title: Difference in characteristics between Endocardially-derived cardiac tissue macrophages (EcTMs) and non-Endocardially-derived cardiac tissue macrophages (non EcTMs)

city: Los Angeles

first: Ayako

last: Shigeta

state: CALIFORNIA

address: 675 C.E. Young Dr

institute: UCLA

summary: [Purpose] To define the traditional profile of EcTMs, RNA seq analysis were parformed on EcTMs and non EcTMs at postnatal day28. [Method] The workflow consists of first-strand synthesis, template switching, adaptor ligation, cleavage of ribosomal cDNA and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on an Illumina Nextseq500 a single read 75 run. Data quality check was conducted on Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program. Reads were aligned to the UCSC mm10 reference genome map using TopHat. DEseq2 was used to identify differentially expressed genes of EcTMs compared to non-EcTMs. 36 upregulated genes in EcTMs compared to non-EcTMs with a padj < 0.05 were subsequently clustered and visualized using R. Gene ontology functional analyses were performed using the database for annotation, visualization, and integrated discovery (DAVID) online tool.[Result] 40 genes were differentially expressed between the two groups: 36 were higher and 4 genes were lower in EcTMs compared to non-EcTMs. Gene Ontology analysis revealed that EcTMs were enriched for genes related to antigen presentation, lysosomes, and phagosomes (H2-Ab1, H2-Aa, H2-Eb1, CD74, Laptm5). [Conclusion] EcTMs would have higher potential for presenting antigen and phagositosis compared to non EcTMs.

overall_design: Examination of 2 kinds of cardiac tissue macrophages

first: Atsushi

last: Nakano


title: Transcriptomic changes in Medicago truncatula and Lotus japonicus root nodules during drought stress

status: Public on Feb 26 2019

city: Warsaw

first: Weronika

last: Czarnocka

address: Nowoursynowska 166

department: Department of Botany

country: Poland

institute: Warsaw University of Life Sciences

type: Expression profiling by high throughput sequencing

summary: Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research we focused on plants from Fabaceae family, which have a unique ability for establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We present the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results prove a decrease in the efficiency of nitrogen fixation as well as extensive changes in plant and bacterial transcriptomes shortly after watering cessation. We show for the first time that not only symbiotic plant component, but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrate that both M. truncatula and L. japonicus root nodules are susceptible to water deprivation, they indicate significant differences in plant and bacterial response to drought between tested species, which may be related to various type of root nodules formed by these species.

sample_organism:
Mesorhizobium loti
Sinorhizobium meliloti
Medicago truncatula
Lotus japonicus

overall_design: RNA was obtained from Medicago truncatula and Lotus japonicus non-inoculated roots (R) and root nodules either subjected to drought for two (T2) or four (T4) days, or well-watered control (T0). Two biological replicates for each sample was obtained. Each biological replicate consisted of roots or nodules harvested from 10-12 plants. RNA obtained from root nodules contained both plant and bacterial RNA. For Medicago truncatula the compatible rhizobium species is Sinorhizobium meliloti, for Lotus japonicus - Mesorhizobium loti.

first: Izabela

last: Sańko-Sawczenko


title: wMelpop strain of Wolbachia infection of Aedes albopictus mosquito C6/36 cells modulates dengue virus-induced host cellular transcripts and induces critical sequence alterations in dengue viral genome

status: Public on Feb 25 2019

city: Philadelphia

first: Klaudia

last: Kuranda

state: PA

address: 3737 Market St

department: Data Sciences

country: USA

institute: Spark Therapeutics

summary: The dengue virus (DENV) cause frequent epidemics infecting ~390 million people annually in over 100 countries. There are no approved vaccines or antiviral drugs for treatment of infected patients. However, there is a novel approach to control transmission of DENV by the mosquito vectors, Aedes aegypti and Ae. albopictus, using Wolbachia symbiont. The wMelPop strain of Wolbachia suppresses DENV transmission and shortens the mosquito life span. However, the underlying mechanism is poorly understood. To clarify this mechanism, either naïve Ae. albopictus (C6/36) or wMelPop-C6/36 cells were infected with DENV2. Analysis of host transcript profiles by RNAseq revealed that the presence of wMelPop had profound effects on mosquito host cell transcription in response to DENV2 infection. The viral RNA evolved from wMelPop-C6/36 contained low frequency mutations (~25%) within the coding region of transmembrane domain-1 (TMD1) of E protein. Mutations with >97 % frequencies were distributed within other regions of E, NS5 RNA-dependent RNA polymerase (NS5POL) domain, the TMDs of NS2A, NS2B, and NS4B. Moreover, while DENV2-infected naïve C6/36 cells showed syncytia formation, DENV2-infected wMelPop-C6/36 cells did not. The Wolbachia-induced mutant DENV2 can readily infect and replicate in naïve C6/36 cells; whereas, in the mutant DENV2- infected BHK-21 or Vero cells, the virus replication was delayed. In LLC-MK2 cells, the mutant failed to produce plaques. Additionally, in BHK-21 cells, many mutations in the viral genome reverted to WT and compensatory mutations in NS3 gene appeared. Our results suggest that wMelPop impacts significantly the interactions of DENV2 with mosquito and mammalian host cells.

overall_design: Cellular mRNA profiles of naïve Ae. albopictus (C6/36) or wMelPop-C6/36 cells infected with DENV2 were generated by RNA-Seq, in triplicate, using Illumina HiSeq.

first: Tadahisa

last: Teramoto

first: Xin

last: Huang

first: Iñaki

last: Iturbe-Ormaetxe

first: Scott

middle: L

last: O’Neill

first: Peter

last: Armbruster

first: Radhakrishnan

last: Padmanabhan


title: Transcriptome analysis of mouse cortical development and characterization of long non-coding RNAs

city: Wuhan

first: Tian

last: Kuan

state: Hubei

address: Luojiashan

country: China

institute: College of Life Sciences at Wuhan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Cortical neural progenitor cells (NPCs) change their competency over time during development, giving rise to distinct cell types sequentially. Many genes that govern cortical development are now known, but it remains elusive how their temporal expression is controlled. Recently, long non-coding RNAs are found to be essential for cell-fate specification and precise gene regulation in many developmental events. In this study, strand-specific RNA sequencing studies unveil large amount of long non-coding RNAs are actively and differentially expressed across mouse cortical development. Integration of RNA sequencing data from key stages of developing mouse cortex enables us to cluster coding and non-coding transcripts into co-expression “modules” to infer functional relationships. Intriguingly, the cortical transcriptome undergoes significant changes in early mouse neurogenesis. Cortical long non-coding RNAs tends to be transcribed from genomic loci adjacent to protein-coding genes related to neural development. Finally, we found large amount of predicted enhancer regions are able to transcribe RNAs.  This study will help us better understand molecularly how cortical NPCs specify their fates during development, especially roles of lncRNAs in this process.

overall_design: Ribosomal-depletion RNA profiles of dorsal forebrain (cortex) tissues from E10.5 and E12.5 mouse embryos were generated using Illumina HiSeq 2000 and totally 410 million paired-end reads were generated.

first: Wei

last: Li

first: Kuan

last: Tian

first: Lili

last: Mu

first: Zhiyuan

last: Luo

first: Wenchen

last: Shen

first: Jing

last: Liu

first: Xiaoling

last: Zhong

first: Yamu

first: Kuanwei

last: Sheng

first: Ying

first: Yan

last: Zhou


title: Selective roles of vertebrate PCF11 in premature and full-length transcript termination (human 3' mRNA-seq)

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including: mNET-seq, 3’ mRNA-seq, chromatin RNA-seq and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and downstream gene silencing. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript, and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination.

overall_design: 3' mRNA-seq in HeLa cells. Control and PCF11 knock-down (4 biological replicates); control and PCF11 PAS1 deletion clones muA and muB (3 biological replicates); control and additional PCF11 PAS1 deletion clones muC and muD (1 replicate).

first: Michal

middle: R

last: Gdula

first: Karin

last: Panser

first: Andrea

last: Pauli

first: Nick

last: Proudfoot


title: Selective roles of vertebrate PCF11 in premature and full-length transcript termination (zebrafish 3' mRNA-seq)

overall_design: 3' mRNA-seq in individual zebrafish embryo heads. Two types of mutants: zPCF11 null and zPCF11 with deletion of PAS1. Wild-type (wt, +/+), heterozygous (het, +/-) and homozygous mutant (hom, -/-) embryos were analyzed. Wild-type and heterozygous animals were phenotypically indistinguishable.


title: Selective roles of vertebrate PCF11 in premature and full-length transcript termination (chromatin-bound RNA-seq)

overall_design: Semi-nascent transcriptome measured by chromatin-bound RNA-seq in HeLa cells. Control and PCF11 knock-down (2 biological replicates) and control and PCF11 PAS1 deletion (4 biological replicates).

middle: J


title: The effect of colorectal cancer (CRC) organoid-derived extracellular vesicles on the expression profile of fibroblasts

city: Budapest

first: Zoltan

last: Wiener

address: Ulloi ut 26

country: Hungary

institute: Semmelweis University

summary: Extracellular vesicles (EV) are membrane-surrounded vesicles secreted by cells that carry biologically important molecules to the target cells. EVs form a heterogenous group and they represent a novel way of intercellular communication. To study the importance of colorectal cancer (CRC)-derived EVs on stromal fibroblasts, we applied CRC patient-derived 3D organoid cultures and commercially available human colon fibroblasts. We studied the gene expression changes in fibroblasts in the presence and absence pf CRC-derived EVs.

overall_design: CRC patient-derived organoids were 3D cultured in Matrigel in chemically defined medium and EVs were isolated after 2 days by differential centrifugation and untracentrifugation. The effect of EV-enriched pellet, suspended in the EV-free supernatant was compared to the EV-free supernatant in human colon fibroblasts


title: Selective roles of vertebrate PCF11 in premature and full-length transcript termination (mNET-seq)

overall_design: T4ph mNET-seq in HeLa cells. Control and PCF11 knock-down (3 biological replicates) and control and PCF11 PAS1 deletion (2 biological replicates).


title: Microarray dataset of TmBER1 gene silencing strain, TmBER2 gene silencing strain, and pSAP2G mock strain

city: Tokyo

first: Herbert

middle: Jimenez

last: Santos

address: 7−3−1, Hongo, Bunkyo-ku

department: School of International Health, Graduate School of Medicine

country: Japan

institute: The University of Tokyo

summary: In order to understand the function of the Entamoeba-specific transmembrane β-barrel on the ER (TmBER) proteins, TmBER1 and TmBER2, we carried out transcriptional gene silencing of the two TmBERs respectively. In this study, we would like to find out which genes are affected by silencing of TmBER1 and TmBER2 with respect to the mock transformant pSAP2-G, which was transfected with an empty vector.

overall_design: We analyzed the expression profile of 9,230 genes in Entamoeba histolytica, when either TmBER1 or TmBER2 is gene silenced (gs) using a custom-generated Affymetrix platform full genome microarray. The transcriptome data from either gs strains were compared with that of the mock transformant to determine the specific effect of gene silencing on E. histolytica.

first: Kenichiro

last: Imai

first: Takashi

last: Makiuchi

first: Kentaro

last: Tomii

first: Paul

last: Horton

first: Akira

last: Nozawa

first: Kenta

last: Okada

first: Yuzuru

last: Tozawa

first: Tomoyoshi

last: Nozaki


title: Small Heterodimer Partner and Fibroblast Growth Factor-19 Inhibit Intestinal Npc1l1 Expression and Cholesterol Absorption

status: Public on Feb 23 2019

city: Urbana

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

summary: Small Heterodimer Partner (SHP/NR0B2) is an unusual orphan nuclear receptor that does not have a DNA binding domain and acts as a co-repressor for many transcriptional factors, including LRH-1, SREBPs, FOXA1, and AhR, which inhibits expression of its target genes. To explore global intestinal functions of SHP, WT and SHP-KO mice were fed for 6 h after fasting overnight. In SHP-KO mice, 1,707 genes were upregulated, and 1,055 genes downregulated by 2-fold or more compared to WT mice. In GO analysis, intestinal genes upregulated with the highest significance were involved in the transport of ions, lipids, and hormones, and in cholesterol metabolic processes; whereas genes downregulated were involved in the cell cycle, the immune response, and apoptosis. Remarkably, expression of genes important for cholesterol absorption, including Npc1l1, sterol biosynthetic genes, including Hmgcr, and key intestinal bile acid transporters, Asbt and Ost-alpha/beta, was altered in SHP-KO mice compared to WT mice. Overall, in this study, SHP was shown to be a gene-specific transcriptional partner of SREBP-2 to epigenetically inhibit cholesterol-regulating genes, including Npc1l1, in the late-fed state.

overall_design: Intestinal mRNA profiles were generated by deep sequencing, were profiled at the intestine (Jejunum and Ileum) in wild-type (WT) and SHP-KO mice fed for 6 h after fasting overnight.

first: Sangwon

last: Byun

first: Sunmi

last: Seok

first: Grace

last: Guo

first: H

middle: E

last: Xu

first: Byron

last: Kemper

first: Jongsook

last: Kim Kemper


title: COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [cell lines]

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Tumor-stromal communication within the microenvironment contributes to initiation of metastasis and may present a therapeutic opportunity. Using serial single cell RNA-sequencing in an orthotopic mouse prostate cancer model, we find upregulation of Prolactin receptor as cancer cells that have disseminated to the lung expand into micrometastases. Secretion of the ligand Prolactin by adjacent lung stromal cells is induced by tumor cell production of the COX-2 synthetic product prostaglandin E-2 (PGE-2). PGE-2 treatment of fibroblasts activates the nuclear orphan receptor NR4A (Nur77), with Prolactin as a major transcriptional target for the NR4A-Retinoid X receptor (RXR) heterodimer. Ectopic expression of Prolactin receptor in mouse cancer cells enhances micrometastasis, while treatment with the COX-2 inhibitor Celecoxib abrogates Prolactin secretion by fibroblasts and reduces tumor initiation. Across multiple human cancers, COX-2, Prolactin, and Prolactin receptor show consistent differential expression in tumor and stromal compartments. Such paracrine crosstalk may thus contribute to the documented efficacy of COX-2 inhibitors in cancer suppression.

overall_design: Five subclonal cell lines were established from CE1-4 prostate cancer cells, derived from tissue-specific inactivation of PTEN [Pubmed ID: 20631921]. RNA-seq was performed on the five subclonal cell lines and the parental line.

first: Yu

last: Zheng

first: David

last: Miyamoto

middle: S

first: Erin

last: Emmons

first: Srinjoy

last: Sil

first: Michael

last: Koulopoulos

first: Katherine

last: Broderick

first: Eric

last: Tai

first: Toshi

last: Shioda

first: Chin-Lee

last: Wu

first: Mehmet

last: Toner

last: Ting

first: Sridhar

last: Ramaswamy

first: Shyamala

last: Maheswaran

first: Daniel

middle: A

last: Haber

first: Valentine

last: Comaills

first: Risa

last: Burr

first: Gaylor

last: Boulay

first: Shruthi

last: Rengarajan

first: Anupriya

last: Kulkarni

first: Miguel

last: Rivera


title: High-throughput identification of the impact of ΔrecA mutation on sensitivities to various chemical compounds in Escherichia coli

status: Public on Feb 24 2019

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

institute: RIKEN Quantitative Biology Center

summary: Antibiotic resistance is currently considered as a global threat to public health. It was shown that adaptive resistance mutation and acquisition of resistance genes by horizontal gene transfer are facilitated by RecA-dependent SOS response during antibiotic treatment. In this study, we performed high-throughput determination of minimal inhibitory concentrations (MICs) of 214 chemicals including not only various kinds of antibiotics but also toxic chemicals of unknown drug action in Escherichia coli wild-type MDS42 strain and the ΔrecA mutant strain. The ΔrecA mutant showed increased sensitivity to DNA-damaging agents, DNA replication inhibitors, and chromate stress. The ΔrecA mutant also showed increased sensitivity to chemicals other than DNA-damaging agents such as S-(2-aminoethyl)- l-cysteine, l-histidine, ruthenium red, D-penicillamine, carbonyl cyanide 3-chlorophenylhydrazone (CCCP), cerulenin, and l-cysteine. Microarray analysis showed that expressions of glnK, nac, and glnLG encoding nitrogen assimilation regulators together with amtB encoding ammonium transporter decreased in the ΔrecA mutant strain. These results suggest that ΔrecA mutation affect not only SOS response but also nitrogen assimilation.

overall_design: Transcriptomes of the ΔrecA mutant strain and the wild-type strain were compared by DNA microarray analysis. Both strains were grown on the modified M9 medium and total RNA was isolated from the cells in the early exponential growth phase. The comparison was performed in triplicate, starting from independent cultures.

first: Tomoya

last: Maeda

first: Takaaki

last: Horinouchi

first: Natsue

last: Sakata

first: Aki

last: Sakai

first: Chikara


title: Transcriptome of nitrogen depleted Dunaliella salina

city: TEDA

first: Hexin

last: Lv

state: Tianjin

address: 29 13th street

institute: Tianjin University of Science and Technology

summary: Illumina HiseqTM2000 RNA-sequencing of Dunaliella salina under nitrogen deprivation condition was performed.

overall_design: Dunaliella salina cells cultured under nitrogen deprivation conditions were harvested and RNA were extracted and sequenced by Illumina HiseqTM2000


title: COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [single cells]

first: Ben

last: Wittner

overall_design: Primary tumors were established by direct prostate inoculation into immunosuppressed NSG mice of CE1-4 prostate cancer cells, derived from tissue-specific inactivation of PTEN [Pubmed ID: 20631921].  These cells, which were GFP-luciferase tagged, are noteworthy in that they have preserved expression of the androgen receptor and epithelial markers and recapitulate biological features of human prostate cancer. Six weeks following intra-prostate inoculation, multiple single DTCs were identified microscopically within the lungs (394 cells/hpf), with a smaller number in liver (54 cells/hpf), brain (9 cells/hpf) and bone marrow (1 cell/hpf). To undertake RNA sequencing of single cells during progression from quiescent DTCs to proliferative lesions, we identified GFP-tagged single tumor cells from lung harvested at various intervals, analyzing these separately from microdissected multicellular lesions. Individual DTCs collected at 6-7 weeks (DTC-I; N=20) and at 9-11 weeks (DTC-II; N=55) were compared with single cells derived from the primary tumor (N=29), lung micro-metastases (N=33), and CTCs isolated by microfluidic capture from blood specimens (N=12) [Pubmed ID: 28181495].

first: Yu

last: Zheng

first: David

last: Miyamoto

first: Erin

last: Emmons

first: Srinjoy

last: Sil

first: Michael

last: Koulopoulos

first: Katherine

last: Broderick

first: Eric

last: Tai

first: Toshi

last: Shioda

first: Chin-Lee

last: Wu

first: Mehmet

last: Toner


title: TNFα and LTβ stimulated UM-SCC 46 gene expression [TNF]

status: Public on Feb 22 2019

city: Bethesda

first: Carter

last: Van Waes

state: MD

address: 10 Center Drive

department: Head and Neck Surgery Branch

institute: NIDCD

summary:
To investigate the regulatory mechanisms and targets of the activation of NF-kB and inflammatory pathways, we treated HPV(-) head and neck cancer line UM-SCC 46 cells with TNFα and LTβ at different time points, and compared the gene expression by microarray. TNFα uniquely induced 172 genes, LTβ specifically induced 202 genes, while 155 genes were induced by both ligands.
Total RNA samples were isolated from UM-SCC 46 cells after TNFα or LTβ treatment at different time points, and the gene expression were compared with untreated cell controls.

overall_design: UM-SCC 46 cells were treated with TNFα (20ng/ml) or LTβ (100ng/ml) for 1, 3, 6, 12, and 24 hours. RNA was isolated and global gene expression was examined by beads based array using Illumina HumanWG-6-v3-BeadChip (Illumina, CA). Raw data were imported to the GenomeStudio software, and normalized data were imported to Parte to detect differentially expressed genes by using an ANOVA test. Hierarchical clustering of altered gene expression when treated with LTβ was compared to untreated cells using MeV software. The heat map represents two-fold increased gene expression when compared to untreated samples.

first: Xinping

last: Yang

first: Tsu-Fan

last: Cheng

first: Zhong

last: Chen


title: Transcriptional characterization of  visceral adipose tissue (VAT) mesenchymal stromal cell (mSC) subtypes in male and female C57BL/6 mice.

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Regulatory T cells (Tregs) are key brakes on the VAT inflammation that regulates local and systemic metabolic tenor. The cytokine, IL-33, expands and sustains the unique Treg population residing within VAT. Making use of  single-cell RNA sequencing, we identified the major IL-33 producers in VAT to be particular mSC subtypes, related to but distinct from adipocyte progenitor cells. We further characterize these subsets by individually isolating them and performing bulk-RNA sequencing. We explored modulation of the VAT-mSC (VmSC) landscape with physiologic variables such as age and sex, as well as pathogenic states like obesity. We uncovered a VAT Treg:stromal-cell negative regulatory loop that keeps the potent effect of IL-33 under rein.

overall_design: Gene expression profiles of VmSC subtypes from young male and female mice. 2-4 mice were pooled for each biological replicate and at least 2 biological replicates were obtained per VmSC subtype.

first: Raul

middle: G

last: Spallanzani

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: TNFα and LTβ stimulated UM-SCC 46 gene expression [LTB]

summary:
To investigate the regulatory mechanisms and targets of the activation of NF-kappaB and inflammatory pathways, we treated HPV(-) head and neck cancer line UM-SCC 46 cells with TNFα and LTβ at different time points, and compared the gene expression by microarray. TNFα uniquely induced 172 genes, LTβ specifically induced 202 genes, while 155 genes were induced by both ligands.
Total RNA samples were isolated from UM-SCC 46 cells after TNFα or LTβ treatment at different time points, and the gene expression were compared with untreated cell controls.


title: COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis

first: Ben

last: Wittner

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: TNFa and LTB stimulated UM-SCC 46 gene expression


title: The effect of miR-204 on mRNA expression profiles of primary mouse chondrocytes

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: mRNA profiles of primary mouse chondrocytes transfected with miR-Ctrl or miR-204 mimics were generated by mRNA sequencing. This study provides insights into the role of miR-204 in chondrocytes.

overall_design: For primary culture of mouse chondrocytes, cells were isolated from femoral condyles and tibial plateaus of 5-day-old ICR mice. Mouse chondrocytes were transfected with miR-Ctrl or miR-204 mimics for 24 hours. mRNA profiles of miRNA-transfected chondrocytes were generated by mRNA sequencing, using Illumina HiSeq 2500 system.

first: J

middle: H

first: D

last: Kang


title: Sequence specific suppression of androgen receptor-DNA binding in vivo by a Py-Im polyamide

city: Pasadena

first: Peter

last: Dervan

state: CA

address: 1200 E. California Blvd., MC164-30

institute: California Institute of Technology

summary: The crucial role of androgen receptor in prostate cancer development is well documented, and its inhibition is a mainstay of prostate cancer treatment.  Here we analyze the perturbations to the androgen receptor cistrome caused by a minor groove binding molecule that is designed to target a sequence found in a subset of androgen response elements.  We find treatment with this pyrrole-imidazole polyamide exhibits sequence selectively in its repression of androgen receptor binding in vivo. Differentially changed loci are enriched for sequences resembling ARE half-sites that match the Py-Im polyamide binding preferences determined in vitro. Comparatively, permutations of ARE half-site bearing single or double mismatches to the Py-Im polyamide binding sequence are not enriched. This study represents an indirect determination of Py-Im polyamide binding preference in vivo using an unbiased approach.

overall_design: ChIP-seq of androgen receptor in 1 prostate cancer cell line with 3 treatments (vehicle, DHT, DHT and Py-Im polyamide)

middle: B

first: Alexis

last: Kurmis


title: LncRNA Spehd regulates hematopoietic stem cells and progenitors and is required for multilineage differentiation

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

summary: Long non-coding RNAs (lncRNAs) show patterns of tissue- and cell-type-specific expression that are very similar to those of protein coding genes and consequently have the potential to control stem and progenitor cell fate decisions along a differentiation trajectory. To understand the roles that lncRNAs might play in hematopoiesis, we selected a subset of mouse lncRNAs with potentially relevant expression patterns and refined our candidate list using evidence of conserved expression in human blood lineages. For each candidate, we assessed its possible role in hematopoietic differentiation in vivo using competitive transplantation. Our studies identified two lncRNAs that were required for hematopoiesis. One of these, Spehd, showed defective multi-lineage differentiation, and its silencing yielded common myeloid progenitors deficient in their oxidative phosphorylation pathway. This effort not only suggests that lncRNAs can contribute to differentiation decisions during hematopoiesis but also provides a path toward the identification of functional lncRNAs in other differentiation hierarchies.

overall_design: Transcriptome analysis was performed on shRNA-expressing sorted bone marrow progenitors cells (LSK, CMP). The animals had been transplanted with hematopoietic stem cells transduced with inducible shRNA vectors against lncRNA12928/Spehd or control knockdown , they were allowed to reconstitute for 10 weeks and administered doxycycline-containing food for 6 days. The objective was to identify transcriptional changes upon lncRNA loss.

first: M

first: Benjamin

middle: T

last: Jackson

first: Gregory

last: Hannon


title: Transcriptional profile of the liver of zebrafish after feeding with 0% or 25% dietary maize substitution

city: Wilrijk

first: Isabelle

last: Gabriëls

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

summary: For the toxicological risk assessment of genetically modified (GM) food components, the European Food Safety Agency advises to use an adapted version of the 90-day oral toxicity study in rodents, originally designed for the toxicity testing of chemicals. Since in GM crop testing scenarios the crop under evaluation is specifically intended as a food / feed component, some testing aspects are conceptually different from testing chemical compounds and thus need careful consideration. One key consideration relates to the appropriate dose level to evaluate the GM crop as a component of the experimental diet. The aim of this study was to develop and optimize methods that are required for advancing the use of zebrafish feeding trials for the toxicological safety evaluation of GM crops. Using maize as a case study, we investigated the effects of an increasing maize substitution dose level in the diets of zebrafish, using non-GM maize. In addition, we investigated the effect of the presence of maize in the diets (0% or 25% of maize substitution levels) on mRNA transcriptional profiles in the zebrafish liver.

overall_design: 0% vs 25% dietary maize substitution, 4 biological replicates, 10 male and 10 female fish per replicate

first: I

first: L

last: Vergauwen

last: De Boevre

first: S

last: Van Dongen

first: R

last: Blust

last: De Saeger

last: Eeckhout

last: De Loose

last: Knapen


title: Genome Wide Methylation Analysis of Organellar DNA in MR219 Indica Rice Cultivar

city: Subang Jaya

first: Kanagesswari

last: Muniandy

state: Selangor

address: Jalan Lagoon Selatan

department: School of Science

country: Malaysia

institute: Monash University Malaysia

type: Methylation profiling by high throughput sequencing

summary:
Purpose:  The chloroplast DNA has not been primiarly analyzed in rice plants before. Hence, the objective of this study is to analyze and compare the differential methylation of chloroplast DNA in MR219 indica rice across different tissues and different developmental stages.
Methods:  We prepared a total of nine sodium bisulfite treated DNA libraries from three developing grain tissues, three leaf tissues at ripening stage and three leaf tissues at vegetative stage and sequenced them in Illumina Miseq platform. We performed quality trimming, alignment followed by methylation calling and differential methylation analysis using Trimmomatic v36, Bismark v16.3 and SeqMonk v40.0 on the sequencing data obtained. Statistical analysis was carried out in SeqMonk software and further validated in SPSS statistical software v22.2.
Results: With an optimized data analysis workflow, we mapped around average of 26000 reads to chloroplast genome.  Differential CpG and CHG methylation in SeqMonk v40.0 revealed that MR219 chloroplast DNA is differentially methylated in grain and leaf tissues and across vegetative stage and ripening stage in the leaf tissues. Chloroplast DNA from leaf at ripening stage was most methylated, followed by grain tissue and lastly leaf tissue from vegetative stage.
Conclusions: Overall, it can be concluded that the organellar DNA in MR219 rice are differentially methylated at different tissues and across different developmental stages. The chloroplast DNA was most methylated in the  leaf at ripening stage, followed by grain at ripening stage and leaf at vegetative stage. The functional significance of the differential methylation observed in this study needs to be investigated.

overall_design: MR219 rice developing grain at ripening stage, leaf tissue at ripening stage and leaf tissue at vegetative stage sequencing data were generated from Illumina Miseq in triplicates.

first: Sadequr

last: Rahman

first: Yin

middle: P

last: Lee


title: Repression of germline genes in C. elegans somatic tissues by H3K9 dimethylation of their promoters [ChIP-seq]

status: Public on Feb 21 2019

city: Milwaukee

first: Lisa

middle: N.

last: Petrella

state: WI

address: 1428 W. Clybourn St

department: Biological Sciences

institute: Marquette University

summary: synMuv B proteins, including LIN-15B, are necessary to repress the expression of germline-promoting genes in the soma during embryonic and early larval development in C. elegans.  The goal of this research was to determine if changes to histone modifications could underlie the misexpression of germline genes in these mutants.  We performed ChIP-seq on four histone modifications in wild type and three synMuv B mutants at two temperatures to assess these changes.

overall_design: Examination of four histone modifications (H3K9me2, H3K27me3, H3K4me3, H3K36me3) by ChIP in WT and three mutant (lin-15B(n744), lin-35(n745), lin-37(n758)) C. elegans at 20°C and 26°C to assess changes in chromatin that may lead to the changes in gene expression seen in mutants.

first: Andreas

last: Rechtsteiner

first: Meghan

last: Costello

first: Thea

last: Egelhofer

first: Jacob

middle: M

last: Garrigues

first: Susan

last: Strome

middle: N


title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm

city: San Francisco

first: M.

middle: Yvonne

last: Kim

address: 3rd st.

institute: UC San Francisco

summary: Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice, however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared to sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion.

overall_design: Examination of DNA methylation in rice sperm and vegetative cell

first: M

middle: Y

first: Akemi

last: Ono

first: Stefan

last: Scholten

first: Tetsu

last: Kinoshita

first: Daniel

last: Zilberman

first: Takashi

last: Okamoto

first: Robert

last: Fischer


title: RNA-sequencing of Wnt-dependent and Wnt-independent of Glioblastoma stem cell cultures

city: Toronto

first: Nishani

last: Rajakulendran

state: Ontario

address: 144 College St. Room 950, Leslie Dan Faculty of Pharmacy

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

summary: Four Wnt-dependent and four Wnt-independent GSC cultures were grown in stem cell media and RNA expression between the two subsets evaluated

overall_design: Four biological replicates each of Wnt-dependent and Wnt-independent GSC cultures

first: Stephane

last: Angers


title: Single cell transcriptomic analysis (InDrops) of mouse mesenchymal stromal cells (mSCs or FAPs, fibro-adipogenic progenitors) isolated from lymph node, muscle and visceral adipose tissue

first: CBDM

last: Lab

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation (InDrops)

first: David

last: Zemmour

first: Raul

last: Spallanzani

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Stroke target identification guided by astrocyte transcriptome analysis

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)


title: A novel role of the stress-activated protein kinase network p38/HOG in coupling growth to division in Candida albicans

status: Public on Feb 20 2019

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

institute: Universite de Montreal

type: Genome binding/occupancy profiling by array

summary: The basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans, is a critical but still poorly understood aspect of eukaryotic cell proliferation. All eukaryotic cells must grow to a critical cell size before commitment to division occurs. This size threshold couples cell growth to division and thereby establishes long-term size homeostasis. Here, to address the problem of cell size control across different species, we performed the first quantitative survey of the size phenome in the pathogenic yeast Candida albicans by focusing on mutants of transcriptional regulators and kinases. We investigate one of the divergent size regulatory pathways in C. albicans, the p38/HOG MAPK module, to uncover a novel stress-independent function for the HOG module in size control. We show that Hog1 inhibits G1/S transcription to delay the G1/S transition and that Hog1 also controls ribosome biogenesis gene expression. These results suggest that Hog1 represents a critical and previously unsuspected nexus between the growth and division machineries. Our study thus delineates the overall genetic basis for size control in C. albicans and identifies, to our knowledge, the first specific conduit that couples cell growth to cell division.

overall_design: To investigate the role of Hog1 in Start control in C. albicans, we performed genome-wide transcriptional profiling by microarray. G1-cells of both hog1 mutant and the parental WT strain were collected by centrifugal elutriation, grown for 10 min at 30°C in fresh YPD medium and their transcriptomes were characterized. Using the same experimental setup, we performed genome wide occupancy experiment (YPD, 30°C) with Hog1-TAP to determine its binding sites.

first: Julien

last: Chaillot

first: Jaideep

last: Malick

first: Faiza

last: Tebbji

middle: R

last: Albert

first: Michael

last: Cook

first: Mike

last: Tyers


title: Stroke target identification guided by astrocyte transcriptome analysis [single animal]

summary: We aimed to investigate the influence of ischemic stroke in mice on their ribosomal mRNA in astrocytes. Therefore, we make use of the conditional Cre/LoxP System in the RiboTag mouse line in order to isolate the ribosomal mRNA of astrocytes. CreERT2 expression under the astrocyte-specific Cx43 promoter is induced by Tamoxifen injection and activates the expression of a haemagglutinin tag on ribosomal proteins.   3 weeks after Tamoxifen induction, mice were subjected to a 60 min middle cerebral artery occlusion (tMCAO), which is an established ischemic stroke model. Control mice were not further treated.

overall_design: Single sample analysis from 3 animals in each group, 2 technical replicates each. From each sample RNA was extracted by IP two times and pooled back together.

first: Cordula

last: Rakers

first: Melvin

last: Schleif

first: Thomas

last: Ulas

first: Kristian

last: Händler

first: Santiago

last: ValleTorres

first: Toni

last: Schumacher

first: Khalid

last: Tai

first: Caroline

last: Dalmoro

middle: L

first: Walker

last: Jackson

first: Gabor

middle: C

last: Petzold


title: Stroke target identification guided by astrocyte transcriptome analysis [pool]

first: Joachim

last: Schultze

overall_design: Pool from 3 animals in each group, 2 technical replicates each. From each sample RNA was extracted by IP two times and pooled back together.


title: Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1-/Δ7 mice

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: The use of Akkermansia muciniphila as potential therapeutic intervention is receiving increasing attention. Health benefits attributed to this bacterium include an improvement of metabolic disorders and exerting anti-inflammatory effects. The abundance of A. muciniphila is associated with a healthy gut in early mid- and later life. However, the effects of A. muciniphila on a decline in intestinal health during the aging process are not investigated yet. We supplemented accelerated aging Ercc1-/Δ7 mice with A. muciniphila for 10 weeks and investigated histological, transcriptional and immunological aspects of intestinal health. The thickness of the colonic mucus layer increased about 3-fold after long-term A. muciniphila supplementation and was even significantly thicker compared to mice supplemented with Lactobacillus plantarum WCFS1. Colonic gene expression profiles pointed towards a decreased expression of genes and pathways related to inflammation and immune function, and suggested a decreased presence of B cells in colon. Total B cell frequencies in spleen and mesenteric lymph nodes were not altered after A. muciniphila supplementation. Mature and immature B cell frequencies in bone marrow were increased, whereas B cell precursors were unaffected. These findings implicate that B cell migration rather than production was affected by A. muciniphila supplementation. Gene expression profiles in ileum pointed toward a decrease in metabolic- and immune-related processes and antimicrobial peptide production after A. muciniphila supplementation. Besides, A. muciniphila decreased the frequency of activated CD80+CD273- B cells in Peyer’s patches. Additionally, the increased numbers of peritoneal resident macrophages and a decrease in Ly6Cint monocyte frequencies in spleen and mesenteric lymph nodes add evidence for the potentially anti-inflammatory properties of A. muciniphila. Altogether, we show that supplementation with A. muciniphila prevented the age-related decline in thickness of the colonic mucus layer and attenuated inflammation and immune-related processes at old age. This study implies that A. muciniphila supplementation can contribute to a promotion of healthy aging.

overall_design: The effects of 10-wk bacterial supplementation of Akkermansia muciniphila on gut barrier and immunity was investigated in 16-week-old accelerated aging Ercc1-/Δ7 mice, which have a median lifespan of ~20wk. Distal ileum and proximal colon tissues were subjected to gene expression profiling.

first: Benthe

last: van der Lugt

first: Adriaan

last: van Beek

first: Steven

last: Aalvink

first: Ben

last: Meijer

first: Bruno

last: Sovran

first: Wilbert

last: Vermeij

first: Renata

last: Brandt

first: Willem

last: de Vos

first: Huub

last: Savelkoul

first: Wilma

last: Steegenga

first: Clara

last: Belzer


title: RNA-seq of selenium treatment in cortical neurons

city: White Plains

first: Rajiv

last: Ratan

state: New York

address: 785 Mamaroneck Ave

department: Research

institute: Burke Neurological Institute

summary: Ferroptosis, a non-apoptotic form of programmed cell death, is triggered by oxidative stress in cancer, heat stress in plants and hemorrhagic stroke. A homeostatic transcriptional response to ferroptotic stimuli is unknown. We show that neurons respond to ferroptotic stress by induction of a transcriptional adaptive response. Pharmacological selenium (Se) augments mitochondrial and nuclear GPX4 and other genes in this transcriptional program, the selenome, via coordinated activation of the transcription factors TFAP2c and Sp1, to protect neurons. This RNA seq data uses primary cortical neurons in cultures treated with either homocysteic acid (HCA), which induces ferroptosis and/or Se, which augments the adaptation to ferroptosis. Both protective (1mM Se) and non-protective (0.1mM Se) of selenium are used. Cells are collected after 6 hours when the transcriptional response is observed.

overall_design: Primary cortical neurons are plated from E15 mouse pups for 24 hours. Then either ferroptosis inhibitor HCA (5mM) and/or sodium selenite (0-1uM) is added to the cultures in bath. Cultures are washed with PBS and scraped for RNA collection. RNA is purified and quality measured. RNA was depleted with Ribo-zero gold and RNA seq was done using Hi seq 4000.

first: Ishraq

last: Alim

first: Vivek

last: Swarup

first: Daniel

last: Geschwind


title: Transcriptomic analysis of iPSC and ESC challenged with atmospheric or physiological oxygen

city: Parkville

first: James

last: Spyrou

state: VIC

address: Royal Parade

department: School of BioSciences

country: Australia

institute: The University of Melbourne

summary: Modulation of metabolism by 5% (physiological) oxygen during reprogramming has been shown to improve reprogramming efficiency, yet it is not known how it may affect the transcriptome and physiology of iPSC. RNA-seq analysis highlighted that iPSC derived under 20% oxygen displayed transcriptomic instability. Consequently, inappropriate modulation of metabolism by atmospheric oxygen during reprogramming significantly impacts the resultant iPSC transcriptional landscape.

overall_design: RNA-Seq analysis of two iPSC lines, and one ESC line, each sub-cultured under 20% and 5% oxygen.

first: David

middle: K

last: Gardner

first: Alexandra

middle: J

last: Harvey


title: Repression of germline genes in C. elegans somatic tissues by H3K9 dimethylation of their promoters

first: Lisa

last: Petrella

type: Genome binding/occupancy profiling by genome tiling array


title: Automated RNAi screening reveals MRG-1/MRG15 as a barrier for germline to neuron reprogramming in C. elegans

city: Berlin

first: Baris

last: Tursun

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

summary: Abstract: Chromatin-regulating factors safeguard cell identities by suppressing ectopic gene expression thereby imposing barriers for transcription factor-induced reprogramming of cell fates. Identifying factors opposing the induction of ectopic cell fates is important to better understand developmental differentiation processes and may improve cellular reprogramming for therapeutic approaches. Reprogramming barriers have previously been studied mostly in tissue cultures. Hence, knowledge about chromatin regulators acting as reprogramming barriers in vivo needs improvement. We therefore made use of the nematode C. elegans as an in vivo gene discovery tool and interrogated its chromatin-regulating factors for being involved in protecting germ cells against reprogramming to neurons by performing automated RNAi screening. We identified the conserved chromodomain factor MRG-1 (MRG15 in humans) as a barrier for converting germ cells into neurons and characterized its protein-protein and genome interactions using IP-MS and ChIP-seq in wild-type animals versus mutants lacking the germline. We found that MRG-1 associates predominantly with genes carrying active histone modifications but it also cooperates with the histone H3K9 methyltransferase SET-26 in order to prevent conversion of germ cells into neurons. Conserved chromatin regulators such as MRG-1 potentially have similar functions in higher organisms as shown previously for the histone chaperone LIN-53 (CAF-1p48/RBBP7). LIN-53 was initially identified as a barrier of C. elegans germ cell reprogramming and was later shown to also block reprogramming in mammals. Such remarkable conservation of reprogramming barriers illustrates that understanding cell fate protection in C. elegans could help to improve the generation of new cell types for therapeutic approaches in humans.

overall_design: Two c. elegans worm strains  ( N2 and glp-4(bn2) ) were analysed in triplicates using ChIP-seq to identify binding regions of chromodomain factor MRG-1 (MRG15 in humans).

first: Martina

last: Hajduskova


title: System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: The compendium of RNA-binding proteins (RBPs) has been greatly expanded by the development of RNA interactome capture (RIC). However, it remained unknown if the complement of RBPs changes in response to environmental perturbations and whether these rearrangements are important. To answer these questions, we developed ‘comparative RIC’ and applied it to cells challenged with an RNA virus, called sindbis (SINV). Over two hundred RBPs display differential interaction with RNA upon SINV infection. These alterations are mainly driven by the loss of cellular mRNAs and the emergence of viral RNA. RBPs stimulated by the infection redistribute to viral replication factories and regulate the capacity of the virus to infect. For example, ablation of XRN1 causes cells to be refractory to SINV, while GEMIN5 moonlights as a regulator of SINV gene expression. In summary, RNA availability controls RBP localisation and function in SINV-infected cells.

overall_design: RNA-seq and iCLIP-seq in SINV infected human cells.

first: Alfredo

last: Castello

first: Shuai

last: Ni

middle: I


title: Malaria Host Pathogen Interaction Center Experiment S01: Host and parasite gene transcript abundances, from cultured cells, of Macaca mulatta infected with Plasmodium knowlesi Pk1(A+), Pk1(B+)1+, Pk1(C+) ex vivo time course.

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

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

sample_organism:
Plasmodium knowlesi
Macaca mulatta

platform_organism:
Plasmodium knowlesi
Macaca mulatta

overall_design: Malaria-naive rhesus macaques (Macaca mulatta), were inoculated with a particular parasite clone and allowed to reach a targeted peak parasitemia of 5% - 10% proportion of infected RBCs. Whole blood was collected at the early ring stage while subjects were under anesthesia, and an ex vivo culture was established using standard protocols, which include but are not limited to the processing of the whole blood by removing platelets and white blood cells. Samples were collected starting at 1.5-2 hours after establishing cultures, followed by collections every 4 hours for a 24 hour period. Blood-stage curative doses of the anti-malarial drug chloroquine were administered to all subjects after whole blood extraction from each subject. Parasitemias were monitored daily by earsticks. Within the MaHPIC, this project is known as ‘Supporting Project 01’.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from 'S01' including proteomics and other MaHPIC Experiments, visit http://plasmodb.org/plasmo/mahpic.jsp. This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).

first: Steven

middle: E

last: Bosinger

first: Jeremy

middle: D

last: DeBarry

first: Allison

last: Hankus

first: Jessica

last: Kissinger

first: Nicolas

last: Lackman

first: Stacey

middle: A

last: Lapp

first: Mustafa

last: Nural

first: Nirav

last: Patel

first: Mariko

middle: S

last: Peterson

first: Gregory

last: Tharp


title: The effect on p53-induced gene transactivation by LIMA1 knockdown.

city: Sapporo

first: Masashi

last: Idogawa

institute: Sapporo Medical University

summary: To explore the effect of LIMA1 on gene transactivation induced by p53, we evaluated the changes in gene expression by RNA-seq in LIMA1 knockdown or control A549 cells.

overall_design: Lung cacncer A549 cells were stably infected with lentivirus expressing shRNA-LIMA1 or negative control shRNA. These cells were treated with nutlin-3a which activates endogenous p53. The change of p53-induced gene transactivation was analyzed.


title: Changes of metabolic genes expression in lungs of bleomycin-treated mice

status: Public on Feb 19 2019

city: Shanghai

first: Daping

last: Yang

address: No.320 Yueyang Road, Xuhui District

institute: SIBS

summary:
Purpose: Explore whether bleomycin treatment will induce changes of metabolic genes expression via next-generation sequencing (NGS) in mouse lung tissues.
Methods: Four groups of wild type mice were intratracheally injected with 25 µl PBS or bleomycin (15 mg/kg) after anesthetization. 10 days after bleomycin treatment, lung tissues were removed for RNA collection. Three samples per group were mixed to one sample and used for next RNA purification. RNA samples were then used for high-throughput sequencing according to standard operation based on RNA BGISEQ-500.
Results: Using an optimized data analysis workflow, we mapped about 21.9 million sequence reads per sample to the mouse genome (build mm10) and identified 1024 upregulated and 936 downregulated genes in lungs of bleomycin-treated mice. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered metabolic changes of many carbohydrates, amino acid and fatty acid. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in metabolism profiling.
Conclusions: Our study represents the first detailed analysis of metabolic changes in lungs of bleomycin-treated mice with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based metabolic genes characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of metabolic genes expression in bleomycin-treated or untreated mice were generated by deep sequencing, in triplicate, using BGISEQ-500.

first: Youcun

last: Qian


title: Effect of different irrigation supply on gene expression of two table grape cultivars

city: Turi

first: Maria Francesca

last: Cardone

state: Bari

address: via Casamassima 148

department: Centro di ricerca Viticoltura ed Enologia (CREA-VE)

country: Italy

institute: Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA)

summary: Grapevine (Vitis vinifera L.) is importantly cultivated worldwide for table grape and wine production. Its cultivation requires irrigation supply, especially in arid and semiarid areas. Water deficiency can affect berry and wine quality mostly depending on the extent of plant perceived stress, which is a cultivar-specific trait.  We tested the physiological and molecular responses to water deficiency of two table grape cultivars, Italia and Autumn royal, and we highlighted their different adaptation. Microarray analyses revealed that Autumn royal reacts involving only 29 genes, related to plant stress response and ABA/hormone signal transduction, to modulate the response to water deficit. Instead, cultivar Italia orchestrates a very broad response (we found 1037 genes differentially expressed) that modifies the cell wall organization, carbohydrate metabolism, response to reactive oxygen species, hormones and osmotic stress.  For the first time we integrated transcriptomic data with cultivar-specific genomics and found that ABA-perception and –signalling are key factors mediating the varietal-specific behaviour of the early response to drought. We were thus able to isolate candidate genes for the genotype-dependent response to drought.  These insights will allow the identification of reliable plant stress indicators and the definition of sustainable cultivar-specific protocols for water management.

overall_design: 3 time points were analysed (OI_FI and WD) of 2 cultivars on one tissue (apexes)

first: Fiammetta

last: Alagna

first: Claudia

last: Catacchio

first: Rocco

last: Perniola

first: Carlo

last: Bergamini

first: Silvia

last: Rotunno

first: Francesco

last: Calabrese

first: Pasquale

last: Crupi

first: Donato

last: Antonacci

first: Mario

last: Ventura

first: Maria

middle: F


title: IL-17B promotes proinflammatory cytokines expression in mouse lung tissues

summary:
Purpose: Explore IL-17B target genes expression via next-generation sequencing (NGS) in mouse lung tissues.
Methods: Overexpress IL-17B in mouse lung tissues via intranasal injection of adenovirus encoding IL-17B (Adv-IL-17B) and empty virus (Adv-EV). Three days after infection lung tisses were removed for RNA collection. Five samples per group were mixed to one sample and used for next RNA purification. RNA samples were then used for high-throughput sequencing according to standard operation based on RNA Hiseq 4000.
Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome (build mm10) and identified 269 upregulated and 99 downregulated genes in lung after IL-17B overexpression. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to lung inflammation and infection. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of IL-17B induced downstream genes with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based downstream genes characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of IL-17B overexpressed lung tissue were generated by deep sequencing, in triplicate, using Illumina RNA Hiseq 4000.


title: piRNA silencing contributes to interspecies hybrid sterility and reproductive isolation in Drosophila

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

summary: The piRNA pathway is an adaptive mechanism for maintaining the stability of the genome by repression selfish genomic elements such as transposons. As a host defense mechanism the piRNA pathway is rapidly evolving with different sets of piRNA silencing different targets in closely-related species. In male germline of D.melanogaster, repression of Stellate genes by piRNA generated from Supressor of Stellate, Su(Ste), locus is required for male fertility, but both Su(Ste) piRNA and their targets are absent in other Drosophila species.  Here we showed that D.melanogaster genome contain non-coding genomic repeats that have sequence similarity to vasa, protein-coding host gene essential for germline development. In male germline Vasa Related (Varel) repeats produce abundant piRNA that are anti-sense to vasa, however, vasa mRNA escape silencing due to imperfect complementarity between piRNA and vasa sequences. Unexpectedly, we found that Varel piRNA of D.melanogaster target vasa  of closely related D. mauritana species in interspecies hybrids. The same hybrids show derepression of harmful Stellate locus due to the absence of Su(Ste) piRNA.  Thus, the piRNA pathway contributes to the reproductive isolation between Drosophila species, causing hybrid male sterility via misregulation of two different host factors.

sample_organism: Drosophila melanogaster x Drosophila mauritiana

overall_design: Examination of piRNA production in small RNA libraries and transcription level of Varel repeats and vasa transcripts in RNA-seq libraries from D.melanogaster, D.mauritiana and interspecies hybrids


title: Identification of spatiotemporal RNA expression and subcellular RNA localization during Drosophila embryonic neurogenesis

first: Alexandra

middle: Louise

last: McCorkindale

address: Robert Roessle-Strasse 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center for Molecular Medicine

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

overall_design: Refer to individual Series


title: Subcellular RNA localization during Drosophila embryonic neurogenesis [fractionation-Seq]

summary:
We isolated whole embryo, nuclear, and cytoplasmic lysates from Drosophila embryos during early and late embryogenesis
In Drosophila melanogaster, cell-type specification during early nervous system development requires precise regulation of gene expression in time and space. To investigate the gene regulation patterns in early neuronal development, we developed a method 'DIV-SortSeq'    to enrich for specific neuroglial cell types for RNA sequencing: from early columnar subdivision and specification, through neuroglial differentiation. DIV-SortSeq recapitulates many of the known protein-coding transcriptome dynamics, as well as novel transcriptional regulatory patterns. We also performed nuclear-cytoplasmic fractionation of whole embryos - Fractionation-Seq - to assess temporal changes in subcellular localization of transcripts during embryogenesis. We present these data as a resource to permit further in-depth investigation into the functional roles of the coding and noncoding transcriptome during early Drosophila neurogenesis.

overall_design: Ribodepleted RNA-Seq data from whole embryos, nuclear and cytoplasmic fractions at 6-8h and 18-22h after egg laying (AEL)

first: Robert

middle: P

last: Zinzen


title: The effect on p53-induced gene transactivation by NEAT1 knockdown.

first: Masashi

summary: To explore the effect of NEAT1 on gene transactivation induced by p53, we evaluated the changes in gene expression by RNA-seq in NEAT1 knockdown or control U2OS cells.

overall_design: Osteosarcoma U2OS cells were transfected with siRNA targeting NEAT1 or negative control siRNA and then treated with nutlin-3a which activates endogenous p53. The change of p53-induced gene transactivation was analyzed.


title: Effect of BB608 on Gene Expression in HNSCC Cell Line

city: Cambridge

first: Harry

last: Rogoff

address: 640 Memorial Dr.

institute: Boston Biomedical, Inc.

summary: Study to determine the genome wide effects on transcripton in FaDu cells treated with BB608, a transcription factor inhibitor

overall_design: 2 samples analyzed, 3 biological replicates per sample

first: Yang

last: Ao

first: Rogoff

last: Harry

first: Zhu

last: Chen

first: Sun

last: Xiangao

first: Li

last: Chiang


title: Novel Form of JARID2 is Required to Regulate Differentiation in Keratinocytes.

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

institute: University of Liverpool

summary: Polycomb repressive complex-2 (PRC2) is a group of proteins that play important role during development and in cell differentiation. PRC2 is a histone-modifying complex that catalyses methylation of lysine 27 of histone H3 (H3K27me3) at differentiation genes leading to their transcriptional repression. JARID2 is a co-factor of PRC2 and is important for targeting PRC2 to chromatin as well as modulating its activity. Here, we show that in many human cells, including human epidermal keratinocytes, JARID2 predominantly exists as a novel low molecular weight form, which lacks the N-terminal PRC2-interacting domain (ΔN-JARID2). We show that ΔN-JARID2 is a cleaved product of full-length JARID2 spanning the C-terminal conserved region consisting of jumonji domains. JARID2 knockout in keratinocytes results in up-regulation of cell cycle genes and repression of many epidermal differentiation genes. Surprisingly, repression of epidermal differentiation genes in JARID2-null keratinocytes can be relieved by expression of ΔN-JARID2 suggesting that this form promotes activation of these genes and has opposing function to that of PRC2 in regulation of differentiation.  We propose that a switch from expression of full-length JARID2 to ΔN-JARID2 is important for the up-regulation of genes during differentiation.

overall_design: RNA-seq analysis of Wildtype and JARID2-null keratinocytes (HaCaTs) on day 0 and day 3 of calcium induced differentiation.


title: miRNA sequencing of synovial fluid derived extracellular vesicles between normal and osteoarthritis  (OA) patients

status: Public on Feb 18 2019

city: Baltimore

first: Jennifer

last: Elisseeff

address: 5031 Smith Building 400 N. Broadway

institute: Johns Hopkins University

summary: To determine whether extracellular vesicles were also present in human disease, we isolated and evaluated extracellular vesicles from synovial fluid from normal and OA patients at relatively advanced ages (70 - 80 years). Here we report the altered expression of synovial fluid extracellular vesicles-derived miRNAs in osteoarthritis compared to normal patients with age-relate degeneration to investigate potential biomarkers for OA diagnosis.  The OA donors had clinical evidence of OA based on pain that led to total joint arthroplasty.

overall_design: Examination of miRNA expression in extracellular vesicles isolated from synovial fluids of normal and osteoarthritis patients

first: Okhee

middle: O

last: Jeon


title: Effect of BB608 on STAT3 DNA Binding in HNSCC Cell Line

summary: Study to determine the genome wide effects on STAT3 binding in FaDu cells treated with BB608, a transcription factor inhibitor.

overall_design: 2 samples DMSO treated, ChIP using STAT1 or STAT3 antibody. 2 samples BB608 treated, ChIP using STAT1 or STAT3 antibody


title: Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system

first: Yun

last: Liu

address: Dongan Road 130

institute: Fudan University

summary: The architecture and function of chromatin are largely regulated by local interacting molecules, such as transcription factors and noncoding RNAs. However, our understanding of these regulatory molecules at a given locus is limited because of technical difficulties. Here, we describe the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and an engineered ascorbate peroxidase 2 (APEX2) system to investigate local chromatin interactions (CAPLOCUS). We showed that with specific small-guide RNA targets, CAPLOCUS could efficiently identify both repetitive genomic regions and single-copy genomic locus with high resolution. Genome-wide sequencing revealed known and potential long-range chromatin interactions for a specific single-copy locus. CAPLOCUS also identified telomere-associated RNA. CAPLOCUS, followed by mass spectrometry, identified both known and novel telomere-associated proteins in their native states. Thus, CAPLOCUS may be a useful approach for studying local interacting molecules at any given chromosomal location.

overall_design:
CAPLOCUS combined with NGS sequencing was carried out on a repetitive region on chromosome 13 (chr13: 112,930,173-112,968,847), a single-copy locus  on chromosome 11 (chr11: 5,497,611-5,497,843), and sgGAL4 control in replicate.
In this method, with sgRNAs targeting a specific genomic region, local proteins were labeled with biotin and can be captured by M-280 Steptavidin Dynabeads. Thus, sgC13-IP and sgC11-IP were transfected with different sgRNAs targeting C13 region or C11 region, but both were pulled down with M-280 Steptavidin Dynabeads.

first: Wenqing

last: Qiu


title: Identification of spatiotemporal RNA expression during Drosophila embryonic neurogenesis [DIV-MARIS]

summary:
We used immunostaining and FACS to enrich for distinct neural cell types at multiple stages of Drosophila neurogenesis for RNA-Seq
In Drosophila melanogaster, cell-type specification during early nervous system development requires precise regulation of gene expression in time and space. To investigate the gene regulation patterns in early neuronal development, we developed a method 'DIV-SortSeq'    to enrich for specific neuroglial cell types for RNA sequencing: from early columnar subdivision and specification, through neuroglial differentiation. DIV-SortSeq recapitulates many of the known protein-coding transcriptome dynamics, as well as novel transcriptional regulatory patterns. We also performed nuclear-cytoplasmic fractionation of whole embryos - Fractionation-Seq - to assess temporal changes in subcellular localization of transcripts during embryogenesis. We present these data as a resource to permit further in-depth investigation into the functional roles of the coding and noncoding transcriptome during early Drosophila neurogenesis.

overall_design: Ribodepleted RNA-Seq data from Intermediate Column, Ventral Column, Neuroblasts, Neurons, and Glia


title: RNASeq of adipocytes from ROSA vs BMPR2 DELX mice

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: We sequenced RNA from adipocytes of ROSA and BMPR2 DELX transgenic mice

overall_design: Expression pattern in BMPR2 DELX mutant mice using ROSA as control


title: hCLE/RTRAF-HSPC117-DDX1-FAM98B: A new cap-binding complex that activates mRNA translation

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: hCLE/C14orf166/RTRAF, DDX1 and HSPC117 are components of cytoplasmic mRNA-transporting granules kinesin-associated in dendrites. They have also been found in cytoplasmic ribosome-containing RNA granules that transport specific mRNAs halted for translation until specific neuronal signals renders them accessible to the translation machinery. hCLE associates to DDX1, HSPC117 and FAM98B in HEK293T cells and all four proteins bind to cap analog-containing resins. Competition and elution experiments indicate that binding of hCLE complex to cap resins is independent of eIF4E; the cap-binding factor needed for translation. Purified hCLE free of its associated proteins binds cap with low affinity suggesting that its interacting proteins modulate its cap association. hCLE silencing reduces hCLE accumulation and that of its interacting proteins and decreases mRNA translation. hCLE-associated RNAs have been isolated and sequenced; RNAs involved in mRNA translation are specifically associated. The data suggest a positive role of hCLE complex modulating mRNA translation.

overall_design: Standard RNA-seq protocol was applied for comparing two sample types (HEK293T cells transfected with hCLE-TAP plasmid or empty TAP) with two biological replicates each. More than 20 million single-end, strand-specific 50 nt reads were generated for each sample.

first: Alejandra

last: Pazo

first: Alicia

last: Pérez-González

first: Maite

last: Huarte

last: Chávez

first: Amelia

last: Nieto


title: Study of the impact of copper levels in bovine blood on transcriptional profile

summary: Blood was drawn and RNA extracted from the ten pooled samples. Transcriptional profile of these samples was obtained using RNASeq.

overall_design: There are ten samples, and each sample is a pool of three individual animals. Samples 5, 7, 8, 9, and 10 are derived from animals that received mineral supplementation to increase copper levels.


title: Expression data from Nasopharyngeal carcinoma (NPC) cell lines treated or untreated with Caffeic acid phenethyl ester (CAPE)

status: Public on Feb 16 2019

city: Nanning

first: Yushan

last: Liang

address: 6# Shuangyong Road

department: Department of Otolaryngology Head & Neck Surgery

institute: First Affiliated Hospital of Guangxi Medical University

summary:
CAPE has anti-bacterial and viral infection, anti-oxidant, anti-inflammatory, and anti-tumor properties.We found that CAPE suppressed the proliferation and colony-formation ability of NPC cells.
We used microarrays to identify differential genes regulated by CAPE in NPC cells and futher analys the potential GO and pathway

overall_design: NPC cell lines (HK1,HK1EBV) treated or untreated with CAPE were included in the microarray.  NPC cell line treated with DMSO as control. There are one sample in each group

first: Xiaoying

last: Zhou

first: Guangwu

last: Huang

first: Zhe

last: Zhang


title: RNA-sequencing uncovers transcriptomes of human diseased, healthy, and disease-modeled retinal pigment epithelial cells.

city: New York

first: Timothy

middle: Adam

last: Blenkinsop

state: NY

address: 1425 Madison Ave, Icahn Building, Floor 13, Room 13-70A

department: Cell, Development and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary: Human donor derived retinal pigment epithelial cells from healthy, diseased, and disease-modeled sources underwent RNA-sequencing to identify unique, gene signatures.

overall_design: Retinal pigment epithelial cell transcriptomes of human healthy, diseased, and disease-modeled cells were uncovered using Illumina RNA-sequencing, in triplicate.

first: Nathan

last: Boles


title: Effect of prolonged exposure to normoxia on miRNA expression of primary mouse chondrocytes

status: Public on Feb 17 2019

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: miRNA profiles of primary mouse chondrocytes exposed to prolonged normoxia, which resulted in accumulation of oxidative stress. The sequencing data were generated by miRNA sequencing, in three biological replicates. This study provides insights into the role of chronic oxidative stress in chondrocytes and helps identification of miRNAs related to OA pathogenesis.

overall_design: Total RNA was isolated from chondrocytes and subjected to small RNA-seq library preparation using the TruSeq kit (Illumina).

first: J

middle: H

first: D

last: Kang


title: The histone demethylase KDM1A is essential for the maintenance and differentiation of spermatogonial stem cells and progenitors

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

institute: McGill University

summary: Little is known of the fundamental processes governed by epigenetic mechanisms in the supplier cells of spermatogenesis, the spermatogonial stem cells (SSCs). The histone H3 lysine demethylase KDM1A is expressed in spermatogonia. We hypothesized that KDM1A serves in transcriptional regulation of SSCs and fertility. Using a conditional deletion of Kdm1a [conditional knockout (cKO)] in mouse spermatogonia, we determined that Kdm1a is essential for spermatogenesis as adult cKO males completely lack germ cells. Analysis of postnatal testis development revealed that undifferentiated and differentiating spermatogonial populations form in Kdm1a-cKO animals, yet the majority fail to enter meiosis. Loss of germ cells in the cKO was rapid with none remaining by postnatal day (PND) 21. To gain insight into the mechanistic implications of Kdm1a ablation, we isolated PND 6 spermatogonia enriched for SSCs and analyzed their transcriptome by RNA sequencing. Loss of Kdm1a was associated with altered transcription of 1206 genes. Importantly, differentially expressed genes between control and Kdm1a-cKO animals included those that are essential for SSC and progenitor maintenance and spermatogonial differentiation. The complete loss of fertility and failure to establish spermatogenesis indicate that Kdm1a is a master controller of gene transcription in spermatogonia and is required for SSC and progenitor maintenance and differentiation.

overall_design: Examination of the effect of the knockout of the histone demethylase KDM1A on the gene expression of GOF/deltaPE-Oct4/GFP mice postnatal spermatogonia isolated by FACS.

first: Sarah

last: Kimmins


title: Effect of KCNK3 mutations on hypoxic mice lungs studied by RNASeq

first: James

last: West

summary: We sequenced RNA from lungs of mice, subjected to hypoxia, with or without KCNK3 knockout mutations

overall_design: Comparison of hypoxic versus normoxic condition in the presence and absence of KCNK3 mutation


title: Comparison of gene expression in seminiferous tubules of 3 month old calf versus 9 month old calf using RNA-Seq

summary: We sequenced RNA from seminiferous tubules of 3 month old calf versus 9 month old calf

overall_design: Single samples of seminiferous tubules of 3 month old calf and 9 month old calf were available. RNA was extracted, sequenced and differential expression analysis performed.


title: An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus

city: Berkeley

first: Britt

last: Glaunsinger

address: 565 Li Ka Shing Center

institute: UC Berkeley

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

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Refer to individual Series


title: RNA sequencing analysis to identify gene targets of Kaposi's sarcoma herpesvirus (KSHV) ORF24

summary: ORF24 is the core component of a virally encoded transcription complex in KSHV that is active during later stages of infection. ORF24 makes interactions with both promoter DNA and host RNA polymerase II. The aim of this study was to identify the targets of the virally encoded transcription complex by sequencing total RNA from cells that express a mutant ORF24 that does not interact with RNA polymerase II and compare it to RNA from a mutant rescue cell line (WT). We observed that most viral genes were down regulated in the absence of the ORF24-Pol II interaction and as expected, majority of them were late genes.

overall_design: iSLK cells latently infected with the mutant KSHV ORF24 (RAAAG) or the mutant rescue (MR) were reactivated in to the lytic cycle using doxycycline and sodium butyrate. 24 or 48 hours post reactivation, the total RNA was extracted from the cells and subject to library preparation for RNA sequencing.

first: Divya

last: Nandakumar


title: Effect of estrogens and BMPR2 on mouse kidney gene expression


title: Inferring population dynamics from single-cell RNA-sequencing time-series data

status: Public on Feb 15 2019

city: Neuherberg

first: David

middle: Sebastian

last: Fischer

address: Ingolstaedter Landstr. 1

department: ICB

institute: Helmholtz Zentrum Munich

summary: This dataset consists of single-cell RNA-seq (Drop-seq) data from thymi of day 14.5 mouse embryos. The sample includes the whole thymus, including mesenchyme, endothelium, epithelium, thymocytes, and other lymphocytes. The mouse is a Rag2-/- knockout.

overall_design: 1 sample

first: Anna

last: Fiedler

first: Eric

middle: M

last: Kernfeld

first: Ryan

last: Genga

first: Aimee

last: Bastidas-Ponce

first: Mostafa

last: Bakhti

first: Heiko

last: Lickert

first: Jan

last: Hasenauer

first: Rene

last: Maehr

first: Fabian

last: Theis


title: Ectopic expression of DNA methyltransferases DNMT3A2 and DNMT3L leads to aberrant hypermethylation and postnatal lethality in mice

city: Setagaya-ku

first: Keisuke

last: Sasaki

state: Tokyo

address: 1-1-1, Sakuragaoka

department: Department of BioScience

institute: Tokyo University of Agriculture

summary: DNA methylation is generally known to inactivate gene expression. The DNA methyltransferases (DNMTs), DNMT3A and DNMT3B, catalyze somatic cell lineage-specific DNA methylation, while DNMT3A and DNMT3L catalyze germ cell lineage-specific DNA methylation. How such lineage- and gene-specific DNA methylation patterns are created remains to be elucidated. To better understand the regulatory mechanisms underlying DNA methylation, we generated transgenic mice that constitutively expressed DNMT3A and DNMT3L, and analyzed DNA methylation, gene expression, and their subsequent impact on ontogeny. All transgenic mice were born normally but died within 20 weeks accompanied with cardiac hypertrophy. Several genes were repressed in the hearts of transgenic mice compared with those in wild-type mice. CpG islands of these downregulated genes were highly methylated in the transgenic mice. This abnormal methylation occurred in the perinatal stage. Conversely, mono-allelic DNA methylation at imprinted loci was faithfully maintained in all transgenic mice, except H19. Thus, the loci preferred by DNMT3A and DNMT3L differ between somatic and germ cell lineages.

overall_design: We generated transgenic mice expressing both DNMT3A2 and DNMT3L ectopically in broad somatic cells throughout the lifetime (DNMTs-Tg mice). All DNMTs-Tg mice  showed delayed postnatal growth and finally died  within 20 weeks after birth. We  hypothesized that the exogenous DNMT3A2 and DNMT3L abnormally methylated some genes to produce these severe phenotypes.  As DNA methylation generally silences gene expression, we conducted comprehensive gene expression analyses in heart tissues of DNMTs-Tg mice to identify genes that were abnormally hypermethylated by exogenous DNMT3A2 and DNMT3L.

first: Satoshi

last: Hara

first: Reina

last: Yamakami

first: Yusuke

last: Sato

first: Saki

last: Hasegawa

first: Tomohiro

last: Kono

first: Kanako

last: Morohaku

first: Yayoi

last: Obata


title: The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells (RNA-seq)

first: Craig

last: Thompson

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

summary: The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the Cd4 gene is stably repressed in CD8+ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for Cd4 repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in Cd4 silencing. When CAF-1 was lacking, Cd4 derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a, but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the Cd4 locus. Instead, Dnmt3a deficiency sensitized CD8+ T cells to Cd4 derepression mediated by compromised functions of histone modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone modifying enzymes.

overall_design: There are 9 samples total. There are 8 samples consisting of sorted CD8+ T cells with or without expression of CD4 after knock-down with shRNAs targeting Dnmt1 or Chaf1a. There is 1 sample consisting of sorted CD8+ T cells after shRenilla knock-down.

first: Charles

last: Ng

first: Martin

last: Aichinger

first: Tung

last: Nguyen

first: Christy

last: Au

first: Tariq

last: Najar

first: Lin

last: Wu

first: Kai

middle: R

last: Mesa

first: Will

last: Liao

first: Jean-Pierre

last: Quivy

first: Benjamin

last: Hubert

first: Genevieve

last: Almouzni

first: Johannes

last: Zuber

first: Dan

last: Littman


title: Genome-wide map of viral transcription factor ORF34 binding in Kaposi's Sarcoma Herpesvirus (KSHV)

first: Britt

last: Glaunsinger

summary: We report the mapping of the genome-wide binding sites of a central component of a viral transcription complex from KSHV. We find that ORF34 binds at several locations on the viral genome but observed no detectable binding to the host genome. A majority of binding sites on the viral genome were upstream of known transcription start sites of mapped genes.

overall_design: Chromatin for immuno-precipitation was prepared from iSLK cells latently infected with HA-ORF34 KSHV and reactivated with doxycycline and sodium butyrate for 48 h.

first: Divya

last: Nandakumar


title: RNA sequencing from FOXM1 knockout HEK293T cells reconstituted with FOXM1 isoforms a, b and c.

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

summary: To study the transcriptional programs of FOXM1 isoforms, we generated a FOXM1 CRISPR knockout cell line then reconstituted it with FOXM1a, b or c and performed RNA sequencing.

overall_design: Methods: HEK293T cells were transfected in triplicate with plasmids expressing empty, FOXM1a, FOXM1c and FOXM1b. Total RNA was harvested at 48 hours and RNA squencing was performed.

first: C

middle: J

last: Barger

first: A


title: Diversity of cytosine methylation across the fungi tree of life

city: Athens

first: Robert

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. DNA MTase genotypes have diversified from the ancestral DNMT1+DNMT5 genotype through numerous loss events, and duplications, whereas, DIM-2 and RID-1 are more recently derived in fungi. Methylation is typically enriched at intergenic regions, which includes repeats and transposons. Unlike certain Insecta and Angiosperm species, Fungi lack canonical gene body methylation. Some fungi species possess large clusters of contiguous methylation encompassing many genes, repetitive DNA and transposons, and are not ancient in origin. Broadly, methylation is partially explained by DNA MTase genotype and repetitive DNA content. Basidiomycota on average have the highest level of methylation, and repeat content, compared to other phyla. However, exceptions exist across Fungi. Other traits, including DNA repair mechanisms, might contribute to interspecific methylation variation within Fungi. Our results show mechanism and genome evolution are unifying explanations for interspecific methylation variation across Fungi.

sample_organism:
Phycomyces blakesleeanus
Saccharomyces cerevisiae
Plenodomus lingam
Aspergillus flavus
Fusarium fujikuroi
Neurospora crassa
Cryptococcus neoformans
Pleurotus ostreatus
Agaricus bisporus
Coprinopsis cinerea
Candida albicans
Aureobasidium pullulans
Laccaria bicolor
Uncinocarpus reesii
Mixia osmundae
Parasitella parasitica
Clavispora lusitaniae
Botrytis cinerea
Sporobolomyces roseus
Tilletiopsis washingtonensis
Coemansia reversa
Lobosporangium transversale
Radiomyces spectabilis
Cordyceps militaris
Wolfiporia cocos
Spinellus fusiger
Hesseltinella vesiculosa
Rhodonia placenta
Flammula alnicola
Microbotryum lychnidis-dioicae
Coemansia spiralis
Candidozyma auris
Kirkomyces cordensis
Metarhizium robertsii
Pseudogymnoascus destructans
Heterobasidion irregulare
Pyricularia oryzae KJ201
Syncephalis fuscata
Podospora anserina
Phanerodontia chrysosporium

platform_organism:
Plenodomus lingam
Fusarium fujikuroi
Pleurotus ostreatus
Agaricus bisporus
Coprinopsis cinerea
Candida albicans
Aureobasidium pullulans
Mixia osmundae
Parasitella parasitica
Clavispora lusitaniae
Botrytis cinerea
Sporobolomyces roseus
Tilletiopsis washingtonensis
Coemansia reversa
Lobosporangium transversale
Radiomyces spectabilis
Wolfiporia cocos
Spinellus fusiger
Hesseltinella vesiculosa
Flammula alnicola
Microbotryum lychnidis-dioicae
Coemansia spiralis
Candidozyma auris
Kirkomyces cordensis
Pseudogymnoascus destructans
Heterobasidion irregulare
Syncephalis fuscata
Podospora anserina
Phanerodontia chrysosporium

overall_design:
MethylC-seq libraries for newly sequenced fungi species were prepared according to the protocol described in (Urich et al. 2015; doi: 10.1038/nprot.2014.114). Libraries were single-end 50, 75, or 150 bp sequenced on an Illumina NextSeq500 machine. Un-methylated lambda phage DNA or mitochondrial genome was used to as a control for sodium bisulfite conversion. WGBS data was aligned to each species respective genome assembly using the methylpy pipeline (Schultz et al. 2015; doi:10.1038/nature14465; https://bitbucket.org/schultzmattd/methylpy/wiki/Home). In brief, reads were trimmed of sequencing adapters using Cutadapt (Martin and Marcel 2011; doi: http://dx.doi.org/10.14806/ej.17.1.200), and then mapped to both a converted forward strand (cytosines to thymines) and converted reverse strand (guanines to adenines) using bowtie v1.1.1 (Langmead et al. 2009; doi: 10.1186/gb-2009-10-3-r25).

This series contains re-analyzed data. Links to re-analyzed GSMs can be found below. Re-analyzed sample information and processed data fiels are available at the foot of this record.

Previously published WGBS data for Aspergillus flavus (Liu, Lin, Wu et al. 2012; doi: 10.1371/journal.pone.0030349) (SRR345557), Cordyceps militaris (Wang et al. 2015; doi: 10.1016/j.funbio.2015.08.017) (SRR1916344, SRR1916345, SRR1916346, and SRR1916347), Cryptococcus neoformans (Huff and Zilberman 2014; doi: 10.1016/j.cell.2014.01.029) (SRR847298), Laccaria bicolor (Zemach et al. 2010; doi: 10.1126/science.1186366) (SRR042632, and SRR042633), Magnaporthe oryzae (Jeon et al. 2015; doi: 10.1038/srep08567) (SRR653493), Metarhizium robertsii (Li et al. 2017; doi: 10.1016/j.funbio.2017.01.002) (SRR3175452), Neurospora crassa (Honda et al. 2012; doi: 10.1073/pnas.1614279113) (SRR3476867), Phycomyces blakesleeanus (Zemach et al. 2010; ; doi: 10.1126/science.1186366) (SRR042643), Postia placenta (Zemach et al. 2010; doi: 10.1126/science.1186366) (SRR042648, and SRR042649), Saccharomyces cerevisiae (Moreselli et al. 2015; doi: 10.7554/eLife.06205) (SRR1916130), and Uncinocarpus reesii (Zemach et al. 2010; doi: 10.1126/science.1186366) (SRR042657) were downloaded from the Short Read Archive (SRA), and processed and aligned identically as described above.

last: Bewick


title: SUCNR1 signaling controls macrophage alternative activation

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

institute: IRB

summary: Sucnr1 signaling promotes M2 polarization

overall_design: Adipose tissue-derived macrophages (ATMs) from 19–21-week-old mice from Sucnr1flox/flox and LysM-Sucnr1-/- were used in this study.

first: Sonia

last: Fernández-Veledo

first: Noelia

last: Keiran

first: María

middle: I

last: Hernández-Alvarez


title: Chromatin accessibility of converted and control dermal BJ fibroblasts

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We report changes in chromatin accessibility following ectopic expression of wildtype or mutant p63+/- KLF4 for 72 hours in dermal BJ fibroblasts.

overall_design: ATAC-seq of dermal BJ fibroblasts following ectopic expression of a control empty vector or wild type/mutant (I537T) p63 +/- KLF4  for 72 hours in biological duplicates (NextSeq500)

first: Lin-Shiao

last: Enrique

first: Berger

last: Shelley


title: Enrichment of p63, KLF4 and H3K27ac at chromatin in converted and control dermal BJ fibroblasts

summary: We report changes in enrichment at chromatin of p63, KLF4 and H3K27ac following ectopic expression of wildtype or mutant p63+/- KLF4 for 72 hours in dermal BJ fibroblasts.

overall_design: p63,KLF4 and H3K27ac ChIP-seq in dermal BJ fibroblasts following ectopic expression of a control empty vector or wild type/mutant (I537T) p63 +/- KLF4  for 72 hours in biological duplicates (NextSeq500)


title: The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-κB signalling via EZH2

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

summary: The protozoan parasite Toxoplasma gondii has co-evolved with its homeothermic hosts (humans included) strategies that drive its quasi-asymptomatic persistence in hosts, hence optimizing the chance of transmission to new hosts. Persistence, which starts with a small subset of parasites that escape host immune killing and colonize the so-called immune privileged tissues where they differentiate into a low replicating stage, is driven by the interleukin 12 (IL-12)-interferon-γ (IFN-γ) axis. Recent characterization of a family of Toxoplasma effectors that are delivered into the host cell, in which they rewire the host cell gene expression, has allowed the identification of regulators of the IL-12-IFN-γ axis, including repressors. We now report on the dense granule-resident effector, called TEEGR (Toxoplasma E2F4-associated EZH2-inducing gene regulator) that counteracts the nuclear factor-κB (NF-κB) signalling pathway. Once exported into the host cell, TEEGR ends up in the nucleus where it not only complexes with the E2F3 and E2F4 host transcription factors to induce gene expression, but also promotes shaping of a non-permissive chromatin through its capacity to switch on EZH2. Remarkably, EZH2 fosters the epigenetic silencing of a subset of NF-κB-regulated cytokines, thereby strongly contributing to the host immune equilibrium that influences the host immune response and promotes parasite persistence in mice.

overall_design: Human (HA and HFF) cells were left uninfected or infected for 24 hours with Pruku80, Pruku80ΔTEEGR or Pruku80ΔTEEGR+TEEGR (complemented) Toxoplasma type II strains before gene expression was measured. Three independent experiments were performed for each condition.

first: Laurence

last: Braun

first: Marie-Pierre

last: Brenier-Pinchart

first: Pierre-Mehdi

last: Hammoudi

first: Dominique

last: Cannella

first: Sylvie

last: Kieffer-Jaquinod

first: Julien

last: Vollaire

first: Véronique

last: Josserand

first: Bastien

last: Touquet

first: Yohann

last: Couté

first: Isabelle

last: Tardieux

first: Alexandre

last: Bougdour

first: Mohamed

last: Hakimi


title: Expression profiling of converted and control dermal BJ fibroblasts

summary: We report transcriptional changes following ectopic expression of wildtype or mutant p63+/- KLF4 for 72 hours in dermal BJ fibroblasts.

overall_design: RNA-seq of dermal BJ fibroblasts following ectopic expression of a control empty vector or wild type/mutant p63 +/- KLF4  for 72 hours in biological duplicates (NextSeq500)