title: Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus plant microbe interaction

status: Public on Jun 14 2020

city: Carbondale

first: Bryan

middle: Manyasi

last: Musungu

state: IL

address: 1125 Lincoln Dr.

department: Plant Biology

institute: Southern Illinois University Carbondale

summary: The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore authors undertook a systems biology approach involving dual RNA-seq to determine simultaneous response from the host and pathogen.  What was dramatically highlighted in the analysis was upon infection there is uniformity in the development of the host and pathogen.  This led to the development of host-pathogen index which was able to categorize the samples for down-stream system biology analysis.   Additionally we were able to determine key genes in the pathways such as jasmonate, ethylene and ROS which were up-regulated in the studyThe stage of infection index used for the transcriptomic analysis revealed that A. flavus does not produce many transcripts initially during pathogenesis.  It was found that when A. flavus was producing an abundance of transcripts, pathways involved the endosomal transport, aflatoxin production, sugar production and many others were up-regulated.  In tandem, Z. mays had multiple resistance pathways, such as the phenylpropaniod, jasmonic acid and ethylene pathways that were up-regulated.  The analysis of the gene regulatory networks revealed that multiple WRKY genes were targeting the activation of the resistance pathways. The analysis also revealed, for the first time, the activation of Z. mays resistance genes targeting A. flavus genes.  Our results show that the plant-microbe interaction has multiple layers and that A. flavus transcriptionally reacts to the hostile environment of Z. mays.   The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore authors undertook a systems biology approach involving dual RNA-seq to determine simultaneous response from the host and pathogen.  What was dramatically highlighted in the analysis was upon infection there is uniformity in the development of the host and pathogen.  This led to the development of host-pathogen index which was able to categorize the samples for down-stream system biology analysis.   Additionally we were able to determine key genes in the pathways such as jasmonate, ethylene and ROS which were up-regulated in the studyThe stage of infection index used for the transcriptomic analysis revealed that A. flavus does not produce many transcripts initially during pathogenesis.  It was found that when A. flavus was producing an abundance of transcripts, pathways involved the endosomal transport, aflatoxin production, sugar production and many others were up-regulated.  In tandem, Z. mays had multiple resistance pathways, such as the phenylpropaniod, jasmonic acid and ethylene pathways that were up-regulated.  The analysis of the gene regulatory networks revealed that multiple WRKY genes were targeting the activation of the resistance pathways. The analysis also revealed, for the first time, the activation of Z. mays resistance genes targeting A. flavus genes.  Our results show that the plant-microbe interaction has multiple layers and that A. flavus transcriptionally reacts to the hostile environment of Z. mays.   The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore authors undertook a systems biology approach involving dual RNA-seq to determine simultaneous response from the host and pathogen.  What was dramatically highlighted in the analysis was upon infection there is uniformity in the development of the host and pathogen.  This led to the development of host-pathogen index which was able to categorize the samples for down-stream system biology analysis.   Additionally we were able to determine key genes in the pathways such as jasmonate, ethylene and ROS which were up-regulated in the studyThe stage of infection index used for the transcriptomic analysis revealed that A. flavus does not produce many transcripts initially during pathogenesis.  It was found that when A. flavus was producing an abundance of transcripts, pathways involved the endosomal transport, aflatoxin production, sugar production and many others were up-regulated.  In tandem, Z. mays had multiple resistance pathways, such as the phenylpropaniod, jasmonic acid and ethylene pathways that were up-regulated.  The analysis of the gene regulatory networks revealed that multiple WRKY genes were targeting the activation of the resistance pathways. The analysis also revealed, for the first time, the activation of Z. mays resistance genes targeting A. flavus genes.  Our results show that the plant-microbe interaction has multiple layers and that A. flavus transcriptionally reacts to the hostile environment of Z. mays.

sample_organism:
Zea mays
Aspergillus flavus

platform_organism:
Zea mays
Aspergillus flavus

overall_design: B73 maize was innoculated with Aspergillus flavus and samples were collected at 0,4,6,8,12,18,24,30,36,42,48,72,96,120,144 hours post inoculation and analyzed using a dual RNA-seq approach

first: Matt

last: Geisler

first: Gary

last: Payne

first: Ahmad

last: Fakhoury

first: Greg

last: Obrien

first: Deepak

last: Bhatnagar

first: Robert

last: Brown


title: mRNA sequencing of human glioma stem like cell and Kaposi's sarcoma assocaited herpesvirs infected human glioma stem like cell.

status: Public on Jun 13 2020

city: Daejeon

first: Hyungtaek

last: Jeon

address: 77 GYERYONG-RO 771BEON-GIL, JUNG-GU

department: school of medicine, Dept. of microbiology and immunology

country: South Korea

institute: Eulji University

type: Expression profiling by high throughput sequencing

summary: Difference of cell growth between KSHV infected human glioblastoma stem like cell and uninfected cell.

overall_design: Examination of KSHV infected glioma stem like cell and mock infected cells.

first: Myung-Shin

last: Lee


title: Piwi-like 4 and piRNA Regulate Neuroinflammation Transcriptionally and Post-transcriptionally

status: Public on Jul 01 2020

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

country: USA

institute: UCSD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Analysis of the impact of Piwil4 suppression on p65 and c-Jun binding to inflammatory genes in microglia

overall_design: ChIP-seq experiments are designed to examined the chromatin binding of p65 and c-Jun in activated microglial BV-2 cells when Piwil4 is knocked down

first: Qidong

last: Hu


title: ELOVL2 is a novel tumor suppressor attenuating tamoxifen resistance in breast cancer via suppressing the AKT pathway

status: Public on Jun 12 2020

city: Goyang

first: Dawoon

last: Jeong

address: 32 Dongguk-ro, Ilsan Dong-gu

department: Life Science

institute: Dongguk University

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: ELOVL2 is a novel tumor suppressor attenuating tamoxifen resistance in breast cancer via suppressing the AKT pathway [methylation 850K]

summary: Genome wide DNA methylation profiling of tamoxifen-resistant(Tam-R) breast cancer cell line MCF-7. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs.

overall_design: Genomic DNA obtained from MCF-7 where acquires tamoxifen-resistance.

first: Sunjung

last: Kim


title: Low and High Dose Progestins Elicit Distinct Breast Cancer Biology

city: Chicago

first: Hari

last: Singhal

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: An incomplete understanding of dose-dependent progesterone receptor (PR) biology has led to the suboptimal exploitation of PR as a therapeutic target. While hormone replacement therapies (HRT) containing low-doses of synthetic progestogens (progestins) have been associated with an increased risk of breast cancer, high-dose progestin therapies have beneficial therapeutic effects in some patients with breast cancer. Herein we report that PR subcellular localization, post-trans3lational modifications, stability, chromatin binding, responsive gene expression and downstream biology differ considerably as a function of progestin concentration. Dose-dependent transcriptional profiling revealed that different concentrations of progestin elicit classic sigmoidal and/or biphasic gene induction at distinct target gene sets. Notably, when compared to high doses of progestin, low-dose treatments lead to minimal nuclear translocation of PR while supporting robust induction of a subset of target genes, indicating that PR occupancy has a complex relationship to target gene induction. Interestingly, high but not low-dose progestin treatments lead to increased phosphorylation at Ser294 and is associated with higher receptor turnover. Furthermore, while low-dose treatments stimulate cell proliferation, high-dose treatments do not result in significant cell cycle progression to S phase. Similar biphasic and sigmoidal patterns of gene induction were observed in human breast tumor explants treated with various concentrations of progestin, underscoring the need to fine tune the dosage of PR-targeting therapies. Given the wide range of medical applications of PR target therapy, our discovery of distinct dose-dependent PR biology may have important clinical implications.

overall_design: Cells were grown in DMEM supplemented with 8% fetal bovine serum (FBS) and 1% penicillin streptomycin. Prior to experiments, cells were cultured for 48 hours in phenol red free media supplemented with 0.1% charcoal-stripped FBS and 1% penicillin streptomycin (steroid-deprived media). R5020 (PerkinElmer #NLP004005MG) dissolved in ethanol (vehicle) was used at a final concentration as mentioned in the manuscript.

first: Myles


title: Tracking epigenetic changes during human leukemogenesis

city: Montreal

first: Thomas

last: Milan

state: Quebec

address: 2950 Chemin de Polytechnique

country: Canada

institute: IRIC

summary: We have developed a human model leukemia system where healthy cord blood (CB) cells from single donors are used to generate dozens of human leukemias driven by KMT2A fusions. These models have been used for the study of the stepwise changes in donor CB cells as they undergo leukemic transformation driven by the KMT2A-MLLT3 (KM3) fusion gene. We specifically studied the epigenetic changes that occur in this specific AML subgroup through ChIP-seq of histone modifications and ATAC-seq and DNA methylation through Methyl-Seq.

overall_design: The overall design is to study epigenetic changes in human Hematopoietic Stem and Progenitor Cells (HSPCs) during leukemogenesis

first: Magalie

last: Celton

first: Karine

last: Lagacé

first: Elodie

last: Roques

first: Safia

last: Safa-Tahar-Henni

first: Eva

last: Bresson

first: Anne

last: Bergeron

first: Josée

last: Hebert

first: Soheil

last: Meshinchi

first: Sonia

last: Cellot

first: Frédéric

last: Barabé

first: Brian

middle: T

last: Wilhelm


title: ELOVL2 is a novel tumor suppressor attenuating tamoxifen resistance in breast cancer via suppressing the AKT pathway [gene expression]

summary: Analysis of tamoxifen-sensitivity recovery effect by genes which are regulated by ELOVL2(Elongation of very long chain fatty acids protein 2) at gene expression level in breast cancer. This study identifies that ELOVL2 regulates AKT or ER signaling-related genes and  ELOVL2 as an essential gene responsible for resistance.

overall_design: Total RNA obtained from tamoxifen-resistant MCF-7(Tam-R MCF-7) where ELOVL2 was overexpressed


title: ELOVL2 is a novel tumor suppressor attenuating tamoxifen resistance in breast cancer via suppressing the AKT pathway [methylation 450K]

summary: Genome wide DNA methylation profiling of tamoxifen-resistant(Tam-R) breast cancer cell line MCF-7. The Illumina Infinium Human Methylation 450k Bead chip was used to obtain DNA methylation profiles across approximately 450,000 CpGs.


title: P0 wild type tooth and skin

status: Public on Jun 27 2020

city: SENDAI

first: Kan

last: Saito

state: Miyagi

address: 4-1 Seiryo-machi

department: Oral Health and Development Sciences

country: Japan

institute: Tohoku University

summary: P0 whole tooth germ cells versus P0 skin cells

overall_design: tooth and skin at P0


title: Transcriptional changes during astrocyte maturation in vivo at single cell resolution

status: Public on Jun 11 2020

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

summary: Analysis of gene expression during striatal astrocyte maturation in vivo in mouse by scRNA-Seq

overall_design: In vivo astrocytes were purified from mice using anti-ACSA2 MACS at indicated ages. Cells were analysed by 10X-Genomics scRNA-Seq.

first: Francois

last: Guillemot

first: Robert

last: Goldstone


title: Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome [Affymetrix]

status: Public on Jun 23 2020

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

institute: The Institute of Cancer Research

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

summary: Combination of CDK4/6 inhibitors and endocrine therapy has been shown to improve clinical outcome in advanced estrogen receptor-positive breast cancer. However, not all patients will benefit and relapse is inevitable making the identification of new therapeutic strategies/biomarkers of particular importance.

overall_design: Affymetrix Genome-wide Human SNP Array 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from the target cell lines using QIAamp DNA mini kit according to the manusfacturer’s instructions (Qiagen).

first: Qiong

first: Ricardo

middle: R

last: Santos

first: Lesley

middle: A

last: Martin


title: Effects of Injectable DMPA and Combined Oral Contraceptive Use on HIV Susceptibility Factors in Pig-tailed Macaques

status: Public on Jun 07 2020

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
Progestin-based contraception may increase the risk of vaginal HIV acquisition to a level greater than the progesterone-rich luteal phase of the menstrual cycle, which has been demonstrated to have a significantly higher transmission rate compared to the follicular phase. We used pig-tailed macaque (Macaca nemestrina) model to evaluate the effects of administration of the oral the combined oral contraceptives (COCs) depot medroxyprogesterone acetate (DMPA) and levonorgestrel (LNG) on mucosal factors that influence HIV susceptibility. We compared the pH and vaginal epithelial thickness data from previous studies, and evaluated contraception-induced molecular changes in the vagina using transcriptional and cytokine profiling.
The administration of  DMPA caused a pronounced thinning of the vaginal epilthelium relative to measurements takein in the follicular or luteal phase. DMPA also induced a significant increase in vaginal IL10 expression. Lastly, using RNA-Seq analyses of vaginal biopsies, we noted that both DMPA- and LNG-based contraception induced a signature of gene expression similar to that of the luteal phase, only more exacerbated, and including widespread down-regulation of HIV-restriction genes. Use of progestin-based contraception might engender a milieu that poses an increased risk of HIV transmission than that of the luteal phase via vaginal thinning, induction of immunosuppressive cytokines, and widespread suppression of HIV restriction factors.

overall_design: 15 animals were divided into 4 sub-phases of the menstrual cycle. Vaginal pinch biopsy samples from pre-treatment (baseline) and post-HC (COC, 5 weeks after first dose; DMPA, 2 weeks post-second injection) were hybridized to Affymetrix GeneChip® Rhesus Macaque Genome Arrays.

first: Sundaram

last: Vishwanathan

first: Steven

middle: E

last: Bosinger

first: Nirav

middle: B

last: Patel

first: Chunxia

last: Zhao

first: Tamika

last: Payne

first: Sharon

middle: D

last: Ostergaard

first: Katherine

last: Butler

first: James

last: Mitchell

first: Shanon

last: Ellis

first: Ellen

middle: N

last: Kersh

first: Janet

middle: M

last: McNicholl


title: Chromatin accessibility changes during astrocyte maturation in vivo and in culture

first: Michael

last: Lattke

summary: Analysis of changes in chromatin accessibility during astrocyte differentiation and maturation in vivo and in vitro in mouse, and investigation of transcription factors and extrinsic conditions influencing maturation

overall_design: In vivo astrocytes were purified from mice using anti-ACSA2 MACS at indicated ages. In vitro astrocytes were differentiated from cultured neural stem/progenitor cells (cultured in EGF/FGF2 medium) using BMP4 for 14 days (without EGF/FGF2). Where indicated, astrocytes in vitro were infected with transgenes and gene expression induced from day 7 to 14, or astrocytes differentiated for 7 days in BMP4 in normal 2D cultures or in 3D cultures were matured for 7 days in basal medium or FGF2 containing medium. Cells were analysed by ATAC-Seq.

first: Francois

last: Guillemot

first: Robert


title: Expression data from Control or TRIB3-silenced A549 cells

status: Public on Jun 09 2020

city: Beijing

first: Jiaojiao

last: Yu

address: 1 Xian Nong Tan Street

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
To determine the critical mediator of TRIB3-enhanced EGFR recycling, we examined the expression profile of genes that might regulate EGFR recycling by using mRNA microarrays.
EGFR tyrosine kinase inhibitors (TKIs) confer first line therapy for patients with non-small-cell lung cancer (NSCLC). However, patients eventually develop disease progression, often driven by inevitable acquisition of EGFR TKI resistant mutations. Currently all EGFR TKIs repress NSCLC through inhibiting the kinase activity of EGFR signaling, highlighting the need for therapeutics with alternative mechanisms of action. Here we report that the elevated TRIB3 expression associates positively with EGFR stability and NSCLC progression. TRIB3 interacts with EGFR and recruits PKCα thereby enhances PKCα-induced T654 phosphorylation, which suppresses EGFR degradation and enhances membrane recycling, EGFR downstream signaling, and NSCLC stemness.

overall_design: Total RNA from A549 cells expressing Control-shRNA or TRIB3-shRNA were obtained. RNA quantity and quality were measured by NanoDrop ND-1000. RNA microarrays were performed.

first: Fang

last: Hua


title: MicroRNA-934 is a novel regulator orchestrating neurogenesis during early human neural development

status: Public on Jun 06 2020

city: Boston

first: Ioannis

middle: S

last: Vlachos

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify microRNAs (miRNAs) with a key role in the molecular mechanisms controlling human neurogenesis, we performed deep sequencing of small and long RNA transcripts at distinct stages of directed neuronal differentiation of human embryonic and induced pluripotent stem cells.

overall_design: We have performed RNA Sequencing (RNA-Seq) and small RNA-Seq in skin fibroblasts, iPSCs, neural progenitor cells (NPCs) and neurons PD and control samples (two clones from each individual), along with HUES 6, HUES 6-derived NPCs and HUES-derived neurons. The two library preparations (RNA-Seq and small RNA-Seq) were performed using the same initial samples.

first: Kanella

last: Prodromidou

first: Maria

last: Gaitanou

first: Georgia

last: Kouroupi

first: Artemis

last: Hatzigeorgiou

first: Rebecca

last: Matsas


title: Single-cell RNA-seq of control and Sendai virus-infected mouse lungs [2wk timpoint]

status: Public on Jun 02 2020

city: Houston

first: Margo

middle: Patricia

last: Cain

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

summary: The Sendai virus infection model induces global changes involving multiple lung cell types. At 2 weeks post-infection, when the virus had been largely cleared and the lung is undergoing repair, proliferation of endothelial cells and alveolar type 2 (AT2) cells is observed, as well as aberrant appearance Trp63/Sox2-expressing basal-like cells reminiscent of pods or lineage-negative epithelial progenitors observed upon severe H1N1 virus infection.

overall_design: FACS-purified control or virus infected whole murine lung epithelial, endothelial, mesenchymal, and immune cells were mixed together in similar proportions and processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics).

middle: P

first: Jichao

last: Chen

first: Belinda

middle: J

last: Hernandez


title: Targeting Germline and Tumor Associated Nucleotide Excision Repair Defects in Cancer

status: Public on Jun 01 2020

city: New York

first: Sabine

last: Topka

state: NY

address: 417 E. 68Th St.Zuckerman Research Bldg.

department: Medicine

institute: MSKCC

summary: Genetic alterations in members of the nucleotide excision repair (NER) pathway are present in a wide spectrum of cancers, but specific treatment options for this patient population are scarce. Here, we show occurrence of putative damaging germline and somatic alterations in NER genes in up to 10% of patients within certain cancer types across a large set of cancers and explored the potential therapeutic role of irofulven for patients with hypomorphic mutations in nucleotide excision repair genes. Gene-edited isogenic pairs of wildtype and mutant ERCC2 or ERCC3 cell lines were used to assess response to irofulven. Both in vitro and in vivo studies showed significantly enhanced irofulven sensitivity in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to the current standard of care agent cisplatin. Hypomorphic ERCC2/3 mutant cells had an impaired ability to repair irofulven induced DNA damage. Transcriptomic profiling of the tumor tissues suggested co-dependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies. The present study provides a molecularly targeted, pre-clinical approach to cancers with mutations in nucleotide excision repair pathway genes, demonstrating preferential sensitivity to the drug irofulven alone, or in combination with other agents.

overall_design: Analysis of mRNA expression in xenografts derived from either wildtype human mammary epithelial (HMLE) cells or HMLE cells gene-edited to harbor a heterozygous mutation in ERCC3 (p.R109X). Tumors from eight vehicle treated mice each and tumors from seven mice each treated with irofulven were used for analysis.

first: Zoe

last: Steinsnyder

first: Vignesh

last: Ravichandran

first: Kaitlyn

last: Tkachuk

first: Yelena

last: Kemel

first: Chaitanya

last: Bandlamudi

first: Mogens

middle: W

last: Madsen

first: Helena

last: Furberg

first: Ouathek

last: Ouerfelli

first: Charles

last: Rudin

first: Gopakumar

last: Iyer

first: Steven

last: Lipkin

first: Semanti

last: Mukherjee

first: David

last: Solit

middle: F

last: Berger

first: Dean

last: Bajorin

first: Jonathan

last: Rosenberg

first: Barry

last: Taylor

first: Elisa

last: DeStanchina

first: Vijai

last: Joseph

first: Kenneth

last: Offit


title: Time-series transcription microarray data of Streptomyces coelicolor M145-OA

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

institute: IMCAS

summary: The present work aimed at selecting appropriate native temporal promoters with the identical profile of the cumate-inducible promoter under the optimal induction condition. This strategy enabled us to optimized the expression of biosynthetic gene cluster of desired secondary metabolites in Streptomyces, while avoid the use of inducer during fermentation. By clustering the genes with quite similar transcriptional profile with that of gfp controlled by the cumate-inducible promoter based on time-series microarray data, 50 qualified genes were identified, which were controlled by 24 putative promoters. Then, the cumate-inducible promoter were replaced by the 24 native temporal promoters, and fermentation results showed the good performance of these promoters compared to that of the cumate-inducible promoter. Therefore, our strategy could be used to fine-tune the expression of target BGCs for production improvement.

overall_design: Transcriptional profiling of S. coelicolor M145-OA at different growth phases (exponential, transitional and stationary phase)

first: Shanshan

last: Li

first: Junyang

last: Wang

first: Weishan


title: Development of gene expression signatures for derivatives of mangiferin

status: Public on Jun 05 2020

city: Shanghai

first: jun

last: Han

address: 800 Xiangyin Rd.

institute: Second Military Medical University, Shanghai, China

summary: To further development of our gene expression approach to pharmacology, we have employed whole genome microarray expression profiling as a discovery platform to identify gene expressionsignatures for 2 derivatives of mangiferin.   3T3-L1 preadipocytes were incubated with X-1 or X-3 for 24 h, and a 19-gene consensus signature was identified that distinguished between treatment and control samples.

overall_design: X-1 or X-3 induced gene expression in 3T3-L1 cells was measured at  24 hours after exposure to 70 µM.  Nine independent experiments were performed at  24 hours.

first: Jun

first: Fengying

last: Liang


title: Exploring acupuncture mechanism in preconditioning of IRI

city: Jinan

first: Qi

middle: Wen

last: Tan

state: Shandong

address: Jingshi Road 16369

department: Acupuncture Department

institute: Shandong University of TCM

summary: JJ group compared with the MX group, 703 differentially expressed genes were screened out, among which 542 were up-regulated and 161 genes were down-regulated; compared with DZ group, 1529 differentially expressed genes were screened, 1212 genes were up-regulated and 317 genes were down-regulated. KEGG Pathway analysis enriched the Wnt pathway, and screened 11 genes; among which 9 genes were up-regulated, including Wnt5b, Wnt9b, Wnt10b, Fzd2, Plch1, Plch2, dkkl1, Amer and Amer3, and 2 were down-regulated, including plcb1 and sapcd2.

overall_design: Rats were randomly divided into sham group(DZ), IRI group(MX), Jiaji group（JJ）, Neiguan group（NG）, Yanglingquan group(YL), Quchi group(QC). After 7 day’s pretreatment of acupuncture, MIRI model was replicated by ligation of the left anterior descending coronary artery in MX group and all acupuncture groups(n=4 respectively).

first: Qiwen

first: Ning

last: Xiao


title: The different genes profiles in NASH-HCC specimens

first: Jian

last: Wu

address: 138 Yixue Yuan Road

institute: Fudan University

summary:
Paraffin-embedded paired tumor and peri-carcinoma tissues (n=4) were obtained from the Biorepository of Fudan University Institute of Liver Cancer, which were used for the Affymetrix microarray analysis
To investigate the progression of NASH to HCC, we established a differential gene expression profile by analyzing significant expression changes in pathologically confirmed NASH-HCC and peri-carcinoma specimens using Affymetrix microarrays.

overall_design: 4 pairs of NASH-HCC tumor and its precarcinoma tissues


title: β-catenin regulates FOXP2 transcriptional activity via multiple binding sites

city: Graz

first: Gesa

last: Richter

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical University Graz

summary: We observed different gene expression by overexpressing the transcription factor FOXP2 in U2OS cells compared to mock-transfected cells. Additionally, we found β-catenin as co-activator binding directly to FOXP2. Activation of Wnt signaling was changing the transcriptional activity of FOXP2. Other functional and regulatory elements were found within FOXP2 and were confirmed by RNA-Seq.

overall_design: Determining gene expression differences by overexpressing an transcription factor (wildtype and mutant) in human osteosarcoma cells and additional activation of an Signaling pathway linked to the function of this transcription factor

first: Tobias

last: Madl


title: Transcriptomic study of NR8383 cells following exposure to multi-walled carbon nanotubes (NM401)

status: Public on May 30 2020

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

country: France

institute: Université de lorraine

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages exposed for 4 h to 0.17 µg/mL of multi-walled carbon nanotubes (NM401) (100 % cell viability). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 686098

overall_design: Changes in gene expression in NR8383 cells incubated without (control) or with (0.17 µg/mL) of multi-walled carbon nanotubes (NM401) for 4 h were measured. For each condition, four biological replicates were performed : C1; C2; C3; C4 as controls, T1; T2; T3, T4 as exposed cells.

first: Ramia

last: Safar

first: Sara

last: Nahlé

first: Bertrand

middle: H

last: Rihn

first: Luc

last: Ferrari


title: Endogenous retroviruses act as enhancers to drive species-specific germline transcriptomes in mammals

status: Public on May 28 2020

city: Cincinnati

first: Akihiko

last: Sakashita

state: Ohio

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary: Gene regulation in the germline ensures the production of high-quality gametes, long-term maintenance of the species, and speciation. Germline transcriptomes undergo dynamic changes after the mitosis-to-meiosis transition in males and have been subject to evolutionary divergence among mammals. However, the mechanism that underlies germline regulatory divergence remains undetermined. Here, we show that endogenous retroviruses influence species-specific germline transcriptomes in mammals. We show that the endogenous retroviruses function as active enhancers to drive evolutionarily young (mouse or rodent specific) spermatogenesis-specific genes after the mitosis-to-meiosis transition in male mice. These ERV loci bear binding motifs for critical regulators of spermatogenesis such as A-MYB. The genome-wide transposition of ERVs might have rewired germline gene expression in a species-specific manner. Notably, these features are present in human spermatogenesis, but independently evolved ERVs are associated with expression of germline genes, demonstrating the prevalence of ERV-driven mechanisms in mammals. Together, we propose a model whereby species-specific transcriptomes are fine-tuned by endogenous retroviruses in the mammalian germline.

overall_design: ChIP-seq analysis using wild-type and A-myb mutant pachytene spermatocytes; RNA-seq analysis using RLTR10B2 targeting CRISPRa mouse embryonic stem cells

first: Satoshi

last: Namekawa


title: Role of DPYSL2A in KLF4-mediated monocytic differentiation in AML cells

status: Public on May 31 2020

city: Kyoto

first: Ken

last: Morita

address: 53 Kawahara-cho, Syogoin, Sakyo-ku

department: Human Health Sciences

institute: Kyoto University

summary:
To compare the global gene expressions in between KLF4- and DPYSL2A-expressed AML cells, we conducted gene expression arrays in THP-1 cells lentivirally-transduced with doxycycline-inducible KLF4 or DPYSL2A.
We identified the pivotal role of KLF4-DPYSL2A axis in differentiating AML cells, which could be theraputically-tageted in conventional therapy-resistant AML patients.

overall_design: THP-1 cells were transduced with lentivirus encoding KLF4 or DPYSL2A under doxycycline responsive promoters. Cells were treated with 3 μM doxyxicline for 48 hours to induce gene expressions.


title: Comparison of LPS-induced gene expression in UBA3-sufficient or -deficient primary macrophages

status: Public on May 26 2020

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

summary: Bone marrow-derived macrophages (BMMs) from Uba3(flox/flox) mice or Uba3(flox/flox; lyz2-cre) mice were stimulated with or without 100ng/ml LPS for 4 hours. The total RNA was prepared and subjected to microarray.

overall_design: Bone marrow mononuclear cells from individual mice were cultured with M-CSF to induce BMMs. In total, 3 Uba3(flox/flox) mice and 3 Uba3(flox/flox; lyz2-cre) mice were used. BMMs from a Uba3(flox/flox) mouse were named as WT, whereas BMMs from a Uba3(flox/flox; lyz2-cre) mouse were named as KO. All the mice are littermates.

first: Zhenjie

last: Ye


title: Exaggerated BMP4 signalling alters human airway basal progenitor cell differentiation to cigarette smoking-related phenotypes

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

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

overall_design: Refer to individual Series


title: Transcriptomic study of PMA-differentiated THP-1 cells following exposure to zinc oxide nanoparticles NM110

summary: To identify differentially expressed genes and key biological pathways that define toxicity following nanoparticles exposure, we performed microarray analyses on PMA-differentiated THP-1 macrophages exposed for 4 h to 8 µg/mL of NP ZnO (50 % cell viability) and to 2 µg/mL of NP ZnO (50 % cell viability divided by 4 ). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 686098

overall_design: Changes in gene expression in PMA-differentiated THP-1 cells incubated without (control) or with (2 or 8 µg/mL) of NP ZnO for 4 h were measured. For each condition, four biological replicates were performed : C1; C2; C3; C4 as controls, Z(2)1; Z(2)2; Z(2)3; Z(2)4, Z(8)1; Z(8)2; Z(8)3; Z(8)4 as exposed cells to 2 or 8 µg/mL respectively.

first: Timéh

last: Saidou


title: Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

institute: Imperial College London


title: Comparison of LPS-induced gene expression in NEDD8-sufficient or -deficient primary macrophages

summary: Bone marrow-derived macrophages (BMMs) from Nedd8(flox/flox) mice or Nedd8(flox/flox; lyz2-cre) mice were stimulated with or without 100ng/ml LPS for 4 hours. The total RNA was prepared and subjected to microarray.

overall_design: Bone marrow mononuclear cells from 3  Nedd8(flox/flox) mice were mixed together to induce NEDD8-sufficient BMMs (WT) with M-CSF. And bone marrow mononuclear cells from 3  Nedd8(flox/flox; lyz2-cre) mice were mixed together to induce NEDD8-defficient BMMs (KO) under the same conditions. All the mice are littermates of C57 BL/6 strain.

first: Jiayang

last: Jin


title: Neutrophil gene expression in adult-onset Still's disease

status: Public on May 22 2020

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

institute: New Markers for Adult-Onset Still's Disease

summary: Adult-onset Still’s disease (AOSD) is a rare autoinflammatory disease, characterized by fever, rash, arthritis and other systemic inflammatory manifestations like hepatosplenomegaly and serositis. Neutrophil activation is the hallmark of AOSD. Here we aimed to identify candidate biomarker and to validate its association with clinical manifestations in AOSD. Transcriptome analysis of neutrophils from treatment-naïve active AOSD patients and healthy donors was performed. Using cut-offs of >2.0 fold change with p<0.05, we identified 864 DEGs in neutrophils from patients with active AOSD compared to healthy donors, including 442 and 422 upregulated and downregulated genes in active AOSD, respectively. By gene ontology (GO) analysis, we identified several strongly enriched terms of biological process. The most significantly indicated GO term was neutrophil degranulation.

overall_design: Transcriptomes from peripheral blood neutrophils of 6 treatment-naïve AOSD patients and 6 healthy controls

first: Qiongyi

last: Hu

first: Mengyan

last: Wang


title: Genome stabilization by RAD51 stimulatory compound-1 enhances efficiency of somatic cell nuclear transfer-mediated reprogramming and full-term development of cloned mouse embryos

status: Public on May 23 2020

city: Seongnam-si

first: Dong Ryul

last: Lee

state: Gyeonggi-do

address: 335, Pangyo-ro

institute: CHA University

summary: Here, we observed that the activity of Rad 51, a key modulator of homologous recombination repair (HRR) is lower in somatic cell nuclear transfer (SCNT)-derived eggs than in conventional IVF, and found a significantly lower level of DNA double-strand breaks (DSBs) in SCNT eggs during reprogramming. To address this difference, supplementation with RS-1, an activator of Rad51, during the activation of SCNT eggs can increase RAD51 expression and DSB foci and thereby overcome the developmental block. This protocol finally increased the efficiency of SCNT reprogramming. Through subsequent single-cell RNA-seq analysis, we observed the reactivation of a large number of genes that were not expressed in SCNT-2-cell embryos by the upregulation of HRR, which may be related to overcoming the developmental block. Additionally, there may be an independent pathway involving histone demethylase that can reduce reprograming resistance regions. This technology can contribute to the production of comparable cell sources for regenerative medicine.

overall_design: Here we perform RNA-Seq experiment in RS-1-treated mouse 2-cell embryos.

first: D

first: A

first: K

last: Hong


title: Transcriptional changes during astrocyte maturation in vivo and in culture

summary: Analysis of gene expression during astrocyte differentiation and maturation in vivo and in vitro in mouse, and investigation of transcription factors and extrinsic conditions influencing maturation

overall_design: In vivo astrocytes were purified from mice using anti-ACSA2 MACS at indicated ages. In vitro astrocytes were differentiated from cultured neural stem/progenitor cells (cultured in EGF/FGF2 medium) using BMP4 for 14 days (without EGF/FGF2). Where indicated, astrocytes in vitro were infected with transgenes and gene expression induced from day 7 to 14, or astrocytes differentiated for 7 days in BMP4 in normal 2D cultures or in 3D cultures were matured for 7 days in basal medium or FGF2 containing medium. Cells were analysed by bulk RNA-Seq.

first: Francois

last: Guillemot

first: Robert

last: Goldstone


title: Time course Total RNA-Seq in Xbp1 flx/flx (WT, wild-type) mice and AlbCre;Xbp1 flx/flx (XBP1 LKO, liver-specific knockout) mice

status: Public on May 24 2020

first: Huan

last: Meng

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: We reported the hepatic total gene expression (starting at CT0 and proceeding every two hours for four complete 12-hour cycles) in the liver of wild-type mice and XBP1 liver-specific knockout mice.

overall_design: Livers were harvested at 2-hour interval for a total of 48 hours from the male Xbp1 flx/flx and AlbCre;Xbp1flx/flx mice under the condition of constant darkness.


title: A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks [tumor]

first: Haojie

last: Chen

state: Shanghai

address: Yueyang Road 320

department: PICB

institute: CAS

summary: Lung adenocarcinoma (LUAD) is a high malignant tumor mostly occurs in adult patients, which is also a highly heterogeneous disease that involved multi different alterations. Some alterations such like EGFR mutations are frequently observed in LUAD patients, but the mechanisms that drive LUAD tumorigenesis and progression remain largely unclear, which need further researches. For example, epigenetic processes play important roles in cancers, but the variations in the enhancer and super enhancer landscapes of LUAD patients have rarely been studied. Here, to provide an in-depth understanding of the epigenomic heterogeneity of LUAD, we investigate the H3K27ac histone modification profiles of the tumor and adjacent normal lung tissues from 42 LUAD patients and explore the role of epigenetic alterations in LUAD progression.

overall_design:
We investigate the H3K27ac histone modification profiles of the tumor and adjacent normal lung tissues from 42 LUAD patients.

>>>Submitter states that raw data are available at: http://www.biosino.org/node/project/detail/OEP000942<<<

first: Chongze

last: Yuan

first: Zhen

last: Shao

first: Yihua

last: Sun


title: A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks


title: A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks [cell lines]

overall_design: We investigate the H3K27ac histone modification profiles of patient derived cell lines.


title: Time-course gene expression profiles of the synovial tissues in collagen-induced arthritis

status: Public on May 19 2020

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary:
We observed resolution of inflammatory response in collagen-induced arthritis (CIA) mice. To identify molecular signatures defining resolution of the CIA, we applied microarray analysis for synovial tissues in the CIA mice in 6 (induction), 9 (peak) and 15 weeks (resolution) after immunization. To identify genes related to CIA resolution, we performed the following comparisons of gene expression profiles: peak versus induction phase and resolution versus peak phase.
We identified that three genes, Itgb1, Ywhaz and Rps3, are the key regulators for the resolution by measuring degree, betweenness and closeness centrality in reconstructed network based on protein-protein interaction data. To confirm this result, we compared the gene and protein expression level of the three regulators between the two phases of inflammation. Furthermore, we showed that the gene and protein expression level of the three regulators are up-regulated in regulatory T cells and type 2 macrophages than other subtypes of CD4+ T cells and macrophages, and also we examined that recombinant peritoneal macrophages of the three regulators can modulate the expression of pro-inflammatory and anti-inflammatory cytokines. Thus, our findings suggest that those regulators can be employed as therapeutic uses for resolving inflammation

overall_design: To identify molecular signatures associated with resolution of inflammation, we isolated mouse synovial tissues from collagen-induced arthritis models in 6, 9, 15 weeks (CIA-6, 9, 15wk, resepctively) after immunization. The individual time points represent induction, peak and resolution phase of the CIA. Duplicates for each of the four conditions (CIA-6, 9, and 15) were used for microarray analysis.

first: Jin-Sun

last: Kong

first: Daehee

last: Hwang

first: Wan-Uk

last: Kim


title: No upregulation of homologous sequence expression in zebrafish larvae homozygous for the hu2787 nonsense mutant allele of fmr1.

city: Adelaide

first: Stephen

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

summary: The zebrafish has proven to be a versatile and valuable model for investigating the molecular and cellular basis of Fragile X syndrome (FXS). Reduction of expression of the zebrafish FMR1-ortholgous gene, fmr1, causes developmental and behavioural phenotypes related to the human syndrome. The hu2787 nonsense mutation allele of fmr1 is now the most widely used zebrafish model of FXS, although the FXS-relevant phenotypes seen from morpholino antisense oligonucleotide (morpholino) suppression of fmr1 transcript translation were not observed when this allele was first described. The subsequent discovery of genetic compensation, whereby morpholino-directed knockdown can give a more “pure” loss-of-function phenotype while mutations causing nonsense mediated decay of transcripts cause compensatory upregulation of homologous transcripts, suggested an explanation for the differences observed. To test for molecular evidence of genetic compensation in fmr1hu2787 homozygous mutants, we compared the transcriptomes of homozygous mutant and wild type larvae at 2 days post fertilisation. We observed statistically significant changes in the expression of a number of gene transcripts, but none with sequence homology to fmr1. Curiously, the majority of differentially expressed genes are located, like fmr1, on chromosome 14. Quantitative PCR tests on genomic DNA did not support that the apparent expression differences were artefacts due to changes in relative chromosome abundance. The coordinate dysregulation of chromosome 14 genes due to mutation of fmr1 supports this gene’s involvement in a chromosome-wide gene regulation complex.

overall_design: Four clutches of zebrafish embryos were obtained from pair-matings of zebrafish homozygous for the hu2787 allele of fmr1. Another four clutches of zebrafish embryos were obtained from wild-type zebrafish. Each clutch was derived from a different pair of parents.

first: Karissa

last: Barthelson

first: Yang

last: Dong

first: Melanie

last: Hand

first: Zac

last: Pujic

first: Morgan

last: Newman

first: Geoffrey

last: Goodhill

last: Richards

first: Michael

last: Lardelli


title: Effect of Cyclin-dependent kinase 2 (CINP) inhibition on TSU-PR1 cell line with stable KLF5 expression  May

status: Public on May 15 2020

city: Tianjin

first: jintang

last: dong

address: Weijin road

institute: Nankai university

summary: To study wither loss of CINP rescues global gene expression by KLF5 overexpression, we compare the effect of siRNA-mediated CINP silencing on K12 cells (TSU-PR1 cell line with stable KLF5 expression).

overall_design: RNA were isolated 48h after transfection with siCtrl or siCINP in K12 cells, then RNA-Seq analysis were performed using BGISEQ-500 at the BGI (ShenZhen, China).

first: Jin-Tang

first: Qiao

last: Wu


title: Ribosomal coverage with codon resulation in response to RPL12 siRNA treatment vs. no treatment

status: Public on May 17 2020

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

summary: Ribosome Profiling was employed to learn about Ribosome A-site occupancies in response to uL11 siRNA treatment or scrambled siRNA treatment in Cystic Fibrosis Bronchial Epithelial (CFBE) cells.

overall_design: Ribosome Profiling of cells 96h after siRNA transfection

first: Kathryn

last: Oliver

first: Robert

last: Rauscher

first: Marjolein

last: Mijnders

first: Wei

last: Wang

first: Matthew

last: Wolpert

first: Jessica

last: Maya

first: Carleen

last: Sabusap

first: Hui

last: Wen

last: Kesterson

first: Kevin

middle: L

last: Kirk

first: Andras

last: Rab

first: Ineke

last: Braakman

first: Jeong

last: Hong

first: John

last: Hartman IV

first: Eric

last: Sorscher


title: Autoimmune arthritis-associated gene expression in B cells isolated from mice with proteoglycan (PG)-induced arthritis (PGIA)

city: Chicago

first: Tibor

middle: T

last: Glant

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

summary:
Autoimmune arthritis was induced in BALB/c mice with three consecutive PG-injections. B cells were affinity purified from arthritic and contol (adjuvant injected - non-arthritic) mice and isolated total RNA samples were analyzed on microarray platforms.
Several hundred disease-associated gene expression changes were detected in B cells

overall_design: Gene expression profiling of arthritic vs non-arthritic mouse spleen using Agilent arrays with design ID 034068


title: the lncRNA expression profiles in fetal liver, adult liver and liver cancer tissues from mice

status: Public on May 21 2020

city: shanghai

first: Yan

last: Liu

address: 800 Xiangyin Road, Shanghai 200433

department: The Department of Medical Genetics

institute: Second Military Medical University, Shanghai 200433, China

summary: A large number of oncofetal molecules were found through expression profiling of a total of lncRNAs(35923)+coding genes(24881) from 17.5-day-old embryonic livers (three independent replicate samples named A1, A2, and A3), 2-month-old adult male mouse livers (three independent replicate samples named B1, B2, and B3) and one-year-old male mouse liver cancer tissues (three independent replicate samples named C1, C2, and C3) using a microarray analysis.

overall_design: To identify some oncofetal transcripts that potentially affect the occurrence and development of HCC, we established a DEN-induced mouse liver cancer model to obtain experimental samples considering the individual differences in human HCC samples, which are referred to as liver cancer in the following narrative. The liver cancer tissues were subjected to haematoxylin-eosin staining (HE staining) and verified according to their cell morphology under a microscope. Then, we analyzed the expression profiles of lncRNAs and protein-coding RNAs in 17.5-day-old embryonic livers (three independent replicate samples named A1, A2, and A3), 2-month-old adult male mouse livers (three independent replicate samples named B1, B2, and B3) and one-year-old male mouse liver cancer tissues (three independent replicate samples named C1, C2, and C3) using a microarray analysis.

first: Fang


title: Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome [Illumina]

status: Public on May 12 2020

city: London

first: Alice

last: Gao

address: 237 Fulham Road

institute: The Institute of Cancer Research

summary: Combination of CDK4/6 inhibitors and endocrine therapy has been shown to improve clinical outcome in advanced estrogen receptor-positive breast cancer. However, not all patients will benefit and relapse is inevitable making the identification of new therapeutic strategies/biomarkers of particular importance.

overall_design: MCF7, MCF7 LTED and T47D human breast cancer cell lines were treated long-term with palbociclib until they develop resistance and RNA extracted from the parental cell line and corresponding resistance cell line in order to interrogate gene changes.

first: Qiong

first: Ricardo

last: Ribas

first: Lesley

middle: A

last: Martin


title: Resistance to Palbociclib involves multiple mechanisms amenable to targeting with drug holidays or drug switching to improve therapeutic outcome


title: Effect of ORY-2001 on hippocampus and prefrontal cortex of SAMP8 mice.

status: Public on May 13 2020

city: Cornella de Llobregat

first: Tamara

last: Maes

state: Barcelona

address: Carrer Sant Ferran 74

department: R&D

country: Spain

institute: Oryzon Genomics S.A.

summary: Gene expression analysis in the hippocampus and prefrontal cortex of vehicle-treated and ORY-2001 treated SAM mice.

overall_design: Compiled data of 2 two-colour experiments, each experiment performed on different brain regions of vehicle-treated and ORY-2001 treated mice. Three replicates per array for each gene probe.

first: Cristina

last: Mascaró

first: David

last: Rotllant

first: Michele

last: Lufino


title: Human Naive Pluripotency Attained by Transient Inhibition of mTOR

city: Buffalo

first: Jian

last: Feng

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

summary: Mouse embryonic stem cells (mESCs) are in naive pluripotency that represents the ground state of development, from which all cells in the mouse embryo are derived. In contrast, human embryonic stem cells (hESCs) are in a primed state of pluripotency with many different properties. Despite intense efforts to generate naive human pluripotent stem cells (hPSCs), it has not been possible to derive naive hPSCs without relying on transgene overexpression or chemicals. Here, we show that a transient treatment with Torin1, a selective inhibitor of mTOR, converted hPSCs from primed to naive pluripotency. The naive hPSCs were maintained in the same condition as mESCs in defined media with 2iLI (MEK inhibitor, GSK3b inhibitor, LIF and Insulin). Like mESCs, they exhibited high clonal efficiency, rapid cell proliferation, active mitochondrial respiration, X chromosome activation, DNA hypomethylation, and transcriptomes similar to those of human blastocysts than primed hESCs. Most importantly, the naive hPSCs significantly contributed to mouse embryos when transferred to mouse blastocysts. mTor inhibition induced nuclear translocation of TFE3, a critical transcription factor at the interplay of autophagy and pluripotency. TFE3 with mutated nuclear localization signal blocked the conversion from primed to naive pluripotency. It appears that by mimicking diapause at the cellular level, naive pluripotency in human can be readily attained from primed hPSCs, thus establishing the unified ground state of pluripotency in mammals.

overall_design: Comparison of DNA methylation signature between primed state and naïve state PSCs.

first: Zhixing

last: Hu

first: Hanqin

last: Li

first: Houbo

last: Jiang

first: Yong

last: Ren

first: Xinyang

last: Yu

first: Jingxin

last: Qiu

first: Aimee

last: Stablewski

first: Boyang

last: Zhang

first: Michael

last: Buck


title: cGAS Senses Translation Stress Through Direct Binding to Ribosomes

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: The cGAS-STING pathway, a central component of the innate immune system, senses cytosolic DNA and induces interferon-stimulated genes (ISGs) to mediate inflammation. Here we report the unexpected discovery that cGAS senses dysfunctional translation. Purified ribosomes interact with and stimulate recombinant cGAS catalytic activity in vitro. Disruption of the ribosome-associated protein quality control pathway, which detects and resolves ribosome collisions, results in cGAS- and STING-dependent ISG expression, and cause the re-localization of cGAS from the nucleus to the cytosol. Other orthogonal perturbations that lead to elevated levels of collided ribosomes cause re-localization of cGAS as well. Thus, the cGAS-STING pathway senses and responds to translation stress. These findings have implications for the inflammatory responses to viral infection and tumorigenesis, both of which substantially reprogram cellular protein synthesis.

overall_design: Nascent gene expression profiles of MRC5VA cells knocked down for non-target control or ASCC3 by siRNA

first: Li

last: Wan

first: Jesper

middle: Q

last: Svejstrup


title: Gene expression data from human intestinal biopsies

status: Public on May 11 2020

city: Lund

first: Jan

last: Marsal

address: BMC D14

country: Sweden

institute: Lund University

summary: Anti-TNFα therapy induces mucosal healing in a large proportion of Crohn’s disease (CD) patients, but the mechanisms underlying this process are not fully elucidated. To this end we examined molecular effects of adalimumab treatment in CD. CD patients (n=10) underwent ileocolonoscopy were sampled for mucosal biopsies before and after three months of adalimumab treatment. Collected material was analyzed using transcriptome microarray analysis. All patients were responders and eight patients reached clinical remission. Mucosal transcriptome analyses demonstrated that anti-inflammatory and tissue-repair gene-sets were upregulated in inflamed mucosa, in addition to proinflammatory and tissue-destruction-related genes. After treatment, genes promoting inflammation or tissue-destruction were downregulated. , and these genes are primarily expressed in innate leukocytes and stromal cells. Expression of anti-inflammatory and tissue-repair-related genes was also downregulated, but to a lesser degree. Of note, various parts of the colon displayed distinct gene-expression profiles. Adalimumab operates by down-shifting several proinflammatory arms of both the innate and adaptive immune-system, but does not disturb regulatory T-cells. Anti-inflammatory and tissue-repair machineries are upregulated already during active inflammation, but are not effective until proinflammatory drivers have been silenced.

overall_design: 76 intestinal samples from 10 patients were analyzed. 4 samples had a second replicates.

first: Mohammad

last: Kadivar

first: Dirk

last: Repsilber


title: External RNA Control Consortium (ERCC) spikes in RNA sequencing (RNA-Seq) data normalization: transcriptome analysis of yellow fever virus-infected cells

city: Lyon

first: magali

last: roche

address: 8 avenue Rockfeller

institute: university lyon 1

summary: We explored the ability of External RNA Control Consortium (ERCC) standards to detect technical biases between batches of sequencing experiments and to set detection thresholds. We compared three normalization methods (FPKM, DESeq2 and RUV) to identify the optimal analysis approach.

overall_design: Total RNA Profiles of YFV wild-type (Asibi), -vaccine (17D) or mock infected (Control) cells were generated using deep sequencing, in quadriplicate, using Illumina technology

first: Magali

last: Roche

first: Nicolas

last: Massé-Deragon

first: Veronique

last: Barban

first: Catherine

last: Legras-Lachuer


title: Chd1p recognizes H3K36Ac to maintain nucleosome positioning near the transcription start site

first: Hyelim

last: Jo

address: 335 Gwahangno, Yuseong-Gu

department: Biological science

institute: KAIST

summary: H3K36Ac promotes the remodeling activity of Chd1p to maintain chromatin stability at the 5’ ends of genes

overall_design: For ChIP experiment: ChIP against H3, H3K36Ac, Pser2,  a-Flag was performed for a wild type strain(w303a) and strains lacking Chd1 and FLAG-tagged Sua7. For ATAC-seq experiment: wild type strain and chd1_deletion strain  incubated with transposase. For MNase experiment: mononucleosomes of wild tye and chd1_deletion strain were obtained using Mnase.

first: Hyunhee

last: Kim

first: Kwoneel

first: Hogyu

middle: D

last: Seo

first: Keunsoo

last: Kang

first: Hee-Sung

last: Park

first: Lothar

last: Hennighausen

first: Jung

middle: K

last: Choi

first: Daeyoup

last: Lee


title: Multi-omics data and stochastic simulations support a cancer heterogeneity framework unifying genetic, epigenetic, and stochastic variabilities [scRNA-seq]

status: Public on May 08 2020

city: Nashville

first: Corey

middle: Eduardo

last: Hayford

state: TN

address: 2220 Pierce Avenue

department: Chemical and Physical Biology

institute: Vanderbilt University

summary: We subject multiple versions and single cell-derived sublines of an archetypal non-small cell lung cancer cell line to experimental scrutiny at the genomic, transcriptomic, and cell population levels. We find evidence of genetic variability among cell line versions and one subline. Additional sublines show no genetic variation but epigenetic differences are detected at the transcriptomic level. Stochastic simulations of subline growth dynamics confirm that one subline likely contains at least two genetic states while all others are isogenic. Overall, our results substantiate a view of intratumoral heterogeneity in which different genetic states give rise to multiple epigenetic “basins of attraction,” across which cells can transition driven by stochastic factors such as gene expression noise and asymmetric cell division. Deconvolving intratumoral heterogeneity into genetic, epigenetic, and stochastic components provides a lens through which to view tumor drug response and acquired treatment resistance that may lead to novel therapeutic strategies in the future.

overall_design: Omics profiling of multiple cell line versions and sublines from the EGFR-mutant non-small cell lung cancer cell line PC9 - Single-cell RNA sequencing

middle: E

first: Darren

middle: R

last: Tyson

first: Charles

last: Robbins

first: Peter

last: Frick

first: Vito

last: Quaranta

first: Leonard

last: Harris


title: Multi-omics data and stochastic simulations support a cancer heterogeneity framework unifying genetic, epigenetic, and stochastic variabilities

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

overall_design: Refer to individual Series


title: Identification of active promotor regions in Wilms tumor cells

status: Public on May 09 2020

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

summary: The goal of this study was to find differences in the chromatin state (active promotor regions) between two Wilms tumor subtypes (blastemal and non-blastemal).

overall_design: Examination of histone modifications (H3K4m3 + H3K27ac) in two different Wilms tumor cell lines.

first: Kathrin

last: Kattler

first: Jenny

last: Wegert


title: CRISPR-Mediated Multiplexed Epigenomic Perturbation of Putatively Functional ASoC Sites in Human Neural Progenitor Cell Model at Single-cell Resolution

status: Public on May 05 2020

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Functional interpretation of noncoding disease variants, which likely regulate gene expression, has been challenging. Chromatin accessibility (openness) strongly influences gene expression in neurodevelopment; however, to what extent genetic variants can alter chromatin openness in the context of brain disorders/traits is largely unknown. Using human induced pluripotent stem cell (iPSC)-derived neurons as a neurodevelopmental model, we identified abundant open-chromatin regions absent in brains and thousands of genetic variants exhibiting allele-specific open-chromatin (ASoC). ASoC variants are overrepresented in brain enhancers, transcription-factor-binding sites, and quantitative-trait-loci affecting histone modifications or DNA methylation. ASoC variants are also highly enriched for those associated with brain disorders/traits. Following-up schizophrenia-associated ASoC variants by multiplex epigenomic perturbation, computational fine-mapping, and CRISPR-editing further confirmed their regulatory activities and cis-targeted genes. Our study provides the first snapshot of neuronal ASoC landscape and a framework for prioritizing functional disease variants.

overall_design: NPC samples were derived from individual cell line #05, #07, and #08. Collected NPC samples were processed with 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions. Sequencing of the prepared library was performed on an Illumina sequencer generating approximately 450M reads in total.

first: Siwei

last: Zhang


title: Immune cells in the bone healing process

status: Public on May 04 2020

city: Giessen

first: Thaqif

last: El Khassawna

address: Aulweg 128

department: Faculty of Medicine

institute: Justus Liebig University of Giessen

summary: Bone is a unique organ able to regenerate after severe traumatic injuries. However, regeneration is governed by the interplay between systems located in the site of injury. The immune system initiates the inflammatory response in the early phase of healing. Therefore, the global role of T-cells and B-cells in the bone regeneration and the resulting bone quality is the focus of this study. A standard unilateral closed fracture was created in the femora to study the overlapping phases of bone healing. Besides wild type (WT) a model of recombination activating gene 1 knockout (RAG1-/-) mice that lacking mature T and B-cells were investigated. In addition, at D7 the individual role of T-cells and B-cells were investigated through the (TCRβδ) and JHT-/- knockouts respectively. Radiological, biomechanical, histological and imaging were utilized along with differential expression analysis. RAG1-/- mice showed higher biomechanical stiffness in intact bone when compared to the WT mice. Higher mineralization at early stage was seen in the RAG1-/- and bone devoid of T-cells (TCRβδ-/-) including. However, healing in bone devoid of B-cells (JHT-/-) was not apparently deviant of that of WT. Interestingly, second harmonic photon microscopy revealed an disorganized collagen fibers in the RAG1-/- contemporary with the expression analysis showing dysregulation in the expression of ColI subunits. Gene network analysis reflected the expected down regulation of T cell related genes in the RAG1-/- but not the B-cell related genes. This can hint to backup mechanism compensating the lack of mature B-cells. Furthermore, differentially expressed genes in RAG1-/- mice showed an impact on angiogenesis, cytokines & growth factors and bone remodeling, and BMP signaling array throughout the healing process. This asserts the focus on the adaptive immune system in two directions: 1) suggested role of T-cells in governing bone quality. 2) indicated importance of B-cells for bone regeneration through backup mechanisms.

overall_design: Fractured bone samples including 1mm diaphyseal bone on either side of the fracture (N = 5 /group per time point) were taken. The experiment was run in triplicates. The samples were collected after (day=D) D0, D3, D7, D14, D21, and D28 from both wild type and RAG1-/- group.

first: Alessandro

last: Serra

first: Ansgar

last: Petersen

first: Claudia

last: Schlundt

first: Ireen

last: Könnecke

first: Deeksha

last: Malhan

first: Hanna

last: Schell

first: Hans-Dieter

last: Volk

first: Katharina

last: Schmidt-Bleek

first: Geord

last: Duda


title: Allele-specific open chromatin in human neurons elucidates functional noncoding disease variants

summary: ASoC variants are prevalent and cell type-specific ASoC variants were over-represented in intergenic regions and active enhancers. The collection includes ATAC-Seq and RNA-Seq data that were taken from human iPS cells and their derived neuronal cells (neural progenitor cells, cortical glutamatergic neurons, GABAergic neurons, and dopaminergic neurons).

overall_design: In order to detect the changes in chromatin accessibility as well as associated changes at the transcriptional level during neuronal differentiation, we applied human induced pluripotent stem cells (hiPSCs) and hiPSC-derived neurons as a neurodevelopmental model. Generally, 8 iPSC lines from RUCDR were induced to differentiate into neural progenitor cells (NPC), 15-day cortical glutamatergic neurons (CN, Glut d15), GABAergic neurons, and dopaminergic neurons. Their open chromatin landscape, as well as transcriptional activities, were measured using ATAC-Seq and bulk RNA-Seq, respectively. An additional 12 lines were used to generate NPC cells and Glut-d15 neurons for ATAC-Seq, with the aim in gaining extended statistic power for ASoC analysis.


title: Active enhancer landscape during spermatogenesis.

status: Public on May 02 2020

city: Cincinnati

first: Satoshi

last: Namekawa

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Active enhancers are identified by H3K27ac ChIP-seq analysis. To determine the dynamics of active enhancers during spermatogenesis, we performed H3K27ac ChIP-seq and detected reagions of active enhancers during spermatogenesis. We analyzed four representative stages of spermatogenesis: Thy1+ undifferentiated spermatogonia, which contains spermatogonial stem cells and progenitor cells; c-Kit+ differentiating spermatogonia from P7 testes; purified pachytene spermatocytes (PS) undergoing meiosis; and postmeiotic round spermatids (RS) from adult testes.

overall_design: ChIP-seq analyses using wild-type and Scml2-KO spermatogenic cells

first: So

last: Maezawa

first: Artem

last: Barski


title: The transcriptomic signature of painful and non-painful human NF2 schwannomas [set1]

status: Public on May 01 2020

city: Boston

first: Gary

last: Brenner

address: 15 Parkman Street

department: Anesthesia Critical Care and Pain Medicine

institute: Massachusetts General Hospital

summary: Schwannomas are benign peripheral nerve sheath tumors that are associated with substantial morbidity including severe, persistent pain. Treatment, essentially limited to surgical resection, is associated with significant morbidity and for many patient’s efficacious treatment of tumor-related pain is not achievable. There is an urgent need to elucidate the molecular mechanisms underlying schwannoma-induced pain as a first step in development of new therapeutics. In this study, we performed next-generation RNASequencing on a small cohort of formalin fixed paraffin-embedded, painful, and non-painful schwannoma samples obtained from Neurofibromatosis type 2 (NF2) patients. Differential gene and isoform level expression analysis revealed significant transcriptomic differences between painful and non-painful tumors; differentially regulated genes included members of the fibroblast growth factor (FGF) family of genes. Using a xenograft model of human-NF2 we demonstrated that over-expression of FGF7 in schwannoma cells was associated with the development of pain-like behaviors. These results demonstrate both the value of RNASeq utilizing formalin fixed tissues and reveal a novel pathway responsible for neoplasm-associated pain.

overall_design: Examined the transcriptomic differences of  formalin fixed, paraffin-embedded (FFPE) painful (n=3 total) and non-painful (n=8 total) peripheral human NF2-schwannomas (Benign Nerve Sheath tumors).

first: Phanidhar

last: Kukutla

first: Sherif G

last: Ahmed

first: Murat

last: Cetinbas

first: Dan

last: Dubreuil

first: Ahmed

last: Abdelanabi

first: Giulia

last: Fulci

first: Berent

last: Aldikacti

first: Anat

last: Stemmer-Rachamimov

first: Brian

last: Wainger

first: Scott

last: Plotkin

first: Ruslan

last: Sadreyev


title: Thyroid Hormone Receptor Beta Induces a Tumor Suppressive Program in Anaplastic Thyroid Cancer

city: Minneapolis

first: Noelle

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

summary: The thyroid hormone receptor beta (TRβ), a key regulator of cellular growth and differentiation, is frequently dysregulated in cancers. Diminished expression of TRb is noted in thyroid, breast, and other solid tumors and is correlated with more aggressive disease. Restoration of TRb levels decreased tumor growth supporting the concept that TRb could function as a tumor suppressor. Yet, the TRb tumor suppression transcriptome is not well delineated and the impact of TRb is unknown in aggressive anaplastic thyroid cancer (ATC). Here, we establish that restoration of TRb expression in the human ATC cell line SW1736 (SW-TRβ) reduces the aggressive phenotype, decreases cancer stem-cell populations and induces cell death in a T3-dependent manner. Transcriptomic analysis of SW-TRβ cells via RNA-sequencing revealed distinctive expression patterns induced by ligand-bound TRβ and revealed novel molecular signaling pathways. Of note, liganded TRβ repressed multiple nodes in the PI3K/AKT pathway, induced expression of thyroid differentiation markers, and promoted pro-apoptotic pathways. Our results further revealed the JAK1-STAT1 pathway as a novel, T3-mediated, anti-tumorigenic pathway that can be activated in additional ATC lines. These findings elucidate a TRb-driven tumor suppression transcriptomic signature, highlight unexplored therapeutic options for ATC, and support TRb activation as a promising therapeutic option in cancers.

overall_design: Transcriptomic profiling of anaplastic thyroid cancer cells transduced to express TRβ.

first: Eric

last: Bolf

first: Seth

last: Frietze

first: Frances

last: Carr


title: The transcriptomic signature of painful and non-painful human NF2 schwannomas


title: The transcriptomic signature of painful and non-painful human NF2 schwannomas [set2]

overall_design: Examined the transcriptomic differences of  formalin fixed, paraffin-embedded (FFPE) painful (n=4) and non-painful (n=3) peripheral human NF2-schwannomas.


title: Phenotypic Correction of Oligodendrocytes by Concurrent Direct Reprogramming and Gene Replacement of Fibroblasts

city: Cleveland

first: Paul

last: Tesar

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Transcription factor-mediated direct reprogramming technologies that can convert one differentiated somatic cell to another, without an intermediate pluripotent stem cell stage, provide a new mechanism to access somatic cell types for disease modeling and possible therapeutic application. Previous efforts have focused on wild-type cells harboring transgenic reporters to signal successful reprogramming events. Outstanding questions remain of whether cells from disease backgrounds without transgenic reporters are capable of direct reprogramming and whether they phenocopy disease pathology. Here we demonstrate that fibroblasts from the shiverer mouse model of myelin disease can be directly reprogrammed to induced oligodendrocyte progenitor cells (iOPCs) by the expression of Sox10, Olig2, and Nkx6.2 without the aid of transgenic selection reporters. Shiverer mice harbor a homozygous ~20-kilobase deletion in the Myelin Basic Protein (Mbp) gene and this substantial deletion leads to abnormal oligodendrocytes resulting in hypomyelination and decreased lifespan. Shiverer iOPCs efficiently differentiated to induced oligodendrocytes (iOLs) which recapitulated the known disease phenotype of impaired axonal ensheathment and myelination capacity. Combining direct reprogramming and genetic supplementation of a minigene carrying regulatory elements and an open reading frame of MBP, restored MBP expression in differentiated iOLs and their ability to track along and ensheath microfibers in an in vitro assay of myelination capacity.   Collectively these results show that iOPCs provide a rapid and accessible system to accurately model myelin disease pathology and provide promise for future therapeutic advancement for genetic myelin disorders.

overall_design:
RNA was collected from whole cells by lysing in 1 ml TRIzol (Invitrogen) and stored at   -80C until processing.  Phase-lock gel tubes (5Prime) were used to enhance chloroform extraction. The aqueous phase was collected, and RNA isolation completed using the miRNeasy Kit (Qiagen) according to manufacturer’s protocol. One microgram was then subject to ribosome depletion, fragmented, and libraries prepared using the TruSeq Stranded Total RNA Kit with Ribo Zero Gold (Illumina) according to the manufacturer’s protocol and indexed using TruSeq adapters. One hundred base pair paired-end reads were generated on the Illumina HISeq 2500 (Case Western Reserve University Sequencing Core; Cleveland, OH).

Samples:
EpiSC5-OPC= OPCs derived from mouse epiblast stem cells

Shiv-MEF= MEFs derived from shiverer mice and depleted using A2B5 microbeads

Shiv-iOPC-MBP= Day 21 shiverer iOPCs without MBP transgene

Shiv-iOPC-Rd1-Dox= Day 21 shiverer MEFs which were infected with the reprogramming factors but were not induced

Shiv-iOPC-Rd1= Day 21 shiverer iOPCs with the MBP transgene (replicate 1)

Shiv-iOPC-Rd2-Dox= Day 21 shiverer MEFs which were infected with the reprogramming factors but were not induced

Shiv-iOPC-Rd2= Day 21 shiverer iOPCs with the MBP transgene (replicate 2)

Shiv-iOPC-Rd3= Day 21 shiverer iOPCs with the MBP transgene (replicate 3)

first: Robert

last: Karl

first: Daniel

middle: C

last: Factor


title: Shared and distinct metabolic demands for innate and adaptive cytotoxic lymphocytes during viral infection

status: Public on Apr 28 2020

city: New York

first: Endi

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: Natural Killer (NK) cells and CD8+ T cells share many characteristics at steady state and during viral infection. In this study, we interrogate the metabolic pathways that fuel NK cell effector function in response to mouse cytomegalovirus (MCMV) infection. This dataset contains transcriptional profiling of wild-type and LDHA-deficient Ly49Hpositive NK cells at steady state and early after infection.

overall_design: RNASeq was performed on wild-type or LDHA-deficient Ly49Hpositive NK cells harvested after 2 days post in vivo infection in a mixed bone chimera setting; 2-3 replicates per group and 20,000-60,000 cells per replicate.

first: Joseph

last: Sun


title: Comparison of the transcription of palmitoylcarnitine induced pluripotent stem cells, normal induced pluripotent stem cells and embryonic stem cells through RNA-seq

city: Nanjing

first: Zhaoyu

last: lin

state: Jiangsu

address: 12 Xuefu Road

institute: Nanjing University

summary: We sequenced mRNA from 2 clones of palmitoylcarnitine induced pluripotent stem cells, 2 clones of normal induced pluripotent stem cells, 1 embryonic stem cell, and 1 mouse embryonic fibroblast strain to compare the expression profiles

overall_design: Examination of mRNA levels in palmitoylcarnitine induced pluripotent stem cells, normal induced pluripotent stem cells and embryonic stem cells

last: Lin


title: Liver tissue expression data from WT and Abhd15-ko mice on normal chow diet at refed state

city: Graz

first: Juliane

last: Bogner-Strauss

address: Petersgasse 10-12/II

institute: Institute of Biochemistry, Graz University of Technology

summary:
Abhd15 is mainly expressed in adipose tissues and highly upregulated upon adipogenesis. Abhd15 expression is correlated with insulin resistance in obese humans, however its physiological function remains unknown. We used the microarray technology to gain insight into ABHD15’s physiological function by identifying dysregulated genes in liver from Abhd15-ko mice in comparison to WT mice.
We used microarrays to detail the global programme of gene expression in liver and identified distinct dysregulated genes in response to refeeding

overall_design: Male WT and Abhd15-ko mice on a clean C57BL/6J background were used. At 14 weeks of age, WT and Abhd15-ko mice were fasted overnight and refed with chow diet for 1 hour prior to harvesting. Liver from WT and Abhd15-ko mice was collected and immediately snap frozen in liquid nitrogen. RNA was isolated for gene expression microarray analyses at the exon level (Affymetrix, Santa Clara, CA, USA). To isolate RNA, the frozen tissue samples were homogenized in TRIzol® reagent (Invitrogen/Life Technologies, Carlsbad, CA, USA) and processed based on the manufacturer’s instruction. Total RNA (200ng) from individual samples was then used for Affymetrix analysis. Terminal-labeled cDNA, hybridization to genome-wide Mouse Gene 2.0 ST Gene Chips and scanning of the arrays were carried out according to the manufacture’s indications (Affymetrix). Output primary row data was analyzed with Expression Console software (Affymetrix).

first: Wenmin

last: Xia

first: Ariane

last: Pessentheiner

first: Melina

first: Evelyn

last: Walenta

first: Hubert

last: Hackl

first: Thomas

last: Rülicke


title: Cisplatin induces inefficiently translated short transcripts in long genes

status: Public on Apr 30 2020

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: We explored the regulation of intronic polyadenylation (IPA) by cisplatin, and its impact on the translatome.

overall_design: To identify regulations of IPA isoform expression relative to the last exon of genes in the processes of cisplatin response and resistance, we performed 3'-seq analyses and compared cisplatin-treated versus mock cells, and  cisplatin-resistant versus sensitive cells (all conditions in triplicates).

first: Martin

last: DUTERTRE

first: Iris

last: TANAKA

first: Mandy

last: CADIX

first: Sophie

last: MICHALLET

first: Ludovic

last: TESSIER

first: Hussein

last: MORTADA

first: Pierre

last: GESTRAUD

first: Virginie

last: RAYNAL

first: Sylvain

last: BAULANDE

first: Didier

last: AUBOEUF

last: SERVANT

first: Stéphan

last: VAGNER

first: Béatrice

last: EYMIN


title: Transcriptome analysis of acute IL-33 or chronic HDM activated murine lung ILC2s

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus Medical Center

summary: We have identified CD25high and CD25low ILC2 subsets in various mouse models of airway inflammation. Transcriptome analysis of acute IL-33 (CD25High) or chronic HDM (CD25Low) activated murine lung ILC2s suggests functional differences between these two ILC2 populations.

overall_design: biological replicate (n=2) RNA-Seq experiments

first: Rudi

last: Hendriks


title: Brown adipose tissue (BAT) expression data from WT or ABHD15-/- on normal chow diet at refeeding state

first: Juliane

last: Bogner-Strauss

summary:
Abhd15 is mainly expressed in adipose tissues and highly upregulated upon adipogenesis. Abhd15 expression is correlated with insulin resistance in obese humans, however its physiological function remains unknown. We used the microarray technology to gain insight into ABHD15’s physiological function by identifying dysregulated genes in BAT from Abhd15-ko mice in comparison to WT mice.
We used microarrays to detail the global programme of gene expression in BAT and identified distinct dysregulated genes in response to refeeding

overall_design: Male WT and Abhd15-ko mice on a clean C57BL/6J background were used. At 14 weeks of age, WT and Abhd15-ko mice were fasted overnight and refed with chow diet for 1 hour prior to harvesting. BAT from WT and Abhd15-ko mice was collected and immediately snap frozen in liquid nitrogen. RNA was isolated for gene expression microarray analyses at the exon level (Affymetrix, Santa Clara, CA, USA). To isolate RNA, the frozen tissue samples were homogenized in TRIzol® reagent (Invitrogen/Life Technologies, Carlsbad, CA, USA) and processed based on the manufacturer’s instruction. Total RNA (200ng) from individual samples was then used for Affymetrix analysis. Terminal-labeled cDNA, hybridization to genome-wide Mouse Gene 2.0 ST Gene Chips and scanning of the arrays were carried out according to the manufacture’s indications (Affymetrix). Output primary row data was analyzed with Expression Console software (Affymetrix).

first: Wenmin

last: Xia

first: Ariane

last: Pessentheiner

first: Melina

first: Evelyn

last: Walenta

first: Hubert

last: Hackl

last: Rülicke


title: In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

first: Derk

last: ten Berge

address: Wytemaweg 80

department: Cell Biology

institute: ErasmusMC

summary: This SuperSeries is composed of the SubSeries listed below. SubSeries GSE105762 contains bulk RNA-Seq data, while SubSeries GSE145726 contains single-cell RNA-Seq data.


title: Key transcriptional regulators in Wilms tumors of blastemal subtype

first: Tim

last: Kehl

summary: The aim of the study was to identify key transcriptional regulators that might be responsible for the increased resistance to chemotherapy of blastemal Wilms tumors.

overall_design: Comparison of gene expression profiles in Wilms tumors of blastemal subtype (n=17) and non-blastemal tumors (n=16).

first: Nicole

last: Ludwig


title: Efficient Propagation of Circulating Tumor Cells: A First Step for Probing Tumor Metastasis.

status: Public on Apr 21 2020

city: Washington

first: Jerry

last: Xiao

state: DC

address: 3900 Reservoir Rd NW, PCS Bldg, Room GR10C

department: Tumor Biology

institute: Georgetown University

summary: Circulating Tumor Cells (CTCs) from metastatic breast cancer patients were harvested and grown in vitro for 30+ days in a novel short-term culture method. Additionally, RNA from the buffy coat of 5 healthy donors were sequenced and subjected to culture conditions; 0/5 cultures successfully grew. This new culture method is highly efficient and allows for the molecular characterization of CTCs and identification of potential targets for therapy against tumor metastasis. Using this method, we established 12/12 cultures of CTCs.

overall_design: One sample each from six MBC patients of various receptor subtype (HER2+ n=2; ER/PR+ n=3, TNBC n=1) were sequenced alongside RNA from 5 healthy donors.

first: J

last: McGill

last: Kassner

first: S

last: Choudhury

first: K

last: Stanton

first: R

last: Schlegel

first: Z

last: Sauna

first: P

last: Pohlmann

last: Agarwal


title: In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

summary: Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. Downregulation of WNT signals in the blastocyst drives transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells (RSCs), a self-renewing naive-primed intermediate. RSCs gain a unique epigenome that includes erasure of constitutive heterochromatin and bivalent marking of primed pluripotency genes. Notwithstanding this primed chromatin landscape, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate where control over pluripotency progression and morphogenesis pivots from WNT to MEK signals.

overall_design: Using Illumina HiSeq, mRNA profiles were generated from mouse embryonic stem cells cultured in various conditions or differentiated to the primed pluripotent state.  As biological replicates, R1 and CGR8 embryonic stem cell lines were used. The cells were cultured in serumfree N2B27 medium supplemented with the cytokine LIF, and either the GSK3-inhibitor CHIR99021 and the MEK-inhibitor PD325901 (L2i), or a combination of PD325901 and the Wnt inhibitor IWP2 (LIM). Furthermore, mRNA profiles were also generated from cells differentiated towards the primed pluripotent state for 35 hrs and for 4 days by culture in the presence of LIF, FGF2, Activin A, and IWP2 (LFAI). Finally, mRNA profiles were generated from time courses of R1 embryonic stem cells switched from LIF+2i to LIF supplemented with either FGF2, Activin A and IWP2 (LFAI), or with IWP2 and PD325901 (LIM). The time courses lasted for 4 days, and mRNA profiles were generated from every day. No replicates were generated for the time courses.

first: Jente

last: Stel

first: A

last: den Dekker

last: Brouwer

first: W

last: van IJcken


title: Dynamic seed transcriptome analysis of japonica to imbibitional tolerance

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: Seeds experience several stress responses from dry to germinated state. To determine the regulators contributing to imbibitional tolerance, dynamic transcriptome analyses were conducted at dry (0 h), imbibed (24 h) and germinated (48 h) stages in japonica Jiucaiqing in this study. Results showed that the differentially expressed genes (DEGs) were pronounced in the early stage (0-24 h) than the late stage (24-48 h); 1,452 transcripts were differentially expressed (648 up-regulated and 804 down-regulated) in the early stage and 625 transcripts (230 up-regulated and 395 down-regulated) in the late stage. Gene ontology and MapMan analyses confirmed that 391 and 164 DEGs at the early and late stage respectively involved in stress responses pathway. These DEGs included the abiotic stress-, hormone-, peroxidases-, signaling-, transcription-, proteolysis- and cell wall-related genes. Nearly all the heat stress-related DEGs, e.g. hsp20 and DnaK family proteins, were down-regulated with seed germination, while the peroxidases- and signaling-related DEGs, e.g. calcium-binding proteins, were up-regulated. Many auxins-, abscisic acid- and ethylene-related DEGs, e.g. 9-cis-epoxycarotenoid dioxygenase, OsFBL16 and OsSAUR33, were involved in stress responses during seed germination. Meanwhile, several transcription factors of bZIP and MYB, ethylene responsive element binding protein family (ERF), and heat stress transcription factor family (HSF) were identified during seed germination. The proteolysis-related DEGs, e.g. ubiquitin-related proteins, were significantly regulated during seed germination. The uniformity between transcriptome data, quantitative trait loci co-localizations and quantitative RT-PCR results confirm the crucial roles of the cell wall-related genes on seed germination. The identified stress-responsive might be useful for the improvement of imbibitional tolerance in rice.

overall_design: mRNA profiles of seeds in the landrace rice Jiucaiqing (Oryza sativa spp. japonica) after 0, 24 and 48 h imbibition were combined respectively from three biological replicates for RNA sequencing.

first: Zhoufei

first: Haoyuan

last: Li

first: Ji

last: Huang


title: Multi-omics data and stochastic simulations support a cancer heterogeneity framework unifying genetic, epigenetic, and stochastic variabilities [Bulk-RNA-seq]

first: Corey

last: Hayford

summary: We subject multiple versions and single cell-derived sublines of an archetypal non-small cell lung cancer cell line to experimental scrutiny at the genomic, transcriptomic, and cell population levels. We find evidence of genetic variability among cell line versions and one subline. Additional sublines show no genetic variation but epigenetic differences are detected at the transcriptomic level. Stochastic simulations of subline growth dynamics confirm that one subline likely contains at least two genetic states while all others are isogenic. Overall, our results substantiate a view of intratumoral heterogeneity in which different genetic states give rise to multiple epigenetic “basins of attraction,” across which cells can transition driven by stochastic factors such as gene expression noise and asymmetric cell division. Deconvolving intratumoral heterogeneity into genetic, epigenetic, and stochastic components provides a lens through which to view tumor drug response and acquired treatment resistance that may lead to novel therapeutic strategies in the future.

overall_design: Omics profiling of multiple cell line versions and sublines from the EGFR-mutant non-small cell lung cancer cell line PC9 - Bulk RNA sequencing

first: Darren

last: Tyson

first: Charles

middle: J

last: Robbins

first: Peter

last: Frick

first: Vito

last: Quaranta

first: Leonard

last: Harris


title: ChIP-seq to profile Pol occupancy in bone marrow-derived macrophages from C57BL/6 mice

status: Public on Apr 20 2020

first: Li

last: Yu

address: Medicial Science Building, Tsinghua University

department: The Institution of Immunology

institute: Tsinghua University

summary: We characterized the PolII occupancy on gene loci in conditions of unstimuated and LPS stimualtion in BMDMs

overall_design: WT BMDMs were left untreated or stimulated with LPS  for 1 hour. PolII was performed and the DNA products were subject to ChIPseq

first: Bin

last: Zhang

first: Yingli

last: Shang


title: Circular RNAs show differential expression profiles and may be potential therapeutic targets by acting as ceRNAs in cholesteatoma

status: Public on Apr 27 2020

first: Hua

last: Yang

address: Department of Otolaryngology, Peking Union Medical College Hospital, Beijing, 100730, China

institute: Peking Union Medical College Hospital

summary: In our present study, we explored the circRNA expression profiles in cholesteatoma by deep RNA-seq analysis. We obtained totally 355 significantly differentially expressed circRNA in cholesteatoma, among which 101 were identified to be up-regulated, and 254 down-regulated. By constructing the circRNA-miRNA-mRNA ceRNA networks, it was discovered that circRNAs might contribute to cholesteatoma formation by functioning as ceRNAs for miRNAs.

overall_design: A genome-wide analysis was performed to profile differences in circRNA expression between 4 pairs of cholesteatoma and matched normal skin samples. All specimens were obtained from 2 female and 2 male patients aged 18-year-old to 32-year-old who received unilateral middle ear cholesteatoma surgeries. The post-auricular skins were taken as control samples from the same patients.

first: Juanjuan

last: Gao


title: Autoimunne arthritis-associated B cell methylome in mice with proteoglycan (PG)-induced arthritis (PGIA) [methylation]

city: Chicago

first: Tibor

last: Glant

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

type: Methylation profiling by genome tiling array

summary:
Autoimmune arthritis was induced by three consecutive PG injections. B cells were affinity purified from mice and methylated DNA fractions were enriched by methylated-CpG island recovery assay (MIRA) method  and investigated on microarray platforms.
Several hundred differentially methylated regions were detected in the investigated B cell epigenomes

overall_design: Four control (non-arthritic) and four arthritic B cell samples were analyzed on NimbleGen's DNA Methylation 385K CpG Island Plus RefSeq Promoter Array

last: Rauch


title: Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 in Arabidopsis

status: Public on Apr 25 2020

city: Cologne

first: Thomas

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

institute: Max-Planck Institute for Plant Breeding Research

summary: Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling in Arabidopsis thaliana and wild tobacco. We used chromatin immunoprecipitation and sequencing (ChIP-seq) of Arabidopsis TPR1-GFP expressing transgenic lines to characterize genome-wide TPR1-chromatin associations.

overall_design: We performed ChIP-seq experiments with α-GFP antibodies in three independent biological replicates using leaves of six-week-old pTPR1:TPR1-GFP in Col-0, a line with constitutive immunity ,and pTPR1:TPR1-GFP in eds1-2 plants lacking constitutive immunity. The pTPR1:TPR1-HA #3 Col-0 line served as a negative control as it is also autoimmune and accumulates similar TPR1 transcript levels as the TPR1-GFP line. Leaf material of 6-week-old plants was used in all three independent biological replicates.

first: Dmitry

last: Lapin

first: Jane

last: Parker

first: Barbara

last: Kracher


title: Transcriptional landscape changes after tolerization adaptive laboratory evolution of Staphylococcus aureus to vancomycin

status: Public on Apr 24 2020

city: La Jolla

first: Henrique

last: Machado

state: CA

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

summary: Eight vancomycin-tolerized strains were selected for transcriptional analysis, along with their pre-evolved counterparts (wild type and one media-adapted strain per medium type).

overall_design: Strains were grown in RPMI or CA-MHB respective to the evolution media, with and without vancomycin (at 1/2 MIC). At OD 0.2, cultures without vancomycin were harvested. At the same OD, cultures were treated with 0.5x MIC of vancomycin, and harvested for RNA 30min after.


title: High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis.

status: Public on Apr 16 2020

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series