the TCGA DLBCL dataset

overall_design: Examination of differentially regulated genes in 2 cell lines treated with CUDC-907

first: Jing

last: Wang


title: A new model for long-range chromatin reorganization linked to enhancer activation [5C]

city: Edinburgh

first: Nezha

last: Benabdallah

address: Crewe Road South

institute: University of Edinburgh

summary:
The most prominent model for long-range enhancer regulation involves direct enhancer-promoter interaction by looping out the intervening chromatin. Using a synthetic biology approach, we have determined that a chromatin unfolding bteween Shh and its enhancers is regulated specifically by the Shh-Brain-Enhancers and is mediated by the recruitment of Poly (ADP-Ribose) Polymerase 1.  This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models.
Using 5C study the enhancer-driven activation of the Sonic hedgehog gene (Shh)

overall_design: 5C oligonucleotides were designed around HindIII restriction sites following an alternative scheme

first: Iain

last: Williamson

first: Robert

last: Illingworth

first: Shelagh

last: Boyle

first: Graeme

last: Grimes

first: Pierre

last: Therizols

first: Wendy

last: Bickmore


title: Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary: Human neocortex expansion likely contributed to the remarkable cognitive abilities of humans. This expansion is thought to primarily reflect differences in proliferation versus differentiation of neural progenitors during cortical development. Here, we have searched for such differences by analysing cerebral organoids from human and chimpanzees using immunohistochemistry, live imaging, and single-cell transcriptomics. We find that the cytoarchitecture, cell type composition, and neurogenic gene expression programs of humans and chimpanzees are remarkably similar. Notably, however, live imaging of apical progenitor mitosis uncovered a lengthening of prometaphase-metaphase in humans compared to chimpanzees that is specific to proliferating progenitors and not observed in non-neural cells. Consistent with this, the small set of genes more highly expressed in human apical progenitors points to increased proliferative capacity, and the proportion of neurogenic basal progenitors is lower in humans. These subtle differences in cortical progenitors between humans and chimpanzees may have consequences for human neocortex evolution.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Single-cell transcriptomes from human and chimpanzee cerebral organoids from multiple time points were analyzed in this study. All single cell samples were processed on the microfluidic Fluidigm C1 platform and contain 92 external RNA spike-ins. Human data were generated from dissociated whole organoids derived from induced pluripotent stem cell line SC102-A1 (iPSC SC102-A1) at 60 days after the start of embryoid body culture. Chimpanzee data were generated from dissociated whole organoids from iPS cell line SandraA at 45 days and PR818-5 at 50 days, 55 days, 61 days and 80 days and microdissected cortical-like regions from chimpanzee iPS cell line PR818-5 at 51 days and 62 days.

first: Sabina

last: Kanton

first: Barbara

last: Treutlein


title: Gene expression study of Pestalotiopsis fici on PDA medium and SA medium

city: Beijing

first: xiaoling

last: zhang

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of microbiology chinese academy of sciences

summary: We studied mitochondrial gene expressions of Pestalotiopsis fici when cultivated on two media.

overall_design: Detection of mitochondrial gene expression of P. fici on PDA and SA substrates after 20 days' incubation.

first: Xiuna

first: Xingzhong

last: Liu


title: Xanthomonas campestris pv. campestris str. 8004 (Xcc 8004; Indian Isolate): Wild type vs xibR mutant, under the both iron-replete and iron-deplete conditions.

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Transcriptional profiling of low-iron stimulon and XibR influenced regulon using wild-type Xcc 8004 and xibR mutant grown under iron-replete and iron-deplete conditions. Trancriptional analysis under iron-deplete condition, mimicking in planta environment, provides greater insights into expression pattern of several virulence-associated functions under low-iron. A genetic screen sggested the involvement of XibR (Xanthomonas iron binding regulator) in iron-uptake and metabolism. Present transcriptional analysis suggested the co-regulation of virulence associated functions including siderophore biosynthesis, motility, chemotaxis and typeIII effectors by a novel transcriptional regulator of NtrC family protein XibR and iron avability.

overall_design: Organism: Xanthomonas campestris, Agilent Custom Xanthomonas campestris 8x15K Array designed by Genotypic Technology Private Limited.

first: Chatterjee

last: Subhadeep

first: Pandey

last: Sheo Shankar


title: Comparison of planktonic and biofilm growth of Group A Streptococcus by high-throughput RNA sequencing (RNA-seq)

city: Nashville

first: Eric

middle: P

last: Skaar

state: Tennessee

address: 1161 21st Avenue South, A5303B MCN

institute: Vanderbilt University Medical Center

summary: Through the use of RNA-seq, we compared the transcriptome of Group A Streptococcus (GAS) at multiple biofilm time points to multiple planktonic time points in order to determine genes that are differentially expressed during biofilm growth.

overall_design: Biological triplicates from four biofilm time points (8 hour biofilm, 16 hour biofilm, 6 day biofilm and 10 day biofilm) were analyzed and compared to biological triplicates from three planktonic time points (early log phase, late log phase, and early stationary phase).

first: Jeffrey

last: Freiberg

first: Yoann

last: Le Breton

first: Kevin

last: McIver

first: Mark

last: Shirtliff


title: Targeted deletion of an Nr4a1 associated enhancer ablates Ly6Clow monocytes while protecting pleiotropic gene function in macrophages [ChIP-seq]

city: La Jolla

first: Graham

middle: David

last: Thomas

address: 9420 Athena Circle

department: Inflammation Biology

institute: La Jolla Institute for Allergy and Immunology

summary: Mononuclear phagocytes are a diverse cell family that occupy all tissues and assume numerous functions to support tissue and systemic homeostasis. Our ability to investigate the roles of individual subsets is limited by an absence of approaches to ablate gene function within specific sub-populations. Using Nr4a1-dependent Ly6Clow monocytes as a representative cell type we show that enhancer deletion addresses these limitations. Combining ChIP-Seq and molecular approaches we identify a single, conserved, sub-domain within the Nr4a1 enhancer that is essential for Ly6Clow monocyte development. Mice lacking this enhancer lack Ly6Clow monocytes but retain Nr4a1 gene expression in macrophages during steady state and in response to LPS. Nr4a1 is a key negative regulator of inflammatory gene expression and decoupling these processes allows Ly6Clow monocytes to be studied without confounding influences. Enhancer targeting possesses greater specificity than cre recombinase-mediated gene deletion, providing a route to generate loss-of-function models in closely related cell types.

overall_design: ChIP-Sequencing for histone modifications H3K4me2 and H3K27ac in primary murine monocyte dendritic cell precursors (MDP), common monocyte progenitors (cMoP), Ly6Chi monocytes and Ly6Clow monocytes sorted from the bone marrow of C57BL/6 mice/

middle: D


title: Targeted deletion of an Nr4a1 associated enhancer ablates Ly6Clow monocytes while protecting pleiotropic gene function in macrophages [RNA-seq]

overall_design: Paired End mRNA sequencing of FACS purified primary murine MDP, cMoP, Ly6Chi and Ly6Clow monocytes from the bone marrow and Ly6Chi and Ly6Clow monocytes from the peripheral blood


title: Tumor-Specific Retrogene NANOGP8 Reprograms Prostate Cancer Cells to Castration Resistance by Engaging the FOXA1/AR Signaling Axis and MYC [ChIP-seq]

city: Smithville

first: Collene

last: Jeter

state: TX

address: 1808 Park Rd 1C, Box 389

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Targeted disruption of the embryonic stem cell (ESC) self-renewal and pluripotency factor NANOG has been shown to diminish cancer cell clonogenic growth in vitro and tumor development in vivo. NANOG has also been shown to augment CSC properties and propel the emergence of castration-resistance prostate cancer (CRPC) phenotypes. Here, we investigate the molecular mechanisms underlying NANOG-mediated oncogenesis and prostate cancer progression to androgen independence.  ChIP-Seq analysis of LNCaP prostate cancer cells overexpressing doxycycline-inducible NANOG (either NANOG1 or NANOGP8 vs pLVX control) reveal that NANOG coordinately occupies regions of chromatin regulated by AR signaling steroid-receptor complex proteins AR, FOXA1 and NKX3.1. Taken together with the NANOG-induced changes in the prostate cancer transcriptome (RNA-Seq), NANOG appears to reprogram prostate cancer cells to castration resistance by converging on steroid-hormone receptor signaling.

overall_design: LNCaP empty vector (pLVX) vs NANOG overexpressing (NANOG1 or NANOGP8) cells cultured +/- doxycycline for 4 days were subject to chromatin immunoprecipitation with anti-NANOG antibody (NgIP) vs IgG control and Illumina sequencing

first: Bigang

first: Yue

last: Lu

first: Dean

middle: G

last: Tang


title: Targeted deletion of an Nr4a1 associated enhancer ablates Ly6Clow monocytes while protecting pleiotropic gene function in macrophages

overall_design: Refer to individual Series


title: Activity-dependent transcriptional changes in human neurons

city: Boston

first: Bulent

last: Ataman

address: 220 Longwood Ave. GB405

department: Neurobiology

institute: Harvard Medical School

summary: We used genome-wide sequencing methods to identify activity-regulated gene expression and regulatory elements in human neurons.  Sensory stimuli drive the maturation and function of the mammalian nervous system in part through the activation of gene expression networks that regulate synapse development and plasticity.  These programs of gene transcription have primarily been studied in mice, and it is not known if there are neuronal activity-regulated genes that control features of brain development and function that are unique to humans.  In this study, we used genome-wide sequencing methods to identify activity-regulated gene expression and regulatory elements in human neurons.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA-seq data was obtained from primary human, mouse, and rat neuronal cultures that are depolarized for 0, 1, and 6 hours, as well as ChIP-seq data using H3K4me1, H3K4me3, and H3K27ac antibodies.

first: Gabriella

middle: L

last: Boulting

first: David

middle: A

last: Harmin

first: Michael

middle: E

last: Greenberg


title: PTEN-deficient synovial sarcoma

city: Salt Lake City

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

institute: University of Utah

summary: Transcriptome comparisons by RNAseq of genetically engineered mouse models of synovial sarcoma, expressing SS18-SSX1 or SS18-SSX2 and having homozygous conditional genetic silencing of Pten or wildtype Pten.

overall_design: 6 primary tumor samples with wildtype Pten, 8 primary tumor and 5 metastatic site tumor samples with homozygous disruption of Pten

first: Jared

middle: J

last: Barrott


title: Global spatial organization of γ proteobacterial nucleoids is determined by specific long-range interactions.

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: GCC was used to determine the response of P. aeruginosa nucleoid structure to different environmental conditions.

overall_design: Pseudomonas aeruginosa strains were stored (-80°C) and cultured (37°C) on/in mineral salts medium (MM) with either 0.05% (w/v) or 0.2% (w/v) NH4Cl. NH4Cl was used as nitrogen source. The cells were cultivated with 2% (w/v) sodium gluconate. For GCC analyses, P. aeruginosa strains were recovered from -80°C on LB-plates for 24 hours prior to starter culture inoculation. Starter cultures were cultured (37°C, 160rpm, O/N) in MM medium (gluconate 2% w/v) with or without nitrogen, as indicated. Test cultures were inoculated, from the starter cultures, in MM media gluconate (2% w/v) with or without nitrogen, grown (37°C, 160rpm) and harvested at an OD600 = 0.6-8 (log phase) or OD600 = 4-5 (stationary phase).

first: R

middle: S

last: Grand

first: B

middle: H

last: Rehm

first: J

middle: M


title: RNA-seq-based transcriptome analysis of a Streptococcus pyogenes mutant expressing cytoplasmically restricted enolase.

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary: We report the mRNA expression profile of Streptococcus pyogenes Type M1 strain M1T15448-derived mutant lacking eukaryote-type Serine threonine kinase.

overall_design: Measuring transcriptome profiling in M1T1SENhb mutants vs M1T1-WT  5448 strain


title: RNA-seq analysis of a Streptococcus pyogenes mutant lacking the eukaryote-type ser/thr kinase (SP-STK)

overall_design: Measuring transcriptome profiling in M1T1DSTK mutants vs M1T1-WT  5448 strain


title: Differential gene expression analysis of 4days post fertilization (dpf) wildtype and flt1ka601zebrafish mutants to identify venous sprouting associated genes

status: Public on Nov 01 2016

city: Karlsruhe

first: Raphael

last: Wild

address: Fritz-Haber-Weg 2

department: Zoology

institute: Karlsruhe Institute of Technology

summary: Formation of organ-specific vasculatures requires cross-talk between developing tissue and specialized endothelial cells. Here we show how developing zebrafish spinal cord neurons coordinate vessel growth through balancing of neuron-derived Vegfaa, with neuronal sFlt1 restricting Vegfaa-Kdrl mediated angiogenesis at the neurovascular interface. Neuron-specific loss of flt1 or increased neuronal vegfaa expression promotes angiogenesis and peri-neural tube vascular network formation. Combining loss of neuronal flt1 with gain of vegfaa promotes sprout invasion into the neural tube. Upon loss of neuronal flt1, ectopic sprouts emanate from veins involving special angiogenic cell behaviors including nuclear positioning and a molecular signature distinct from primary artery or secondary venous sprouting. Manipulation of AV identity or Notch signaling established that ectopic sprouting in flt1 mutants requires venous endothelium. Conceptually our data suggest that spinal cord vascularization proceeds from veins involving two-tiered regulation of neuronal sFlt1 and Vegfaa via a novel sprouting mode.

overall_design: Examination of wildtype (3 biological replicates, with two technical replicates each) and flt1ka601 homozygous mutants (3 biological replicates, with two technical replicates each)

first: Ferdinand

last: le Noble


title: Robust extracellular pH modulation by Candida albicans during growth in carboxylic acids

city: Houston

last: Lorenz

address: 6431 Fannin

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

summary:
Purpose:  Candida albicans avidly uses multiple carbon sources that are less preferred by related species.  This project compared transcriptional profiles of cells growing in media containing these nutrients relative to glucose
Methods: C. albicans strain SC5314 was incubated in minimal YNB media containing 2% glucose, casamino acids, glutamate or a-ketoglutarate for five hours.  RNA was prepared and subjected to deep sequencing.
Results: Substantial overlap was seen in the transcriptional changes in all alternative carbon sources relative to the glucose control.  Source-specific changes reflected the unique metabolism of each nutrient.
Conclusions: C. albicans is well-adapted to use a range of nutrients that can be found in the mammalian host and has a common transcriptional response to limiting carbon environments.

overall_design: Cells were grown in the indicated nutrient conditions for ~5 hours before Illumina deep sequencing.  Duplicate samples were processed and the read number (100 bp, paired end) for any replicate ranged from 39-48 million.