title: RealTime quantitative PCR of cardiac at risk area samples obtained from a mouse model of ischemia and reperfusion injury

status: Public on Jul 07 2019

city: San Donato Milanese

first: Marco

last: Piccoli

address: piazza Malan 1

institute: IRCCS Policlinico San Donato

summary: Mice were exposed to cardiac ischemia/reperfusion injury and sacrificed after 1 or 4 days. Hearts were stained with Evans blu/TTC to isolate the at risk area. Hearts were divided into 1mm slices, the at risk area of any slice were pooled together before RNA extraction. Mice were divided into 3 different groups: Sham animals have been subjected to the surgical procedure without the induction of the ischemia and reperfusion injury and represent the control animals; LAD group is represented by animals subjected to the surgical procedure and the induction of the ischemia and reperfusion imjury; MLAD group is represented by animals subjected to the surgical procedure and the induction of the ischemia and reperfusion injury, followed by myriocin treatment (SLN/Myr) at the beginning of reperfusion.

overall_design: qPCR gene expression profiling. Samples were obtained from 5 to 7 animals per group (Sham; LAD; MLAD). For any given target gene, the average expression value of all the sham animals has been compared to the expression value of each animal from LAD and MLAD group to calculate their relative expression levels. Statistical analyses were performed comparing: LAD vs Sham; MLAD vs Sham; LAD vs MLAD at both time points of reperfusion.

first: Fabiola

last: Bonezzi

first: Paola

last: Signorelli


title: Transcriptomic analysis of PHHs isolated from hCLiP-transplanted mouse chimeric liver

status: Public on Jul 04 2019

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

country: USA

institute: University of Pennsylvania

summary: Transcriptome of PHHs isolated from hCLiP-transplanted mouse chimeric liver was compared with those of cryopreserved PHHs.

overall_design: hCLiPs at passage 0 (FCL and DUX) or passage 1 (JFC) were transplanted to cDNA-uPA/SCID mice, and repoulation was performed for 11 weeks. Then, repopulated human hepatocytes were isolated by two-step collagenase perfusion followed by mouse cell depletion via MACS.

first: Takahiro

last: Ochiya


title: Hepatic induction of hCLiPs

summary: hCLiPs at passage 1 were induced into mature hepatocytes, and transcritptome was analyzed in comparison with PHHs.

overall_design: Transcriptome of hCLiPs before hepatic induction or those cultured with or without hepatic inducing factors for 8 days were compared with primary cultured human hepatocytes.


title: Ef-cd locus shortens rice maturity duration without yield penalty

status: Public on Jul 03 2019

city: Shanghai

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: The contradiction between ‘high-yielding’ and ‘early-maturing’ hampers further improvement on annual rice yield. Here we reported the positional cloning of a major maturity duration-regulatory gene, Early flowering-completely dominant (Ef-cd), and demonstrated that natural variation in Ef-cd could be used to overcome the above contradictory. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition. Field test comparisons of early-maturing Ef-cd near-isogenic lines (NILs) with their wild types as well as the derivative early-maturing hybrids with their wild-type hybrids conducted under different latitudes determined that early-maturing Ef-cd allele shortens maturity duration (ranging from 7 to 20 days) without a concomitant yield penalty. Ef-cd facilitates nitrogen utilization and also improves the photosynthesis rate. Analysis of 1,439 elite hybrid rice varieties revealed that the 16 homozygotes and 299 heterozygotes possessing Ef-cd matured significantly earlier. Therefore, Ef-cd could be a vital contributor of elite early-maturing hybrid varieties in balancing grain yield with maturity duration.

overall_design: Total RNA was extracted from the fresh leaf blades of 40 d seedling of early-maturing NIL D248 (BC5F11) and its recurrent parent SH881 (Shuhui881) using TRIzol reagent (Invitrogen, USA). 2 biological replications were collected.

first: Jun

last: Fang

first: Fantao

last: Zhang

first: Xiaojian

last: Deng

first: Chengcai

last: Chu


title: Reprogramming of primary human hepatocytes (PHHs) into hCLiPs

summary: PHHs were cultured in the presence of small molecules and converted to proliferative progenitor cells named human chemcically induced progenitors (hCLiPs).

overall_design: PHHs were reprogrammed into hCLiPs by culturing them with FBS and two small molecules A83-01 and CHIR99021 (termed AC). PHHs cultured with FBS in the absence of AC were used as control.


title: Gene expression data from IMR90 control, IMR90 shRRM2 and shRRM2/shp16

status: Public on Jul 02 2019

city: Hershey

first: Raquel

last: Buj

address: 500 University Drive

department: Physiology

institute: Penn State College of Medicine

summary: Transformed and tumorigenic cells require increased deoxyribonucleotide synthesis to fuel the genome replication that sustains their unregulated cell cycle and proliferation. Therefore, it is likely that the cell cycle and nucleotide metabolism are linked. The cell cycle inhibitor p16 is a critical tumor suppressor that is lost as an early event in many human cancers. While loss of p16 is known to play a role in deregulating the cell cycle, whether loss of p16 expression affects nucleotide metabolism is unknown.

overall_design: mRNA profiles of IMR90 control, dNTP depletion-induced senesnce (shRRM2) and dNTP depletion-induced senescence bypass (shRRM2/shp16)  were generated by deep sequencing, in triplicate, using  HiSeq 2500 sequencer (Illumina)

first: Chi-Wei

first: Erika

middle: S

last: Dahl

first: Kelly

middle: E

last: Leon

first: Ross

last: Kuskovsky

first: Natella

last: Maglakelidze

first: Lydia

last: Kutzler

first: Holly

last: Lacko

first: Yiling

last: Lu

first: Mils

middle: B

last: Gordan

first: Raghavendra

last: Gowda

first: Gavin

middle: P

last: Robertson

first: Joshua

middle: I

last: Warrick

first: Meenhard

last: Herlyn

first: Yuka

last: Imamura

first: Scot

middle: R

last: Kimball

first: David

middle: J

last: DeGraff

first: Nathaniel

middle: W

last: Snyder

first: Katherine

middle: M

last: Aird


title: Ectopic CTCFL/BORIS expression in ovarian cancer precursor cells enhances cellular motility and invasion through GALNT14 and alters CTCF chromatin occupancy

status: Public on Jul 01 2019

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: High-grade serous carcinoma (HGSC) is the most aggressive and predominant form of epithelial ovarian cancer and the leading cause of gynecological cancer death. We have previously shown that CTCFL (also known as BORIS, Brother of the Regulator of Imprinted Sites) is expressed in a large proportion of ovarian cancers, which is associated with global and promoter-specific DNA hypomethylation, advanced tumor stage, and poor prognosis. To explore its functional role in HGSC, we expressed BORIS in human fallopian tube secretory epithelial cells (FTSEC), the presumptive cell of origin for HGSC. BORIS-expressing cells exhibited increased motility and invasion, and BORIS expression was associated with alterations in several cancer-associated gene expression networks, including fatty acid metabolism, TNF signaling, cell migration, and ECM-receptor interactions. Importantly, GALNT14, a glycosyltransferase gene previously implicated in cancer cell migration and invasion, was highly induced by BORIS, and GALNT14 knockdown significantly abrogated BORIS-induced cell motility and invasion.  In addition, in silico analyses provided evidence for BORIS and GALNT14 co-expression in several human cancers.  Finally, ChIP-seq demonstrated that expression of BORIS in FTSEC cells was associated with de novo and enhanced binding of CTCF at hundreds of loci, many of which correlated with activation of transcription at target genes, including GALNT14. Taken together, our data indicate that BORIS may promote cell motility and invasion in HGSC via upregulation of GALNT14, and suggests BORIS as a potential therapeutic target in this malignancy.

overall_design:
Genome-wide mapping of CTCF and BORIS occupancy in FT282 cells ectopically expressed either EV (Empty Vector) or BORIS.
Expression profiling by high throughput sequencing (RNA-seq) of FT282 cells ectopically expressed either EV (Empty Vector) or BORIS.

first: Joanna

middle: C

last: Hillman

first: Michael

last: Higgins


title: Characterization of long term-cultured of hCLiPs

first: Takeshi

last: Katsuda

summary: hCLiPs generated from 2 lots of PHHs (FCL and DUX) were characterized at various time points until passage 10.

overall_design: Transcriptome analysis was performed using hCLiPs at P0, P3, P5, P7 and P10

first: Takahiro

last: Ochiya


title: Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted multiple genome-scale CRISPR screens for essential CTCF loop anchors in the human K562 erythroid cell line. Surprisingly, the primary drivers of apparent ``hits'' in this screen were single guide RNAs (sgRNAs) with low sequence specificity. After removing these confounders, we found that no CTCF loop anchors among the ones we screened are essential for cell growth in culture. We also observed analogous effects in independent non-coding screens densely tiling regulatory elements and genomic neighborhoods near previously known essential genes. Strikingly, we found that low-specificity guides also result in strong confounding growth effects in screens employing epigenetic perturbations that do not cause DNA damage, such as CRISPRi and CRISPRa. Remarkably, the set of confounded guides is distinct for each perturbation mode. Promisingly, strict filtering of CRISPRi libraries using GuideScan-aggregate specificity scores removed these confounded sgRNAs and allowed for the identification of essential enhancers, which we validated extensively. Our stduy presents the first genome-scale functional characterization of CTCF binding sites in the human genome, while also identifying the limitations on and outlining the future prospects for the detailed functional dissection of regulatory elements in the genome using Cas9.

overall_design: This series contains dataset of several different types: 1) pooled CRISPR screens of non-coding genomic elements (tiling screens, screens targeting CTCF loop anchor sites, "fine-mapping" screens for insulator and enhancer elements) in the K562 cell line and 2) ATAC-seq, RNA-seq, ChIP-seq experiments examining the changes in gene expression, chromatin accessibility, and protein occupancy in a set of validation cell lines generated using individual sgRNAs)

first: Josh

last: Tycko

last: Wainberg

middle: K

first: Oana

last: Ursu

first: Gaelen

middle: T

last: Hess

first: William

last: Greenleaf

first: Anshul

last: Kundaje

last: Bassik


title: The transcription factor Deaf-1 modulates Engrailed-1 expression to regulate the specification of skin appendage fate

first: Yana

last: Kamberov

address: Curie bvld

institute: University of Pennsylvannia

summary: The goal of this study was to search for Deaf1 enrichment regions in the En1 locus. Thus we were able to confirm predicted Deaf1 DNA binding sites upstream of the ORF of En1 and to discover new Deaf1 enrichment region in the putative En1 TAD

overall_design: We perform ChIP-seq using an existing human keratinocytes cellular line (GMA24A1F), that expressed En1 and Deaf1 endogenously

first: Daniel

last: Aldea


title: Notch signaling controls periodontal ligament maturation through regulating Lamin A

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Tooth eruption is a continuous biological proces with dynamic changes at cellular and tissue levels particularly within the periodontal ligament (PDL). Occlusion completion is a significant physiological landmark of dentintion establishment. However the implication and molecular networks engaging in of this event on the the final  PDL maturation are still largely unknown. In this study, using rat and mouse molar teeth and transgenic approaches, as well as a human PDL cell line by combining RNAseq and proteomic analysis systematically, we screened the key molecular links in regulating PDL maturation before and after occlusion establishiment. We discovered Notch, a key molecular pathway in regulating stem cell fate and differentiation, is a major player in the event. Intercepting Notch pathway by deleting its key canonical transtripitonal factor: RBP-Jkappa using conditional knocking out strategy in the mice delayed PDL maturation. We also identified that  Lamin A, a cell nuclear lamina member, is one unique marker of PDL maturation and its expression is under the control of Notch signalling. Our study therefore provides a deep insight of how PDL maturation is regulated molecularly and we expect the outcomes to be applied to better understand the molecular regulation networks and physiological conditions such as tooth eruption and movement, and also for periodontal diseases.

overall_design: Comparison of PDL expression upon occlusal contact establishment (occurs between P18 and P28).

first: Balazs

last: Denes

first: Chloe

last: Bolton

first: Charlotte

last: Illsley

first: Wailing

last: Kok

first: Jemma

middle: V

last: Walker

first: Ansgar

last: Poetsch

first: Stavros

last: Kiliaridis

first: Bing

last: Hu


title: Single-cell transcriptomic profiling of the aging mouse brain

city: Cambridge

first: Lee

last: Rubin

state: MA

address: 7 Divinity Ave

institute: Harvard University

summary: The mammalian brain is complex, with multiple cell types performing a variety of diverse functions, but exactly how each cell type is affected in aging remains largely unknown. Here we performed a single-cell transcriptomic analysis of young and old mouse brains. We provide comprehensive datasets of aging-related genes, pathways and ligand–receptor interactions in nearly all brain cell types. Our analysis identified gene signatures that vary in a coordinated manner across cell types and gene sets that are regulated in a cell-type specific manner, even at times in opposite directions. These data reveal that aging, rather than inducing a universal program, drives a distinct transcriptional course in each cell population, and they highlight key molecular processes, including ribosome biogenesis, underlying brain aging. Overall, these large-scale datasets provide a resource for the neuroscience community that will facilitate additional discoveries directed towards understanding and modifying the aging process.

overall_design: Total of 16 mice brains with raw data for 50,212 single cells and processed data for 37,089 single cells

middle: L

first: Methodios

last: Ximerakis

first: Scott

last: Lipnick

first: Joshua

last: Levin


title: Molecular Evaluation of Impacted Reproductive Physiology in Fathead Minnow Testes Provides Mechanistic Insights into Insensitive Munitions Toxicology (IMX-101)

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary:
Abstract —  Previous toxicological investigations of the insensitive munition (IM), 3-nitro-1,2,4-triazol-5-one (NTO), demonstrated histopathological and physiological impacts in mammalian testes.  The implications of these findings for fish was unknown, therefore we investigated the effects of chronic (21 day) exposures to NTO and an NTO-containing IM formulation called IMX-101 (composed of 2,4-dinitroanisole (DNAN), nitroguanidine (NQ), and NTO) in adult male fathead minnows to assess if impacts on testes were conserved.  The NTO exposure caused no significant mortality through the maximum exposure concentration (720 mg/L, measured), however NTO elicited testicular impacts causing significant asynchrony in spermatogenesis and necrosis in secondary spermatocytes at the two highest exposure concentrations (383 mg/L and 720 mg/L) and testicular degeneration at the highest exposure.  Microarray-based transcriptomics analysis identified significant enrichment of steroid metabolism pathways and mTORC-signal control of spermatogonia differentiation in NTO exposures each having logical connections to observed asynchronous spermatogenesis.  Additionally, NTO impaired transcriptional expression for genes supporting sperm structural and flagellar development including sperm-associated antigen 6 (Spag6).  These functional transcriptomic responses are logical contributors underlying impacted reproductive physiology in NTO exposures that ultimately lead to reductions in spermatozoa.  In contrast to NTO, the IMX-101 formulation elicited significant mortality at the two highest exposure concentrations of 25.2 and 50.9 mg/L (DNAN nominal + NTO measured + NQ measured).  Unlike NTO and NQ, the DNAN component of the IMX-101 formulation underwent significant transformation in the 21d exposure.  From previous investigations, neither NTO or NQ caused mortality in fish at >1000 mg/L suggesting that mortality in the present study arose from DNAN / DNAN-attributable transformation products.  The 12.6 mg/L IMX-101 exposure caused significant sublethal impacts on testes including sperm necrosis, interstitial fibrosis, and Sertoli-like cell hyperplasia.  Transcriptional profiles for IMX-101 indicated significant enrichment on multiple signaling pathways supporting spermatogenesis, mitosis / meiosis, and flagellar structure, all logically connected to observed sperm necrosis.  Additionally, pronounced transcriptional increases within the PPARα-RXRα pathway, a known DNAN target, has been hypothesized to correspond to Sertoli cell hyperplasia, presumably as a compensatory response to fulfill the nurse-function of Sertoli cells during spermatogenesis.  Overall, the transcriptional results indicated unique molecular responses for NTO and IMX-101.  Regarding chemical hazard, NTO impacted testes and impaired spermatogenesis, but at high exposure concentrations (≥ 192 mg/L), whereas the IMX-101 formulation, elicited mortality and impacts on reproductive physiology likely caused by DNAN and its transformation products present at concentrations well below the NTO-component concentration within the IMX-101 mixture formulation.
see previous row.

overall_design: Two separate microarray assays were conducted within this study.  The two experiments investigated 2 unique chemical exposures in dose-series assays including:  1. NTO and 2. the IMX-101 formulation which contains a mixture of NTO, DNAN and NQ.  This GEO entry represents analysis number 2. IMX-101:   Subchronic (21 day) toxicity tests employing adult male P. promelas were conducted as static renewal assays conducted at 23 °C.  Exposures were performed in 7.6 L glass fish tanks with a test solution volume of 6.0 L following ASTM general guidance.  Partial water renewals were conducted thrice weekly on Mondays, Wednesdays and Fridays by removing and replacing 3.0 L of exposure solution.  Two fish were exposed in each tank to IMX-101 at 0 (control), 6.2, 12.6, 25.2 and 50.9 mg/L (DNAN nominal + NTO measured + NQ measured) where each experimental treatment included 5 replicate tanks.  The reason for using the nominal concentration for IMX-101 is that the measured mean concentration of DNAN and DNAN primary transformation products, 2- and 4-amino-nitroanisole (2A-4NAN and 4A-2NAN), in the in-water and out-water corresponded to only 4% or less of the target concentrations, indicating substantial transformation of the parent compound to unknown yet biologically affective products in the IMX-101 exposure assays.  All fish surviving until the conclusion of the 21d assay were euthanized by immersion in an overdose solution of MS-222 (300 mg/L) for at least 10 minutes after cessation of movement.  After euthanasia, each fish was weighed (g) and then necropsied where one testis was fixed in 10% neutral-buffered formalin for histopathological evaluation and the other fixed for transcriptomics by flash freezing in liquid nitrogen.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).

first: Guilherme

last: Lotufo

first: Thiyagarajah

last: Arunthavarani

first: Natalie

middle: D

last: Barker

first: Qing

last: Ji

first: Karin

last: Marshall

first: Mitchell

last: Wilbanks

first: Pornsawan

last: Chappell


title: High-throughput sequencing of  Pol IV and RDR2 transcripts, and their DCL3-diced products, generated from an M13mp18 (+) strand DNA template

city: Bloomington

first: Craig

middle: S.

last: Pikaard

state: Indiana

address: 915 E. Third Street

department: Department of Biology and Department of Molecular and Cellular Biochemistry

institute: Howard Hughes Medical Institute, Indiana University

summary: In plants, the biogenesis of 24 nt and 23 nt small interfering RNAs (siRNAs) requires NUCLEAR RNA POLYMERASE IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). We show that single-stranded M13 bacteriophage DNA can be used as a template for siRNA synthesis in vitro. Deep sequencing of RNAs produced from the in vitro reactions of Pol IV, RDR2 and DCL3 shows that Pol IV transcribes the DNA into first-strand RNAs which RDR2 then uses as templates to synthesize complementary second strands. These siRNA precursor transcripts made by Pol IV and RDR2 are mostly 30-50 nt. An untemplated 3' terminal nucleotide is a characteristic of RDR2 transcripts. DCL3 dicing of double-stranded precursor RNAs synthesized by Pol IV and RDR2 generates siRNAs that are mostly 24 nt, with a smaller population of 23 nt also produced.

overall_design:
Deep sequencing of siRNA precursors produced by in vitro activities of Pol IV-RDR2, and mature siRNAs produced by DCL3 with a single-stranded M13 bacteriophage DNA template. Briefly, we purified recombinant NUCLEAR RNA POLYMERASE IV (Pol IV) and recombinant RNA-dependent RNA POLYMERASE 2 from Arabidopsis thaliana tissues, and incubated them with single-stranded bacteriophage M13 DNA that serves as a template to synthesize small RNA precursors. These precursors were then processed by recombinant DCL3 proteins that were expressed in Sf9 insect cells to produce small RNAs in vitro. These precursors and small RNAs were subject to high-throughput sequencing. RNAs synthesized by purified recombinant Pol IV from an rdr2 mutant background were served as a control for the deep-sequencing experiment.

Please note that the processed data is clean reads which are mappable to the M13 ssDNA template that we used as a template for in vitro transcription. To investigate the size distributions, sequence preferences/characteristics of small RNA as well as their precursors in this study, the clean reads that are derived from Pol IV RDR2 and DCL3 activities by using a ssDNA template would be important for readers to understand our conclusion. Therefore, read sequences, read sizes and strandedness are provided in the processed datasets.

first: Feng

last: Wang

first: Jasleen

last: Singh

middle: S


title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy

city: La Jolla

first: David

last: Schlaepfer

state: CA

address: 3855 Health Sciences Dr.

department: Moores Cancer Center

institute: UCSD

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

overall_design: Refer to individual Series


title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy [ID8 and ID8-IP / KMF cells]

summary: Gene copy number changes, cancer stem cell (CSC) increases, and platinum chemotherapy resistance contribute to poor prognosis in patients with recurrent high grade serous ovarian cancer (HGSOC). CSC phenotypes involving Wnt-b-catenin and aldehyde dehydrogenase activities, platinum resistance, and tumor initiating frequency are here associated with spontaneous genetic gains, including genes encoding KRAS, MYC and FAK, in a new murine model of ovarian cancer (KMF). Noncanonical FAK signaling was sufficient to sustain human and KMF tumorsphere proliferation, CSC survival, and platinum resistance. Increased FAK tyrosine phosphorylation occurred in HGSOC patient tumors surviving neo-adjuvant platinum and paclitaxel chemotherapy and platinum resistant tumorspheres acquired FAK dependence for growth. Importantly, combining a pharmacologic FAK inhibitor with platinum overcame chemoresistance and triggered apoptosis in vitro and in vivo. Knockout, rescue, genomic and transcriptomic analyses collectively identified more than 400 genes regulated along a FAK/b-catenin/Myc axis impacting stemness and DNA repair in HGSOC, with 66 genes gained in a majority of Cancer Genome Atlas samples. Together, these results support combinatorial testing of FAK inhibitors for the treatment of recurrent ovarian cancer.

overall_design: mRNA profiles of ID8 and ID8-IP / KMF cells were generated in triplicate using an Illumina NovaSeq 6000 Sequencing System

first: Carlos

last: Díaz Osterman

first: Duygu

last: Ozmadenci

first: Elizabeth

middle: G

last: Kleinschmidt

first: Kristin

middle: N

last: Taylor

first: Allison

last: Barrie

first: Shulin

last: Jiang

first: Lisa

last: Bean

first: Florian

last: Sulzmaier

first: Christine

last: Jean

first: Isabelle

last: Tancioni

first: Kristen

last: Anderson

first: Sean

last: Uryu

first: Edward

last: Cordasco

first: Jian

last: Li

first: Xiao

last: Chen

first: Guo

last: Fu

first: Marjaana

last: Ojalill

first: Pekka

last: Rappu

first: Jyrki

last: Heino

first: Adam

last: Mark

first: Guorong

last: Xu

first: Kathleen

last: Fisch

first: Vihren

last: Kolev

last: Weaver

first: Jonathan

last: Pachter

first: Balázs

last: Győrffy

first: Michael

last: McHale

first: Denise

last: Connolly

first: Alfredo

last: Molinolo

first: Dwayne

last: Stupack


title: Particulate radiation-induced gliomas

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Trangenic mice with brain-targeted deletion of one allele of p53 and one allele ot Pten were irradiated with particulate radiation. Radiation induced gliomas were analyzed to identify copy number variations

overall_design: DNA extracted from one non-irradiated, non-tumor bearing mouse brain tissue and tumor tissue from seven mice with radiation-induced gliomas.  Thus, a single DNA extraction from normal mouse brain was produced, labeled with Cy3 and co-hybridized with each of the 7 irradiated samples.

first: Pavlina

last: Todorova

first: Eliot

last: Fletcher-Sananikone

first: Bipasha

last: Mukherjee

first: Rahul

last: Kollipara

first: Vamsidhara

last: Vemireddy

first: Xian

last: Xie

first: Peter

last: Guida

last: Story

first: Kimmo

last: Hatanpaa

first: Amyn

last: Habib

first: Robert

last: Bachoo

last: Hromas

first: John

last: Floyd

first: Sandeep

last: Burma


title: human hepatocytes (PHHs) and human chemcically induced progenitors (hCLiPs) study

first: Takeshi

last: Katsuda


title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy [KMF parental, KMF clone KT13 (FAK-/-), KT13 + GFP-FAK, KT13 + GFP-FAK R454, and KT13 + deltaGSK beta-catenin]

first: David

last: Schlaepfer

overall_design: mRNA profiles of KMF parental, KMF clone KT13 (FAK-/-), KT13 + GFP-FAK, KT13 + GFP-FAK R454, and KT13 + deltaGSK beta-catenin cells were generated in triplicate using an Illumina NovaSeq 6000 Sequencing System

first: Carlos

last: Díaz Osterman

first: Duygu

last: Ozmadenci

first: Elizabeth

last: Kleinschmidt

first: Kristin

last: Taylor

first: Allison

last: Barrie

first: Shulin

last: Jiang

first: Lisa

last: Bean

first: Florian

last: Sulzmaier

first: Christine

last: Jean

first: Isabelle

last: Tancioni

first: Kristen

last: Anderson

first: Sean

last: Uryu

first: Edward

last: Cordasco

first: Jian

last: Li

first: Xiao

last: Chen

first: Guo

last: Fu

first: Marjaana

last: Ojalill

first: Pekka

last: Rappu

first: Jyrki

last: Heino

first: Adam

last: Mark

first: Guorong

last: Xu

first: Kathleen

last: Fisch

first: Vihren

last: Kolev

last: Weaver

first: Jonathan

last: Pachter

first: Balázs

last: Győrffy

first: Michael

last: McHale

first: Denise

last: Connolly

last: Molinolo

last: Stupack


title: mTC and mTN cells

city: Stockholm

first: Martin

last: Bergö

address: Hälsovägen 7C (Neo building)

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute


title: Maternal Vitamin C regulates DNA demethylation and devlopment of the mouse embryonic germline [Cut&Run]

city: San Francisco

first: Stephanie

last: Parker

address: 35 Medical Center Way

institute: UCSF

summary: Maternal Vitamin C is required in vivo for proper DNA demethylation and development of fetal germ cells in a mouse model of Vitamin C deficiency. Withdrawal of Vitamin C from the maternal diet does not affect overall embryonic development but leads to defects in the fetal germline, which persist well after Vitamin C re-supply during late gestation. The transcriptome of germ cells from Vitamin C-deficient embryos is remarkably similar to that of embryos carrying a mutation in Tet1, which is responsible for DNA demethylation and activation of regulators of meiosis. In agreement with these results, Vitamin C deficiency leads to an aberrant DNA methylation profile that includes incomplete demethylation of key regulators of meiosis and transposable elements. These findings reveal that deficiency in Vitamin C during gestation recapitulates a mutation in Tet1 and disrupts germline reprogramming and development. Our work further indicate that the embryonic germline is sensitive to perturbations of the maternal diet, providing a potential intergenerational mechanism for adjusting fecundity to environmental quality.

overall_design: Examination of H3K9me2 genome-wide enrichment in gonadal PGCs or soma from E13.5 female Gulo -/- embryos developed with and without Vitamin C supplementation. 3-5 biological replicates per condition.

first: Michelle

last: Percharde

first: Miguel

last: Ramalho-Santos


title: Long non-coding RNA expression profiling reveals LINC00271 as a prognostic marker in adrenocortical carcinoma

city: Hatfield

first: Floryne

middle: Ottilie

last: Buishand

address: Hawkshead Lane

department: Clinical Science and Service

country: United Kingdom

institute: Royal Veterinary College

summary:
Adrenocortical carcinoma (ACC) is an aggressive malignancy with a low but variable overall survival rate. Even after complete tumor resection, over half of patients develop recurrent disease. Long noncoding RNAs (lncRNAs) have been found to be involved in cancer initiation/progression and as markers of cancer prognosis. The role of lncRNAs in ACC is poorly understood. Thus, in this study we performed lncRNA expression profiling in ACC, adrenocortical adenoma (ACA) and normal adrenal cortex (NAC).  Total RNA was extracted from fresh frozen tissue samples (11 ACA, nine ACC and five NAC samples) with histopathological confirmed diagnosis. ArrayStar Human LncRNA/mRNA Expression Microarray V3.0 was used for transcriptome analysis. Differentially expressed lncRNAs were validated using TaqMan real-time quantitative PCR in a validation cohort including an additional 10 ACCs. The ACC dataset from the Cancer Genome Atlas (TCGA) project was used to evaluate the prognostic utility of lncRNAs found to be differentially expressed in ACC. Survival curves were plotted by Kaplan-Meier analysis, and differences in survival rates were assessed using a log-rank test. P < 0.05 was considered significant. Gene Set Enrichment Analysis (GSEA) was performed to identify lncRNA-associated biological signaling pathways.  Unsupervised hierarchical and heat map clustering showed distinct clustering of ACC samples compared with NAC and ACA samples by lncRNA expression profiles. A total of 874 lncRNAs were differentially expressed between ACC and NAC, including known carcinogenesis-related lncRNAs such as HOTTIP, HOXA11-AS1, CRNDE, LINC00271 and TBXAS1. One thousand seventy-six lncRNAs were differentially expressed between ACC and ACA. LINC00271 was a prognostic marker, with patients with low LINC00271 expression surviving significantly shorter than patients with a high LINC00271 expression. Median survival time (MST) for the low-expression group was 1788 days, whereas the MST was not reached for the high-expression group (P < 0.019). Importantly, low LINC00271 expression was positively associated with WNT signaling, cell cycle, chromosome segregation and tissue morphogenesis pathways.
ACC has a distinct lncRNA expression profile. LINC00271 is a prognostic marker in ACC and is involved in biological pathways commonly dysregulated in ACC.

overall_design: 11 ACA, nine ACC and five NAC samples

middle: O

first: Yi

last: Liu-Chittenden

first: Yu

last: Fan

first: Amit

last: Tirosh

first: Dhaval

last: Patel

first: Daoud

last: Meerzaman

first: Electron

last: Kebebew


title: Maternal Vitamin C regulates DNA demethylation and devlopment of the mouse embryonic germline [soma RNA-seq]

overall_design: Examination of the transcriptional profile of single E13.5 female Gulo -/- embryos developed with and without Vitamin C supplementation. 5 biological replicates per condition.


title: RNAseq of WFU3 mouse prostate epithelial stem cells with knockdown of Map3k7, Chd1, and both

city: Aurora

first: Lauren

last: Jillson

state: Colorado

address: 12801 E 17th Avenue, Room L18-6213, Mail stop 8303

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

summary:
Purpose: The goal of this study is to identify transcriptome-wide changes that occur in a mouse prostate cell line with knockdown of Map3k7(Tak1) and Chd1. We utilize this cell line as a model of an aggressive prostate cancer subtype consisting of loss of both MAP3K7 and CHD1 in human patients. RNAseq comparing shControl, shMap3k7(Tak1), shChd1, and shDouble (both) was used to identify transcriptome changes resulting from loss of these genes of interest in order to identify potential therapeutic vulnerabilites.
Cell line: The generation of the WFU3 cell line has been previously described (Barclay, W.W et al. The Prostate. 2005; PMID:15599944). Breifly, anterior prostate lobes of adult B1/6; 129/SVEV mice were harvested, minced, and extensively digested, and resulting organoids were separated from stromal cells using a Percoll density gradient. These organoids were then plated on rat-tail collagen coated plates in complete growth media, and after 4-5 passages were transferred to uncoated plates. These prostatic epithelial progenitor stem cells are maintained in supplemented 50:50 Dulbecco’s modified Eagle’s medium (DMEM)/Ham’s F-12 medium (F12). Complete media components are described in the Barclay, W.W paper.

overall_design: mRNA profiles of mouse prostatic epithelial cells (WFU3) with shControl, shMap3k7, shChd1, and both (shMap3k7&shChd1) were generated by RNAsequencing and compared to identify differentially expressed genes between the groups.

first: Satoshi

last: Washino

first: James

last: Costello

first: Scott

last: Cramer


title: Methylation Heterogeneity within Human Lung Carcinoids (LCs) Tumors

city: New Brunswick

first: SAURABH

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

type: Methylation profiling by genome tiling array

summary:
DNA CpG methylation profiling of LC patients samples were performed to understand genotype to phenotype corrlelations , novel molecular subtypes and cell of origins
Lung carcinoids (LCs) are rare and slow growing primary lung neoplasms that are understudied.   Here, we performed targeted exome sequencing using a 354-cancer gene panel (n=29), mRNA sequencing (n=30) and DNA methylation assay (n=18) on macro-dissected lung carcinoids. The mutations we identified were enriched for genes involved in covalent histone modification/chromatin remodeling (34.5%) (MEN1, ARID1A, KMT2C and KMT2A were recurrently mutated) as well as DNA repair (17.2%) pathways. Unsupervised clustering and principle component analysis on gene expression and DNA methylation profiles showed 3 robust molecular subtypes (LC1, LC2, LC3) with distinct clinical features.  MEN1 gene mutations were found to be enriched and exclusively in the LC2 subtype (p-value<0.001).  The LC3 subtype is predominately found at endobronchial lung and earlier age of diagnosis. Immunohistochemical staining of two biomarkers, ASCL1 and S100, is sufficient to stratify the three subtypes. This molecular classification of lung carcinoids into three subtypes may help improve treatment decision and clinical management.

overall_design: 18 LCs tumor specimens were obtained from MKSCC and samples were probed for DNA CpG methylation using Illumina Methylation 450K array and processed as per manufacturers instructions

first: Saurabh

last: Laddha

first: Chang

last: Chan

first: Laura

last: Tang


title: Human Lung Carcinoids


title: Transcriptomic profiling of human Lung Carcinoids (LCs)

summary: Lung carcinoids (LCs) are rare and slow growing primary lung neoplasms that are understudied. Here, we performed targeted exome sequencing using a 354-cancer gene panel (n=29), mRNA sequencing (n=30) and DNA methylation assay (n=18) on macro-dissected lung carcinoids. The mutations we identified were enriched for genes involved in covalent histone modification/chromatin remodeling (34.5%) (MEN1, ARID1A, KMT2C and KMT2A were recurrently mutated) as well as DNA repair (17.2%) pathways. Unsupervised clustering and principle component analysis on gene expression and DNA methylation profiles showed 3 robust molecular subtypes (LC1, LC2, LC3) with distinct clinical features.  MEN1 gene mutations were found to be enriched and exclusively in the LC2 subtype (p-value<0.001).  The LC3 subtype is predominately found at endobronchial lung and earlier age of diagnosis. Immunohistochemical staining of two biomarkers, ASCL1 and S100, is sufficient to stratify the three subtypes. This molecular classification of lung carcinoids into three subtypes may help improve treatment decision and clinical management.

overall_design: Genomic and Transcriptomic Characterization of Lung Carcinoids


title: microRNA array of LoVo cells and LoVo-Small Extracellular Vesicles

city: Hangzhou

first: yingkuan

last: Shao

address: Jiefang Road 88

institute: Zhejiang Universit

summary:
LoVo cells were cultured in sEV-depleted (160,000xg, 16h) complete medium and the supernatant were collected after 72h. sEVs were purified and centrifuged at 100,000xg for 2.5h using a Beckman SW41Ti rotor
to know the miRNA in LoVo cells and LoVo-Small Extracellular Vesicles

overall_design: LoVo cells were cultured in sEV-depleted (160,000xg, 16h) complete medium and the supernatant were collected after 72h. After three successive centrifugations at 300×g (5 min), 1,200×g (20 min), and 10,000×g (30 min) at 4℃, sEVs were purified with Amicon Ultra-15 centrifugal filters with a nominal molecular weight limit of 100 kDa and Millex-GP syringe membrane filters with a 0.22-µm pore size (Millipore Express, US) to eliminate debris, then centrifuged at 100,000×g (70 min at 4℃). Vesicles resuspended were loaded onto the top of a step gradient comprising layers of 0.25, 0.5, 1.0, 1.25, and 2M (mol/L) sucrose (S9378, Sigma). The gradients were centrifuged at 100,000xg for 2.5h using a Beckman SW41Ti rotor

first: Yingkuan

first: Shu

last: Zheng


title: High-throughput sequencing of plasma microRNA in elderly men fed a high protein diet in relation to the PBMC transcriptome: A 10 week randomized controlled trial

city: Grafton

first: FARHA

last: RAMZAN

state: AUCKLAND

address: 85 Park road

department: Liggins Institute

country: New Zealand

institute: University of Auckland

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Thirty one healthy men older than age 70 were randomized to consume either the recommended dietary allowance (RDA; 0.8 g/kg/day) or twice the RDA (2xRDA; 1.6g/kg/day) of protein for 10 weeks.

first: Farha

last: Ramzan


title: Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline [RRBS]

first: Stephanie

last: Parker

type: Methylation profiling by high throughput sequencing

overall_design: Examination of the DNA methylation (RRBS) profiles of single E13.5 female Gulo -/- embryos developed with and without Vitamin C supplementation. 6 biological replicates per condition.

first: Miguel

last: Ramalho-Santos


title: Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline


title: Maternal Vitamin C regulates DNA demethylation and development of the mouse embryonic germline [RNA-Seq]

overall_design: Examination of the transcriptional profile of single E13.5 female Gulo -/- embryos developed with and without Vitamin C supplementation. 6 biological replicates per condition.


title: DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [Ribo-Seq]

city: Würzburg

first: Markus

last: Sauer

address: Am Hubland, Biozentrum - Lehrstuhl für Biochemie

country: Germany

institute: University of Würzburg

summary: DHX36 is a ATP-dependent, 3´-5´ RNA helicase of the DEAH family. Previous publications reported this helicase to associate with AU-rich elements and to specifically unwind G-quadruplex structures. Here, we performed Ribosome footprintin in triplicats of HEK293 wildtype cells and DHX36-KO-HEK293 cells to identify changes in ribosome occupancy on mRNAs upon presence or absence of this helicase. After sequencing and mapping to the human genome at nucleotide-resolution level we analysed the coverage of ribosomes on target mRNAs, identified in this study (see PAR-CLIP). Our analyses show that only minor changes upon DHX36 knockout can be observed.

overall_design: Examination of ribosome footprints in HEK293 wildtype cells and DHX36-KO-HEK293 cells

first: Stefan

last: Juranek

first: Daniel

last: Benhalevy

first: Xiantao

last: Wang

last: Hafner

first: Katrin

last: Paeschke


title: DHX36 is the missing link to understand RNA G-quadruplex structures, mRNA stability, and translation [RNA-seq]

summary: DHX36 is a ATP-dependent, 3´-5´ RNA helicase of the DEAH family. Previous publications reported this helicase to associate with AU-rich elements and to specifically unwind G-quadruplex structures. Here, we performed RNA-seq in triplicats of HEK293 wildtype cells and DHX36-KO-HEK293 cells to identify changes in RNA abundance upon presence or absence of this helicase. After sequencing and mapping to the human genome at nucleotide-resolution level we analysed the mRNA abundance of target mRNAs, identified in this study (see PAR-CLIP). Our analyses show that binding of DHX36 to 3´UTRS of target mRNAs significantly reduce their abundance.

overall_design: Examination of RNA abundance in HEK293 wildtype cells and DHX36-KO-HEK293 cells


title: DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [ChrRNA-seq]

overall_design: Examination of nascent RNA levels in HEK293 wildtype cells and DHX36-KO-HEK293 cells


title: DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation

overall_design: Refer to individual Series


title: Leo1 is essential for dynamic regulation of heterochromatin and gene expression during cellular quiescence [RNA-Seq]

status: Public on Jun 30 2019

city: Huddinge

first: Eriko

last: Oya

address: Blickagången 16

institute: Karolinska Institutet

summary: Cellular quiescence is a reversible differentiation state when cells are changing the gene expression programme to reduce metabolic functions and adapt to a new cellular environment. The epigenetic changes that accompany these alterations are not so well understood. Here we investigate the role of Leo1, a subunit of the conserved Paf1 (RNA polymerase-associated factor 1) complex, in the quiescence process using fission yeast as a model organism. Fission yeast cells enter the G0 phase of the cell cycle when exposed to nitrogen starvation and the heterochromatin regions become very dynamic. The reduction of heterochromatin in early G0 correlates with the reduced activity of target of rapamycin, TORC2, signalling. Cells lacking the Leo1 show reduced survival in G0.  In these cells heterochromatin regions including subtelomeres are stabilized and many genes, including membrane transport genes, fail to be expressed. Our results suggest that Leo1 is essential for dynamic regulation of heterochromatin and gene expression during cellular quiescence.

overall_design: RNA profiles in wt/leo1D during quiescence; total 20 samples; biological duplicates

first: Mickaël

last: Dubief

first: Adiel

last: Cohen

first: Catherine

last: Schurra

first: Jun-ichi

last: Nakayama

first: Ronit

last: Weisman

first: Benoit

last: Arcangioli

first: Karl

last: Ekwall


title: Gene expression profiling of the Arabidopsis  glucosinolate deficient mutants, ref5-1 and ref2-1 and med5 mutants

city: West Lafayette

first: Clint

last: Chapple

state: IN

address: 175 S. University St.

department: Department of Biochemistry

institute: Purdue University

summary:
Purpose:  To identify changes in gene expression in ref5-1 and ref2-1 compared with wild type and ref5-1 med5 and ref2-1 med5 compared to ref5-1 or ref2-1 respectively
Methods: Gene expression profiles were generated from 18-day-old, pooled Arabidopsis rosettes in biological quadruplicate, by paired-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR.
Results: We identified 71 genes that were differentially expressed in both ref5-1 and ref2-1 compared to wild type but their altered expression is restored.

overall_design: Gene expression profiles of wild type and mutants were generated in biological triplicate from 18-day-old Arabidopsis rosettes by deep sequencing using Illumina HiSeq 2500.

first: Jeong

middle: I

last: Kim


title: Circular RNA CircFndc3b Modulates Cardiac Repair after Myocardial Infarction via FUS/VEGF-A axis

status: Public on Jun 29 2019

city: Wallingford

first: Venkata

middle: Naga Srikanth

last: Garikipati

state: Pennsylvania

address: 3500 N, Broad St, 908B MERB

institute: Temple University

summary: In this study we found differential expression of circular RNA in the mouse hearts 3 days post MI compared to sham operated hearts

overall_design: Here we performed a microarray two biological replicates of MI or sham surgery mouse hearts at day 3

first: Raj

last: Kishore


title: Gene Expression Profiling of Oligodendrocyte Precursor Cells Conditioned with Interferon gamma

city: Baltimore

first: Peter

middle: Arthur

last: Calabresi

address: 600 N. Wolfe St

department: Neurology

institute: Johns Hopkins Univbersity

summary: Interferon Gamma suppresses genes associated with OPC differentiation and induces genes associated with antigen presentation

overall_design: In vitro conditioning of OPCs from threee separate rat donors with PDGF vs PDGF withdrawal and either T3, IFNg or both at 8, 24, 48 and 96 hours

first: Leslie

last: Kirby

first: Jingya


title: An improved method for circular RNA purification that efficiently removes linear RNAs containing G-quadruplexes or structured 3’ ends

status: Public on Jun 28 2019

city: Philadelphia

first: Jeremy

middle: E.

last: Wilusz

address: 363 Clinical Research Building, 415 Curie Boulevard

department: Department of Biochemistry & Biophysics

institute: University of Pennsylvania Perelman School of Medicine

summary: Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3’-5’ exonuclease RNase R. Here, we demonstrate that standard protocols involving RNase R fail to digest >20% of all highly expressed linear RNAs, but that these shortcomings can be easily overcome. RNAs with highly structured 3’ ends, including snRNAs and histone mRNAs, are naturally resistant to RNase R, but can be efficiently degraded once a poly(A) tail has been added to their ends. In addition, RNase R stalls in the body of many mRNAs, especially at G-rich sequences that have been previously annotated as G-quadruplex (G4) structures. Upon replacing K+ (which stabilizes G4s) with Li+ in the reaction buffer, we find that RNase R is now able to proceed through these sequences and fully degrade the mRNAs in their entirety. In total, our results provide important improvements to the current methods used to isolate circular RNAs as well as a way to reveal RNA structures that may naturally inhibit degradation by cellular exonucleases.

overall_design: RNA-seq experiments: (1) Two replicates of HeLa cell derived RNA were treated with either RNase R or KCl containing buffer for 15 min. (2) Three replicates of HeLa cell derived RNA were treated by E-PAP followed by digestion with RNase R in LiCl containing buffer. The correspoding three controls were treated with LiCl containing buffer alone.

first: Mei-Sheng

last: Xiao

middle: E


title: Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement on the X chromosome [RNA-seq]

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: In D. melanogaster males, X chromosome monosomy is compensated by chromosome-wide transcription activation. We found that complete dosage compensation during embryogenesis takes surprisingly long. Although the activating Dosage Compensation Complex (DCC) associates with the chromosome and acetylates histone H4 early, many genes are not compensated. Acetylation levels on gene bodies continue to increase for several hours after gastrulation in parallel with progressive compensation. Constitutive genes are compensated earlier than developmental genes. Remarkably, later compensation correlates with longer distances to DCC binding sites. This time-space relationship suggests that DCC action on target genes requires maturation of the active chromosome compartment.

overall_design: RNA-seq in 8 embryonic stages in total 54 single embryos.

first: Khairunnadiya

last: Prayitno

middle: B

last: Becker


title: DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [cPDS-RNA-seq]

first: Markus

last: Sauer

overall_design: Examination of RNA abundance in HEK293 wildtype cells and DHX36-KO-HEK293 cells upon treatment with RNA-G4 stabilizing ligand carboxyPyridostatin

first: Stefan

last: Juranek

first: Daniel

last: Benhalevy

first: Xiantao

last: Wang

last: Hafner

first: Katrin

last: Paeschke


title: Nrf2 activation promotes lung cancer metastasis by blocking degradation of Bach1

city: New York

first: Shaowen

last: Jiang

state: NY

address: 227 East 30th

department: Department of Pathology

institute: NYU Langone

summary:
Purpose: The goal of this study is to analyze the transcriptional pathways regulated by Fbxo22 and Keap1 in mouse lung adeno carcinoma cells.
Methods: mouse lung adeno carcinoma cells either Keap1 wild type (KP) or mutant (KPK), have been transfected for 3 days with siRNA targeting Fbxo22. Knock down efficiency has been evaluated by western blot (using specific antibody for Fbxo22) and qPCR  (using specific oligos for Fbxo22) .
Results: The transcriptomic analysis helps us to support our finding that loss of either Keap1 or Fbxo22 induces metastases

overall_design: All 12 samples generated by deep sequencing in triplicate

first: Luca

last: Lignitto

first: Michele

last: Pagano


title: Transcriptomic comparison of mouse lung adenocarcinoma cell lines derived upon treatment with urethane

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: We repeatedly injected FVB and C57BL/6 intraperitonealy with urethane. Mice developed lung tumours. We sacrificed the mice, harvested their lungs and cultured the tumour cells. After over 60 passages we established 3 novel mouse lung adenocarcinoma cell lines. The aim of this study os to compare their transcriptomic profile.

overall_design: We established 3 mouse lung adenocarcinoma cell lines, two from the FVB  and one from the C57BL/6  background. All samples were analyzed using Genespring 12.5 GX to obtain the  data.

first: Nikolaos

last: Kanellakis


title: Transcriptomic comparison of FVB mouse strain lung Cells and epithelial trachea cells.

summary: We injected 12 (6 males, 6 females) FVB mice 8 weeks old, with either saline or urethane. One week later we sacrificed  and harvested their lungs. The dissected lungs were assayed to RNA extraction (via trizol).  Moreover we cultured mouse tracheal epithelial  cells. We compared all samples in order to identify each specific transcriptomic signature.

overall_design: Samples from FVB mice lung cells and epithelial trachea cells were analyzed using Genespring 12.5 GX to obtain the  data.


title: Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement on the X chromosome [ChIP-seq]

overall_design: Covaris sheared ChIP-seq: H4K16ac, H3K36me3 and Input in 2 embryonic stages and in 2 biological replicates. MNase ChIP-seq: MSL2, MOF, H4K16ac, Input in 2 embryonic stages and in 3 biological replicates.

first: Peter


title: Gene expression profiling of mouse bone marrow derived macrophages exposed to B16F10 mouse melanoma cell line

summary: Naïve macrophages were cultured from murine bone marrow

overall_design: Bone marrow-derived macrophages were exposed to non-conditioned, or B16F10 mouse melanoma cells conditioned media


title: Crisaborole and atopic dermatitis skin biomarkers: an intrapatient randomized trial

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: Crisaborole ointment, 2%, is a nonsteroidal phosphodiesterase 4 (PDE4) inhibitor for the treatment of mild-to-moderate atopic dermatitis (AD). The mechanism of action (MOA) of crisaborole and its effects on lesional measures of disease severity are not yet well-defined. This phase 2a, single-center, vehicle-controlled, intrapatient study was designed to further characterize the MOA of crisaborole through evaluation of clinical efficacy and changes in skin biomarkers in adults (N = 40) with mild-to-moderate AD.

overall_design: Two target lesions were randomized intrapatient (1:1) to double-blind crisaborole:vehicle, applied twice daily for 14 days. Patients then applied crisaborole (open-label) to all affected areas for 28 days. Punch biopsy specimens were collected for biomarker analysis at baseline, day 8 (optional), and day 15.

first: Robert

last: Bissonnette

first: Aisleen

last: Diaz

first: John

last: Werth

first: Chuanbo

last: Zang

first: Ivana

last: Vranic

first: Vivek

last: Purohit

first: Michael

last: Zielinski

first: Bonnie

last: Vlahos

first: Yeriel

last: Estrada

first: Etienne

last: Proulx

first: William

middle: C

last: Ports

first: Emma

last: Guttman-Yassky


title: DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [PAR-CLIP-seq]

first: Markus

last: Sauer

summary: DHX36 is a ATP-dependent, 3´-5´ RNA helicase of the DEAH family. Previous publications reported this helicase to associate with AU-rich elements and to specifically unwind G-quadruplex structures. Here, we performed PAR-CLIP in duplicates to specifically crosslink DHX36 and helicase-dead DHX36 E335A to its RNA binding targets in HEK293 cells. After sequencing and mapping to the human genome at nucleotide-resolution level we combined sequencing reads to a total of over 60000 binding clusters on more than 9000 transcripts. Distribution analyses revealed that DHX36 binds mainly to CDSs and 3´UTRS of mRNAs. Also, a G-rich binding motif for DHX36 was identified.

overall_design: Examination of DHX36 and the helicase-dead mutant DHX36 E335A in duplicates to identify binding targets in HEK293 cells

first: Stefan

last: Juranek

first: Daniel

last: Benhalevy

first: Xiantao

last: Wang

last: Hafner

first: Katrin

last: Paeschke


title: Specificity assessment of allele selective Zinc Finger Protein Repressors in HD fibroblasts

city: Richmond

first: Bryan

last: Zeitler

address: 501 Canal Blvd.

institute: Sangamo Therapeutics

summary: Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder caused by a CAG trinucleotide expansion in the huntingtin gene (HTT), which codes for the pathologic mutant HTT (mHTT) protein. Since normal HTT is thought to be important for brain function, we engineered zinc finger protein transcription factors (ZFP-TFs) to target the pathogenic CAG repeat and selectively lower mHTT as a therapeutic strategy. Using patient-derived fibroblasts and neurons, we demonstrate that ZFP-TFs selectively repress >99% of HD-causing alleles over a wide dose range, while preserving expression of >86% of normal alleles. Other CAG-containing genes are minimally affected, and virally delivered ZFP-TFs are active and well tolerated in HD neurons beyond 100 days in culture and at least 9 months in the mouse brain. Using three HD mouse models, we demonstrate improvements in a range of molecular, histopathological, electrophysiological, and functional endpoints. Our findings support the continued development of an allele-selective ZFP-TF for the treatment of HD.

overall_design: Four treatments (ZFP-A, ZFP-B, ZFP-C, control) were tested in HD fibroblasts (GM02151). For each treatment, 6 replicate transfections were conducted yielding 6 biological replicates. Cells were harvested 24 hours later and processed for total RNA isolation and Affymetrix sample Prep. The control treatment was a non-CAG targeted ZFP-TF. One control-treated replicate was excluded from the analysis based on an exploratory grouping analysis which identified it as an outlier.

first: Steven

last: Froelich

first: Kimberly

last: Marlen

first: David

last: Shivak

first: Qi

last: Yu

first: Davis

last: Li

first: Jocelynn

middle: R

last: Pearl

first: Jeffrey

last: Miller

first: Lei

last: Zhang

last: Paschon

first: Sarah

middle: J

last: Hinkley

first: Irina

last: Ankoudinova

first: Stephen

last: Lam

first: Dmitry

last: Guschin

first: Lexi

last: Kopan

first: Jennifer

middle: M

last: Cherone

first: Hoang-Oanh

last: Nguyen

first: Guijuan

last: Qiao

first: Yasaman

last: Ataei

first: Matthew

last: Mendel

first: Rainier

last: Amora

first: Richard

last: Surosky

first: Josee

last: Laganiere

first: B

last: Vu

first: Anand

last: Narayanan

first: Yalda

last: Sedaghat

first: Karsten

last: Tillack

first: Christina

last: Thiede

first: Annette

last: Gärtner

first: Seung

last: Kwak

first: Jonathan

last: Bard

first: Ladislav

last: Mrzljak

first: Larry

last: Park

first: Taneli

last: Heikkinen

first: Kimmo

middle: K

last: Lehtimäki

first: Marie

last: Svedberg

first: Jenny

last: Häggkvist

first: Lenke

last: Tari

first: Miklós

last: Tóth

first: Andrea

last: Varrone

first: Christer


title: Gene expression profiling of  mT/mG;Lyz2.Cre vs IKKbetaf/f;Lyz2.Cre mouse bone marrow derived macrophages

first: Georgios

last: Stathopoulos

summary: Gene expresion comparison between tomato Lyz2 Cre and IKKbeta flox/flox Lyz2 Cre bone marrow derived macrophages

overall_design: Gene expression profiling of tomato and IKKbeta deleted mouse bone marrow derived macrophages.

first: Nikolaos

last: Kanellakis


title: RNA-Seq data for Trp53/Brca1-null premalignant mammary epithelial cells with a K8+ luminal origin

status: Public on Jun 27 2019

city: Boston

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: BRCA1 mutation-carriers are predisposed to develop Basal-like breast cancer (BLBC), and p53 mutations are present in the majority of human BLBC cases, suggesting loss of these two tumor suppressors play key roles in development of BLBC.  Recent studies suggest that the majority of human breast cancers, including BLBC, may originate from mammary epithelial cells (MECs) in the luminal lineage.  However, how loss of p53 and BRCA1 contributes to development of BLBC from luminal MECs remains largely elusive.  We developed a novel genetic targeting and lineage tracing approach based on intraductal injection of Cre-expressing adenovirus under the control of the pan-luminal Keratin 8 (K8) promoter (Ad-K8-Cre).  We performed intraductal injection of Ad-K8-Cre to female mice carrying conditional knockout alleles of Brca1 (Brca1L) and Trp53 (Trp53L).  The injected females developed mammary tumors similar to human BLBC within 12 months after injection. Here we characterized MECs targeted by Ad-K8-Cre one month after the intraductal injection.

overall_design: YFP+ wild-type (WT), or p53-deficient, or p53/BRCA1-deficient mammary epithelial cells were sorted from Rosa26-Stop-YFP (R26Y), or Trp53L/L;R26Y, or Trp53L/L;Brca1L/L;R26Y female mice 1 month after intraductal induction of Ad-K8-Cre adenovirus, respectively; total RNAs were prepared from each sorted cell populations and subjected to RNAseq expression profiling.

first: Dongxi

last: Xiang


title: Transcriptome analysis of cultured human alveolar epithelial type 2 cells

city: Noda, Chiba

first: Kazushige

last: Shiraishi

address: Yamasaki 2669

country: Japan

institute: Tokyo University of Science

summary: We investigated whether in vitro expansion of human alveolar epithelial type II cells is possible. We found that human endogenous human alveolar epithelial type II cells can be cultured and passaged. The culture system enabled retroviral gene transduction into human alveolar epithelial type II cells. We performed RNA sequencing of human alveolar epithelial type II cells transduced with mutant surfactant protein C or control vector.

overall_design: Cultured human alveolar epithelial type II cells were transfected with retroviral vector containing mutant surfactant protein C or control retroviral vector. The retroviral vector contained LNGFR as a marker. After gene transduction, transduced cells were purified by magnetic-activated cell sorting. The transcriptome of the cells was generated by 5’Tag-seq using Ion Genestudio S5 Sequencer.

first: Shigeyuki

last: Shichino


title: Single-cell RNA-seq reveals distinct gene expression profiles underlying the cellular heterogeneity of the sinoatrial node (SAN) cells

city: New Orleans

first: YiPing

last: Chen

address: 6400 Freret Street

institute: Tulane University

summary: We use single cell RNA-sequencing to profile SAN cells (included atrium) from Shox2Cre/+;R26RmTmG at E13.5.

overall_design: Single-cell RNA-seq of E13.5  Shox2Cre/+;R26RmTmG SAN cells including atrial cells.

first: Hua


title: Impact of DNA MMR activity on antiviral gene expression in H441 cells infected with influenza A virus

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: H441 cells lacking DNA MMR activity have reduced expression of antiviral and stress response genes during influenza A virus infection.

overall_design: H441 cells were depleted of control or DNA MMR genes MSH2+MSH6 and then infected with mock or influenza A virus for 24 h before toral RNA collection and RNAseq.

first: Benjamin

middle: S

last: Chambers


title: Aspergillus fumigatus Colony Biofilm Morphology Impacts Hypoxia Fitness, Inflammation, and Disease Progression

city: Riverside

first: Jason

last: Stajich

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

summary: We report gene expression differences in Aspergillus fumigatus wild type, hrmA mutant, and overexpression under hypoxia and normoxia conditions

overall_design: Examination of 5 genotypes (WT, hrmA deletion, hrmA OE, hrmA_REV, EVOL).

first: Caitlin

middle: H

last: Kowalski

first: Joshua

middle: D

last: Kerkaert

first: Ko-Wei

last: Liu

first: Carey

last: Nadell

first: Robert

middle: A

last: Cramer


title: Effect of Toxoplasma gondii efector TgIST on global transcriptome of human foreskin fibroblasts (HFFs) upon type I IFN activation

city: St. Louis

first: Sumit

middle: Kumar

last: Matta

state: MO

address: 660 S. Euclid

department: Molecular Microbiology

institute: Washington University in St. Louis

summary: TgIST is an effector secreted by Toxoplasma gondii into the host cell that translocates to the nucleus and block STAT1 mediated transcription. STAT1 is involved in type I and II interferon (IFN) mediated upregulation of range of anti-parasitic molecules.  A total of 544,234,059 read sequences generated from 3 independent biological replicates were mapped to human hg19 reference genome. Type I IFN activation of HFFs infected with TgIST knockout parasites showed upregulation of genes involved in interferon signaling compared to wild type parasites.

overall_design: HFFs were infected with wild type (RH) or TgIST knockout (RH KO) T. gondii parasites for 12 hours, followed by stimulation with or without human IFN-β for 6 hours. Uninfected cells with or without IFN-β treatment were used as controls. RNA samples isolated from 3 independent replicates were used for next-generation mRNA sequencing to analyze the ability of TgIST to regulate type I IFN responses in host cells.

first: L

last: Sibley


title: Gene expression profiling of mouse mast cells exposed to B16F10 mouse melanoma cell line

first: Georgios

last: Stathopoulos

summary: Naïve mast cells were cultured from murine bone marrow using incubation with IL-3 alone (samples 1 and 2) or IL-3 and KITL (samples 3 and 4).

overall_design: IL-3 only or IL-3/KITL-matured bone marrow-derived mast cells were exposed to non-conditioned, or B16F10 mouse melanoma cells conditioned media

first: Nikolaos

middle: I


title: Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq]

city: Wuhan

first: Rui

last: Xiao

state: Hubei

address: Medical Research Institute, Wuhan University

department: Medical Research Institute

institute: Wuhan University

summary:
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also showed strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.
As part of the ENCODE consortium, we embarked on a large-scale RBP ChIP-seq analysis, revealing broad presence of RBPs in active chromatin regions in the human genome.  Like transcription factors (TFs), RBPs also show great preference for hotspots in the genome, particularly gene promoters, where their binding is frequently linked to transcriptional output. Self-organizing map reveals extensive co-binding events between TFs and RBPs, as exemplified by those between YY1, a known RNA-dependent TF, and RBM25, an RBP involved in alternative splicing. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may bridge specific TF-RNA interactions to control transcription.

overall_design: Examination of RBP-dependent transcription regulation by GRO-seq with 2 replicated experiments in HepG2 cells

first: Jia-Yu

first: Xiang-Dong

last: Fu


title: Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture?

city: Antwerpen

first: Nicolas

last: De Neuter

address: Middelheimlaan 1

country: Belgium

institute: University of Antwerp

summary:
Background: Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated with a significant morbidity and mortality. Bacterial meningitis requires antibiotics, as opposed to enteroviral meningitis, which only requires supportive therapy. Clinical presentation is usually not sufficient to differentiate between viral and bacterial meningitis, thereby necessitating cerebrospinal fluid (CSF) analysis by PCR and/or time-consuming bacterial cultures. However, collecting CSF in children is not always feasible and a rather invasive procedure.

Methods: In 12 Belgian hospitals, we obtained acute blood samples from children with signs of meningitis (49 viral and 7 bacterial cases). (aged between 3 months and 16 years). After pathogen confirmation on CSF, the patient was asked to give a convalescent sample after recovery. 3’mRNA sequencing was performed to determine differentially expressed genes (DEGs) to create a host transcriptomic profile.

Results: Enteroviral meningitis cases displayed the largest upregulated fold change enrichment in type I interferon production, response and signaling pathways. Patients with bacterial meningitis showed a significant upregulation of genes related to macrophage and neutrophil activation. We found several significantly DEGs between enteroviral and bacterial meningitis. Random forest classification showed that we were able to differentiate enteroviral from bacterial meningitis with an AUC of 0.982 on held-out samples.

Conclusions: Enteroviral meningitis has an innate immunity signature with type 1 interferons as key players. Our classifier, based on blood host transcriptomic profiles of different meningitis cases, is a possible strong alternative for diagnosing enteroviral meningitis.

overall_design: Gene expression profiles of host blood can be used to differentiate between different types of meningitis.  Libraries were sequenced in 4 lanes and each sequencing lane is represented as a column in the processed data files.

first: Esther

last: Bartholomeus

first: Annelies

last: Lemay

first: Luc

last: Pattyn

first: David

last: Tuerlinckx

last: Weynants

first: Koen

last: Van Lede

first: Gerlant

last: van Berlaer

first: Dominique

last: Bulckaert

first: Tine

last: Boi

first: Ann

last: Vander Auwera

first: Marc

last: Raes

first: Dimitri

last: Van der Linden

first: Helene

last: Verhelst

first: Susanne

last: Van Steijn

first: Tijl

last: Jonckheer

first: Joke

last: Dehoorne

first: Rik

last: Joos

first: Hilde

last: Jansens

first: Arvid

last: Suls

first: Pierre

last: Van Damme

first: Kris

last: Laukens

first: Geert

last: Mortier

first: Pieter

last: Meysman

first: Benson

last: Ogunjimi


title: RNAseq expression in CD45+/CD3-/NK1.1+/CD122+ uterine NK cells

status: Public on Jun 26 2019

city: Spring House

first: Kasper

last: Hoebe

state: PA

address: 1400 McKean rd

department: Immunology

institute: J&J

summary: The study compares RNAseq expression in gd8.5 uNK cells isolated from the placentas from WT C57BL/6J and Gab3-KO pregnant females.

overall_design: Gab3-KO vs. WT

first: Anna

last: Sliz


title: Single cell RNA-Seq data for Trp53/Brca1-null premalignant mammary epithelial cells and tumor cells with a K8+ luminal origin

first: Zhe

last: Li

summary: BRCA1 mutation-carriers are predisposed to develop Basal-like breast cancer (BLBC), and p53 mutations are present in the majority of human BLBC cases, suggesting loss of these two tumor suppressors play key roles in development of BLBC. Recent studies suggest that the majority of human breast cancers, including BLBC, may originate from mammary epithelial cells (MECs) in the luminal lineage. However, how loss of p53 and BRCA1 contributes to development of BLBC from luminal MECs remains largely elusive. We developed a novel genetic targeting and lineage tracing approach based on intraductal injection of Cre-expressing adenovirus under the control of the pan-luminal Keratin 8 (K8) promoter (Ad-K8-Cre). We performed intraductal injection of Ad-K8-Cre to female mice carrying conditional knockout alleles of Brca1 (Brca1L) and Trp53 (Trp53L). The injected females developed mammary tumors similar to human BLBC within 12 months after injection. Here we characterized MECs targeted by Ad-K8-Cre at different time points after the intraductal injection, as well as mammary tumors developed in this model, by single cell expression analysis.

overall_design: YFP+ p53/BRCA1-deficient mammary epithelial cells were sorted from Trp53L/L;Brca1L/L;Rosa26-Stop-YFP (R26Y) female mice ~2 weeks or 5 months after intraductal induction of Ad-K8-Cre adenovirus, respectively, and were subjected to single cell RNA-seq analysis. In addition, single cell suspensions were prepared from two mammary tumors developed in this mouse model and were subjected to single cell RNA-seq analysis.

first: Dongxi

last: Xiang


title: LncRNA-induced spread of Polycomb controlled by genome architecture, RNA abundance, and CpG island DNA [RIP-seq]

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

summary: Long noncoding RNAs (lncRNAs) cause Polycomb Repressive Complexes (PRCs) to spread over broad regions of the mammalian genome. We report that in mouse trophoblast stem cells, the Kcnq1ot1 and Airn lncRNAs induce PRC-dependent chromatin modifications over multi-megabase domains. Throughout the Airn-targeted domain, extent of PRC-dependent modification correlated with intra-nuclear distance to the Airn locus, pre-existing genome architecture, and the abundance of Airn itself. Specific CpG islands displayed characteristics indicating that they nucleate the spread of PRCs upon exposure to Airn. Chromatin environments surrounding Xist, Airn, and Kcnq1ot1 suggest common mechanisms of PRC engagement and spreading. Our data indicate that lncRNA potency can be tightly linked to lncRNA abundance, and that within lncRNA-targeted domains, PRCs are recruited to CpG islands via lncRNA-independent mechanisms. We propose that CpG islands that autonomously recruit PRCs interact with lncRNAs and their associated proteins through 3-dimensional space to nucleate the spread of PRCs in lncRNA-targeted domains.

overall_design: RNA IP sequencing data in mouse trophoblast stem cells and SM33 mouse embryonic stem cells.

first: Megan

last: Schertzer


title: KMT9 writes the H4K12me1 histone mark and controls metabolism and proliferation of castration-resistant prostate cancer cells [ChIP-seq]

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

summary: KMT9 is formed by the assembly of KMT9a and KMT9b and writes the H4K12me1 mark. The objectives of this study is to identify KMT9a, KMT9b, and H4K12me1 locations by ChIP-seq in the androgen-independent PC-3M prostate cancer cells and to show that upon KMT9a knockdown the levels of H4K12me1 mark decrease.

overall_design: 16 samples correponding to ChIP and input samples were used for the study

first: Roland

last: Schüle

first: Dominica

last: Willmann


title: Reduced representation bisulfite sequencing (RRBS) of WT, Tet1-/-, Tet2-/-, Tet1-/-:Tet2-/- (DKO), and Tet1-/-:Tet2-/-:Tet3-/- (TKO) murine embryonic stem under normal culture conditions.

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: RRBS was used to investigate the methylation status of CpG dinucleotides in different Tet knockouts.

overall_design: RRBS libraries were generated for 3 WT, 3 Tet1-/-, 2 Tet2-/-, DKO, and TKO clones. Sequencing was done on a Illumina NextSeq 500 for all paired end reads.

first: Kirthi

last: Pulakanti

first: Michael

last: Reimer


title: Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

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

overall_design: Refer to individual Series


title: System Analysis of The Functional Cross-Talk Between PPARα, LXR and FXR in HepaRG Liver Cells

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

institute: Swiss Institute of Bioinformatics

summary: The purpose of the present study was to explore in liver cells the connectivity that operates between three nuclear receptors in the liver, LXR, FXR, and PPARa, all three known to act on lipid and glucose metabolism, and also on inflammation. The human cell line HepaRG was selected for its proximity to human primary hepatocytes. Global gene expression of differentiated HepaRG cells was assessed after 4 hours and 24 hours of exposure to GW3965  (LXR agonist), GW7647  (PPARα agonist), and GW4064 and CDCA (FXR synthetic and natural agonist, respectively).

overall_design: The study includes 36 samples from two time points, 4h and 24h. The two time points were analyzed separately. The cell cultures received six different treatments: four ligands binding to nuclear receptors (CDCA, FXR-L, LXR-L and PPARα-L) and two control treatments (DMSO vehicle control and untreated control).  There were three replicate cell cultures for each treatment. For the data analysis, DMSO and untreated control were lumped together into a single control group.

first: Cristina

last: Casals-Casas

first: Michaël

last: Baruchet

first: Khanh

last: Trang

first: Sylvain

last: Pradervand

first: Aurélien

last: Naldi

first: Béatrice

last: Desvergne


title: Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells (ChIP-seq)

summary: The development of CRISPR-Cas systems for targeting DNA and RNA in diverse organisms has transformed biotechnology and biological research. Moreover, the CRISPR revolution has highlighted bacterial adaptive immune systems as a rich and largely unexplored frontier for discovery of new genome engineering technologies. In particular, the class 2 CRISPR-Cas systems, which use single RNA-guided DNA-targeting nucleases such as Cas9, have been widely applied for targeting DNA sequences in eukaryotic genomes. Here, we report DNA-targeting and transcriptional control with class I CRISPR-Cas systems. Specifically, we repurpose the effector complex from type I variants of class 1 CRISPR-Cas systems, the most prevalent CRISPR loci in nature, that target DNA via a multi-component RNA-guided complex termed Cascade. We validate Cascade expression, complex formation, and nuclear localization in human cells and demonstrate programmable CRISPR RNA (crRNA)-mediated targeting of specific loci in the human genome. By tethering transactivation domains to Cascade, we modulate the expression of targeted chromosomal genes in both human cells and plants. This study expands the toolbox for engineering eukaryotic genomes and establishes Cascade as a novel CRISPR-based technology for targeted eukaryotic gene regulation.

overall_design: Examination of genome-wide Cascade binding in human cells with 3 different crRNAs in triplicate.

first: Adrian

last: Pickar-Oliver

first: Joshua

last: Black

first: Mae

last: Lewis

first: Kevin

last: Mutchnick

first: Stephen

middle: L

last: Gasior

first: Alejandro

last: Barrera

first: Luke

last: Bartelt

first: Timothy

last: Reddy

first: Chase

last: Basiel

first: Rodolphe

last: Barrangou

last: Young

last: Gerbasch


title: Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription

first: Rui

last: Xiao


title: Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]

summary: Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also showed strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.

overall_design: Examination of RBP ChIP-seq with 2 replicated experiments in HepG2 and K562 cells

first: Jia-Yu

last: Chen

first: Xiang-Dong

last: Fu


title: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [RNA-seq]

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages.

overall_design: RNA-Seq: 9 cell types, with a total of 34 individual replicates.

first: Hisashi

last: Miura

first: Saori

last: Takahashi

first: Rawin

last: Poonperm

first: Shin-ichiro

last: Takebayashi


title: Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]

overall_design: Examination of RBM25-dependent chromatin structure by BL-Hi-C with 2 replicated experiments in HepG2 cells

first: Zheng-Yu

last: Liang


title: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [HiC-seq]

overall_design: Hi-C: 10 cell types, with a total of 22 individual replicates (in duplicates or triplicates).

first: Akie

last: Tanigawa


title: LncRNA-induced spread of Polycomb controlled by genome architecture, RNA abundance, and CpG island DNA

first: J

last: Calabrese

department: Pharmacology


title: Polymorphisms in RocA contribute to the molecular pathogenesis of serotype M28 group A streptococcus

status: Public on Jun 25 2019

city: Houston

first: Paul

last: Bernard

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: RNA-seq experiments of serotype M28 group A streptococcus strains with mutations in rocA at two time points

overall_design: RNA-seq data 53 strains at 2 time points in duplicate (clinical isolates) and 7 strains at 2 time points in triplicate (isogenics)

first: Randall

last: Olsen


title: Next Generation Sequencing of Wild Type and Gata2-/- LSCs

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

summary: Gata2, a zinc finger TF, is essential for the generation and survival of HSCs in the embryo and has been implicated in the pathogenesis of AML, yet the requirement for Gata2 in adult HSCs and LSCs remains unclear. Using a conditional mouse model where Gata2 was deleted specifically in hematopoietic cells, we show that knockout of Gata2 leads to a rapid and complete cell-autonomous loss of adult HSCs. In Meis1a/Hoxa9 driven AML, deletion of Gata2 impedes maintenance and self-renewal of LSCs. We then performed RNA-seq from sorted control and Gata2 KO LSCs (CD45.2+ c-Kit+) after pIpC treatment in transplanted mice.

overall_design: Wild Type and Gata2-/- Meis1a/Hoxa9 LSCs were harvested from mice 24 days after pIpC administration

first: Juan

last: Gonzalez

first: Neil

last: Rodrigues


title: Single-cell RNA expression profiling of mouse common lymphoid progenitors with or without dox-induction of LIN28B

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

summary: To reprogram adult HSPCs in vivo, we used a mouse engineered to express LIN28B in a Doxycycline (Dox)-inducible manner (iLIN28B). We performed single cell RNA-seq to compare the transcriptomes of common lymphoid progenitor (CLP) cells isolated from mouse FL, adult BM of wildtype mice, adult BM of iLIN28B treated with Dox (+Dox), and adult BM of littermate controls +Dox.

overall_design: 4 Chromium Single Cell 3' llbraries were prepared and sequenced from CLP populations as described above.

first: Saifeng

last: Wang

first: Madeline

last: Wong

first: Bryan

last: Chim

first: Amir

last: Foroushani

first: Markus

last: Hafner


title: Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells (RNA-seq)

first: Charles

last: Gersbach

overall_design: Examination of transcriptome-wide changes in gene expression with Cascade-mediated activation of endogenous genes.

first: Adrian

last: Pickar-Oliver

first: Joshua

last: Black

first: Mae

last: Lewis

first: Kevin

last: Mutchnick

first: Stephen

last: Gasior

first: Alejandro

last: Barrera

first: Luke

last: Bartelt

first: Timothy

last: Reddy

first: Chase

last: Basiel

first: Rodolphe

last: Barrangou

last: Young

last: Gerbasch


title: LncRNA-induced spread of Polycomb controlled by genome architecture, RNA abundance, and CpG island DNA [ChIP-Seq]

first: J

last: Calabrese

overall_design: ChIP-seq data from three mouse cell types: trophoblast stem cells, cortical neurons, and embryonic stem cells. F1 hybrid cell lines were generated from crosses between CAST/EiJ (Cast) and C57BL/6J (B6) mice.

first: Megan

last: Schertzer


title: KMT9 writes the H4K12me1 histone mark and controls metabolism and proliferation of castration-resistant prostate cancer cells [ChIP-Seq 2]

first: Eric

last: Metzger

summary: The aim of the study is to identify KMT9a target genes in PC-3M cells

first: Roland

last: Schüle

first: Dominica

last: Willmann


title: Functional genomic analysis of WT, Tet1-/-, Tet2-/-, Tet1-/-:Tet2-/- (DKO) murine embryonic stem cells

first: Sridhar

last: Rao


title: LncRNA-induced spread of Polycomb controlled by genome architecture, RNA abundance, and CpG island DNA [RNA-Seq]

overall_design: RNA-seq data compares gene expression in mouse trophoblast stem cells upon modulation of the Airn and Kcnq1ot1 lncRNAs or upon knockdown of HNRNPK.


title: KMT9a writes the H4K12me1 histone mark and controls metabolism and proliferation of castration-resistant prostate cancer cells [RNA-seq]

summary: The aim of the RNA-seq was to identify the KMT9 transcriptome in PC-3M cells. The MCF10A breast epithelial cells that do not express KMT9a were used to show that the siRNA against KMT9 show no off-target effects.

overall_design: 12 samples correponding to 4 times 3 replicates were used for the study


title: RNA-seq of WT, Tet1-/-, Tet2-/-, Tet1-/-:Tet2-/- (DKO), and Tet1-/-:Tet2-/-:Tet3-/- (TKO) murine embryonic stem cells following six days of LIF withdrawal.

summary: The goal of this study was to identify transcriptional differences between varying combinations of Tet deletion clones following six days of LIF withdrawal. These libraries were generated from cells under normal culture conditions.

overall_design: RNA-seq libraries were generated for 3 WT, 3 Tet1-/-, 2 Tet2-/-, DKO, and TKO clones. Sequencing was done on a Illumina NextSeq 500 for all paired end reads

first: Kirthi

last: Pulakanti

first: Michael

last: Reimer


title: RNA-Seq analysis of wild-type and Hdac3-null E16.5 neurospheres and P0 cerebral cortex

city: Montreal

first: Xiang-Jiao

last: Yang

state: Quebec

address: 1160 Pine Ave W

country: Canada

institute: McGill University

summary:
Histone deacetylase 3 (HDAC3) is a unique epigenetic regulator forming stoichiometric complexes with several other proteins. Patients with mutations in genes encoding these proteins display intellectual disability, implying an important role of HDAC3 in this prevalent disease. Here we report that cerebrum-specific inactivation of the mouse gene causes striking developmental defects in the neocortex, hippocampus and corpus callosum; post-weaning lethality; and abnormal behaviors, including hyperactivity and anxiety. The developmental defects are due to rapid loss of neural stem and progenitor cells (NSPCs), starting at E14.5. Premature neurogenesis and abnormal neuronal migration in the mutant brain alter NSPC homeostasis. Mutant cerebral cortices display augmented DNA damage, apoptosis, and histone hyperacetylation. In agreement with these results, mutant NSPCs are impaired in forming neurospheres in vitro, and treatment of wild-type NSPCs with the HDAC3-specific inhibitor RGFP966 abolishes neurosphere formation. Transcriptomic analyses of neonatal cerebral cortices and cultured neurospheres support that HDAC3 regulates various transcriptional programs through interaction with multiple transcription factors, including NFIB. These findings establish HDAC3 as a major deacetylase critical for perinatal development of the mouse cerebrum and NSPCs, thereby suggesting a direct link of this enzymatic epigenetic regulator to human cerebral and intellectual development.

To study the impact of cerebrum specific (Emx1-Cre) deletion of Hdac3 on embryonic neurospheres (cultured in vitro from E16.5 cerebrum) and neocortex from newborn pups (P0).

overall_design: For neurospheres, cerebrums were dissected out from E16.5 embryonic brains (2 wild-type and 2 Hdac3 cKO), and cultured in neural stem cell culture media till day 4. The neurospheres were colleted for RNA isolation. For cerebral cortex, the dorsal part of the cerabral cortices from P0 brains (2 wild-type and 2 Hdac3 cKO) were collected for RNA isolation. The RNA samples were sequenced using the Illumina TruSeq stranded mRNA kit on HiSeq2500.

first: Lin

last: Li


title: Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene

first: Guillaume

last: Lettre

address: 5000 Rue Bélanger

institute: Montreal Heart Institute


title: Cell-Specific Image-guided Transcriptomics of Ischemic Acute Kidney Injury

status: Public on Jun 24 2019

city: Seattle

first: Neal

last: Paragas

state: WA

address: 850 Republican St

institute: University of Washington

summary: The highly heterogeneous nature of the kidney's tubular epithelium has made it challenging to identify unique, cell-specific pathways particularly when renal injury causes the loss of fiduciary landmarks. Here, we combine a cell-specific luciferase reporter system with a chemo-selective substrate to identify specific Òat riskÓ tissues. We demonstrate that this platform system has the power to identify both cell-specific pathophysiological events and cell-specific transcriptional changes and consequently can identify novel therapeutic targets. Using the kidney ischemia-reperfusion model (iAKI), we found that lipid peroxidation mirrored H2O2 generation but with entirely different timing and sensitivity to ischemia depending on the nephron segment. We found the collecting duct demonstrated intensive ROS generation and transcriptional analysis demonstrated mitochondrial distress. In fact, pretreatment with a single bolus of a mitochondrial antioxidant, MitoTEMPO delayed ROS generation and significantly reduced acute oxidative stress associated injury. These data demonstrate that iAKI differentially targets different nephron segments, demonstrating the complexity of kidney injury includes multiple segments. Our in vivo ROS detection system can explore complex injuries in heterogeneous organs by leveraging image guidance for tissue interrogation.

overall_design: Kidney collecting duct cell mRNA profiles of mice after ischemia/reperfusion injury or control (sham), n=4 per condition,  were generated by deep sequencing,using Illumina HiSeq.

first: Sina

last: Gharib


title: Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene (RNAseq)

summary: Genome-wide association studies (GWAS) have identified 100s of loci associated with coronary artery disease (CAD) and blood pressure (BP)/hypertension. Many of these loci are not associated with traditional risk factors, nor include obvious candidate genes, complicating their functional characterization. We hypothesized that many GWAS loci associated with vascular diseases modulate endothelial functions. Endothelial cells play critical roles in regulating vascular homeostasis (e.g. selective barrier, inflammation, hemostasis, vascular tone) and endothelial dysfunction is a hallmark of atherosclerosis and hypertension. We generated an integrated map of gene expression (RNA-sequencing), open chromatin regions (ATAC-sequencing), and 3D interactions (Hi-C) in resting and TNFα-treated human endothelial cells. We showed that genetic variants associated with CAD and BP are enriched in open chromatin regions identified in endothelial cells. We used physical loops identified by Hi-C to link open chromatin peaks that include CAD or BP SNPs with the promoter of genes expressed in endothelial cells. This analysis highlighted 4,548 combinations of regulatory elements-promoters, including 108 pairs that involve a differentially open chromatin site and a differentially expressed gene following TNFα treatment. At a CAD locus, we validated one of these pairs by engineering a deletion of the TNFα-sensitive regulatory element using CRISPR/Cas9 and measuring an effect on the expression of the novel CAD candidate gene AIDA. Our data support an important role played by genetic variants acting in the vascular endothelium to modulate inter-individual risk in CAD or hypertension

overall_design: RNAseq of TNF-alpha treated endothelial cells (teloHAEC and HCAEC) for 0, 4h or 24h

first: Simon

last: Lalonde

first: Valérie-Anne

last: Codina-Fauteux

first: Sébastian

last: Méric de Bellefon

first: Francis

last: Leblanc

first: Mélissa

last: Beaudoin

first: Rola

last: Dali

first: Tony

last: Kwan

first: Ken

last: Sin Lo

first: Tomi

last: Pastinen


title: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [BrdU-IP Repli-chip]

first: Ichiro

last: Hiratani

overall_design: BrdUIP Repli-chip: 10 cell types, with a total of 20 individual replicates (all in duplicates).

first: Hisashi

last: Miura

first: Saori

last: Takahashi

first: Rawin

last: Poonperm

first: Shin-ichiro

last: Takebayashi