title: Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin [DRIP-Seq]

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

summary: Genome wide distribution of R-loops in Wild Type and RNAi dH1 Drosophila melanogaster S2 cells

overall_design: S9.6 DRIP Seq in Drosophila melanogaster S2 WT and RNAi dH1 cells, treated (R+) or not (R-) with RNase H

first: Aleix

last: Bayona

last: Casas-Lamesa

last: Reina

first: Jordi

last: Bernués

first: Fernando

last: Azorin


title: RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of AIM2.

status: Public on Aug 18 2017

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

type: Expression profiling by high throughput sequencing

summary: Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Chronic inflammation has been recognized as a risk factor for cSCC and inflammation is a typical feature of the progression of actinic keratosis lesions to invasive and metastatic cSCC. Inflammasomes are important components of the innate immune response involved in onset of inflammation. Inflammasome component AIM2 serves as a sensor for cytoplasmic double-strand DNA, and this way plays a key role in response to bacterial and viral colonization. Activation of inflammasome by cytoplasmic DNA in epidermal keratinocytes can promote the initiation of inflammation in autoimmune and autoinflammatory skin diseases. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) and oligonucleotide array-based expression analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=5) revealed overexpression of AIM2 in cSCC cells (GSE66412 and GSE66368, respectively). We wanted to futher study the RNA expression profile of AIM2 knockdown cSCC cells.

overall_design: Total RNAs from negative control and AIM2 siRNA transfected cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina sequencing.

first: Mehdi

last: Farshchian

first: Veli-Matti

last: Kähäri


title: Paramutation of natural epialleles in tomato

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: Refer to individual Series


title: The neuropeptide Neuromedin U stimulates innate lymphoid cells and promotes type 2 inflammation

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

country: USA

institute: NYU Langone Health


title: Paramutation of natural epialleles in tomato [sRNA]

summary: By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. Analysing the segregation of the methylation patterns for a subset of these regions shows variations in the penetrance of paramutation-like interactions.

platform_organism: Solanum lycopersicum x Solanum pennellii

overall_design: sRNA of M82, S. pennellii and their F1 for leaf/flower/pollen, sRNA for Micro-Tom and S. pimpinellifolium seedlings, methylome data of M82 and introgression lines IL1-1, IL2-5 and IL8-3


title: Global regulatory roles of the cAMP/PKA pathway revealed by phenotypic, transcriptomic, and phosphoproteomic analyses in a null mutant of PKA catalytic subunit in Candida albicans

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

summary: The conserved cAMP-dependent protein kinase (PKA) holoenzyme is composed of two catalytic and two regulatory subunits. It plays critical roles in the regulation of many biological processes in eukaryotic organisms. In the human fungal pathogen Candida albicans, the PKA kinase has been extensively investigated for its importance in the regulation of morphological transitions and virulence. It has been long thought that the PKA catalytic subunit is essential for cell viability in C. albicans. Paradoxically, the single adenylyl cyclase-encoding gene, CRY1, which is required for the production of cAMP in C. albicans, is not essential for cell growth. In this study, we successfully generated a null double mutant of TPK1 and TPK2 (tpk2/tpk2 tpk1/tpk1 or t2t1), which encode two isoforms of the PKA catalytic subunit in C. albicans. We reevaluated the roles of the PKA catalytic subunit in cell growth and phenotypic transitions. Inactivation of the PKA catalytic subunit by deletion of both TPK1 and TPK2 blocked filamentation and dramatically attenuated the ability of white-to-opaque switching, but promoted sexual mating in C. albicans. Tpk2 plays a major role in these regulations, while Tpk1 generally functions as a negative regulator in morphological transitions and sexual mating. A comparative transcriptomic analysis demonstrated that the t2t1 and cyr1/cyr1 mutants exhibited similar global gene expression profiles. Compared to the WT strain, the general transcriptional activity and expression of genes involved in metabolism, translation, biosynthesis, adhesion and filamentation are significantly decreased in both the t2t1 and cyr1/cyr1 mutants. And a portion of stress-response and cell wall-related genes were upregulated in these mutants, which is consistent with their increased ability of anti-stresses. To further explore the global regulatory role of the PKA kinase, we performed quantitative phosphoproteomics analysis. Combining with bioinformatics analyses, we identified 181 potential PKA phosphorylation targets, which represent 148 unique proteins involved in a wide spectrum of biological processes. Cell wall and membrane-related proteins (e.g. Ecm3, Bni1, and Smi1) were enriched in Tpk1-specific targets, while Tpk2-specific substrates include transporters, filamentation and cytoskeleton-related proteins (e.g. Smf3, Sep7, and Mhp1). There were also many Tpk1 and Tpk2 overlapped and coordinately regulated-substrates. Our study clarifies the essentiality of the PKA catalytic subunit and shed new insights into the global regulatory features of the cAMP/PKA pathway in C. ablicans. The t2t1 null mutant generated in this study would also be a new resource for the field to study this important pathway.

overall_design: total RNA profiles of wild type,tpk2/tpk2 tpk1/tpk1 double mutant, and cyr1/cyr1 mutant

first: Guanghua

last: Huang

first: Chengjun

last: Cao


title: Effects of Inhibition of CDK8/19 Mediator Kinase by Senexin B in HCT116 cells treated with or without TNF-alpha

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

summary: We have investigated the effects of CDK8/19 inhibitor Senexin B on NFκB-mediated transcription, induced by a canonical NFκB activator, TNFα.

overall_design: HCT116 cells were pre-treated with or without 1 μM Senexin B for 1 hour, followed by 2 hour treatment with 10 ng/ml TNFα. Each treatment condition was done in biological triplicate.

first: Jiaxin

last: Liang

first: Hao

last: Ji

first: Zhengguan

last: Yang

first: Serena

last: Altilia

first: Bing

last: Hu

first: Adam

last: Schronce

first: Martina

last: McDermott

first: Gary

middle: P

last: Schools

first: Chang-uk

last: Lim

first: David

last: Oliver

first: Michael

middle: S

last: Shtutman

first: Tao

last: Lu

first: George

middle: R

last: Stark

first: Donald

middle: C

last: Porter

first: Eugenia

middle: V

last: Broude

first: Igor

middle: B

last: Roninson


title: Replication stress affects epigenetic stability

city: Hangzhou

first: Xiangwei

last: He

state: Zhejiang

address: NanoTech Bd., Zhejiang Univ., 388 Yuhangtang Rd.

department: Life Sciences Institute

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Replication stress affects genome-wide H3K9me2 nucleosome maps of chromatin state.

overall_design: Examine H3K9me2 nucleosomes in wt and cdc22-23 mutant cells

first: Wenzhu

last: Li

first: Jia

last: Yi


title: Profiling of gene expression in lung tissue in C57Bl/6 and DBA/2 mouse strains following exposure to carbon nanotubes

city: Cincinnati

first: Evan

last: Frank

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati

summary: Carbon nanotubes (CNTs) are fibrous particulates made up of elemental carbon and a novel nanomaterial known for its variety of industrial applications.  It has been shown that lung exposure to CNTs may cause adverse effects inclunding lung inflammation and remodeling in experimental models.  We investigated the impact of genetic background on the development of adverse outcomes by comparing several common inbred mouse strains and found that C57Bl/6 and DBA/2 strains were polarized in their sensitivity to adverse changes at 4 weeks following an exposure to 4 mg/kg CNT.  Here we compare underlying gene expression profiles which may inform the understanding of lung biology underpinning genetic susceptibility to adverse outcomes following environmental or occupational exposure to CNTs.

overall_design: Changes in mRNA profiles were compared between CNT-exposed animals and vehicle-treated controls (n=3/group) of either C57Bl/6 or DBA/2 strains.

middle: A


title: Whole transcriptomic screening the RNA from control (O), photon radiotherapy (X) and proton therapy (P) tumors

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: The general purpose of the experiment is to compare the therapeutic effect of photon (X) radiotherapy versus proton (P) therapy for head and neck carcinoma. For that purpose we have generated cells that have resisted to multi irradiations by X or P. We have then injected these human cells in nude mice. Whereas these cells proliferate less than the control (0, non-irradiated cells) in vitro, they formed bigger tumors in mice compared to 0 cells. Hence, the hypothesis is that they secreted factors that educate the microenvironment. We have observed that although the tumors generated by the P cells are as big as those generated by the X cells, the lymphangiogenic/metastatic capacity is greater for the X cells. Hence, we would like to compare within a whole transcriptomic screening the RNA from 0, X and P tumors. The provided samples consist of a mix of human and mouse RNA.

overall_design: Three conditions with three replicates : control (O), photon radiotherapy (X) and proton therapy (P)

first: M

last: Plesu

first: G

last: Pages

first: K

first: P

last: Barbry


title: Estrogen receptor coregulator binding modulators (ERXs) effectively target estrogen receptor positive human breast cancers

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We examined the transcriptional chagnes modulated by ECBI-11 by perfroming global transcriptome analysis. ZR75 cells were treated with either control or ECBI-11 in the presence of E2 for 48 h and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that ECBI modulated several genes that are involved in cell cycle, breast cancer signaling, estrogen signaling and apoptosis.

overall_design: Total RNA was isolated from the ZR75  cells that were treated with vehicle or ECBI for 48 h. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Ratna

middle: K

last: Vadlamudi


title: Methyl-Spec-seq data for HOXB13

status: Public on Aug 17 2017

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

summary: We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse HOXB13 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.

overall_design: Except different methylation types of DNA, the overall design is the same as conventional Spec-seq, which we have published work before.


title: Transcriptome analysis of quorum sensing-dependent genes in Burkholderia gladioli BSR3.

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

country: South Korea

institute: Pusan National University

summary: In Burkholdeira gladioli BSR3, quorum sensing (QS) signal plays a pivotal role in many bacterial behaviors, including motility, toxin production and oxalogenesis. To understand transcriptional profiling of QS-dependent genes, we carried out RNA-Seq analysis of the wild type B. gladioli BSR3, and a QS-defective mutant under different culture states (10h and 24h after incubation), representing exponential phase and stationary phase.

overall_design: 2 samples examined: Burkholderia gladioli BSR3 wild type, and a QS-defective mutant, COK94 (BSR3 bglu_2g11050::lacZ). Two conditions: cultured in LB media for 10h or 24h.

first: Sunyoung

last: Kim

first: Young-Su

last: Seo


title: RiboZero Gold paired-end RNA-seq data from postmortem tissue of the dorsolateral prefrontal cortex of autism spectrum disorder samples and healthy control samples

city: Baltimore

first: Carrie

last: Wright

address: 855 N Wolfe St

institute: Lieber Institute for Brain Development

summary:
Purpose: The goals of this study was to compare the expression of histamine related genes in ASD patients and controls.
Methods: RNA-Seq was performed using strand-specific Ribosomal RNA depletion (RiboZero) library preparation and the TruSeq RNA Sample Preparation v2 kit from Illumina. One hundred base pair paired-end sequencing was run on the HiSeq 2000. TopHat (v2.0.4) was used to enforce strand specificity and to align the sequencing reads to known transcripts of the Ensembl Build GRCh37.67. FeatureCounts (v1.4.4) was used to count the total number of reads overlapping each gene using the default settings, with paired-end and reverse-stranded counting specified using the Ensembl Build GRCh37.67 gtf file. These counts were merged from both reads of the paired-end sequencing and normalized by library size and coding gene length to form Reads Per Kilobase of Gene per Million mapped reads (RPKM) values. The influence of diagnosis on expression was analyzed with linear regression transcriptome-wide and further evaluated using a gene set analysis.
Results: There was no significant diagnosis effect on any of the individual genes but expression of the gene set of HNMT, HRH1, HRH2, and HRH3 was significantly altered.
Conclusions: Our study represents the first specific analysis of the expression of histamine related genes in ASD and suggests that these genes may collectively be dysregulated.

overall_design: Comparison of gene expression of 13 ASD cases and 39 matched controls.

first: Joo

middle: H

last: Shin

first: Andrew

middle: E

last: Jaffe

first: Anandita

last: Rajpurohit

first: Amy

last: Deep-Soboslay

first: Nicholas

middle: J

last: Brandon

first: Thomas

middle: M

last: Hyde

first: Joel

last: Kleinman

first: Alan

last: Cross

first: Daniel

last: Weinberger


title: Statins modulate endothelial transcriptional profile by inhibiting EZH2

city: Rochester

first: Suowen

last: Xu

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

summary: Statins protect against the development of atherosclerosis via cholesterol-dependent and –independent mechanisms. Understanding the molecular mechanisms mediating simvastatin induced atheroprotective effects is critical for designing anti-atherosclerotic agents. Here, we showed that simvastatin decreases the expression of the Polycomb methyltransferase EZH2 in endothelial cells. To better understand the influence of the simvastatin-induced EZH2 downregulation on endothelial transcriptome, we performed RNA-sequencing study to evaluate differential gene expression after overexpression of EZH2 in the presence of simvastatin treatment. We found simvastatin treatment altered a subset of genes that can be rescued with EZH2 overexpression. Therefore, simvastatin treated endothelial cells display an atheroprotective phenotype by downregulating EZH2.

overall_design: Human Umbilical Vein Endothelial Cells (HUVEC, passage 3 to passage 5) were seeded in 0.2% gelatin-coated 6-well plate the day before experiment. The next day, HUVECs were treated with control adenovirus (AdCon) or EZH2 adenovirus (AdEZH2, #1371, Vector Biolab) for 24 hours, before stimulation with simvastatin (1 µM, dissolved in DMSO) for 48 hours in the presence of adenovirus. After treatment, RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN). High quality RNA samples (pre-assessed by Nanodrop measurements) were further processed in the Genome Research Center of the University of Rochester Medical Center. The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3’ adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome. Sequenced reads were cleaned using Trimmomatic-0.32 before mapping some of to the human reference genome (GRCh38.p2) with STAR-2.4.2a. Raw read counts were obtained using HTSeq and gencode 23 human gene annotations. DESeq2-1.10.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05. Then, Cufflinks-2.0.2 Software was used with the gencode 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05.

middle: G

last: Jin

first: John

last: Ashton

first: Jason

last: Myers


title: 4β-Hydroxywithanolide E Modulates Alternative Splicing of Apoptotic Genes in Human Hepatocellular Carcinoma Huh-7 Cells

city: Taichung

first: Chien Chih

last: Lee

address: 2 Yuh-Der Road

country: Taiwan

institute: China Medical University Hospital

summary: Alternative splicing is a mechanism for increasing the protein variety of a limited number of genes. Studies have shown that aberrant regulations of the alternative splicing of apoptotic gene transcripts may contribute to the development of cancer. In this study, we isolated 4β-Hydroxywithanolide E (4bHWE) from the traditional herb Physalis peruviana, and analyzed its biological effects in cancer cells. The results demonstrated that 4bHWE modulates the alternative splicing of apoptotic genes (e.g., HIPK3, SMAC/DIABLO, and SURVIVIN), changes the expression level of splicing factors (e.g., hnRNP C1/C2, ASF/SF2, SRp20, and SRp55), and induces histone tail posttranslational modifications (e.g., H3K27me1, H3K27me2, H3K36me3, and H3K79me1). Pretreatment with okadaic acid to inhibit protein phosphatase-1 could partly relieve the effects of 4bHWE on the alternative splicing of HIPK3 and SMAC/DIABLO transcripts, as well as on the dephosphorylation of ASF/SF2. Genome-wide detection of alternative splicing further indicated that several other apoptosis-related genes are also regulated by 4bHWE, including APAF1, CARP-1, and RIPK1. Moreover, we extended our study to apoptosis-associated molecules, detecting an increasing level of CASPASE-3 activity and cleavage of poly ADP-ribose polymerase in 4bHWE-induced apoptosis. Furthermore, in vivo experiments showed that the treatment of tumor-bearing mice with 4bHWE resulted in a marked decrease of tumor size and weight. Taken together, this study is the first to show that 4bHWE affects alternative splicing through the modulations of splicing factors, providing a novel view of the antitumor mechanism of 4bHWE.

overall_design: Examination of the global genes with altered alternative splicing in 4bHWE-treated Huh-7 cells.

first: Jan-Gowth

last: Chang

first: Chien-Chih


title: RNA-seq of Arabidopsis thaliana seedlings growing in the presence of a bacterial synthetic community under full and low phosphate conditions

city: Stanford

first: Sur

last: Herrera Paredes

address: 371 Serra Mall,  Gilbert Building Room 109

department: Biology

institute: Stanford University

summary: This study evaluates the transcriptome of Arabidopsis thaliana seedlings growing in the presence of a diversity of synthetic bacteria communities under different phosphate availability.

overall_design:
Arabidopsis seeds (wild-type Col-0) were germinated on Johnson medium containing 0.5 % sucrose with either 1 mM Pi (in the form of KH2PO4), or no Pi added. Plants were then transferred to 30 µM Pi (low) or 100 µM Pi in the absence of sucrose alone or with one of the synthetic communities.

Please note that the different values (e.g. I1I2, I2I3 etc.) in the 'sample characterics: bacteria' field represents different "synthetic communities" (ie groups of bacteria applied together). There are 9 blocks (P1,P2,P3,I1,I2,I3,N1,N2,N3) each of 8-9 bacterial strains, and each synthetic community is made by combining two blocks; for example, samples that say P1P2 were grown in the presence of a synthetic community that had all the strains from both P1 and P2.

first: Gabriel

last: Castrillo

first: Paulo

last: Teixeira

first: Jeff

last: Dangl


title: Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells [RNA-seq]

city: Pardess hana

first: Uri

last: Weissbein

state: Please Select

address: Haalon 4

country: Israel

institute: Hebrew University of Jerusalem

summary: Human pluripotent stem cells (hPSCs) are an important player in disease modeling and regenerative medicine. Nonetheless, multiple studies uncovered their inherent genetic instability upon prolonged culturing, where specific chromosomal aberrations provide cells with a growth advantage. These positively selected modifications have dramatic effects on multiple cellular characteristics. Epigenetic aberrations also possess the potential of changing gene expression and altering cellular functions. In the current study, we assessed the landscape of DNA methylation aberrations during prolonged culturing of hPSCs, and defined a set of genes which are recurrently hypermethylated and silenced. We further focused on one of these genes, testis-specific Y-encoded like protein 5 (TSPYL5), and demonstrated that when silenced, differentiation-related genes and tumor-suppressor genes are downregulated, while pluripotency- and growth-promoting genes are upregulated. This process is similar to the hypermethylation-mediated inactivation of certain genes during tumor development. Our analysis highlights the existence and importance of recurrent epigenetic aberrations in hPSCs during prolonged culturing.

overall_design: RNA sequencing experiment of human embryonic stem cells after TSPYL5 knockdown, as well as after 5-aza-2'-deoxycytidine treatment.

first: Nissim

last: Benvenisty


title: CDK4/6 inhibition and tumor immunity

city: Melbourne

first: Shom

last: Goel

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptomic analysis in PDX mammary carcinoma after CDK4/6 inhibition

summary: We measured changes in expression of 20,812 human genes PDX tumors growing in mice after treatment with abemaciclib

overall_design: Examination of changes in gene expression


title: Next-generation sequencing measuring ribosome mRNA occupancy and translation efficiency in CD4+ T cells isolated from Mettl3 KO and WT mice

city: New Haven

first: Huabing

last: Li

state: CONNECTICUT

address: 1 Gilbert Street, S570

department: Immunobiology

institute: Yale University School of Medicine

summary: 50 million CD4+ naive T cells were isolated from Mettl3 KO and WT mice by StemCell CD4+ T cell isolation kits. The ribosome protected fragments and inputs were prepared strictly following the manual of Illumina TruSeq Ribo Profile (Mammalian) Kit. The libraries were generated using the same kit and subjected to sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat, and anlayzed by Tuxedo suite & HTseq.

overall_design: Ribosome protected fragments were isolated following Illumina TruSeq Ribo Profile Kit with CD4+ T cells from Mettl3 KO and WT mouse, and subjected to deep sequencing, in duplicate, using Illumina HiSeq 2000.

first: Richard

last: Flavell


title: Transcriptomic analysis in breast cancer cell lines after CDK4/6 inhibition

summary: We measured changes in expression of 20,812 genes in human breast cancer cell lines after treatment with abemaciclib

overall_design: Examination of changes in gene expression in 3 cell lines, in triplicate


title: Transcriptomic analysis in murine mammary carcinoma tissue after treatment with control vehicle or abemaciclib

summary: We measured changes in expression of 3,826 genes in MMTV-rtTA/tetO-HER2 mammary carcinoma tissue after treatment with control vehicle or abemaciclib

overall_design: Examination of changes in gene expression in 23 tumors (11 control, 12 abemaciclib)

first: Goel

last: Shom


title: Next-generation sequencing measuring m6A enrichment in CD4+ T cells isolated from WT mice

summary: CD4+ T cells were isolated by StemCell CD4+ T cell isolation kit of spleen and lymph nodes WT mice. Total RNAs were isolated from the pure CD4+ T cells, subjected to standard m6A RIP protocol. The libraries were generated with IPed and Input RNAs and subjected to sequencing. Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat, and gene expression levels were measured by Cufflinks.

overall_design: m6A modified RNAs were immunoprecipitated and enriched with m6A specific antibody from WT mouse CD4+ T cells, and subjected to deep sequencing, in duplicate, using Illumina HiSeq 2000.


title: Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals

status: Public on Aug 20 2017

city: Townsville

first: Catalina

last: Aguilar

state: Queensland

address: 1 James Cook Dr.

department: Collegue of Public Health, Medical and Veterinary Sciences

institute: James Cook University

summary:
Purpose: Corals are major sources of dimethylsulphoniopropionate (DMSP), a compound that plays a central role in the global sulphur cycle. While DMSP biosynthesis pathways have been investigated in plants and algae, the molecular basis for its production by corals is unknown. Given its potential role as an osmolyte, the effect of salinity stress on levels of DMSP was investigated in both adults and juveniles (lacking photosynthetic symbionts) of the coral Acropora millepora. This study used transcriptomic data to analyse the effects of salinity over the coral A. millepora and to identify coral genes likely to be involved in DMSP biosynthesis.
Methods: Adults coral transcriptomic libraries were constructed from samples exposed during 1 and 24 hours of salinity treatment (25 PSU) and control (35 PSU) conditions (n=5 per condition). Juveniles coral transcriptomic libraries were constructed from samples exposed to 24 and 48 hours of salinity treatment (28 PSU) and control (35 PSU) conditions (n=6 per condition). All libraries were sequenced by 100 bp paired-end in a HiSeq 2000. Reads were mapped onto the Acropora millepora genome using TopHat2 to produce a count data gene expression matrix for subsequent gene expression analysis using DESeq2 package.
Results: In adult coral samples, 5.5 - 10.2 million RNAseq reads were obtained for each treatment sampling time while 3.4 - 8.8 million reads were obtained for each juvenile coral sample. The count matrix of the 26,622 A. millepora gene predictions were generated using htseq-count workflow. BlastP analysis of the A. millepora gene predictions led to the identification of coral members of gene families implicated in DMSP biosynthesis in other organisms, while RNA-seq data was used to identify the differentially expressed ones in response to hyposaline stress and on this basis were considered to be candidates for roles in DMSP biosynthesis in corals.
Conclusions: Hyposaline stress increased DMSP production in both adults and aposymbiotic juvenile corals, and transcriptomic analyses highlighted the potential involvement of specific candidate genes in the production of DMSP via an alga-like pathway. The biochemistry of DMSP production is not well established for any eukaryotic system and, as the first animals in which it has been demonstrated, this is particularly true in the case of corals. Our RNA-seq results enabled the identification of candidates for roles in DMSP biosynthesis in corals but, given its critical roles in diverse biological processes, a thorough investigation of the molecular mechanisms leading to its production by corals is required.

overall_design: RNA-seq profiles of Acropora millepora coral adults (n=18) and juveniles (n=23) under hyposaline stress were generated by 100 bp paired-end sequencing using HiSeq 2000.

first: Jean-Baptiste

last: Raina

first: Cherie

last: Motti

first: Sylvain

last: Fôret

first: David

last: Hayward

first: Bruno

last: Lapeyre

last: Bourne

last: Miller


title: Striatal transcriptome analysis of Shank3-overexpressing mice

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

institute: Korea University College of Medicine

summary: Shank3 is a core excitatory postsynaptic protein enriched in the striatum. We have previously generated and characterized Shank3-overexpressing transgenic mice, and found that these mice exhibited manic-like behavioral phenotypes. To understand molecular mechanisms underlying the behavioral changes, we performed transcriptome (RNA-sequencing) analysis of the striatal tissues from 12-week-old wild-type and Shank3 transgenic mice.

overall_design: Striatal transcriptome of 12-week-old wild-type and Shank3 transgenic (TG) mice.

first: Yeunkum

last: Lee

first: Hyojin

last: Kang


title: UTX ChIP sequencing in non-treated MCF-7 cells

city: Beijing

first: Guojia

last: Xie

address: No.38, Xueyuan Rd

institute: PKUHSC

summary: UTX is implicated in embryonic development and lineage specification. However, how this X-linked histone demethylase contributes to the development and progression of breast cancer remains to be investigated. Here we report that UTX is physically associated with estrogen receptor (ER) and functions in ER-regulated transcription. We showed that UTX coordinates with JHDM1D and CBP to direct H3K27 methylation-acetylation transition and to create a permissive chromatin state on ER targets. Genome-wide analysis of the transcriptional targets of UTX by ChIP-seq identified a cohort of genes including chemokine receptor CXCR4 that are critically involved in breast cancer tumorigenesis and metastasis. We demonstrated that UTX promotes the proliferation and migration of ER+ breast cancer cells. Interestingly, UTX itself is transactivated by ER, forming a feed-forward loop in the regulation of hormone response. Indeed, UTX is upregulated during ER+ breast cancer progression, and the level of its expression is positively correlated with that of CXCR4 and negatively correlated with the overall survival of ER+ breast cancer patients. Our study identified a feed-forward loop between UTX and ER in the regulation of hormonally responsive breast cancer carcinogenesis, supporting the pursuit of UTX as a potential target for the intervention of certain ER+ breast cancer with specific epigenetic vulnerability.

overall_design: Examination of UTX target genes in MCF-7 cells

first: Jing

last: Liang


title: Lin37 is essential for repression of cell-cycle genes in quiescence

city: Leipzig

first: Gerd

last: Müller

address: Semmelweisstrasse 14

department: Medical School

country: Germany

institute: University of Leipzig

summary: The DREAM complex represses cell-cycle gene transcription in quiescence. To investigate the role of the DREAM component Lin37, we created Lin37 knockout cells by CRISPR/Cas9-nickase. pRTS episomal vectors expressing luciferase or Lin37 were introduced in two independent knockout clones (411-27 and 632-2) to create Lin37 knockout and rescue cells. To exit the cell cycle and to enter quiescence, cells were serum starved for 60h. RNA-seq was applied to identify genes de-regulated by loss of Lin37 during quiescence.

overall_design: The following samples are included: clone 411-27 – two biological replicates of each Lin37 knockout and rescue cells; clone 632-2 – two biological and one technical replicate for both Lin37 knockout and rescue cells

first: Christina

last: Mages

first: Axel

last: Wintsche

first: Stephan

last: Bernhart

last: Muller


title: Epididymal adipose tissue gene expression in wildtype mice and mice with inactivated mesoderm specific transcript

city: Scarborough

first: Robert

last: Koza

state: Maine

address: 81 Research Drive

department: Center for Molecular Medicine

institute: Maine Medical Center Research Institute

summary:
The goal of this study is to compare transcriptome profiles of epididymal adipose tissue from wildtype mice and mice with a targeted inactivation of mesoderm specific transcript (Mest) fed a high fat diet from 8 to 16 weeks of age to gain insight for MEST function.
Gene expression profiling resulted in relatively few changes (~36 targets; FDR padj<0.1) in gene expression in epididymal WAT from wildtype mice and mice with inactivated paternal allele for Mest. A less stringent analyses of the dataset (P ≤ 0.05; with mean of ≥ 50 sequence tags for at least one group) identified 395 genes more highly expressed in epididymal adipose tissue of wildtype mice and 301 genes more highly expressed in mice with a paternal inactivation of Mest.
Gene pathway analyses of differentially expressed genes showed decreased expressed of genes associated with immune response and inflammation in high fat diet-fed mice with inactivated Mest compared with wildtype mice. Transcritome analyses supported phenotypic measurements which indicated improved glucose homeostasis in mice with inactivated Mest.

overall_design: Epididymal white adipose tissue RNA was purified from wildtype mice (n=6) and mice with Mest inactivated on the paternal allele (N=5) that were fed a high fat diet (D12231; Research Diets) ad libitum from 8 to 16 weeks of age.  Quality and quantity of RNAs were confirmed using an Agilent 2100 Bioanalyzer.


title: Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

summary:
Background: Despite an early response to platinum-based chemotherapy in advanced stage high-grade serous ovarian cancer (HGSOC), the majority of patients will relapse with drug-resistant disease. Aberrant epigenetic alterations like DNA methylation are common in HGSOC. Differences in DNA methylation are associated with chemoresponse in these patients. The objective of this study was to identify and validate novel epigenetic markers of chemoresponse using genome-wide analysis of DNA methylation in extreme chemoresponsive HGSOC patients.

Methods: Genome-wide next-generation sequencing was performed on methylation-enriched tumor DNA of two HGSOC patient groups with residual disease, extreme responders (≥18 months progression-free survival (PFS), n = 8) and non-responders (≤6 months PFS, n = 10) to platinum-based chemotherapy. DNA methylation and expression data of the same patients were integrated to create a gene list. Genes were validated on an independent cohort of extreme responders (n = 21) and non-responders (n = 31) using pyrosequencing and qRT-PCR. In-silico validation was performed using publicly available DNA methylation (n = 91) and expression (n = 208) datasets of unselected advanced stage HGSOC patients. Functional validation of FZD10 on chemosensitivity was done in ovarian cancer cell lines using siRNA-mediated silencing.

Results: Integrated genome-wide methylome and expression analysis identified 45 significantly differentially methylated and expressed genes between two chemoresponse groups. Four genes FZD10, FAM83A, MYO18B and MKX were successfully validated in an external set of extreme chemoresponsive HGSOC patients. High FZD10 and MKX methylation was related with extreme responders and high FAM83 and MYO18B methylation with extreme non-responders. In publicly available advanced stage HGSOC datasets, FZD10, MYO18B and MKX methylation levels were associated with PFS. High FZD10 methylation was strongly associated with improved PFS [HR=0.43, 95%CI=0.27-0.65, p=0.0002]. Consistently, low FZD10 expression was associated with improved PFS [HR=1.36, 95%CI=0.99-1.88, p=0.058]. FZD10 silencing caused significant sensitization towards cisplatin treatment in survival assays and apoptosis assays.

Conclusions: By applying genome-wide integrated methylome analysis on extreme chemoresponsive HGSOC patients, we identified novel clinically relevant, epigenetically-regulated markers of platinum-sensitivity in HGSOC patients. The clinical potential of these markers in predictive and therapeutic approaches has to be further validated in prospective studies.

first: Tushar

last: Tomar

first: Tim

last: de Meyer

first: Wim

last: van Criekinge

first: Steven

last: de Jong

first: G

last: Wisman


title: Next-generation sequencing measuring mRNA expression in naïve T cells isolated from Mettl3 KO and WT mice

first: Huabing

last: Li

summary: Naïve T cells were obtained by StemCell CD4+ T cell isolation kit of spleen from Mettl3 KO and WT mice followed by FACS sorting (CD4+CD25-CD45RB-Hi). Raw sequencing reads were aligned to the mouse genome (mm10) with Tophat, and gene expression levels were measured by Cufflinks.

overall_design: Mettl3 KO & WT mouse naïve T cells mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.

first: Richard

last: Flavell


title: HTS-Seq analysis of Kdm4a wildtype and knockout females at 2.5 dpc

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

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

overall_design: Refer to individual Series


title: A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital


title: Transcrptional profiles of Cryptococcous neoformans Gsb1 at non-stress and oxidative stress conditions

first: Seon Ah

last: Cheon

address: 84 Heukseok-ro

institute: Chung-Ang University

summary:
Purpose: To identify the downstream genes whose expression levels are affected by the deletion of gsb1 under non-stress and oxidative stress conditions, we compared the RNA-seq based transcriptional profiles of wild-type and gsb1 cells.
Methods: mRNA profiles of cells grown at non-stress and oxidative stress conditions were generated by RNA-seq using Illumina GAIIx. The sequence reads that passed quality filters were mapped to reference genome and the normalized RPKM values were calculated by CLC Genomics Workbench.
Results: RNA-Seq analysis during normal growth revealed increased expression of a number of genes involved in mitochondrial respiration and cell cycle, but decreased expression of several genes involved in the mating-responsive MAPK signaling pathway. Moreover, RNA-Seq analysis under oxidative stress revealed that several genes involved in ROS defense, cell wall remodeling, and protein glycosylation were highly induced in the wild-type strain but not in gsb1.
Conclusions: This study proposed that Gsb1 is a key transcriptional regulator modulating growth, anti-stress responses, differentiation, and virulence in C. neoformans.

overall_design: mRNA profiles of cells grown at non-stress and oxidative stress conditions were generated by RNA-seq using Illumina.

first: Seon

first: Hyun

last: Kang


title: 2.5 dpc female HPG axis RNASeq of Kdm4a wildtype and knockout mice

summary: Purpose: We performed RNA-Seq on 2.5dpc mouse hypothalamus, pituitary, ovary and uterus of 8-10 week old littermate female control and Kdm4a knockout mice. Upon observing for the extent of altered genes of physiological relevance to observed female infertility phenotype, this would help us narrow down the most relevant tissue to perform genome wide ChipSeq binding profiles for Kdm4a, H3K4me3 and H3K9me3. This dataset would present likely target genes under direct control of Kdm4a.

overall_design: Wildtype and Kdm4a knockout mice were set up for natural timed mating. At 2.5 dpc (days post coitus), females were sacrificed and checked for presence of preimplantation embryos by flushing the oviduct. Whole uterus, hypothalamus, pituitary and ovaries were dissected and immediately cleaned of fat and flash frozen in liquid nitrogen. RNA was extracted using Qiagen RNAeasyPlus mini kit following homogenization in RLTplus buffer., tissue RNA quality was measured using an Agilent 2100 Bioanalyzer system (Agilent, #G2940CA) and RNA 6000 Nano reagents (Agilent, #5067-1511). RIN scores were at least 8 for samples used in the RNA Seq with three biological replicates for each tissue


title: Knock-down of Ror1 in MDA-MB-231 cell line decreases cell invasiveness

city: Göttingen

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Göttingen

summary:
RNA-Seq profiling of triple-negative MDA-MB-231 cell line with know-down of non-canonical WNT signaling receptor Ror1.
The MDA-MB231 cells were either transfected with a non-sense control shRNA (shCTL) or with a ROR1 shRNA (shROR1) construct. The objective was to find expression-responsive targets of these perturbations as potential drivers of MDA-MB231 cell invasiveness.

overall_design: Two conditions of  MDA-MB-231 cells each in 3 replicates:  1. non-sense control shRNA (shCTL),  2. ROR1 shRNA (shROR1)

first: Michaela

last: Bayerlová

first: Alexander

last: Wolff

first: Florian

last: Klemm

first: Annalen

last: Bleckmann


title: A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development [ATAC-seq]

summary: The neural crest is a dynamic progenitor cell population that arises at the border of neural and non-neural ectoderm. The inductive roles of FGF, Wnt, and BMP at the neural plate border are well established, but the signals required for subsequent neural crest development remain poorly characterized. Here, we conducted a screen in primary zebrafish embryo cultures for chemicals that decrease neural crest formation, as read out by crestin:EGFP expression. We found that the natural product caffeic acid phenethyl ester (CAPE) disrupts neural crest gene expression, migration, and melanocytic differentiation by reducing Sox10 activity. CAPE inhibits PI3K/Akt signaling specifically in FGF-stimulated cells, and neural crest defects in CAPE-treated embryos are suppressed by constitutively active Akt1. Inhibition of Akt activity by constitutively active PTEN similarly decreases crestin expression and Sox10 activity. Our study has identified Akt as a novel intracellular pathway required for neural crest development.

overall_design: To evaluate the effect of CAPE on chromatin accessibility in zebrafish neural crest cells, we treated sox10:GFP transgenic embryos with 10 micromolar CAPE or DMSO control at 2 ss, then sorted GFP+ cells at 17 or 20 ss for analysis by ATAC-seq.

first: Christie

last: Ciarlo

first: Charles

last: Kaufman

first: Beste

last: Kinikoglu

first: Jonathan

last: Michael

first: Song

last: Yang

first: Christopher

last: D’Amato

first: Sasja

last: Blokzijl-Franke

first: Jeroen

last: den Hertog

first: Thorsten

last: Schlaeger

first: Yi

last: Zhou

first: Eric

last: Liao


title: Epigenomic diversification within the genus Lupinus

city: Poznan

first: karolina

last: susek

address: Strzeszynska

country: Poland

institute: Institute of Plant Genetics, Polish Academy of Sciences

summary: Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organization of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment. In order gain a better understanding of the epigenetic organization of genomes in lupins we applied the immunostaining of methylated histone H3 and DNA methylation as well as whole-genome bisulfite sequencing. We revealed variations in the patterns of chromatin modifications at the chromosomal level among three crop lupins, i.e. L. angustifolius (2n=40), L. albus (2n=50) and L. luteus (2n=52), and the legume model plant Medicago truncatula (2n=16). Different chromosomal patterns were found depending on the specific modification, e.g. H3K4me2 was localised in the terminal parts of L. angustifolius and M. truncatula chromosomes, which is in agreement with the results that have been obtained for other species. Interestingly, in L. albus and L. luteus this modification was limited to one arm in the case of all of the chromosomes in the complement. Additionally, H3K9me2 was detected in all of the analysed species except L. luteus. DNA methylation sequencing (CG, CHG and CHH contexts) of aforementioned crop but also wild lupins such as L. cosentinii (2n=32), L. digitatus (2n=36), L. micranthus (2n=52) and L. pilosus (2n=42) supported the range of interspecific diversity. The examples of epigenetic modifications illustrate the diversity of lupin genomes and could be helpful for elucidating further epigenetic changes in the evolution of the lupin genome.

sample_organism:
Lupinus albus
Lupinus angustifolius
Lupinus luteus
Lupinus cosentinii
Lupinus digitatus
Lupinus micranthus
Lupinus pilosus

overall_design: Examination of 7 lupin species; DNA was extracted from young leaves; plants were grown in a greenhouse under controlled (temp. 22/18ºC, photoperiod 16/8h, RH 60%)

first: Robert

last: Schmitz

first: Adam

last: Bewick

first: Karolina

last: Susek


title: Dynamics of gene expression during devepolement and expansion of vegetative stem internodes of bioenergy sorghum

city: college station

first: brian

middle: adam

last: mckinley

state: tx

address: 2128 tamu

department: biochemistry and biophysics

institute: texas A&M University

summary: Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analysis of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020.

overall_design: A developmental time course of four sucessive internodes located in the zone of internode elongation each harvested in triplicate for RNA-seq analysis.

first: Tesfamichael

last: Kebrom

first: Brian

last: McKinley

first: John

last: Mullet


title: A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development [RNA-seq]

first: Leonard

last: Zon

overall_design: To evaluate the effect of CAPE on gene expression in zebrafish neural crest cells, we treated sox10:GFP transgenic embryos with 10 micromolar CAPE or DMSO control at 2 ss, then sorted GFP+ cells at 17 ss for analysis by RNA-seq.

first: Christie

last: Ciarlo

first: Charles

last: Kaufman

first: Beste

last: Kinikoglu


title: Genome-wide expression profiling of grapevine (Vitis vinifera cv Cabernet Sauvignon) woody stems and asymptomatic leaves during a time course of infection by Neofusicoccum parvum

city: Davis

first: Mélanie

last: Massonnet

state: California

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

summary: Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of grape and N. parvum genes in stem (local) and leaf (distal) tissues during an extensive interaction time course.

overall_design: Potted V. vinifera cv. Cabernet Sauvignon clone FPS 19 plants were inoculated with N. parvum UCD646So mycelia (ATCC number: MYA-3706). Stems and leaves were collected at seven time points: 0 hour post-inoculation (hpi), 3 hpi, 24 hpi, 2 weeks post-inoculation (wpi), 6 wpi, 8 wpi, and 12 wpi. Three biological replicates, corresponding to a pool of leaves from four plants for the distal sampling and to individual stems (-1 cm) in the case of the local sampling, were used for RNA extraction.

first: Erin

last: Galarnau

first: Rosa

last: Figueroa-Balderas

first: Daniel

last: Lawrence

first: Shiho

last: Miki

first: Qiang

last: Sun

first: Christopher

last: Wallis

first: Kendra

last: Baumgartner

first: Dario

last: Cantu


title: Expression profiles of wild-type and mcrA-deleted cells in a glucose minimal medium

city: Nagoya

first: Tomohiro

last: Akashi

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Advanced Medical Science

country: Japan

institute: Nagoya University Graduate School of Medicine

summary: Expression profiles of wild-type and mcrA-deleted cells cultured in a glucose minimal medium for 1 day.

overall_design: mRNA profiles of wild-type and mcrA-deleted cells were generated by deep sequencing, in triplicate, using Illumina MiSeq.


title: RNA-seq Analysis of the stem of Wild Type and CEP1 Transcriptomes

status: Public on Aug 16 2017

first: Hui

last: Li

address: Qinghua East Road No.35

department: Biochemistry and Molecular Biology

institute: Beijing Forestry University

summary: RNA-seq was performed to examine the differential expressed transcriptomes in cep1 plants during stem development compare to wild type plants.

overall_design: To examine the differential expressed transcriptomes in cep1 plants during stem development, the stem from cep1 mutants and wild type plants at 25-days after flowering were collected for RNA-seq analysis. No replicates include in each samples.


title: NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: Burkholderia cenocepacia is a versatile opportunistic pathogen that survives in a wide variety of environments, which can be limited in nutrients such as nitrogen. We previously showed that B. cenocepacia sigma factor s54 played a major role in control of nitrogen assimilation and virulence. In this work, we investigated the role of the s54 enhancer binding protein NtrC in controlling the response to nitrogen limitation and virulence. RNA-Seq analyses and phenotypical analysis on a ntrC mutant strain showed that, in addition to orchestrating uptake of nitrogen sources, NtrC is also regulating exopolysaccharide (EPS) production and motility. A search for NtrC consensus sequences identified a potential binding sequence in the promoter region of gene clusters involved in EPS formation and flagellar rotation suggesting that NtrC directly controls the expression of these phenotypic traits in B. cenocepacia H111.

overall_design: NtrC regulon in B. cenocepacia

first: Yilei

last: Liu

first: Martina

last: Lardi

first: Alessandro

last: Pedrioli

first: Leo

last: Eberl


title: DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA

first: Yueyi

last: Shi

address: No.28, Fuxing Road

department: Department of Stomatology

institute: Chinese PLA General Hospital

summary: In this study, we have developed MB-seq, a novel DNA methylome profiling technology combining MeDIP-seq with bisulfite conversion, which can precisely detect the 5mC sites and determine their DNA methylation level at single-base resolution in a cost-effective way. In addition, we have developed a new alternative method, MRB-seq (MeDIP-repetitive elements removal-bisulfite sequencing), which interrogates 5mCs in functional regions by depleting nearly half of repeat fragments enriched by MeDIP. Comparing MB-seq and MRB-seq to whole-genome BS-seq using the same batch of DNA from YH peripheral blood mononuclear cells. We found that the sequencing data of MB-seq and MRB-seq almost reaches saturation after generating 7-8 Gbp data, whereas BS-seq requires about 100 Gbp data to achieve the same effect. In comparison to MeDIP-seq and BS-seq, MB-seq offers several key advantages, including single-base resolution, discriminating the methylated sites within a CpG and non-CpG pattern and overcoming the false positive of MeDIP-seq due to the non-specific binding of 5-methylcytidine antibody to genomic fragments.

first: Rongfa

last: Bu


title: An integrated expression atlas of miRNAs and their promoters in human and mouse

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary: MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. We created the first integrated expression atlas of miRNAs and their promoters in mammalian cells by deep sequencing matched short RNA (sRNA) and Cap Analysis Gene Expression (CAGE) libraries from 492 RNA samples. Most samples were derived from human primary cells, allowing us to annotate each human miRNA by its sRNA expression profile across primary cell types. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species, reflecting the importance of transcriptional regulation of miRNA expression. As primary and mature miRNA expression levels in the matched libraries were correlated, CAGE expression of primary miRNAs could be used as a proxy for the expression level of mature miRNAs, allowing us to extend the miRNA expression survey to the 1,829 human and 1,029 mouse CAGE libraries in FANTOM5. We thus provide the first broad atlas of miRNA expression in primary cells, as well as the largest map of miRNA promoters to date, establishing the foundation for detailed analysis of expression patterns and transcriptional control regions of miRNAs.

overall_design: Validation of miRNA promoters by RACE in monocytes, macrophages and dendritic cells.

first: Claudia

last: Gebhard

first: Michiel

last: de Hoon


title: Quantitative Analysis of Wild Type and Tlx3f/f;SNS-cre dorsal root ganglion Transcriptomes by RNAseq

first: Zijing

address: Fengtai District, #20 East St.

institute: Beijing Institute of Biotechnology

summary: purpose: to analyse the differentially expressed genes in dorsal root ganglion between Wild Type and Tlx3f/f;SNS-cre mice

overall_design: methods: total RNA from dorsal root ganglion of Wild Type and Tlx3f/f;SNS-cre mice were obtained for RNAseq,in triplicate, using Illumina HiSeq4000

first: Chengcheng

last: Huang


title: Deciphering the nature of the coral-Chromera association

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

institute: CSIRO

summary: Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has attracted interest because of its unique evolutionary position between the photosynthetic dinoflagellates and the parasitic apicomplexans. The nature of the relationship between Chromera and its coral host is controversial. Is it a mutualism, from which both participants benefit, or is Chromera a parasite, harming its host? To better understand the interaction, larvae of the common Indo-Pacific reef-building coral Acropora digitifera were experimentally infected with Chromera and the impact on the host transcriptome assessed at 4, 12, and 48 h post-infection using Illumina RNA-Seq technology. The transcriptomic response of the coral to Chromera was complex and implies that host immunity is strongly suppressed, and both phagosome maturation and the apoptotic machinery modified. These responses differ markedly from those described for infection with a competent strain of the coral symbiont Symbiodinium, instead resembling those of vertebrate hosts to parasites and/or pathogens such as Mycobacterium tuberculosis. Consistent with ecological studies suggesting that the association may be accidental, the transcriptional response of A. digitifera larvae leads us to conclude that Chromera is more likely to be a coral parasite, commensal, or accidental bystander, but certainly not a beneficial mutualist

overall_design: The goal of the study is to determine the nature of the coral-Chromera association based on host transcriptional response post-Chromera infection.There were 2 conditions (Chromera-infected and control). Samples were taken at 3 time points post-Chromera infection; 4h, 12h and 48h. There were 3 biological replicates per condition. RNA was isolated and 17 RNA-Seq libraries were sequenced on Illumina Hi-Seq 2000 platform. Samples were analysed to infer differential gene expression, comparing the Chromera-infected samples to the control ones at each time point

first: Vivian

last: Cumbo

first: Saki

last: Harii

first: Chuya

last: Shinzato

first: Cheong

middle: X

last: Chan

first: Mark

last: Ragan

first: Nori

last: Satoh

first: Eldon

last: Ball

first: David

last: Miller


title: Transcriptome analysis of the Novosphingobium resinovorum SA1 strain grown on sulfanilic acid and glucose

status: Public on Aug 15 2017

city: Szeged

first: Botond

last: Hegedüs

address: Közép fasor 52.

department: Department of Biotechnology

country: Hungary

institute: University of Szeged

summary: Novosphingobium resinovorum strain SA1 is one of few strains capable of degrading sulfanilic acid which is a widely used representative of sulfonated aromatic compounds. In order to identify the elements involved in the biodegradation process and to understand the metabolic responces of the cells exposed to this aromatic compound, we performed a whole transcriptome analysis of cells grown on sulfanilic acid and glucose.  Additionally, for distinguish the potential stress/starvation effects of the xenobiotic we compared the transcript profiles of samples taken from both the exponential and stationary growth phases.

overall_design: 8 samples -  including two replicas in each point - were analyzed as follows. 2-2 paralel samples were taken from the exponential phase cells grown on sulfanilic acid and glucose. These are for comparing the transcript profiles of the actively growing cells using sulfanilic acid (xenobiotic) and glucose (control) as substrates. For modeling the starvation effect, 2-2 samples/replicas were taken from the stationary phase cells grown on glucose and sulfanilic acid.

first: Péter

last: Kós

first: Gábor

last: Bende

first: Naila

last: Bounedjoum

first: Gergely

last: Maróti

first: Krisztián

last: Laczi

first: Márk

last: Szuhaj

first: Katalin

last: Perei

last: Rákhely


title: Sox9-eGFP cell sorted intestinal cells

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: The different cell populations of intestinal crypts were sorted based on the expression of Sox9eGFP expression.

overall_design: Separation of intestinal crypts into subpopulations

first: Matt

last: Kanke


title: Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Parascaris)

city: Aurora

first: Jianbin

last: Wang

state: CO

address: 12801 East 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado Denver

summary: Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. Here, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum and the horse parasite Parascaris univalens. In addition, we carried out in-depth analyses of DNA elimination in the parasitic nematode of humans, Ascaris lumbricoides, and the parasitic nematode of dogs, Toxocara canis. Our analysis of nematode DNA elimination reveals that in all species, repetitive sequences (that differ among the genera) and germline-expressed genes (approximately 1000-2000 or 5%-10% of the genes) are eliminated. Thirty-five percent of these eliminated genes are conserved among these nematodes, defining a core set of eliminated genes that are preferentially expressed during spermatogenesis. Our analysis supports the view that DNA elimination in nematodes silences germline-expressed genes. Over half of the chromosome break sites are conserved between Ascaris and Parascaris, whereas only 10% are conserved in the more divergent T. canis. Analysis of the chromosomal breakage regions suggests a sequence-independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our genome assemblies and annotations also provide comprehensive resources for analysis of DNA elimination, parasitology research, and comparative nematode genome and epigenome studies.

overall_design: A total of 6 samples are used for this study, including male germline, female germline, embryo, intestine and carcass, and a mixed sample for 5'-end RNA sequencing.

first: Maxim

last: Zagoskin

first: Shenghan

last: Gao

first: Richard

last: Davis


title: Gene expression of ectoplacental cones of early post-implantation embryos (6.5 days post-coitus) from control and obese dams

city: Philadelphia

first: Rebecca

last: Simmons

state: PA

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

summary: We used a low-input strand specific total RNA library preparation kit to obtain transcriptomes from sexed ectoplacental cones of embryos from control and diet-induced obese dams.  We compared expression profiles to determine which genes and pathways are altered in the tissue that will go on to develop into the placenta and extraembryonic tissue.

overall_design: Examination of impact of diet-induced obesity on gene expression in the early post-implantation mouse embryo.

first: Kathleen

last: O'Neill

last: Condon


title: Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris)

overall_design: A total of 11 Ascaris samples are used for this study, including regions of the male germline (1, mitotic region; 2, spermatogenesis; 3, post-meiotic region; 4, seminal vesicle; and 5, spermatids), regions of the female germline (1, mitotic region; 2, early pachytene; 3, late pachytene; 4, diplotene; and 5, oocyte), and a mixed sample for 5'-end SL and TeloPrime RNA-seq.


title: Expression signature in a human colorectal cancer cell lines, HCT116 and RKO, transfected with miR-101

city: Chuo-ku

first: Naoto

last: Tsuchiya

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center Research Institute

summary: Understanding of molecular system how tumor-suppressor p53 selectively activates and/or completes appropriate tumor-suppressor pathway in response to various stresses is still one of the most important issues to be clarified. We analyzed a molecular mechanism for the completion of p53-dependent ribosome stress responsible pathway by miR-101. To this end, expression microarray analyses were conducted in the presence or absence of miR-101. We found that miR-101 induces the activation of p53-dependent G2 phase cell cycle arrest through the increased phosphorylation of ATM, leading to the p53-depdent apoptosis.

overall_design: HCT116 or RKO cells were transfected with a Pre-miR-101 miRNA Precursor Molecule (Ambion) or Pre-miR miRNA Molecules Negative Control #2 (Ambion) at a final concentration of 5 nM. After incubtion for 3 days, total RNAs were extracted and gene expression signatures were determined. Three independent experiments were performed for each transfection.

first: Yuko

last: Fujiwara


title: 2.5 dpc Uterus Chip-Seq of Kdm4a mice

first: Aditya

last: Sankar

address: Ole Maaloes Vej 5

institute: University of Copenhagen

summary: Purpose: ChipSeq allows us to identify binding sites of target proteins of interest in the genome, helping create a global profile for the same. Kdm4a is a H3K9me3 histone demethylase that acts to prevent spurious accumulation of this repressive mark at H3K4me3 positive transcription start sites. To complement transcriptome data from Kdm4a mice, we performed Chip-Seq on 2.5dpc mouse uterus of 8-10 week old littermate control and Kdm4a knockout mice for Kdm4a, H3K9me3 and H3K4me3. This would help us check which of the target genes with changed gene expression was due to the direct change in histone lanscape in absence of Kdm4a.

overall_design: Wildtype and Kdm4a knockout mice were set up for natural timed mating. At 2.5 dpc, we harvested pre-receptive uterus from mice after confirming the presence of embryos by flushing the oviduct. The uteri were subsequently cross-linked with 1% paraformaldehyde, homogenized mechanically and  chromatin extracted and sheared by sonication.  1mg for Kdm4a and 100 uG for histone IPs were used as input. ChipSeq Libraries were then constructed using Illumina from eluates using 2ng of IP-ed DNA as input material. The profiles are compared between wildtype and Kdm4a knockout conditions.


title: Targets of ROR2 overexpression in MCF-7 cells revealed a differentially regulated module of non-canonical WNT signaling pathway

first: Tim

last: Beissbarth

address: Humboldtallee 32

institute: University Medical Center Göttingen

summary:
RNA-Seq profiling of estrogen-receptor-positive MCF-7 cell lines with different perturbations of non-canonical WNT signaling .
The MCF-7 cells were either transfected with an empty vector (pcDNA) or with a ROR2 overexpression construct, in parallel with or without stimulation with recombinant WNT5A. The objective was to find expression-responsive targets of these perturbations as potential drivers of increased cell invasiveness.

overall_design: Four conditions of MCF-7 cells each in 3 replicates:  1. empty vector (pcDNA),  2. empty vector (pcDNA) with WNT5A stimulation, 3. ROR2 overexpression construct, 4. ROR2 overexpression construct with WNT5A stimulation

first: Michaela

last: Bayerlová

first: Kerstin

last: Menk

first: Florian

last: Klemm

first: Annalen

last: Bleckmann


title: RNA transcriptome in Drosophila melanogaster embryos mutant for serine hydroxymethyl transferase (SHMT)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We report the analysis of the transcriptome in Drosophila embryos with two genotypes (1: wild type, 2: embryos from germline clones of a SHMT mutant (allele X238)) and two developmental stages (1: pre-blastoderm, stage 1 and stage 2, 0–1h after egg lay, 2: late blastoderm/cellularisation stage 5, 1.5–2.5 h after egg lay)

overall_design: Examination of transcription in two genotypes and two developmental stages

first: Franziska

last: Winkler

first: Jörg

last: Großhans


title: Bovine follicular fluid extracellular vesicles RNA contents

city: Pirassununga

first: Juliano

last: da Silveira

state: Sao Paulo

address: Duque de Caxias 225

department: Veterinary Medicine

country: Brazil

institute: University of Sao Paulo

summary: The goal of this experiment was to determine the RNA contents of extracellular vesicles isolated from 3-6mm bovine ovarian follicles.

overall_design: We performed RNA-seq analysis of extracellular vesicles isolated from a pool of ovaries in order to determine the highly abundant RNA molecules within these vesicles.


title: Epigenetic and transcriptional analysis of mesoderm progenitor cells identifies HOPX as a novel regulator of hemogenic endothelium

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

summary: We analyzed chromatin dynamics and transcriptional activity of human embryonic stem cell (hESC)-derived cardiac progenitor cells (CPCs) and KDR+/CD34+ endothelial cells generated from cardiogenic or hemogenic mesoderm. Using an unbiased algorithm to hierarchically rank genes modulated at the level of chromatin and transcription, we identified novel candidate regulators of mesodermal lineage determination. HOPX, a non-DNA binding homeodomain protein, was identified as a candidate regulator of blood-forming endothelial cells. We used HOPX reporter and knockout hESCs, as well as hopx loss of function studies in zebrafish, to show the requirement of HOPX in vivo and in vitro in hemato-endothelial lineage specification. Loss of HOPX does not impact endothelial fate specification but markedly reduces primitive hematopoiesis acting at least in part through suppression of Wnt/β-catenin signaling. Single cell RNA-seq data during mouse hematopoietic development in vivo confirm a role for HOPX in hematopoietic fate. Taken together, we show that HOPX is a novel regulator of hemato-endothelial fate specification in vitro and in vivo that functionally regulates Wnt signaling to modulate primitive hematopoiesis.

overall_design: 2 biological replicates were isolated from cardiac progenitor cells (CPCs) and endothelial populations derived from cardiogenic mesoderm (C-ECs) and hemogenic mesoderm (H-ECs). RNA-seq and ChIP-seq (H3K4me3 and H3K27me3) was performed for each replicate.

first: Nathan

last: Palpant

first: Yuliang

last: Wang


title: TREM2 is a global regulator of microglia energetic and biosynthetic metabolism during steady state and in Alzheimer’s disease

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: The most common form of senile dementia, Alzheimer’s disease (AD), is  characterized by Aβ plaques and neurofibrillary tangles in the CNS.  AD genetic studies have identified high-risk hypomorphic variants in TREM2, a myeloid cell surface receptor that enables concerted microglial responses to Aβ plaques and neuronal cell death, including proliferation, survival, clustering and phagocytosis. How TREM2 promotes these responses is not known. Here, we demonstrate that TREM2 drives mTOR signaling, which maintains high ATP levels, supports biosynthetic pathways and suppresses AMPK phosphorylation and autophagy. In vitro, TREM2-deficient macrophages undergo dramatically increased autophagy and die in response to growth factor limitation or ER stress. Excessive autophagy is also evident in microglia from Trem2-/- 5XFAD mice and in post-mortem specimens from AD patients carrying TREM2 risk variants. Metabolic derailment, autophagy and cell death can be circumvented by engaging alternative energy production pathways. Thus, restoring microglial energetic and anabolic levels may be a future therapeutic avenue for TREM2-associated neurological disease.

overall_design: Bone marrow-derived macrophages (BMDMs) from WT and Trem2–/– mice were cultured in either 0.5% or 10% LCCM overnight in complete RPMI. Some samples cells were stimulated with 10 ng/ml LPS for 4 hours.

first: Tyler

last: Ulland

first: Wilbur

last: Song

first: Stanley

last: Huang

first: Jason

middle: D

last: Ulrich

first: Alexey

last: Sergushichev

first: Wandy

middle: L

last: Beatty

first: Alexander

last: Loboda

first: Nigel

last: Cairns

first: Amal

last: Kambal

first: Ekaterina

last: Loginicheva

first: Susan

last: Gilfillan

first: Marina

last: Cella

first: Herbert

middle: W

last: Virgin

first: Emil

last: Unanue

first: Yaming

middle: N

first: David

last: Holtzman

first: Marco

last: Colonna


title: Evidence for inducer function of 2-keto-3-deoxy-L-galactonate in D-galacturonic acid induced gene expression in Aspergillus niger

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: In Aspergillus niger, the enzymes encoded by gaaA, gaaB, gaaC and gaaD catabolize D-galacturonic acid (GA) consecutively into L-galactonate, 2-keto-3-deoxy-L-galactonate, pyruvate and L-glyceraldehyde, and glycerol. We show here that deletion of gaaB or gaaC results in severely impaired growth on GA and accumulation of pathway intermediates L-galactonate and 2-keto-3-deoxy-L-galactonate, respectively. Expression levels of several GA-induced genes were specifically elevated in the ∆gaaC mutant on GA as compared to the reference strain or other GA catabolic pathway deletion mutants. The hyper-induction of GA-induced genes in ∆gaaC indicates that 2-keto-3-deoxy-L-galactonate is the inducer of genes required for GA utilization.

overall_design:
In this study, we constructed GA catabolic pathway deletion mutants (∆gaaA, ∆gaaB, ∆gaaC and ∆gaaD) to gain insight into regulation of GA-induced genes in A. niger. Comparative analysis of all the GA catabolic pathway deletion mutants indicates that 2-keto-3-deoxy-L-galactonate acts as the physiological inducer of the GA-induced genes.
-----------------------------------------------------
This represents the ΔgaaC mutant only

first: Ebru

last: Alazi

first: Claire

last: Khosravi

first: Tim

last: Homan

first: Saskia

last: du Pré

first: Mark

last: Arentshorst

first: Marcos

last: Di Falco

first: Thi

last: Pham

first: Mao

last: Peng

first: Maria

middle: V

last: Aguilar-Pontes

first: Adrian

last: Tsang

first: Jaap

last: Visser

middle: P

first: Arthur

last: Ram


title: Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence (RNA-seq)

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

summary: Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which cause Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement of chromatin reorganization, including the formation of senescence-associated heterochromatic foci (SAHF). The nuclear lamina (NL) is an important contributor to genome organization and has been involved in cellular senescence and organismal aging. It interacts with multiple regions of the genome called lamina-associated domains (LADs). Some LADs are cell type-specific, while others are conserved between cell types and are referred to as constitutive LADs. Here, we used DamID to investigate the changes in genome-NL interactions in a model of OIS triggered by the expression of the BRAFV600E oncogene.  Results. We found that OIS cells lose most of their constitutive LADs (cLADS), suggesting the loss of a specific mechanism that targets cLADs to the NL. In addition, multiple genes relocated to the NL. Unexpectedly, they were not repressed, implying the abrogation of the repressive activity of the NL during OIS. Finally, OIS cells displayed an increased association of telomeres with the NL.  Conclusions. Our study reveals that senescent cells acquire a new type of LAD organization and suggest the existence of as yet unknown mechanisms that tether cLADs to the NL and repress gene expression at the NL.

overall_design: Examination of gene expression in cycling cells, after oncogene induced senescence, and after quiescence

first: Christelle

last: Lenain

first: Ludo

last: Pagie

first: Bas

last: van Steensel

first: Daniel

last: Peeper


title: H4K16ac modification profile difference between Peg3-WT and KO MEF cells

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

summary: PEG3 (Paternally Expressed Gene 3) is an imprinted gene encoding a DNA-binding protein.  Two components of the mammalian MSL (Male-Specific Lethal) complex, Msl1 and Msl3, are known to be the genomic targets of PEG3.  In this report, we performed genome-wide ChIP-seq experiments profiling H4K16ac levels using a set of MEF cells (Mouse Embryonic Fibroblast), the WT and KO of Peg3.  The results indicated that about 10% of the mouse gene catalog showed high levels of H4K16ac levels in Peg3-KO MEFs than in Peg3-WT MEFs.  This further suggests that mammalian Peg3 may control its downstream genes through the MSL complex.

overall_design: Comparison of H4K16 ac levels between Peg3-WT and Peg3-KO MEFs.

first: An

last: Ye


title: Transcriptional changes in the primary somatosensory cortex upon sensory deprivation

city: Nijmegen

first: Koen

last: Kole

address: Heyendaalsweg 135

department: Neurophysiology

institute: Donders Institute for Brain Cognition and Behaviour

summary: Experience-dependent plasticity (EDP) is essential for anatomical and functional maturation of sensory circuits during development and can be readily studied is the rodent barrel cortex. Using this model we aimed to uncover changes on the transcriptome level and applied RNA sequencing upon altered sensory experience in juvenile mice in a cortical column and layer specific manner. From column- and layer-specific barrel cortical tissue, high quality RNA was purified and sequenced. The current dataset entails an average of 50 million paired-end reads per sample, 75 base pairs in length.

overall_design: Wild type mice were deprived of their C-row whiskers from P12 until P23-P24, after which acute brain slices were prepared and tissues were excised from L2/3 and L4 from specific barrel columns. RNA isolated from these tissue sections was then subjected to RNA-sequencing.

first: Yutaro

last: Komuro

first: Jan

last: Provaznik

first: Jelena

last: Pistolic

first: Vladimir

last: Benes

first: Paul

last: Tiesinga

first: Tansu

last: Celikel


title: Post-Transcriptional Regulation of Mouse Neurogenesis by Pumilio Proteins [RNA-Seq]

city: New Haven

first: Haifan

last: Lin

state: Connecticut

address: 10 Amistad St.

department: Cell Biology

institute: Yale Univeristy

summary: We employ mRNA-seq to investigate transcriptome of  Pum1-Knockout, Pum2-Knockout and WT conditons

overall_design: In order to investigate whether Pum1 and Pum2 regulate their targets at their RNA levels, we used 1/10 of the samples from the Pum1 and Pum2 iCLIP experiments (four biological repeats of WT, P1KO, and P2KO neonatal brains) to extract total RNAs for RNA deep sequencing. And we also collected three Ndcko neonatal brains for RNA deep sequencing.

first: Meng

last: Zhang

first: Jing

last: Xia


title: Post transcriptional modifications of miRNAs in the cnidarian Nematostella vectensis

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

summary: MicroRNAs of bilaterian animals undergo posttranscriptional modifications such as methylation, tailing and trimming that regulate miRNA stability and function.  To gain insight on the evolution of miRNA posttranscriptional modification, we studied regulation of miRNA stability by methylation in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister group of Bilateria.

overall_design: Employ height throughput sequence of endogenous small RNAs

first: V

last: Modepalli

first: Y

last: Moran


title: Post-Transcriptional Regulation of Mouse Neurogenesis by Pumilio Proteins

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

overall_design: Refer to individual Series


title: Post-Transcriptional Regulation of Mouse Neurogenesis by Pumilio Proteins [RIP-Seq]

summary: we employ crosslinking immunoprecipitation (iCLIP) to reveal Pum1 and Pum2 binding mRNAs

overall_design: To unravel the molecular mechanisms mediated by Pum1 and Pum2, we performed individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) to identify Pum1 and Pum2 target RNAs and to delineate the Pum binding sites at the single nucleotide resolution. We used neonatal wildtype brains for Pum1 iCLIP and Pum2 iCLIP, with neonatal brains from Pum1 global knockout (P1KO) and Pum2 global knockout (P2KO) mice, as the negative controls, respectively. Two biological duplicates were carried out for each condition.


title: Genome-wide binding sites for RGA in Arabidopsis inflorescence apices

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

institute: JIC

summary:
The Arabidopsis thaliana REPRESSOR OF GA gene (RGA) encodes a DELLA protein that associates with multiple transcription factors to control plant growth in response to the hormone gibberellin (GA) (1). As part of a screen for genes that mediate the function of RGA in stem growth and shoot meristem function, we performed ChIP-seq to identify genome-wide loci associated with RGA in inflorescence apices. To detect genes controlled by RGA in a gain-of-function semi-dwarf background, we used a GFP-tagged, gibberellin-insensitive version of RGA (RGAp:GFP-rga-delta17) (2).
(1) J.-M. Daviere, P. Achard, Gibberellin signaling in plants. Development 140, 1147-1151 (2013).
(2) A. Dill, T. P. Sun, Synergistic derepression of gibberellin signaling by removing RGA and GAI function in Arabidopsis thaliana. Genetics 159, 777-785 (2001).

overall_design:
Plants expressing a GFP-tagged, gibberellin-insensitive version of RGA (RGAp:GFP-rga-delta17) were used for ChIP-seq with anti-GFP antibodies; wild-type controls (Landsberg-erecta) were used as epitope-negatve controls.
The files that resulted from comparing the combined RGAp:GFP-rga-delta17 replicates with the combined control replicates are linked as Series supplementary files.

first: Antonio

last: Serrano-Mislata

first: Stefano

last: Bencivenga


title: sRNA-seq data over Arabidopsis thaliana germination

city: Heidelberg

first: Quentin

last: Gouil

state: VIC

address: Studley Road

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.

overall_design: Total RNA was extracted from Arabidopsis seeds at 10 time points during germination in triplicate. The time points were: freshly harvested seed (H), seeds following 15 days of ripening (0 h), seeds after; 1 h of stratification (1 h S), 12 h of stratification (12 h S), 48 h of stratification (48 h S), followed by seed collected 1 hour into the light (1 h SL), 6 hours into the light (6 h SL), 12 hours into the light (12 h SL), 24 hours into the light (24 h SL) and 48 hours into the light (48 h SL).

first: Reena

last: Narsai


title: RNA-seq data over Arabidopsis thaliana germination

summary: RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.


title: methylC-seq data over Arabidopsis thaliana germination

summary: methylC-seq profiling of 4 time points during germination in Arabidopsis, from mature seed, through  stratification, germination and to post-germination.

overall_design: gDNA was extracted from Arabidopsis seeds at 4 time points during germination in triplicate. The time points were: following 15 days of ripening (0 h), after 48h of stratification (48hS), 6 hours into the light (6 h SL), 24 hours into the light (24 h SL) and 48 hours into the light (48 h SL).


title: Klf1 and Klf3 compete for promoters and enhancers to fine-tune transcription

city: Woolloongabba

first: Melissa

last: Ilsley

state: Queensland

address: 36 Kent street

institute: Mater Research

summary: Reciprocal gene regulation by Krüppel-like factors

overall_design: ChIP-seq of KLF3 and KLF1 in erythroid cell lines. 4sU-RNA-seq before and after induction of KLF3-ER in erythroid cell lines.

first: Kevin

middle: R

last: Gillinder

first: Stephen

last: Huang

first: Andrew

middle: C

last: Perkins


title: Transcriptome analysis and identification of genes associated with lemon floral transition and flower development during floral inductive water deficits

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

summary: Water deficit is the key induction factors known to induce flowering in many woody plants, whereas reports on the molecular mechanisms underlying floral induction by water deficit are scarce. Here, we analyzed morphology, cytology and different hormone level of lemon buds during floral inductive water deficits. Higher levels of ABA were observed and the floral buds initiated differentiation by paraffin sections analysis. Total 1,638 differentially expressed genes (DEGs) were identified by RNA-sequencing. Some DEGs were related to flowering, while others were associated with hormone biosynthesis or metabolism.

overall_design: In this experiment, terminal bud and the following five buds (the major node position for flower formation) from flushes were sampled at three stages (stage 1: one week before water deficit, stage 2: one week after the beginning of water deficit, and stage 3: one week after rehabilitation of irrigation).

first: Chun-Gen

last: Hu

first: Jin-Zhi


title: CTCF translates IL-2- and αKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs [HiC-Seq]

city: Birmingham

first: Amy

last: Weinmann

address: 1825 University Blvd

department: Department of Microbiology

country: USA

institute: University of Alabama at Birmingham

summary: We found that aspects of the IL-2-sensitive effector gene program in CD4+ Th1 and CD8+ Tc1 cells are regulated by glutamine and alpha-ketoglutarate (αKG)-induced events, in part through changes in DNA and histone methylation states. We further identified a novel mechanism by which IL-2- and αKG-sensitive metabolic changes regulate the association of CTCF with select genomic sites.  αKG-sensitive CTCF sites were often associated with loci containing IL-2- and αKG-sensitive genome organization patterns and gene expression in T cells.  Surprisingly, IL-2- and αKG-sensitive CTCF sites in T cells were also associated with genes from developmental pathways that had αKG-sensitive expression in ES cells.  The data collectively support a novel mechanism wherein CTCF serves to translate αKG-sensitive metabolic changes into context-dependent differentiation gene programs.

overall_design: To address whether IL-2- and aKG-sensitive CTCF binding events might influence genome organization, we performed an in situ Hi-C analysis on CD4+ T cells polarized in Th1 conditions and maintained in high IL-2, low IL-2, or low IL-2 with aKG. Data from the Hi-C analysis were analyzed to define changes in genome organization associated with each condition.

first: Danielle

last: Chisolm

first: Daniel

last: Savic

first: Amanda

middle: J

last: Moore

first: Andre

last: Ballesteros-Tato

first: Beatriz

last: Leon

first: David

middle: K

last: Crossman

first: Cornelis

last: Murre

first: Richard

last: Myers

middle: S


title: CTCF translates IL-2- and αKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs [ATAC-Seq]

overall_design: Antigen specific CD8+ T cells were generated during the course of an influenza infection in mice. 7-9 days after the initial influenza infection, tetramer positive NP antigen specific or OTI specific CD8+ T cells were sorted into CD25high or CD25low populations.

middle: M


title: CTCF translates IL-2- and αKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs [ChIP-Seq]

overall_design: We performed a ChIP-seq analysis examining H3K27me3 states in CD4+ Th1 cells maintained in high IL-2, low IL-2, or low IL-2 with αKG. We also performed a CTCF ChIP-seq analysis with CD4+ Th1 cells maintained in high IL-2, low IL-2, or low IL-2 with αKG to define the sites associated with CTCF in each condition. In addition, we performed an H3K27Ac ChIP-seq analysis with Th1 cells maintained in high IL-2, low IL-2, or low IL-2 with αKG to examine potential enhancer regions in each condition.


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 102651

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Global transcriptional analysis of EPEC/ETEC hybrid isolates.

overall_design: RNA sequencing was performed on seven E. coli during growth in laboratory media and conditions that have been previously demonstrated to induce expression of virulence genes.

first: Tracy

last: Hazen

first: Amol

last: Shetty

last: Rasko


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 401140


title: CTCF translates IL-2- and αKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs [RNA-Seq]

overall_design: We conducted an RNA-seq analysis on CD4+ Th1 or CD8+ Tc1 cells maintained in high IL-2, low IL-2, or low IL-2 with aKG to define the composition of the IL-2-sensitive gene program that is impacted by metabolic changes related to aKG.  We also performed an RNA-seq analysis on CD4+ T cells polarized in Th1 conditions to define the role for glutamine in the IL-2- and aKG-sensitive program. For these experiments, primary CD4+ T cells were isolated and were stimulated with aCD3 and aCD28 in Th1 polarizing conditions either in the presence or absence of glutamine. After 3 days, the cells were split and maintained in Th1 polarizing conditions in either the presence or absence of glutamine in either high or low environmental IL-2 conditions. In addition, an RNA-seq analysis was performed in the mouse ES cell line E14Tg2a, with cells cultured in glutamine free-conditions either left untreated or exposed to aKG for 2 days.  This study was performed to address whether a subset of genes associated with aKG-sensitive CTCF peaks in Th1 cells might be induced by aKG in the context of a cell type where they are naturally expressed.


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 402290


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli H10407


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Pax9-/- Palate shelves Transcriptomes

city: Salt Lake City

first: Shihai

last: Jia

state: ut

address: 20 South 2030 East, Room 320 BPRB

department: Department of Neurobiology

institute: University of Utah

summary: Nonsyndromic clefts of the palate and/or lip are common birth defects arising in about 1/700 live births worldwide. They are caused by multiple genetic and environmental factors, can only be corrected surgically and require complex post-operative care that imposes significant burdens on individuals and society. Our understanding of the molecular networks that control palatogenesis has advanced through studies on mouse genetic models of cleft palate.  In particular, the transcription factor Pax9 regulates palatogenesis through the Bmp, Fgf and Shh pathways in mice.  But there is still much to learn about Pax9’s relationship with other signaling pathways in this process. Expression analyses and unbiased gene expression profiling studies offer a molecular explanation for the resolution of palatal defects by showing that Wnt and Eda/Edar-related genes are expressed in normal palatal tissues and that the Wnt and Eda/Edar signaling pathway is downstream of Pax9 in palatogenesis.

overall_design: E13.5 mouse embryos palate were micro-dissceted, control and mutant samples were seperated and individually lyzed for the RNA extraction.

first: Rena

last: D'Souza


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli HS


title: Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli E2348/69

sample_organism:
Escherichia coli HS
Escherichia coli O127:H6 str. E2348/69


title: CTCF translates IL-2- and aKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs


title: RNA-sequencing in WT and Fmr1-/- (KO) neurons treated with Jq1 and THZ

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Widespread epigenetic disruptions in FXS mice leads to transcriptional changes that likely contribute to the neuronal phenotpyes underlying FXS.

overall_design: 7DIV cultured cortical neurons from WT or Fmr1 KO mice were treated for 24 hours with vehicle, Jq1, or THZ, performed in triplicate.


title: The Genomic Landscape of Atypical Fibroxanthoma

city: San Francisco

first: Kevin

last: Lai

state: CA

address: 2340 Sutter Street

department: Dermatology

institute: University of California, San Fransico

summary: In this study, we used exome sequencing and RNA sequencing to describe the genomic landscape of Atypical Fibroxanthoma (AFX). Using exome sequencing data, we identified several genes commonly mutated in our samples such as CSMD3, COL11A1, and FAT1. We also identified deletions in chr9p and chr13q in the AFX tumors. Using our RNA-sequencing data, we identified 8591 differentially expressed genes, of which 3524 genes had at least a 2 log fold change between AFX tumors and normal keratinocytes. We also identified several pathways that are dysregulated in AFX, such as epithelial to mesenchymal transition and tumor-associated macrophage response.

overall_design:
Eight atypical fibroxanthoma samples were collected during Mohs surgery and wide local excision. The samples were snap frozen and embedded in Tissue-Tek. Laser capture microdissection was used to isolate the tumor and normal keratinocytes. Exome sequence libraries were prepared with the Nimblegen SeqCap EZ Exome 3.0 capture kit. The RNA samples were reversed transcriped using the Nugen's Ovation RNA-Seq system-kit and prepared using Nugen's Ovation Ultralow kit. 101bp paired-end sequencing was performed on an Illumina HiSeq 2500 for the exome and RNA-Seq libraries. The normal keratinocytes were used as controls in this study when compared to the tumor.
RNA-seq data in this Series.

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