title: MeCP2 interacts with chromosomal microRNAs in brain

status: Public on May 22 2018

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

summary: Although methyl CpG binding domain protein-2 (MeCP2) is commonly understood to function as a silencing factor at methylated DNA sequences, recent studies also show that MeCP2 can bind unmethylated sequences and coordinate gene activation. MeCP2 displays broad binding patterns throughout the genome, with high expression levels similar to histone H1 in neurons. Despite its significant presence in the brain, only subtle gene expression changes occur in the absence of MeCP2. This may reflect a more complex regulatory mechanism of MeCP2 to complement chromatin binding. Using an RNA immunoprecipitation of native chromatin technique, we identify MeCP2 interacting microRNAs in mouse primary cortical neurons. In addition, comparison with mRNA sequencing data from Mecp2-null mice suggests that differentially expressed genes may indeed be targeted by MeCP2-interacting microRNAs. These findings highlight the MeCP2 interaction with microRNAs that may modulate its binding with chromatin and regulate gene expression.

overall_design: Chromatin RIP-seq using antibody specific for MeCP2 in mouse primary cortical cells. RIP was performed on untreated cells as well as depolarised neurons. Total chromatin RNA was processed in parallel as a background control. Small RNA-seq libraries were constructed using the Illumina Small RNA v1.5 protocol.

first: Abdul

middle: W

last: Khan

first: Haloom

last: Rafehi

first: Scott

last: Maxwell

first: Giuseppe

last: Ciccotosto

first: Assam

last: El-Osta


title: Transcriptomic Differences Associated with TSC2 Gene Expression Loss in Lymphangioleiomyomatosis [mouse cells]

status: Public on May 23 2018

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary:
Pulmonary Lymphangioleiomyomatosis (LAM), a rare lung disease that affects predominantly women, is characterized by proliferation of smooth muscle-like cells in the lungs, destruction of lung tissue, upregulation of VEGF-D, and growth of lymphatic vessels inducing a loss of pulmonary function. TSC2 gene mutations that render TSC2 inactive are a common finding associated with LAM. To better understand the function of the TSC2 gene, we sought to characterize differences in the transcriptome of cells where TSC2 is inactivated.
RNA-Seq was used to measure transcript expression differences between TSC2-null mouse embryonic fibroblasts and TSC2-expressed mouse embryonic fibroblasts. The Illumina TruSeq method was used to prepare stranded poly(A)-selected RNA-Seq libraries, and 100bp paired-end reads were generated with an Illumina Hi-Seq 2500 instrument in high output mode. RNA-Seq data was analyzed using kallisto (http://pachterlab.github.io/kallisto/) and R.

overall_design: Transcriptomic profiles obtained via RNA-Seq of mouse embryonic fibroblasts (TSC2-expressed and TSC2-null) and from kidney epithelial cells which were treated with rapamycin or left untreated.

first: Vera

middle: P

last: Krymskaya


title: ChAHP (Adnp, Chd4, HP1) mediates sequence-specific recruitment of HP1 independent of H3K9 methylation

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Activity-dependent neuroprotective protein (ADNP) is one of the most frequent autism spectrum disorder-associated gene products known to date. Here we show that Adnp interacts with the chromatin remodeler Chd4 and the heterochromatin protein HP1 to form a stable complex, which we refer to as ChAHP. Genetic ablation of ChAHP components or DNA binding sites in embryonic stem cells prematurely activates lineage-specific genes, revealing an important role for Adnp in restraining the differentiation capacity of pluripotent cells. Adnp targets the ChAHP complex to specific sequence motifs at euchromatic loci, representing an H3K9 methylation-independent mechanism of HP1 recruitment and gene silencing.

overall_design:
ChIP-seq, RNA-seq and ATAC-seq experiments were performed in mouse ES cells of isogenic background, each experiment was performed in biological replicates.

Please note that each bed file (linked to the Series records) belongs to the following samples;
Adnp_peak_positions.bed: ChIPseq for Adnp in wt mES cells rep1-3 [GSM2582357-GSM2582359]
HP1g_peaks_wo_Adnp_motif_positions.bed: ChIPseq for HP1g in wt mES cells rep1-3 [GSM2582375-GSM2582377], ChIPseq for HP1g (Cbx3) in Adnp knock-out mES cells rep1-3 [GSM2582389-GSM2582391]

first: Veronika

last: Ostapcuk

first: Sarah

middle: H

last: Carl

first: Marc

last: Bühler


title: Retinoic acid induced expression of Hnf1β and Fzd4 is required for pancreas development in Xenopus laevis

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Retinoic acid (RA) is required for pancreas specification in Xenopus and other vertebrates. However, the gene network that is directly induced by RA-signalling in this context remains to be defined. We identified the transcription factor Hnf1β and the Wnt-receptor Fzd4/Fzd4s as direct RA-target genes through RNA-sequencing of in vitro generated pancreatic explants. Functional analyses of Hnf1β and Fzd4/Fzd4s in programmed pancreatic explants and whole embryos revealed their requirement for pancreatic progenitor formation and differentiation. Hnf1β and Fzd4/Fzd4s thus appear to be involved in pre-patterning events of the embryonic endoderm allowing for pancreas formation.

overall_design: VegT/Noggin/Cyp26a1 programmed animal cap explants from Xenopus laevis, untreated and treated with RA/CHX and collected  2 hours after RA addition at the equivalent of gastrula stage 11; two replicates A and B for each condition

first: Tomas

last: Pieler

first: Maja

middle: B

last: Gere

first: Claudia

last: Pommerenke

first: Thomas

last: Lingner


title: Transcriptomic data of MDA-MB-231 cells adapted to culture in media containing different sugars (glucose or fructose) and cultured as mammospheres

city: Southampton

first: Jeremy

middle: Paul

last: Blaydes

state: Hampshire

address: Southampton General Hospital, Tremona Road

department: Faculty of Medicine

country: United Kingdom

institute: University of Southampton

summary: We report the single-cell RNA sequencing data obtained from MDA-MB-231 breast cancer cells cultured in standard DMEM with 25 mM glucose, or adapted to culture in DMEM with 10 mM fructose to reduce glycolysis, and then cultured as mammospheres

overall_design: Examination of transcriptomic changes in MDA-MB-231 breast cancer cells mammospheres in response to restriction of glycolysis

first: Matthew

middle: J

last: Rose-Zerilli


title: Transcriptomic Differences Associated with TSC2 Gene Expression Loss in Lymphangioleiomyomatosis [human cells]

summary:
Pulmonary Lymphangioleiomyomatosis (LAM), a rare lung disease that affects predominantly women, is characterized by proliferation of smooth muscle-like cells in the lungs, destruction of lung tissue, upregulation of VEGF-D, and growth of lymphatic vessels inducing a loss of pulmonary function. TSC2 gene mutations that render TSC2 inactive are a common finding associated with LAM. To better understand the function of the TSC2 gene in LAM , we sought to characterize differences in the transcriptome of cells where TSC2 is inactivated.
RNA-Seq was used to measure transcript expression differences between a human TSC2-null angiolipoma cell line derived from an individual with LAM, and the same cell line with re-expressed TSC2 to serve as a control. The Illumina TruSeq method was used to prepare poly(A)-selected stranded RNA-Seq libraries, and 100bp paired-end reads were generated with an Illumina Hi-Seq 2500 instrument in high output mode. RNA-Seq data was analyzed using kallisto (http://pachterlab.github.io/kallisto/) and R.

overall_design: Transcriptomic profiles obtained via RNA-Seq for human TSC2-null angiolipoma cell line derived from an individual with LAM; the same cell line with TSC2 re-expressed served as a control; cells were treated with Rapamycin, STAT3, or left untreated.


title: Preliminary Report of Transplantation of Human Fetal Retinal Pigment Epithelial Cells on Age-related Macular Degeneration Patients

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

summary:
Background:  Different sources of retinal pigment epithelial cells (RPE) were transplanted to treat Age-related Macular Degeneration. But the mechanisms of therapeutic effect are unclear till now, and GMP level fetal RPE (fRPE)   need further evaluation for treatment.
Methods: Modified GMP fRPE primary culture system was founded. These RPE were tested on Mer-/- mice and sodium iodate induced retinopathy primate model for safety and feasibility. Five dry-AMD patients and one Stargardt’s Disease patient were enrolled, and received sub retinal transplantation of hfRPE with three dosage cohorts(1×105，2×105，5×105). ETDRS, optic coherent tomographic imaging (OCT), color fundus (CF), fluorescent angiography (FFA), autofluorescence, microperimetry examination were conducted before surgery, and during follow-up period. The studies are registered with ClinicalTrials.gov, numbers NCT02868424.
Findings: GMP level fRPE from modified primary culture system has good proliferative capacity and full functions of RPE in vitro. Human fetal RPE can survive long period in sub-retinal space in mice and monkey models of RPE degeneration, and showed therapeutic effect on Mer-/- mice. During our nine-months follow-up of six clinical cases, no endophthalmitis, no vitreous hemorrhage, no proliferative vitreoretinopathy was observed, and epiretinal memrbrane was the only complication. Among the patients, four of them achieved increase in  ETDRS visual acuity (VA), of which the greatest improvement was 18 letters, and one kept steady while the other had 9 letters decreased VA. Color fundus photos and OCT demonstrated the existence of the fRPE cells, and improved retinal sensitivity as well as the changes observed in auto fluorescence also can tell the situation of grafted cells to some extent.
Interpretation: GMP level fRPE from modified culture system exhibited satisfactory results on in vitro and preclinical experiments. Preliminary clinical trial proved safety of the fRPE subretinal transplantation, and substantiated it a promising therapy for dry AMD including the converted from exudative AMD.

overall_design: Retinal mRNA profiles of human fetal RPE cells cultured in xeno-free medium were conducted from 3 aborted fetus.

first: Qinghuai

last: Liu

first: Songtao

last: Yuan

first: Han

last: Shen


title: Arachidonic acid targets pneumococcal fatty acid homeostasis

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

summary: Free fatty acids play an important role during infection by modulating immune responses, but also by directly functioning as antimicrobials. Particularly, the host’s long chain polyunsaturated fatty acids, not commonly found in bacterial pathogens, have significant antibacterial potential. Of these arachidonic acid (AA) is in high abundance, and in this study we show that upon infection with the Streptococcus pneumoniae the AA concentration in the blood increases. Hence, we investigated the transcriptmoic effects of AA on this extremely problematic bacterial pathogen.

overall_design: Wild-type Streptooccus pneumoniae D39 cells were grown in C+Y media with or without supplementation of 62.5 uM arachidonic acid. Cells were grown from OD600 = 0.05 to 0.3. Total RNA was then isolated and the transcriptomes of treated and untreated cells was determined. Each sample represents a pool of three biological replicates.

middle: A

first: Stephanie

middle: L

last: Begg

first: Christopher

last: McDevitt


title: Transcriptomics but not DNA methylomics find Tp73, Cebpd, Pax6 and Spi1 transcription factors as treatment targets for traumatic brain injury

city: Kuopio

first: Anssi

last: Lipponen

address: Neulaniementie 2

department: A. I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

type: Methylation profiling by high throughput sequencing

summary: TBI was induced with lateral fluid-percussion injury in adult male rats. MBD-seq of the perilesional cortex, ipsilateral thalamus and ipsilateral hippocampus was performed at 3 months post-TBI. The data was used to identify differential methylation of gene promoter, gene body, and exons in the perilesional cortex , thalamus and hippocampus.

overall_design: TBI was induced to 5 rats, 5 sham operated served as a controls.

first: Assam

last: El-Osta

first: Antony

last: Kaspi

first: Mark

last: Ziemann

first: Ishant

last: Khurana

first: K

middle: N

last: Harikrishnan

first: Vicente

last: Ferrandis

first: Noora

last: Puhakka

first: Jussi

last: Paananen

first: Asla

last: Pitkänen


title: Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma [ChIP-Seq]

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Transcriptional dysregulation plays a major role in the development and progression of human tumors such as pediatric neuroblastoma. Therefore, we sought to elucidate the relationship between genes required for neuroblastoma cell growth and survival and the transcriptional core regulatory circuitry (CRC) that controls the gene expression program. A genome-scale CRISPR-Cas9 screen for oncogenic dependencies revealed that 143 genes are essential for cell survival and growth in neuroblastoma relative to other cancers, including many super-enhancer (SE) regulated transcription factors. Genome-wide occupancy analysis of transcription factor binding demonstrated that at least six of these transcription factors were both dependency genes and components of the CRC in MYCN-amplified neuroblastoma including: HAND2, ISL1, PHOX2B, GATA3, TBX2, and MEIS2.  Binding sites for these transcription factors were clustered within a few hundred base pairs in their own enhancers and the enhancers of downstream target genes, which surprisingly included  40% of the independently determined neuroblastoma dependency genes. This profound level of transcriptional control of oncogenesis through self-reinforcing transcriptional circuits led us to test combinatorial pharmacological inhibition of transcriptional initiation and elongation, which synergistically induced tumor cell death, supporting Òdrugging transcriptionÓ  as a means to advance the treatment of high risk neuroblastoma.

overall_design: ChIP-Seq for transcription factors in neuroblastoma cell types

first: Adam

last: Durbin

last: Zimmerman

first: Neekesh

middle: V

last: Dharia

first: Brian

last: Abraham

first: Amanda

last: Balboni

first: Nina

last: Weichert-Leahey

first: Shuning

last: He

first: John

middle: M

last: Krill-Burger

first: Francisca

last: Vazquez

first: David

last: Root

first: Aviad

last: Tsherniak

first: William

middle: C

last: Hahn

first: Todd

middle: R

last: Golub

first: Kimberly

last: Stegmaier

first: A

middle: T

last: Look


title: Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma [ATAC-Seq]

overall_design: ATAC-Seq in neuroblastoma cell types

first: Mark


title: Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower

city: Athens

middle: James

last: Bewick

state: GA

address: 120 East Green Street

department: Genetics

institute: University of Georgia

summary: The importance and applications of polyploidy have long been recognized, from shaping the evolutionary success of flowering plants to improving agricultural productivity. Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant - having both retained more genes and being more highly expressed - a phenomenon termed subgenome dominance. How quickly one subgenome dominates within a newly formed polyploid, if immediate or after millions of years, and the genomic features that determine which genome dominates remain poorly understood. To investigate the rate of subgenome dominance emergence, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural less than 140 year old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and diploid progenitors (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of two divergent genomes and that subgenome expression dominance significantly increases over generations. Additionally, CHH methylation levels are significantly reduced in regions near genes and within transposons in the first generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and submissive subgenomes in the natural allopolyploid. Our analyses reveal that the subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following the hybridization. These findings not only provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events, but may also contribute to uncovering the mechanistic basis of heterosis and subgenomic dominance.

sample_organism:
Erythranthe guttata
Erythranthe lutea x Erythranthe guttata
Erythranthe lutea
Mimulus peregrinus

overall_design: Whole Genome Bisulfite Sequencing (WGBS) of leaf tissue from Mimulus guttatus and M. luteus, a hybrid, and natural and lab-generated allopolyploids.

first: Joshua

last: Puzey


title: Super-enhancer Driven Core Regulatory Circuitry in MYCN-amplified Neuroblastoma

first: Richard

last: Young

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

overall_design: Refer to individual Series


title: Itraconazole targets cell cycle heterogeneity in colorectal cancer

status: Public on May 21 2018

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute


title: Identifying dormant cells in colorectal cancer spheroids

summary: Cellular dormancy and heterogeneous cell cycle lengths provide important explanations for treatment failure following adjuvant therapy with S-phase cytotoxics in colorectal cancer (CRC) yet the molecular control of the dormant versus cycling state remains unknown.  In CRCs dormant cells are found to be highly clonogenic and resistant to chemotherapies.  We sought to understand the molecular features of dormant CRC cells to facilitate rationale identification of compounds to target both dormant and cycling tumour cells.

overall_design: Six colorectal cancer cell lines (DLD1, HCT15, HT55, SW948, RKO and SW48) were labelled with the cell permeable dye CFSE and then grown in non-adherent spheroid culture for 6 days to enable identification of dormant cells that retain CFSE (LRC) and cycling cells (BULK).  LRCs and BULK populations were then FACS sorted from each cell line in quadruplicate. As a control experiment, to identify off-target effects of the CFSE dye and culture artefacts, BULK populations from DLD1 cells at d1 and d6 after seeding both with and without CFSE labelling were included in the RNAseq analysis.  RNA was extracted using the RNAeasy Micro Plus kit (Qiagen) and quantified using the Qubit RNA Assay Kit (Thermo Fisher Scientific).  RNA quality was assessed using the Agilent Bioanalyser system as per manufacturer’s instructions.  Following normalisation and sample randomisation, Truseq library (Illumina) preparation was carried out at the CRUK CI genomics facility and subsequent single end, 50bp sequencing using the HiSeq system (Illumina).  Following human genome alignment (hg19), read counts were normalised and differential expression tested using the DEseq protocol.

first: Simon

last: Buczacki


title: Identifying the molecular mode of action of itraconazole in colorectal cancer

summary: Two cell lines (HT55 and SW948) were found responsive to itraconazole treatment.  To identify the mode of action cells were treated with itraconazole or control (DMSO) and then subjected to RNAseq analysis once the phenotype had developed

overall_design: HT55 and SW948 cells were seeded in adherent culture and treated with 5uM itraconazole or DMSO for 6 days.  Cells then underwent RNA extraction using the RNAeasy Micro Plus kit (Qiagen) and quantified using the Qubit RNA Assay Kit (Thermo Fisher Scientific).  RNA quality was assessed using the Agilent Bioanalyser system as per manufacturer’s instructions.  Following normalisation and sample randomisation, Truseq library (Illumina) preparation was carried out at the CRUK CI genomics facility and subsequent single end, 50bp sequencing using the HiSeq system (Illumina).  Following human genome alignment (hg19), read counts were normalised and differential expression tested using the DEseq protocol.


title: Downregulation of miR-218-5p promotes invasion of oral squamous cell carcinoma cells via activation of CD44-ROCK signaling

city: dalian

first: Xiaojie

last: Li

address: No. 9 of Lvshun South Road

country: China

institute: Dalian Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The invasion front of oral squamous cell carcinoma (OSCC) harbors the most aggressive cells of the tumor and is critical for cancer invasion and metastasis. MicroRNAs (miRNAs) play an important role in regulating OSCC invasion. In this study, we modeled the OSCC invasion front on a microfluidic chip and investigated differences in miRNA profiles between cells in the invasion front and those in the tumor mass by small RNA sequencing and bioinformatic analysis. We found that miR-218-5p was downregulated in invasion front cells; a luciferase reporter assay confirmed that cluster of differentiation (CD)44 was a direct target of miR-218-5p. Inhibiting miR-218-5p in invasion front cells activated CD44- Rho-associated protein kinase (ROCK) signaling and promoted cell invasion by inducing cytoskeletal reorganization. These findings indicate that miR-218-5p negatively regulates OSCC invasiveness by targeting the CD44–ROCK pathway and may be a useful therapeutic target for OSCC. Moreover, our method of modeling and isolating invasion front cells using a microfluidic chip is a time-saving alternative to in vivo models.

overall_design: The small RNA of the OSCC cells (UM-SCC6) and the invasion front cells of OSCC (UM-SCC6-M) were analyzed by Next Gen RNA Sequencing.

first: XIAOJIE

last: LI

first: JIANYA

last: HE

first: MIAOMIAO

last: SHAO

first: FEI

last: PENG

first: BAI

last: CUI

first: JIAO

first: YAN

last: RAN

first: XUESONG

last: YANG

first: YONG

last: LUO

first: YAO

last: LU

first: BINGCHENG

last: LIN

first: TINGJIAO

last: LIU


title: Genome-wide profiling of H3K4me3 and H3K27me3 modifications during and after vernalization in Brachypodium

city: Beijing

first: Qing

last: Huan

address: No.20 Nanxincun Xiangshan, Haidian District

institute: Institute of Botany, Chinese Academy of Sciences

summary: Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture.

overall_design: Examination of 2 different histone modifications (H3K4me3 and H3K27me3) in 3 differently vernalized Brachypodium seedlings (V0,V30 and V30N). And another one H3K4me3 sequencing in non-vernalized seedlings (H3K4me3_V0_2) is the biological replication.


title: Control of maize vegetative and reproductive development, fertility and rRNAs silencing by HISTONE DEACETYLASE 108

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

summary: Histone deacetylases (HDACs) catalyze the removal of acetyl groups from acetylated histone tails that consequently interact more closely with DNA, leading to chromatin state refractory to transcription. Zea mays HDA108 belongs to the Rpd3/HDA1 HDAC family and is ubiquitously expressed during development. The newly isolated hda108/hda108 insertional mutant exhibited many developmental defects: significant reduction in plant height, alterations of shoot and leaf development, alterations of inflorescence patterning and fertility. Western blot analyses and immunolocalization experiments revealed an evident increase in histone acetylation, accompanied by a marked reduction in H3K9 dimethylation, in mutant nuclei. The DNA methylation status, in the CHG sequence context, and the transcript level of ribosomal sequences were also affected in hda108 mutants, while enrichment in H3 and H4 acetylation characterizes both repetitive and non-repetitive transcriptional up-regulated loci. RNA-Seq both of young leaf and anthers indicated that transcription factor expression is highly affected and that the pollen developmental programme results as disrupted in hda108 mutants. Crosses between hda108/hda108 and epiregulator mutants did not produce any double mutant progeny indicating possible genetic interactions of HDA108 with distinct epigenetic pathways. Our findings indicate that HDA108 is directly involved in regulation of maize development, fertility and epigenetic regulation of genome activity.

overall_design: Total RNA-Seq analysis of maize developing leaves (3 biological replicates) collected from wild-type and hda108 mutant plants. Strand-specific sequencing on a Illumina HiSeq2500

first: Silvia

last: Farinati

first: Jacques

last: Rouster

first: Hervé

last: Lassagne

first: Massimiliano

last: Lauria

first: Nicola

last: DalFerro

first: Serena

last: Varotto


title: Control of maize vegetative and reproductive development, fertility and rRNAs silencing by HISTONE DEACETYLASE 108 [PMeA and MiA]

overall_design: Total RNA-Seq analysis of maize anthers at post-meiotic (PMeA) and mitotic (MiA) stages. 2 biological replicates for stage, each obtained by pooling anthers from three tassels per genotype were collected from wild-type and hda108 mutant plants. Strand-specific sequencing on a Illumina HiSeq2500


title: Familial resemblances in human whole blood transcriptome

status: Public on May 18 2018

city: Quebec

first: Bénédicte L.

last: Tremblay

state: Quebec

address: Pavillon des Services, 2440 Hochelaga Blvd

department: School of Nutrition

country: Canada

institute: Institute of Nutrition and Functional Foods (INAF), Laval University

summary: The objective is to quantify the contribution of genetic and common environmental effects in the familial resemblances of whole blood genome-wide gene expression levels. We also make comparisons with familial resemblances in blood leukocytes genome-wide DNA methylation levels in the same cohort in order to further investigate biological mechanims.

overall_design: A total of 48 subjects from 16 families were recruited in the Greater Quebec City area, in Canada, as part of the GENERATION Study. Parents had to be in good general health, non-smokers, with BMI ranging between 18 and 35 kg/m2, and free of any metabolic conditionds requiring treatment. Children also had to be non-smokers and in good general health. Families living under the same roof comprised at least the mother and one child aged between 8 and 18. Blood samples were collected from an antecubital vein into PAXgeneTM tubes after 12-h overnight fast and 48-h alcohol abstinence. Total RNA was isolated and purified from whole blood using PAXgene Blood RNA Kit (QIAGEN) for all 48 subjects.

first: Bénédicte

first: Frédéric

last: Guénard

first: Benoît

last: Lamarche

first: Louis

last: Pérusse

first: Marie-Claude

last: Vohl


title: Identification of genes involved in metabolism and signaling of abscisic acid and gibberellins during Epimedium pseudowushanense B.L.Guo seed morphophysiological dormancy

first: Yimian

last: Ma

address: No. 151 Malianwa North Road, Haidian District

institute: The Institute of Medicinal Plant Development (IMPLAD)

summary: The molecular mechanism of seed morphophysiological dormancy of Epimedium pseudowushanense B.L.Guo. remains largely unknown. The endogenous ABA and GA content of E. pseudowushanense seeds at three developmental stages was quantitatively determined. The result showed the levels of ABA in E. pseudowushanense seeds decreased during the seed embryo growing and development, levels of GA3 increased during seed embryo growing, and levels of GA4 increased during seed dormancy releasing and seed sprouting. High-throughput sequencing method was used for reveal the E. pseudowushanense seed transcriptome. The transcriptome data were assembled as 178,613 unigenes and the numbers of differentially expressed unigenes between the seed development stages were compared. By computer analysis of the KEGG reference pathways, twelve candidate genes were likely to be involved in metabolism and signaling of abscisic acid and gibberellins. The expression patterns of these genes were revealed by real-time quantitative RT-PCR. Phylogenetic relationships among the deduced E. pseudowushanense proteins and their homologous in other plant species were analyzed. The results indicate EpNCED1, EpNCED2, EpCYP707A1 and EpCYP707A2 are likely to be involved in ABA biosynthesis and catabolism. EpSnRK2 is likely implicated in ABA signaling during seed dormancy. EpGA3ox is likely to be involved in gibberellin biosynthesis, and EpDELLA1 and EpDELLA2 are likely implicated in GA signaling. This study was the first to provide the E. pseudowushanense seed transcriptome and the key genes involved in metabolism and signaling of abscisic acid and gibberellins, and so it is valuable for studies on seed morphophysiological dormancy mechanism

overall_design: The transcriptome of three Epimedium pseudowushanense B.L.Guo seed samples were examined.

first: Baolin

last: Guo


title: Identification of genes related to embryonal control of yellow seed coat in B. napus

status: Public on May 19 2018

city: Hangzhou

first: Fei

last: Xu

address: 198 Shiqiao Road

institute: Zhejiang Academy of Agricultural Sciences

summary: Seed coat colour is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds, such as seed dormancy, longevity, oil content, protein content and fibre content. In Brassica napus, inheritance of seed coat colour is related to maternal effects and pollen effects (xenia effects). In this research, we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus with pollen effect. Microcopy of transverse sections of the mature seed shows pigment is deposited only in the epidermal cells, the first cell layer of seed coat. By Illumina Hiseq 2000 sequencing technology, a total of 12 G clean data, 116x coverage of coding sequences of B. napus, was achieved from 26-day old brown and yellow seeds. It was assembled into 172,238 independent transcripts and 55,637 unigenes by Trinity. A total of 150 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus. Only 49 of the TT orthologous genes are transcripted in seeds. However transcription of all the orthologs was independent of the embryonal control of seed coat colour. Of all the Trinity-assembled unigenes, only 55 genes were found to be differentially expressed between the brown seeds and yellow mutant. Among them 50 were up-regulated and 5 were down-regulated in the yellow seeds as compared to the brown counterpart. By KEGG classification, 14 metabolic pathways were enriched significantly. Of these, 5 pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were produced at higher levels in the embryo of yellow seeds as compared to brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the 26-day embryo of yellow seeds. Pigment indispensable substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe and disappearance of pigment in the yellow seeded mutant indicate that embryonal control of seed coat colour is related with Phe and Ala metabolism in the embryo of B. napus.

overall_design: Examination of 26-day-old seeds of 2 near isogenic lines with distinct seed coat colour.

first: Renhu

last: Liu

first: Fulin

last: Wang


title: Priming and Activation of ERα Enhancers Through Ordered and Cooperative Interactions Between p300 and Mediator

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center


title: Conservative alteration of chromosomal expression pattern across human solid tumor types

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

institute: Yunnan university of Chinese Medicine

summary: We used RNASeq technology to get whole transcription profilings of 2 control samples (MCF7), 2 replicates of MCF7_sh_XIST_1 and 2 replicates of MCF7_sh_XIST_2. Our goal is to find the differentially expressed genes by comparing knockdown of XIST in MCF7 and control MCF7 in Breast cancer cell line.

overall_design: Examination of  differentitally expressed genes by comparing expression profiles of MCF7 (4 sh_XIST samples) and control (2 MCF7 samples).

first: Baowei

last: Jiao


title: Quantitative Proteomics Reveals a Unique Wiring of Signaling Pathways that Protects Human Regulatory T Cell Identity

city: Amsterdam

first: Eloy

last: Cuadrado

address: Plesmalaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin

summary: Regulatory CD4+ T cells (Tregs) are functionally distinct from conventional CD4+ T cells (Tconvs). To understand Treg identity, we have compared by proteomics and transcriptomics human naïve (n) and effector (e)Tregs, Tconvs and transitional FOXP3+ cells. Among these CD4+ T cell subsets, we detected differential expression of 421 proteins and 640 mRNAs, with only 48 molecules shared. Fifty proteins discriminated Tregs from Tconvs. This common Treg protein signature indicates altered signaling by TCR-, TNF receptor-, NFkB-, PI3 kinase/mTOR-, NFAT- and STAT pathways and unique cell biological and metabolic features. Another protein signature uniquely identified eTregs and revealed active cell division, apoptosis sensitivity and suppression of NFkB- and STAT signaling. eTreg fate appears consolidated by FOXP3 outnumbering its partner transcription factors. These features explain why eTregs cannot produce inflammatory cytokines, while transitional FOXP3+ cells can. Our collective data reveal that Tregs protect their identity by a unique “wiring” of signalling pathways

overall_design: mRNA profiles of 5 CD4+ T cell populations were generated by deep sequencing, in triplicate

first: E

first: Maartje

last: van den Biggelaar

first: Yi-yen

last: Chen

first: Sander

last: de Kivit

first: Manon

last: Slo

first: Ihsane

last: Doubal

first: Alexander

last: Meijer

first: Rene

last: van Lier

first: Jannie

last: Borst

first: Derk

last: Amsen


title: Hepatic transcriptome analysis for differential gene expression between steers of divergent feed efficiency phenotypes in three Canadian beef breeds

status: Public on May 17 2018

city: Edmonton

first: Changxi

last: Li

state: Alberta

address: Agriculture/Forestry Centre

department: Agricultural, Food & Nutritional Science

institute: University of Alberta

summary:
The objective of this study was to identify differentially expressed genes in the liver of steers with divergent Residual Feed Intake (RFI).
Methods:In total 50 purebred Angus, 48 purebred Charolais and 158 Kinsella Composite breed steers were tested for individual feed intake using the GrowSafe system for an average period of 70 to 73 days. During the feedlot test animals were fed at ad libitum with a finishing diet composed of 75% barley grain, 20% barley silage and 5% rumensin pellet. Body weight of each animal was measured at an interval of 28days and ADG for each animal was obtained from a linear regression of serial body weight (BW) measurements (Kgs) on time (days). MWT was calculated as midpoint BW0.75, where midpoint BW was computed as the sum of initial BW of the animal and the product of its ADG multiplied by half the number test days. DMI of each animal was calculated as the average daily feed intake of the animals for the time during the feedlot test (days). The expected DMI for each animal was predicted using the regression intercept and regression coefficients of ADG and MWT on actual DMI, and RFI was computed as the difference between the standardized daily DMI and the expected DMI. At the end of the test, animals were slaughtered and liver tissue was collected immediately after slaughter separately bagged in plastic bags, labeled and flash frozen in liquid nitrogen. The frozen samples were transferred to the laboratory on ice and stored at -80C until RNA extraction. From the frozen samples, 20 samples from each breed were selected for total RNA extraction including six samples  with extreme high and six samples  extreme low-RFI phenotypes for each breed. Complementary DNA (cDNA) libraries were constructed for each of the 60 animals and consequently single end sequenced using Illumina Hiseq 2500 sequencer. The raw reads were aligned and mapped to the bovine reference genome UMD 3.1 using Tophat2 aligner with default alignment parameters. Thereafter, reads aligned uniquely to each annotated transcript of gene in the bovine genome were counted using HTSeq-count package with default parameters. Read counts from HTSeq-count, sample information (sample id, sire, feed efficiency group and sequencing mode) and gene annotation table from ENSEMBL Biomart were used for differential expression analysis within each breed using the edgeR package in R for the six extreme low-RFI and six extreme high-RFI samples.
Results: At a false discovery rate of 0.05 and fold change > 2 , we identified 72, 41 and 175 differentially expressed genes for Angus, Charolais and KC RFI divergent steers respectively.

overall_design: RNA-seq of Angus, Charolais and Kinsella Composite male liver with either low or high Residual Feed Intake (RFI).

first: Robert

last: Mukiibi

first: Michael

last: Vinsky

first: Kate

last: Keogh

first: Carolyn

last: Fitzsimmons

first: Paul

last: Stothard

first: Sinead

last: Waters


title: Short-term pIFN-α2a treatment does not significantly reduce the viral reservoir of SIV-infected, ART-treated rhesus macaques

city: Atlanta

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Objective: To evaluate the effect of short-term type I IFN treatment on the latent viral reservoir in SIV-infected rhesus macaques on ART; Methods: We infected twelve RMs intrarectally with 10,000 TCID of SIVmac239. After 6 weeks of infection, all RMs started a three-class, four-drug ART regimen. Once viral loads were consistently undetectable, six animals were administered 1 dose of pegylated IFN-α2a per week for 4 weeks with each weekly intramuscular application being 6 µg/kg.

overall_design: We infected twelve RMs intrarectally with 10,000 TCID of SIVmac239. After 6 weeks of infection, all RMs started a three-class, four-drug ART. Once viral loads were consistently undetectable, six animals were administered 1 dose of pegylated IFN-α2a per week for 4 weeks with each weekly intramuscular application being 6 µg/kg.

first: David

last: Palesch

first: Steven

last: Bosinger

first: Maud

last: Mavigner

first: James

last: Billingsley

first: Cameron

last: Mattingly

first: Diane

last: Carnatha

first: Mirko

last: Paiardini

first: Ann

last: Chahroudi

first: Thomas

last: Vanderford

first: Guido

last: Silvestri

first: Nirav

last: Patel


title: Priming and Activation of ERα Enhancers Through Ordered and Cooperative Interactions Between p300 and Mediator [GRO-seq]

first: W. Lee

last: Kraus

summary: Estrogen receptors alpha (ERα) converges estrogen signaling by orchestrating estrogen (E2)-dependent transcription regulation.  Upon binding to the chromatin, ERα serves as a nucleation site for de novo formation of transcription enhancer complexes.  Steroid receptor coactivators family proteins (SRCs, a.k.a p160) and Mediator complex are the two coregulators for ERα that directly interact with the receptors and control enhancer activity by regulating recruitment of other coregulators and transcription machinery.  Lysine acetyltransferase p300/CBP is also a critical coregulator for ERα that is recruited through SRCs in stable ERα enhancer complex.  ERα enhancers exhibit common enhancer features including enrichment of enhancer-specific histone modification (e.g. H3K4me1 and H3K27ac), coregulator recruitment, and active transcription.  Despite of recognition of those enhancer characteristics, the order of assembly and functions and the functional relationships among enhancer features during active enhancer complex formation is not well understood.  Using the time course genomics and molecular biology assays, we dissect the order of assembly and functions of ERα enhancer complex formation.  We describe the mechanism of SRC-independent p300 recruitment mediated by Mediator, leading to initial partial activation of the ERα enhancer for enhance priming.  Maturation of the enhancer in turn switches the p300 recruitment mechanism to an SRC-dependent manner, resulting in the maximum enhancer activity and transcription outcomes.  Thus, our results illustrate the role of SRC in enhancing the activity of primed enhancers.  Furthermore, we show that forced recruitment of p300 to inactive enhancers establishes active enhancer marks and induces ERα-target gene expression.  Together, we demonstrate the molecular mechanisms of ERα enhancer complex formation where p300 plays a pivotal role in enhancer activation and target gene expression controlled by distinctive mechanisms through different stages of ERα enhancer complex formation.

overall_design: GRO-seq datasets were generated using E2-treated MDA-MB-231 cells expressing ERα wt and L540Q mutant to define ERα enhancers and to determine enhancer complex formation and activity.

first: Shino

last: Murakami

first: Anusha

last: Nagari

first: W


title: Mirror bisulfite sequencing – a method for single-base resolution of hydroxymethylcytosine

city: Irvine

first: Xueguang

last: Sun

state: CA

address: 17062 Murphy Ave

institute: zymo research corp

summary: While the role of 5-methylcytosine has been well studied, the biological role of 5-hydroxymethylcytosine still remains unclear due to the limited methods available for single-base detection of 5-hydroxymethylcytosine (5hmC). Here we present Mirror bisulfite sequencing for the detection of 5hmC at a single CpG site by synthesizing a DNA strand to mirror the parental strand. This semi-conservative duplex is sequentially treated with β-glucosyltransferase and M.SssI methylase. A glucosyl-5hmCpG in the parental strand inhibits methylation of the mirroring CpG site, and after bisulfite conversion, a thymine in the mirroring strand indicates a 5hmCpG site in the parental strand whereas a cytosine indicates a non-5hmC site. Using this method, the 5hmC levels of various human tissues and paired tumor liver tissues were mapped genome-wide.

overall_design: developing a new assay for genomic profiling of 5hmC

first: Darany

last: Tan

first: Tzu

last: Chung

first: Xi-Yu

last: Jia


title: Isolating Independent Effects of Diet/Energy Balance and Body Weight on Behavior and Metabolic Health

city: Philadelphia

first: Isaac

last: Perron

address: 125 S 31st St, Auite 2100

department: Medicine

institute: University of Pennsylvania

summary: Associated with numerous metabolic and behavioral abnormalities, obesity is classified by metrics reliant on body weight (such as body mass index). However, overnutrition is the common cause of obesity, and may independently contribute to these obesity-related abnormalities.  The goal of this study is to isolate ‘diet/energy balance’ effects independent from ‘body weight’ effects on various metabolic and behavioral parameters using the Diet Switch feeding paradigm in mice. [We conducted] unbiased gene expression analysis of the nutrient-sensing circumventricular hypothalamus [using RNA-seq]. Remarkably, only two genes responded to diet/energy balance (neuropeptide y [npy] and agouti-related peptide [agrp]), while others were related only to body weight. Furthermore, linear regression models revealed that npy and agrp showed similar modifiability by diet/energy balance and body weight compared to electroencephalographic-measured sleep/wake behavior.

overall_design: Purified polyA-enriched mRNA from circumventricular hypothalamus (CVH) punches in mice under various dietary conditions: 1) Regular chow (RC) only (n=5); 2) High-fat diet (HFD) only (n=5); 3) Chornic RC followed by acute HFD (RC.HFD; n=6); 4) Chronic HFD follwed by acute RC (HFD.RC; n=5)

first: Brendan

last: Keenan

first: Karthikeyani

last: Chellappa

first: Nicholas

middle: F

last: Lahens

first: Nichole

last: Yohn

first: Keith

last: Shockley

first: Allan

middle: I

last: Pack

first: Sigrid

last: Veasey


title: RNA sequencing of prostate cancer and normal tissue from African Americans and European Americans

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary: Background:African American men (AAM) are at higher risk of being diagnosed with prostate cancer (PCa) and are at higher risk of dying from the disease compared to European American men (EAM). We sought to better understand PCa molecular diversity that may be underlying these disparities. We ran RNA-sequencing data analysis on high-grade PCa to identify genes showing differential tumor versus normal adjacent tissue expression patterns unique to AAM or EAM.

overall_design: Matched high-grade (GS≥7(4+3)) prostate tumor and adjacent normal specimens from 16 patients (8 AAM and 8 EAM) were subjected to two replicate runs of RNA-sequencing.

first: Cristina

last: Mitrea

first: Emily

last: Girsch


title: ChIP-seq targeting Myc-tagged UL34 from human fibroblasts infected with human cytomegalovirus at 48 hours post infection

first: Mark

middle: Daniel

last: Slayton

state: Ohio

address: 7 Depot Street

department: Biomedical Sciences

institute: Ohio University

summary:
Purpose: To identify interactions of the viral DNA-binding protein, UL34, with the viral genome during lytic-phase replication.
Methods: Human fibroblasts were infected with human cytomegalovirus expressing Myc-tagged UL34 in biological duplicate.  At 48 hours post infection, ChIP was performed with anti-Myc tag antibody (Cell Signaling) and the resulting DNA fragments were sequenced on Illumina MiSeq.  Reads were trimmed and duplicates removed.  Reads passing quality filter were aligned to a custom reference genome containing both the human genome with the human cytomegalovirus genome as an additional chromosome to prevent read assignment bias with CLC Genomics Workbench verison 9.0.  Enrichment of UL34 in the viral origin of lytic replication (oriLyt) was calculated by dividing read counts from the ChIP'd samples (Myc-UL34-1, Myc-UL34-2) by those from non-ChIP whole cell lysate (Input) with a 125bp sliding window (25bp overhang) after adjusting for total read count variances.  An additional sample containing DNA that was subjected to the ChIP protocol in the absence of antibody (No Antibody) was compared to the Input to determine background enrichment.
Results: Several peaks were identified when comparing the Myc-UL34-ChIP samples to Input.  UL34 is bound to the viral oriLyt at 48 hours post infection near the three previously defined UL34-binding sites to varying degrees, as well as additional locations within the region.  No peaks were identified when comparing the No Antibody and Input samples.

overall_design: Occupancy of HCMV UL34 in the viral oriLyt.

first: Bonita

last: Biegalke


title: Comparative Transcriptomic Analysis of Hematopoietic System Across Species by Microwell-Seq

city: hangzhou

first: guoji

last: guo

state: zhejiang

address: yuhangtang road 388

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

summary: Traditional single-cell RNA-seq technologies have shown limitations for large scale experiments. Here, we constructed a single-cell resolution transcriptomic atlas of (HSPCs) in human and mouse,including a total number of 71,729 single cells clustered into 39 subpopulations by computational analysis. In human, we found 20 progenitors primed with unique lineages like megakaryocyte, neutrophil and B cell progenitor can project directly from HSPCs. Within the c-Kit positive cells from mouse bone marrow, we described 19 progenitor subgroups at single cell resolution.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We sampled 7 batches (CD34+_b1-7) of Human CD34+ mobilized peripheral blood stem cells (PBSCs); 2 batches (CD34+_thawed_l6-7) of thawed Human CD34+ mobilized peripheral blood stem cells (PBSCs) and 2 batches (CD34-_b1-2) of thawed Human CD34- mobilized peripheral blood stem cells (PBSCs), around 5000 single cells per sample.
1 batch of mouse-transferred CD34+ cells; 3 batches of Mouse c-kit+ cells and 5 batches of mouse bone marrow cells.1 batch of zebrafish kidney marrow-derived hematopoietic cell.
Human CD34+ cells were selected by human CD34 selection kit (StemCell Technologies Cat #18056), following the protocol provided by the manufacturer. After spin at 300 x g for 5min, the supernatant was removed and CD34+ cells were suspended in 1x DPBS + 2mM EDTA and diluted to ~ 100,000/mL for Microwell-seq. After thawing in IMDM medium, human CD34+ cells were suspended in 100μL of PBS+5% FBS for exposure of antibodies. mPB CD34+ cells were transplanted into sublethally irradiated NCG (NOD-Prkdcem26Cd52Il2rgem26Cd22/Nju, Nanjing Biomedical Research Institute of Nanjing University) mice via an injection into the femur cavity (approximately, 1X105 cells per mouse). Two months after transplantation, hCD45+CD34+ cells (mouse-transferred CD34+ cells) were sorted from mice bone marrow cells collected from the femur and tibia. Mouse c-kit + cells were were sorted by flow cytometry, following the protocol provided by the manufacturer. The following antibodies were used for MPP(CD34+CD38-Thy1-CD45RA-CD49f-) cell sorting: CD34 PE (Biolegend, clone 581, cat #343506), CD34 FITC (BD bioscience, clone 581, cat #555821), CD38 PE-Cy7 (BD bioscience, clone HIT2, cat #560677), CD90 APC (BD bioscience, clone 5E10, cat #559869), CD45RA APC/Fire 750 (Biolegend, clone HI100, cat #304151), CD49f BV421 (Biolegend, clone GoH3, cat #313623).

first: Gguoji

last: Guo

first: Shujing

last: Lai


title: TOX expression governs the encephalitogenic potential of microbe-induced autoreactive CD8+ T cells by reducing immune checkpoint sensitivity

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary: We report that TOX represses a terminal differentiation signature in CD8+ T cells by repressing Id-2 expression

overall_design: Examination of TOX-specific peaks in OT-1 genome

first: Doron

last: Merkler

first: Nicolas

last: Page


title: GATA2 is Dispensable for Generation of Hemogenic Endothelium But Required for Endothelial-to-Hematopoietic Transition

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

summary: Using loss-of- and restoration-of-function approaches, we found that GATA2 function is mainly focused on enthothelial-to-hematopoietic transition (EHT) other than formation of hemogenic endothelial cells (HECs) in hematopoietic development of human ESCs. In addition, our study found that small portion of hematopoietic progenitors (HPs) can be generated even in the absence of GATA, which was proved to have similar character to that of GATA2-independent HPs lacking CFU-G and CFU-GM potential but retaining lymphoid potential.

overall_design: Intermediate precursors at different stage of hematopoietic development were subject to gene expression profiling using genetically engineered hESCs. genetically intact (no genetic engineering) hESCs were used as intact control.

first: Igor

last: Slukvin

first: HyunJun

last: Kang

first: Scott

last: Swanson


title: Priming and Activation of ERα Enhancers Through Ordered and Cooperative Interactions Between p300 and Mediator [ChIP-seq]

first: W. Lee

last: Kraus

overall_design:
ChIP-seq (ERα, Med1, SRC, p300, and H3K27ac) and GRO-seq datasets were generated using E2-treated MDA-MB-231 cells expressing ERα wt and L540Q mutant to define ERα enhancers and to determine enhancer complex formation and activity.

ChIP antibody information;
ERa, rabbit polyclonal antiserum generated in the Kraus Laboratory against the 1-113 of human ERa
Med1, Cat. # A300-793A, Lot # A300-793A-2
SRC, rabbit polyclonal antiserum generated in the Kraus Laboratory against the 624-1130 of mouse SRC2
H3K27ac, Cat. # ab4729, Lot # GR254711-1
p300, Cat. # sc-584x, Lot #  I1715

first: Shino

last: Murakami

first: Anusha

last: Nagari

first: W


title: Direct interaction of MYCN and p53 regulate transcriptional responses in neuroblastoma

city: Houston

first: Jason

last: Shohet

address: One Baylor Plaza

department: Pediatrics

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Differentially expressed genes post knock down of lincDUSP26

city: Cleveland

first: Ahmad

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Total RNA from V703 and V481 cells (negative control vs KD of lincDUSP) were subjected to next generation RNA-seq (100bp, paired-end, strand-specific). The expression of mRNAs was calculated as FPKM values.

overall_design: Three biological of negative control vs KD were utilized for RNA isolation from each cell line (V703 and V481).


title: Differential roles of TAp63α and deltaNp63α in chicken myogenic differentiation

status: Public on May 16 2018

city: Guangzhou

first: Wen

last: Luo

state: Guangdong

address: Wushan

institute: South China Agricultural University

summary: We constructed chicken TAp63α and deltaNp63α overexpression vectors, and then transfected into chicken primary myoblast. After 48 hours transfection, we collected total RNA and conducted RNA-sequencing by using BGISEQ-500. GFP overexpression vector was used as control.

overall_design: Examination of TAp63α and deltaNp63α functions in chicken primary myoblast

first: Xiquan

last: Zhang


title: WGBS assessment of global methylation alterations in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

summary: Using WGBS we assessed global DNA methylation changes in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells. Compared with WT cells, Dnmt3aKO cells but not Dnmt3bKO cells showed genome-wide hypomethylation.

overall_design: Genomic DNA from WT, Dnmt3aKO or Dnmt3bKO J1 ES cells wes isolated, treated with bisulfite and sequenced with Illumina HiSeq sequencing systems.

first: Sean

last: Cullen

first: Xueqiu

last: Lin

first: Wei

last: Li

first: Margaret

last: Goodell


title: Total RNA was extracted from three samples of CD33 CAR or control T cells from three different donors

city: Memphis

first: Lance

middle: E

last: Palmer

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: In vivo persistence of chimeric antigen receptor (CAR) T cells correlates with therapeutic efficacy, yet CAR-specific factors that support persistence are not well resolved. Using a CAR containing a single chain variable fragment (scFv) specific for CD33 linked to a 4-1BB and CD3 zeta signaling domain that is currently in advanced clinical trials, we show that CAR-expression, in a ligand-independent manner, alters T cell differentiation during ex vivo expansion. CAR-transduced T cells displayed decreased naïve and stem memory populations and increased effector subsets relative to vector-transduced control cells, and this was associated with reduced in vivo persistence. Altered persistence was not due to antigen specificity or tumor presence, but was linked to tonic signaling through the CAR, most notably CD3 zeta ITAMs, prior to transfer. We identified the PI3K/AKT pathway in CD33 CAR T cells as responsible. Treatment with a PI3K inhibitor modulated the differentiation program of CAR T cells, preserved a less differentiated state without affecting T cell expansion, and improved in vivo persistence relative to control cells. These results help resolve mechanisms by which tonic signaling modulates CAR T cell fate, and identifies a novel pharmacologic approach to enhance the durability of CAR T cells for cell-based immunotherapy.

overall_design: RNA-Seq differential expression analysis comparing CD33 CAR T-cells vs control T-cells from three healthy indivduals

first: Wenting

last: Zheng

first: Carol

last: O'Hear

first: Rajshekhar

last: Alli

first: Jacob

last: Basham

first: Lindsay

last: Jones

first: Terrence

last: Geiger


title: Next Generation Sequencing of CNS-infiltrating Tox-sufficient and -deficient OT-1 cells in ODC-OVA mice 7 days after LCMV-OVA infection

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the transcriptome of CNS-infiltrating OT-1 WT and Tox-deficient cells during effector phase (7 days after infection with LCMV-OVA)

overall_design: OT-1 mRNA profiles of 7-weeks old ODC-OVA mice adoptively transfered with 10^5 OT-1 CD45.1 cells (WT and Tox-deficient) 7 days after i.v. infection with LCMV-OVA (deep sequencing, in triplicate, using Illumina).

first: Doron

last: Merkler

first: Nicolas

last: Page


title: RNA-seq analysis of transcriptomic changes caused by Egg/dSETDB1 in Drosophila

city: Seoul

first: Jae Yun

last: Lim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Egg/dSETDB1, the ortholog of the human methyltransferase SETDB1, is the only H3K9 methyltransferase essential for viability and fertility in Drosopila. To understand the role of Egg in oogenesis, we adopted high throughput RNA sequencing (RNA-seq) and identified putative target genes regulated by Egg.

overall_design: To obtain total RNAs and cDNAs, ovaries were dissected from 2- to 4-day-old wild type (w1118) or egg mutant (egg2138/Df(2R)Dll-Mp) females and frozen in liquid nitrogen.

first: Lim

last: Yun

first: Moon

last: Woongjoon

first: Shin

last: Chanseok


title: Next Generation Sequencing of splenic- and CNS-infiltrating OT-1 cells in ODC-OVA mice upon LCMV-OVA and Lm-OVA infection

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the transcriptome of OT-1 cells during priming (3 days after infection) and during effector phase ( 7 days after infection) in ODC-OVA mice after LCMV-OVA and Lm-OVA infection

overall_design: OT-1 mRNA profiles of 7-weeks old ODC-OVA mice adoptively transfered with 10^5 OT-1 CD45.1 cells 3 and 7 days after i.v. infection with LCMV-OVA and Lm-OVA (deep sequencing, in triplicate, using Illumina).


title: Direct interaction of MYCN and p53 regulate transcriptional responses in neuroblastoma [RNA-Seq]

first: Jason

last: Shohet

summary: The net transcriptome of a cancer cell is defined by relative levels of transcription factors, activators, suppressors and co-factors. These in turn are controlled by epigenetic, genetic and metabolic restraints. Here we used RNA-Seq, ChIP-qPCR, and ChIP-Seq to determine the impact of MYCN protein levels on p53 and MYCN mediated transcription in neuroblastoma, a p53 wild-type neural crest derived pediatric malignancy. Of note, about 25% of neuroblastoma is MYCN amplified and expresses 10-100 fold higher levels of MYCN protein than non-amplified tumors. We hypothesized that p53 functions would be globally altered by extreme MYCN levels and this could help to explain aggressive biology and poor long term survival which distinguishes MYCN-amplified neuroblastoma. In fact, we found that in the context of high MYCN levels, activation of p53 results in marked changes in transcription of specific p53 and MYCN target loci regulating apoptosis, DNA repair and cell cycle progression. Co-immunoprecipitation of endogenous and GST-fused proteins, as well as ChIP-qPCR confirms formation of p53/MYCN complexes and enrichment of both transcription factors at active loci. This p53/MYC interaction is independent of MYC/MAX complexes. Together, these data demonstrate MYCN to be a direct co-factor modulating p53 transcriptional output in MYCN amplified cancer.

overall_design: To explore the interaction of the MYCN and p53 transcriptional programs, we utilized a MYCN-inducible system to evaluate p53 transcriptional responses by RNA-Seq in the presence of high and low MYCN levels.  MDM2 inhibitor Nutlin3a was used to increase p53 levels in a MYCN inducible cell line.

first: Saurabh

last: Agarwal


title: Direct interaction of MYCN and p53 regulate transcriptional responses in neuroblastoma [ChIP-Seq]

overall_design: To explore the MYCN binding at genomic locations under MYCN low and MYCN high conditions


title: Quantitative analysis of WT, Dnmt3a-/-, Dnmt3b-/- and Tet1-/- J1 ES cell transcriptomes

first: xueqiu

last: lin

summary: In order to figure out the roles of Dnmt3 and Tet1 in gene regulation, we assessed global gene expression changes in Dnmt3aKO, Dnmt3bKO and Tet1KO ES cells.

overall_design: mRNA profiles of WT, Dnmt3a-/- and Dnmt3b-/- ES cells; WT and Tet1-/- ES cells were generated by deep sequencing, in replicate, using Illumina HiSeq sequencing systems.

first: Sean

last: Cullen

first: Xueqiu

last: Lin

first: Tianpeng

last: Gu

first: Wei

last: Li

first: Margaret

last: Goodell


title: Next Generation Sequencing for Quantitative Transcriptomic Profiling of TLR3, TLR7 and TLR8 Activation in Neurons

status: Public on May 15 2018

city: Taipei

first: Yi-Ping

last: Hsueh

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: The goal of this study is to compare gene expression of mouse cultured cortical and hippocampal neurons in response to TLR3, TLR7 and TLR8 activation

overall_design: At 4 day in vitro, wild-type mouse cortical and hippocampal neurons were treated with vehicle control, poly IC (for TLR3 activation) and CL075 (for TLR7 activation). Tlr7-/- neurons were treated with vehicle control and CL075/poly dT (for TLR8 activation). Six hr after treatment, total RNAs were extracted for deep sequencing, in triplicate, using the NextSeq500 High-output v2 (75 cycle) sequencing kit on the Illumina NextSeq500 instrument.

first: Yun-Fen

last: Hung

first: Chiung-Ya

last: Chen


title: Adult CNS Myelin Enhances Axonal Outgrowth From Neural Stem Cells

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: The growth of neural stem cells is strongly enhanced on myelin in vitro and in vivo. To identify the mechanisms associated with this phenome, we compared RNA expression from mouse E12 derived spinal cord cells on stimulation substrates (laminin and myelin) to permissive substrates (PDL). We identified Negr1 as mediator of the stimulatory effects of myelin.

overall_design: Examination of transcripts in embryonic spinal cord cells stimulated by laminin and myelin substrates in vitro.

first: Gunnar

last: Poplawski

first: Richard

last: Lie

first: Matt

last: Hunt

first: Hiromi

last: Kumamaru

first: Paul

last: Lu

first: Michael

last: Schaefer

first: Grace

last: Woodruff

first: Jacob

last: Robinson

first: Jeniffer

last: Dulin

first: Cedric

last: Geoffroy

first: Lutz

last: Mezel

first: Binhai

last: Zheng

first: Giovanni

last: Coppola

first: Mark

last: Tuszynski


title: Genome-wide maps of Dnmt3a1 binding in WT and Tet1-/- J1 ES cells

first: xueqiu

last: lin

summary: By biotin-streptavidin ChIP, we found that Dnmt3a1 enriched at diatal promoter regions and its binding was elevated by Tet1 deletion.

overall_design: Biotin-tagged Dnmt3a1 J1 ES cell line were generated and Tet1 was deleted in the cell by CRISPR-Cas9. Then biotin-streptavidin ChIP-seq was performed in these cell lines.

first: Sean

last: Cullen

first: Xueqiu

last: Lin

first: Wei

last: Li

first: Margaret

last: Goodell


title: Dnmt3a KO CMS-Seq

summary: Dnmt3a KO vs. WT CMS-Seq in 129S4/SvJae background

overall_design: Dnmt3a KO vs. WT CMS-Seq


title: G9a regulates temporal preimplantation developmental program and lineage segregation in blastocyst

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

summary: Early mouse development is regulated and accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2). Previously, we provided insights into its role in post-implantation development (Zylicz et al., 2015). Here we explore the impact of depleting the maternally inherited G9a in oocytes on development shortly after fertilisation. We show that H3K9me2 normally accumulates at 8- cell stage to promote timely repression of a subset of 4-cell stage specific genes. Loss of maternal inheritance of G9a disrupts the gene regulatory network resulting in developmental delay and destabilisation of inner cell mass lineages by the late blastocyst stage. Our results indicate a vital role of this maternally inherited epigenetic regulator in creating conductive conditions for developmental progression and on cell fate choices.

overall_design: Single embryo RNAseq was performed at E2.5 8-cell stage  from 10 control and 10 maternally depleted Ehmt2 embryos.

first: Jan

last: Zylicz

first: Maud

last: Borensztein

first: Yun

last: Huang

first: Caroline

last: Lee

first: M

last: Surani


title: Role of liquid sugar in regulating the hepatic transcriptome in a high fat Western diet model of NAFLD

city: Auburn

first: Michael

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

department: Nutrition

institute: Auburn University

summary:
Purpose:  The goals of this study are to use hepatic transcriptome profiling (RNA-seq) to examine the role of liquid sugar consumption in the progression of NAFLD.
Methods: Hepatic mRNA profiles of 12-week chow (n=4), high fat Western diet (n=5), and high fat Western diet + fructose/sucore in the drinking water (n=5) fed mice were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: We mapped about 100 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the livers of mice. RNA-seq data confirmed stable expression of X known liver specific genes. Approximately 10% of the transcripts showed differential expression between the XXX, with a fold change ≥1.5 and p value <0.05. Altered expression of XX genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several pathways that may contribute to NAFLD progression. RNA-seq data had a linear relationship with qRT–PCR: a goodness of fit (R2) of xxxx.
Conclusions:

overall_design: Hepatic mRNA profiles of chow, HFWD, and HFWD+F/S fed mice were generated by deep sequencing.


title: Genome-wide maps of MBD1 in mouse dentate gyrus

first: Xinyu

last: Zhao

address: 1500 HIGHLAND AVE, T513 Waisman Center

department: Department of Neuroscience

summary: We report the MBD1 binding profiles in mouse dentate gyrus by sequencing MBD1 chromatin immunoprecipitated DNA

overall_design: Examination of MBD1 in mouse dentate gyrus.

first: Yu

last: Gao

first: Brian

last: Eisinger


title: Gene expression profiles in cardiac specific overexpression of Glut1 transgenic mice

status: Public on May 14 2018

city: Seattle

first: Dan

last: Shao

state: WA

address: 850 Republican Street, N130

department: Mitochondria and Metabolism Center

institute: University of Washington

summary: Cardiac-specific Glut1 transgenic (Glut1-TG) mice exhibited higher glucose uptake and utilization compared with wild type mice. Cardiac pathological hypertrophy is accompanied by a switch of substrate metabolism from fatty acid oxidation to glucose use, resulting in a fetal like metabolic profile. However, the role of increasing glucose utilization in regulating cardiomyocyte growth is poorly understood. In order to identify novel pathways that is regulated by glucose, we performed microarray analyses using hearts from Glut1-TG and WT mice. The microarray analyses revealed that many genes that are involved in branched-chain amino acids (BCAAs) were downregulated in Glut1-TG mice.

overall_design: Two groups of cardiac-specific transgenic mice were used for this study, control and Glut1-TG mice. Hearts were dissected from 11-12 weeks old male mice (FVB background). Total RNA was prepared from the hearts to conduct the microarray analyses.

first: Yan

last: Jie

first: Rong

last: Tian


title: Translation elongation factor 4 (LepA) contributes to tetracycline susceptibility by stalling elongating ribosomes

city: Beijing

first: Bin

last: Liu

state: Beijing

address: Hai Dian

department: School of Life Sciences

institute: Tsinghua University

summary:
Purpose: We use the ribosome profiling protocol to understand EF4 mediated translation events.
Methods: We used ribosome profiling data to analyze by plastid software. The ribosome were purified by sucrose gradient separation.
Results: Using sequencing data, we found that EF4 mediates the 1-nucleotide conformational change of ribosomes. We also found that many genes involved in translation after tetracycline treatment. Finally, we found that EF4 stalls the elongating ribosomes globally.
Conclusions: Our results suggest that EF4 mediates both 30S biogenesis and translation elongation process, in particular, EF4 stalls the elongating ribosomes globally.

overall_design: Ribosome footprints from WT and ΔEF4 strains and the two strains treated with tetracycline were sequenced, in two replicates, using Illumina HiSeq 2500.

first: Chunlai

last: Chen


title: Liver transcriptomic and plasma metabolic profile of fattening lambs is modified by feed restriction during the suckling period.

city: León

first: Alba

middle: Santos

last: Baza

state: León

address: Finca Marzanas, Grulleros

department: Nutrición y Producción de Herbívoros

country: Spain

institute: Instituto de Ganadería de Montaña (CSIC)

summary:
Purpose: The present study was designed to identify both differentially expressed (DE) genes in the liver tissues of fattening Merino lambs and differences in metabolites accumulated in plasma, thus trying to identify modified metabolic pathways as a consequence of milk restriction during the suckling period.
Methods: Twenty-four male Merino lambs were assigned to 2 different groups (n=12 per dietary treatment). The first group (ad libitum, ADL) was kept permanently with the dams whereas the other group (restricted, RES) was milk restricted. When they reached 15 kg of live body weight, all the lambs were offered the same complete pelleted diet at the same level to ensure no differences in dry matter intake. All the lambs were slaughtered with 27 kg.  For transcriptomic analysis, 4 liver samples representative from each group (8 samples in total) were selected for RNA sequencing methodology (RNA-seq).
Results: 38 DE annotated genes were identified by RNA-seq, with 23 DE genes being down-regulated and 15 up-regulated in the liver of RES relative to the ADL group (P < 0.10). In general, those genes and pathways involved in protein synthesis or protease inhibitors were down-regulated in the RES group, whereas those related to proteolytic degradation were up-regultated, thus suggesting a higher catabolism of proteins in these lambs. Contrarily, RES lambs showed over-expression of xenobiotic metabolism pathways, whereas those genes related to β-oxidation of fatty acids were down expressed.
Conclusions: According to the data obtained, early feed restriction during the suckling period of Merino lambs promoted long-term effects on hepatic transcriptomic profile and plasma metabolic profile wich might have modified fatty acids metabolism, catabolism of proteins and detoxification of xenobiotics, thus reducing feed efficiency of fattening period.

overall_design: A transcriptomic analysis was carried out using next-generation sequencing (RNA-seq) from liver samples: 4 animals from ADL group and 4 animals from RES group, 8 samples in total.

last: Santos

first: Francisco

last: Giráldez

first: Erminio

last: Trevisi

first: Luigi

last: Lucini

first: Javier

last: Frutos

first: Sonia

last: Andrés


title: RNAseq analysis of wildtype and Nrf2-/- advanced lung tumors

city: East Lansing

first: Karen

last: Liby

state: MI

address: 1355 Bogue Street

department: Pharmacology&Toxicology

institute: Michigan State University

summary: Nrf2 plays a critical role in lung cancer. We investigated the gene expression profile in Nrf2 wildtype and knockout tumors. Nrf2 wildtype and knockout mice were injected with 2 or 4 doses of vinyl carbamate (16 mg/kg). Lung tumors were then dissected and pooled from each group to isolate total RNA. RNAseq was then performed to analyze the differential expression profiles between groups.

overall_design: mRNA profiles of two Nrf2 wild type (WT) and two knockout (KO) mice were generated by deep sequencing, using Illumina 2000.

first: Di

last: Zhang

first: Jonathan

last: Rennhack


title: Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis [CE_RNA-seq]

city: New York

first: Itai

last: Yanai

address: 430 East 29th St., Office 510

department: Biochemistry and Molecular Pharmacology

institute: New York University, School of Medicine

summary: miRNAs play essential roles in the mechanics of gene regulation, however, on an organismal-scale, the processes in they are deployed are not well understood. Here, we adopt an evolutionary developmental approach to study miRNA function by examining their expression throughout embryogenesis in both C. elegans and D. melanogaster. We find that, in both species, the miRNA complement of the transcriptome shifts in a punctuated fashion during the previously identified mid-developmental transition specifying two dominant modes of miRNA expression: an early and a late profile. Strikingly, we find that phylogenetically conserved miRNAs are expressed late, while early expressed miRNAs are inversely expressed with their targets suggesting strong target-inhibition. Our work exposes two distinct strategies of miRNA function comprising late-expressed physiological roles and early expressed repressive roles. In summary, the expression of miRNAs throughout embryogenesis in two species implicates their role in the canalization of cell-types during late phases of embryogenesis and repressing targets to lock-down misexpression.

overall_design: A timecourse of mRNA expression in C. elegans embryonic developmet

first: Gal

last: Avital

first: Gustavo

middle: S

last: França


title: Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis [CE_miRNA-seq]

overall_design: A timecourse of miRNA expression in C. elegans embryonic developmet


title: A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila [RNA-Seq]

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary: Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that bind Piwi proteins to silence transposons and to regulate gene expression. In Drosophila germ cells, the Aubergine (Aub)-Argonaute 3 (Ago3)-dependent ping-pong cycle generates most germline piRNAs. Loading of anti-sense piRNAs amplified by this cycle enables Piwi to enter the nucleus and silence transposons. Nuclear localization is crucial for Piwi function in transposon silencing, but how this process is regulated remains unknown. It is also not known whether any of the components of the nuclear pore complex (NPC) directly function in the piRNA pathway. Here, we show that nucleoporin 358 (Nup358) and Piwi interact with each other and that a germline knockdown (GLKD) of Nup358 with short hairpin RNA prevents Piwi entry into the nucleus. The Nup358 GLKD also activated transposons, increased genomic instability, and derailed piRNA biogenesis because of a combination of decreased piRNA precursor transcription and a collapse of the ping-pong cycle. Our results point to a critical role for Nup358 in the piRNA pathway, laying the foundation for future studies to fully elucidate the mechanisms by which Nup358 contributes to piRNA biogenesis and transposon silencing.

overall_design: mRNA profiles from mat>Luc (Control) and Nup358 germline knockdown ovaries.


title: Transcriptional profiling of mouse prostate tumors with conditional mutations in the Pten, Apc, or Tgfbr2 genes

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: We report the changes in gene expression in mouse prostate comparing normal wild type prostate to tumors generated by Cre mediated deletion of Pten or Apc, either with or without deletion of Tgfbr2. Pten single mutant tumors were isolated at either 8 weeks or 22 weeks of age, with high grade prostate intraepithelial neoplasia (HGPIN) as the main phenotype. Pten;Tgfbr2 double mutants were isolated at 8 weeks (primarily HGPIN), or at 11-14 weeks with extensive locally invasive cancer. Apc single mutants were isolated at 36 weeks old with adenosquamous HGPIN, or at 21-24 weeks of age for the Apc:Tgfbr2 double mutants, which had adenosquamous carcinoma. Ages for the two double mutant groups were based on initial signs of excess tumor burden. Wild type control prostates were isolated at around 20 weeks of age.

overall_design: Ventral prostates were isolated rapidly and frozen for RNA isolation. Where individual lobes were no longer recognizable due to extensive tumor formation, a piece of the tumor was used. We analyzed multiple replicates fro each group by RNA-seq: 8 week Pten and Pten;Tgfbr2, Apc (at 36 weeks) and Apc;Tgfbr2 (at 20 to 24 weeks) samples - three replicates each. Wild type and 22 weeks Pten single mutants - four replicates each. Pten;Tgfbr2 double mutants at 11 to 14 weeks - five replicates.


title: RNA-Seq transcriptome profiling of soleus from adult and aged mice following disuse muscle atrophy and recovery

city: Orlando

first: Paul

last: Coen

state: FL

address: 301 East Princeton Street

department: Translational Research Institute for Metabolism and Diabetes

institute: Florida Hospital

summary: Rodent hind limb unloading was used as a model for reduced muscle activity and eventual atrophy. After a 10 day period of unloading, mice in this study were “reloaded” for 3 days and regained use of their hind limbs. We report the application of Next-generation sequencing (NGS) technology for high-throughput profiling of mRNA in soleus muscle of adult (6 mo) and aged (22-24 mo) mice. Our goal was to determine the effects of hind limb unloading and reloading on mRNA profiles in soleus muscle and compare between adult and aged mice. We find that there are distinct response in the profile of fatty acid oxidation, TCA cycle, ETC oxidative phosphorylation gene expression patterns in response to unloading and reloading. The repsonses are generally simialr between young and old mice.

overall_design: RNA-Seq was performed with total RNA isolated from snap frozen soleus muscle. Male C57BL/6J mice (Adult 6 mo and Old 22-24 mo) were obtained from the NIA's Aged Rodent Colony Charles River Laboratories, Madison, WI) and were subjected to the following experimental conditions: 1) hind limb unloaded for 10 days, 2) hind limb unloaded for 10 days and reloaded for 3 days, or 3) maintained under control conditions for 10 days. Mice were fed ad libitum with a standard chow diet (#2916, Harlan-Teklad, Houston, Tx) and water/hydrogel (ClearH2O, Westbrook, ME, US) and housed at 22C with a 12-h light/dark cycle. All soleus samples were harvested following a 4 hour fast and mice were sacrificed at ~11am by CO2 asphyxiation and cervical dislocation.

first: Xiaolei

first: Rick

middle: B

last: Vega


title: Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis [DM_miRNA-seq]

overall_design:
A timecourse of miRNA expression in D. melanogaster embryonic development

Please note that the data for the DM_mRNA-seq was already published (Levin et al., 2016, PMID 26886793) and the corresponding samples of the DM_miRNA are represented in the current study.


title: Two evolutionary developmental strategies for miRNA gene regulation in animal embryogenesis

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

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster

overall_design: Refer to individual Series


title: Maturation of polycistronic mRNA by RNase Y and its associated Y-complex in Gram-positive bacteria

status: Public on May 12 2018

city: Cambridge

first: Aaron

last: DeLoughery

state: MA

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

summary: Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability and discordant abundance among co-transcribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity towards the cggR-gapA operon, an event that differentiates the expression of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified that is also required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. However, whether the Y-complex is broadly required for RNase Y activity is unknown. Here we used end-enrichment RNA sequencing (Rend-seq) to globally identify operon mRNAs that undergo maturation post-transcriptionally by RNase Y and the Y-complex. We found that the Y-complex is required for the majority of RNase Y-mediated mRNA maturation events and affects riboswitch abundance in B. subtilis. In contrast, noncoding RNA maturation by RNase Y often do not require the Y-complex. Furthermore, deletion of RNase Y has more pleiotropic effects on the transcriptome and cell growth than deletions of the Y-complex. We propose that the Y-complex is a specificity factor for RNase Y, with evidence that its role is broadly distributed across low-GC Firmicutes.

sample_organism:
Staphylococcus aureus
Bacillus subtilis

platform_organism:
Staphylococcus aureus
Bacillus subtilis

overall_design: 16 Rend-seq experiments in B. subtilis and Staphylococcus aureus

middle: J

first: Jean-Benoit

last: Lalanne

first: Byoung-Mo

last: Koo

first: Richard

last: Losick

first: Gene-Wei

last: Li


title: Gene expression responses to ABA and to osmotic stress in the pyl112458 379101112 mutant

city: Shanghai

first: Yang

last: Zhao

state: Shanghai

address: 300 Fenglin RD

institute: Shanghai Center for Plant Stress Biology, and CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Nearly all of the transcript level responses to ABA in WT seedlings were diminished in the 112458 379101112 mutant.  However, only a relatively small percentage of the transcript level responses to osmotic stress was abolished in the 112458 379101112 mutant, and the majority of the responses was maintained, although the levels of up- or down-regulation of many of the transcripts were reduced in the mutant.

overall_design: Wild type and mutant seedlings were grown vertically for 9 days before treatment. These seedlings were mock treated, or treated with 100 µM ABA or 300 mM mannitol for 24 hours on filter papers.  The transcriptome were analyzed by deep sequencing, in triplicate, using Illumina HiSeq 2500.


title: Induction of Prolonged Early G1 Arrest by CDK4/CDK6 Inhibition Reprograms Lymphoma Cells for Durable PI3Kδ Inhibition Through PIK3IP1

first: Selina

last: Chen-Kiang

state: NY

address: 1300 York Avenue, C338

institute: Weill Cornell Medical College

summary: The RNA-seq data presented in this study include libraries from Mantle Cell Lymphoma (MCL) tumor cells of 4 patients, Peripheral Blood B Cells from 3 healthy volunteers and JEKO-1 MCL cell lines

overall_design: RNA-Seq on MCL patient samples

first: D

last: Chiron

first: M

last: Di Liberto

first: C

last: Mason

first: S


title: 4C-seq analysis of interactions with the Albumin promoter in mouse liver

status: Public on May 11 2018

city: Boston

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21, and 4C-seq analyses in male and female mouse liver centered at an Albumin promoter viewpoint. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C.  Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. This allows high expression of super enhancer target genes and individual genes within inactive TADs, and may be a broadly conserved mechanism of genomic regulation.

overall_design: 4C-seq for the promoter of Albumin in mouse liver

first: Bryan

last: Matthews


title: Sp8 and Sp9 Coordinately Promote Striatal Medium Spiny Neuron Production through Activating Six3 Expression [RNA-seq]

first: Qifei

last: Liang

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
Purpose: To assess changes in gene expression profiles from the E16.5 no cre littermate control striatum and conditional double knockout of Dlx5/6-CIE; Sp8 Flox/Flox; Sp9 Flox/Flox mice.
Methods: Total RNA was isolated and sequenced from the striatum of the E16.5 no cre littermate control or Dlx5/6-CIE; Sp8 Flox/Flox; Sp9 Flox/Flox mice in duplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed  which performed fold-change>=2 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of Sp8 and Sp9.
Results: 80 genes were significantly increased and 120 genes were significantly decreased in expression level due to the loss of Sp8 and Sp9 expression.

overall_design: Total RNA was isolated and sequenced from the striata of the E16.5 no cre littermate control or Dlx5/6-CIE; Sp8 Flox/Flox; Sp9 Flox/Flox mice in duplicate using an illumina high-seq 2500.

first: Zhejun

last: Xu

first: Zhenmeiyu

first: Yan

last: Wen

first: Guoping

last: Liu

first: Dashi

last: Qi

first: Zhuangzhi

last: Zhang

first: Min

last: Wang

first: Chunyang

first: Teng

last: Guo

last: Song

last: You

first: Bin

last: Chen

first: Kenneth

last: Campbell

first: John

middle: L

last: Rubenstein

first: Zhengang

last: Yang


title: Transcriptomic analysis of neuroepithelium and sorted neural progenitors in the murine cortex duirng early stages of development

status: Public on May 10 2018

first: Kevin Fongching

last: Chau

address: Enders Building. Room 1150, 300 Longwood Avenue

institute: Boston Children's Hospital

summary: Relatively little is known about how the identity of early neuronal stem cells changes before and after neural tube closure (neurulation). We performed RNA sequencing on microdissected forebrain precursors and revealed sharp reductions in expresion of protein biosynthetic machinery after neurulation. These reductions were paralleled by down-regulation of Myc, which regulated forebrain precursor ribosome ribosome biogenesis. To study consequences of Myc dysregulation, we overexpressed Myc in Nestin+ neural progenitors, sorted these progenitors for RNA sequencing, and identified 135 genes that are differentially expressed between Myc-overexpressed embryos and their wildtype littermates.

overall_design:
The first RNA sequencing dataset contains micordissected neuroepithelium from E8.5 and E10.5 mouse embryos, two biological replicates for each age.
The second RNA sequencing dataset contain FACS isolated Pax6+ neural progenitors form the cortex of E13.5 MYC-overexpressed embryos and their wildtype littermates, three biological replicates for each genotype.

first: Kevin

first: Matthew

last: Johnson

first: Mark

last: Springel

first: Maria

last: Lehtinen


title: IsomiR and miRNA Profiling in Colorectal Neoplasia

city: Rochester

first: Wilson

last: Wu

state: MN

address: 200 First Street SW

department: Gastroenterology and Hepatology

institute: Mayo Clinic

summary: Using miRDeep2 and a custom NGS data analysis workflow to annotate and quantify isomiRs in normal and neoplastic colorectal tissues.

overall_design: Establishment and validation of a custom workflow, study isomiR profile and differential expression in colorectal neoplasia

first: Chung Wah

first: Jared

last: Evans

first: David

last: Ahlquist


title: AMPKα1 and α2 knockout and usage of alternative polyadenylation sites

status: Public on May 09 2018

city: Pullman

first: Zhihua

last: Jiang

address: Veterinary and Biomedical Research Building, Room 151

department: Animal Science

institute: Washington State University

summary: Role of alternative polyadenylation in muscle development remains largely undetermined.  Our WTTS-seq approach to capture 3'-end of RNAs clearly revealed alternaitve polyadenylation events responsible for reduced muscle mass in AMPK α1, but increased muscle mass in AMPK α2 knockout mice.

overall_design: Total RNA samples obtained from muscle tissue of knockout (KO) mice and wild-type (WT) mice were used to construct WTTS-seq libraries. Eight WTTS-seq libraries including two AMPKα1 KO mice, two AMPK α2 KO mice, two AMPKα1 WT mice and two AMPK α2 WT mice were involved in this submission.

first: Xiang

last: Zhou

first: Shuwen

first: Jennifer

last: Michal

first: Yangzi

last: Du


title: Identification of a small molecule that facilitates the differentiation of human iPSCs/ESCs into pancreatic endocrine cells

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

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

country: Japan

institute: CyberomiX Inc

summary: Pancreatic beta cell generation from induced pluripotent stem cells (iPSCs) offers an alternative donor tissue source; however, the efficiency of induction of INSULIN (INS)+ cells from human iPSCs (hiPSCs) is low. We aimed to establish an efficient differentiation protocol for generating INS+ cells from hiPSCs by identifying novel inducers. We screened small molecules that increased the induction rate of INS+ cells from hiPSC-derived PDX1+ pancreatic progenitor cells by using high-throughput screening (HTS) system. We identified one compound, sodium cromoglicate (SCG) out of about 1,250 small molecules that we screened. When SCG was combined with the previously described protocol, the induction rate of INS+ cells increased up to 15–20%, and the cells developed the ability to secrete C-peptide in vitro. We found that SCG facilitates the differentiation of multiple endocrine cell types, including INS+ cells, in both hiPSC differentiation cultures and mouse embryonic pancreas explants by inducing NEUROG3+ endocrine precursor cells. We also confirmed that the mechanisms of action by which SCG induces the pancreatic endocrine differentiation include the inhibition of BMP4 signaling.

overall_design: We performed RNA sequencing analyses to compare the gene expression profiles of cells that were differentiated from hiPSC-derived PDX1+ PP cells after 8 days of treatment with SCG and those that were treated with H2O (control); we also compared the gene expression profiles of cells that were treated with 4Fs and SCG and those that were treated with 4Fs alone.

first: Yasushi

last: Kondo

first: Taro

last: Toyoda

first: Kenji

last: Osafune


title: Transcriptional Analysis of Wild Type and KLF4-/- Peritoneal Macrophages

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

summary: Krüppel-like factor 4 (KLF4) is a critical regulator of macrophage activation. Here, we report transcriptomic differences in peritoneal macrophages isolated from Lysozyme M Cre (control) and myeloid-specific KLF4 knockout mice.

overall_design: Peritoneal macrophages were isolated from lysozyme M Cre (wt) and myeloid-specific KLF4 knockout (K4KO) mice 72 hours after thioglycolate injection. Three mice per group were used.  cDNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit and sequenced on a Illumina HiSeq 2500 platform. Reads from each sample were aligned to the mouse genome (UCSC mm10) using TopHat2 (Kim et al., 2013). Macrophage gene expression was quantitated as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (Trapnell et al., 2010).

first: Xudong

last: Liao

first: Derin

last: Tugal

first: Chen

last: Fu

first: Yuyan

last: Shen