title: Deep mutagenesis of HLA-A*02:01 reveals elements of folded structure necessary for MHC-I-specific chaperone interactions and plasma membrane trafficking

city: Urbana

first: Erik

last: Procko

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The loading of high affinity peptides onto nascent class I MHC (MHC-I) molecules is facilitated by chaperones, including the class I-specific chaperone TAP-binding protein-related (TAPBPR).  NMR experiments reveal that conformational dynamics of specific MHC-I allotypes, especially around regions known to be in physical proximity to the TAPBPR interface, are correlated with TAPBPR binding affinity.  HLA-A*02:01 residues in the alpha1 and alpha2 domains were deep mutationally scanned to determine the effects of nearly all single amino acid substitutions on HLA-A2 surface expression and TAPBPR interactions.  Surface trafficking, which demands HLA-A2 be properly folded with bound peptide, imposes strict sequence constraints on the HLA-A2 core, surfaces contacting the beta2-microglobulin and alpha3 domains, and on the A, B and F pockets that ‘grip’ peptide anchor residues.  However, TAPBPR binding is permissive to many mutations of HLA-A2, both in the core and on the surface, with the exceptions of two conserved clusters of hydrophobic residues that pack the alpha2-1 and alpha2-2 helices against the beta-sheet.  TAPBPR binding is therefore dependent on a local conformation of the alpha2 domain, most likely with a widened peptide binding groove based on published crystal structures.  Overall, the data are consistent with a conformational selection model for MHC-I/TAPBPR interactions, in which high MHC-I dynamics increases representation in the structural ensemble of appropriate conformers for TAPBPR recognition.

overall_design: A c-myc tag was fused to the extracellular N-terminus of HLA-A*02:01 for surface detection.  Interactions between HLA-A2 and TAPBPR were investigated using bimolecular fluorescence complementation (BiFC), in which the N-terminus (VN) of split fluorescent Venus was fused to the cytosolic tail of HLA-A2, and the C-terminus (VC) of split Venus was fused to the cytosolic tail of TAPBPR.  The native transmembrane helix and cytosolic tail of TAPBPR were replaced with a generic transmembrane domain to allow TAPBPR to escape intracellular compartments; this means the experiment reports on TAPBPR/HLA-A2 interactions regardless of where HLA-A2 mutants localize.  A library encoding nearly all single amino acid substitutions in the alpha1 and alpha2 domains of HLA-A2 was generated by overlap extension PCR, and the plasmid library was transfected into human Expi293F cells (a suspension culture derivative of HEK 293) under conditions where each cell typically acquires no more than one coding variant.  Using FACS, wild-type Expi293F cells expressing endogenous tapasin were collected that displayed high surface HLA-A2, based on fluorescent antibody staining for the c-myc tag. For FACS-based collection of cells showing high BiFC between TAPBPR and HLA-A2, the library was transfected in to cells stably expressing VC-fused TAPBPR.  RNA transcripts in the collected cell populations were deep sequenced and compared to the naive plasmid library.  The enrichment or depletion of all HLA-A2 variants was calculated and is used as a proxy for relative phenotypic fitness under the selection regime.  All deep mutational scans were independently replicated (n = 2).

first: Christine

middle: A

last: Devlin


title: DNase-seq from tibial nerve (ENCSR754WNA)

status: Public on Nov 01 2019

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

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


title: Transcriptome analysis reveals significant differences between primary plasma cell leukemia and multiple myeloma even when sharing a similar genetic background

status: Public on Oct 29 2019

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

summary: Primary plasma cell leukemia (pPCL) is a highly aggressive plasma cell dyscrasia characterized by short remissions and very poor survival. Deletions of 17p13 are much more frequent in pPCL than in multiple myeloma (MM). Although the 17p deletion is associated with poor outcome and extramedullary disease in MM, its presence does not confer the degree of aggressiveness observed in pPCL. The comprehensive exploration of the transcriptome, including isoform expression and RNA splicing events, may provide novel information about biological differences between the two diseases carrying a 17p deletion. Transcriptomic studies were carried out with the Human Transcriptome Array in nine newly diagnosed pPCL and ten MM samples, all of which harbored the 17p deletion.   Unsupervised cluster analysis clearly distinguished pPCL from MM samples. Indeed, 3,584 genes and 20,033 isoforms were found to be deregulated between pPCL and MM, most of which were underexpressed in pPCL. Pathway enrichment analysis at the gene and isoform levels revealed seven overlapping pathways mainly related to mRNA processing. There were 2,727 significantly deregulated isoforms of non-differentially expressed genes. Strangely enough, significant differences were observed in the expression of spliceosomal machinery components between pPCL and MM, in respect of the gene and isoform expression, and of the alternative splicing events. Furthermore, most of the deregulated exons have binding sites for most serine/arginine-rich proteins.  In summary, transcriptome analysis revealed significant differences in the relative abundance of isoforms between pPCL and MM, even when they both had the 17p deletion. Importantly, the mRNA processing pathway including RNA splicing machinery emerged as one of the most remarkable mechanisms underlying the biological differences between the two entities.

overall_design: Nine patients with newly diagnosed pPCL and ten with newly diagnosed MM were selected for the study based on the presence of 17p deletion.

first: Elizabeta

last: Rojas

first: Luis

last: Corchete

first: María

middle: V

last: Mateos

first: Ramón

last: García Sanz

first: Irena

last: Misiewicz-Krzeminska

first: Norma

middle: C


title: SOX21 ensures rostral forebrain identity by suppression of WNT8B during neural regionalization of human embryonic stem cells

status: Public on Oct 28 2019

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

type: Expression profiling by high throughput sequencing

summary: Generation of brain region-specific progenitors from human embryonic stem cells (hESCs) is critical for their application. However, transcriptional regulation of neural regionalization in human embryos is poorly understood. Here, we report that transcription factor SOX21 is required for telencephalic fate specification from hESCs. SOX21 knockout (KO) impairs telencephalic fate specification, concomitant with the activation of diencephalic genes and Wnt signaling. Inhibition of Wnt signaling restores telencephalic specification from SOX21 KO hESCs. Analysis of global SOX21 DNA binding profiles and SOX21-regulated genes identifies SOX21 targets. SOX21 interacts with b-catenin and interferes with TCF4/b-catenin binding to the enhancer of WNT8B. Double KO of SOX21 and WNT8B restores telencephalic specification, indicating that SOX21 specifies the telencephalic fate through repressing WNT8B expression. Moreover, the high and low levels of SOX21 in the telencephalon and diencephalon, respectively, in developing human brains support its role in telencephalic fate specification. Collectively, this study unveils previously unappreciated roles of SOX21 and sheds light on the transcriptional control of telencephalic patterning in humans.

overall_design: To dissect the transcriptional network controlling the rostrocaudal specification of early neural differentiation, we generated NPCs from hESCs with defined regional identities ranging from the rostral forebrain to the spinal cord based on published protocols (Imaizumi et al., 2015; Kirkeby et al., 2012; Kriks et al., 2011). Generally, rostrocaudal patterning was established by the dose-dependent activation of WNT signaling. Inhibition of Wnt signaling by IWP2 (2 uM) induced the rostral forebrain fate, while activation of Wnt signaling by CT induced the diencephalic, mesencephalic and rhombencephalic fate, depending on CT concentrations ranging from 0.4 to 4.0 uM. RA (1.0 uM) coupled with 4.0 uM CT (CT4.0RA) was used to induce the spinal cord fate. We then carried out RNA sequencing (RNA-seq) for cell samples collected from 19 groups (each with two biological replicates), covering 3 time points (days 0, 4, 8) and 9 differentiation conditions (IWP2, CT0.0, CT0.4, CT0.8, CT1.0, CT2.0, CT3.0, CT4.0, CT4.0RA).

first: Xinyuan

last: Liu

first: Yang

last: Zhou

first: Jing

last: Wen

first: Fan

last: Tang

first: Ying

last: Jin


title: Profiling of the host small non-coding RNAome in Mycobacterium tuberculosis infection

city: Hannover

first: Leonardo

middle: SILVA

last: de Araujo

address: Feodor-Lynen strasse 7

country: Germany

institute: Twincore

type: Non-coding RNA profiling by high throughput sequencing

summary: We report a study about differentially expressed small non-coding RNAs in the blood of humans harboring a latent (LTBI) or active tuberculosis (TB) infection in comparison with exposed controls (ExC) and treated LTBI (LTBItt). All non-TB subjects enrolled in this study were recent close contacts (rCt) of a newly diagnosed contagious TB cases enrolled in Rio de Janeiro, Brazil. The detailed methodology is described below.   According to Brazilian Ministry of Health (BMH) guidelines, the screen to detect LTBI among recent contacts comprises a clinical evaluation by a physician specializing in pulmonary diseases, a chest X-ray (CXR), and a tuberculin skin test (TST, cut-off 5mm). Additionally, as part of this study, blood was collected for short- (st) and long-term (lt) IGRA. St-IGRA was performed by stimulating whole blood with the Mtb antigen ESAT6:CFP10 (expressed as a fusion protein) for 22h (cut-off 10pg/mL). Lt-IGRA involved stimulating peripheral blood mononuclear cells (PBMC) with this same antigen for 5 days (cut-off 100 pg/mL).   Cases were defined as follows: ExC were recent close contacts of a TB index case and had a negative response to both TST and in house interferon-gamma release assay (IGRA) by stimulating blood-derived specimens with ESAT6:CFP10 indicating absence of Mycobacterium tuberculosis (Mtb) infection. LTBI was defined as (1) a TST induration >5 mm measured 72 h after intradermal injection of Mtb purified protein derivative (PPD) and (2) a positive IGRA response (to either st-IGRA or lt-IGRA, or both); if indicators of active disease were observed on CXR, (3) the absence of acid-fast bacilli (AFB) and negative Lowenstein-Jensen (LJ) culture of clinical specimens were also required. LTBItt consisted of LTBI cases (TST+/IGRA+ at enrollment) who completed a 6-month course of IPT. Their blood samples were collected >2 months after the end of isoniazid (INH) preventive treatment (IPT). Active TB was defined as (1) respiratory symptoms suggestive of TB, and/or (2) detection of AFB and/or positive LJ culture in sputum, bronchoalveolar lavage or biopsy, followed by (3) remission of symptoms upon anti-TB chemotherapy. Their blood samples were obtained before initiation of treatment.  Whole blood was collected in PAXgene RNA tubes (PreAnalytiX, SWZ) and was stored at -80°C for <2 years before RNA extraction.   sncRNA libraries. Total RNA (including small RNA) was isolated using the PAXgene Blood miRNA Kit (PreAnalytiX, SWZ), which is indicated for the isolation and purification of total RNA longer than 18 nucleotides. The manufacturer’s instructions were followed at both stages. Total RNA was quantified with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, EUA) and RNA integrity was assessed via agarose gel electrophoresis. One microgram RNA was used for cDNA library preparation (TruSeq Small RNA Sample Preparation® Kit, Illumina, San Diego, CA) following the manufacturer’s protocols. RNAseq was performed on an Illumina HiSeq® 2500 Sequencing System (Illumina, San Diego, CA), generating 50 bp single reads and ≈16 million reads passing filter for each sample.   Pre-processing and differential expression. The FASTQ files were preprocessed (FastQC 0.11.2), adaptors trimmed (Cutadapt 1.7.1), aligned to the human genome (STAR 2.4.1d), counted (featureCounts 1.4.6) on the Oasis 2.0 web platform.  Transcripts with <5 reads in at least one sample were excluded. Then, normalized and evaluated for differentially expressed (DE) transcripts using DESeq2 (v. 1.16) on the Oasis 2.0 web platform (https://oasis.dzne.de/).

overall_design: We collected blood samples from recent close contacts at recruitment and monitored them for 1 year. All TB cases were treatment-naïve. An active TB sncRNA signature was derived from whole blood RNA sequencing data by comparing TB and non-TB groups. Notably, it classified all TB cases correctly and reclassified 8 presumed LTBI cases as TB, 5 of whom turned out to have features of Mycobacterium  tuberculosis infection on chest radiographs.

middle: S

first: Steven

last: Talbot

first: Aravind

last: Tallam

first: Robert

last: Geffers

first: Maria Helena

middle: F

last: Saad

first: Frank

last: Pessler


title: Human Islet Response to Selected Type 1 Diabetes Associated Bacteria

status: Public on Oct 30 2019

city: Omaha

first: Ahmed

middle: M

last: Abdellatif

state: NE

address: 42 and Emile

department: Surgery-Transplant

institute: University of Nebraska Medical Center

summary: Type 1 diabetes (T1D) is a chronic autoimmune disease that results from destruction of pancreatic β-cells. T1D subjects were recently shown to harbor distinct intestinal microbiome profiles. Based on these findings, the role of gut bacteria in T1D is being intensively investigated. The mechanism connecting intestinal microbial homeostasis with the development of T1D is unknown.  Specific gut bacteria such as Bacteroides dorei (BD) and Ruminococcus gnavus (RG) show markedly increased abundance prior to the development of autoimmunity. One hypothesis is that these bacteria might traverse the damaged gut barrier, and their constituents elicit a response from human islets that causes metabolic abnormalities and inflammation. We have tested this hypothesis by exposing human islets to BD and RG in vitro, after which RNA-Seq analysis was performed. The bacteria altered expression of many islet genes. The commonly upregulated genes by these bacteria were cytokines, chemokines and enzymes, suggesting a significant effect of gut bacteria on islet antimicrobial and biosynthetic pathways. Additionally, each bacteria displayed a unique set of differentially expressed genes (DEGs). Ingenuity pathway analysis of DEGs revealed that top activated pathways and diseases included TREM1 Signaling and Inflammatory Response, illustrating the ability of bacteria to induce islet inflammation. The increased levels of selected factors were confirmed using immunoblotting and ELISA methods. Our data demonstrate that islets produce a complex anti-bacterial response. The response includes both symbiotic and pathogenic aspects. Both oxidative damage and leukocyte recruitment factors were prominent, which could induce beta cell damage and subsequent autoimmunity.

overall_design: In the present study, we experimentally tested the hypothesis that intestinal dysbiosis and leakage of bacteria into the human pancreas could trigger an islet anti-bacterial immune response. This response could lead to subsequent recruitment of immune cells to islets, initiating autoimmunity. To achieve that aim, isolated human islets were exposed to Bacteroides dorei and Ruminococcus gnavus, two bacteria overrepresented in the gut just before/at incidence of autoimmunity and Escherichia coli, a ubiquitous bacterium associated with accelerated maturation of the gut microbiome for 6h or 24h. Islets exposed to the potent cytokine IL-1β for the same time periods were used as positive controls. Islets exposed to serum-free medium were additionally used as negative controls.

first: Heather

middle: J

last: Smith

first: Nora

middle: E

last: Sarvetnick


title: A Novel LincRNA HERES Epigenetically Regulates Wnt Signaling Pathway via Interaction with EZH2 in Esophageal Squamous Cell Carcinoma

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

summary: Esophageal squamous cell carcinoma (ESCC), a major type of primary esophageal cancer in developing countries, displays a very poor clinical outcome in five-year survival rate. Although long non-coding RNAs (lncRNAs) exert critical roles in cancer development, the promising therapeutic targets of ESCC-expressed lncRNAs have not been comprehensively examined and their cancer-driving roles remain largely unknown at the mechanistic level. In this study, we aimed to identify ESCC-driving lncRNAs in the transcriptome level and exploit a therapeutic target with understanidng their modes of action.

overall_design: High-throughput RNA sequencing (RNA-seq) was performed with rRNA-depleted, total RNAs prepared from paired cancerous and non-cancerous tissues of 23 Korean ESCC patients, and the RNA-seq data were profiled to identify ESCC-driving lncRNAs.

first: Sang-Kil

last: Lee


title: Inactivation of Irf1 causes susceptibility to colitis-associated colorectal cancer

status: Public on Oct 31 2019

city: MONTREAL

first: Philippe

last: Gros

state: QC

address: 3649 Sir William Osler Street, Rm 370, Rm 370

country: Canada

institute: McGill University

summary: The incidence of colorectal cancer (CRC) is increased in patients afflicted by inflammatory bowel diseases (IBD) The cellular and molecular mechanisms that link chronic inflammation of the gut and increased CRC susceptibility are poorly understood. Risk of IBD is strongly influenced by genetic factors, including the IBD5 locus (5q31), harboring the IRF1 gene. A cause to effect relationship between chronic inflammation and CRC, and a possible role of IRF1 were studied in Irf1-/- mutant mice in a model of colitis associated CRC (CA-CRC) induced by azoxymethane and the irritant dextran sulfate. Loss of Irf1 causes hyper-susceptibility to CA-CRC, with early onset and increased number of tumors leading to rapid lethality. Transcript profiling (RNA-seq) and immunostaining of colons shows heightened inflammation, enhanced crypt cells proliferation and reduced tissue repair in Irf1-/- mutants, and this prior to appearance of tumors. A considerable infiltration of leukocytes is seen at this early stage in Irf1-/- colons, this infiltrate being composed primarily of proinflammatory Gr1+ Cd11b+ myeloid cells, mast cells, and CD3+ lymphoid cells. Studies in bone marrow chimeras show that differential susceptibility to CA-CRC of Irf1-/- vs. B6 controls is fully transferable by hematopoietic cells. Studies in human datasets confirm that transcripts signatures seen in Irf1-/- mice in response to AOM/DSS are enriched in clinical specimens from patients with IBD and with CRC. In addition, IRF1 expression in the colon is significantly decreased in late stage CRC (stages 3, 4) associated with poorer prognosis. These studies suggest that partial or complete loss of IRF1 expression alters the type, number, and function of immune cells in situ in gut establishing microbial-driven chronic inflammation and possibly creating a tumor promoting environment.

overall_design: We had found that interferon regulatory factor 1 (Irf1) knockout mice developed significantly higher colorectal tumor burden upon AOM/DSS treatments compared to resistant control B6 mice. Based on these results, we decided to investigate the molecular mechanisms by which these genes contribute to CA-CRC through transcriptome profiling. RNA sequencing was done on the colons of B6 and Irf1-/- untreated mice and mice at day 26 after one AOM and one DSS treatment (mice received one injection 7mg/kg of AOM (d1) followed by one 4-day cycle of DSS (2%; d8-d11) and were sacrificed at d26). The D26 timepoint was selected to elucidate how the biological systems in the colon were altered in our CA-CRC susceptible mice prior to the establishment of tumorigenesis. Colons of untreated and 26 days post-AOM/DSS treated B6 WT and Irf1 KO mice were examined by transcriptional profiling using three biological replicates per group.

first: Thiviya

last: Jeyakumar

first: David

last: Langlais


first: Zhuoqing

last: Fang

overall_design: To analyze the function of SOX21 in early neural differentiation, we compared the gene expression profiles between wild type and SOX21-/- H9 cells at 3 time points (Day 0, 4, 8) during neural differentiation by mRNA sequencing.

first: Xinyuan

last: Liu


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

overall_design: Refer to individual Series


title: A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Technology

country: Estonia

institute: University of Tartu

summary:
Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood–Ljungdahl
pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterization of acetogen metabolism has recently improved, key transcriptional features such as promoter motifs and transcriptional regulators are still unknown in acetogens. Here, we use differential RNA-sequencing to identify a previously undescribed promoter motif associated with essential genes for autotrophic growth of the model-acetogen Clostridium autoethanogenum. RNA polymerase was shown to bind to the new promoter motif using a DNA-binding protein assay and proteomics enabled the discovery of four candidates to potentially function directly in control of transcription of the WLP and other key genes of C1 fixation metabolism. Next, in vivo experiments showed that a TetR-family transcriptional regulator (CAETHG_0459) and the housekeeping sigma factor (sA) activate expression of a reporter protein (GFP) in-frame with the new promoter motif from a fusion vector in Escherichia coli. Lastly, a protein–protein interaction assay with the RNA polymerase (RNAP) shows that CAETHG_0459 directly binds to the RNAP. Together, the data presented here advance the fundamental understanding of transcriptional regulation of C1 fixation in acetogens and provide a strategy for improving the performance of gas-fermenting bacteria by genetic engineering.

overall_design: Differential RNA sequencing of gas and fructose-grown Clostridium autoethanogenum. Two samples for each condition: one enriched for processed (TAP-) and one for primary (TAP+) transcripts.

first: Renato

middle: D

last: Lemgruber

first: Christopher

last: Bakker

first: Robin

middle: W

last: Palfreyman

first: Ricardo

last: Gonzalez Garcia

first: Ryan

last: Tappel

first: Michael

last: Köpke

first: Séan

last: Simpson

first: Lars

middle: K

last: Nielsen

first: Esteban

last: Marcellin


title: Genome-wide map of SOX21 occupancy in human embryonic stem cell-derived neural progenitor cells [ChIP-seq]

summary: To understand how SOX21 regulates neural fate specification, we differentiated wild type and SOX21 knockout hESC into neural epithelial cells (NECs) using dual SMAD inhibition protocol. We collected cells at neural differentiation day 5 and performed SOX21 ChIP-seq to investigate the genome-wide binding profiles. Meanwhile, we also carried out b-catenin ChIP-seq in wild type and SOX21 knockout NECs to dissect the role of SOX21 in Wnt signaling inhibition, thus providing important information for the mechanism underlying SOX21's functions in early neural fate specification.

overall_design: Examination of genome-wide binding profile of SOX21 in neural epithelial cells (NECs). Comparison of b-catenin occupies between wild type and SOX21 knockout NPCs.

first: Ying

last: Jin


title: Functional Significance of U2AF1 S34F Mutation in Lung Adenocarcinomas

status: Public on Oct 25 2019

first: Mohammad

last: Shahrokh Esfahani

address: 265 Campus Drive

institute: Stanford University

summary: We conducted RNA-Seq and iCLIP for dox-inducible constructs of FLAG-HA tagged U2AF1 in the wild-type and mutant forms.

overall_design: The wild-type and mutant versions of U2AF1 were generated in HCC78. The goals of this study were to find differential binding and expression of wild type and mutant U2AF1. We generated stable doxycycline-inducible U2AF1 wild-type and mutant cell lines in HCC78 and induced each isoform with doxycycline. We observed that compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3’ splice junctions. The presence of S34F caused a shift in binding at 3’ splice sites, which was significantly associated with alternative splicing of skipped exons. Expression of U2AF1 S34F also induced the expression of genes involved in the epithelial-mesenchymal transition (EMT), with corresponding increases in tumor cell invasion. Finally, consistent with its RNA binding affinities, S34F preferentially induced splicing of the long over the short SLC34A2-ROS1 isoform, and overexpression of the long isoform increased invasiveness.

last: Flynn

first: Ash

last: Alizadeh

first: Maximilian

last: Diehn


title: Multiomic Fermentation Using Chemically Defined Synthetic Hydrolysates Revealed Multiple Effects Of Lignocellulose-Derived Inhibitors On Cell Physiology and Xylose Utilization In Zymomonas mobilis

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

institute: University of Wisconsin

summary: The conversion of sugars in lignocellulosic hydrolysates to bioethanol represents an industrially relevant system for understanding microbial physiology associated with production of bio-based fuels and chemicals. To this end we have developed a new version of synthetic hydrolysate (SynH) modeled on highly concentrated 9% AFEX-pretreated cornstove hydrolysate (ACSH) with and without lignocellulose-derived inhibitors (LDIs) added, termed SynH3 and SynH3- respectively. We profiled the cellular responses of xylose-utilizing Z. mobilis 2032 grown in both SynH3- and SynH3 via collection and analysis of multiple omics-based data (multiomics) including transcriptomics, proteomics, and metabolomics. Our study was focused on answering the following two questions. First, how does Z. mobilis respond to LDIs in SynH3 and how does this compare to our previous studies with E. coli in 6% ACSH SynH? Second, what is the potential cause for the poor xylose conversion in the presence of LDIs? Addressing these questions will provide critical information for engineering of Z. mobilis strains with improved productivities in lignocellulosic hydrolysates.

overall_design: Samples consist of four time points with three biological replicates each of cells either grown in control medium SynHv3.8 (aka SynH3- which does not contain lignocellulose-derived inhibitors) or SynHv3.11 (aka SynH3 which does include lignocellulose-derived inhibitors)

first: Yaoping

last: Zhang

first: Jessica

last: Vera

first: Dan

last: Xie

first: Jose

last: Serate

first: Edward

last: Pohlman

first: Jason

last: Russel

first: Alexaner

last: Hebert

first: Joshua

last: Coon

first: Shabda

last: Gajbhiye

first: Trey

last: Sato

first: Donna

last: Bates


title: Host-microbe interactions following L. plantarum administration in SIV-infected and uninfected rhesus macaques

status: Public on Oct 23 2019

city: Davis

first: Satya

last: Dandekar

address: 415 Health Sciences Dr

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary: We used microarrays to detail the global gene expression changes in the ileum of SIV-infected and uninfected macaques following administration of L. plantarum.

overall_design: A total of 8 rhesus macaques were enrolled in the study, 4 of which were infected intravenously with SIVmac251 for 10 weeks and 4 of which served as SIV-negative controls. At 10-weeks post-infection, all macaques underwent ligated ileal loop surgery to assess the effects following L. plantarum administration compared to control media MRS administration.

first: Katti

middle: R

last: Crakes


title: RNA-seq analysis of distal gene expression changes during nodulation

status: Public on Oct 24 2019

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: Legume plants form symbiotic relationships with diazotrophic bacteria called rhizobia. During such symbiosis, plants provide bacteria with preferred carbon sources such as malate and succinate in return for essential reduced nitrogen. Compatible interactions result in a series of plant root modifications that eventually result in nodule formation. Bacteria living in the nodule cells fix nitrogen via the nitrogenase enzyme complex. Interestingly, as in plant-pathogen interactions, incompatibility in legume-rhizobia associations is also regulated in a genotype-specific manner. For example, the dominant Rj2 gene is presumed to help exclude poor nitrogen-fixing or less-beneficial rhizobia such as B. japonicum USDA122 (U122). The process likely involves recognition of bacterial effectors by host receptor proteins similar to the perception of pathogenic microbes. Our results show that genetic exclusion of incompatible rhizobia in the root requires conserved molecular components of the plant immune response pathway and results in the induction of systemic signaling in the distal tissue. To better understand the mechanism underlying incompatible rhizobia-induced systemic signaling, we compared the transcriptional changes in the foliar tissue of Rj2 plants inoculated with compatible or incompatible rhizobia strains, using RNA-Seq analysis.

overall_design: Overall, 1 control (mock), 2 treatments (treated with Incompatible Glycine max L76-1988 with Bradyrhizobium japonicum USDA122 and Glycine max L76-1988 with Sinorhizobium fredii USDA257), each with 3 replicates.

first: M

middle: B

last: Shine

first: R

last: Chowda-Reddy

first: Asheesh

last: Singh

first: Pradeep

last: Kachroo

first: Aardra


title: DNA methylation Profiling in Autoimmune encephalitis (AE): DNA methylation profile in healthy control (HC) sujects and acute-phase AE subjects

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

type: Methylation profiling by genome tiling array

summary:
DNA methylation analysis of DNA samples from total WBC collection
The DNA samples from each subject was first subject to bisulfite conversion, followed by sample preparation and microarray experiment.

overall_design: We analyzed 3 healthy control DNA samples and 5 acute-phase AE DNA samples

first: Meng-Han

last: Tsai


title: Copy Number Variations identified in 225 Diffuse Large B-Cell Lymphoma tumors

city: Bron

first: Sylvain

last: Mareschal

address: Centre de Biopathologie Est, 59 boulevard Pinel

department: NGS-HCL platform

country: France

institute: Hospices Civils de Lyon

type: Genome binding/occupancy profiling by genome tiling array

summary: Copy Number Variations (CNVs) were identified performing Comparative Genomic Hybridization (CGH) on 225 patients after whole-genome amplification, using Agilent SurePrint G3 4x180K microarrays. CNVs were further integrated with gene expression (Affymetrix U133+2 arrays) and mutations (targeted DNA resequencing). Complete description of the methods, array quality checks and called segments are available as supplemental material in the corresponding publication.

overall_design: 225 DNA samples extracted from frozen Diffuse Large B-Cell Lymphoma (DLBCL) tumors were hybridized against a commercial DNA pool. 6 arrays were discarded before analysis due to incomplete patient or expression data to correlate with. 29 more arrays were discarded after analysis due to an unrecoverable amplification bias (see the correspong publication for details), resulting in 190 exploitable arrays.

first: Sydney

last: Dubois

first: Martin

last: Figeac

first: Céline

last: Villenet

first: Bruno

last: Tesson

first: Fabrice

last: Jardin


title: Transcriptomics analysis of trimester-specific full-term placentas from three Zika virus-infected women

status: Public on Oct 22 2019

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Effects of Zika virus (ZIKV) infection on placental development during pregnancy are unclear. In this study, full-term placentas from three women, each infected with ZIKV during specific pregnancy trimesters, were harvested for anatomic, immunologic and transcriptomic analysis. Each woman exhibited a unique immune response with raised IL-1RA, IP-10, EGF and RANTES expression, and neutrophil numbers during the acute infection phase. Although ZIKV NS3 antigens co-localized to placental Hofbauer cells, the placentas showed no anatomical defects. Transcriptomic analysis of samples from the placentas revealed that infection during trimester 1 caused a disparate cellular response centered on differential eIF2 signalling, mitochondrial dysfunction and oxidative phosphorylation. Despite these, the babies were delivered without any congenital anomalies. Nevertheless, these findings should translate to improve clinical prenatal screening procedures for virus-infected pregnant patients.

overall_design: Three ZIKV-positive pregnant women were recruited to the study, who had been infected with ZIKV in different trimesters following the ZIKV outbreak that happened in Singapore in 2016. Transcriptome profiling of the placenta discs and foetal membranes of the placentas was used to investigate the cellular host response during ZIKV infection. Both tissues were digested to obtain a single-cell suspension: the placenta disc was further separated into CD45+ immune and CD45- non-immune fractions, to define the drivers of ZIKV-induced cellular changes. Tissue samples were collected in triplicate to account for tissue heterogeneity, except those obtained from Patient 3, where the sample was processed as a whole, due to technical difficulties. Placental samples from two healthy women were included as controls.

first: Lisa

last: Ng


title: Characterization of the Placental Transcriptome through Mid to Late Gestation in the Mare

city: Lexington

first: Shavahn

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

summary: The placenta is a dynamic organ which undergoes extensive remodeling throughout pregnancy to support, protect and nourish the developing fetus. Despite the importance of the placenta, very little is known about its gene expression beyond very early pregnancy and post-partum. Therefore, we utilized RNA-sequencing to characterize the transcriptome from the fetal (chorioallantois) and maternal (endometrium) components of the placenta from mares throughout gestation (4, 6, 10, 11 m). Within the endometrium, 47% of genes changed throughout pregnancy, while in the chorioallantois, 29% of genes underwent significant changes in expression. Further bioinformatic analyses of both differentially expressed genes and highly expressed genes help reveal similarities and differences between tissues. Overall, the tissues were more similar than different, with ~ 95% of genes expressed in both tissues, and high similarities between the most highly expressed genes (9/20 conserved), as well as marked similarities between the PANTHER pathways identified. The most highly expressed genes fell under a few broad categories, including endocrine and immune-related transcripts, iron-binding proteins, extracellular matrix proteins, transport proteins and antioxidants. Serine protease inhibitors were particularly abundant, including SERPINA3, 6 and 14, as well as SPINK7 and 9. This paper also demonstrates the ability to effectively separate maternal and fetal components of the placenta, with only a minimal amount of chorioallantoic contamination in the endometrium (~8%). This aspect of equine placentation is a boon for better understanding gestational physiology and allows the horse to be used in areas where a separation of fetal and maternal tissues is essential. Overall, these data represent the first large-scale characterization of placental gene expression in any species and include time points from multiple mid- to late-gestational stages, helping further our understanding of gestational physiology.

overall_design: We analyzed paired chorioallantois and endometrium from mares at 4, 6, 10 and 11 m of gestation (4 per time point) via RNA-sequencing. Chorioallantois samples were submitted separately (GSE108279).

first: Pouya

last: Dini

first: Hossam

last: El-Sheikh Ali

first: Theodore

last: Kalbfleisch

first: Barry

last: Ball


title: Genome binding/occupancy profiling of Tox2 in Tfh-like cells

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

country: China

institute: Tsinghua University

summary: T Follicular helper (Tfh) cell is an effector CD4+ T cell subset specialized in helping B cells in germinal centers (GC) reactions. Although Bcl6 was identified as a Tfh-specific transcription factor essential for their development, the molecular mechanisms underlying Bcl6 regulation and Tfh cell commitment remain unclear. Here, we report that Tox2 transcription factor is highly expressed in Tfh cells, regulated by Bcl6 and STAT3. Forced expression of Tox2 drives Bcl6 expression and Tfh development. Mechanistically, Tox2 directly binds to Tfh-associated genes, including Bcl6, and functions to promote their chromatin accessibility and modulate the activities of other Tfh-regulating factors. Conversely, genetic deletion of Tox2 results in defective Tfh differentiation, and inhibiting both Tox and Tox2 in T cells abolishes Tfh differentiation and GC response. Thus, our results demonstrate that Tox2 is a key transcription factor that regulates Bcl6 expression and Tfh development and suggest a Tox2-Bcl6 axis in feed-forward regulation of Tfh program.

overall_design: Because the commercial Tox2 antibody did not work well in western blot, we constructed a retrovirus expressing an HA tag at Tox2 C-terminus, with similar function as wild-type Tox2 in CD4+ T cells, for the ChIP experiment using T cells activated under Tfh-like condition.

first: Wei

last: Xu

first: Xiaohong

last: Zhao


title: mRNA structure regulates protein expression through changes in functional half-life

city: Cambridge

first: David

middle: Michael

last: Mauger

state: MA

address: 200 Technology Square

department: Platform Research

institute: Moderna, Inc.

summary: A SHAPE-MaP structure probing experiment was performed on 39 firefly luciferase mRNAs containing uracil, 1-methyl-psuedouracil, or 5-methoxy-uracil.  For each mRNA, SHAPE-MaP includes a sample treated with 1M6 ('MOD'), a minus reagent ('NC'), and a denatured control ('DEN'). The 1M6 reagent preferenctially reacts with unpaired bases in RNA and subsequently induces mutations during the reverse transcription step of library preparation. After sequencing and alignment, the 'mutational profiles' of the 'p', 'm', and 'd' samples are used to calculate the SHAPE reactivity of each base.

overall_design: SHAPE-MaP on 39 firefly luciferase mRNAs containing modified uracils

first: B

last: Cabral

first: Vladimir

last: Presnyak

first: Melissa

last: Moore


title: Single cell RNA sequencing analysis of CD45low/+ lineagelow lung cells from adult and neonatal (12-day-old) RORα lineage tracer mice

city: Vancouver

first: Maryam

last: Ghaedi

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

institute: BC Cancer Agency

summary: To fully characterize the heterogeneity and gene expression profile of mouse lung ILC2s, We generated RORα lineage tracer mice by crossing RoraIRES-Cre (Chou et al., 2013) and R26R-EYFP mice, which have a loxP-flanked stop sequence followed by the gene encoding yellow fluorescent protein (YFP) in the ROSA26 locus. In these RORα-YFP mice, cells expressing Rorα during their development should be irreversibly labeled by YFP. Flow cytometric analyses of lymphocytes in RORα-YFP mice showed that innate lymphoid cells type 2 (ILC2s) were marked by YFP expression. However, both adult and neonatal lung Lin−YFP+ cells were heterogeneous and included not only ILC2s (GATA-3+Thy1+) but also GATA-3−Thy1− and GATA-3lowThy1+ cells. In order to fully assess the lung ILC2 heterogeneity, we analyzed all CD45low/+Linlow cells from adult (6-week-old) and neonatal (12-day-old) RORα-YFP mouse lungs by droplet-based scRNA-seq. Unsupervised clustering of the cells revealed distinct clusters of stromal, B, T, NK cell, DC and ILC2 based on their expression of well-characterized marker genes. We then isolated the ILC2 cluster and performed a second round of unsupervised clustering to examine the existence of possible ILC2 subsets. In both adult and neonatal datasets, ILC2s were divided into subsets with each subset expressing a distinct set of ILC2-associated genes. We validated the existence of distinct ILC2 subsets in adult and neonatal lungs using flow cytometry. We also comprehensively assessed the genes that were specifically and/or differentially expressed by ILC2s compared to other immune and non-immune cell populations in our datasets. This analysis revealed the expression of well-characterized ILC2 genes such as Gata3, Rora, Areg and Il7r as well as other genes with potential immune regulatory functions.

overall_design: Examination of lung ILC2 heterogeneity during neonatal and adult periods

first: Fumio

last: Takei


title: Gene expression data of organoids derived from traditional serrated adenomas

city: Tokyo

first: Kohta

last: Toshimitsu

address: 35, Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University

summary: Traditional serrated adenomas (TSAs) are rare colorectal polyps characterized by unique histology features. Fusions in R-spondin genes have been found in TSAs, but it is not clear whether these are sufficient for TSA development. We established 2 patient-derived TSA organoid lines, and engineered chromosome rearrangements that involve R-spondin genes into human colonic organoids using CRISPR-Cas9. Consequently, we highlighted the similarity of the gene expression patterns between TSA organoids and engineered organoids.

overall_design: We analyzed gene expression of 2 patinet-derived traditional serrated adnoma, 3 genetically engineered and 1 normal colonic organoids. Total RNA were extracted from organoids and hybridized to GeneChip PrimeView Human Gene Expression Array, and scanned with GeneChip Scanner 3000 7G.

first: Kenta

last: Kawasaki


title: TLR5 dependent gene expression in H. pylori infection

city: Erlangen

first: Pachathundikandi

last: Suneesh Kumar

state: Bayern

address: Staudtstrasse 5

department: Chair of Microbiology

institute: FAU Erlangen-Nuremberg

summary: HEK293 cells overexpressing TLR5 (TLR5+) and parent cell lines were infected with H. pylori to differentiate the gene expression through increased TLR5 signalling.

overall_design: The experiment was designed to analyze the differential gene expression in H. pylori infected TLR5+ and parent cell lines  at 6h by comparing with respective mock controls. It was envisaged to understand the most prominent differential gene expression due to over expression of TLR5 in HEK293 cells as compared with parental cells at the stipulated time period of H. pylori infection.

first: Suneesh

last: Kumar Pachathundikandi

first: Steffen

last: Backert


title: Gene expression profiling of zebrafish (Danio rerio) in response to nutritional supplementation with mastic essential oil from Pistacia lentiscus var. chia

status: Public on Oct 21 2019

city: Ioannina

first: Thomais

last: Papamarkaki

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

summary: To analyse the gene expression profile of zebrafish in response to nutritional supplementation with mastic essential oil, mRNA was isolated at 42dpf and subjected to DNA microarray analysis. Gene ontology characterisation indicated that most of the differentially expressed genes were related to the immune defense against pathogens, immunometabolic processes and mucin function.

overall_design: Gene expression profiling of control and mastic essential oil supplemented zebrafish at 42 dpf with the Affymetrix Zebrafish Gene 1.0 ST Array.

first: Eleni

last: Tzima

first: Iliana

last: Serifi

last: Papamarcaki


title: Brain-to-cervical lymph node signaling after stroke

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Microarray analysis of isolated lymphatic endothelial cells from cervical lymph nodes (CLNs) of ischemic mice showed the activation of transmembrane tyrosine kinase pathways.

overall_design: The experiment is comprised of 6 Mouse Gene 2.0 ST arrays, comparing lymphatic endothelium samples derived from CLNs of mice at 3 hours post reperfusion after a 1 hour transient focal ischemia (3H) to those from sham controls (n=3 per experimental group, each sample representing pooled CLNs from 4 animals).

first: Kazuhide

last: Hayakawa


title: Retroelement insertion in a CRISPR/Cas9 editing site in the early embryo intensifies genetic mosaicism

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

institute: KRIBB

type: Genome variation profiling by high throughput sequencing

summary: Continued CRISPR/Cas9-mediated editing activity that allows differential and asynchronous modification of alleles in successive cell generations expands allelic complexity. To understand the earliest events during CRISPR/Cas9 editing and the allelic selection among the progeny of subsequent cell divisions, we inspected in detail the genotypes of 4- and 8-cell embryos and embryonic stem cells (ESCs) after microinjection of a CRISPR toolkit into the zygotes. We found a higher editing frequency in 8-cell embryos than in 4-cell embryos, indicating that the CRISPR/Cas9 activity persisted through the 8-cell stage. Analysis of a CRISPR/Cas9 transgenic founder mouse revealed that four different alleles were present in its organs in different combinations and that its germline included three different mutant alleles, as shown by the genotypes of the pups. The indel depth, which measured the extent of indels at the sequence level within single embryos, decreased significantly as the embryos advanced to form ESCs, suggesting that exclusion of fatal indels occurred in the subsequent cell generations. Interestingly, we discovered that the CRISPR sites frequently contained introduced retroelement sequences and that this occurred preferentially with certain classes of retroelements. Therefore, in addition to CRISPR/Cas9’s innate mechanism of separate, differential enzymatic modifications of alleles, the frequent retroelement insertions that occur in early mouse embryos during CRISPR/Cas9 editing further expand the allelic diversity and mosaicism in the resulting transgenic founders.

overall_design: Genotyping of CRISPR/Cas9 modified genomic regions by the highthrouput sequencing technology

first: Jeehyun

last: Jeon


title: The Cyclic AMP Receptor Protein Regulates Quorum Sensig and Global Gene Expression in Yersinia pestis During Planktonic Growth and Growth in Biofilms

city: Chicago

first: Jeremy

middle: T

last: Ritzert

state: IL

address: 1032 W. Sheridan Road

department: Biology

institute: Loyola University Chicago

summary: We use RNA-seq to identify Crp-regulated, Biofilm-regulated and Glucose-regulated genes in Yersinia pestis grown in planktonic and biofilm growth states.

overall_design: Comparing transcripts between Y. pestis and Y. pestis ∆crp growin in glucose, glycerol, in planktonic and biofilm states

first: Karla

last: Satchell


title: Assessment of the Diagnostic Utility of Serum MicroRNA Classification in Patients with Diffuse Glioma

status: Public on Oct 19 2019

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

summary: A serum miRNA combination could be a powerful classifier for the detection of patients with brain tumors.

overall_design: Serum microRNA profiles of diffuse gliomas, other primary brain tumors, primary central nervous system lymphomas (PCNSL), metastatic brain tumors (Meta), benign brain tumors, spinal schwannomas, trauma, infarction, benign disease controls, and prospectively collected non-cancer controls in a clinic.

first: Makoto

last: Ohno

first: Juntaro

last: Matsuzaki

first: Junpei

last: Kawauchi

first: Yoshiaki

last: Aoki

first: Junichiro

last: Miura

first: Ken

last: Kato

first: Hiromi

last: Sakamoto

first: Yuko

last: Matsushita

first: Masamichi

last: Takahashi

first: Yasuji

last: Miyakita

first: Koichi

last: Ichimura

first: Yoshitaka

last: Narita

first: Takahiro

last: Ochiya


title: Improved retinal organoid differentiation by modulating signaling pathways revealed by comparative transcriptome analyses with development in vivo

status: Public on Oct 18 2019

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: This study provides analysis of developing mouse retina organoids derived from induced pluripotent stem cells . RNA-seq profiling was performed on 2 time points during retinal organoids supplemented with docosahexaenoic acid (DHA), linoleic acid (LA), and/or FGF1. Alignment, transcript and gene quantitation, and normalization was performed.

overall_design:
Retina organoids were collected in duplicate or triplicate at 2 time points during differentiation (day (D) 26 and 32) with and without DHA and FGF1 supplementation.

Please note that the Gene_Normalized-CPM.tsv contains 18 data columns as 5 samples were eliminated for the particular analysis. The other processed data files contain the complete data for all 23 samples.

first: Holly

middle: Y

last: Chen

first: Ryan

last: Kelley

first: Anupam

last: Mondal

first: Tiansen

last: LI

first: Vijender

last: Chaitankar

first: Anand

last: Swaroop


title: Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

institute: University of Illinois at Urbana-Champaign

summary: The aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways.

overall_design: Two stages of flower bud development: pre-meiosis (size: 1-6 mm) and post-meiosis (size: 7-12 mm) and three different sex-types: male (variety 'AU9'), female (variety 'AU9') and hermaphrodite (variety 'SunUp').

first: Ray

last: Ming

first: Jennifer

last: Wai

first: Ming-Li

last: Wang


title: Gene expression in rice roots after Pythium arrhenomsnes infection versus mock infection

city: Ghent

first: Ruben

last: Verbeek

address: Coupure links 653

department: Department of Biotechnology

country: Belgium

institute: Ghent University

summary: Next to their essential roles in plant growth and development, phytohormones play a central role in plant immunity against pathogens. In this study we examined the role of hormones in the antagonism of the plant-pathogenic oomycete Pythium arrhenomanes against the root-knot nematode Meloidogyne graminicola in rice roots. Hormone measurements and gene expression analyses showed that the jasmonate (JA) pathway is induced early upon P. arrhenomanes infection. Exogenous application of methyl-jasmonate (MeJA) on the plant confirmed that JA is needed for basal defence against both P. arrhenomanes and M. graminicola in rice. Whereas M. graminicola suppresses root JA levels to increase host susceptibility, Pythium inoculation boosts JA accumulation up to levels that can no longer be repressed by the nematode in double-inoculated plants. Exogenous MeJA supply phenocopied the defence-inducing capacity of P. arrhenomanes against the root-knot nematode, whereas the antagonism was weakened in JA-insensitive mutants. Transcriptome analysis confirmed upregulation of JA biosynthesis and signalling genes upon P. arrhenomanes infection, and additionally revealed induction of genes involved in biosynthesis of diterpenoid phytoalexins, consistent with strong activation of the gene encoding the JA-inducible transcriptional regulator DITERPENOID PHYTOALEXIN FACTOR. Next to that, our results provide evidence for induced expression of genes encoding ERF83, and related PR proteins, as well as auxin depletion in P. arrhenomanes infected rice roots, which potentially further contributes to the reduced nematode susceptibility seen in double-infected plants.

overall_design:
Seeds were grown in Gamborg B5 medium as described above, using 0.6-cm PDA plugs of a 7-days-old culture of P. arrhenomanes (PT60). Samples from mock-inoculated and Pythium-infected seedlings were collected 2 days post inoculation (dpi).
Three biological replicates were sampled, where each biological replicate represents a pool from at least 20 individual plants, giving a total of six RNA samples (two treatments × three biological replicates).
Please note that the experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated). The associated raw data file is indicated in the corresonding sample description field.

first: Evelien

last: Van Buyten

first: Md

middle: Z

last: Alam

first: David

last: De Vleesschauwer

first: Jonas

last: Van Bockhaven

first: Shoshi

last: Kikuchi

first: Ashley

last: Haeck

first: Kristof

last: Demeestere

first: Godelieve

last: Gheysen

first: Monica

last: Höfte

first: Tina

last: Kyndt


title: Temperature-dependent regulation of upstream open reading frame translation in s. cerevisiae

first: Shardul

last: Kulkarni

address: 49 Convent Drive, Rm 2C08

institute: NICHD, NIH

summary: Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. cerevisiae. Initiation from NCCs or AUGs in the 5’-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. Using reporter assays, we found that changes in growth temperature can affect translation from NCC start sites in yeast cells, suggesting the possibility that gene expression could be regulated by temperature by altering use of different uORF start codons. Using ribosome profiling, we provide evidence that growth temperature regulates the efficiency of translation of nearly 200 uORFs in S. cerevisiae. Of these uORFs, most that start with an AUG codon have increased translational efficiency at 37 ˚C relative to 30 ˚C and decreased efficiency at 20 ˚C. For translationally regulated uORFs starting with NCCs, we did not observe a general trend for the direction of regulation as a function of temperature, suggesting mRNA-specific features can determine the mode of temperature-dependent regulation. Consistent with this conclusion, the position of the uORFs in the 5’-leader relative to the 5’-cap and the start codon of the main ORF correlates with the direction of temperature-dependent regulation of uORF translation. We have identified several novel cases in which changes in uORF translation are inversely correlated with changes in the translational efficiency of the downstream main ORF. Our data suggest that translation of these mRNAs is subject to temperature-dependent, uORF-mediated regulation. Overall, our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae.

overall_design: We examined the effect of changes in culture temperature on usage of alternate start sites upstream of the annotated start codon AUG (translation of upstream open reading frame i.e. uORF). We calculated global translational efficiencies (TEs) by ribosome footprint profiling of BY4741 cells cultured at multiple temperatures. The study includes 12 samples, comprised of 6 mRNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates of cells cultured at 20 °C, 30 °C. and 37 °C. The ribo-seq data generated in this study are previously published (Martin-Marcos et al., 2017, eLife 2017;6:e31250 DOI: 10.7554/eLife.31250). The ribo-seq data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) with accession numbers GSM2895484, GSM2895485, GSM2895488, GSM2895489, GSM2895490, GSM2895491.

first: Fujun

last: Zhou

first: Neelam

last: Se

first: Hongen

last: Zhang

first: Alan

middle: G

last: Hinnebusch

first: Jon

last: Lorsch


title: RNA-seq Analysis of Castration-Resistant Prostate Cancer With Knock-down of E2F1

city: Nanning

first: Qingniao

state: Guangxi

address: 22 Shuangyong road

institute: Guangxi Medical Universtiy

summary: From castration resistant prostate cancer (CRPC) regulatory network, we found over 90% negative feedback loop went through E2F1. And we detected PC3 and DU145 cells with depletion of E2F1 through the invasion, migration, proliferation and apoptosis experiments. In order to identify which genes trigger these phenomenon and regulatory mechanism of E2F1 in CRPC, we performed the gene expression between the vector and under the knockdown of E2F1 in PC3 and DU145 cells by RNA sequencing (RNA-seq). To investigate differentially expressed genes (false discovery rate (FDR) <0.05, |log2 (Fold Change)| > 1) between vector control and shE2F1 of CRPC cells, we performed processing RNA-Seq data using the Basespace. Then we verified some common two cells’ differentially expressed genes through quantitative real-time PCR.

overall_design: RNA-seq transcriptome profiling of PC3 and DU145 cells with knock-down of E2F1

first: Yanling

last: Hu


title: Effector differentiation potential determined at the level of human CD8+ naïve T cell subsets [microarray]

status: Public on Oct 17 2019

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

summary: Antigen recognition by CD8+ naïve T cells induces immune activation and rapid effector differentiation that ensures elimination of virally-infected and malignant cells. While signals from the extracellular milieu and downstream of the TCR have long been known to play a crucial role, it is currently unknown whether heterogeneity within the naïve CD8+ T cell pool shapes the potency of effector differentiation. We report the identification of two discrete subsets of human CD8+ TN cells, defined by positive and negative expression of the chemokine receptor CXCR3, with different potential to generate fully-differentiated effector T cells following antigen-specific stimulation. The CXCR3+ are more abundant than the CXCR3– naïve in peripheral blood and lymphoid tissues, retain enhanced expression of effector-related genes ex vivo and display features of the T cell receptor chain repertoire indicating enhanced capacity to bind the peptide:major histocompatibility complex. Likewise, a phenotypically equivalent murine CD8+ naïve population expressing high levels of CD5, a surrogate indicator of enhanced TCR sensitivity for self, preferentially generates short-lived effector cells following infection. Our findings imply that CD8+ T cell effector differentiation potential in humans is shaped by heterogeneity in the preimmune repertoire

overall_design: 12 samples

first: Gabriele

last: De Simone

first: Emilia

first: Enrico

last: Tagliafico

first: Elena

last: Tenedini

first: Clelia

last: Peano

first: Francesco

last: Ferrari

last: Lugli


title: Effector differentiation potential determined at the level of human CD8+ naïve T cell subsets [RNA-Seq]

overall_design: 18 samples


title: Effector differentiation potential determined at the level of human CD8+ naïve T cell subsets

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: NPM and NPM-MLF1 interact with chromatin remodeling complexes and influence their recruitment to specific genes

city: Montréal

first: Eric

last: Milot

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: HMR research center/Université de Montréal

summary: Nucleophosmin (NPM1) is either frequently mutated or subjected to chromosomal translocation in acute myeloid leukemia (AML). NPM protein is primarily located in the nucleus, but the recurrent NPMc+ mutation is characterized by cytoplasmic localization and leukemogenic properties. Similarly, the NPM-MLF1 translocation product favors the partial cytoplasmic retention of NPM. Regardless of their common cellular distribution, NPM-MLF1 malignancies engender different effects on hematopoiesis compared to NPMc+ counterparts, highlighting possible aberrant nuclear function(s) of NPM in NPMc+ AML. We performed a proteomics analysis and found that NPM and NPM-MLF1 interact with chromatin remodeling complexes of the ISWI family, as well as with NuRD and P/BAF complexes. Accordingly, NPM and NPM-MLF1 are recruited to transcriptionally active or repressed genes along with NuRD and P/BAF elements. Although the overall gene expression program in NPM knockdown cells is similar to that resulting from NPMc+ and is consistent with loss of nuclear function of NPM, NPM-MLF1 expression differentially altered gene transcription regulated by NPM. The abnormal gene regulation imposed by NPM-MLF1 is characterized by enhanced recruitment of NuRD to gene regulatory regions. Thus, different mechanisms orchestrate the deregulation of NPM function in NPMc+- versus NPM1-MLF1-associated leukemia.

overall_design: Gene expression profil was determinated by Ion Ampli Sequencing in K562 sh Scramble (contrôle) and K562 shNPM cells, in triplicate.


title: Clostridioides difficile responses to calprotectin

city: Nashville

first: Christopher

last: Lopez

state: Tennessee

address: 1161 21st Avenue South, Medical Center North

institute: Vanderbilt University Medical Center

summary: The intestines house a diverse microbiota that must compete for nutrients to survive, but the specific limiting nutrients that control pathogen colonization are not clearly defined. Clostridioides difficile colonization typically requires prior disruption of the microbiota, suggesting that outcompeting commensals for resources is key in establishing C. difficile infection (CDI). The immune protein calprotectin (CP) is released into the gut lumen during CDI to chelate zinc (Zn) and other essential nutrient metals. Yet, the impact of Zn limitation on C. difficile colonization is unknown. To define C. difficile responses to Zn limitation, we performed RNA sequencing on C. difficile exposed to CP. In media with CP, C. difficile upregulated genes involved in metal homeostasis and amino acid metabolism.

overall_design: Six total samples were analyzed; three samples were biological replicates of C. difficile grown in media alone and three samples were biological replicates of C. difficile grown in media containing recombinant calprotectin

middle: A

middle: P

last: Skaar


title: A single-cell atlas of the human cortex reveals drivers of transcriptional changes in  Alzheimer’s disease in specific cell subpopulations

status: Public on Oct 16 2019

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

institute: Duke-NUS Medical School

summary: There is currently little information about how individual cell types contribute to Alzheimer’s disease (AD). Here, we applied single-nucleus RNA-seq (snRNA-seq) on the entorhinal cortex from control and AD brains of twelve individuals, yielding a total of 13,214 high quality nuclei. We detail cell-type-specific gene expression patterns, unveiling how transcriptional changes in specific cell subpopulations contribute to AD. We report that the AD risk gene, APOE, is specifically repressed in AD oligodendrocyte progenitor cells and astrocyte subpopulations, and upregulated in an AD-specific microglial subopulation. Integrating transcription factor regulatory modules with AD risk loci revealed drivers of cell-type-specific fate transitions towards AD. For example, transcription factor EB, a master regulator of lysosomal function, regulates multiple disease genes in a specific AD astrocyte sub-population. These results provide insights into the coordinated control of AD risk genes and their cell-type specific contribution to disease susceptibility and are available at http://adsn.ddnetbio.com.

overall_design: Single Nuclei RNA sequencing of 8 10x libraries with each library containing 2 individuals (n =16)

first: Alexendra

last: Grubman

first: John

middle: F

last: Ouyang

first: Oweb

last: Rackham

first: Jose

last: Polo

last: Petretto


title: Gastric organoid single-cell RNA-seq I

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Meta3 and Meta4 gastric organoids from Mist1-creERT2/+;KrasLSL/+ mice

overall_design: Meta3 vs. Meta4

first: Alan

last: Simmons

first: Eunyoung

last: Choi


title: Gastric organoid single-cell RNA-seq II

summary: Meta4 gastric organoids from Mist1-creERT2/+;KrasLSL/+ mice treated with vehicle or Selumetinib

overall_design: Meta4+DMSO vs. Meta4+Selumetinib


title: Transcriptional profile of TCX2 mutant

status: Public on Oct 15 2019

city: Ames

first: Natalie

middle: M

last: Clark

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

summary: RNAseq profile of the tcx2-3 mutant and whole root and cell type-specific profiling of the tcx2 mutant

overall_design: RNA was extracted from 3 replicates of 5 day old tcx2-3 mutant and WT roots and sequenced. RNAseq analysis also performed on tcx2 mutant plants crossed with various cell-specific GFP markers

first: Rosangela

last: Sozzani


title: Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

type: Methylation profiling by high throughput sequencing

summary: Epigenetic aberrations are widespread in cancer, yet the underlying mechanisms and causality remain poorly understood. A subset of gastrointestinal stromal tumors (GISTs)  lack canonical kinase mutations but instead have succinate dehydrogenase (SDH)-deficiency and global DNA hyper-methylation. Here we associate this hyper-methylation with changes in genome topology that activate oncogenic programs. To investigate epigenetic alterations systematically, we mapped DNA methylation, CTCF insulators, enhancers, and chromosome topology in KIT-mutant, PDGFRA-mutant, and SDH-deficient GISTs. Although these respective subtypes shared similar enhancer landscapes, we identified hundreds of putative insulators where DNA methylation replaced CTCF binding in SDH-deficient GISTs. We focused on a disrupted insulator that normally partitions a core GIST super-enhancer from the FGF4 oncogene. Recurrent loss of this insulator alters locus topology in SDH-deficient GISTs, allowing aberrant physical interaction between enhancer and oncogene. CRISPR-mediated excision of the corresponding CTCF motifs in an SDH-intact GIST model disrupted the boundary and strongly up-regulated FGF4 expression. We also identified a second recurrent insulator loss event near the KIT oncogene, which is also highly expressed across SDH-deficient GISTs. Finally, we established a patient-derived xenograft (PDX) from an SDH-deficient GIST that faithfully maintains the epigenetic state of the parental tumor, including hyper-methylation and insulator defects. This PDX model is highly sensitive to FGF receptor (FGFR) inhibitor, and more so to combined FGFR and KIT inhibition, validating the functional significance of the underlying epigenetic lesions. Our study reveals how epigenetic alterations can drive oncogenic programs in the absence of canonical kinase mutations, with implications for mechanistic targeting of aberrant pathways in cancers.

overall_design:
RNA-seq, CTCF occupancy characterization, histone H3K27 acetylation profiling and DNA bisulfite sequencing in GIST patient specimens, xenograft and the GIST-T1 cell line + Hi-C and CTCF HiChIP in GIST T1 line.

Due to patient privacy concerns, raw data is available through dbGaP, accession phs001906.

first: William

last: Flavahan

first: Bradley

last: Bernstein


title: Root Meristem Growth Factor 1 (RGF1) controls root meristem size through reactive oxygen species (ROS) signaling

city: Durham

first: Philip

middle: Norman

last: Benfey

state: NC

address: Science Drive, Biology Department, Box 90338

institute: Duke University & HHMI

summary:
Purpose: Although five receptors of RGF1 have recently been identified, the downstream signaling mechanism remains unknown. The goal of this study is to elucidate signaling events following RGF1 action.
Methods: mRNA profiles of the root meristematic zone from Arabidopsis seedlings with or without RGF1 treatment were generated by deep sequencing, in triplicate. The sequence reads were analyzed using Tophat and DESeq2. The mutants of selected differentially expressed genes were generated for phenotyping.
Results: Our study uncovered a series of signaling events following RGF1 action. The RGF1-receptor pathway controls distribution of reactive oxygen species (ROS) along the developmental zones of the Arabidopsis root. We identify a novel transcription factor, RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), which plays a central role in mediating RGF1 signaling. Manipulating RITF1 expression leads to redistribution of ROS along the root developmental zones. Changes in ROS distribution, in turn, enhance the stability of the PLETHORA2 (PLT2) protein, a master regulator of root stem cells.
Conclusions: Our study clearly depicts a signaling cascade initiated by RGF1 and links the RGF1 peptide to ROS regulatory mechanisms.

first: Masashi

last: Yamada

first: Xinwei

last: Han


title: Gastric organoid single-cell RNA-seq


title: Cell type transcriptomic profile of the Arabidopsis root stem cell niche

summary: We used fluorescence activated cell sorting (FACS) to isolate the different cell populations in the Arabidopsis root stem cell niche

overall_design: GFP marker lines were grown for 5 days. Roots were protoplasted and cells were collected using FACS. RNA was extracted from cells and sequenced. 3 or 4 biological replicates were collected for each stem cell population.

first: Adam

last: Fisher

first: Maria

last: de Luis Balaguer


title: In vitro FRC-conditioned, IL6-conditioned or control (anti-CD3/CD28)-stimulated CD8+ T cells

status: Public on Oct 14 2019

city: Charlestown

first: Debattama

last: Sen

department: Cancer Center

institute: MGH/Harvard


title: Transcriptome profiling of lung tissue from influenza-infected mice treated with plasma gelsolin

first: Lester

last: Kobzik

address: 665 Huntington Ave

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

summary: Recombinant human plasma gelsolin (rhu-pGSN) improves survival and reduces morbidity of mice infected with influenza. The goal of this study was to investigate the transcriptome profile of lung tissue from infected mice, treated with either rhu-pGSN or vehicle.

overall_design: Mice were infected intranasally with H1N1 (A/Puerto Rico/8/1934) and treated by subcutaneous injections with rhu-pGSN or vehicle daily starting on day 7 after infection. Lung tissue was harvested on days 7 and 9 for RNA analysis.


title: Deletion of intestinal Hdac3 remodels the lipidome of enterocytes and protects mice from diet-induced obesity

status: Public on Oct 12 2019

city: Heidelberg

first: John

last: Mariadason

state: Victoria

address: Austin Health, 145 Studyley Road

department: Gastrointestinal Cancers

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: Histone deacetylase 3 (Hdac3) regulates the expression of lipid metabolism genes in multiple tissues, however its role in regulating lipid metabolism in the intestinal epithelium is unknown. Here we demonstrate that intestine-specific deletion of Hdac3 (Hdac3IKO) protects mice from diet induced obesity. Intestinal epithelial cells (IECs) from Hdac3IKO mice display co-ordinate induction of genes and proteins involved in mitochondrial and peroxisomal b-oxidation, have an increased rate of fatty acid oxidation, and undergo marked remodelling of their lipidome, particularly a reduction in long chain triglycerides. Many HDAC3-regulated fatty oxidation genes are transcriptional targets of the PPAR family of nuclear receptors, Hdac3 deletion enhances their induction by PPAR-agonists, and pharmacological HDAC3 inhibition induces their expression in enterocytes. These findings establish a central role for HDAC3 in co-ordinating PPAR-regulated lipid oxidation in the intestinal epithelium, and identify intestinal HDAC3 as a potential therapeutic target for preventing obesity and related diseases.

overall_design: Intestinal epithelial cells (IECs) were isolated from the entire small intestine from Hdac3IKO and Hdac3WT mice by incubation of the small intestine in 15 mM EDTA for 15 minutes. For samples to be used for gene expression analysis, the buffer was supplemented with RNA secure (ThermoFisher Scientific, Waltham MA, USA).

first: Mercedes

last: Dávalos-Salas

first: Sheren

last: Al-Obaidi


title: ATAC-seq profiling of in vitro FRC-conditioned, IL6-conditioned or control (anti-CD3/CD28)-stimulated CD8+ T cells

summary: To broadly assess which pathways FRCs regulate in CD8+ T cells, we sorted CD8+ T cells for ATAC-seq following activation in whole splenocyte mixtures via soluble anti-CD3/CD28 (0.25μg/ml) for 48 hours (Stim), activated with anti-CD3/CD28 in the presence of Nos2–/– FRCs (FRC) or activated with anti-CD3/CD28 plus 100 ng/ml recombinant IL-6 (IL-6). Here we demonstrate that FRC-derived signals, including IL-6, act in concert with TCR signaling and co-stimulation to remodel chromatin and render essential transcription factor binding motifs accessible in activated CD8+ T cells. Signals from FRCs led to increased binding regions for MYC, HIF-1α and HIF-1β, which are known to promote metabolic pathways following T cell activation. Additionally, FRC-derived signals promoted activity of transcription factors that regulate survival and memory programs in T lymphocytes such as BATF and BACH2.

overall_design: CD8+ T cells were sorted for ATAC-seq following activation in whole splenocyte mixtures via soluble anti-CD3/CD28 for 48 hours (Stim), activated with anti-CD3/CD28 in the presence of Nos2–/– FRCs  (FRC) or activated with anti-CD3/CD28 plus 100 ng/ml recombinant IL-6 (IL-6). Three biological replicates were used for each condition.

first: Flavian

last: Brown


title: RNA-seq profiling of in vitro FRC-conditioned, IL6-conditioned or control (anti-CD3/CD28)-stimulated CD8+ T cells

summary: To broadly assess which pathways FRCs regulate in CD8+ T cells, we sorted CD8+ T cells for RNA-seq following activation in whole splenocyte mixtures via soluble anti-CD3/CD28 for 48 hours (Stim), activated with anti-CD3/CD28 in the presence of Nos2–/– FRCs  (FRC) or activated with anti-CD3/CD28 plus 100 ng/ml recombinant IL-6 (IL-6). Here we demonstrate that FRC-derived signals, including IL-6, act in concert with TCR signaling and co-stimulation to promote the expression of MYC and HIF-1-dependent glycolytic genes and vital pro-survival genes (encoding BCL-2 family members, inhibitors of apoptosis [IAPs] members and Cflar) in activated CD8+ T cells.

overall_design: CD8+ T cells were sorted for RNA-seq following activation in whole splenocyte mixtures via soluble anti-CD3/CD28 for 48 hours (Stim), activated with anti-CD3/CD28 in the presence of Nos2–/– FRCs  (FRC) or activated with anti-CD3/CD28 plus 100 ng/ml recombinant IL-6 (IL-6). The following number of biological replicates were used for each condition: Stim (2), FRC (3), IL-6 (2)


title: A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

status: Public on Oct 11 2019

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Specific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the α-globin enhancers are distributed between multiple promoters in a mouse model in which the α-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non- membrane bound nuclear compartments.

overall_design: Tri-C is a 3C-based technique that can analyze multi-way interactions. It combines 3C library preparation (NlaIII restriction enzyme) with oligonucleotide capture enrichment for viewpoints of interest and the fragments they interact with. The capture step has been optimized to capture two or more interacting fragments with high efficiency. We have used this to analyze the 3D structure of the active mouse alpha globin locus in primary erythroid cells.

first: A

first: Jim

last: Hughes


title: Time course of the Arabidopsis root stem cells

first: Natalie

last: Clark

country: USA

summary:
The goal of this dataset was to transcriptionally profile the Arabidopsis root stem cells over developmental time.
To accomplish this, we protoplasted roots expressing PET111:GFP every 8 hours from 4 days to 6 days old. We then collected GFP negative cells from the PET111:GFP line using cell sorting, as these cells represent the stem cell population. RNA was extracted from cells, libraries were prepared, and RNA-seq was performed. FPKM values were calulcated using Cufflinks.

overall_design: Arabidopsis roots expressing PET111:GFP were protoplasted every 8 hours from 4 days to 6 days post-stratification. GFP-negative cells were collected, RNA was extracted, and RNA-seq was performed.

first: Rosangela

last: Sozzani


title: Edematous Severe Acute Malnutrition is Characterized by Hypomethylation of DNA

city: Houston

first: Neil

middle: A.

last: Hanchard

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: A slower transmethylation of one-carbon substrates in the edematous form of severe acute malnutrition (ESAM) suggests that downstream aberrations in DNA methylation could drive differences in acute pathogenesis between ESAM and non-edematous malnutrition (NESAM). Here, we integrate genome-wide assessments of DNA methylation with corresponding gene expression profiles and sequence variation to show that relative to NESAM, acute ESAM is characterized by significant hypomethylation at 99% of differentially methylated loci in two SAM cohorts, whereas recovered adults show no significant differences in methylation. Hypomethylated loci correlate with both up- and down-regulation of proximal genes, which are associated with the clinical sub-phenotypes of kwashiorkor and enriched for GWAS hits linked to over-nutrition, including fatty liver and diabetes. Methylation at these loci also appears to be influenced by nearby genetic variation in a manner that varies with nutritional status. Our findings implicate epigenetic and genetic variation in ESAM pathophysiology and support methyl-group supplementation in ESAM management.

overall_design: DNA obtained from buccal epithelial cells of 309 children with severe acute malnutrition and 65 adults with a history of severe acute malnutrition, who have since recovered, was bisulfite converted and hybridized to the Illumina Infinium HumanMethylation450K BeadChip array. We then compared genome-wide methylation between 164 acutely ill children with edematous malnutrion (ESAM) to that of 145 children with non-edematous malnutrition (NESAM) to identify epigenetic differences between the two manifestations of severe acute malnutrition. Of these acutely ill children, 109 were Jamaican (ESAM n=61, NESAM n=48) and 200 were Malawian (ESAM n=103, NESAM=97). Genome-wide methylation comparison was repeated between recovered adults from Jamaica, of which 31 had a history of ESAM and 34 of NESAM.

first: Katharina

middle: V

last: Schulze

first: Shanker

last: Swaminathan

first: Sharon

last: Howell

first: Aarti

last: Jajoo

first: Natasha

middle: C

last: Lie

first: Orgen

first: Roa

last: Sadat

first: Nancy

last: Hall

first: Liang

last: Zhao

first: Kwesi

last: Marshall

first: Thaddeus

last: May

first: Marvin

middle: E

last: Reid

first: Carolyn

last: Taylor-Bryan

first: Xueqing

last: Wang

last: Belmont

first: Yongtao

last: Guan

first: Mark

middle: J

last: Manary

first: Indi

last: Trehan

first: Colin

last: McKenzie


title: Genomic analysis of a subterrestrial nematode, Halicephalobus mephisto

status: Public on Oct 09 2019

city: Washington

first: John

middle: Russell

last: Bracht

state: DC

address: 4400 Massachusetts Ave NW

institute: American University

summary: Gene annotation and expression analysis

overall_design: RNA-seq was performed on 25 degree C (n=3 replicates), 38 degree C (n=3 replicates), and 40 degree C samples (n=6 replicates)

middle: R


title: Drosophila, which Lacks Canonical Transcription-Coupled Repair Proteins, Performs Transcription-Coupled Repair

city: Chapel Hill

first: Yanyan

last: Yang

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

type:
Other
Third-party reanalysis

summary: Previous work with the classic T4 Endonuclease V digestion of irradiated Drosophila DNA followed by Southern hybridization led to the conclusion that Drosophila lacked transcription-coupled repair (TCR). This conclusion was reinforced by the Drosophila Genome Project which revealed that Drosophila lacked CSA, CSB, or UVSSA homologs, whose orthologs are present in eukaryotes that carry out TCR ranging from Arabidopsis to humans.  A recently developed in vivo excision assay and the Excision Repair-sequencing (XR-seq) method have enabled genome-wide analysis of nucleotide excision repair in various organisms at single nucleotide resolution and strand-specific manner. Using these methods, we have discovered that Drosophila S2 cells carry out robust TCR comparable to that observed in mammalian cells.  Our findings provide new insights into the mechanisms of TCR among various species.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
We apply XR-seq in S2-DGRC , the cells were obtained from the Drosophila Genetic Resources Center. For UV treatments, cells were inoculated into R-150 plates and grown to about 25 to 80 percent confluence.  Media was gently removed from the semi-adherent monolayer, cells were irradiated with UV-C, and then fresh media containing sterilized, conditioned media was added to cells, and cells were incubated at 27 degrees.  Following predetermined repair times, plates were placed on ice and cooled cells were harvested by scraping and rinsing with ice-cold PBS. Cells were pelleted, transferred to Eppendorf tubes, washed with cold PBS, and resuspended in 340 ul of cold TE.  samples were immunoprecipitated with anti-CPD antibody, and then ligated to adapters and processed for sequencing (XR-seq).
This series includes re-analysis of XR-seq of UV-treated normal human fibroblast cells and Cockayne syndrome cells.  GSE76391: GSM1985849  GSM1985850 GSM1985851 GSM1985852 GSM1985853 GSM1985854; GSE67941:GSM1659164 GSM1659165

first: Nazlı

last: Deger

first: Laura

last: Lindsey-Boltz

first: Aziz

last: Sancar

first: Christopher

last: Selby


title: Heterozygous deletion of the SHOX gene enhancer in two females with clinical heterogeneity associating with skewed XCI and escaping XCI

status: Public on Oct 08 2019

city: hangzhou

first: yixi

last: sun

state: zhejiang

address: XUESHI ROAD 1

institute: Zhejiang University

summary: Skewed X-chromosome inactivation (XCI) plays an important role in the phenotypic heterogeneity of X-linked disorders. However, the role of skewed XCI in XCI–escaping gene SHOX regulation is unclear. Here, we focused on a heterozygous deletion of SHOX gene enhancer with clinical heterogeneity. Using SNP array, we detected that the female proband with Leri-Weill dyschondrosteosis (LWD) carried an 857 kb deletion on Xp22.3 (encompassing SHOX enhancer) and a 5,707 kb large-fragment deletion on Xq25q26. XCI analysis revealed that the X-chromosome with the Xq25q26 large-fragment deletion was completely inactivated, which forced the complete activation of the other X-chromosome carrying SHOX enhancer deletion. While the Xp22.3 deletion locates on the escaping XCI region, under the combined action of skewed XCI and escaping XCI, transcription of SHOX gene was mainly from the activated X-chromosome with SHOX enhancer defect, involving in the formation of LWD phenotype. Interestingly, this SHOX enhancer deletion was inherited from her healthy mother, who also demonstrated completely skewed XCI. However, the X-chromosome with SHOX enhancer deletion was inactivated, and the normal X-chromosome was activated. Combing with escaping XCI, her phenotype was almost normal. In summary, this study was a rare report of SHOX gene enhancer deletion in a family with clinical heterogeneity due to skewed inactivation of different X-chromosomes, which can help in the genetic counseling and prenatal diagnosis of disorders in females with SHOX defect.

overall_design: Karyotyping and SNP array were performed and showed the presence of an 857kb deletion in Xp22.33 (chrX:784,064-1,640,746) in the male fetus III1. To verify the results, SNP array was also performed on samples of the pregnant woman II2 and her husband II1. Surprisingly, not only a deletion of 857 kb in Xp22.33, but also a 5,707 kb deletion (chrX:127,915,006-133,621,667) in Xq25q26.3 was observed in the woman

first: Yixi

last: Sun

first: Minyue

last: Dong


title: Gene expression in protoapothecia from Ascodesmis nigricans

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

summary: The aim of this analysis was to analyze gene expression in young fruiting bodies (protoapothecia) of the filamentous ascomycete Ascodesmis nigricans. Young fruiting bodies were isolated by laser microdissection, RNA was extracted, amplified and used for RNA-sequencing. The resulting data were compared to data from total vegetative and sexual mycelium.

overall_design: Two independent biological replicates were performed and sequenced.

first: Stefanie

last: Poeggeler


title: High-resolution custom array spanning Xq22 region to study patients carrying PLP1 copy number gain

first: Vahid

last: Bahrambeigi

state: Texas

address: 1 Baylor Plaza

department: Human Molecular Genetics

institute: Baylor College Of Medicine

type: Genome variation profiling by genome tiling array

summary: We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array and breakpoint junction sequence analysis. Analysis of these data enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array and breakpoint junction sequence analysis.

overall_design: The goal of this experiment was to determine the size, genomic extent and gene content of each Xq22 rearrangement.

first: James

last: Lupski

first: Grace

last: Hobson


title: Long noncoding RNA LINC01111 suppresses pancreatic cancer aggressiveness by regulating DUSP1 expression via microRNA-3924

status: Public on Oct 05 2019

city: Wuhan

first: Pan

last: Shutao

state: State...

address: Wuhan, Hubei Province, China

institute: Tongji Hospital

summary: Dysfunction in long noncoding RNAs (lncRNAs) is reported to participate in the initiation and progression of human cancer; however, the biological functions and molecular mechanisms through which lncRNAs affect pancreatic cancer (PC) are largely unknown. Here, we report a novel lncRNA, LINC01111, that is clearly downregulated in PC tissues and plasma of PC patients and acts as a tumor suppressor. We found that the LINC01111 level was negatively correlated with the TNM stage but positively correlated with the survival of PC patients. The overexpression of LINC01111 significantly inhibited cell proliferation, the cell cycle, and cell invasion and migration in vitro, as well as tumorigenesis and metastasis in vivo. Conversely, the knockdown of LINC01111 enhanced cell proliferation, the cell cycle, and cell invasion and migration in vitro, as well as tumorigenesis and metastasis in vivo. Furthermore, we found that high expression levels of LINC01111 upregulated DUSP1 levels by sequestering miR-3924, resulting in the blockage of SAPK phosphorylation and the inactivation of the SAPK/JNK signaling pathway in PC cells and thus inhibiting PC aggressiveness. Overall, these data reveal that LINC01111 is a potential diagnostic biomarker for PC patients, and the newly identified LINC01111/miR-3924/DUSP1 axis can modulate PC initiation and development.

overall_design: There are six RNA samples from pancreatic cancer cell line used for analysis, three as control (NC1, NC2, NC3) and three as LINC01111-upregulated (UP1, UP2, UP3).

first: Shutao

last: Pan

first: Ming

last: Shen

first: Min

last: Zhou

first: Xiuhui

last: Shi

first: Ruizhi

last: He

first: Taoyuan

last: Yin

last: Wang

first: Xingjun

last: Guo

first: Renyi

last: Qin


title: AUF-1 affected genes in human skin cells

status: Public on Oct 10 2019

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

institute: Jiangsu Jiangyin People's Hospital

summary:
This study aims to evaluate the effect of AUF-1 knokdown on the function and global gene expression in human skin cells. Cells with AUF1 silencing were compared with control cells by RNA-Seq.
Cell senescence is a tightly controlled, programmed process. Although the mechanism of cell senescence is unclear, the concept that cell aging is an interaction results  between enviomental and genetic factors has been accepted. Changes in the expression of related genes are the genetic basis of cell senescence. AUF1 gene has been proved that can recognize classical mRNA and regulated its expression level. These classical mRNA include those encoding cecle-regulating proteins, apoptotic regulators, cytokines and proto-oncogenes. Our study use overexpression and interference lentivirus of AUF1 to  transfect WS1 cell to process cell transcriptome sequencing. Through the Bioinformatics analysis results, we want to see some different expressed genes related to cell cecle, cell apoptosis and so on. Our study can provide basis research to further expound AUF1 gene, play an important role of aging mechanism.

overall_design: Overexpression vectors and interference vectors were constructed and transfected into WS1 cells respectively. After 48h culture, second-generation sequencing was arranged

first: S

last: Zhang


title: Transcriptomics and chromatin accessibility analysis of MLL-AF9 early responses in mouse bone marrow cells

city: New Haven

first: Shangqin

state: CT

address: 10 Amistad St

department: Cell Biology

institute: Yale University

summary: We investigated early changes of gene expressions and chromatin accessibilities in hematopoietic stem and progenitor cells (HSPCs) in response to MLL-AF9 oncogene expressions. Using RNA-Seq and ATAC-Seq, we analyzed HSPCs briefly exposed to MLL-AF9 for one or two days. Such analysis addressed the initial changes during malignant transformation, and provided insights into the primary functions of MLL-AF9 oncogene.

overall_design: Early cellular responses to MLL-AF9 oncogene expression were determined using RNA-Seq and ATAC-Seq of HSPCs exposed to MLL-AF9 for one or two days. Freshly isolated HSPCs and HSPCs cultured without MLL-AF9 expression were used as controls, in duplicates.

first: Xinyue

last: Chen

first: Daniel

last: Burkhardt


title: DNA copy number alteration analysis of radioresistant and radiosensitive prostate cancer cell lines

city: Dresden

first: Michael

last: Seifert

address: Fetscherstr. 74

institute: TU Dresden

summary: Prostate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection. Radioresistant (RR) sublines were generated form these original parental radiosensitive (RS) cell lines. aCGH profiles of radiosensitive (RS) and radioresistant (RR) prostate cancer cell lines were measured and compared to normal DNA.

overall_design: One aCGH experiment was performed for each cell line.

first: Anna

last: Dubrovska

first: Claudia

last: Peitzsch

first: Vasyl

last: Lukiyanchuk

first: Klink

last: Barbara


title: MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [GRO-Seq]

status: Public on Oct 03 2019

city: Guangzhou

first: Jiajian

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

summary: Evidence of widespread transcription at active enhancers became apparent. However, our understanding about the functions of enhancer RNAs (eRNAs) and their mechanistic roles remains incomplete. Here, we study eRNA regulation and function using skeletal myoblast differentiation as a paradigm. We provide a panoramic view of enhancer transcription and uncover reprogramming in enhancer transcription occurring during myogenic differentiation. We demonstrate the critical role of MyoD in activating eRNAs production. Results from in depth dissection of two eRNAs transcribed from super enhancers (seRNA-1 and -2) suggest that seRNAs can promote myogenic differentiation in vitro and in vivo; the induction of the seRNAs is in coordination with the activation of the neighboring genes and seRNA loss largely impairs their expression. Mechanistically, we elucidate these seRNAs specifically bind to heterogeneous nuclear ribonucleoprotein L (hnRNPL) and modulate hnRNPL binding to the target promoter. A CAAA tract on the seRNA was identified to be essential in mediating the interaction between seRNA-1 and hnRNPL. Disruption of seRNA-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the target genes, in coincidence with the reduction of their expression. Furthermore, analyses of hnRNPL binding transcriptome-wide reveals its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction contributes to target mRNA activation.

overall_design: 2 RNA-seq, 1 hnRNPL CLIP-seq, 8 GRO-seq experiments performed.

first: Huating

first: Hao

last: Sun

first: Yu

last: Zhao

first: Liangqiang

first: Kun

first: Xiaona

first: Yuying

last: Li


title: MyoD induced enhancer RNA interacts with hnRNPL protein via CAAA motif to activate target gene transcription during myogenic differentiation [RNA-Seq]

last: Zhou

last: He