title: Effect of SPINK1 and IL-6 knockdown in JHOC9 and JHOC5 ovarian clear cell carcinoma cells

status: Public on Nov 10 2019

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary: Response of JHCO9 and JHOC5 cells to infection with NT (control) lentivirus or one of two knockdown lentiviruses, SPINK1 KD or  IL-6 KD.

overall_design: Cells were plated in 35 mm dishes, infected with NT lentivirus, SPINK1 KD #9; (NM_003122.2-208s1c1, Sigma) and IL-6 KD#58 (NM_000600.3-912s21c1, Sigma)

middle: C


title: Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages

status: Public on Nov 27 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies.

overall_design: High-resolution, genome-wide chromatin accessibility maps were determined by ATAC-seq at several stages of pure avian neural crest populations and non-neural crest cells isolated from developing chick embryos.

first: Irving

last: Ling


title: Transposon mutagenesis screening of Newcastle disease virus (NDV)

status: Public on Oct 04 2019

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

country: USA

institute: Icahn school of medicine at Mount Sinai

summary: We report the genetic plasticity of Newcastle disease virus. We introduced insertional mutation in the virus genome and checked fitness by  comparing distribution of mutants in passage 1 and passage 2.

overall_design: 3 independent trials

first: Satoshi

last: Ikegame

first: Shannon

last: Beaty

first: David

last: Sachs


title: Incidence of phosphate variations on nutrient transports in a symbiocosm formed by poplar, sorghum and Rhizophagus irregularis.

status: Public on Oct 27 2019

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

type: Expression profiling by high throughput sequencing

summary: We analyzed the impact of different phosphate levels on the regulation of plant and fungal transcriptomes.

sample_organism:
Populus trichocarpa
Sorghum bicolor
Rhizophagus irregularis

overall_design: Symbiocosms containing a poplar plant and a sorghum plant connected by a common mycelial network were used to assess the impact of phosphate content on their gene expression.

first: Silvia

last: Calabrese

first: Alexis

last: Sarazin

first: Cusant

last: Loïc

first: Annette

last: Niehl

first: Alexander

last: Erban

first: Daphnée

last: Brulé

first: Ghislaine

last: Recorbet

first: Daniel

last: Wipf

first: Joachim

last: Kopka

first: Thomas

last: Boller

first: Pierre-Emmanuel

last: Courty


title: Expression array of mouse bone marrow-derived macrophages and osteoclasts

status: Public on Oct 03 2019

city: Ann Arbor

first: Lingxin

last: Zhu

state: Michigan

address: 210 Washtenaw Ave, Life Sciences Institute, Room 5008

institute: Univeristy of Michigan in Ann Arbor

summary:
In response to the cytokines, macrophage colony-stimulating factor and receptor activator of NF-kB ligand, monocyte precursors differentiate into bone marrow-derived macrophages (BMDMs) that ultimately fuse to form multi-nucleated osteoclasts, following a tightly controlled genetic program where specific sets of genes are differentially expressed.
We used microarrays to examine the gene expression profile underlying mouse osteoclast differentiation.

overall_design: Bone marrow-derived macrophages and osteoclasts were lysed at specified stages of differentiation for RNA extraction and hybridization to Affymetrix microarrays for a time-dependent profile of the BMDM-osteoclast transition. We selected BMDM-osteoclasts at five time-points: before differentiation, i.e. BMDMs (day 0), during differentiation (day 1, 2 and 3) and the mature osteoclasts (day 5).

first: Stephen

last: Weiss


title: Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [MNase-Seq]

status: Public on Oct 29 2019

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Methylation profiling by high throughput sequencing

summary: We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

overall_design: Extract the nucleosome 147bp DNA for analysis

first: Yu-Xi

last: Luo

first: Xiao-Mei

last: Hou


title: The effects of Mkp-1 knockout and systemic E. coli infection on the transcriptome of the liver

status: Public on Oct 01 2019

city: Chicago

first: Irina

last: Buhimschi

state: IL

address: 820 S. Wood St.

department: Department of Obstetrics & Gynecology

institute: University of Illinois at Chicago College of Medicine

summary: Previously, I have found that Mkp-1 knockout exacerbates inflammation, perturbs lipid metabolism, increases organ damage, mortality, and bacterial burdens.  To understand the role of Mkp-1 in the regulation of host defense, we performed RNA-seq analysis using total RNA isolated from livers of uninfected and E. coli-infected wildtype and Mkp-1 knockout mice. Specifically, Mkp-1 wildtype and knockout (both on the C57/129 background) mice were infected with E. coli (O55:B5, ATCC 12014) at a dose of 2.5×107 CFU/g of body weight i.v., or given same volume of PBS.  Mice were sacrificed 24 h post-infection to harvest organs.  Livers were frozen clamping in liquid nitrogen, and stored at -80°C .  Total RNA was isolated with Trizol and used for RNA-seq.  RNA-seq results indicate that both E. coli infection and Mkp-1 knockout caused profound changes in the transcriptomes in the mouse livers.

overall_design: Examination of the transcriptomal changes caused by E. coli sepsis in both Mkp-1 wildtype and knockout mice.

first: Yusen

last: Liu

first: Markus

last: Hafner


title: Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis

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

overall_design: Refer to individual Series


title: Transcriptome analyses of iPSC-derived neural stem/progenitor cells and cerebral organoids from monozygotic twins discordant for schizoaffective bipolar disorder

status: Public on Sep 30 2019

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

summary: To investigate the disease-associated differences in gene expression pattern during neuro developmental stage between the discordant twins, we performed RNA sequecing-based transcriptome analyses of iPSC-derived neural cells.

overall_design:
For bulk RNA-seq, two clones of iPSC-derived neural stem/progenitor cells from each twin were analyzed. For single-cell RNA-seq, four clones of iPSC-derived cerebral organoids for each twin were analyzed. Two organoids for each clone were subjected to the analysis.
[Ethics committee]  Wako 1st Research Ethics Committee of RIKEN
[Ethics approval number] Wako-1st-15-4(23)

first: Tomoyo

last: Sawada

first: Tadafumi

last: Kato

first: Mika

last: Yoshimura

first: Kaori

last: Tanaka

first: Yohei

last: Sasagawa

last: Nikaido


title: Relevance of temozolomide for elderly patients with MGMT promoter-methylated malignant astrocytomas outside the RTK I methylation group [HD collective]

status: Public on Oct 31 2019

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: The data contains Illumina 450k/EPIC array methylation files from 380 glioblastoma patients of the Heidelberg Neuro-Oncology Center

overall_design: FFPE or KRYO tissue from 380 patients with glioblastoma was analyzed with Illumina 450k/EPIC methylation arrays. Note that this dataset contains only samples with a methylation classifier assignment of either RTK I, RTK II or mesenchymal

first: Antje

last: Wick

first: Michael

last: Platten

first: Christoph

last: Meisner

last: Bamberg

first: Ulrich

last: Herrlinger

first: Jörg

last: FElsberg

first: Astrid

last: Weyerbrock

first: Clemens

last: Seidel

first: Joachim

middle: P

last: Steinbach

last: Sabel

first: Jan

last: Esper

first: Jürgen

last: Debus

first: Felix

last: Sahm

last: Meixensberger

first: Ralf

last: Ketter

first: Regine

last: Mayer-Steinacker

first: Andreas

last: von Deimling

first: Guido

last: Reifenberger

last: Weller

first: Wolfgang


title: The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells [GRO-seq]

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

summary: The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood due to poor sensitivity and/or resolution of current chromatin structure-based assays. Consequently, it is not well established if enhancers operate individually and/or in clusters to coordinate gene transcription. In the current study, we introduce Nodewalk, which uniquely combines high sensitivity with high resolution to enable the analysis of chromatin networks in minute input material. The >10,000-fold increase in sensitivity over other many-to-all competing methods uncovered that active chromatin hubs identified in large input material, corresponding to 10 000 cells, flanking the MYC locus are primarily virtual. Thus, the close agreement between chromatin interactomes generated from aliquots corresponding to less than 10 cells with randomly re-sampled interactomes, we find that numerous distal enhancers positioned within flanking topologically associating domains (TADs) converge on MYC in largely mutually exclusive manners. Moreover, when comparing with several enhancer baits, the assignment of the MYC locus as the node with the highest dynamic importance index, indicates that it is MYC targeting its enhancers, rather than vice versa. Dynamic changes in the configuration of the boundary between TADs flanking MYC underlie numerous stochastic encounters with a diverse set of enhancers to depict the plasticity of its transcriptional regulation. Such an arrangement might increase the fitness of the cancer cell by increasing the probability of MYC transcription in response to a wide range of environmental cues encountered by the cell during the neoplastic process.

overall_design: Examination of nascent mRNA profiles in normal human colonic epithelial cells (HCEC) and human colorectal carcinoma cells (HCT116) generated by sequencing, in duplicate, using Illumina MiSeq.

first: Noriyuki

last: Sumida

first: Emmanouil

middle: G

last: Sifakis

first: Barbara

middle: A

last: Scholz

first: Alejandro

last: Fernandez-Woodbridge

first: Narsis

last: Kiani

first: David

last: Gomez-Cabrero

first: Peter

middle: J

last: Svensson

first: Jesper

last: Tegner

first: Anita

last: Göndör


title: The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells [RNA-seq]

overall_design: Examination of mRNA profiles in normal human colonic epithelial cells (HCEC) and human colorectal carcinoma cells (HCT116) generated by sequencing, in duplicate, using Illumina MiSeq.


title: The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells [Nodewalk-seq]

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Examination of intra- and interchromosomal chromatin interactions in normal human colonic epithelial cells (HCEC) and human colorectal carcinoma cells (HCT116) generated by Nodewalk, a novel 3C-based assay.


title: Impact of GDF15 expression of ovarian cancer cell on stroma and Cisplatin responses

status: Public on Sep 05 2019

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary: We report the RNAseq data from xenografts mouse models generated from human ovarian cancer cell lines A2780 with GDF15 expression knockdown with shRNA

overall_design: The gene expression profiles of tumors from cisplatin treated xenograft mouse models generated with A2780 with two independent shRNA targeting GDF15 are compared to that of A2780 with non-target shRNA


title: miRNA profiling in radiated mice bone marrow and hypothalamus pretreated with radioprotectants.

status: Public on Sep 07 2019

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

summary: To further understanding of miRNA expression during radioprotectation, we used microarray analysis to determine the differential expression of miRNAs in the bone marrow of mice exposed to high-dose IR with and without pretreatment with three types of radioprotectants: Amifostine (WR2721), CBLB502, and Nilestriol, as well in the hypothalamus of mice exposed to IR with and without pretreatment with amifostine. Overall, amifostine treatment led to a similar expression pattern of miRNAs to that of CBLB502 but not to that of nilestriol in bone marrow. The radioprotectants exhibited mostly opposite effects against IR-induced miRNAs. These results expand the biological function of miRNAs in mediating the activity of radioprotectants, further offering insights into the molecular mechanism underlying radioprotection.

overall_design: Radiation induced miRNA expression in mice bone marrow and hypothalamus pretreated with amifostime, CBLB502 and nilestriol was measured at 12 hours after exposure to doses of 8 Gy gamma-rays.  The bone marrow from three animals were pooled in one sample for each treatment.

first: Baolei

last: Tian

first: Hanjiang

last: Fu

first: Bin

last: Liu

first: Jie

last: Zhu

first: Xiaofei

last: Zheng


title: The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells

first: Rolf

last: Ohlsson


title: lncRNA and mRNA profiling in radiated mice bone marrow and hypothalamus pretreated with radioprotectants

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To further understanding of lncRNA and mRNA expression during radioprotectation, we used microarray analysis to determine the differential expression of lncRNAs, and mRNAs in the bone marrow of mice exposed to high-dose IR with and without pretreatment with three types of radioprotectants: Amifostine, CBLB502, and Nilestriol, as well in the hypothalamus of mice exposed to IR with and without pretreatment with amifostine. Overall, the induction of lncRNAs and mRNAs was increased by pretreatment with all three radioprotectants. Amifostine treatment led to a similar expression pattern of lncRNAs, and mRNAs to that of CBLB502 but not to that of nilestriol. The radioprotectants exhibited mostly opposite effects against IR-induced lncRNAs, and mRNAs in bone marrow, and might induce a potential common mechanism of histone gene downregulation only in the face of IR, mainly via nucleosome assembly and related signaling pathways, which may be a common response to IR-induced biological changes and could explain the radioprotection mechanism. These results expand the biological function of lncRNAs, and mRNAs in mediating the activity of radioprotectants, further offering insights into the molecular mechanism underlying radioprotection.

overall_design: Radiation induced lncRNA and mRNA expression in mice bone marrow and hypothalamus pretreated with amifostime, CBLB502 and nilestriol was measured at 12 hours after exposure to doses of 8 Gy g-rays. The bone marrow from three animals were pooled in one sample for each treatment.


title: Transcriptomics-based drug repurposing approach identifies novel drugs against sorafenib-resistant hepatocellular carcinoma

status: Public on Sep 01 2019

city: Columbus

first: Kelly

last: Regan

state: Ohio

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: The Ohio State Univ

summary: Hepatocellular carcinoma (HCC) is frequently diagnosed in patients with late-stage disease who are ineligible for curative surgical therapies. Furthermore, the majority of patients become resistant to sorafenib. Recently, computational methods for drug repurposing have shown great promise to accelerate the discovery of new uses for existing drugs. In order to identify novel drugs for use against sorafenib resistant (SR)-HCC, we employed a transcriptomics-based drug repurposing method termed connectivity mapping. We conducted a comprehensive analysis of available in vitro and in vivo gene signatures of (SR)-HCC, and generated our own in vitro model using the Huh7 HCC cell line. We compared coverage of SR-HCC gene signatures across seven patient-derived HCC gene expression datasets, and observed that patients harboring the Huh7 SR-HCC gene signature had significantly reduced survival. Utilizing the Huh7 SR-HCC gene signature, we applied connectivity mapping to drug-induced gene expression profiles (n= 3,740 drugs) in the HepG2 HCC cell line from the LINCS database in order to find drugs that could oppose sorafenib resistance. We validated the use of two non-receptor tyrosine kinase inhibitors, dasatinib and fostamatinib, to reduce viability of sorafenib-resistant HCC cells and confirmed up-regulated activity of Src family kinases, the targets of dasatinib, in our SR-HCC models. We prospectively validated predicted gene expression changes in fostamatinib treated Huh7-SR via RNA-seq analysis.

overall_design: Gene expression profiles of Huh7-SR hepatocellular carcinoma cells resistant to sorafenib were generated by RNAseq (Illumina HiSeq 4000) following treatment with fostamatinib and vehicle control.

middle: E

last: Regan-Fendt

first: Ding

last: Li

first: Kalpana

last: Ghoshal


title: RNA-seq in WT and sir2∆, sir4∆ and sum1∆ in K. lactis yeast strains

status: Public on Sep 28 2019

first: Lisha

address: 7000 fannin st

institute: UT Health Science Center at Houston

summary: Evaluation of the differential expression of mRNA between WT and sir2∆, WT and sir4∆, WT and sum1∆ in K. lactis yeast strains.

overall_design: There are two technical replicates of WT mRNA (2 samples) and two technical replicates of sir2∆, sir4∆ and sum1∆ mRNA (2 samples each)

first: Kristen

last: Humphrey

first: Tao

first: Laura

last: Rusche


title: Transcriptomics of an in vitro model of sorafenib resistance in Huh7 hepatocellular carcinoma cell line

summary: Hepatocellular carcinoma (HCC) is often diagnosed in patients with advanced disease who are ineligible for curative surgical therapies. Sorafenib, a multi-kinase inhibitor, is currently the only approved drug used in treating such patients. However, patients rapidly become unresponsive due to inherent and acquired drug resistance. To better understand the molecular mechanisms underlying sorafenib resistance in HCC at a global level in an unbiased manner, we conducted gene expression analysis using in vitro models of HCC sorafenib resistance using the Huh7 cell line, including a resistant pool of cells and a specific clone derived from the resistant pool.

overall_design: Untreated parental Huh7 HCC cells (n=3), Sorafenib-resistant pool Huh7 cells (n=3), Sorafenib-resistant clone A7 Huh7 cells (n=3)

first: Ryan

last: Reyes

first: Samson

middle: T

last: Jacob

first: Tasneem

last: Motiwala


title: Functional module detection through integration of single-cell RNA sequencing data with protein–protein interaction networks

status: Public on Sep 09 2019

first: Enrique

middle: M

last: Toledo

address: Innovation Building, Old Road Campus, Roosevelt Drive

department: R&D

institute: Novo Nordisk

summary:
Recent advances in single-cell RNA sequencing (scRNA-seq) have allowed researchers to explore transcriptional function at a cellular level. In this study, we present scPPIN, a method for integrating single-cell RNA sequencing data with protein–protein interaction networks to detect active modules in cells of different transcriptional states. We achieve this by clustering RNA-sequencing data, identifying differentially expressed genes, constructing node-weighted protein–protein interaction networks, and finding the maximum-weight connected subgraphs with an exact Steiner-tree approach. As a case study, we investigate RNA-sequencing data from human liver spheroids but the techniques described here are applicable to other organisms and tissues. scPPIN allows us to expand the output of differential expressed genes analysis with information from protein interactions. We find that different transcriptional states have different subnetworks of the PPIN significantly enriched which represent biological pathways. In these pathways, scPPIN also identifies proteins that are not differentially expressed but of crucial biological function (e.g., as receptors) and therefore reveals biology beyond a standard differentially expressed gene analysis.
Human primary hepatocytes from a mixture of 10 donors grown in a 3D spheroid, were purchased from InSphero AG (Switzerland) and maintained in the culture medial provided by the company. Single cell libraries were prepare with a 10X Genomics 3’ v2 kit and sequenced in an Illumina NextSeq 500. Sequencing data demultiplexing and alignment was carried out with CellRanger with default parameters.

overall_design: Single cell RNA sequencing of human primary liver spheroids from InSphero with chromium 10X  3' v2 kit.

first: Florian

last: Klimm

first: Thomas

last: Monfeuga

first: Fang

last: Zhang

first: Charlotte

last: Deane

first: Gesine

last: Reinert


title: Systematic discovery of endogenous human ribonucleoprotein complexes

status: Public on Sep 19 2019

city: Austin

first: Anna

last: Battenhouse

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

summary: An exploration of human protein complexes in the presence and absence of RNA reveals endogenous ribonucleoprotein complexes

overall_design: A robust biochemical fractionation-mass spectrometry (MS) strategy to identify RNP complexes proteome-wide by their sensitivity to RNase A-treatment

middle: L

last: Mallam

first: Wisath

last: Sae-Lee

first: Jeffery

last: Schaub

first: Fan

last: Tu

first: Yu

last: Jang

first: Jonghwan

last: Kim

first: John

middle: B

last: Wallingford

first: Ilya

last: Findelstein

first: Edward

last: Marcotte

first: Kevin

last: Drew


title: Profiling in radiated mice bone marrow and hypothalamus pretreated with radioprotectants

first: Changhui

last: Ge


title: Identifying a high-risk cellular signature in the multiple myeloma bone marrow microenvironment_3

status: Public on Aug 31 2019

city: La Jolla

first: Samuel

last: Danziger

state: CA

address: 10300 Campus Point Dr

institute: Celgene

summary: The multiple myeloma (MM) tumor microenvironment is thought to influence patient outcomes. To test this, we computationally enumerated relevant cell populations in 436 newly diagnosed MM patients. Unsupervised clustering identified 5 clusters, with patients in Cluster 5 having significantly worse outcomes: 13 fewer months of progression-free survival (P = 0.002) and 8 fewer months of overall survival (P = 0.040). Cell type analysis showed that patients in Cluster 5 had elevated CD8+ T cell and B cell populations, but low granulocyte levels. A granulocyte signature identified an additional 14% of patients with elevated risk but lacking International Staging System stage III or GEP-70 high- risk status

overall_design: To determine how the cellular content in the microenvironment contributes to patient outcome RNA extracted from whole bone marrow (WBM) biopsies were analyzed subtracting the signal derived from the malignant plasma cells to focus on the non-tumor cells. A custom algorithm was developed to define and quantitate the impact of cellular subcomponents of the bone marrow (BM) microenvironment on outcome and applied it to a series of WBM trephine biopsies.

first: Mark

last: McConnell

first: Jake

last: Gockley

first: Mary

middle: H

last: Young

first: Adam

last: Rosenthal

first: Frank

last: Schmitz

first: David

last: Reiss

first: Phil

last: Farmer

first: Daisy

middle: V

last: Alapat

first: Amrit

last: Singh

first: Cody

last: Ashby

first: Michael

last: Bauer

first: Yan

last: Ren

first: Kelsie

last: Smith

first: Suzana

middle: S

last: Couto

first: Frits

last: van Rhee

first: Faith

last: Davies

first: Maurizio

last: Zangari

first: Nathan

last: Petty

first: Robert

middle: Z

last: Orlowski

first: Madhav

last: Dhodapkar

first: Wilbert

last: Copeland

first: Brian

last: Fox

first: Antje

last: Hoering

first: Alison

last: Fitch

first: Katie

last: Newhall

first: Bart

last: Barlogie

first: Matthew

middle: W

last: Trotter

last: Hershberg

last: Walker

first: Andrew

last: Dervan

first: Alexander

last: Ratushny

first: Gareth

last: Morgan


title: Identifying a high-risk cellular signature in the multiple myeloma bone marrow microenvironment_2

first: Samuel

last: Danziger

first: Mark

last: McConnell

first: Jake

last: Gockley

first: Mary

last: Young

first: Adam

last: Rosenthal

first: Frank

last: Schmitz

first: David

last: Reiss

first: Phil

last: Farmer

first: Daisy

last: Alapat

first: Amrit

last: Singh

first: Cody

last: Ashby

first: Michael

last: Bauer

first: Yan

last: Ren

first: Kelsie

last: Smith

first: Suzana

last: Couto

last: van Rhee

last: Davies


title: Identifying a high-risk cellular signature in the multiple myeloma bone marrow microenvironment_1

last: Danziger

first: Frits

first: Faith

first: Maurizio

last: Zangari

first: Nathan

last: Petty

first: Robert

last: Orlowski

first: Madhav

last: Dhodapkar

first: Wilbert

last: Copeland

first: Brian

last: Fox

first: Antje

last: Hoering

first: Alison

last: Fitch

first: Katie

last: Newhall

first: Bart

last: Barlogie

first: Matthew

last: Trotter

last: Hershberg

last: Walker

first: Andrew

last: Dervan

first: Alexander

last: Ratushny

last: Morgan


title: Gene expression in the livers of rats with no infection and at 2 and 4 weeks after Clonorchis sinensis infection

status: Public on Aug 29 2019

city: Jinju

first: Byoung-Kuk

state: Gyeongnam

address: Jinjudaero 816

department: Department of Parasitology and Tropical Medicine, and Institute of Health Sciences

country: South Korea

institute: Gyeongsang National University

summary: We examined gene expression profiles (27028 genes) in the livers of Sprague-Dawley rats with no infection and at 2 and 4 weeks after Clonorchis sinensis infection using Whole Rat Genome Microarray 4x44K v3 (GPL14745, Agilent-028282)

overall_design: Clonorchis sinensis induced gene expression in rat livers was measured at 2 weeks (n=2) and 4 weeks (n=2) after post-infection, compared to control group (n=2).


title: Transcriptome characterization of embryogenesis at a single cell resolution [Panagrellus redivivus]

city: Vienna

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: By collecting and processing individual embryonic cells from sequentially older embryos we have generated a single cell transcriptome dataset describing embryogenesis from the fertilized zygote and the first cell divisions for all founder cell lines.

overall_design: Individual embryos were dissociated manually and single cells were collected for processing. Each cell was barcoded, and samples were multiplexed into a single sequencing library for each embryo processed.

first: Itai

last: Yanai


title: Next generation sequencing quantitatively analyzes transcriptomes of primary CLL cells co-culture with Wild Type or prkcb-/- bone marrow mesenchymal stromal cells

status: Public on Aug 15 2019

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: RNA-seq profiles of patient-derived primary CLL cells when co-cultured with bone marrow derived mesenchymal stromal cells (BMSC) from either wildtype or Prkcb-/- mice, in normal condition or under venetoclax (ABT-199) treatment.

overall_design: mRNA profiles of primary CLL cells co-culture with wildtype or prkcb-/- BMSCs were generated by deep sequencing,in both biological and techical triplicate.

first: Jingyu

last: Chen


title: Role of TCHHL1 (trichohyalin-like 1) on the proliferation of normal human epidermal keratinocytes

status: Public on Aug 22 2019

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
TCHHL1 (trichohyalin-like 1) protein is a novel member of the fused-type S100 protein gene family. Previous findings suggest that TCHHL1 may play a role in the proliferation of keratinocytes.
In the present study, to clarify a role of TCHHL1 in the proliferation of keratinocytes, we performed global-scale gene expression analysis in TCHHL1-Knockdown keratinocytes using an Affymetrix GeneChip® system.

overall_design: Normal human epidermal keratinocytes (negative control siRNA), and normal human epidermal keratinocytes (siRNA for TCHHL1) were used. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Teruhiko

last: Makino


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 and H1 after SNAI1 deletion at Day2 after human early hematopoietic differentiation .

status: Public on Jul 26 2019

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to verify SNAI1 deletion is suffice to downregulate other MAGs during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and SNAI1-knockout samples collected at day 2 after hematopoietic differentiation.
Methods: mRNA profiles of hESC samples collected at day 2 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Knockout of SNAI1 indeed suppresses the expression of other MAGs

first: Hongtao

last: Wang


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived  CD31+ cells and H1 after HAND1-overexpression derived  CD31+ cells at Day8 after human early hematopoietic differentiation .

summary:
Purpose: The goals of this study are to verify HAND1 overexpression is suffice to upregulate other MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and HAND1-overexpressed samples collected at day 8 after hematopoietic differentiation.
Methods: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: HAND1 overexpression is suffice to upregulate other MAGs during early hematopoietic differentiation of H1 cells.


title: Next generation sequencing quantitatively analyzes transcriptomes of bone marrow derived mesenchymal stromal cells from Wild Type or prkcb-/- mice

summary: RNA-seq profiles of Wild Type or Prkcb-/- mouse bone marrow derived mesenchymal stromal cells (BMSCs), either monocultured or co-cultured with primary CLL cells.

overall_design: mRNA profiles of wildtype or Pkcb-/- BMSCs, either monocultured or co-cultured with patient derived primary CLL cells, were generated by deep sequencing, in biological triplicate.


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of BC1, BC1 derived APLNR+ cells, CD31+CD34+ cells and CD43+ cells during human early hematopoietic differentiation

summary:
Purpose: The goals of this study are to verify the dynamic changes of MAGs in BC1 derived different population of cells during human early hematopoietic differentian.
Methods: mRNA profiles of hESC samples collected from day 0 to day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions:MAGs showed convincingly dynamic expression during early hematopoietic differentiation of BC1 cells


title: Identifying a high-risk cellular signature in the multiple myeloma bone marrow microenvironment

first: Samuel

last: Danziger

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

overall_design: Refer to individual Series


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without SB431542 treatment at Day8 after human early hematopoietic differentiation .

summary:
Purpose: The goals of this study are to verify the inhibition of TGFb signaling is suffice to surpress the expression of MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and samples with SB431542 treatment collected at day 8 after hematopoietic differentiation.
Methods: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Inhibiting TGFb signaling is suffice to significantly surpressed the expression of MAGs.


title: Temporal comparison of leaf transcriptomes between early-flowering Arabidopsis thaliana atx1/atx3/atx4 triple mutants and vegetative WT Col-0 plants of the same age.

status: Public on Jul 12 2019

city: Lakewood

first: Will

last: Hinckley

address: 4440 Gondar Ave

department: Biology

institute: CSULB

summary: atx1/atx3/atx4 triple mutants display significantly early flowering and early leaf senescence phenotypes. RNA-seq was used to identify gene expression changes occuring at the time of bolting, independent of leaf age.

overall_design:
Two homozygous atx1/atx3/atx4 triple T-DNA insertion mutants were isolated (TM1 and TM2). Both have the same T-DNA mutant alleles but come from different crosses so they may contain different background mutations. atx triple mutants display significant early flowering and significant early leaf senescence phenotypes. Previous phenotype analyses show that early leaf senescence was detected at day 33 in the triple mutants. RNA-seq was used to identify gene expression changes occurring at the time of bolting that might be promoting the onset of leaf senescence, thus coupling the early flowering phenotype to the early leaf senescence phenotype (see "Timeseries Design Infographic"). Triple Mutants bolting at the peak of triple mutant bolting (Days 24 and 25, see "Peak of Triple Mutant Bolting Info" for details) were pooled and then 1/4th of these bolting plants were harvested. Plants were then randomly selected for harvesting from this pool in two day increments, three times. Thus, harvesting days were 25, 27, 29, and 31 days after stratification. This strategy was used to ensure the TM plants harvested at each time point were developmentally similar. The sixth leaf to emerge was harvested from each plant. Three replicates were generated per line, per time point (4 time points), totaling to 12 cDNA libraries per genotype. The 36 cDNA libraries were prepared using the BrAD-seq protocol and were then sequenced at the University of California, Irvine Genome High-throughput Facility.
"Peak of Triple Mutant Bolting Info", "Timeseries Design Infographic", "BrAD-seq Info". These images were included to help understand the experimental design.

first: Judy

last: Brusslan

first: Keykhosrow

last: Keymanesh


title: Human and murine transcriptome profiling identifies cross-species homology in pulmonary mononuclear phagocytes [DCs and Monocytes]

status: Public on Jun 19 2019

city: Denver

first: Claudia

last: Jakubzick

state: Colorado

address: 1400 Jackson St

department: Pediatrics

institute: National Jewish Health

summary: The mononuclear phagocyte (MP) system consists of macrophages, monocytes, and dendritic cells. MP subtypes play distinct functional roles in steady-state and inflammatory conditions. Though murine MPs are well characterized, their human homologues remain poorly understood, particularly in the lung and draining lymph nodes (LNs). Understanding these homologies, and their similarities and differences with murine MPs, is critical for identifying human genetic targets and thus developing human immunotherapies. To address this gap, we performed transcriptome-based alignment across fifteen distinct human and nine distinct murine lung and LN MPs. As controls to validate the analytical quality of cross-species pulmonary MP analysis, human blood and murine spleen MPs were used. Constrained canonical correlation, t-SNE and catplot visualization was used to align human and mouse MPs and identify MP subtypes with maximal correspondence across species. Among the top marker genes expressed in corresponding human-mouse MP pairs, only 30-10% of the genes overlapped, indicating a need for caution when identifying human gene variants and functions from mice. For instance, SPP1 is highly expressed in human interstitial macrophages but not alveolar macrophages (AMs), whereas in mice SSP1 is only expressed in AMs. Moreover, human LN dendritic cells (DCs) align best with murine LN DCs but not murine splenic DCs indicating cross-species similarity in tissue. Lastly, in both species, CD88 was the most useful cell surface marker for distinguishing monocyte/macrophages from DCs. Overall, these data provide a reference for analyzing cross-species transcriptome data and evaluating whether specific murine genes are suitable guides to identify the functionality of human MPs, or conversely, whether pursuing specific human genes in mice, is likely to be a valid and fruitful approach.

overall_design: RNA-sequencing of mouse mononuclear phagocytes from lung-draining lymph nodes and spleen.

first: Sophie

last: Gibbings

first: Sandy

last: Larson

first: Thomas

last: Danhorn

first: Sonia

last: Leach


title: RNA-sequencing of pretreatment AB1 (mesothelioma) and Renca (kidney cancer) tumours mice both respondant and non-respondant to immunotherapy with CTLA4 and PD-L1

status: Public on Jul 18 2019

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

summary:
Purpose: Cancer immunotherapy has shown outstanding results in the past few years. Specifically, antibodies targeting immune checkpoints can prolong survival in some patients with various cancer types. However, most patients do not respond, and it is not fully understood what biological processes determine an effective outcome. This lack of understanding hinders the development of rational combination treatments.
Methods: Here, we analysed bulk RNAseq data obtained from pretreatment responding and non-responding tumour samples from mice treated with antibodies against CTLA4 and PD-L1.
Results: We found that responsive tumours displayed an inflammatory gene expression signature which was consistent with positive upstream regulation by not only IFNγ/STAT1, but also TLR3 and negative regulation by IL-10.  Our results identify a pre-treatment cellular microenvironment and molecular signature associated with benefit from immune checkpoint blockade that can be therapeutically attained to improve treatment efficacy.

overall_design: 48 samples in total: 24 samples from AB1 pretreatment tumours (12  responders, 12 non-responders) and 24 samples from Renca pretreatment tumours (12 responders, 12 nonresponders). Each sample represents an individual biological replicate (i.e. no duplicate samples from the same mouse). Response to immunotherapy determined….

first: Rachael

last: Zemek

first: Wee

last: Chin

first: Vanessa

last: Fear

first: Tom

last: Casey

first: Cath

last: Forbes

first: Danika

last: Hope

first: Louis

last: Boon

first: Alistair

middle: R

last: Forrest

first: Daithi

middle: O

last: Muiri

first: Michael

last: Millward

first: Anna

middle: K

last: Nowak

first: Timo

last: Lassmann

first: Anthony

last: Bosco

first: Richard

last: Lake

first: Willem

last: Lesterhuis


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without IWP2 treatment at Day2 after human early hematopoietic differentiation .

first: Jiaxi

last: Zhou

summary:
Purpose: The goals of this study are to verify the inhibition of Wnt signaling is suffice to surpress the expression of MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and samples with IWP2 treatment collected at day 2 after hematopoietic differentiation.
Methods: mRNA profiles of hESC samples collected at day 2 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Inhibiting Wnt signaling is suffice to significantly surpressed the expression of MAGs.

first: Hongtao

last: Wang


title: Human and murine transcriptome profiling identifies cross-species homology in pulmonary mononuclear phagocytes

first: Claudia

last: Jakubzick


title: MUTHEC

status: Public on Apr 05 2019

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

institute: Centre de Recherche des Cordeliers

summary: We analyzed 801 primary HCC developed in 720 patients. Samples were collected from 1992 to 2016 in three French tertiary liver centers  in patients treated by liver resection, liver transplantation (surgical samples) and in patients treated by radiofrequency ablation and with advanced HCC  treated by non-curative therapies (tumor biopsies).   All samples obtained from surgical samples or tumor biopsy were immediately frozen in liquid nitrogen and stored at -80°C prior extraction. We  assessed mRNA expression by quantitative RT-PCR in a subset of 757 liver tumor samples. 517 to 782 HCC, according to the gene considered, were sequenced for 30 driver genes (TERT, TP53, CTNNB1, AXIN1, PIK3CA, ARID1A, ARID2, RPS6KA3, NFE2L2, CDKN2A, IL6ST, BRAF, STAT3, HNF1A, JAK1, KRAS, GNAS, KEAP1, IRF2, HRAS, NRAS, TSC2, APOB, TSC1, ALB, CDKN1A, MAP1B, SETD2, ATM and MLL2).

overall_design: Quantitative RT-PCR and target sequencing on human hepatocellular carcinoma (HCC)

first: Jean

last: Charles Nault

first: Jessica

last: Zucman-Rossi


status: Public on Apr 01 2019

city: Cincinnati

first: LungMAPP

last: DCC

state: OH

address: 3333 Burnet Ave

institute: LungMAP DCC

summary: The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on postnatal day 1. Distinct populations of epithelial, endothelial, mesenchymal, and immune cells were identified, each containing distinct subpopulations. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://www.lungmap.net/

overall_design:
Time course RNA-seq profiling of mouse sorted AT2 cells
contributor: LungMAP Consortium

first: Jeffrey

last: Whitsett

first: Yan

last: Xu


status: Public on Mar 29 2019

summary: The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on several time points. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://www.lungmap.net/

overall_design:
Time course RNA-seq profiling of mouse sorted Pdgfra+ fibroblasts
Contributor: LungMAP Consortium

first: Anne

last: Perl


title: TP53/DNA Damage Response Pathway is Activated and Contributes to the Pathogenesis of Dilated Cardiomyopathy Caused by Lamin A/C Mutations

status: Public on Apr 17 2019

city: Houaton

first: Ali

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

summary: To gain insights into the molecular pathogenesis of DCM caused by LMNA mutation, a doxycycline-inducible (Dox-Off) gene expression system was used to express either a wild type (WT) or a mutant LMNA containing the pathogenic variant p.Asp300Asn (LMNAD300N) in cardiac myocytes. The LMNAD300N is associated with DCM in patients with atypical progeroid/Werner syndrome and non-syndromic cardiac progeria. Expression of the mutant LMNAD300N protein in cardiac myocytes led to severe fibrosis, apoptosis, cardiac dysfunction, and premature death.  RNA-seq was performed (prior to onset of cardiac dysfunction) to identify  gene signatures and transcriptional regulators responsible for this phenotype. Mechanistic studies identified activation of E2F/TP53/DDR, as a major mechanism responsible for the pathogenesis of DCM caused by the LMNAD300N mutation.

overall_design: RNA-seq analysis   from  2-week old WT and mice expressing mutant LMNA  (LMNAD300N)

first: Suet

middle: N

last: Chen

first: Raffaella

last: Lombardi

first: Jennifer

last: Karmouch

first: Judy

last: Tsai

first: Grace

last: Czernuszewicz

first: Matthew

last: Taylor

first: Luisa

last: Mestroni

first: Cristian

last: Coarfa

first: Priyatansh

last: Gurha


title: Transcriptomic analyses of co-infection of Mycoplasma gallisepticum and Escherichia coli in chicken lungs

status: Public on Apr 19 2019

city: Harbin

first: Zhiyong

last: Wu

address: 600 Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

summary:
Purpose:In order to assess the respiratory toxicity of co-infection in chicken lung, we established a co-infection model to investigate transcriptome profiles of chicken lung.
Methods: RNA extracted by Trizol reagent (Invitrogen) was utilized to construct the final library (BGISEQ-500 RNA-Seq Library) based on the manufacturer’s instructions. Library was validated on the Agilent Technologies 2100 bioanalyzer. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecule. The DNBs were load into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by synthesis. Whole transcriptome sequencing data was filtered and mapped to Chicken genome (Gallus genome Version 5.0.1 NCBI). DEG-seq method was based on Poisson distribution (Fold Change > 2 and Adjusted P value < 0.001)
Results: Sampling directly from the lung yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 18,043 Gallus gallus genes.
Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-infection (MG and E.coli) and their underlying mechanisms.

overall_design: mRNA profiles of control and three infected groups of chicken lungs were generated by deep sequencing. The sequence reads that passed quality filters were analyzed at the transcript

first: J

last: Li

first: Z

last: Wang


title: Combined Targeting of Estrogen Receptor alpha and XPO1 prevent Akt activation, remodel metabolic pathways and induce autophagy to overcome tamoxifen resistance

status: Public on May 26 2019

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

summary: Majority of breast cancer specific deaths in women with ERα (+) tumor occur due to metastases that are resistant to endocrine therapy. There is a critical need for novel therapeutic approaches to resensitize recurrent ERα (+) tumors to endocrine therapies. The objective of this study was to elucidate mechanisms of improved effectiveness of combined targeting of ERα and XPO1, a nuclear transport protein in overcoming endocrine resistance. Selinexor (SXR), an XPO1 antagonist, has been evaluated in multiple later stage clinical trials in patients with relapsed and /or refractory hematological and solid tumor malignancies. Using human phosphokinase array to profile kinase signaling pathways, we found that 4-OH Tamoxifen, SXR or their combination induced differential Akt phosphorylation profiles, changing the phosphorylation status and activity of the kinase. Also, our RNA sequencing data indicated that 4-OH Tamoxifen+SXR combination treatment causes gene expression changes distinct from 4-OH Tamoxifen and SXR treatments alone in tamoxifen-resistant cell lines. Since we observed dramatic changes in Akt activity and we saw a differential gene expression pattern with individual and combined 4-OH Tamoxifen and SXR treatments, we hypothesized that metabolic profile of breast cancer cells would change in the presence of 4-OH Tamoxifen and SXR.  Using Seahorse metabolic profiler and cell viability experiments in limited media conditions, we showed that tamoxifen resistant cells were more dependent on mitochondria for energy production. Their glucose and fatty acid dependency decreased in the presence of SXR and cells were more dependent on glutamine as the mitochondrial fuel source.    We demonstrated that combined targeting of XPO1 and ERα rewires metabolic pathways and shuts down both glycolytic and mitochondrial pathways that would eventually lead to autophagy.  Remodelling metabolic pathways to regenerate new vulnerabilities in endocrine resistant breast tumors is novel, and given the need for better strategies for improving therapy response of relapsed ERα (+) tumors, our findings show great promise for uncovering the role of ERα-XPO1 crosstalk plays in reducing cancer recurrences.

overall_design: RNASeq analysis was performed as previously described [17; 18; 19]. Briefly, BT474 cells were treated with Veh (0.5% EtOH), 10-7 M 4-OH Tamoxifen (Sigma, St. Louis, MO), 10-7 M Selinexor (SXR) (Selleckchem, Houston, TX) or 4-OH Tamoxifen and SXR combination for 24 hours. Total RNA was extracted with TRIzol reagent (Life Technologies) according to manufacturer protocol and cleaned using QIAGEN clean-up kit. RNA quality was assessed using bioanalyzer. Total RNA from each sample (3 per treatment group) were sequenced at the sequencing center at UIUC, and data was generated in Fastqc file format to compare the expressions between four treatment groups.

first: Eylem

last: Kulkoyluoglu-Cotul

first: Brandi

middle: P

last: Smith

first: Kinga

last: Wrobel

first: Yiru

middle: C

last: Zhao

first: Karen

first: Kadriye

last: Hieronymi

first: Ozan

last: Imir

first: Caitlin

last: O'Callaghan

first: Aditi

last: Mehta

first: Yosef

last: Landesman


title: UAB LungMAP Consortium Data

first: LungMAPP

last: DCC


title: Defining the inflammatory gene signature at day 7 postpartum associated with the development of bovine uterine disease

city: Dunsany

first: Kieran

middle: Gerard

last: Meade

state: Co. Meath

address: Grange

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary:
Background: Physiological inflammation of the uterus postpartum is essential for the reparative processes of involution after calving. In the majority of cows, this inflammation is resolved and homeostasis is restored. However, in a significant subset, inflammation persists and contributes to tissue damage, pathology and subfertility. Transcriptomic differences of immune genes between cattle that resolve inflammation and those that develop uterine disease have been detected as early as 7 days postpartum (DPP) suggesting that the host immune response plays an important role in disease outcome.
Results: Here, we extensively characterise the immune response at the transcriptomic level in endometrial epithelial cells from post-partum dairy cows phenotyped for both clinical and sub-clinical forms of uterine disease. We address the hypothesis that excessive expression of endometrial inflammatory molecules contributes to development of endometritis. Classification of cattle (n=112) as healthy or with uterine disease (purulent vaginal discharge; PVD and cytological endometritis; CYTO) was based on vaginal mucus score and >18% polymorphonuclear cell infiltrate into the endometrium at 21 DPP. RNA-seq analysis of endometrial epithelial cells collected using cytobrushes identified differential expression of 294 genes (FDR <0.05) between cows that subsequently resolved inflammation (n=10) and those that developed disease (n=20). Pathway over-representation analysis of differentially expressed genes (DEG) identified significant changes in immune-related pathways, including the NOD-like receptor signalling pathway, cytokine-cytokine receptor interaction pathway and the Toll-like receptor signalling pathway which were up-regulated in cattle that subsequently developed disease. The majority of the DEG were upregulated in cows that developed PVD, and included all genes upregulated in CYTO cows, suggesting a core inflammatory gene signature early post-partum contributes to the onset of uterine disease. This inflammatory signature was validated by qPCR in an independent group of cows (n=56) and included upregulation of pro-inflammatory genes (including TLR2, TLR4, NLRP3, IL1A, IL1B, IL8, and S100A8) at day 7 postpartum in cows that failed to resolve inflammation.
Conclusions: Despite a large amount of inter-animal heterogeneity, these results suggest that excessive activation and inappropriate regulation of the inflammatory response early postpartum is a key feature of the subsequent development of uterine disease.
Keywords: Endometritis, Inflammation, Transcriptome, Next generation sequencing, Dairy cattle, Uterine involution, Immune response

overall_design: Examination of endometrial transcriptome of healthy and endometritic cows at 7 days postpartum.

first: Amy

last: Brewer

first: Paul

last: Cormican

first: Joseph

middle: J

last: Lim

first: Aspinas

last: Chapwanya

first: Cliona

last: O’ Farrelly

middle: G


title: growth competition assay of Sendai virus and mumps virus

status: Public on Mar 21 2019

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

summary: We evaluate the individual growth of 8 mutants of Sendai virus in the competitive  condition under the cultured cells. We also evalate the growth of 6 mutants of mumps virus in the similar competitive condition.

sample_organism:
Mumps orthorubulavirus
Respirovirus muris

overall_design:
3 independent trial in Sendai virus and mumps virus
Mumps virus (7 mutants);
Insert will be 1386, 1781, 1858, 1881, 2892, 3436.
Sendai virus (8 mutants);
Insert will be 1405, 1606, 1694, 1721, 2659, 2703, 2748, 2909.
All positions are base on my excel file (showing a coverage).
The sequence of 15bp insert is 'TGCGGCCGCANNNNN'.
Last 5N is variable depending on the position where insert occurs.

first: Satoshi

last: Ikegame

first: Shannon

last: Beaty


title: A time course study by mRNA Sequencing to identify transcriptional changes in mice lung development

status: Public on Mar 19 2019

summary: Mammalian fetal lung development is a complex biological process.Despite considerable progress, a comprehensive understanding of the dynamic regulatory networks that govern postnatal alveolar lung development is still lacking. The purpose of this study as part of the LungMAP consortium (www.lungmap.net)  is to understand the transcriptional  changes in the process of mammalian lung development.

overall_design: Method:  We isolated alveolar septa from c57BL/6 mice  by laser capture microdissection from 14 time points (E16.5, P0.5, P1, P1.5, P2.5, P4, P5, P7, P10, P13.5, P15, P19, P23, and P28) and performed RNA-Sequencing by Illumina Hi-Seq 2500 .

first: Farida

last: Ahangari

first: Teodora

last: Nicola

first: Namasivayam

last: Ambalavanan

first: Naftali

last: Kaminski


title: Time course RNA-seq profiling in sorted endothelial, epithelial, and immune cells from WT C57BL6 mice

summary: The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on postnatal day 1. Distinct populations of epithelial, endothelial, and immune cells were identified, each containing distinct subpopulations. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://www.lungmap.net/

overall_design: Time course RNA-seq profiling in sorted endothelial, epithelial, immune, and mesenchymal-derived cells from E16.5, E18.5, P7 and P28 wild-type C57BL6 mice

first: Jeffrey

middle: A

last: Whitsett

first: Yan

last: Xu


title: Transcriptome analysis of TNFR1-knockout mouse colon

status: Public on Mar 15 2019

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

summary:
We have compared mRNA expression in full-thickness mouse colon between wildtype mice and mice with a genetic deletion in tumor necrosis factor receptor 1 (TNFR1, encoded by the Tnfrsf1a gene). This experiment was motivated by our observation that Il10-/- Tnfr1-/- double-knockout mice develop very-early-onset colitis at the time of weaning, significantly earlier than disease onset in Il10-/- single-knockout mice. This suggests that TNFR1 mediates protection from colitis. To understand these protective mechanisms at the transcript level in a non-inflammatory context, we performed transcriptome profiling (mRNA-Seq) on colons from 12-week-old Tnfr1-/- mice, which do not develop colitis, and wildtype littermates. These experiments revealed that an estimated 510 transcripts were upregulated and 377 downregulated in colonic tissue of Tnfr1-/- mice. We aggregated the transcript information to calculate gene expression and performed gene set enrichment analysis to identify signaling pathways altered in Tnfr1-/- mice. When queried against a high-confidence set of 50 signaling pathways, the Tnfr1-/- gene expression profile was associated with reduced mitosis and increased glycolysis, transforming growth factor beta signaling, DNA repair, and reactive oxygen species signaling. Gene ontological analysis classified some of the differentially expressed genes into cytokines, junctional proteins, and transcription factors, but within these groups there was no consensus on the direction of regulation.
We also examined how differentially expressed transcripts (called the TNFR1-regulated transcriptome) compared to differentially expressed colonic transcripts from previously collected Tnfr2-/- animals (or the TNFR2-regulated transcriptome, available at the NCBI Gene Expression Omnibus under the accession GSE65408). The raw data were re-analyzed with the current pipeline to enable comparison. There was almost no correlation between TNFR1- and TNFR2-regulated transcripts. Only 30 (~3%) TNFR1-regulated transcripts were also TNFR2-regulated transcripts, and ~4% of the TNFR2-regulated genes were also TNFR1-regulated genes. Of the few co-regulated transcripts, there was a significant negative correlation in their direction of regulation in Tnfr1-/- versus Tnfr2-/- colons. Collectively these results indicate that TNFR1 and TNFR2 have mostly different and opposing effects on gene expression in the mouse colon.
MANUSCRIPT ABSTRACT:  BACKGROUND & AIMS: Very-early-onset inflammatory bowel disease (VEO-IBD) is a devastating disease beginning in early childhood, refractory to anti-tumor necrosis factor (anti-TNF) therapies, and associated with mutations in the interleukin 10 (IL-10) pathway. Contrary to mainstream clinical practice, cellular and animal studies have shown beneficial roles of TNF signaling in colitis, but how these roles are encoded through TNF’s receptors remains unknown. Here we examined the role of TNF receptor 1 (TNFR1, or p55) in modulating the onset and severity of colitis in the interleukin 10 (IL-10)-deficient mouse model.  METHODS: Colitis severity was compared between Il10-/- Tnfr1-/- and Il10-/-- littermate mice at 2-12 weeks of age. To assess dysbiosis as a potential pathogenic mechanism, Il10-/- Tnfr1-/- mice were treated with neomycin and metronidazole and their cecal contents analyzed by 16S rRNA sequencing. Gene expression, barrier function, and epithelial proliferation and apoptosis were examined in adult colitis-free Tnfr1-/- wildtype littermates.  RESULTS: In contrast to relatively healthy Il10-/- mice, Il10-/- Tnfr1-/- mice developed severe, antibiotic-treatable colitis shortly after weaning. Microbiotal composition was similar between Il10‑/- Tnfr1-/- mice and Il10-/- littermate controls. Tnfr1-/- mice expressed transcripts associated with reactive oxygen species and DNA repair pathways. Tnfr1-/- mice exhibited focal areas of crypt branching, higher colonic epithelial permeability, and hallmarks of DNA damage.  CONCLUSIONS: TNFR1 promotes epithelial homeostasis and regulates commensal exposure. The lack of TNFR1 accelerates the onset and severity of IBD in the absence of tolerogenic signaling (i.e., lack of IL-10). Il10-/- Tnfr1-/- mice may serve as a valuable model of very-early-onset IBD (VEO-IBD).

overall_design: Total RNA from whole colons of 12 week-old male wildtype C57Bl/6 and TNFR1-/- mice (n=3 each) was isolated using the PureLink RNA kit (Ambion, Life Technologies). RNA samples were submitted to the Genomic Services Lab at the HudsonAlpha Institute for Biotechnology (Huntsville, AL) for multiplex library preparation, mRNA enrichment, and sequencing. Sequencing was performed to an average depth of 30M paired-end 50bp reads per sample (HiSeq, Illumina, San Diego, CA). Data files containing raw reads were aligned to the mouse genome using kallisto, and statistical tests for differential expression were performed with sleuth.

first: Sharon

last: Tam

middle: Y

first: Philip

middle: E

last: Dubé

first: Shivesh

last: Punit

first: Rabea

last: Alhosh

first: Nandini

last: Girish

first: D

last: Polk


title: LungMAP Consortium Data

status: Public on Mar 25 2019

first: LungMAPP

last: DCC

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


title: Genome-wide miRNA and piRNA profiles of the vector whitefly, Bemisia tabaci during feeding on Tomato yellow leaf curl virus-infected tomato

status: Public on Feb 28 2019

city: Charleston

first: Kai-Shu

last: Ling

state: SC

address: 2700 Savannah Hwy

institute: USDA-ARS

type: Non-coding RNA profiling by high throughput sequencing

summary: The whitefly, Bemisia tabaci MEAM1 is a devastating vector capable of transmitting hundreds of plant viruses, including Tomato yellow leaf curl virus (TYLCV), to important food and fiber crops. Here we performed genome-wide profiling of micro RNAs (miRNAs) and piwi-interacting RNAs (piRNAs) in whiteflies after feeding on TYLCV-infected tomato or uninfected tomato for 24, 48 and 72 h. Overall, 160 miRNAs were discovered, 68 of which were conserved and 92 were B. tabaci-specific miRNAs. Majority of the genes that were predicted to be targeted by miRNAs had gene ontologies related to metabolic processes. We identified two miRNAs that were differentially expressed in whiteflies when fed on TYLCV-infected tomato compared to whiteflies that fed on uninfected tomato. The identified piRNAs were expressed as clusters throughout the whitefly genome. A total of 53 piRNA clusters were expressed across all time points and treatments, while 5 piRNA clusters were exclusively expressed in whiteflies that fed on TYLCV-infected tomato, and 24 clusters were exclusively expressed in whiteflies that fed on uninfected tomato. Approximately 62% of all identified piRNAs were derived from non-coding sequences that included intergenic regions, introns, and UTRs with unknown functions.  The remaining 38% of piRNAs were derived from coding sequences (CDS) and repeat elements. Transposable elements targeted by piRNA clusters included both class I retrotransposons such as Gypsy, Copia, and LINEs and class II DNA transposons such as MITE, hAT, and TcMar. Lastly, six protein coding genes were targeted in whiteflies that fed on TYLCV-infected tomato. Information on how TYLCV influences miRNA and piRNA expression in whiteflies provides a greater understanding of regulatory pathways involved in mediating whitefly-virus interactions, and will facilitate the identification of novel targets for RNAi control.

overall_design: Deep sequencing of small RNAs was isolated from total RNA from whiteflies fed on either TYLCV-infected tomato or uninfected tomato for 24, 48, and 72 h. Three biological replicates were performed for each time point.

first: Md

last: Shamimuzzaman

first: Daniel

last: Hasegawa


title: RNA-seq of  control and Lmna -/- mice heart samples

status: Public on Feb 08 2019

first: Ali

last: Marian

summary: RNA-sequencing analysis from  whole heart ribosome depleted RNA  from the 2-week old WT and Lmna-/- mice (N=5) . Strand specific RNA seq libraries where prepared form   ribosome-depleted cardiac RNA samples using the Illumina TruSeq stranded total RNA library preparation kit. The samples weresequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate100 base paired  end reads.

overall_design: Cardiac RNA profiles from 14-day old wild type (WT) and Lmna -/- mice were generated by deep sequencing from 5 mice in each genotype.

first: Cristian

last: Coarfa


title: Transposon mutagenesis screening of Sendai virus and mumps virus

status: Public on Feb 01 2019

first: satoshi

last: ikegame

summary: We report the genetic plasticity of Sendai virus and mumps virus. We introduced insertional mutation in the virus genome and checked fitness by comparing distribution of mutans in passage 1 and passage 2.

platform_organism:
Mumps orthorubulavirus
Respirovirus muris

overall_design: 3 independent trial in Sendai virus and mumps virus

first: Satoshi

last: Ikegame

first: Shannon

last: Beaty

first: David

last: Sachs


title: HIV-1 Vpu exerts broad immunosuppressive effects by inhibiting NF-κB-dependent gene expression

status: Public on Feb 05 2019

city: La Jolla

first: Lars

last: Pache

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Using an unbiased RNA sequencing approach of primary CD4+ T cells infected with three wild type primary HIV-1 isolates and selective mutants thereof, Langer et al. show that the HIV-1 accessory protein Vpu exerts broad immunosuppressive effects, inhibiting the induction of innate and adaptive immune responses. Transcription factor network analyses reveal that Vpu suppresses the expression of NF‑κB rather than IRF3 target genes. As a result, Vpu impairs the production of pro-inflammatory cytokines such as IFNβ, CXCL10 and IL-6.

overall_design: Human CD4+ T cells, isolated from 4 independent healthy donors, A1, X, Y and Z (corresponding to A, B, C and D in the publication), were infected with equal amounts of three different HIV-1 primary isolates, two of them being clade B viruses (HIV-1 CH077 and HIV-1 STCO1) and one of them being a clade C virus (HIV-1 CH293). In addition, CD4+ T cells were infected with mutant viruses of the aforementioned primary isolates. Specific mutations were introduced in these viruses to either abrogate Vpu expression ("vpu stop"), or selectively abrogate Vpu-mediated counteraction of the antiviral protein tetherin ("A20L/A24L" or "A15L/A19L") or NF-kB inhibition ("R50K" or "R45K"). Global RNA of  infected cells was collected 72 hours post infection and processed for RNA-Seq analysis.

first: Simon

last: Langer

first: Christian

last: Hammer

first: Paul

middle: D

last: De Jesus

first: Kristina

middle: M

last: Herbert

first: Sumit

last: Chanda

first: Jacques

last: Fellay

last: Sauter


title: Stimulative effect of low-dose neonicotinoid pesticide, clothianidin on human neuroblastoma SH-SY5Y cells by disrupting intracellular signaling

status: Public on Feb 06 2019

first: Tetsushi

last: Hirano

address: 2630 sugitani

summary:
Neonicotinoids are one of most widely used pesticides targeting nicotinic acetylcholine receptors (nAChRs) of insects and suspected to have adverse effects on mammals by laboratory testing on rodents. Recent epidemiological evidence revealed the increasing amounts of neonicotinoids detected from human samples, rising a critical question whether neonicotinoids affect to human health.
We investigated potential effects of a neonicotinoid pesticide, clothianidin (CTD) on human neuroblastoma SH-SY5Y cells as a model of nervous systems of human. Transcriptional analyses using GeneChip system were also performed to understand the effects of CTD on global gene expression.

overall_design: Total RNA was extracted from SH-SY5Y cells exposed to 1uM of CTD or vehicle (0.1%DMSO) for 24 hours. Quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Clariom S array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Yoshiaki

last: Tabuchi


title: Regulation of Translation Elongation Revealed by Ribosome Profiling

status: Public on Jan 27 2019

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

sample_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans
Homo sapiens

overall_design: Refer to individual Series


title: Regulation of Translation Elongation Revealed by Ribosome Profiling [Dataset_4]

summary: Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. These distinct ribosome conformational states revealed by ribosome profiling are seen in all eukaryotes tested including fungi, worms and mammals. This high-resolution ribosome profiling approach reveals the anticipated Rck2-dependent inhibition of translocation through eEF2 phosphorylation during hyperosmotic stress. These same approaches reveal a strong translation elongation arrest during oxidative stress where the ribosomes are trapped in a pre-translocation state, but in this case the translational arrest is independent of Rck2-driven eEF2 phosphorylation. These results provide new insights and approaches for defining the molecular events that impact translation elongation throughout biology.

platform_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans
Homo sapiens

overall_design: 24 biological samples are included for ribosome footprinting samples. These include HeLa, MB-MDA-231 and yeast cells and C. elegans embryos.

first: Rachel

last: Green


title: A developmental model of human early cardiac valvulogenesis (II)

status: Public on Jan 23 2019

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

institute: INSERM

summary: One third of cardiac congenital diseases affect cardiac valves. Genetically modifiedmice have advancedourunderstandingof valve development and related pathologies. However, little is known with regard tohuman valve development.We aimed to derive a novel human pluripotent stem cellmodel in order to decode the early steps of human valvulogenesis.Human MesP1+mesodermal cells were differentiated toward the fate of second heart field progenitors and then to a selected population of pre-valvular endocardial cells. Gene arrays revealed that these human prevalvular cells (HPVC) express patterns of genes similar to those expressed in theatrioventricular canal (AVC) endocardium of E9.0 mouse embryos. In mice this developmental time precedes endocardial mesenchymal transition (EndoMT),which is required for mature valve formation.HPVC treated with BMP2, cultured onto chick or mouse AVC cushions, or transplanted into the outflow tract or AVC of embryonic chick and mouse hearts, underwent EndoMTin both a Notch-dependent and independent-manner and expressed markers of valve mesenchymal cells and fibroblasts.Similar to the previously described valve interstitial cells (VICs), HPVC also differentiate into tendinous/chondrogenic cells.   Our study indicates thathuman pluripotent stem cells canrecapitulate early valvulogenesis and thus provide a powerful model to further decipher the origin and lineage contributionof different valvular cell typesin humans.

overall_design: experiments were performed in triplicates

first: Stephane

last: Zaffran

first: Michel

last: Puceat

first: Randy

last: Faustino


title: RNA-Seq of WT and constitutively methylated mESCs

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: WT J1 and 3B3L cells (in which Dnmt3B and Dnm3L are constitutively expressed from an exogenous construct) were cultured under both serum/LIF and 2i/LIF conditions. 3B3L cells do not show ground state-associated hypomethylation phenotype. This experiment sought to analyse the gene expression changes between the two conditions.

overall_design: Three biological replicates per condition J1 serum, J1 2i, 3B3-3l serum, 3B3-3l 2i.

first: Katy

last: McLaughlin

first: Ilya

last: Flyamer

first: John

last: Thomson

first: Heidi

last: Mjoseng

first: Ruchi

last: Shukla

first: Iain

last: Williamson

first: Robert

middle: S

last: Illingworth

first: Ian

last: Adams

first: Sari

last: Pennings

first: Wendy

last: Bickmore

first: Richard

last: Meehan


first: LungMAPP

last: DCC

summary:
Mammalian fetal lung development is a complex biological process.Despite considerable progress, a comprehensive understanding of the dynamic regulatory networks that govern postnatal alveolar lung development is still lacking. The purpose of this study as part of the LungMAP consortium (www.lungmap.net)  is to understand the transcriptional  changes in the process of mammalian lung development.
Method:  We isolated endothelial and type II pneumocyte cells from c57BL/6 mice from different time points and performed miRNA array by NanoString technology.

overall_design:
Time course NanoString microRNA expression profiling in sorted endothelial cells and type II pneumocytes from WT C57BL6 mice

contributor: LungMAP Consortium

first: Farida

last: Ahangari

first: Teodora

last: Nicola

first: Namasivayam

last: Ambalavanan

first: Naftali

last: Kaminski


title: Manganese detoxification by Staphylococcus aureus

status: Public on Jan 01 2019

city: Nashville

first: Eric

last: Skaar

state: TN

address: 1161 21st Avenue South, Medical Center North A5102

department: Department of Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

summary: Manganese (Mn) is an essential micronutrient critical for the pathogenesis of Staphylococcus aureus, a significant cause of human morbidity and mortality. Paradoxically, excess Mn is toxic, therefore maintaining intracellular Mn homeostasis is required for survival. To identify gene candidates that contribute to manganese detoxification, we compared the transcriptional response of S. aureus cells exposed to 1 mM MnCl2 and those that were untreated.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Cultures of S. aureus were exposed to either 1 mM MnCl2 or untreated media. The experiment was performed in biological triplicate for a total of 6 samples.

first: Caroline

last: Grunenwald

first: Lillian

last: Juttukonda

first: Andy

last: Weiss


title: Pseudomonas aeruginosa CLJ3 genome sequencing, transcriptomics, and proteomics [transcriptomics]

status: Public on Nov 30 2018

city: Grenoble

first: Ina

last: Attrée

address: 17 avenue des Martyrs

department: Laboratory Biology of Cancer and Infection

institute: Biosciences and Biotechnology Institute of Grenoble

summary:
Gene expression profiles of two Pseudomonas aeruginosa taxonomic outlier clinical isolates, CLJ1 and CLJ3 [CLJ3]

Pseudomonas aeruginosa taxonomic outliers emerged recently as infectious for humans, provoking hemorrhagic pneumonia. Those bacteria lack classical type III secretion system, and utilize the pore-forming toxin for infection. Two clones CLJ1 and CLJ3 belonging to these taxonomic outliers have been isolated from the same patient at two different times during hospitalization. P. aeruginosa CLJ3 displays antibiotic resistance phenotype, while CLJ1 is more cytotoxic on epithelial and endothelial cells.

overall_design: Total RNA was isolated from CLJ3 and sequenced in duplicate using Illumina HiSeq to compare their genome-wide transcription levels and relate these to protein levels and genome sequence.

first: Erwin

last: Sentausa


title: From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo

status: Public on Dec 07 2018

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: The neural crest (NC) is a transient embryonic stem cell population characterised by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant versus wild-type cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. Strikingly, foxd3 then gradually switches from an activator to its previously well-described role as a transcriptional repressor. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from ‘permissive’ to ‘repressive’ nucleosome/chromatin organisation to maintain multipotency and define cell fates.

overall_design: Examination of RNA-seq, ATAC-seq, histone ChIP-seq, Biotin ChIP-seq in wild-type and foxd3 mutant context at epiboly stages and in neural crest cells; single-cell RNA-seq

first: Martyna

last: Lukoseviciute

first: Daria

last: Gavriouchkina

first: Ruth

last: Williams

first: Tatiana

last: Hochgreb-Hagele

first: Upeka

last: Senanayake

first: Vanessa

last: Chong-Morrison

first: Supat

last: Thongjuea

first: Emmanouela

last: Repapi

first: Adam

last: Mead


title: Relevance of temozolomide for elderly patients with MGMT promoter-methylated malignant astrocytomas outside the RTK I methylation group

status: Public on Oct 31 2019

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The data contains Illumina 450k/EPIC array methylation files from 104 patients of the NOA-08 study comparing temozolomide alone vs. radiotherapy in elderly patients with glioblastoma

overall_design: Out of the 373 patients included in the NOA-08 study, tissue for biomarker analysis was available in 104 patients. PPFE tissue was used to characterize methylation profiles of these patient tumors with 450k/EPIC arrays

first: Antje

last: Wick

first: Michael

last: Platten

first: Christoph

last: Meisner

last: Bamberg

first: Ulrich

last: Herrlinger

first: Jörg

last: Felsberg

first: Astrid

last: Weyerbrock

first: Clemens

last: Seidel

first: Joachim

last: Steinbach

last: Sabel

first: Jan

last: Vesper

first: Jürgen

last: Debus

first: Felix

last: Sahm

last: Meixensberger

first: Ralf

last: Ketter

first: Regine

last: Mayer-Steinacker

first: Andreas

last: von Deimling

first: Guido

last: Reifenberger

last: Weller

first: Wolfgang


title: Genome-wide linkage analysis in Spanish melanoma-prone families

city: Barcelona

first: joan anton

last: Puig Butille

address: Villarroel 170

country: Spain

institute: Hospital Clínic

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array


title: CCHMC LungMAP Consortium Data

status: Public on Apr 01 2019

city: Cincinnati

first: LungMAPP

last: DCC

address: 3333 Burnet Ave

institute: LungMAP DCC


title: GDF15 is a secretary protein from ovarian cancer cell A2780 and induced by cisplatin in vivo

status: Public on Nov 08 2018

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary:
A2780 is a cisplatin sensitive ovarian cancer cell line. A2780 ovarian cancer cells was treated with different doses of cisplatin in an attempt to identify biomarkers that can be used to predict chemoresponse.
We used microarrays to identify genes induced by cisplatin in a time dependent manner.

overall_design: A2780 ovarian cancer cell lines were treated with two acute doses of cisplatin (5μM or 10μM) and treated cells were harvested at different times for gene expression profiling.

first: Daisy

middle: I

last: Izaguirre


title: Intricate genetic program underlying hypoxia-induced dormancy in Mycobacterium tuberculosis revealed by high-resolution transcriptional time-course

status: Public on Mar 04 2019

city: Seattle

first: Eliza

last: Peterson

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Transcriptional profiling (RNA-seq) of Mycobacterium tuberculosis during transitions between normoxia and hypoxia.

overall_design: Cultures of Mycobacterium tuberculosis were grown in reactors with mass flow controllers to control the amount of nitrogen and air flowing into the reactors. Fiber optic technology non-invasively measured the dissolved oxygen content of the cultures, and specially-designed sampling ports were used to draw out samples while preventing oxygen from leaking into the cultures. Samples were collected along a 5 day time-course and harvested for mRNA expression profiling by Illumina sequencing, in triplicate. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.

first: Abrar

last: Abidi

first: Nitin

last: Baliga


title: Pseudomonas aeruginosa CLJ1 genome sequencing, transcriptomics, and proteomics [transcriptomics]

first: Ina

last: Attrée

summary:
Gene expression profiles of two Pseudomonas aeruginosa taxonomic outlier clinical isolates, CLJ1 and CLJ3 [CLJ1]

Pseudomonas aeruginosa taxonomic outliers emerged recently as infectious for humans, provoking hemorrhagic pneumonia. Those bacteria lack classical type III secretion system, and utilize the pore-forming toxin for infection. Two clones CLJ1 and CLJ3 belonging to these taxonomic outliers have been isolated from the same patient at two different times during hospitalization. P. aeruginosa CLJ3 displays antibiotic resistance phenotype, while CLJ1 is more cytotoxic on epithelial and endothelial cells.

overall_design: Total RNA was isolated from CLJ1 and sequenced in duplicate using Illumina HiSeq to compare their genome-wide transcription levels and relate these to protein levels and genome sequence.

first: Erwin

last: Sentausa


title: Similarities and differences in the regulation of HoxD genes during chick and mouse limb development [Capture Hi-C]

status: Public on Nov 27 2018

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences

summary: Hoxd genes are important for limb development in all tetrapods examined thus far. In mouse, they are controlled by a complex bimodal regulation, which regulates first the proximal patterning, then the distal structure, allowing at the same time the formation of the wrist and ankle articulations. We analyzed the existence of this regulatory mechanism in chicken, i.e. in an animal where large morphological differences exist between fore- and hindlimbs. We report that while this bimodal regulation is globally conserved between mammals and avian, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancer and the position of the TAD boundary and the forelimb versus hindlimb comparative regulations. Some aspects of these regulations seem to be more conserved between chick and bats than with the mouse situation, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their functions.

overall_design: Capture Hi-C datasets of chick whole fore- or hindlimb buds at HH20

first: N

first: L

last: Lopez-Delisle

first: C

last: Bolt

first: D

last: Duboule


title: The ultra-sensitive Nodewalk technique identifies stochastic from virtual, population-based enhancer hubs regulating MYC in 3D: Implications for the fitness of cancer cells [ChIP-seq]

status: Public on Sep 30 2019

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

institute: Karolinska Institutet

summary: The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood due to poor sensitivity and/or resolution of current chromatin structure-based assays. Consequently, it is not well established if enhancers operate individually and/or in clusters to coordinate gene transcription. In the current study, we introduce Nodewalk, which uniquely combines high sensitivity with high resolution to enable the analysis of chromatin networks in minute input material. The >10,000-fold increase in sensitivity over other many-to-all competing methods uncovered that active chromatin hubs identified in large input material, corresponding to 10 000 cells, flanking the MYC locus are primarily virtual. Thus, the close agreement between chromatin interactomes generated from aliquots corresponding to less than 10 cells with randomly re-sampled interactomes, we find that numerous distal enhancers positioned within flanking topologically associating domains (TADs) converge on MYC in largely mutually exclusive manners. Moreover, when comparing with several enhancer baits, the assignment of the MYC locus as the node with the highest dynamic importance index, indicates that it is MYC targeting its enhancers, rather than vice versa. Dynamic changes in the configuration of the boundary between TADs flanking MYC underlie numerous stochastic encounters with a diverse set of enhancers to depict the plasticity of its transcriptional regulation. Such an arrangement might increase the fitness of the cancer cell by increasing the probability of MYC transcription in response to a wide range of environmental cues encountered by the cell during the neoplastic process.

overall_design: ChIP-Seq for H3K27me3 in HCT116 colon cancer cells (2 replicates).

first: Noriyuki

last: Sumida

first: Emmanouil

last: Sifakis

first: Barbara

last: Scholz

first: Alejandro

last: Fernandez-Woodbridge

first: Narsis

last: Kiani

first: David

last: Gomez-Cabrero

first: Peter

last: Svensson

first: Jesper

last: Tegner

first: Anita

last: Göndör


title: RNA-Seq data of NCI-H82 cells expressing a Dox-On pRB (pTripZ RB1) grown in the presence or absence of DOX and then treated with vehicle or AZD2811.

status: Public on Sep 28 2018

city: Boston

first: Matthew

last: Oser

state: MA

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

summary: We report changes in gene expression in response to reexpression of pRB in NCI-H82 cells and how AZD2811 differentially affects the transcriptome of these cells depending on whether or not pRB is expressed.

overall_design: Two biological replicates (10_18 and 10_21) for analysis of gene expression (RNA-Seq) in NCI-H82 cells that are grown in the presence (pRB+) or absense (pRB-) of DOX and treated with AZD2811 or not.

first: William

last: Kaelin Jr.


title: Functional significance of the HIV-1 Tat signature amino acid residues

status: Public on Oct 25 2018

city: Bengaluru

first: Ranga

last: Udaykumar

state: Karnataka

address: Jakkur post

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: We sequenced the mRNA from a stably transduced Human T-cell line expressing the HIV-1 Tat protein. The inducible Tat expression has been used to understand and compare the cellular molecules and pathways being modulated by the wild type subtype-C Tat versus its single signature amino acid residue variant.  Additionaly, the HIV-1 subtype B and C Tat comparitive analysis has also been included in the study to evaluate the  gene expression profile as a reponse to subtype specific Tat proteins.

overall_design: Evaluation of the genes and pathways differentially modulated by the epression of the variant HIV-1 Tat proteins or suntype specific Tat proteins in a Human T-cell line using RNASeq analysis.

first: M

last: Menon

first: K

last: Bankar

last: Vasudevan

first: U

last: Ranga


title: Genome-wide map of DNA replication origin in Schizosaccharomyces pombe

status: Public on Jan 19 2019

city: Tokyo

first: Takashi

last: Sutani

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: DNA replication origins, or DNA sites pre-RC is bound to, were identified by ChIP-seq of pre-RC components, Orc4 and Mcm2. DNA copy number analysis revealed that ~40% of the detected sites were efficient and early-firing origins.

overall_design: ChIP-seq of Orc4 and Mcm2 in G1 cells. Both ChIP-purified and input DNA were sequenced to accurately map the binding sites. Genome DNA of cells arrested in early-S and G2 phases were also sequenced to map early replicated genome regions. 6 samples in total.

first: Koji

last: Masuda


title: Patient adipose stem cell-derived adipocytes reveal genetic variation that predicts anti-diabetic drug response

status: Public on Jan 11 2019

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: Thiazolidinedione drugs (TZDs) target the transcriptional activity of PPARg to reverse insulin resistance in type 2 diabetes, but side effects limit their clinical use. Here, using human adipose stem cell-derived adipocytes, we demonstrate that single-nucleotide polymorphisms (SNPs) were enriched at sites of patient-specific PPARg binding, which correlated with the individual-specific effects of TZD rosiglitazone (rosi) on gene expression. Rosi induction of ABCA1, which regulates cholesterol metabolism, was dependent upon SNP rs4743771, which modulated PPARg binding by influencing the genomic occupancy of its cooperating factor NFIA. Conversion of rs4743771 from the inactive SNP allele to the active one by CRISPR/Cas9-mediated editing rescued PPARg binding as well as rosi-induction of ABCA1 expression. Moreover, rs4743771 is a major determinant of undesired serum cholesterol increases in rosi-treated diabetics. These data highlight human genetic variation that impacts PPARg genomic occupancy and patient responses to antidiabetic drugs, with implications for developing personalized therapies for metabolic disorders

overall_design: hACSs derived from obstity patient were differentiated into adipocytes; then treated with rosiglitazone

first: Wenxiang

last: Hu