title: Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence [ChIP-seq]

first: Gregory

last: Donahue

overall_design:
This study compares genome-wide ChIP-seq profiles of several histone post-translational modifications in proliferating and senescent fibroblasts. The PTMs studied include the acetylation marks H3K18ac, H3K23ac, H3K27ac, H3K122ac, H4K5ac, and the methylation mark H3K4me1. Each PTM chIP-seq was done in two replicates in both proliferating and replicative senescent cells. To control for sonication efficiency bias, whole histone subunit H3 and H4 along with input and IgG were sequenced over four replicates in both proliferating and replicative senescent cells. Additionally, chIP-seq for the enhancer decorating histone PTMs H3K4me1 and H3K27ac was also performed in cells undergoing irradiation-induced senescence (IR); this experiment was performed using whole histone subunit H3 along with input and IgG as a control for sonication efficiency, and all samples were sequenced in two replicates. Finally, chIP-seq for histone acetyltransferases CBP and p300 was performed along with a separate input and IgG in proliferating and replicative senescent cells, and all samples were sequenced in two replicates.

Please note that several processed data files were generated from multiple samples as indicated in the the correponding sample description field and thus are avilable as Series supplementary file.

first: Payel

last: Sen

first: Yemin

last: Lan

first: Catherine

last: Li

first: Simone

last: Sidoli

first: Greg

first: Adam

last: Field


title: SMARTer single cell total RNA sequencing

status: Public on Jan 01 2019

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Blastemal progenitors modulate immune signaling during early limb regeneration.

city: Cambridge

first: Douglas

middle: A.

last: Melton

state: MA

address: 7 Divinity Ave.

country: USA

institute: Harvard University

summary: Blastema formation is a hallmark of limb regeneration that requires proliferation and migration of progenitors derived from many tissues to the amputation plane. To better understand the genetic programs that initiate limb regeneration, we reasoned that blastemal progenitors would be among early proliferating cells in the stump following amputation. Here we separately profiled dividing and non-dividing stump tissues, as well as the wound epidermis, during early axolotl limb regeneration to examine transcriptional programs of blastemal progenitors. We provide a description of the changes in gene expression specific to early dividing cells at the site of amputation, inclusive of progenitors for the regenerating limb. This work collectively  demonstrates differential suppression/activation of core developmental signaling pathways in subsets of the early regenerating limb and further suggests that interleukin-8 (il-8) signaling is important for regeneration.

overall_design: To identify transcripts that were differentially expressed and enriched within early dividing cells during axolotl limb regeneration, we separately sequenced stump-derived 4N, stump-derived 2N, and wound epidermis at 0, 4, and 5 days post-amputation (dpa). We sequenced a total of 27 samples, 3 biological replicates per timepoint. These samples were multiplexed and sequenced on 1 Illumina Nextseq 500 run and also across 6 lanes on a Hiseq 2500.

first: Stephanie

middle: L

last: Tsai

first: Clara

last: Baselga-Garriga

middle: A


title: Gut Microbiota from Human Autism Spectrum Disorder Induces Behavioral Deficits in Mice

status: Public on Feb 01 2019

city: Pasadena

first: Gil

last: Sharon

state: CA

address: 1200 E California Blvd

institute: California Institute of Technology

summary: We transplanted gut microbiota via fecal transfer from TD and ASD children into germ-free wild-type mice, and reveal that colonization with ASD microbiomes induces hallmark changes in sociability, vocalization, and stereotypies. The brains of mice receiving gut microbiota from ASD individuals display alternative splicing patterns for genes dysregulated in the human ASD brain.

overall_design: Offspring of colonized mice (3 TD and 5 ASD donors) were saccrificed at P45 and striatum and prefrontal cortex were dissected.

first: Sharon

last: Gil

first: Gandal

last: Michael


title: RNA-seq profiles after SP-2509 Treatment of LNCaP, C42B, and PC3 cells

status: Public on Dec 31 2018

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

summary:
LSD1 (also known as KDM1A) is a histone demethylase and a key regulator of gene expression in embryonic stem cells and cancer.1,2 LSD1 was initially identified as a transcriptional repressor via its demethylation of active histone H3 marks (di-methyl lysine 4 [2MK4]).1  In prostate cancer, specifically, LSD1 also co-localizes with the AR and demethylates repressive 2MK9 histone marks from androgen-responsive AR target genes, facilitating androgen-mediated induction of AR-regulated gene expression and androgen-induced proliferation in androgen-dependent cancers.3,4  Recently, it was shown that treatment with high doses of androgens (e.g.10-fold higher doses than those required for induction of expression of androgen-activated genes such as PSA) recruits LSD1 and AR to an enhancer within the AR; this AR and LSD1 recruitment represses AR transcription.5 Thus, LSD1 appears to play a role in mediating both the proliferative and repressive phases of the biphasic androgen dose-response curve. For these reasons, we hypothesized that LSD1 might be important for maintenance of AR signaling in castration-resistant prostate cancer (CRPC) tumors.
However, in this report, we describe a distinct role of LSD1 as a driver of proliferation and survival of prostate cancer cells, including CRPC cells, irrespective of androgens or even AR expression. Specifically, LSD1 activates expression of cell cycle, mitosis, and embryonic stem cell maintenance pathways that are enriched in lethal prostate cancers – pathways not activated by androgens. Finally, we observe that treatment with a new LSD1 inhibitor potently and specifically suppresses LSD1 function and suppresses CRPC growth and survival in vitro and in vivo. Our data place LSD1 as a key driver of androgen-independent survival in lethal prostate cancers and demonstrate the potential of LSD1-directed therapies in the near-term.
1. Shi Y, Lan F, Matson C, et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. Dec 29 2004;119(7):941-953.
2. Whyte WA, Bilodeau S, Orlando DA, et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature. Feb 9 2012;482(7384):221-225.
3. Metzger E, Wissmann M, Yin N, et al. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature. Sep 15 2005;437(7057):436-439.
4. Yamane K, Toumazou C, Tsukada Y, et al. JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell. May 5 2006;125(3):483-495.
5. Cai C, He HH, Chen S, et al. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell. Oct 18 2011;20(4):457-471.

overall_design: RNA-sequencing experiments after treating prostate cancer cell lines with the LSD1 inhibitor SP-2509.


title: Analysis of seeds from Aethionema arabicum Turkish (TUR) and Cyprus (CYP) accession in response to light

status: Public on Jan 30 2019

city: Wien

first: Zsuzsanna

last: Mérai

address: 1030 Wien Dr. Bohr-Gasse 3.

country: Austria

institute: Gregor Mendel Institute

summary:
The seed germination in response to light shows natural variation in two accessions of Aethionema arabicum (Brassicaceae). One accession from Turkey (TUR) germinates well in darkness and light, while another closely related accession from Cyprus (CYP) germinates only in the dark. To understand the transcriptional differences between the two accession, we performed RNA-seq analysis from imbibed seeds, which were kept either in darkness or under light for 23 hours.
Results provide the first transcriptional comparison from light-neutral (TUR) and light-sensivite (CYP) seeds kept in darkness or exposed to light.

overall_design: Imbibed seeds of TUR and CYP seeds were kept in darkness or exposed to white light (100 µmol m-2s-1) for 23 hours. mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. In total, 12 samples were analyzed (2 accessions x 2 conditions x 3 repetitions)

first: Kai

last: Graeber

first: Per

last: Willhelmsson

first: Stefan

last: Rensing

first: Gerhard

last: Leubner-Metzger

first: Ortrun

last: Mittelsten Scheid


title: DNA re-replication is susceptible to nucleotide level mutagenesis

status: Public on Dec 27 2018

city: San Francisco

first: duyen

last: Bui

state: CALIFORNIA

address: 600 16th street

institute: UCSF

summary: The sources of genome instability, a hallmark of cancer, remain incompletely understood.  One potential source is DNA re-replication, which arises when the mechanisms that prevent re-initiation of replication origins within a single cell cycle are compromised. Using the budding yeast Saccharomyces cerevisiae, we previously showed that DNA re-replication is extremely potent at inducing gross chromosomal alterations and that this arises in part because of the susceptibility of re-replication forks to break. Here, we examine the ability of DNA re-replication to induce nucleotide level mutations. During normal replication these mutations are restricted by three overlapping error avoidance mechanisms: the nucleotide selectivity of replicative polymerases, their proofreading activity, and mismatch repair. Using lys2InsEA14, a frameshift reporter that is poorly proofread, we show that re-replication induces up to a 30x higher rate of frameshift mutations and that this mutagenesis is due to passage of the re-replication fork, not secondary to re-replication fork breakage.  Re-replication can also induce comparable rates of frameshift and base substitution mutations in a more general mutagenesis reporter CAN1, when the proofreading activity of DNA polymerase ε is inactivated.  Finally, we show that the induction of lys2InsEA14 frameshift mutations by re-replication is dependent on mismatch repair. These results suggest that the mismatch repair associated with re-replication is attenuated, although at most sequences DNA polymerase proofreading provides enough error correction to mitigate the mutagenic consequences. Thus, re-replication can facilitate nucleotide level mutagenesis in addition to inducing gross chromosomal alterations, broadening its potential role in genome instability.

overall_design:
The arrays in this series are primary comparative genomic hybridizations to determine genomic changes after re-replication or other genomic stresses. Genomic DNA was purified from reference Saccharomyces cerevisiae cells or survivors of re-replication or other genomic stresses, differentially labeled with Cy3 and Cy5, and competitively hybridized to a spotted microarray containing ORF and intergenic PCR products. Cy5/Cy3 ratios are normalized so that the average ratio of all elements was 1. A small number of the arrays were used to determine the extent and location of re-replication under different conditions. For those, genomic DNA was purified from non-replicating and re-replicating cells. Series contains a total of 12 hybridizations. 90% of the re-replicating DNA preparation and 1 µg of the reference DNA were labeled, respectively, with Cy3 and Cy5 fluorescent dye (Fisher Scientific 45-001-270).  Arrays were then scanned using an Axon Scanner 4B.  GenePix Pro6.0 and BatchReplicationAnalyzer4.2 were then used to generate copy number information across the genome.
More information on the strains used in this study is available in the file Strains_GEO_submission.xlsx available at the foot of this page.

first: Duyen

middle: T

first: Joachim

middle: J

last: Li


title: Mouse ES Cells: Wild type vs. Zscan5b knockout

city: Tokyo

first: Seiji

last: Ogawa

country: Japan

institute: Keio University

summary: Transcriptional profiling of mouse embryonic stem cells comparing control untreated ES cells with Zscan5b knockout ES cells

overall_design: Two-condition experiment, Wild type ES vs. Zscan5b knockout ES cells. Biological replicates: 3 wild type replicates, 3 Zscan5b knockout replicates.

first: Mitsutoshi

last: Yamada


title: Transcriptome wide gene expression analysis with inducible silencing of YY1 in AW8507 oral cancer cells

status: Public on Jan 19 2019

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: In order to study the role of the transcription factor YY1 in oral cancer progression, transcriptome wide gene expression analysis was performed with inducible silencing of YY1 in a grade III, tongue derived oral cancer cell line, AW8507 (Established and characterized by Tatake RJ et al. 1990) stable for tet-ON-shYY1.

overall_design: AW8507 cells were transfected with TRIPZ-tet-ON-shYY1 plasmid and tet-ON-shYY1 stable cells were obtained by selection with puromycin followed by FACS for RFP positivity. The AW8507 cells stable for tet-ON-shYY1 were treated with doxycycline to induce tet-ON system, therefore expression of shRNA against YY1, which resulted in silencing of YY1 mRNA (Confirmed by qRT-PCR). Total RNA was isolated from control and doxycycline group and transcriptome wide gene expression changes were analyzed via microarray based approach.

first: Amit

middle: K

last: Behera

first: Madavan

last: Vasudevan

first: Tapas

last: Kundu


title: Genome-wide transcriptional profiles of Kupffer cells and alveolar macrophages from naïve and LPS-injected mice

city: Seongnam-si

first: Daun

last: Jung

state: Gyeonggi-do

address: Bundang-gu, 삼평동 689

department: Department of Pathology

country: South Korea

institute: CHA Bundang Medical Center

summary: To reveal early responses to one of septic agents, lipopolysaccharide (LPS), in tissue resident macrophages, we isolated Kupffer cells as well as alveolar macrophages from bolus LPS-injected mice at 1 and 4 hours (hr) of early time points and performed quantitative RNA sequencing

overall_design: mRNA profiles of Kupffer cells and alveolar macrophages from naïve and LPS-injected mice were generated by sequencing, in triplicate, using NextSeq 500 (Illumina, Inc., USA)

first: Yirang


title: Long non-coding RNAs discriminate the stages and gene regulatory states of the human humoral immune response

status: Public on Jan 17 2019

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: human tonsilar naïve and germinal center B cells and diffuse large B cell lymohoma cell lines

overall_design: Genome-wide ChIPseq binding sites in human tonsilar Naïve and Germinal Center B cells and GCB derived cell lines

middle: S

first: Ari

last: Melnick

first: Cem

last: Meydan


title: Universal correction of blood coagulation factor VIII in patient-derived induced pluripotent stem cells using CRISPR/Cas9

status: Public on Jan 05 2019

city: Seoul

first: Chul-Yong

last: Park

address: Yonsei-ro 50-1

department: Physiology

institute: Yonsei University

summary:
Confirmation of the nuclease acivities at the On- and Off-target sites;
Hemophilia A (HA) is caused by genetic mutations in the blood coagulation factor VIII (FVIII). Genome editing approaches can be used to target the mutated site itself in patient-derived induced pluripotent stem cells (iPSCs). However, these approaches can be hampered by difficulty preparing thousands of editing platforms for each corresponding variant found in HA patients. Here, we report a universal approach to correct the various mutations in HA patient iPSCs by the targeted insertion of the FVIII gene into the human H11 site via CRISPR/Cas9. We derived corrected clones from two types of patient iPSCs with frequencies of up to 64% and 66%, respectively, without detectable unwanted off-target mutations. Moreover, we demonstrated that endothelial cells differentiated from the corrected iPSCs successfully secreted functional protein in vitro and functionally rescued the disease phenotype in vivo. This strategy may provide a universal therapeutic method for correcting all genetic variants found in HA patients.

overall_design: Triplicate samples are analyzed in the HEK293 cells. Single sample is analyzed in the iPSCs.

first: Dong-Wook

last: Kim


title: Genome-wide transcriptomic analysis of Arabdiopsis mutants controling nuclear size in comparison to the wildtype

status: Public on Jan 14 2019

city: Norwich

first: Pawel

last: Mikulski

address: Colney Lane

department: CDB

country: United Kingdom

institute: John Innes Centre

summary: We report genome-wide transcriptomic profile of 2 week-old Arabidopsis seedlings from pwo1 and crwn1 crwn2 mutants in comparison to the wildtype (Col-0)

overall_design: Arabidopsis thaliana seedlings of Col-0, pwo1 and crwn1 crwn2 were grown vertically on MS plates in long-day conditions for 2 weeks. Afterwards, RNA from 3 biological replicates per genotype was isolated using RNeasy Plant Mini Kit (Qiagen) and NGS library created using TruSeq RNA Library Prep Kit v2 (Illumina). Paired-end sequencing was performed on HiSeq 2500 platform (Illumina).

first: Daniel

last: Schubert


title: ChIP-seq in human tonsilar Naïve and Germinal Center B cells and DLBCL cell lines

status: Public on Jan 16 2019


title: Infiltrating monocyte-derived macrophages polarizes in to anti-inflammatory and neuro-protective phenotype in a rat model of cerebral ischemia

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: To summarize our results, we found microglia and MDMs are functionally heterogeneous population contributing differently to the disease phenotype. Our data, suggest that during post-ischemic inflammation microglia exhibit pro-inflammatory phenotype, while infiltrating MDMs display anti-inflammatory and neuro-protective phenotype. Apart from up-regulation of some of the classical M2 marker in MDMs, our gene expression profiling using RNA-sequencing revealed a unique signature of MDMs with the up-regulation of genes associated with wound healing, MHCII antigen-presentation and tissue repair. Our results strongly suggest that MDMs infiltrating the CNS parenchyma during the sub-acute of post-ischemic inflammation might contribute to the endogenous mechanism of neuroprotection.

overall_design: RNAseq profilling of sorted microglia and macrophages after MCAO compared to sham

first: Wenson

last: Karunakaran


title: Peripheral Blood Transcriptomic and miRNA Transcriptomic Analyses for Salmonella Infection in Pig

status: Public on Jan 03 2019

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

type: Non-coding RNA profiling by high throughput sequencing


title: Analysis of SOD1 binding sites by next generation sequencing under different redox environments

status: Public on Dec 20 2018

city: Wuhan

first: Xiang

last: Li

state: Hubei

address: No.152 Luoyu Road

department: School of Chemistry

institute: Central China Normal University

summary: We report the application of ChIP-Seq technology for analyzing the DNA binding sites of SOD1 in the nucleus of HeLa cells. By obtaining a plenty of sequence from chromatin immunoprecipitated DNA, we generated genome-wide DNA binding sites of SOD1. After sequencing of ChIP samples, 42,737,195, 49,950,032, and 38,825,768 clean reads for control group, H2O2 treated group and LD100 (a specific inhibitor of SOD1) treated group were obtained through trimming the raw reads. We find that SOD1 occupies DNA sites with distinct sequence preference in the nucleus. The treatment with either H2O2 or LD100 was found to decrease the strength of SOD1 binding to DNA, indicating that the H2O2 exposure- or SOD1 inhibition-mediated redox dyshomeostasis may result in decreased genes that are reasonably regulated through alteration of SOD1 structures compared to control.

overall_design: Examination of SOD1 binding to DNA in the nucleus under different redox conditions

first: Changlin

last: Liu


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of DTA-1 treatment on sorted mouse adipose tissue ILC2 Transcriptomes

city: Los Angeles

first: Lauriane

last: Galle

state: California

address: 1450 Biggy Street NRT 5509

institute: University of Southern California

summary: Metabolic syndrome is characterized by disturbances in glucose homeostasis and the development of low-grade systemic inflammation, which increase the risk to develop type-2 diabetes mellitus (T2DM). Type-2 innate lymphoid cells (ILC2s) are a recently discovered immune population secreting Th2-cytokines. While previous studies show how ILC2s can play a critical role in the regulation of metabolic homeostasis in the adipose tissue, a therapeutic target capable of modulating ILC2 activation has yet to be identified. Here, we show that GITR, a member of the TNF superfamily, is expressed on both murine and human ILC2s. Strikingly, we demonstrate that GITR engagement of activated, but not naïve, ILC2s improves glucose homeostasis, resulting in both protection against insulin-resistance onset and amelioration of established insulin-resistance. Together, these results highlight the critical role of GITR as a novel therapeutic molecule against T2DM and its fundamental role as an immune checkpoint for activated ILC2s.

overall_design: mRNA profiles of sorted mouse adipose tissue ILC2s treated either with the isotype control or DTA-1 were generated by deep sequencing, in triplicate, using a NextSeq 500 (Illumina) system.

last: Galle-Treger

first: Benjamin

middle: P

last: Hurrell


title: Differential requirement for centriolar satellites in cilium formation and ciliary signaling among different vertebrate cells

status: Public on Nov 28 2018

city: Istanbul

first: seref

last: gul

address: Yalikoy Mh., Beykoz

department: Institute of Life Sciences and Biotechnology

country: Turkey

institute: Bezmialem Vakif University

summary: Centriolar satellites are an array of membrane-less granules that localize and  move around the vertebrate centrosome/cilium complex. They have recently  emerged as key regulators of the biogenesis and function of the  centrosome/cilium-complex and their mutations are linked to ciliopathies.  Although centriolar satellites are ubiquitous structures of the vertebrate cells,  their precise function and molecular mechanism of action in different cell types  remain poorly understood. Here, we generated kidney and retinal epithelial cells  that lack centriolar satellites by genetically ablating their scaffolding protein  PCM1 and investigated the cellular and molecular consequences of satellite loss  in cells. We showed that centriolar satellites are required for cilium assembly,  regulation of ciliary content, timely response to Hedgehog signals and three-  dimensional epithelial cell organization, but not for cell proliferation, cell cycle  progression and centriole duplication. Importantly, the requirement for centriolar  satellites in cilium assembly varied between retinal and kidney epithelial cells and  we identified the differences in the efficiency of targeting key ciliogenesis factors  to the centrosome including Mib1 and Talpid3 as the likely molecular basis for  this phenotypic variability. Quantitative global transcriptomic and proteomic  profiling of satellite-less cells showed that loss of centriolar satellites does not  lead to a major transcriptional response, but leads to a significant rearrangement  of the global proteome. Together, our findings identify important roles for  centriolar satellites in key cilium-related cellular processes through regulating the  proteostasis and centrosomal/ciliary targeting of proteins and provide insight into  the disease mechanisms of ciliopathies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed global transcriptome analysis of wild type (WT) and PCM1 knock-out cells by using two different cells: human RPE1, and mouse IMCD3 cells. Deep sequencing technique was utilized via  illumina HiSeq4000 platfrom in two biological replicates for each condition.

first: S

last: Gul

first: I

middle: H

last: Kavakli


title: Open chromatin profiling in adipose tissue marks genomic regions with functional roles in cardiometabolic traits

city: Chapel Hill

first: Karen

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary:
Identifying the regulatory mechanisms of genome-wide association study (GWAS) loci affecting adipose tissue has been restricted due to limited characterization
of adipose transcriptional regulatory elements. We profiled chromatin accessibility in three frozen human subcutaneous adipose tissue needle biopsies and
preadipocytes and adipocytes from the Simpson Golabi-Behmel Syndrome (SGBS) cell strain using an assay for transposase-accessible chromatin (ATAC-seq).
We identified 68,571 representative accessible chromatin regions (peaks) across adipose tissue samples (FDR<5%). GWAS loci for eight cardiometabolic traits
were enriched in these peaks (p<0.005), with the strongest enrichment for waist-hip ratio. Of 110 recently described cardiometabolic GWAS loci colocalized
with adipose tissue eQTLs, 59 loci had one or more variants overlapping an adipose tissue peak. Annotated variants at the SNX10 waist-hip ratio locus and
the ATP2A1-SH2B1 body mass index locus showed allelic differences in regulatory assays. These adipose tissue accessible chromatin regions elucidate genetic
variants that may alter adipose tissue function to impact cardiometabolic traits.

overall_design:
ATAC-seq on adipose tissue from three individuals from the METSIM study and two replicates of SGBS preadipocytes and three replicates of differentiated SGBS adipocytes

Authors' note:
Please note that the METSIM study does not allow unrestricted access to fastq files and other files that allow individual identity to be determined.
Therefore, the raw data for the adipose tissue ATAC-seq samples will be submitted to dbGaP where researchers can request access to them.
We do have permission to share ATAC-seq peaks and bigWig signal tracks because it is not possible to identify an individual from these files.

first: Maren

middle: E

last: Cannon

first: Kevin

middle: W

last: Currin

first: Kristin

last: Young

first: Hannah

last: Perrin

first: Swarooparani

last: Vadlamudi

first: Alexias

last: Safi

first: Lingyun

last: Song

first: Ying

last: Wu

first: Martin

last: Wabitsch

first: Markku

last: Laakso

first: Gregory

last: Crawford


title: SW480 cells undergoes postmitotic neuron-like differentiation in response to EZH2 knockdown

city: Nanjing

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

summary:
Formerly we found that combined inhibition of class I HDACs, DNMTs, EZH2 and LSD1 with chemical inhibitors in a variety of cancer cells caused neuronal differentiation. Our recent study demonstrated that functional knockdown of EZH2 alone in SW480 cells can also lead to significant neuronal differentiation.
We used microarray to analyze global gene expression change in SW480 cells after neuronal differentiation induced by EZH2 knockdown.

overall_design: EZH2 function was blocked in SW480 cells via shRNA knockdown. Cells underwent significant morphological change after 6 days of EZH2 knockdown, as compared control SW480 cells that was infected with lentivirus carrying empty vector. Control and EZH2 knockdown cells were then collected and subjected to microassay analysis. Two samples, one was control SW480 cells and the other was SW480 cells with EZH2 knockdown, were used for microarray assay.

first: Anhua

last: Lei


title: Next generation sequencing reveals no change in mtDNA deletions upon the loss of mitochondrial fusion in mouse hearts

status: Public on Dec 28 2018

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

summary:
Aim: To determine whether mtDNA deletions arise upon the loss of mitochondria fusion in heart tissue
Method: DNA was isolated heart mitochondria from control and heart-specific double mitofusin1-2 (dMfn) KO animals and used to generate libraries for sequencing to detect mtDNA deletions. Total genomic DNA from the Deletor mouse was provided by Anu Suomalainen-Wartiovaara and used as a positive control for the detection of mtDNA rearrangements. A standard Illumina TrueSeq paired-end library was prepared with ~500 base pair fragment inserts. Paired-end 100 base pair sequencing was conducted using an Illumina HiSeq 2500. The reads were mapped to the genomic sequence without the mitochondria using bowtie (VN: 2.1.0) to remove nuclear-genomic sequences. The unmapped reads were then mapped to the mitochondrial sequence (GenBank JF286601.1) using bwa (n=0.04, VN: 0.6.2-r126)  with unmapped reads undergoing an additional mapping round after trimming fastx_trimmer, VN: 0.0.13.2) to ensure higher mapping results. Using samtools (VN: 1.0: samtools –f1 –F14) reads, where the two paired sequences were observed to be greater than 600 base pair apart were identified as those containing deletion breakpoints. These reads were extracted for additional analysis.
Results: Control and dMfn KO samples showed similar frequencys of breakpoints, while the positive control (Deletor mouse) showed a high frequecny of large breakpoints.

overall_design: Heart DNA from littermate control (3 replicates), dMfn KO (3 replicates), Deletor mouse as positive control (1 replicate)

first: Arnaud

last: Mourier


title: Expression data from retinoic acid-sufficient and retinoic acid-deficient mouse airway smooth muscle [mouse ASMs]

status: Public on Dec 25 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Observational studies in human suggest involvement of vitamin A/retinoic acid (RA) signaling in the regulation of airway smooth muscle (ASM) function, but the precise mechanisms by which RA impacts ASM phenotype is not clear.  Here, we generated trascriptional profiles from two different models of RA-sufficient and RA-deficient mouse ASM in order to determine the molecular targets of RA in ASM (VAS/VAD, CTR/BMS)
Mouse ASMs were isolated from Acta2-hrGFP;Cspg4-DsRED adult mice using flow cytometry.  VAS mice were given normal, vitamin A-sufficient diet (15 IU vitamin/g) while the VAD mice were given 3 days of vitamin A-deficient diet (< 0.1 IU vitamin/g).  CTR/BMS mouse ASMs were also isolated from Acta2-hrGFP;Cspg4-DsRED adult mice using flow cytometry.  CTR mice were given 3 days of powdered, vitamin A sufficient diet mixed with vehicles (corn oil) while the BMS diet were given 3 days of powdered, vitamin A sufficient diet mixed with a potent pan-RA-receptor antagonist (BMS, 5 mcg/g).

overall_design: Mouse ASMs from 3 mice in each experimental condition were collected and pooled for microarray analysis.

first: Felicia

last: Chen


title: Knock-down of phosphoserine phosphatase gene effects rather N- than S-metabolism in Arabidopsis thaliana

status: Public on Dec 26 2018

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: Elucidating the relative contribution of three serine biosynthesis pathways, i.e. (i) the glycolate pathway, (ii) the phosphorylated pathway and (iii) the glycerate pathway.

overall_design: Arabidopsis thaliana plants [Wildtype Col-0 and three mutant lines in Col-0 background: (i) bou (At5g46800), (ii) psp17, (iii) psp18 (both: At1g18640)] were grown in biological triplicates under high CO2 (3000 ppm) for 35 days, 12 hr light / 12 hr dark and then shifted to ambient CO2 24 hours before harvesting. Samples for RNASeq were taken two hours before (“end of night”, EON) and two hours after (“beginning of day”, BOD) the onset of light.

first: Sladja

last: Samuilov

first: Nadine

last: Rademacher

first: Dominik

last: Brilhaus

first: Tabea-Mettler

last: Altmann

first: Marion

last: Eisenhut

first: Heinz

last: Rennenberg


title: Expression data from retinoic acid-sufficient and retinoic acid-deficient human airway smooth muscle [human primary ASMs]

summary: Observational studies in human suggest involvement of vitamin A/retinoic acid (RA) signaling in the regulation of airway smooth muscle (ASM) function, but the precise mechanisms by which RA impacts ASM phenotype is not clear.  Here, we generated trascriptional profiles from primary human ASM from 3 unrelated donoros cultured in control medium or medium containing BMS493 (an retinoic acid receptor antagonist)

overall_design: Human primary ASMs from 3 unrelated donors were cultured in control medium, BMS-containing medium (1 micromolar) and DEAB-containing medium (10 micromolar) for 24 hours prior to the extraction of RNA for transcriptional profile analysis.


title: Global expression profiling of osteogenic differeintiation with retinoic acid or without retinoic acid for two days from hiPSC

status: Public on Dec 21 2018

city: Kyoto

first: Hiroyuki

last: Yoshitomi

address: 53, Kawahara-Cho, Shogoin,

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

summary: Comparison of gene expressions among osteogenic differentiated cells with retinoic acid, those without retinoic acid and cells before induction

overall_design: Osteogenic differentiation from hiPSC with or without retinoic acid

first: J

last: Toguchida

first: H

first: S

last: Kawai


title: Aberrant transcriptomes and DNA methylomes define pathways that drive pathogenesis and loss of brain laterality/asymmetry in schizophrenia and bipolar disorder [Illumina]

status: Public on Nov 26 2018

summary: Although the loss or reversal of brain laterality is one of the most consistent modalities in schizophrenia (SCZ) and bipolar disorder (BD), its molecular basis remains elusive. Our limited previous studies indicated that epigenetic modifications are key to the asymmetric transcriptomes of brain hemispheres. We used whole-genome expression microarrays to profile post-mortem brain samples from subjects with SCZ, psychotic BD [BD(+)] or non-psychotic BD [BD(-)], or matched controls (n=10/group, corresponding to different brain hemispheres) and performed whole-genome DNA methylation (DNAM) profiling of the same samples (n=3-4/group) to identify pathways associated with SCZ or BD(+) and genes/sites susceptible to epigenetic regulation. qRT-PCR and quantitative DNAM analysis were employed to validate findings in larger sample sets (n=35/group). Gene Set Enrichment Analysis (GSEA) demonstrated that BMP signaling and astrocyte and cerebral cortex development are significantly (FDR q<0.25) coordinately upregulated in both SCZ and BD(+), and glutamate signaling and TGFβ signaling are significantly coordinately upregulated in SCZ. GSEA also indicated that collagens are downregulated in right versus left brain of controls, but not in SCZ or BD(+) patients, and Ingenuity Pathway Analysis predicted that TGFB2 is an upstream regulator of these genes (p=0.0012). While lateralized expression of TGFB2 in controls (p=0.017) is associated with a corresponding change in DNAM (p≤0.023), lateralized expression and DNAM of TGFB2 are absent in SCZ or BD. Loss or reversal of brain laterality in SCZ and BD corresponds to aberrant epigenetic regulation of TGFB2 and changes in TGFβ signaling, indicating potential avenues for disease prevention/treatment.

overall_design: RNA samples were extracted from the dissects of post-mortem brains (Brodmann’s area 46, dorsolateral prefrontal cortex) of patients with SCZ or BD or control subjects (n=35 per group), obtained from the Stanley Medical Research Center (SMRC). The samples used in the analysis were matched for sex, ethnicity, brain laterality, age and other demographics.  A subset of n=10 samples per group were used for gene expression profiling.

first: Hamid

last: Abdolmaleky

first: Sam

last: Thiagalingam


title: Mild traumatic brain injury in mice beneficially alters structural and metabolic protein expression in mouse lung to enhance survival after Pseudomonas aeruginosa infection

status: Public on Nov 08 2018

summary:
Female ICR mice 6-8 weeks old and weighing 23-28 grams received a mild traumatic brain injury via weight drop model.
48 hours after trauma, the mice were sacrificed and RNA was extracted from lungs to examine what pulmonary gene expression changes may have been triggered by the brain injury using microarray analysis.

overall_design: RNA is extracted from mouse lung 48 hours after a traumatic brain injury to see what changes may have been illicited by the trauma.

first: Max

last: Vaickus

first: Daniel

last: Remick


title: The extent of liver injury determines hepatocyte fate toward senescence or cancer

city: Shanghai

first: Pu

last: You

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: Induction of hepatocyte senescence is known to inhibit hepatocellular carcinoma (HCC). Until now, it has not been clear how the degree of liver injury dictates hepatocyte senescence and carcinogenesis. In this study, we investigated whether the severity of injury determines cell fate decisions between hepatocyte senescence and carcinogenesis. After testing of different degrees of liver injury, we found that hepatocyte senescence is strongly induced in the setting of severe acute liver injury. Longer-term, moderate liver injury did not result into hepatocyte senescence, but instead led to a significant incidence of HCC. In addition, carcinogenesis was significantly reduced by the induction of severe acute injury after chronic moderate liver injury. We conclude that severe acute liver injury leads to hepatocyte senescence along with a low incidence of HCC, whereas chronic moderate injury allows hepatocytes to proliferate rather than to enter into senescence, and correlates with a high incidence of HCC. This study improves our understanding in hepatocyte cell fate decisions and suggests a potential clinical strategy to induce senescence to treat HCC.

overall_design: moderate chronic liver injury for 8 weeks or 12 weeks or moderate chronic liver injury for 8 weeks plus severe liver injury 4 weeks

first: Chao

last: Wang


title: Next-Generation Sequencing of Human Mitochondrial DNA (mtDNA) from Postmortem Brain and Blood

status: Public on Nov 01 2018

city: Irvine

first: Brooke

middle: E.

last: Hjelm

address: 837 Health Sciences Rd

department: Department of Psychiatry and Human Behavior

institute: University of California, Irvine

type: Genome variation profiling by high throughput sequencing

summary:
Purpose: To develop a pipeline (Splice-Break) for high-resolution quantification of mtDNA deletions, provide a catalogue of human mtDNA deletion breakpoints, and evaluate mtDNA deletions in brains from subjects with psychiatric disorders.
Methods: 93 samples from human postmortem brain and blood were obtained from the Southwest Brain Bank (SBB) and University of California, Irvine (UCI) Brain Bank. Total DNA was extracted from frozen homogenate tissue and mtDNA was amplified/enriched using a single long-range PCR. Mitochondrial amplicons were purified by bead purification to retain both wild-type and deleted molecules (i.e., no gel excision was performed). mtDNA-enriched PCR amplicons were prepared for sequencing using standard Illumina protocols for DNA. Samples were sequenced 150-mer paired-end reads, in multiplex (96x per lane), on an unpatterned flowcell (HiSeq 2500). Fastq files were processed using our Splice-Break pipeline for the detection and relative quantification of mtDNA deletions.
Results: A catalogue of 4,489 putative mitochondrial DNA (mtDNA) deletions, including their frequency and relative read rate, was produced. Analyses of 93 samples from postmortem brain and blood found 1) the 4,977bp “common deletion” was neither the most frequent deletion nor the most abundant; 2) brain contained significantly more mtDNA deletions than blood; 3) many high frequency deletions were previously reported in MitoBreak, suggesting they are present at low levels in metabolically active tissues and are not exclusive to individuals with diagnosed mitochondrial pathologies; 4) many individual deletions (and cumulative deletion metrics) had significant and positive correlations with age; and 5) the highest deletion burdens were observed in a subset of subjects with major depressive disorder (MDD), and these subjects had mtDNA deletion levels at or above those detected in typical deletion pathologies (e.g., Kearns-Sayre syndrome (KSS) muscle).
Conclusions: Collectively, these data suggest the Splice-Break pipeline can detect and quantify mtDNA deletions at a high level of resolution.

overall_design: 93 samples from human postmortem brain and blood are from 41 subjects with and without psychiatric diagnoses. SBB samples include paired anterior cingulate cortex (ACC) and dorsolateral prefrontal cortex (DLPFC) from 32 subjects. UCI samples include paired DLPFC and BLOOD samples from 9 subjects, 3 of which also had additional brain regions of the ACC, caudate nucleus (CAUN), hippocampus (HIPP), and putamen (PUT) evaluated.

first: Brandi

last: Rollins

first: Peter

middle: M

last: Thompson

first: Marquis

last: Vawter


title: Effect of Ikaros deletion on gene expression in CD4 T cells

status: Public on Dec 12 2018

first: Boston University

last: Microarray and Sequencing Resource

summary: The goal of this experiment is to define how lack of Ikaros impacts gene expression in mature CD4 T cells, both in the resting and activated state. To do this, a conditional knockout mouse model was generated using Cre/lox technology. The floxed allele was designed such that the last translated exon and 3' UTR of the Ikaros gene (Ikzf1) are deleted in mature T cells (mediated by distal Lck-driven Cre). CD4 T cells from mice with floxed alleles that did not express Cre (Cre-) and those that did express Cre (Cre+) were analyzed.

overall_design: The experiment is comprised of 12 Mouse Gene 2.0 ST arrays, profiling CD4+ T cells isolated from the spleens of Cre- and Cre+ mice. The cells were either left untreated or activated for 24 hours with plate bound anti-CD3 and soluble anti-CD28. Each experimental group is represented in triplicate.

first: Susan

last: Winandy


title: RNA-seq of WT and Nocturnin knockout A549 cells

status: Public on Dec 08 2018

city: Princeton

first: Alexei

last: Korennykh

state: New Jersey

address: 216 Shultz Laboratory

department: Molecular Biology

institute: Princeton University

summary: mRNA regulation by the circadian protein Nocturnin in A549 cells.

overall_design: Total RNA from WT and NOCT KO A549 cells were subject to poly-A pulldown and RNA-seq.

first: Du

last: Jin

first: Chitrakar

last: Alisha

first: Prangley

last: Eliza

first: Korennykh

last: Alexei


title: Knockdown of GRHL2 affects active enhancers (H3K27ac sites) enriched for ER binding

status: Public on Dec 07 2018

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

summary: Differential ChIP-Seq data monitoring changes in active enhancer marks (H3K27ac sites) after treatment with siGRHL2 in MCF7 and T47D breast cancer models. Comparing sites altered by treatment with siGRHL2 after 48hours revealed these sites to be enriched for Estrogen Receptor (ER) binding.

overall_design: ChIP-seq data monitoring H3K27ac in MCF7 and T47D cells after treatment with siGRHL2 and siCTRL for 48 hours.

middle: N

first: Florian

last: Markowetz


title: Transcriptome analysis of PPN1 knock-out and overproducing yeast strains grown in control and manganese excess media

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: We report RNA-Seq data of S.cerevisiae PPN1 knock-out yeast strain and PPN1 overproducing transformant yeast strain grown to logarithmic stage in control medium and in the medium containing 5mM manganese.

overall_design: Yeast were grown to logarithmic growth stage in control YPD medium and in YPD medium with 5 mM MnSO4.

first: Tatiana

last: Kulakovskaya

first: Alexey

last: Penin


title: Expression data from mouse atrial Angiotensin II treated for 0,1,2,3 weeks

status: Public on Oct 20 2018

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
AF is characterized by structural and electrical remodeling, including atrial enlargement, fibrosis, inflammation, and ion-channel alteration, which frequently results in arrhythmia recurrence and maintenance.However, the gene expression profiles signaling pathways in the atria during the development of AF induced by Ang II remain unknown
All mice were infused with Ang II (2000 ng/kg/min) using an osmotic pump for 1, 2 and 3 weeks. At the end of Ang II infusion, intracardiac pacing was performed in these animals by inserting an eight-electrode catheter (1.1 F, octapolar EP catheter, Science) through the jugular vein and advancing it into the right atrium and ventricle.

overall_design: All mice were euthanized by an overdose of pentobarbital on weeks 1, 2 and 3 of  Angiotensin II  treatment. Total RNA was isolated with TRIzol (Invitrogen) from atrials (n=4 per group) at each time point according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix GeneChip mouse Genome 430 2.0 array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). On the GeneChip Mouse Genome 430 2.0 Array, over 45,000 probe sets analyze the expression level of over 39,000 transcripts and variants from over 34,000 well characterized mouse genes.

first: Yu-Xuan

last: Wu


title: All-RNA-seq data used in "Genetic resistance to DEHP-induced transgenerational endocrine disruption"

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

summary: We Investigate the persistence of negative impacts on sperm parameters for more than one generation in C57BL/6J and in strain FVB/N subjected to prenatal exposure to di(2-ethylexyl)phthalate (DEHP) using in utero exposures followed by Computer-Aided Sperm Analysis (CASA)  sampling and all-RNA-seq analysis of germ cells transcripts.

overall_design: Pairwise comparisons and hierarchical clustering of: 1) 5 mouse C57BL/6J of the first generation that were exposed in utero to corn oil vehicle (C57.CTL.F1), 2) 5 mouse C57BL/6J of the first generation that were exposed in utero to DEHP (C57.D300.F1),  3) 5 mouse C57BL/6J of the second generation (C57.D300.2), 4) 5 mouse FVB/N of the first generation that were exposed in utero to corn oil vehicle (FVB.CTL.F1), 5) 5 mouse FVB/N of the first generation that were exposed in utero to DEHP (FVB.D300.F1).

first: Rita

last: Rahban

first: Julien

last: Prados

first: Serge

last: Nef

first: Ariane

last: Paoloni-Giacobino


title: Derivation and characterization of putative craniofacial mesenchymal stromal cells from human induced pluripotent stem cells

status: Public on Oct 22 2018

first: Boston University

last: Microarray and Sequencing Resource

summary:
The introduction and widespread adoption of induced pluripotent stem cell (iPSC) technology has opened new avenues for craniofacial regenerative medicine. Neural crest cells (NCCs) are the precursor population to many craniofacial structures, including dental and periodontal structures, and iPSC-derived NCCs may, in the near future, offer an unlimited supply of patient-specific cells for craniofacial repair interventions.
Here, we used an established protocol involving simultaneous Wnt signaling activation and TGF-β signaling inhibition to differentiate three human iPSC lines to cranial NCCs. We then derived a putative craniofacial mesenchymal progenitor (PCMP) population with chondrogenic and osteogenic potential from cranial NCCs and investigated their similarity to widely studied human postnatal dental or periodontal stem/progenitor cells. PCMPs were quite distinct from both their precursor cells (NCCs) and bone-marrow mesenchymal stromal cells, a stromal population of mesodermal origin. Despite their similarity with dental stem/progenitor cells, PCMPS were clearly differentiated by a core set of 66 genes, including ACKR3 (CXCR7), whose expression (both at transcript and protein level) appear to be peculiar to PCMPs. Altogether, our data demonstrate the feasibility of craniofacial mesenchymal progenitor derivation from human iPSCs through a neural crest-intermediate and set the foundation for future studies regarding their full differentiation repertoire and their in vivo existence.

overall_design: We performed microarray analysis of triplicate samples for six different human cell populations, namely human iPSC-derived neural crest cells (NCCs), human NCC-derived putative craniofacial mesenchymal progenitors (PCMPs), stem cells of the apical papilla (SCAP), dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs).

first: Mohamed

last: Jamal

first: Laertis

last: Ikonomou


title: Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons

status: Public on Oct 13 2018

city: New York City

first: Felix

last: Richter

address: 1470 Madison Ave, New York, NY 10029

institute: Icahn School of Medicine at Mount Sinai

summary: Isolation of cell populations is untangling complex biological interactions, but studies comparing methodologies lack in vivo complexity and draw limited conclusions about the types of transcripts identified by each technique. Furthermore, few studies compare FACS-based techniques to ribosomal affinity purification, and none do so genome-wide. We addressed this gap by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification in the context of D1 or D2 dopamine receptor-expressing medium spiny neuron (MSN) subtypes of the nucleus accumbens (NAc), a key brain reward region. We find that nuclear-FACS-seq generates a substantially longer list of differentially expressed genes between these cell types, and a significantly larger number of neuropsychiatric GWAS hits than the other two methods. RiboTag-seq has much lower coverage of the transcriptome than the other methods, but very efficiently distinguishes D1- and D2-MSNs. We also demonstrate differences between D1- and D2-MSNs with respect to RNA localization, suggesting fundamental cell type differences in mechanisms of transcriptional regulation and subcellular transport of RNAs. Together, these findings guide the field in selecting the RNAseq method that best suits the scientific questions under investigation.

overall_design: Forty-nine samples constituting 39 samples from male mice: 16 whole cell-FACS (D1 n=9, D2 n=7), 11 nuclear-FACS (D1 n=6, D2 n=5), and 12 RiboTag (D1 n=6, D2 n=6), and 10 samples from female mice (D1 n=5, D2 n=5).

first: Hope

last: Kronman

first: Benoit

last: Labonté

first: Ramesh

last: Chandra

first: Shan

last: Zhao

first: Gabriel

last: Hoffman

first: Mary

last: Lobo

first: Eric

last: Schadt

last: Nestler


title: The impact of DSF and C23 on P. aeruginosa physiology

status: Public on Sep 30 2018

city: Belfast

first: Shi-qi

last: An

address: Lisburn Road

institute: Queen's University Belfast

summary:
To verify the imapct of DSF and C23 on P. aeruginosa during infection
We used microarray to compare the effects of adding either DSF alone or DSF with C23 on P. aeruginosa gene expression during mouse lung infection relative to the gene expression of P. aeruginosa in the mouse lung with no compound.

overall_design: For the in vivo RNA samples, infected animals as described above were euthanized 24 h post-infection. RNA was isolated from airway homogenate pellets using Trizol according to the manufacturer's instructions. Samples were treated with DNAse, then rRNA was removed from 1 to 5 μg of total RNA using the RiboZero kit for Gram-negative bacteria (Epicentre). rRNA-depleted samples were concentrated by EtOH precipitation. cDNA synthesis and hybridization to Affymetrix GeneChip P. aeruginosa genome arrays.


title: Aberrant transcriptomes and DNA methylomes define pathways that drive pathogenesis and loss of brain laterality/asymmetry in schizophrenia and bipolar disorder

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

overall_design: Refer to individual Series


title: A core set of venom proteins are secreted by entomopathogenic nematodes in the genus Steinernema

first: Ali

last: Mortazavi

address: 2300 E biological science 3

institute: University of California Irvine

summary: We investigated the transcriptional profiles of individual Stienernema feltiae nematodes from in vivo infections and compared them to the profiles of individuals exposed to insect tissue in vitro.

overall_design: Examination of individual Steirnenema feltiae nematodes exposed either to homogenate of the waxworm Galleria mellonella for certain lengths of time or directly dissected out of G. mellonella after infecting them for certain lengths of time.

first: Dennis

last: Chang

first: Lorrayne

last: Serra

first: Dihong

last: Lu

first: Adler

middle: R

last: Dillman


title: Glucocorticoids inhibit macrophage differentiation towards a pro-inflammatory phenotype upon wounding without affecting their migration

status: Public on Nov 17 2018

city: Leiden

first: Yufei

last: Xie

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

summary: Glucocorticoid drugs are widely used to treat immune-related diseases, but their use is limited by side effects and by resistance, which especially occurs in macrophage-dominated diseases. In order to improve glucocorticoid therapies, more research is required into the mechanisms of glucocorticoid action. In the present study, we have used a zebrafish model for inflammation to study glucocorticoid effects on the innate immune response. In zebrafish larvae, the migration of neutrophils towards a site of injury is inhibited by the synthetic glucocorticoid beclomethasone, while migration of macrophages is glucocorticoid resistant. RNA sequencing was done on on Fluorescence-Activated Cell Sorting (FACS)-sorted macrophages.The results show that the vast majority of the wounding-induced transcriptional changes in these cells are inhibited by beclomethasone, whereas a small subset is glucocorticoid-insensitive. As a result, beclomethasone decreases the number of macrophages that differentiate towards a pro-inflammatory (M1) phenotype, which we demonstrated using a tnfa:eGFP-F reporter line and analysis of macrophage morphology. We conclude that the glucocorticoid resistance of the wounding-induced macrophage migration is due to the insensitivity of the induction of macrophage-specific chemoattractants to glucocorticoid inhibition, which may explain the relative resistance of macrophage-dominated diseases to glucocorticoid therapy. However, the induction of pro-inflammatory genes in macrophages is strongly attenuated, which inhibits their differentiation to an M1 phenotype.

overall_design: After anesthesia with 0.02% aminobenzoic acid ethyl ester (tricaine, Sigma Aldrich), the tails of 3 days post fertilization (dpf) embryos were partially amputated with a 1mm sapphire blade (World Precision Instruments) on 2% agarose-coated Petri dishes under a Leica M165C stereomicroscope (Chatzopoulou et al., 2016). Amputated and non-amputated (control) embryos were pretreated for 2 hours with 25 μM beclomethasone (Sigma Aldrich) or vehicle (0.05% dimethyl sulfoxide (DMSO)) in egg water prior to amputation and received the same treatment after the amputation. Macrophages were sorted from Tg(mpeg1.4:mCherry-F) embryos as previously described (Rougeot et al., 2014; Zakrzewska et al., 2010) at 4 hours post amputation (hpa). The sorted cells were collected in QIAzol lysis reagent (Qiagen) for RNA isolation. Extracted total RNA was amplified using the SMART-seq V4 kit (Clontech) for sequencing. The RNA seq libraries generated with the SMART-seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides.

first: Sofie

last: Tolmeijer

first: Annemarie

last: Meijer

first: Marcel

last: Schaaf


title: Transcriptomic analysis of acute mitochondrial pyruvate carrier inhibition using UK5099 in ABL prostate cancer cells

status: Public on Nov 11 2018

city: Houston

first: Sean

last: McGuire

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: ABL cells (derivative of LNCaP) were treated with 100µM UK5099 or vehicle (control) for 72 hours, at which time total RNA was collected and analyzed using RNA-sequencing

overall_design: ABL cells, vehicle vs 100µM UK5099, 72 hour treatment in biological triplicate

first: David

middle: A

last: Bader

first: Rui

last: Chen

first: Kimal

last: Rajapakshe

first: Cristian

last: Coarfa


title: Transcriptome of undifferentiated bovine trophoblast cells

status: Public on Nov 13 2018

city: Ithaca

first: Vimal

last: Selvaraj

address: 204 Morrison Hall

department: Animal Science

institute: Cornell University

summary: Quantitative examination of transcripts expressed in bovine blastocyst derived trophoblasts. These data showcase the fundamental physiology of bovine trophectoderm and indicate hallmarks of the self-renewing undifferentiated state akin to trophoblast stem cells described in other species.

overall_design: RNA-sequencing of three independent collections of bovine blastocyst derived trophoblast colonies

first: Viju

last: Pillai


title: Aberrant transcriptomes and DNA methylomes define pathways that drive pathogenesis and loss of brain laterality/asymmetry in schizophrenia and bipolar disorder [Affymetrix]

first: Boston University

last: Microarray and Sequencing Resource

summary: Although the loss or reversal of brain laterality is one of the most consistent modalities in schizophrenia (SCZ) and bipolar disorder (BD), its molecular basis remains elusive. Our limited previous studies indicated that epigenetic modifications are key to the asymmetric transcriptomes of brain hemispheres. We used whole-genome expression microarrays to profile post-mortem brain samples from subjects with SCZ, psychotic BD [BD(+)] or non-psychotic BD [BD(-)], or matched controls (n=10/group, corresponding to different brain hemispheres) and performed whole-genome DNA methylation (DNAM) profiling of the same samples (n=3-4/group) to identify pathways associated with SCZ or BD(+) and genes/sites susceptible to epigenetic regulation. qRT-PCR and quantitative DNAM analysis were employed to validate findings in larger sample sets (n=35/group). Gene Set Enrichment Analysis (GSEA) demonstrated that BMP signaling and astrocyte and cerebral cortex development are significantly (FDR q<0.25) coordinately upregulated in both SCZ and BD(+), and glutamate signaling and TGFβ signaling are significantly coordinately upregulated in SCZ. GSEA also indicated that collagens are downregulated in right versus left brain of controls, but not in SCZ or BD(+) patients, and Ingenuity Pathway Analysis predicted that TGFB2 is an upstream regulator of these genes (p=0.0012). While lateralized expression of TGFB2 in controls (p=0.017) is associated with a corresponding change in DNAM (p≤0.023), lateralized expression and DNAM of TGFB2 are absent in SCZ or BD. Loss or reversal of brain laterality in SCZ and BD corresponds to aberrant epigenetic regulation of TGFB2 and changes in TGFβ signaling, indicating potential avenues for disease prevention/treatment.

overall_design: RNA samples were extracted from the dissects of post-mortem brains (Brodmann’s area 46, dorsolateral prefrontal cortex) of patients with SCZ or BD or control subjects (n=35 per group), obtained from the Stanley Medical Research Center (SMRC). The samples used in the analysis were matched for sex, ethnicity, brain laterality, age and other demographics.  A subset of n=10 samples per group were used for gene expression profiling.

first: Hamid

last: Abdolmaleky

first: Sam

last: Thiagalingam


title: DNase-seq in eWAT, iWAT, and BAT-derived adipocytes.

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we have employed DNase-seq combined with deep sequencing to map and compare DNase hypersensitive sites in in vitro differentiated primary mouse adipocytes isolated from epididymal and inguinal white adipose tissus as well as  brown adipose tissue.

overall_design: Examination of DNA hypersensitive sites in in vitro differentiatied adipocytes isolated from three different adipose depots.

first: Anne

last: Loft

first: Majken

last: Siersbæk

first: Ronni

last: Nielsen


title: Ferret animal model of severe fever with thrombocytopenia syndrome phlebovirus   for human lethal infection and pathogenesis

status: Public on Oct 30 2018

city: Los Angeles

first: Angela

last: Park

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

institute: University of Southern California

summary: Severe fever with thrombocytopenia syndrome phlebovirus (SFTSV), listed in the WHO most dangerous pathogens, has 12-30% fatality rates with a characteristic thrombocytopenia syndrome. With a majority of clinically diagnosed SFTSV patients older than ~50 years, age is a critical risk factor for SFTSV morbidity and mortality. Here, we report an age-dependent ferret model of SFTSV infection and pathogenesis that fully recapitulates the clinical manifestations of human infections. While young adult ferrets (≤2 years old) did not show any clinical symptoms and mortality, SFTSV-infected aged ferrets (≥4 years old) demonstrated severe thrombocytopenia, reduced white blood cells, and high fever with 93% mortality rate. Moreover, significantly higher viral load was observed in aged ferrets. Transcriptome analysis of SFTSV-infected young ferrets revealed strong interferon-mediated anti-viral signaling, whereas inflammatory immune responses were markedly upregulated and persisted in aged ferrets. Thus, this immunocompetent age-dependent ferret model should be useful for anti-SFTSV therapy and vaccine development.

overall_design: Two groups of young adults (20-24 months, ≤2Y) and aged ferrets (48-50 months), ≥4 Y) were inoculated via the IM route with 107.6 TCID50 of the SFTSV CB1/2014 strain. PBMCs were isolated at 2 and 4 dpi from each group of ferrets (n=3) by density gradient centrifugation using Ficoll-Paque Plus  according to the manufacture’s protocol.

first: Su-Jin

first: Young-Il

last: Kim

first: Hyeok-Il

last: Kwon

first: Eun-Ha

first: Young-Jae

last: Si

first: Min-Suk

last: Song

first: Chul

last: Lee

first: Kyle

last: Jung

first: Woo-Jin

last: Shin

first: Younho

last: Choi

first: Jianxiong

last: Zeng

first: Jae

middle: U

first: Young


title: Translation of upstream open reading frames in a model of neuronal differentiation

status: Public on Sep 07 2018

city: Stanford

first: Caitlin

last: Rodriguez

address: 450 Serra Mall

department: Department of Genetics

institute: Stanford University

summary: Upstream open reading frames (uORFs) initiate translation within mRNA 5’ leaders,and have the potential to altermain coding sequence(CDS) translationontranscripts in which they reside. Ribosome profiling(RP)studies suggest that translating ribosomes are pervasive within 5’ leadersacross model systems. However, the significance of this observationremains unclear. To explore a role for uORF usage in neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells. Using a spectral coherence algorithm (SPECtre),we identify4,954uORFsacross31%of all neuroblastoma transcripts. These uORFspredominantly utilize non-AUG initiationcodonsand exhibit translational efficiencies(TE)comparable to annotated coding regions. Usage of both AUG initiated uORFs and aconservedandconsistently translated subset of non-AUG initiated uORFs correlateswith repressed CDS translation. Ribosomal protein transcripts are enriched in uORFs, and select uORFs on such transcripts were validated for expression. Withneuronal differentiation, we observedan overall positive correlation between translational shifts in uORF/CDSpairs. However,a subset of transcripts exhibit inverse shifts in translation of uORF/CDSpairs. TheseuORFsare enriched in AUG initiation sites, non-overlapping, and shorterin length. Cumulatively, CDSs downstream of uORFs characterized by persistent translation show smaller shifts in TE withneuronal differentiation relative to CDSs without a predicted uORF, suggesting that fluctuations in CDS translation are buffered by uORF translation. In sum, this work provides insights into the dynamic relationshipsand potential regulatory functionsof uORF/CDS pairs in a model of neuronal differentiation.

overall_design: Examination of upstream open reading frame dependent translation regulation across non-differentiated and RA-differentiated SH-SY5Y cells

first: Peter

last: Todd


title: Iron and Heme Coordinate Erythropoiesis through HRI-Mediated Regulation of Protein Translation and Gene Expression

status: Public on Sep 03 2018

city: Cambridge

first: Shuping

last: Zhang

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: Iron and heme play central roles in red blood cell production. However, the mechanisms by which iron and heme levels coordinate erythropoiesis remain incompletely understood. HRI is a heme-regulated kinase that controls translation by phosphorylating eIF2a. Here, we investigate the global impact of iron, heme and HRI on protein translation in vivo in murine primary erythroblasts using ribosome profiling. By defining the underlying changes in translation during iron and HRI deficiencies, we validate known regulators of this process, including Atf4, and identify novel pathways such as co-regulation of ribosomal protein mRNA translation. Surprisingly, we found that heme and HRI pathways, but not iron-regulated pathways, mediate the major protein translational and transcriptional responses to iron deficiency in erythroblasts in vivo and thereby identify previously unappreciated regulators of erythropoiesis. Our genome-wide study uncovers the major impact of the HRI-mediated integrated stress response for the adaptation to iron deficiency anemia.

overall_design: Primary basophilic erythroblasts from E14.5 fetal livers (FLs) of Wild-type (Wt) and Hri-/- mice maintained under +Fe or -Fe conditions were sorted. FLs from embryos of the same mother were pooled before sorting. Two and three biological replicas of each condition were collected for preparations of Ribo-seq and mRNA-seq libraries, respectively.

first: Jane-Jane

last: Chen


title: DNA is Methylated on N4-Cytosine in Eukaryotes

status: Public on Sep 01 2018

city: Buffalo

first: Jie

last: Wang

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a key mechanism for regulation of DNA repair, DNA replication, and gene expression. In bacteria, DNA is modified by methylation on C5-cytosine (5mC), N6-adenine (6mA) and N4-cytosine (4mC). Metazoans were thought to only use 5mC to regulate gene expression until the recent discovery of N6-adenine methylation in DNA of diverse metazoan species, including mammals. Here we show by dot blot, immunoprecipitation with 4mC-specific antibodies, and ultra-high performance liquid chromatography coupled with triple-quadrupole mass spectrometry that 4mC also occurs in most eukaryotes. We further characterize 4mC sites on a near genome-wide scale by single molecule real time (SMRT) sequencing in the nematode C. elegans. In C. elegans, 4mC is found in all chromosomes but is relatively sparse on the X chromosome. 4mC is relatively enriched on introns, depleted on exons, and co-localizes with 6mA.  In human cells, 4mC is anti-correlated with 5mC. Moreover, 4mC modifications are associated with increased gene expression. Transfection of human cells with a 4mC-modified luciferase reporter plasmid increases luciferase expression as compared to the unmethylated plasmid. These data suggest that 4mC promotes gene transcription, playing an opposing role to 5mC, which generally represses transcription. Thus 4mC modification of DNA is a previously unrecognized mechanism of gene regulation in eukaryotes, providing evidence for a complex epigenetic DNA code.

overall_design: C. elegans L4 stage wildtype SMRTseq data

first: Zach

last: O'Brown

first: Konstantinos

last: Boulias

first: Lisheng

first: Hiroki

last: Shibuya

first: Steven

last: Burger

first: Aliya

last: Feroe

first: Miao

last: Yu

first: Chuan

last: He

first: Tao

last: Liu

first: Eric

middle: L

last: Greer


title: Exon Level Expression Profiling analysis of early stage NSCLC suffering rapidly relapse

status: Public on Oct 27 2018

city: Chongqing

first: Liang

address: No. 10 Changjiang Zhi Rd., Yuzhong Dist

institute: Cancer Center of Daping Hospital, Third Military Medical University

summary: Postoperative recurrence is the main cause of poor prognosis in early stage lung adenocarcinoma (LUAD). Factors that can predict recurrence risk are critically needed.we designed a screening procedure based on gene profile data.The differentially expressed genes (DEGs) between patients with recurrence-free survival (RFS)<1 year and RFS>3 years were found.Cox proportional hazards model, IHC and Kaplan-Meier survival analysis were preformed to validate these biomarkers in TCGA and Daping validation sets.

overall_design: To identify DEGs between the RFS<1 year (n=7)and >3year(n=7) subgroups in the Daping discovery set, transcriptome analysis was performed. Tissue cores with >70% tumor content was obtained from formalin-fixed and paraffin-embedded (FFPE) tissue. RNA was extracted from deparaffinized and proteinase K–treated FFPE tissue (20–40 mg) using the RNA prep Pure FFPE Kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions. RNA concentration and quality were assessed by absorbance spectrometry on a NanoDrop (Thermo Fisher Scientific, Wilmington, DE). We performed gene expression profiling of the 14 FFPE-derived LUAD tissues using a GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA). The total RNA input was 500 pg–10 µg. Data were processed by Affymetrix® Transcriptome Analysis Console software 3.0.

first: Dong

first: Mengxia

last: Li


title: Microarray data from BM-MSCs exposed to DMSO, LG268, Rosi, TPhP, TBT, and MEHP

status: Public on Sep 06 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

institute: Boston University

summary: Primary mouse bone marrow mesenchymal stromal cells (BM-MSCs) cultured for bone differentiation were exposed to vehicle (DMSO), synthetic RXR ligand (LG100268), type 2 diabetes therapeutic and PPARγ ligand (Rosiglitazone), and environmental PPARγ ligands (Tributyltin, Triphenyl Phosphate, and MEHP) to evaluate differential gene expression as well as nuclear receptor expression and downstream PPARG target gene expression between all chemical exposures

overall_design: Primary mouse BM-MSCs were isolated and induced to undergo osteogenesis.  At initial differentiation stage, the primary cell cultures are treated with either the vehicle (DMSO) or test chemicals. Total RNA from samples were isolated 1 day or 4 days after treatment/differentiation began and hybridized on Affymetrix microarrays.  There are 4 replicates of each experimental condition.

first: Stefano

last: Monti

first: Jennifer

last: Schlezinger


title: Induced MIST1 and PTF1a Expression in Pancreatic Ductal Adenocarcinoma Cells

city: Frederick

first: Brad

middle: LaMar

last: Jakubison

state: MD

address: 1050 Boyles St., Building 539, Room 106

department: Mouse Cancer Genetics

institute: National Cancer Institute

summary:
Purpose: The goal of the study was to determine the effects of forced expression of the acinar transcription factors MIST1 and PTF1a in PDAC cells.
Methods: Doxycycline inducible MIST1myc and PTF1amyc Panc-1 cells were generated using Clontech's Tetone System and subjected to RNA-Sequencing following doxycycline treatment.
Results: 50 million sequence reads were mapped to the human genome. Data suggests acinar associated molecules were induced upon doxycyline treatment.
Conclusions: MIST1 and PTF1a retain functional activity and can promote acinar gene expression in the context of pancreatic cancer cells.

overall_design: Panc-1 tet-inducible MIST1 and PTF1a cells were treated in the absence or presence  of 1 μg/ml doxycycyline for 72 hours.

first: Stephen

middle: F

last: Konieczny


title: Transcriptional remodeling effects of the nuclear receptor NR4A2 in adult rat ventricular myocytes

status: Public on Nov 27 2018

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

summary: Sustained elevation of sympathetic activity is an important contributor to pathological cardiac hypertrophy, ventricular arrhythmias, and left ventricular contractile dysfunction in chronic heart failure. The orphan nuclear receptor NR4A2 is an immediate early response gene activated in the heart under beta-adrenergic stimulation. The goal of this study was to identify the transcriptional remodeling events induced by NR4A2 expression in cardiomyocytes, and their impact on the physiological response of those cells to sustained beta-adrenergic stimulation. Treatment of adult rat ventricular myocytes (ARVMs) with isoproterenol induced a rapid (< 4 hours) but transient (< 24 hours) increase in NR4A2 expression levels that was accompanied by increased nuclear localization of the transcription factor. Adenovirus-mediated overexpression of NR4A2 modulated the expression of genes linked to adrenoceptor signaling, calcium signaling, cell growth and proliferation, and counteracted the increase in protein synthesis rate and cell surface area mediated by chronic isoproterenol stimulation. In consistence with those findings, NR4A2 overexpression also blocked the phosphorylative activation of ERK1/2, Akt, and of their downstream effector in protein synthesis p70S6K. Prominent among the transcriptional changes induced by NR4A2 was the > 7-fold up-regulation of the dual-specificity phosphatases DUSP2 and DUSP14, two known inhibitors of ERK1/2. Pre-treatment of NR4A2-overexpressing cardiomyocytes with the DUSPs inhibitor BCI prevented the inhibition of ERK1/2 and p70S6K following isoproterenol stimulation. In conclusion, our results suggest that NR4A2 acts as a novel negative feedback regulator of the beta-adrenergic receptor-mediated growth response in cardiomyocytes, and this at least partly through DUSP-mediated inhibition of ERK1/2 signaling.

overall_design: Isolated adult rat ventricular myocytes (ARVMs) were transduced at 50 m.o.i. with a recombinant adenovirus containing the full-length cDNA of human NR4A2 under the transcriptional control of the CMV promoter (Vector Biolabs Ad-h-NR4A2; Cat. No: ADV-217057). ARVMs transduced with a recombinant eGFP adenovirus (Vector Biolabs Ad-GFP; Cat. No. 1060) were used as the cell transduction control. At 48 hours post transduction, total RNA was etracted. A total of six independent experiments were performed using ARVMs isolated from different Sprague Dawley rats.

first: Sadia

last: Ashraf

first: Yassmin

middle: K

last: Hegazy


title: High throughput analysis of the human and mouse spinal cord neural stem cell niche

status: Public on Aug 14 2018

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

country: France

institute: inserm inm u1191

summary: Anamniotes, rodents and man maintain a pool of adult neural stem cells around the central canal in the spinal cord representing an attractive cellular source for endogenous repair. Cell diversity and genes specific for this niche are still ill-defined in mammals. To identify genes specifically expressed in the niche, we microdissected (with laser) the central canal region and the adjacent tissue in human and mice adult tissues. Total RNA was isolated and used to probe affymetrix microarrays

overall_design: We microdissected 2 human (aged 17 and 46) and 4 mouse (3 months old) samples. Central canal and adjacent tissues were microdissected with PALM micro beam equipment. RNA extraction was performed using the ReliaPrep RNA cell Miniprep System (Promega, Madison, USA) . RNA profiling was performed using affymetrix microarray technology.Hybridization targets were obtained following a double amplification procedure according to the protocol developed by Affymetrix (GeneChipTwo-Cycle Eukaryotic Target Labeling Assay; Affymetrix, USA). A hybridization mixture containing 10 µg of biotinylated cRNA was generated. The biotinylated cRNA was hybridized to HT_HG-U133_Plus_PM (human) and HT_MG-430_PM (mouse) Affymetrix microarrays. Four mouse and two human samples (EZ and periEZ regions each) were analyzed in total. The microarrays were scanned using the Affymetrix Gene Atlas scanner.The data files were generated with Affymetrix Expression Console v1.2.1 and gene expression data were normalized with GC-RMA algorithm.

first: Jean-Philippe

last: Hugnot

first: Bernard

last: Rothhut

first: Chantal

last: Ripoll

first: Hussein

last: Ghazale

first: Daria

last: Mamaeva


title: Murine host response to Neisseria gonorrhoeae upper genital tract infection reveals a common transcriptional signature, plus distinct inflammatory responses that vary between reproductive cycle phases

status: Public on Aug 27 2018

summary:
The emergence of fully antimicrobial resistant Neisseria gonorrhoeae has led global public health agencies to identify a critical need for next generation anti-gonococcal pharmaceuticals. The development and success of these compounds will rely upon valid pre-clinical models of gonorrhoeae infection. We recently developed and reported the first model of upper genital tract gonococcal infection. During initial characterization, we observed significant reproductive cycle-based variation in infection outcome. When uterine infection occurred in the diestrus phase, there was significantly greater pathology than during estrus phase. The aim of this study was to evaluate transcriptional profiles of infected uterine tissue from mice in either estrus or diestrus phase in order to elucidate possible mechanisms for these differences. Genes and biological pathways with phase-independent induction during infection showed a chemokine dominant cytokine response to Neisseria gonorrhoeae. Despite general induction being phase-independent, this common anti-gonococcal response demonstrated greater induction during diestrus phase infection. Greater activity of granulocyte adhesion and diapedesis regulators during diestrus infection, particularly in chemokines and diapedesis regulators, was also shown. In addition to a greater induction of the common anti-gonococcal response, Gene Set Enrichment Analysis (GSEA) identified a diestrus-specific induction of type-1 interferon signaling pathways. This transcriptional analysis of murine uterine gonococcal infection during distinct points in the natural reproductive cycle provided evidence for a common anti-gonococcal response characterized by significant induction of granulocyte chemokine expression and high proinflammatory mediators. The basic biology of this host response to N. gonorrhoeae in estrus and diestrus is similar at the pathway level, but varies drastically in magnitude. Overlaying this, we observed type-1 interferon induction specifically in diestrus infection where greater pathology is observed. This supports recent work suggesting this pathway has a significant, possibly host-detrimental, function in gonococcal infection. Together these findings lay the groundwork for further examination of the role of interferons in gonococcal infection. Additionally, this work enables the implementation of the diestrus uterine infection model using the newly characterized host response as a marker of pathology and its prevention as a correlate of candidate vaccine efficacy and ability to protect against the devastating consequences of N. gonorrhoeae-associated sequelae.
Murine microarrays were used to examine transcriptional differences underlying significantly different phenotypes associated with uterine N. gonorrhoeae infection in the estrus versus diestrus phases of the natural reproductive cycle.

overall_design: For each animal in the study, tissue was extracted 6 hours after treatment, mRNA was extracted from whole-organ lysate and run on a single array (1 array per animal). Four animals and arrays were run in each of the infected estrus, infected diestrus, and PBS treated diestrus experimental groups. Three aninals and arrays were run for the PBS treated estrus experimental group.

first: Ian

middle: P

last: Francis

first: Lee

last: Wetzler


title: Peripheral Blood Transcriptomic Analysis for Salmonella Infection in Pig

status: Public on Aug 07 2018

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

summary: Peripheral blood transcriptome is an important intermedia data source for investigation of the mechanism of Salmonella invasion, proliferation, and transmission but its development in pig is quite limited. We challenged four weeks old piglets (Duroc × Landrace × Yorkshire crossbred) with Salmonella enterica serovar Typhimurium LT2 and investigated the peripheral blood gene expression profile before treatment (d0) and at 2 and 7 day post inoculation (dpi) using deep sequencing technology.

overall_design: Twelve healthy piglets (3 groups × 4 replicates) that were challenged with Salmonella. Peripheral blood was collected from the pigs and transcriptome at day 0 and 2, 7 days post infection was determined by Hiseq 2000.

first: H

last: Tinghua

first: Y

last: Min


title: microRNA expression in gastrocnemicus muscle of control, SB431542 treated and cachectic mice

status: Public on Sep 28 2018

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

summary: Cancer mediated activation of the ActRIIB-ALK4/5 heterodimer by myostatin is strongly associated with muscle wasting. Progressive skeletal muscle wasting, with or without loss of adipose tissue, is observed in up to 50 per cent of all cancer patients. This multifactorial syndrome is known as cachexia, and cannot be fully reversed by conventional nutritional support. Cachexia leads to progressive functional impairment. We investigated in vitro and in vivo the efficacy of ALK4/5 receptor blockers like SB431542 in preventing muscle wasting and in this context determined muscle-related miRNA expression profiles in non-tumor bearing control mice, in SB431542 treated C26 tumor-bearing mice and in cachectic C26 tumor-bearing mice.

overall_design: The miRNA expression profile was determined in the gastrocnemicus muscles of non-tumor bearing control mice (n=4, control), of tumor bearing SB431542 treated mice (n=3, SB431542 treated) and of tumor bearing cachetic mice (n=4, cachectic). The miRNA expression of each muscle sample was analyzed in duplicate.

first: S

last: Levolger

first: E

first: J

last: van Vugt

last: Huisman

first: M

middle: G

last: van Vledder

last: van den Engel

first: G

last: Ambagtsheer

last: IJzermans

first: R

last: de Bruin


title: Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression

status: Public on Oct 05 2018

city: New York

first: Joseph

middle: Charles

last: Mays

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU School of Medicine

summary: The vertebrate pineal gland is dedicated to the production of the hormone melatonin, which increases at night to influence circadian and seasonal rhythms.  This increase is associated with dramatic changes in the pineal transcriptome.  Here, single-cell analysis of the rat pineal transcriptome was approached by sequencing mRNA from ~17,000 individual pineal cells, with the goals of profiling the cells that comprise the pineal gland and examining the proposal that there are two distinct populations of pinealocytes differentiated by the expression of Asmt, which encodes the enzyme that converts N-acetylserotonin to melatonin.  In addition, this analysis provides evidence of cell-specific time-of-day dependent changes in gene expression.  Nine transcriptomically distinct cell types were identified: ~90% were classified as melatonin-producing α- and β-pinealocytes (1:19 ratio).  Non-pinealocytes included three astrocyte subtypes, two microglia subtypes, vascular and leptomeningeal cells, and endothelial cells.  α-Pinealocytes were distinguished from β-pinealocytes by ~3-fold higher levels of Asmt transcripts.  In addition, α-pinealocytes have transcriptomic differences that likely enhance melatonin formation by increasing the availability of the Asmt cofactor S-adenosylmethionine, resulting from increased production of a precursor of S-adenosylmethionine, ATP.  These transcriptomic differences include ~2-fold higher levels of the ATP-generating oxidative phosphorylation transcriptome and ~8-fold lower levels of the ribosome transcriptome, which is expected to reduce the consumption of ATP by protein synthesis.  These findings suggest that α-pinealocytes have a specialized role in the pineal gland:  efficiently O-methylating the N-acetylserotonin produced and released by β-pinealocytes, thereby improving the overall efficiency of melatonin synthesis.  We have also identified transcriptomic changes that occur between night and day in seven cell types, the majority of which occur in β-pinealocytes and to a lesser degree in α-pinealocytes; many of these changes were mimicked by adrenergic stimulation with isoproterenol.  The cellular heterogeneity of the pineal gland as revealed by this study provides a new framework for understanding pineal cell biology at single-cell resolution.

overall_design: mRNA profiles of rat pineal gland single-cells during daytime (2 biological replicates) and nighttime (2 biological replicates); mRNA profiles of rat pineal gland single-cells treated with Isoproterenol (single sample) and PBS vehicle control (single sample).

middle: C

first: Michael

last: Kelly

first: Steven

last: Coon

first: Lynne

last: Holtzclaw

first: Martin

last: Rath

first: Mathew

last: Kelley

first: David

last: Klein


title: Deep sequencing of transcript levels of human embryonic stem cell derived mesothelium (epithelial and mesenchymal forms) and mesothelium from neonatal mouse E15.5 of the heart, lung, liver and gut and ChIP-seq data of the mesenchymal form of mesothelium

status: Public on Oct 06 2018

city: Athens

first: Stephen

last: Dalton

state: GA

address: 325 Riverbend Rd

department: Biochemistry & Molecular Biology

institute: University of Georgia

summary: Mesothelium is a multipotent resident progenitor cell of the coelomic organs that functions in organogenesis, repair and possible regeneration. We used hESCs to generate mesothelium of the epithelial and mesenchymal forms. Mesenchymal derivatives of mesothelium have been previously reported to function in tissue repair by promoting and participating in angiogenesis and neovascularization. We uncovered that hESC-derived mesothelium of the mesenchymal form (MesoT) are multipotent and generate smooth muscle cells, endothelial cells and pericytes and self-assemble into vessel-like networks in vitro. MesoT cells contribute to nascent coronary vessels in the repair zone of mechanically damaged neonatal mouse hearts. MesoT cells seeded onto vascular scaffolds self-assemble into vasculature capable of supporting peripheral blood flow following transplantation. Our findings demostrate the potential utility of MesoT cells in tissue repair and vascular engineering applications.

overall_design: Profiles of mRNA transcripts levels were generated for hPSC-derived mesothelium and neonatal mouse by deep sequencing on an Illumina Hisec 2500 and Illumina NxtSeq 500 platform. Cells were generated from WA09 human embryonic stem cells (hESCs). Cell types include mesothelium of the epithelial form (MLC), mesothelium of the mesenchymal form (MesoT), mouse neonatal mesothelium isolated from lineage traced WT1 cells of the heart, lung, liver and gut, and hPSC-derived splanchnic mesoderm-derived smooth muscle cells to use as a comparison for PCA analysis.

first: Thomas

last: Colunga

first: Miranda

last: Hayworth

first: Luoman

last: Chen

first: Kristopher

last: Nazor


title: Fly Boolean Implication Network

status: Public on Aug 29 2018

city: La Jolla

first: Debashis

last: Sahoo

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

type:
Expression profiling by array
Third-party reanalysis

summary: Numerous gene expression datasets from diverse fly tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions.  We propose here a new large scale meta-analysis of all of the publicly available fly datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

overall_design: 2,687 published fly microarray samples assayed on the GPL1322 were re-analyzed. RMA was used to normalize the RAW CEL files all together.


title: The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells

status: Public on Aug 01 2018

city: Shanghai

first: Bo

last: Wen

address: 130 DongAn Road

department: Institutes of Biomedical Sciences

institute: Fudan University

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

overall_design: Refer to individual Series


title: The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells II

summary: The naive embryonic stem cells (nESCs) display unique characteristics mirroring naive pluripotency in vivo, but the molecular mechanisms underlying the self-renewal of nESCs remain incompletely understood. Here we analyzed stranded transcriptomes in mouse nESCs and epiblast-like cells (EpiLCs), and identified 135 long non-coding RNAs (lncRNAs) preferentially expressed in nESCs. We further investigated the functions of Lncenc1, a highly abundant lncRNA in mouse nESCs. Knockdown or knockout of Lncenc1 in mouse nESCs leads to significantly decreased expression of core pluripotency genes and significant reduction of colony formation capability. Furthermore, depletion of Lncenc1 down-regulates the glycolysis pathway, as indicated by significant decreases of glycolysis genes expression, glucose consumption, lactate production and Seahorse data. Mechanically, Lncenc1 associates with RNA-binding proteins PTBP1 and HNRNPK functionally. Together, we demonstrate that Lncenc1 regulates the glycolysis in mouse nESCs, suggesting novel functions of lncRNAs in linking energy metabolism and pluripotent stem cells.

overall_design: RNAseq data in nESCs and Lncenc1 KD nESCs

first: Zihao

last: Sun

first: Minzhe

last: Zhu

first: Pin

last: Lv


title: Plant Boolean Implication Network

summary: Numerous gene expression datasets from diverse plant tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions.  We propose here a new large scale meta-analysis of all of the publicly available plant datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

overall_design: 4,306 published Arabidopsis microarray samples assayed on the GPL198 were re-analyzed. RMA was used to normalize the RAW CEL files all together.


title: Biotin pull-down assay of microRNA-25-3p-specific mRNA targets in human hepatic stellate cells

status: Public on Aug 28 2018

city: Herston

first: Berit

last: Genz

state: Queensland

address: 300 Herston Road

department: Cell and Molecular Biology

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Hepatic stellate cells (HSCs) are considered to be the main source of extracellular matrix in liver fibrosis. During chronic liver injury HSCs become activated and transdifferentiate into pro-fibrotic myofibroblasts. This process is associated with major changes in gene expression as well as intracellular signaling and can potentially be regulated by microRNAs (miRNA). In a recent study we found miRNA-25-3p (miR-25) to be upregulated in serum of children with Cystic Fibrosis (CF) who have no evidence of liver disease, compared to children with CF liver disease and healthy individuals. In this study we investigated the role of miR-25 in HSC biology and on the development of liver disease.

overall_design: LX-2 (Hepatic stellate cells) were transfected with biotynilated miR-25a-3p synthetic duplexes. Total cell lysate was used as control and miRNA coupled with its target mRNA were pulled sown with streptavidin and compared to the control.

first: Grant

last: Ramm


title: Peripheral Blood miRNA Transcriptomic Analysis for Salmonella Infection in Pig

status: Public on Sep 21 2018

first: Tinghua

last: Huang

summary: Peripheral blood transcriptome is an important intermediate data source for investigation of the mechanism of Salmonella invasion, proliferation, and transmission but its development in pig is quite limited. We challenged four-week-old piglets (Duroc × Landrace × Yorkshire crossbred) with Salmonella enterica serovar Typhimurium LT2 and investigated the peripheral blood miRNA expression profile before treatment (d0) and at 2 days post inoculation (dpi) using deep sequencing technology.

overall_design: Six healthy piglets (2 groups × 3 replicates) that were challenged with Salmonella. Peripheral blood was collected from the pig and miRNA transcriptome at day 0 and 2 days post infection was determined by Hiseq 2000.

first: H

last: Tinghua

first: Y

last: Min


title: The Long Noncoding RNA Lncenc1 Regulates Glycolysis in Naive Mouse ES Cells I

overall_design: RNAseq data in nESCs and EpiLSCs cells.

first: Mingzhe


title: Transcriptomic elucidation of itaconic acid production by Methylorubrum extorquens AM1 and its phaR mutant derivative

status: Public on Jul 27 2018

city: Hong Kong

first: Chee Kent

last: Lim

address: Kowloon Tong

department: School of Energy and Environment

country: Hong Kong

institute: City University of Hong Kong

summary: Methylorubrum extorquens AM1 is engineered to produce itaconic acid by heterologous expression of cis-aconitic acid decarboxylase. Mutation was also performed on phaR in Methylorubrum extorquens AM1, which regulate poly-beta-hydroxybutyrate accumulation, in attempt to increase carbon flux toward itaconic acid production. However, in our case, itaconic acid production by phaR mutant strain was not higher than that of the wildtype. Transcriptomic analysis was utilized in order to examine the cause for this phenomenon. RNA-seq analysis revealed that phaR mutation in the itaconic acid-producing strain might result in a complex regulatory rewiring at the gene expression level, which could cause a reduced resource flux toward ITA production. Also, RNA profiling gave a hint at the broad regulatory role of PhaR.

overall_design: Comparison of RNA profiles between Methylorubrum extorquens AM1 wildtype strain carrying pTE101 control plasmid, wildtype strain with itaconic acid-producing plasmid (pTE101a-CAD) and its phaR mutant derivative carrying the itaconic acid-producing plasmid using RNA-seq.

first: Chee

first: Juan

last: Villada

first: Patrick

last: Lee


title: NanoString nCounter Dx Human Stem Cell Panel analysis of microRNA-25-3p-transfected HSCs

status: Public on Aug 25 2018