title: Genome-wide effect of AML engraftment on bone marrow endothelial cells

city: London

first: Diana

last: Passaro

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: We analysed the transcriptional signature in endothelial cells extracted from the bone marrow of mice engrafted with human AML and compared it to the one of mice engrafted with human normal hematopoietic cells

overall_design: Immunodeficient mice were transplanted with human AML cells derived from patients, or with normal human hematopoietic cells derived from cord blood. Mice were sacrificed once assessed the bone marrow engraftment, and the bones were processed to isolate endothelial cells using the CD31 marker. RNA was extracted, sequencing libraries were prepared and sequenced.

first: Dominique

last: Bonnet

first: Probir

last: Chakravatry


title: An NF-κB-dependent, lineage-specific transcriptional program regulates Treg identity and function [RNA-seq]

status: Public on Sep 13 2017

city: New York

first: Hyunju

last: Oh

state: NY

address: 701 West 168th Street

department: Microbiology and Immunology

country: USA

institute: Columbia University Medical Center

type: Expression profiling by high throughput sequencing

summary: We found a NF-κB-dependednt transcriptional program specific in Treg cells compared to Tconv cells by performing multiple RNAseq analyses using various knockout systems.

overall_design: Examination of genome-wide RNA expression in different T cell types

first: Sankar

last: Ghosh


title: MicroRNA Profiling of Endothelial Cells

status: Public on Sep 09 2017

city: Kuopio

first: Suvi

last: Kuosmanen

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, the miRNA expression of human vascular endothelial cells from tissue-derived cells and cultured cells were profiled using miRNA sequencing. The data analysis revealed a striking switch in endothelial miRNA profile as the cells adapted from tissue to cell culture environment and the overall miRNA expression decreased significantly in cultured endothelial cells compared to tissue-derived endothelial cells. In addition to changes in mechanosensitive miRNA expression, alterations in senescence-associated and endothelial-to-mesenchymal-transition-associated miRNAs were observed in aging cells. Collectively, the data illustrates the plasticity of endothelial cells, and elucidates the multifaceted nature of the cell-specific miRNA profiles, clearly emphasising that the cellular miRNA profile consists of fluid collection of miRNAs, which mirror the prevailing cellular status.

overall_design: The samples were collected at endothelial cell extraction from umbilical cords (S0) and from three subsequent cell passages (S1-S3). S0 samples represent the tissue-derived endothelial cells, and S1 to S3 samples are adjusted to static cell culture conditions. S2 samples are from aging cells and S3 from old cells. S0 samples originate from three different donors, S1-S3 from four.

middle: M

first: Emilia

last: Kansanen

first: Anna-Liisa

last: Levonen


title: RNA-seq analysis of FET cells treated with RSPO1 or TGFβ1

city: Omaha

first: Jing

last: Wang

address: S 42 St and Emile St

institute: University of Nebraska Medical Center

summary: To determine whether RSPO1 and TGFβ1 activate similar transcription, RNA-seq analysis was performed to compare gene profiles after treatment by RSPO1 or TGFβ1. FET cells were treated with RSPO1 or TGFβ1 in triplicates for 4 hours and RNAs extracted from these cells were used for RNA-seq analysis. When gene expression profiles were compared, it was found that 153 genes were commonly regulated by either RSPO1 or TGFβ1. Interestingly, the majority of genes regulated by TGFβ1 were also regulated by RSPO1.

overall_design: FET cells were treated with RSPO1 or TGFβ1 in triplicates for 4 hours and RNAs extracted from these cells were used for RNA-seq analysis. Genes with log2 based fold change ≥1 and FDR < 0.05 were considered upregulated genes and those with log2 based fold change ≤ -1 and FDR < 0.05 were considered downregulated genes.

first: Xiaolin

last: Zhou

first: Liying

last: Geng

first: Degeng

first: Haowei

last: YI

first: Geoffrey

last: Talmon


title: Transcriptomic analysis of DJ-1 knockout rat brains using RNA-Seq

status: Public on Sep 11 2017

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary: Mutations in the DJ-1 gene cause rare forms of autosomal recessive Parkinson's disease in humans. Recently, DJ-1 knockout rats have been generated and they have been reported to have subtle motor defects and neurodegeneration. We hypothesized that measuring the differences in mRNA expression in the brains of wildtype and DJ-1 knockout rats would provide insight into the mechanisms underlying these phenotypes. Using RNA-Seq, we were able to measure differential expression of over 2,000 genes in the DJ-1 knockout rat brains.

overall_design: 8 wildtype male rats, 6 DJ-1 knockout male rats

first: David

middle: N

last: Hauser

first: Allissa

middle: A

last: Dillman


title: Concentration dependent binding states of the Bicoid Homeodomain Protein

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We have measured by ChIP-seq the distribution of Bicoid protein in Wild Type embryos, and in embryos in which the sole source of Bicoid is expressed at single concentrations representative of individual positions along the morphogen gradient. In addition, we have measured chromatin accessibility and nucleosome positioning by ATAC seq in Wild Type, bicoid mutant, uniform bicoid, and zelda mutant embryos.

overall_design: Chromatin Immunoprecipitation in Drosophila melanogaster embryos of GFP-tagged Bicoid with 1) wild-type (graded) protein distribution; 2) at three different uniform levels of expression; and 3) wild-type (graded) protein distribution lacking posterior and terminal patterning cues (nos and tsl). ATAC-seq of single embryos staged at 12 minutes into nuclear cycle 14 in seven genotypes: wild-type, bcd[E1], zelda[294], bcd[E1] nos[L7] tsl[4], and three transgenic lines expressing uniform bicoid.

first: Colleen

middle: E

last: Hannon

first: Eric

middle: F

last: Wieschaus


title: The effect of genetic and chemical inhibition of NF-kB subunits on the regulatory T cell (Treg) transcriptome

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

country: France

institute: Cancer Research Center of Lyon

summary: We report here the transcriptome analysis on murine total, resting and activated Treg cells after chemical (using the drug pentoxifylline) and genetic (using conditional KO strain) inhibition of NF-kB.

overall_design:
RNA-sequencing (30 million reads/sample) on :
1- Foxp3+ WT mouse Treg(treated with H2O or pentoxifylline), and c-Rel deficient Treg.
2-Foxp3+ CD62Lhi CD44lo rTreg and CD62Llo CD44hi aTreg sorted from WT, p65KO and cRelKO spleen+LN, ex vivo processed for RNA extraction.
All experiments were performed in duplicates.


title: Small RNA deep sequencing of Arabidopsis DRB mutants

city: Callaghan

first: Kate

last: Hutcheon

state: New South Wales

address: University Drive

country: Australia

institute: University of Newcastle

summary: Arabidopsis thaliana (Arabidopsis) encodes five DOUBLE-STRANDED RNA BINDING (DRB) proteins, DRB1 to DRB5, that predominantly act as non-catalytic cofactors for DICER-LIKE (DCL) proteins in the double-stranded RNA (dsRNA) processing stages of small RNA (sRNA) production pathways. In the nucleus, DRB1 is required for microRNA (miRNAs) processing from imperfectly dsRNA precursors by DCL1. Similarly, DRB4 is required by DCL4 for small-interfering RNAs (siRNAs) production from endogenous or exogenous perfectly dsRNA templates. DRB2 has been recently demonstrated to be required for miRNA and siRNA production in developmentally-important tissues of Arabidopsis while the requirement of either DRB3 or DRB5 in sRNA production remains unclear. Here, we analyse in parallel, the contribution of all five DRB protein family members to the global sRNA landscape of Arabidopsis floral tissues. In depth bioinformatic analysis of sRNA sequencing datasets generated from floral tissues of DRB knockout mutant (drb) plant lines, drb1, drb2, drb4, drb12, drb14, drb24, and drb35 and their comparison to the floral sRNA profile of wild-type Arabidopsis, has enabled confident assignment of the requirement of DRB1, DRB2 and DRB4 for the production of specific miRNA and siRNA subclasses in this tissue. Our analyses have additionally identified novel and/or expanded roles for DRB2 in miRNA, trans-acting siRNAs (tasiRNAs) and natural antisense transcript siRNAs (natsiRNAs) production.

overall_design: Eight samples are included in the study, corresponding to floral small RNA deep sequencing results for wild-type and seven DRB mutant lines; drb1, drb2, drb4, drb12, drb14, drb24, and drb35. This study has been submitted as BioProject PRJNA295898.

first: Andrew

middle: L

last: Eamens


title: REV-ERBα Ameliorates Heart Failure Through Transcription Repression

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Heart failure remains a major unmet clinical need and current therapies  targeting neurohomonal and hemodynamic regulation have limited efficacy. We report that pharmacological activation of the transcriptional repressor REV-ERBa prevents expression of a pathological gene program and cardiomyocyte hypertrophy. In vivo,  REV-ERBa agonism prevents development and halts progression of heart failure in mouse models. Thus, modulation of gene networks by targeting REV-ERBa represents a novel approach to heart failure therapy.

overall_design: We performed RNAseq on NRVM at baseline and after PE stimulation (4 hr and 48 hr) in the presence or absence of SR9009 (SR or Veh were given 24 hr prior to PE).

first: Lilei

last: Zhang

first: Mukesh

last: Jain


title: Functional diversified kaurene synthase like genes in Isodon rubescens shed light on chemical diversity evolution of diterpenoids in Lamiaceae

status: Public on Sep 08 2017

city: Beijing

first: Tong

last: Chen

address: No 16 Nan-xiao-jie Dong-zhi-men-nei

department: State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica

country: China

institute: China Academy of Chinese Medical Sciences

summary: The Lamiaceae family contains numerous diterpenoids, offering a valuable model system for the study of diterpenoid chemical diversity. In this study we report that the ent-kaurene diterpenoids in I. rubescens have the largest diTPS gene family identified in Lamiaceae. Three genes are predicted to be involved in ent-kaurene diterpenoid synthesis while another two KSL genes are functional enzymes utilizing ent-CPP as a substrate. We also showed the presence of a normal-CPP mediated biosynthesis pathway in I. rubescens and that three KSL genes possessing different domain architectures are involved in this pathway. This study provides new information regarding the understanding of diterpenoid chemical diversity and this compounds’ evolution  in  the Lamiaceae family.

overall_design: RNA-seq of Isodon rubescens leaf tissue in Spring

first: Guanghong

last: Cui

first: Baolong

last: Jin


title: Cell-cycle-resolved analysis of RNA expression in neuroblastoma cells upon MYCN knockdown

status: Public on Sep 12 2017

city: Heidelberg

first: Chunxuan

last: Shao

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

summary: Previous studies of c-MYC or MYCN effects on the cellular transcriptome have been performed with unsynchronized tumor cell populations. We reasoned that these results might have been influenced by different cell-cycle profiles of cells with high or low MYC levels  as the expression of a large part of the genome varies with cell-cycle phase. To correct for this potentially confounding effect, we performed RNA sequencing in cell-cycle-synchronized neuroblastoma cells and then compared the transcriptomes of cells with high and low MYCN in equivalent cell-cycle phases.

overall_design: IMR5/75 neuroblastoma cells with tetracycline-inducible MYCN shRNA were arrested at G1:S transition by thymidine treatment for 18 h. After washout, transcriptome was measured at 11 time points over 22h (2 biological replicates).

first: Emma

last: Bell

first: Mona

last: Friedrich


title: Progesterone Regulation of Extracellular Vesicles in the Uterine Luminal Fluid of Sheep (miRNA-Seq)

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Progesterone (P4) acts via the endometrium to modify the uterine environment and promotes conceptus growth for elongation and pregnancy establishment. Ewes were ovariectomized and treated with P4 for 14 days or P4 for 14 days and RU486, a progesterone receptor antagonist, from days 8 to 14. Small RNA sequencing of endometrium and EVs from the uterine lumen detected expression of 768 miRNAs and P4 regulation of 9 endometrial and 7 extracellular vesicle miRNAs.

overall_design: Endometrium from P4-treated (n=5) or P4+RU486-treated ewes (n=5); Extracellular vesicles from the uterine lumen of P4-treated (n=4) or P4+RU486-treated ewes.

first: Gregory

middle: W

last: Burns

first: Kelsey

last: Brooks

first: Eleanore

middle: V

last: O'Neil

first: Darren

last: Hagen

first: Susanta

middle: K

last: Behura


title: Experience-dependent Epigenomic Reorganization in the Hippocampus

city: Lewiston

middle: John

last: Kennedy

state: ME

address: 5 Andrews Rd, Dana 322

department: Chemistry

institute: Bates College

type: Methylation profiling by high throughput sequencing

summary: To further investigate epigenetic regulation of memory, we utilized whole-genome sequencing tools to systematically characterize memory-related changes in gene expression and DNA methylation status following memory acquisition.

overall_design: Experience-dependent alternations in gene expression and DNA methylation in the CA1 area of the hippocampus of Sprague-Dawley rats were observed 1 hr and 24 hr after contextual threat recognition training.

middle: J

first: Jeremy

last: Day

first: John

middle: D

last: Sweatt


title: Comparing gene expression profiles of wild-type and the ∆phcA mutant strains of Ralstonia solanacearum during tomato colonization

city: Madison

first: Caitilyn

last: Allen

state: Wisconsin

address: 1630 Linden Drive

department: Department of Plant Pathology

institute: UW-Madison

summary:
Purpose: To comprehensively identify traits controlled by the PhcA quorum sensing system, and to better understand how this regulator affects pathogen behavior in its natural host environment
Method: 21 day-old tomato plants were inoculated with approximately 2000 cells of either wild-type Rs strain GMI1000 or ΔphcA through a cut petiole. After 72 h in a 28°C growth chamber (12h day/night cycle), 0.1 g of stem tissue spanning the petiole was harvested and transferred immediately to a tube containing 900 µl of pre-chilled transcription stop solution (5% [vol/vol] water-saturated phenol in ethanol) and ground using a Powerlyzer. RNA was isolated from these ground samples using hot phenol method. Total RNA was treated with RiboZero kits to reduce bacterial and plant rRNA, followed by tomato mRNA reduction using polyA selection and used to make libraries with the Illumina TruSeq strand-specific mRNA sample preparation system. After RNA fragmentation, strand-specific libraries were constructed by first-strand cDNA synthesis using random primers, sample cleanup and second-strand synthesis using DNA Polymerase I and RNase H. A single 'A' base was added to the cDNA fragments followed by ligation of the adapters. The final cDNA library was further purified and enriched with PCR, and quality checked using the Bioanalyzer 2100. The libraries were sequenced using the Illumina HiSeq2500, yielding ~20 million 1x50bp reads per sample
Conclusion: Defining the PhcA in planta regulon identified traits that make R. solanacearum successful at high cell density during bacterial wilt disease, but also identified traits that help it survive at low cell densities

overall_design: Bacterial mRNA profiles of wild-type and ΔphcA mutant were generated by using the Illumina HiSeq2500, yielding ~20 million 1x50bp reads per sample. There were biological replicates per treatment.

first: Devanshi

last: Khokhani

first: Tiffany

last: Lowe-Power

first: Tuan

last: Tran


title: The chromatin remodelling factor ATRX suppresses R-loops in transcribed telomeric repeats

city: Headington

first: Richard

last: Gibbons

address: John Radcliffe Hospital

department: MHU, WIMM

institute: University of Oxford

summary: ATRX is a chromatin remodelling factor found at a wide range of tandemly repeated sequences including telomeres (TTAGGG)n. Acquired mutations in ATRX are found in nearly all tumours which maintain their telomeres via the alternative lengthening of telomere (ALT) pathway and ATRX is known to suppress this pathway. Here we show that recruitment of ATRX to telomeric repeats is dependent on their number, their orientation and, critically, on their transcription. Importantly, the transcribed telomeric repeats form RNA-DNA hybrids (R-loops) whose abundance correlates with the recruitment of ATRX. Here we show loss of ATRX is also associated with an increase in R-loop formation. These findings suggest that the presence of ATRX at telomeres may reflect a central role in suppressing deleterious DNA secondary structures which form at transcribed telomeric repeats, and this may account for the increases in DNA damage, stalling of replication and homology directed repair previously observed upon loss of ATRX function.

overall_design: ATRX ChIP-seq in Suv39h1/2 KO MEFs, WT MEF and WT erythroid foetal liver

first: Hsiao

middle: P

last: Voon


title: Single cell RNA-sequencing of Mbd3-null and control lymphoid progenitor cells

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: To determine the role of Mbd3/NuRD in lymphopoiesis, gene expression in single Mbd3-deleted and control lymphoid progenitor cells was analysed using single cell RNA-seq

overall_design: Single Mbd3-deficient and control lymphoid progenitors were isolated from mouse bone marrow by flow cytometry, including lymphoid-primed multipotent progenitors (LMPPs), all-lymphoid progenitors (ALPs) and B cell-biased lymphoid progenitors (BLPs). Single cell RNA-seq was performed as described previously (Picelli et al. (2014) Nature protocols 9:171).

first: Stephen

last: Loughran

first: Fiona

last: Hamey


title: The NANCI-Nkx2.1 gene duplex buffers Nkx2.1 expression to maintain lung development and homeostasis

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: A subset of long-noncoding RNAs (lncRNAs) are spatially correlated with transcription factors (TFs) across the genome, but how these lncRNA-TF gene duplexes regulate tissue development and homeostasis is unclear. We have identified a feedback loop within the NANCI-Nkx2.1 gene duplex that is essential for buffering Nkx2.1 expression, lung epithelial cell identity, and tissue homeostasis. Within this locus, Nkx2.1 directly inhibits NANCI, while NANCI acts in cis to promote Nkx2.1 transcription. Although loss of NANCI alone does not adversely affect lung development, concurrent heterozygous mutations in both NANCI and Nkx2.1 leads to persistent Nkx2.1 deficiency and reprogramming of lung epithelial cells to a posterior endoderm fate. This disruption in the NANCI-Nkx2.1 gene duplex results in a defective perinatal innate immune response, tissue damage, and progressive degeneration of the adult lung. These data point to a mechanism where lncRNAs act as rheostats within lncRNA-TF gene duplex loci that buffer TF expression, thereby maintaining tissue specific cellular identity during development and postnatal homeostasis.

overall_design: E18.5--analysis of 3 samples per genotype (NANCI-+/+, NANCI-CreERT2:RFP/CreERT2:RFP, Nkx2.1-GFP/+, and NANCI-CreERT2:RFP/+:Nkx2.1-GFP/+.      6 month--analysis of NANCI-+/+ (3 samples), Nkx2.1-GFP/+ (3 samples), and NANCI-CreERT2:RFP/+:Nkx2.1-GFP/+ (4 samples).

last: Herriges

first: Edward

last: Morrisey


title: Smooth muscle cell-specific deletion of Col15a1 unexpectedly leads to impaired development of advanced atherosclerotic lesions

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

summary: Atherosclerotic plaque rupture with subsequent embolic events is a major cause of sudden death from myocardial infarction or stroke. Although smooth muscle cells (SMC) produce and respond to collagens in vitro, there is no direct evidence in vivo that SMC are a critical source of collagens impacting lesion development or fibrous cap formation. We sought to determine how conditional SMC specific knockout of collagen type XV (COL15A1) in SMC lineage tracing mice effects advanced lesion formation. COL15A1 was chosen because: 1) we previously identified a Col15a1 sequence variant associated with age related atherosclerosis; 2) COL15A1 is a matrix organizer that enhances tissue structural integrity; and 3) siRNA mediated Col15a1 knockdown increased migration and decreased proliferation of SMC in vitro. We hypothesized that SMC derived COL15A1 is critical in advanced lesion pathogenesis and fibrous cap formation. Surprisingly, we demonstrate that SMC specific Col15a1 knockout mice fed a Western diet for 18 weeks failed to form advanced lesions. SMC Col15a1 knockout lesions have a drastic reduction in overall lesion size, cell accumulation, and the absence of a SMC and ECM- rich lesion or fibrous cap. In vivo RNA-seq analysis on lesions +/- SMC Col15a1 knockout suggests the mechanism for these effects is complex and associated with reductions in multiple pro-atherogenic inflammatory pathways in multiple cell types involved in lesion development. These results thus provide the first direct evidence that a SMC derived collagen is critical during lesion pathogenesis. Additionally, we conclude that SMC Col15a1 knockout unexpectedly inhibited rather than exacerbated lesion pathogenesis.

overall_design: In vivo: mRNA profiles of 18 week fed Western diet wild type (WT) and Col15a1-/- mice were generated by deep sequencing, three animals per group, using Illumina HiSeq 2000.

first: Brittany

middle: G

last: Durgin

first: Olga

last: Cherepanova

first: Delphine

last: Gomez

first: Themistoclis

last: Karaoli

first: Gabriel

last: Alencar

first: Joshua

middle: T

last: Butcher

first: Yuging

last: Zhou

first: Michelle

last: Bendeck

first: Brant

last: Isakson

first: Jessic

last: Connely


title: RNA Sequencing of Pancreatic Islets from Intrauterine Growth Restricted and Normally-Grown Near Term Sheep Fetuses

city: Tucson

first: Sean

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

summary: The study objective was to determine differentially expressed mRNA transcripts in pancreatic islets from fetal sheep with placental insufficiency-induced intrauterine growth restricted.

overall_design: Islets were isolated for high-throughput sequencing from sheep fetuses with placental insufficiency-induced IUGR and controls.

first: S

first: Amy

middle: C

last: Kelly

first: Christopher

last: Bidwell


title: Steatohepatitis progresses to cancer via immunosuppression of HCC directed CD8+ T cells

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: We  show that chronic inflammation and fibrosis in mice with non-alcoholic fatty liver disease (NASH) is accompanied by accumulation of immunoglobulin A (IgA) positive plasmocytes. These cells suppress activation of cytotoxic T cells (CTL) derived from liver infiltrating CD8+ cells. CD8+ T cell ablation greatly accelerates HCC appearance, genetic or pharmacological targeting of IgA and PD-L1 expressing plasmocytes attenuates hepatic carcinogenesis and induces CTL-dependent regression of established HCC.

overall_design: RNA were isolated  from liver /tumor of healthy HFD-fed control  mice, mice with NASH, and HCC, and were analyzed using RNA-seq.

first: Shabnam

last: Shalapour

first: Michael

last: Karin


title: Transcriptomics analysis of gene expressions, m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 (Illumina) in paired-read mode, creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of gene expressive levels, m6A enrichment levels, m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells

first: Chunxia

last: Zhang

first: Baofa

first: Feng

last: Liu

first: Yuigui

last: Yang


title: Comparative temporal analysis of wild-type Ptf1a, Neurog2 and mutant Ptf1a (Ptf1aW224A/W242A) overexpressing Xenopus explant transcriptomes after 6 and 25 hours of DEX induction.

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: RNA-seq reveals the downstream gene regulatory network of wild-type Ptf1a, Neurog2 and Ptf1aW224A/W242A

overall_design: X.laevis embryos were injected in the animal pole of both blastomeres at the two-cell stage with 20 pg mRNA encoding for ptf1a-GR, GR-neurog2 or ptf1aW224A/W242A-GR. At blastula stage, inijected DEX-treated animal caps served as controls (CC).

first: Kristine

last: Henningfeld

first: Tomas

last: Pieler

first: Marie

last: Hedderich

last: Salinas-Riester

first: Thomas

last: Lingner


title: RNA-seq in endometrial stromal tumors

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

institute: Stanford University

summary: We describe the first analysis of gene expression in endometrial stromal tumors by RNA-seq. We demonstrate that undifferentiated uterine sarcomas have a unique gene expression profile that is distinct from other uterine mesenchymal tumors.

overall_design: Paired-end whole-transcriptome sequencing was performed on 19 endometrial stromal tumors (8 low-, 3 high-grade ESS and 8 UUS).

first: Matt

last: van de Rijn

first: Maria

last: Debiec-Rychter


title: Gene expression profiling of mouse brown and white adipose tissues

city: Houston

first: Quincy

last: Mo

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Gene expression profiling of supraclavicular brown, interscapular brown, inguinal white, and epididymal white adipose tissues from C57BL/6 male mice was performed by RNA-sequencing.

overall_design: Total of 12 RNA samples (3 RNA samples from each adipose tissue type) from adipose tissues were used for RNA-sequencing analysis.

first: Qianxing

first: Eric

last: Jaehnig

first: Miao-Hsueh

last: Chen


title: Transcriptional dynamics of paternal X chromosome reveals different epigenetic memory of the inactive state in the inner cell mass

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: This study concerns the dynamics of reprogramming of the inactive X chromosome in the inner cell mass of the E3.5-4.5 mouse blastocysts. We use single cell, allele-specific transcriptomic analyses to define the precise timing of paternal X-linked gene reactivation, as well as nascent RNA FISH and immunuofluorescence to follow the loss of chromatin marks such as H3K27me3. We find evidence that different genes show very different timing of reactivation indicating an epigenetic memory of the inactive state in some cases but not in others. In exploring whether PRC2 might be part of this memory we uncover a role for the X-linked histone demethylase Utx (a gene that actually escapes XCI), in the efficiency of H3K27me3 erasure and reactivation of of the paternal X. This work describes the precise timing and potential mechanisms of X-chromosome reactivation in vivo for the first time.

overall_design: 40 single-cells RNAseq from mouse pre-implantation embryos.

first: Maud

last: Borensztein

first: Laurène

last: Syx

first: Servant

last: Nicolas

first: Edith

last: Heard


title: Genome-wide mapping of nucleosome positioning in Toxoplasma gondii implicates nucleosome-free regions as the major gene regulatory regions

city: Bronx

first: Kami

last: Kim

state: New York

address: 1300 Morris Park Avenue

department: Medicine

institute: Albert Einstein College of Medicine

summary: Nucleosome organization is critical for the regulation of gene expression, and genome-scale mapping of nucleosomes has revealed a conserved, highly ordered pattern in nucleosome positioning. Most genome-wide studies have been performed in model organisms and little is known about nucleosome positioning in evolutionarily divergent eukaryotes. We generated a high-resolution nucleosome map of the protozoan parasite Toxoplasma gondii from four high quality MNase-Seq datasets. T. gondii nucleosomes are organised in phase around the transcription start sites (TSSs) with a canonical pattern that is conserved across eukaryotes. Nucleosome occupancy in exons is influenced by several factors, including GC content, length of exons and strength of splice sites. Poly(dA:dT) is enriched at the +1 nucleosome rather than nucleosome-free regions (NFRs) and serves as the key sequence associated with nucleosome formation in T. gondii. Motif analysis of sequences in NFR1, adjacent to the transcription start site, revealed enrichment of DNA-binding motifs recognized by members of the plant-like ApiAP2 transcription factor family that is conserved across Apicomplexa. Genes associated with the two most common motifs are enriched in genes upregulated during two major waves of mRNA accumulation within the cell cycle. Genome-wide peaks from T. gondii assays for transposase-accessible chromatin using sequencing (ATAC-seq) coincide with NFR1, consistent with the enrichment of T. gondii open chromatin regulatory regions localizing to close to transcription initiation sites. Finally, by integrating the map of nucleosome positions with ChIP-seq we suggest that nucleosome positioning and placement of histone variants and histone modifications play roles in splicing of genes in T. gondii.

overall_design: Examination of nucleosome positioning in intracellular Toxoplasma gondii tachyzoites by Mnase-seq

first: Xiaonan

last: Wang

first: Natalie

last: Silmon de Monerri

first: Sheila

last: Nardelli

first: Matthew

middle: M

last: Croken

first: Gos

last: Micklem

first: James

last: Ajioka


title: Dynamic Strain- and Stage-specific tRNA Transcription and Codon Usage in divergent Toxoplasma gondii strains

summary: tRNAs are critical linker molecules that couple mRNA to protein translation and their availability is a limiting factor for translation. tRNA transcription and the composition of the tRNA pool are both dynamically regulated in response to environmental cues. Recent work suggests that they also play an important role in regulating cell growth and differentiation. Toxoplasma gondii is a highly adaptable, early eukaryotic protozoan that is able to replicate in virtually any nucleated cell and many different host organisms, thus requiring fine-tuning of protein expression. A key feature of parasite pathogenesis is the ability to differentiate between fast growing tachyzoite and slow growing bradyzoite cyst forms, in response to stress e.g. nutrient starvation. Differentiation is accompanied by changes to the mRNA transcriptome and proteome but little is known about translational regulation. In this study, we used comparative genomics to catalogue the repertoire of tRNA genes in T. gondii and their genomic distribution. Interestingly, many tRNAs occur in regulatory regions and intronic sequences of protein-coding genes, which correlates with increased gene expression. To characterize the tRNA pool of T. gondii during stress and differentiation, we surveyed levels of precursor tRNA molecules in the tRNA population by small RNA-seq in three divergent parasite strains with varying bradyzoite differentiation competencies, cultured in normal or bradyzoite differentiation-inducing (pH shock) conditions. Almost all tRNA genes are constitutively transcribed in T. gondii tachyzoites and transcription of individual tRNA genes differs significantly between strains. The abundance of individual tRNAs in the tRNA pool reflects proteomic codon usage, suggesting that tRNA levels are tightly controlled according to the demands of translation. Together, this work suggests that modulation of the tRNA pool is a mechanism by which the protein landscape in T. gondii is regulated in different strains and developmental stages.

overall_design: Three divergent Toxoplasma gondii strains were cultured in tachyzoite (pH7) or bradyzoite (pH8) growth conditions and subjected to small RNA-seq.

first: Louis

last: Weiss

first: Ian

last: Willis


title: Expression profile of hematopoietic stem and progenitor cell (HSPC) compartment of FLT3-ITD and FLT3-ITD miR-155-/- mice

city: Salt lake city

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr East

department: Pathology

institute: University of Utah

summary: The miR-155-dependent differences in gene expression in the HSPC compartment of FLT3-ITD mice is unknown. In this experiment, we performed RNA sequencing on FLT3-ITD and FLT3-ITD miR-155-/- mouse LKS cells.

overall_design: RNA sequencing was performed on RNA extracted from Lin-, cKit+, Sca1+ cells isolated via flow cytometry from FLT3-ITD and FLT3-ITD miR-155-/- mice. 3 samples were submitted for sequencing for each experimental group. Each sample contains RNA from 3 mice, in order to get enough RNA from this rare stem cell population.

first: Jared

last: Wallace


title: Proteogenomic Reveals Biomarkers and Therapeutic Targets in Lymphoid Cancer

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

institute: University of Pennsylvania

summary: Here we find the transcriptional network regulated by ALK oncogenic activitiy in two Anaplastic Large Cell Lymphoma cell lines.

overall_design: The role of ALK in regulating the transcriptome of ALK positive ALCL cell lines was studied.

middle: B

first: Delphine

last: Rolland


title: Logical modelling of lymphoid and myeloid cell specification and trans-differentiation [ChIPseq]

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure

summary: To identify nez putative transcriptionnal regulations controlling the specification of B cell and Macrophage, we performed ChIPSeq in a pre-B cell line containing an inducible form of the transcription factor C/EBPa (C10). We performed ChIP-seq against Foxo1 in uninduced b cell, and for Ebf1 in uninduced or after several times of C/EBPa induction.

overall_design: Genome binding/occupancy of transcription factor Pu1 and histones (H3K4me1/2/3 and H3K27me3) by ChIPseq in uninduced Bcell (Control), after induction Cebpa for 6h (Pulse) and after 6 days of wash (Chase).

first: Samuel

first: Chris

last: van Oevelen

first: Thomas

last: Graf

first: Denis

last: Thieffry


title: FOXP1-SHQ1 deletion cooperates with PTEN deletion in oncogenesis

city: New York

first: Haley

last: Hieronymus

address: 1275 York Ave.

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq was carried out on prostate tumors from mice with prostate-conditional PTEN knockout with and without prostate-conditional FOXP1-SHQ1 locus deletion (12 month old PTEN-flox/flox Pb-Cre4 mice  and FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 mice )

overall_design: Frozen prostate tumors from 12 month old PTEN-flox/flox Pb-Cre4 mice (n=3) and FOXP1-SHQ1-flox/flox PTEN-flox/flox Pb-Cre4 mice  (n=3) were analyzed by RNA-seq

first: H

first: C

last: Sawyers


title: Embryonic retinal development

city: Madrid

first: Patricia

last: Boya

state: Comunidad de Madrid

address: Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biológicas

summary: Embryonic retinal development

overall_design: Mouse retinas at different embryonic developmental stages were isolated and mRNA expression was determined by RNA sequencing

first: Lorena

last: Esteban-Martinez

first: Osvaldo

last: Graña


title: small RNAs produced in the mutant Dicer-2 transgenic flies

city: BALTIMORE

first: Ryuya

last: Fukunaga

address: 725 N. Wolfe St. 521A Physiology Bldg

department: Department of Biological Chemistry

institute: Johns Hopkins University School of Medicine

summary: Examine the abundance and length of siRNAs produced by mutant Dicer-2 in vivo and in vitro in order to understand the mechanism by which Dicer-2 produces highly precise 21 nt siRNAs.

sample_organism:
Drosophila melanogaster
synthetic construct


title: The mechanism of restoration ovarian function using female germline stem cell

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: Germ stem cells are the only stem cells which can produce gametes in vivo. Recently, accumulating evidence demonstrates the isolation and culture of female germline stem cells (FGSCs) from adult mice and humans. Here, we established FGSCs line from single EGFP transgenetic mouse, and traced their differentiation in vivo. Then we compared the follile development from transplanted FGSCs mice (F-TF) with that from wide type mice (F-WT) by RNA-Seq. qRT–PCR validation was performed using SYBR Green assays. Using Illumina HiSeq2500 sequencer, we generated 51.5 Gb of sequencing data from the 8 samples. On average, we detected expression of 20 966 transcripts. Under the criteria fold change > 2 or < 0.5, we obtained 7005 and 5764 differential expressed genes (DEGs) from F-TF or F-WT,respectively. Weighted correlation network analysis (WGCNA) analysis identified core genes and two potential networks during folliculogenesis which were mainly down-regulated after preantral follicle. This study was the first to analyze the development of transplanted FGSCs progressively and would provide the theoretical basis for clinical translational research of FGSCs.

overall_design: Examination of preantral follicle (PF) and small antral follicle (SAF) from transplanted FGSCs and wild type mice.

first: Changqing


title: Assessment of Histone Tail Modifications and Transcriptional Profiling During Colon Cancer and Role of fish oil/pectin Diet Against Colon Carcinogen

city: College Station

first: Jennifer

last: Goldsby

state: TX

address: 112 Cater-Mattil

department: Nutrition and Food Sciences

institute: Texas A&M University

summary: In an effort to gain insight into the extensive dimension of post-translational modifications in histones (including H3K4me3 and H3K9ac) and elucidate the chemoprotective impact of dietary bioactive compounds on transcriptional control in a colon cancer preclinical model, we generated high-resolution genome-wide RNA (RNA-Seq) and “chromatin-state” (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed bioactive (i) fish oil  (ii) butyrate (in the form of a fermentable fiber a rich source of SCFA), (iii) a combination of fish oil plus butyrate or (iv) control diets.  Poor correlation was observed between differentially transcribed (DE) and enriched genes (DERs) at multiple epigenetic levels in fat x fiber dietary combinations and in the presence/absence of carcinogen.  We also demonstrated that the combinatorial diet (fish oil + pectin) was synergistically chemoprotective, and uniquely affected epigenetic profiles in the intestinal epithelium, e.g., upregulating lipid catabolism and beta-oxidation associated genes.

overall_design: Examination of 2 different histone modifications in rat colonocytes in a 2x2x2 factorial study cancer x oil x fiber

middle: S

last: Chapkin

first: Karen

last: Triff


title: Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes

status: Public on Sep 07 2017

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: To study the contribution of long non-coding RNAs (lncRNAs) to beta-cell failure and the development of type 2 diabetes, we used RNA-sequencing coupled with de novo annotation to search for novel transcripts dysregulated in islets of diet-induced obese mice. We identified about 1500 novel lncRNAs, a number of which were differentially expressed in obese mice. The expression of two lncRNAs highly enriched in beta-cells, βlinc2 and βlinc3, correlated to body weight gain and glycaemia levels in obese mice and was also modified in diabetic db/db mice. The expression of both lncRNAs was also modulated in vitro in isolated islets cells by glucolipotoxic conditions. Moreover, the expression of the human orthologue of βlinc3 was altered in the islets of type 2 diabetic patients and was associated to the BMI of the donors. Modulation of the level of βlinc2 and βlinc3 by overexpression or downregulation in MIN6 and mouse islets cells, did not affect insulin secretion but increased beta-cell apoptosis. Taken together, the data show that lncRNAs are modulated in a model of obesity-associated type 2 diabetes and that variations in the expression of some of them may contribute to beta-cell failure during the development of the disease.

overall_design: Performed RNA sequencing coupled with de novo annotation to search for known (protein and long non coding RNAs) and novel transcripts (lncRNAs) dysregulated in pancreatic islets of diet-induced obesity mice versus mice fed a normal diet. (C57BL/6 mice 14 weeks old at sacrifice, fed for 8 weeks)

first: Anna

last: Motterle

first: Sonia

last: Gattesco

first: Marie-Line

last: Peyot

first: Jonathan

last: Esguerra

first: Frédéric

first: Ana

last: Gomez-Ruiz

first: D

middle: R

last: Laybutt

first: Patrick

last: Gilon

first: Lena

last: Eliasson

first: Marc

last: Prentki

first: Romano

last: Regazzi


title: Combinatorial Signal Preception in the BMP Pathway

city: Pasadena

first: Yaron

middle: E

last: Antebi

address: 1200 E California Blvd, MC114-96

department: Biology and Bioengineering

institute: Caltech

summary: These data consist of an expression survey of three receptor cell lines and the parental cell types was performed to determine expression of BMP related genes.

overall_design: Sequence libraries for three cell types were constructed using NEBNext Ultra RNA-seq (NEB #E7530) and sequenced on Illumnia HiSeq2500.

first: James

last: Linton

first: Heidi

last: Klumpe

first: Bogdan

last: Bintu

first: Mengsha

last: Gong

first: Christina

last: Su

first: Reed

last: McCardell

first: Michael

last: Elowitz


title: Effect of Ppargc1a overexpression in mouse heart

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

institute: university of eastern finland

summary: Ppargc1a overexpression in heart tissue measured using RNA sequencing

overall_design: RNA expression profiles were generated using RNA-seq from control (N=3) and Ppargc1a overexpressing (N=3) mice

first: Tomi

last: Tuomainen

first: Pasi

last: Tavi


title: ENAP1 is involved in ethylene response

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

summary: We report that ethylene regulate the ENAP1 binding. We perform a dual cross-linking procedure using the additional cross-linker ethylene glycol bis-succinimidylsuccinate (EGS; Thermo Scientific) along with formaldehyde according to (Pedmale et al. 2016) for Chip-sequencing (ChIPseq) of ENAP1, as well as ENAP1 ChIP- EIN2 reChIPseq (ChIP-reChIPseq), which were used chromatins isolated from 3-day old etiolated Col-0 seedlings treated with ethylene or air gas. Results show that ENAP1 is involved in the EIN2 dependent ethylene response.

overall_design: Examination of 2 different protein binding in 1 Arabidopsis lines which under 2 different treatment.

first: Likai

last: Wang

first: Fan

last: Zhang


title: Malaria Host Pathogen Interaction Center Experiment 04R: Host and parasite gene transcript abundances, from whole blood, of Macaca mulatta infected Plasmodium cynomolgi treated with artemether over 7 time points in a 100 day study

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

summary: This project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support from the Defense Advanced Research Project Agency (DARPA) and others. The MaHPIC generates many data types (e.g., clinical, hematological, parasitological, metabolomics, functional genomics, lipidomics, proteomics, immune response, telemetry) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates (NHPs), and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC:  Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), and Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director).

sample_organism:
Macaca mulatta
Plasmodium cynomolgi strain B

overall_design: Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs primaquine and chloroquine were administered to all remaining subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 04R’. This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E04R and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public. E04R is a 'resequencing' of the same samples from E04. Resequencing for E04R was processed with SOPs and technology consistent with that used for E23R, E24, and  E25 so that results from these experiments could be reliably compared.  E04R does not replace E04, these are distinct datasets. Relative to E04, E04R is only for MaHPIC Yerkes Sequencing and Functional Genomics results.  Only E04R is intended for comparison with E23R, E24, and E25.The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).

first: Dalia

last: Arafat

first: Steve

last: Bosinger

first: Monica

last: Cabrera-Mora

first: Jeremy

last: DeBarry

first: Jay

last: Humphrey

first: Ebru

last: Karpuzoglu

first: Jessica

last: Kissinger

first: Stacey

middle: A

last: Lapp

first: Regina

last: Joice-Cordy

first: Chester

last: Joyner

first: Esmeralda

last: Meyer

first: Alberto

last: Moreno

first: Vishal

last: Nayak

first: Mustafa

last: Nural

first: Suman

last: Pakala

first: Nirav

last: Patel

first: Yan

last: Tang

first: Greg

last: Tharp


title: RNA sequencing identifies differentially expressed genes in embryonic cardiomyocytes following knockdown of DNMT3a or DNMT3b expression

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

summary: Purpose: This study aims to identify the differentially expressed genes in embryonic cardiomyocytes following the knockdown of DNMT3a or DNMT3b expression. Methods: Primary cardiomyocytes were isolated from mouse embryonic day (E) 13.5 ventricles, and cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT3a siRNA (#GS13435), DNMT3b siRNAs (#GS13436), or AllStars negative control siRNA (#1027281) at 0.012 pmol using lipofectamine RNAiMAX (n=3 per treatment). At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA) and magnetically sorted using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). Total RNA was isolated from the sorted cardiomyocytes with the RNAqueous®-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA). RNA-Seq libraries were prepared with the NEBNext® mRNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (NEB, Ipswich, MA). The nine Illumina-adapted libraries were pooled at equal molar ratio and sequenced with one High Output 1x75 cycles run on a NextSeq500 sequencer (Illumina). The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-seq reads were performed with HTSeq. Differential expression (DE) of genes between treatments was analyzed using two methods: R packages EdgeR and DEseq2, with Ensembl Mus_GRCm38.79.gtf as the reference annotation. Genes with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Unique DE genes were identified by combining the results generated from the two analytical methods. Results: DE analysis by DEseq2 and EdgeR software revealed that 524 genes were up-regulated, and 586 genes were down-regulated after knockdown of DNMT3a expression for 72 h. With the same analytical methods and criteria, the results of DE analysis showed that the knockdown of DNMT3b increased the expression of 655 genes and decreased the expression of 378 genes.

overall_design: mRNA profiles in embryonic cardiomyocytes with knockdown of DNMT3a or DNMT3b expression were generated by deep sequencing (n=3 for negative siRNA, n=3 for DNMT3a siRNA, n=3 for DNMT3b siRNA), using Illumina NextSeq500.

first: Scott

last: Rivkees

first: Christopher

last: Wendler


title: Genome-wide study reveals dual function of histone binding protein ENAP1 in ethylene signaling

first: Hong

last: Qiao

summary: Purpose: Next-generation sequencing (NGS) has been used to study the gene expression in different samples under air and ethylene treatment. The goal of this study is to uncover how ENAP1 and H3K23Ac dynamically coordinate with EIN3 to regulate gene expression in response to ethylene.

overall_design: Whole seedling mRNA profiles of 3-day old ein2, ein3eil1, ENAP1ox/ein2 and ENAP1ox/ein3eil1 (in COL background) were generated by sequencing, in 2 replications, using Illumina HiSeq 2000

first: Likai

last: Wang

first: Fan

last: Zhang


title: H3K23me1 is an evolutionary conserved histone modification associated with CG DNA methylation in Arabidopsis

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

summary: Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a novel histone modification in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. Chromatin immunoprecipitation followed by high-throughput sequencing in Arabidopsis thaliana showed that H3K23me1 was highly enriched in pericentromeric regions and depleted from chromosome arms. In transposable elements, it co-localized with CG, CHG and CHH DNA methylation as well as with the heterochromatic histone mark H3K9me2. Transposable elements are often rich in H3K23me1 but different families vary in their enrichment: LTR-Gypsy elements are most enriched and RC/Helitron elements are least enriched. The histone methyltransferase KRYPTONITE and normal DNA methylation were required for normal levels of H3K23me1 on transposable elements. Immunostaining experiments confirmed the pericentromeric localization and also showed mild enrichment in less condensed regions. Accordingly, gene bodies of protein coding genes had intermediate H3K23me1 levels, which coexisted with CG DNA methylation. Enrichment of H3K23me1 along gene bodies did not correlate with transcription levels. Together, this work establishes H3K23me1 as a novel component of the plant histone code.

overall_design: Characterization of the genome-wide distribution of the new histone mark H3K23me1 in Arabidopsis using ChIP-seq. Correlation of the presence of H3K23me1 with additional epigentic modifications and correlation with gene expression.

last: Trejo-Arellano

first: Mahrez

last: Walid

first: Hennig

last: Lars


title: Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage

status: Public on Sep 06 2017

city: Porto Alegre

first: Janette

middle: Palma

last: Fett

state: Rio Grande do Sul

address: Avenida Bento Gonçalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing).

overall_design: To identify and characterize novel genes and metabolic pathways involved in rice cold tolerance, we used two indica rice genotypes (previously identified as cold-tolerant and cold-sensitive by Adamski et al. 2016) in parallel transcriptomic analyses under cold treatment (10 °C for 6 h).  Plants were in the three-leaf stage when cold treatment was applyed. RNA was extracted from leaves.

first: Raul

last: Sperotto


title: Multiplex bisulfite sequencing identifies differentially methylated regions in target genes in embryonic cardiomyocytes following knockdown of DNMT3a or DNMT3b expression

summary: Purpose: This study aims to identify the differentially methylated regions in target genes in embryonic cardiomyocytes following the knockdown of DNMT3a or DNMT3b expression. Methods: Primary cardiomyocytes were isolated from mouse embryonic day (E) 13.5 ventricles, and cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT3a siRNA (#GS13435), DNMT3b siRNAs (#GS13436), or AllStars negative control siRNA (#1027281) at 0.012 pmol using lipofectamine RNAiMAX (n=3 per treatment). At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA) and magnetically sorted using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). DNA was extracted with the Quick-gDNA™ MicroPrep kit (Zymo Research, Irvine, CA). Genomic DNA was treated with sodium metabisulfite for bisulfite conversion. Target gene regions for fifteen target genes (two promoter regions per gene) were PCR-amplified from the bisulfite-converted DNA with ZymoTaq™ PreMix (Hot start DNA taq polymerase, ZYMO Research, Irvine, CA). The fifteen genes include Myh6, Myh7, Myh7b, Nppa, Nppb, Tnnc1, Tnni3, Tnnt2, Camta1, Camta2, Cdkn1A, Cdkn1B, Cdkn1C, Mef2c, and Mef2d. PCR products were cleaned with the ZR-96 DNA Clean & Concentrator™-5 kit (ZYMO Research). PCR products from the same genomic DNA sample were pooled at equal concentration ratio and made into an indexed sequencing library with the Nextera XT DNA Library Preparation kit and the Nextera XT Index Kit (Illumina, San Diego, CA). The nine Illumina-adapted libraries were pooled at equal molar ratio, spiked with 20% PhiX control libraries (Illumina), and sequenced with one 1x150 cycles run (v3) on a MiSeq sequencer (Illumina). The fastq files generated from MiSeq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. A reference genome with the amplicon sequences was built and bisulfite converted in silico with Bismark Bisulfite Mapper. The high quality sequence reads were aligned to the reference genome using Bowtie 2. Cytosine methylation counting was performed with the Bismark methylation extractor. Differential methylation was analyzed with the Methylkit package. CpG sites with false discovery rate (FDR) less than 0.05 and absolute percent methylation difference greater than 5% were considered as significant. Results: Following knockdown of DNMT3a for 72 h, differentially methylated regions were identified in the promoter CpG sites of Myh7, Myh7b, Tnni3, Tnnt2, Nppa, Nppb, Mef2c, Mef2d, and Cdkn1C. Following knockdown of DNMT3b expression for 72 h, differentially methylated regions were identified in the promoter CpG sites of Myh6, Myh7b, Tnni3, Tnnt2, Nppa, Nppb, Mef2d, Cdkn1A, and Cdkn1C.

overall_design: The DNA methylation patterns of target promoters in embryonic cardiomyocytes with knockdown of DNMT3a or DNMT3b expression were generated by deep sequencing (n=3 for negative siRNA, n=3 for DNMT3a siRNA, n=3 for DNMT3b siRNA), using Illumina MiSeq.


title: Single cell RNA-seq of smooth muscle actin cell in the lung.

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: In this study we characterize mesenchymal cell populations expressing Lgr5 and Lgr6 in the adult lung. We show that Lgr5 and Lgr6 expression can be used to identify distinct mesenchymal lineages that drive lineage-specific differentiation of epithelial progenitor cells in adult lung.

overall_design: Mouse lungs were disassociated, sorted by FACS and expression level were quantified using the SmarySeq2.

first: Joo-Hyeon

last: Lee

first: Carla

middle: F

last: Kim


title: ENAP1 is involoved in the Histone H3K23 acetylation- and EIN3- mediated ethylene response

summary: We report that ethylene reduce the ENAP1 binding. We perform Chip-sequencing of ENAP1 using chromatins isolated from 3-day old etiolated Col-0/ein2/ein3eil1 seedlings treated with ethylene or air gas. Results show that ethylene reduce ENAP1 binding in TSS region of EIN3 targeted genes that are regulated at the transcriptional level by ethylene.

overall_design: Examination of 1 different protein binding in 3 Arabidopsis lines which under 2 different treatment.


title: Investigation of the molecular mechanism of liver regeneration by the multi-omics approach (ChIP-seq)

city: Sendai

first: Yoshihiro

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Biochemistry

country: Japan

institute: Tohoku University

summary: Liver regeneration has fascinated the field of regenerative medicine due to its outstanding capacity to undergo a substantial regeneration. The capacity to regenerate is likely to be encoded as a plasticity of molecular networks within the liver. While several reports have utilized massive molecular profiling approaches, a bird-like view of the molecular processes is still lacking. Here, by applying a combination of comprehensive analysis of epigenome, transcriptome and proteome, we depict the molecular landscape of liver regeneration. We demonstrate that histone H3K4 was tri-methylated at promoter regions of many loci, among which only a fraction including cell cycle related genes were transcriptionally up-regulated. Cistrome analysis guided by the histone methylation patterns and transcriptome identified FOXM1 as the key transcription factor to promote liver regeneration, which was confirmed using hepatocytes in vitro. Conditional protein degradation was also observed. These sets of informational resources will be useful to further investigate liver regeneration.

overall_design: We performed portal vein branch ligation in mouse, and hypertrophic right lobe was collected at 3 days after surgery. Then we performed the ChIP-seq analysis using anti-H3K4me3 and H3K27me3 antibodies. We prepared sham operated mice as a control. For peak calling, we used input-DNA as control.

first: Mitsuyo

last: Matsumoto

first: Ryo

last: Funayama

first: Keiko

last: Nakayama

first: Kazuhiko

last: Igarashi


title: Stochastic Principles Governing Alternative Splicing of RNA

city: BETHESDA

first: Jianfei

last: Hu

state: MD

address: 40 CONVENT DR

department: Vaccine Research Center

institute: NIH

summary: The goal of the study was to analyze the principles governing the usage of alternatively spliced transcript isoform of four types of T-cells (Naïve, Central Memory, Transitional Memory and Effector Memory) between resting and activated status. However, the principles discovered in the T cells were universal and can also be applied to other cell type and tissues.

overall_design:
Four types of T cells were sorted and whole transcriptome analysis was performed using an Illumina machine
The readme.txt contains the column headers and description for the processed data files.

first: Daniel

last: Douek

first: Eli

last: Boritz

first: William

last: Wylie


title: Transcriptome Profiling of a Pathogenic Response to a Viral Infection in Jamaican Fruit Bats Artibeus jamaicensis Experimentally Infected With Tacaribe Virus

city: Burlington

first: Diana

middle: Lea

last: Gerrard

state: VT

address: 89 Beaumont Ave C141C Given

department: Cellular molecular and biomedical sciences

institute: University of Vermont

summary: Bats are a widespread group of mammals thought to host a variety of viruses and other disease agents. Here we performed RNA-sequencing on Artibeus jamaicensis infected with the New World arenavirus, Tacaribe Virus, to generate an extensive bat transcriptome.

overall_design: RNA-sequencing of Tacaribe Virus infected and uninfected Artibeus jamaicensis bats with a total of 12-pooled samples (kidney, liver, and spleen) with duplicates for each condition was performed.

first: Seth

last: Frietze

first: Ann

last: Hawkinson


title: RNASeq analysis of Vitis vinifera (cv. Sauvignon blanc) grape berries exposed to elevated light

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

country: Italy

institute: Universita' degli Studi di Verona

summary: By implementing a leaf-removal treatment in the berry bunch zone, grapes were predominantly exposed to elevated light and their complete transcriptomes (as generated by RNASeq) were compared at four developmental stages.

overall_design: Comparison of the transcriptomes of control and exposed Sauvignon blanc grape berries sampled at four developemental stages (EL31, EL33, EL34, EL38)

first: Kari

last: du Plessis

first: Philip

last: Young

first: Hans

last: Eyeghe-Bickong

first: Melane

last: Vivier


title: CD27 marks embryonic hematopoietic stem cells

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

summary: Cell surface markers of adult hematopoietic stem cells (HSCs) are well established, but fewer markers are available for embryonic HSCs and their immediate precursors (pre-HSCs) in the major arteries. We performed RNA-Seq on a population of cells from the major arteries of embryonic day 11.5 mouse embryos enriched for lymphoid progenitors, pre-HSCs, and HSCs. We determined that Tnfrsf7, encoding CD27, a member of the tumor necrosis factor receptor superfamily, is upregulated in this population. CD27 is found on ~5% of hematopoietic cluster cells in the major arteries, and enriches for progenitors with lymphoid potential, embryonic HSCs, and Type II pre-HSCs (CD144+CD45+), and fetal liver HSCs. It does not, however, enrich for yolk sac derived erythro-myeloid progenitors. Collectively, those data show that CD27 is a new cell surface marker of embryonic HSCs and Type II pre-HSCs.

overall_design: Major arteries in dorsal aorta, umbilical, vitelline (A+U+V) from 122 embryonic day 11.5 Ly6a-GFP+ embryos were dissected and disaggregated with collagenase, and 53,000 Ly6a-GFP+ hematopoietic cluster cells (CD31+ CD144+ ESAM+ c-Kit+), 413,000 Ly6a-GFP- hematopoietic cluster cells, 377,000 Ly6a-GFP+ endothelial cells (CD31+ CD144+ ESAM+ c-Kit-), and 791,000 Ly6a-GFP- endothelial cells collected. Cells were sorted into TRIzol-LS (Invitrogen) and pooled into three independent biological samples. The cells were lysed in TRIzol-LS and the aqueous phase was collected after adding chloroform. The aqueous phase was homogenized by 70% ethanol and RNA isolated using Qiagen RNeasy micro kit. Isolated RNA was treated with TURBO DNA-free DNA Removal Kit to remove contaminating DNA.

first: Yan

last: Li

first: Brandon

last: Hadland

first: Kai

last: Tan

first: Nancy

last: Speck


title: KLHL41 stabilizes skeletal muscle sarcomeres by nonproteolytic ubiquitination

city: Dallas

first: Andres

last: Ramirez-Martinez

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UTSW Medical Center

summary: Maintenance of muscle function requires assembly of contractile proteins into highly organized sarcomeres. Mutations in Kelch-like protein 41 (KLHL41) cause nemaline myopathy, a fatal muscle disorder associated with sarcomere disarray. We generated KLHL41 mutant mice, which display lethal disruption of sarcomeres and aberrant expression of muscle structural and contractile proteins, mimicking the hallmarks of the human disease. We show that KLHL41 is poly-ubiquitinated and acts, at least in part, by preventing aggregation and degradation of nebulin, an essential component of the sarcomere. Furthermore, inhibition of KLHL41 poly-ubiquitination prevents its stabilization of nebulin, suggesting a unique role for ubiquitination in protein stabilization. These findings provide new insights into the molecular etiology of nemaline myopathy and reveal a mechanism whereby KLHL41 stabilizes sarcomeres and maintains muscle function by acting as a molecular chaperone. Similar mechanisms for protein stabilization likely contribute to the actions of other Kelch proteins.

overall_design: Gene expression profile was generated comparing wild type (WT) and KLHL41 knockout mice, by deep sequencing, with three biological replicates, using Illumina HiSeq 2500.

first: Eric

middle: N

last: Olson


title: Transcriptome profiling of human erythroblast cells knocking down NCOA4

city: Cambridge

first: Xiaofei

state: MA

institute: Whitehead Institute for Biomedical Research

summary:
Purpose: Knocking down NCOA4 disrupted Thyroid hormone receptor beta agonist,GC-1, mediated terminal human erythroblast differentiation. Therefore, we conducted RNA-seq to profile the transcriptome changes in NCOA4 knocked down human erythroblasts..
Methods: Human CD34+ cells were transduced by lentiviruses encoding shRNAs targeting either LacZ (control) or NCOA4 atday 1 of culture. At day 14, cells were switched to terminal differentiation medium.
Results: Using an optimized data analysis workflow, we have identified an ensemble of genes whose expression are discrupted by NCOA4 knockdown.
Conclusions: There is a significant correlation between the degree of GC-1-mediated gene activation and the degree of NCOA4 knockdown-mediated gene repression.

overall_design: Transcriptome profiles of human erythroblasts transduced with LacZ(control) or NCOA4 shRNA were generated by Illumina HiSeq sequencer in duplicates

first: Harvey

last: Lodish


title: Next Generation Sequencing: Epignetics 300 CRISPR sgRNA screen in THP-1 Acute Myelogenous Leukemia Cells

city: Princeton

first: Trinna

middle: L.

last: Cuellar

state: New Jersey

address: Lewis Thomas Lab, Washington Rd/MOF223C

institute: Princeton University

summary:
Purpose: To identify critical epigenetic regulators of acute myeloid leukemia cell surival (AML), we performed a CRISPR screen with an sgRNA library containing 6121 sgRNAs against the epigenome and controls. We collected samples at day 7 (reference) and day 21 to look for sgRNAs that dropped out of the population and hence, may be critical for for AML cell growth or survival.
Conclusions: Our study reveals a novel epigenetic regulator of innate immunity in AML. This gene is critical for AML surivival and loss of this gene induces a type I IFN response. This particular dataset show the dropout of this gene at day 21, as well as other potential genes that regulate AML cell survival or growth.

overall_design: Genomic DNA was profiled from 3 samples treated with the lentiviral sgRNA library at day 7 and 3 samples at day 21. One sample at day 21 was dropped in the final analysis due to low quality.

middle: L

first: Brad

last: Friedman


title: DNMT3b ChIP-Seq in enteric precursor cells

city: Seville

first: Villalba

last: Leticia

address: Avda. Manuel Siurot s/n

institute: FISEVI

summary: With the aim to elucidate the mechanism underlying the DNMT3b role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) analysis to identify the DNMT3B target genes in enteric precursor cells (EPCs) from mice.

overall_design: Identification of DNMT3b target genes in enteric precursor cells. 12 ChIPs and 12 Inputs were sequenced and analyzed.

first: Salud

last: Borrego

first: Leticia

last: Villalba-Benito

first: Ana

last: Torroglosa


title: RNAseq to determine gene expression changes following depletion of SETDB1 in THP-1 AML Cells

summary:
Purpose: To determine how loss of SETDB1 effects gene expression in THP-1 AML cells.

Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits.

Results: Using an optimized data analysis workflow, we mapped 23 million or more sequence reads per sample to the human genome (GRCh38) with GSNAP for obtaining standard gene expression measurements. Since SETDB1 is also know to regulate repetitive elements we also mapped sequences to a pseudogenome containing tranposable elements from hg19 repeatmasker annotations using RepEnrich and following the pipeline published on GitHub (https://github.com/nskvir/RepEnrich).

Conclusions: Our data determined that immediately following the disruption of SETDB1, a strong type I Interferon response can be observed at day 4. In addition, many repetitive elements are also significanly induced, including L1 LINEs, Endogenous Retroviruses, and Satellite repeats.

overall_design: THP-1 RNA samples treated with 2 different SETDB1 sgRNAs (6, and 9) or NTC sgRNAs and collected at days 4 and 7 in triplicate for a total of 18 samples.

first: Steffen

last: Durinck


title: Novel KDM1A inhibitors induce differentiation and apoptosis of glioma stem cells via unfolded protein response (UPR) pathway

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We examined the transcriptional changes modulated by KDM1A inhibitor NCD-38 by performing global transcriptome analysis. Glioma Stem Cells (GSC10) were treated with either vehicle or NCD-38 for 24 h and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that NCD-38 modulated several genes that are involved in unfolded protein response, endoplasmic reticulum stress pathway and NRF-2 mediated oxidative stress response.

overall_design: Total RNA was isolated from the GSC10 cells that were treated with vehicle or NCD-38 for 24 hours. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Ratna

middle: K

last: Vadlamudi


title: Measuring gene expression profiles of E. coli synthetic rescue strains

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: This goal of these experiments is to assess steady-state transcript levels in a set of E. coli mutants (ppk, dgk, zwf, entC, and dapF null strains) that grow slowly in M9 glucose, and to compare these transcript levels to corresponding synthetic rescue strains (i.e. spontaneous suppressor strains in which slow growth is rescued to wild-type levels).

overall_design:
To isolate total RNA, all strains were grown in triplicate to an equivalent OD in mid-logarithmic phase.  Cells were pelleted, lysed, and total RNA was isolated for analysis by RNA-seq. Steady-state transcript levels in each synthetic resucue strain were compared to the correspoding slow-growing primary (single gene deletion) mutant strains.
zwf.txt: Rockhoppper analysis; tab delimited text of gene expression (zwf deletion mutant versus synthetic rescue suppressors; sup)
dgk.txt: Rockhoppper analysis; tab delimited text of gene expression (dgk deletion mutant versus synthetic rescue suppressors; sup)
ppk.txt: Rockhoppper analysis; tab delimited text of gene expression (ppk deletion mutant versus synthetic rescue suppressors; sup)
dapF.txt: Rockhoppper analysis; tab delimited text of gene expression (dapF deletion mutant versus synthetic rescue suppressors; sup)
entC.txt: Rockhoppper analysis; tab delimited text of gene expression (entC deletion mutant versus synthetic rescue suppressors; sup)

first: Jonathan

last: Willett

first: Aretha

last: Fiebig

first: Thomas

last: Wytock

first: Adilson

last: Motter


title: HIV Reprograms Human Airway Basal Stem/Progenitor Cells to Acquire a Tissue Destructive Phenotype

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: While the survival rate of HIV-infected individuals has dramatically improved with the development of highly active anti-retroviral therapy, HIV-infected individuals have an increased risk for chronic disorders, including the development of COPD, manifesting as emphysema. The mechanisms of HIV-associated emphysema are not understood. Based on the knowledge that human airway basal cells (BC) function as stem/progenitor cells capable of differentiation into specialized ciliated and secretory cells during natural turnover and repair in response to injury, we hypothesized that HIV interacts with, and consequently induces pathologic programming of the BC that contributes to the development of emphysema.

overall_design: Studies were designed to assess: (1) if HIV binds to, infects and/or replicates in BC; (2) identify which BC receptor(s) are responsible for HIV capture; and (3) the reprogramming of BC biology upon HIV exposure. Infectious HIVNL4-3 was used for all studies. Soluble heparan sulfate and heparinase III were used to prevent HIV/BC interactions. BC phenotypes after HIV exposure were assessed by TaqMan quantitative PCR, ELISA, phospho-MAPK array, protease array, cell invasion assay, and zymography.

first: Nancy

middle: P

last: Chung

first: Xuemei

last: Ou

first: K

last: Faisal Khan

first: Jacqueline

last: Salit

first: Robert

middle: J

last: Kaner

first: Ronald

middle: G

last: Crystal


title: Balanced activation of IspG and IspH to eliminate intermediate accumulation and improve isoprenoids production in Escherichia coli

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

summary:
Purpose: To understand the dynamic transcriptional response of Escherichia coli cells to intracellular HMBPP accumulation.
Methods: RNA-seq libraries were constructed for three samples, including (I) CAR005, which used as control; (II) IspG1, which strong over-expressed ispG in CAR005; (III) G4H14, which simultaneously over-expressed ispG and ispH in CAR005.For preparation of RNA samples, single colonies were inoculated into 15x100 mm tubes containing 4 ml LB, and grown at 30ºC and 250 rpm overnight. 100 μl seed culture was inoculated into a 100 ml flask containing 10 ml LB medium, and grown at 30ºC and 250 rpm. After 5 h, 1 ml culture was harvested by centrifugation, frozen in liquid nitrogen and sent to Beijing Genomics Institute (BGI, Shenzhen, China). The three 90-nt paired-end RNA-seq libraries were generated commercially at Beijing Genomics Institute by using the HiSeq™ 2000 platform. Sequencing data was handled essentially with Bowtie2, Tophat2, NOIseq. Expression levels are presented as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Results: We assessed expression levels of a 5 hour culture of ispG1 and compared to the parent strain CAR005. Among the 4200 predicted genes in E. coli ATCC 8739, relative expression levels for 504 genes were found changed in strain ispG1, with 166 markedly up-regulated and 338 repressed. FunCat was used to analyze the biological processes represented by these genes and found categories related to “nucleotide/nucleoside/nucleobase metabolism” (P=7.76E-05), “ribosome biogenesis,” (P=1.06E-20), “translation,” (P=4.26E-12) and “nucleobase binding” (P=1.86E-06) were markedly enriched in the repressed genes set, suggested that HMBPP accumulation might exert deterious effect on cell growth and viability. As for G4H14, only 64 genes were found down-regulated in G4H14. Biological processes associated with macromolecular synthesis no longer markedly enriched, suggesting that cell growth and viability tended to be restored to control level after eliminating HMBPP accumulation.
Conclusions: Transcriptome profiling exhibited additional evidence to the cytotoxicity of HMBPP, meanwhile, demonstrated that activating downstream IspH could contribute to attenuation of such deterious effects.

overall_design: mRNA profiles of Escherichia coli ATCC8739 genetically engineered strain CAR005,IspG1, and G4H14  by deep sequencing, using Illumina HiSeq™ platform.

first: Qingyan

last: Li

first: Feiyu

last: Fan

first: Chen

last: Yang

first: Changhao

last: Bi

first: Jinlei

last: Tang

first: Tao

last: Liu

first: Yanhe

last: Ma

first: Xueli

last: Zhang


title: Tet1 in nucleus accumbens regulates stress responses

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Depression is a leading cause of disease burden, yet current therapies fully treat <50% of affected individuals. Increasing evidence implicates epigenetic mechanisms in depression and antidepressant action. Here, we examined a possible role for the newly identified methylcytosine oxidase, ten eleven translocation protein 1 (TET1), in depression-related behavioral abnormalities. We show that chronic social defeat stress, an ethologically validated mouse model of depression, decreased Tet1 expression in nucleus accumbens (NAc), a key brain reward region, in stress susceptible mice only. Surprisingly, selective knockout of Tet1 in NAc neurons of adult mice produced antidepressant-like effects in several behavioral assays. To identify Tet1 targets that mediate these actions, we performed RNAseq on NAc after Tet1 knockout and found that immune-related genes are the most highly regulated. Interestingly, many of these genes are also upregulated in NAc of resilient mice after chronic social defeat stress. Together, these findings link Tet1 to stress responses and identify novel targets for future antidepressant drug discovery efforts.

overall_design: mRNA was collected from TET1 loxp/loxp mouse nucleus accumbens 4 weeks after AAV-Cre injection with AAV-GFP as control. RNAseq was then performed.

first: Jian

last: Feng

first: Eric

last: Nestler


title: Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro

status: Public on Sep 05 2017

city: Dresden

first: Michell

middle: M

last: Reimer

state: Saxony

address: Fetscherstrasse 105

department: CRT Dresden

institute: TU Dresden

summary: Endogenous oligodendrocyte progenitor cells (OPCs) are a promising target to improve functional recovery after spinal cord injury (SCI) by remyelinating denuded, and therefore vulnerable, axons. Demyelination is the result of a primary insult and secondary injury, leading to conduction blocks and long-term degeneration of the axons, which subsequently can lead to the loss of their neuron. In response to SCI, dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes (OLs). Therefore, researchers strive to control OPC responses, and utilize small molecule screening approaches in order to identify mechanisms of OPC activation, proliferation, migration and differentiation.

overall_design: DEG analysis of primary OPC and OL populations, 5 biological replicates per population

first: Volker

last: Kroehne

first: Vasiliki

last: Tsata

first: Lara

last: Marrone

first: Claudia

last: Froeb

first: Susanne

last: Reinhardt

first: Anne

last: Gompf

first: Andreas

last: Dahl

first: Jared

last: Sterneckert


title: RNA-sequencing of pediatric idiopathic dilated cardiomyopathy patients and healthy controls

city: Aurora

first: Philip

middle: David

last: Tatman

state: Colorado

department: Department of Pharmacology

institute: University of Colorado

summary: We used NGS of rna to understand transcriptome wide changes that occur in the left ventricles of pediatric idiopathic dilated cardiomyopathy patients.

overall_design: Left ventricles were harvested from failed or healthy control patients and rna was sequenced

first: Phil


title: Neuropathic pain promotes gene expression adaptations in brain networks involved in stress and depression

first: Venetia

last: Zachariou

address: 1425 Madison Ave Icahn School of Medicine

summary: Neuropathic pain is a complex chronic condition, characterized by a wide range of sensory, cognitive, and affective symptoms. Indeed, a large percentage of neuropathic pain patients are also afflicted with depression and anxiety disorders -- a pattern that is reliably replicated in animal models. Mounting evidence from clinical and preclinical studies indicates that chronic pain corresponds with adaptations in several brain networks involved in mood, motivation, and reward. Chronic stress is also a major determinant for depression. However, whether chronic pain and chronic stress affect similar mechanisms, and whether chronic pain can affect gene expression patterns known to be involved in depression, remains poorly understood. We employed the spared nerve injury model (SNI) of neuropathic pain in adult C57BL\6 mice and performed next-generation RNA-sequencing in order to monitor changes in gene expression in three brain regions known to be implicated in the pathophysiology of depression and in the modulation of pain: the nucleus accumbens (NAc), the medial prefrontal cortex (mPFC), and the periaqueductal grey (PAG). We observed mostly unique transcriptome profiles across the three brain regions but found common intracellular signal transduction pathways and biological functions were affected. A large amount of genes showing SNI-induced altered expression have been implicated in depression, anxiety, or chronic pain. In addition, we identified genes that are similarly regulated in a murine model of depression: chronic unpredictable stress. Our study provides the first unbiased characterization of neuropathic pain-induced long-term gene expression changes in three distinct brain regions, and presents evidence that neuropathic pain affects the expression of several genes that are also regulated by chronic stress.

overall_design: RNA-seq samples were generated from 3 brain regions (nucleus accumbens, medial prefrontal cortex, and periaqueductal grey) of adult male mice, 2.5 months after sham or spared nerve injury to the sciatic nerve.

first: Giannina

last: Descalzi

first: Li

last: Shen


title: Genome-wide analysis of developmentally regulated microRNAs in Hami melon fruit

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary:
Background: MicroRNAs (miRNAs) represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Although Hami melon is an attractive model for valuable biological traits analysis, the role of miRNA action in the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the Hami melon miRNA profiles at four fruit developmental stages
Results: Small RNA sequencing yielded raw reads in eight libraries. miRNAs expression profiles were variable at different fruit developmental stages. The expression levels of five known miRNAs were validated by quantitative real-time PCR. Among the identified miRNAs, several miRNAs showed developmentally regulated and differentially expressed pattern during fruit development.
Conclusions: Our results present a first comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis for further research on the critical role of miRNAs in melon fruit development.

overall_design: Eight samples, including eight Hami melon flesh mesocarp samples for two separate small RNA sequencing to obtain biological replicates.

first: Hong

last: Zhang

first: Lan

last: Yin

first: Huaisong

last: Wang

first: Guangzhi

first: Xinli

last: Ma

first: Meihua

last: Li

first: Qiushi

last: Fu

first: Yi

first: Hongping

last: Yi


title: MicroRNA differentially expressed in diapausing versus HCl-treated Bombyx embryos

city: Guanzhou

first: Jianrong

last: Lin

state: Guandong

address: WuShan

institute: South China Agricultural University

summary: Differentially expressed microRNAs (miRNAs) were detected to explore the molecular mechanisms of diapause termination. The total small RNA (sRNA) of diapause-destined silkworm eggs and HCl-treated eggs was extracted and then sequenced using HiSeq/MiSeq high-throughput method. 44 novel miRNAs were discovered. Compared to those in the diapause-destined eggs, 61 miRNAs showed significant changes in the acid-treated eggs, with 23 being up-regulated and 38 being down-regulated. The potential target genes of differentially expressed miRNAs were predicted by miRanda. Gene Ontology and KEGG pathway enrichment analysis of these potential target genes revealed that they were mainly located within cells and organelles, involved in cellular and metabolic processes, and participated in protein production, processing and transportation. Two differentially expressed genes, Bombyx mori SDH (BmSDH) and Bmo-miR-2761-3p, were further analyzed with qRT-PCR. BmSDH was significantly up-regulated in the HCl-treated eggs, while Bmo-miR-2761-3p was down-regulated. These results suggested that these two genes were well coordinated in silkworm eggs. Dual luciferase reporter (DLR) assay demonstrated that Bmo-miR-2761-3p inhibited the expression of BmSDH.

overall_design: Examination of different miRNA expression in 2 silkworm egg types.

first: Wentao

last: Fan

first: Yangsheng

last: Zhong

first: Mingyue

last: Qin

first: Bimin

first: Fangyan

first: Huichao

last: Yan

first: Wenchu


title: Gene expression changes in ketogenic and high-fat diets

city: San Francisco

first: John

middle: C

last: Newman

state: CA

address: 1650 Owens Street

department: Geriatrics

institute: UCSF

summary: The ketone body β-hydroxybutyrate (BHB) is produced during dietary restriction, fasting, and exercise. A ketogenic diet (KD) results in long-term production of BHB outside of these contexts. We sought to determine a protein-matched, non-obese ketogenic diet (KD) would affect the longevity and healthspan of C57BL/6 male mice. We find that feeding KD every-other-week to prevent obesity (cyclic KD) reduces mid-life mortality but does not affect maximum lifespan. Similar feeding of a non-ketogenic high-fat/low-carbohydrate (HF) diet may have an intermediate effect on mortality. Cyclic KD improves memory performance in old age, while modestly improving composite measures of healthspan. RNAseq gene expression analysis identifies down-regulation of insulin, TOR, and fatty acid synthesis pathways as possible longevity mechanisms common to KD and HF. However, up-regulation of fasting-related PPARα target genes is unique to KD, consistent across tissues, and preserved in old age, suggesting a mechanism for an incremental benefit from KD. In all, we show that a non-obese ketogenic diet improves survival, memory, and healthspan into old age. These gene expression studies were carried out on 12 month-old male C56BL/6 mice from the NIA Aged Rodent Colony, habituated to AIN-93M control diet and then either maintained on this diet or switched for one week to a 75% kcal fat non-ketogenic high-fat diet or a 90% kcal fat ketogenic diet (all diets with 10% kcal from carbohydrates). Tissues were harvested in the middle of the nighttime feeding period (MN-3am).

overall_design: Control diet N=5, high-fat diet N=6, ketogenic diet N=7. Pairwise comparisons between all three conditions. These gene expression studies were carried out on 12 month-old male C56BL/6 mice from the NIA Aged Rodent Colony, habituated to AIN-93M control diet and then either maintained on this diet or switched for one week to a 75% kcal fat non-ketogenic high-fat diet or a 90% kcal fat ketogenic diet (all diets with 10% kcal from carbohydrates). Tissues were harvested in the middle of the nighttime feeding period (MN-3am).

first: Eric

last: Verdin


title: Tis11 mediated mRNA degradation regulates intestinal stem cell quiescence in Drosophila melanogaster

city: Rochester

first: Benoit

last: Biteau

address: KMRB 2-9905 601 Elmwood Ave

department: Genetics

institute: University of Rochester

summary: we show that Tis11, an Adenine-uridine Rich Element (ARE) binding protein that promotes mRNA degradation, is required to re-establish basal proliferation rates of adult Drosophila intestinal stem cells (ISC) after a regenerative episode. We find that Tis11 limits ISC proliferation specifically after proliferation has been stimulated in response to heat stress or infection, and show that Tis11 expression and activity are increased in ISCs during tissue repair.  Based on stem cell transcriptome analysis and RNA immunoprecipitation, we propose that Tis11 activation represents an integral part of a negative feedback mechanism that limits the expression of key components of several signaling pathways that control ISC function and proliferation. Our results identify Tis11 mediated mRNA decay as an evolutionarily conserved mechanism of re-establishing basal proliferation rates of stem cells in regenerating tissues.

overall_design: stem cell transcriptome analysis of sorted Drosphila ISC (control, Tis11 gain-of-function and Tis11 loss-of-function) and RNA immunoprecipitation of  FLAG- tagged Tis11 bound mRNAs (FLAG-Tis11 expressed specifically in ISCs) performed in duplicate (control IgG precipitation and FLAG precipitiation)

first: McClelland

last: Lindy

first: Jasper

last: Heinrich

first: Biteau

last: Benoit


title: Analysis of non-methylated islands, sites of accessible chromatin and nascent transcriptome in C127 mouse cell line. [C127_BioCAP-ATAC-4sU]

city: Oxford

first: Vincenzo

last: Di Cerbo

address: South Parks Road

institute: University of Oxford

summary: Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed suggesting that the normal targeting and function of SET1 complex is central to creating an appropriately functioning vertebrate promoter associated epigenome.

overall_design: C127 mouse cell line was employed to determine (i) genomic regions enriched for non-methylated DNA using BioCAP assay, (ii) genomic regions of accessible chromatin using ATAC-seq, (iii) nascent transcriptome using an in vivo pulse labelling with 4-thiouridine (4sU) followed by massively parallel sequencing (4sU-seq).

first: David

last: Brown

first: Angelika

last: Feldmann

first: Rob

last: Klose