title: Expression data from "sensitized" mice exposed via respiratory tract to chemical (methylene diphenyldiisocyanate)-glutathione conjugates +/- chloride channel inhibitor (crofelemer)

city: New Haven

first: Adam

last: Wisnewski

state: Connecticut

institute: Yale

summary:
Methylene diphenyl diisocyanate is a chemical known to cause asthma. The present study uses mice to investigate exposure-induced changes in lung gene expression and effects of a chloride channel inhibitor
We used microarrays to detail global whole lung gene expression following respiratory tract exposure to methylene diphenyl diisocyanate (MDI) vs. control exposure in mice immune-sensitized to MDI by prior skin exposure. In some studies mice were given a chloride channel inhibitor (crofelemer) via the respiratory tract before MDI.

overall_design: Mice were immune-sensitized to methylene diphenyl diisocyanate by repeated skin exposure. Immune sensitized mice were subsequently exposed to methylene diphenyl diisocyanate (reaction products with glutathione) intranasally under isoflurane and perfused (airway lavaged) lung tissue was obtained 48 hours after final exposure. Stuudies were done in BalbC, C57BL6, and B-cell deficient mice. In some studies mice were given a chloride channel inhibitor (crofelemer) via the respiratory tract before MDI.


title: Identification of miRNAs and Their targets in Colorectal Cancer (degradome)

status: Public on Mar 02 2020

city: Shanghai

first: Fangbin

last: Zhou

state: State...

address: Siping Road 1239

country: China

institute: Tongji University School of Medicine

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The roles of microRNAs (minRNAs) in mRNA destabilization and translational repression of this disease are well appreciated, their involvement in endonucleolytic cleavage of target mRNAs is poorly understood. Methods: Degradome sequencing was used to identify cleaved targets of some regulated miRNAs. Results: A sum of 9685 potential target genes were characterized for 268 conserved miRNAs and a total of 202 potential target genes were identified for 33 novel miRNAs by degradome sequencing. Target genes were further predicted to be involved in proteoglycans in cancer and AMPK signaling pathway. Five pairs of DEmiRNAs and directed target genes were randomly selected and their negative correlations were validated by RT-qPCR. Conclusions: A number of potential genes targeted by miRNAs were identified and endonucleolytic miRNA-directed mRNA cleavages occur in CRC. Our findings may lead to a better understanding of the novel role of miRNA in the gene regulation of CRC.

overall_design: Potential targets of miRNAs in CRC were generated by degradome sequencing through Illumina Hiseq 2500

first: Yong

last: Dai


title: Transcriptome-wide mapping of RNA:protein interactions of SRSF7 variants in P19 cells by iCLIP and piCLIP

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

country: Germany

institute: Goethe University Frankfurt

summary: We used P19 cells that overexpress GFP-tagged SRSF7 by 3.4-fold and expression-matched SRSF7 mutants that either lack a functional Zinc-knuckle domain or a part of their RS-domain and compared the extent and pattern of binding to mRNAs. For this we performed iCLIP using anti-GFP antibodies. We also performed iCLIP from monosomal and polysomal fractions. In addition we performed iCLIP using anti-SRSF7 antibodies to compare the binding patterns of SRSF7-GFP, endogenous SRSF7 protein and its truncated SRSF7_RRM variant.

overall_design: For each GFP-tagged SRSF7 protein,  2-3 biological replicates were subjected to the iCLIP procedure with UV-crosslinking at 254 nm. For IPs either an anti-GFP antibody was used or an anti-SRSF7 antibody.


title: RNA sequencing of lung innate lymphoid cell (ILC) populations

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

country: USA

institute: National Jewish Health

summary: A transitory, interleukin-25-responsive, KLRG1high Group 2 innate lymphoid (ILC2) cell subset that migrates to mucosal tissues early during type-2 inflammation was recently identified. This study focuses on understanding the significance of this population in relation to tissue-resident ILC2 cells in the lung and intestine.  RNA-sequencing and unbiased pathway analysis revealed the AP-1 factor BATF as a potential modulator of ILC2 cell fate. For RNAseq, KLRG1-postive and KLRG1-neagive populations were sorted and compared.

overall_design: Examination of transcrimptome in 2 ILC cell types.

middle: L

first: Thomas

last: Danhorn

first: Mindy

middle: M

last: Miller

first: Preeyam

last: Patel

first: Brian

last: O'Connor


title: Effect of 6-TG on apoptosis and cell cycle in MCF-7 breast cancer cells and its mechanisms through the regulation of DNMT1

city: 长春市

first: 昊

last: 李

address: 新竹路1977号

institute: 吉林大学

summary: Thioguanine (6-TG) as conventional drug has anti-tumor activity in various cancer cell lines. However, the effect of 6-TG on luminal subtypes breast cancer (ER+, PR+) is elusive. In this study, effect of 6-TG on MCF-7 breast cancer cell line (ER+, PR+) and its mechanisms were investigated. MCF-7 cells were treated with 6-TG and IC50 value was measured by cell counting kit-8 assay. DEGs were confirmed by RNA-seq. Apoptosis and cell cycle consequences were checked by flow cytometry and western blot. Our results showed that colony formation decreased obviously after 6-TG treatment. Moreover, with the treatment of 6-TG cell apoptosis percentage increased. DNMT1 mRNA and protein expression decreased and FAS expression increased in both expression level. Meanwhile, 6-TG treatment also induced MCF-7 cells to occur G2/M phase cell cycle arrest. Overall, our results indicated that 6-TG suppressed cell proliferation, induced G2/M phase arrest through DNMT1 mediated p53-dependent p21 signaling, and accelerated cell apoptosis through activated extrinsic apoptosis pathway which was caused by DNMT1 mediated FAS signaling.

overall_design: Effect of 6-TG on MCF-7 cells.

first: Hao

last: Li

first: Xinglan

last: An


title: Empty SV40 capsids (VLPs) significantly improve survival and recovery of septic rats

city: Jerusalem, ISRAEL

first: Ariella

last: Oppenheim

state: Jerusalem

address: 21 HaAhayot Rd

country: Israel

institute: Hebrew University

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

overall_design: Refer to individual Series


title: Expression data of mouse alveolar macrophage cell (MH-S) colonies stimulated with LPS

city: Sockholm

first: Fredrik

last: Wermeling

state: Stockholm

address: Visionsgatan 18, Center for molecular medicine, Karolinska University Hospital

department: Division of Rheumatology, Department of Medicine, Solna

country: Sweden

institute: Karolinska Institute, Stockholm, Sweden

summary:
Under microscope, MH-S cells show a heterogenous population. By clonal dilution, we generated single cell colonies and found that a set of clones that secreted higher the IL-4Ra regulating protein (“High IL-4Ra activity clones”) and set of colonies secreted lower amount (“Low IL-4Ra activity clones”).
We performed microarrays to detail the global gene expression analysis comparing high IL-4Ra activity and low IL-4Ra activity MH-S clones stimulated with or without LPS.  At this time point, roughly 50 genes annotated as “extracellular” were significantly upregulated more than two-fold in LPS stimulated clones compared to unstimulated ones. Of these, only seven genes showed higher expression in the high IL-4Ra activity clones compared to  low IL-4Ra activity clones.

overall_design: Three high IL-4Ra activity and three low IL-4Ra activity MH-S clones stimulated with or without LPS for 16 hrs were selected for RNA extraction and hybridization on Affymetrix microarrays. Total 12 samples were analysed.

first: Sudeepta

middle: K

last: Panda


title: Distinct signaling and transcriptional pathways regulate peri-weaning development and cold-induced recruitment of beige adipocytes

city: San Francisco

first: Yixuan

last: Wu

state: CA

address: 555 Mission Bay Boulevard South

department: Physiology

institute: University of California, San Francisco

summary: Adipose tissue provides a defense against starvation and environmental cold. These dichotomous functions are performed by three distinct cell types: energy-storing white adipocytes, and thermogenic beige and brown adipocytes. Previous studies have demonstrated that exposure to environmental cold stimulates the recruitment of beige adipocytes in the white adipose tissue (WAT) of mice and humans, a process that has been extensively investigated. However, beige adipose tissue also develops during the peri-weaning period in mice, a developmental program that remains poorly understood. Here, we address this gap in our knowledge using genetic, imaging, physiologic, and genomic approaches. We find that, unlike cold-induced recruitment in adult animals, peri-weaning development of beige adipocytes occurs in a temperature- and sympathetic nerve-independent manner. Instead, the transcription factor B cell leukemia/lymphoma 6 (BCL6) acts in a cell autonomous manner to regulate the commitment but not the maintenance phase of beige adipogenesis. Genome-wide RNA-seq studies reveal that BCL6 regulates a core set of genes involved in fatty acid oxidation and mitochondrial uncoupling, which are necessary for development of functional beige adipocytes. Together, our findings demonstrate that distinct transcriptional and signaling mechanisms control peri-weaning development and cold-induced recruitment of beige adipocytes in mammals.

overall_design: RNA sequencing of murine inguinal white adipose tissue samples from peri-weaning or adult mice that were housed at various temperatures.

first: Ajay

last: Chawla


title: Analysis of pathways elicited by empty SV40 capsids (VLPs) in septic rats 24 hours post 2CLP operation

summary: During the first hours after infection, before SV40 DNA enters the nucleus, empty capsids (VLPs) and the wild-type virus have the same effect on cellular signaling. VLPs were previously found to ameliorate toxic acute kidney injury (AKI) in a mouse model, counteracting apoptosis by inducing the Akt-1 survival pathway. Here we tested their effect on severe sepsis in rats. VLP pre-treatment increased survival and recovery from zero to 75%. RNAseq studies demonstrated that unlike AKI, here the VLPs did not induce survival pathways. Instead they affected thousands of genes and many cellular functions, eliminating deleterious pathways and inducing beneficial ones: immune response, resolution of inflammation, regeneration and cell and system homeostasis. In contrast, only four genes were affected following VLP administration to healthy rats. We propose that SV40 VLPs respond specifically to perturbation in cellular activities. The study suggests that diseases with complex pathophysiology may require treatments affecting wide-spectrum functions.

overall_design: Sprague-Dawley rats were randomly divided into 4 groups, each containing 3 replicates: Control rats that received vehicle (saline) only (VO), a second control, rats that received VLPs only (VLPs), and two groups of 2CLP-insulted rats, one that received vehicle only (2CLP+VO) and the second received VLPs (2CLP+VLP). VLPs were injected through the tail-vein at a dose of 0.3 mg/kg, on 3 consecutive days (0.1 mg/kg daily) prior to the insult. Lungs were harvested 24 hours post the 2CLP insult.

first: Orly

last: Ben-nun-Shaul

first: Sharona

last: Elgavish

first: Yuval

last: Nevo

first: Hadar

last: Benyamini

first: Arieh

last: Eden


title: Lactobacillus rhamnosus GG Genomic and Phenotypic Stability in an Industrial Production Process

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

type: Genome variation profiling by high throughput sequencing

summary: Lactobacillus rhamnosus GG has become one of the most widely marketed and studied probiotic strains. Several genes important for probiotic function have been identified, including the spaCBA-srtC1 gene cluster encoding pili, which have been shown to be important for certain of its probiotic properties. The spaCBA-srtC1 gene cluster has been reported to be unstable in L. rhamnosus GG isolated from liquid dairy products and therefore the present study examined the L. rhamnosus GG genome stability throughout an industrial production process from the original deposit to the freeze-dried products including intermediate fermentations and single colony isolates prepared from these samples. The results showed that the original deposit was identical to the reference ATCC and that the genome sequence stayed fully intact throughout the production process. No SNPs or larger genomic changes occurred in any of the samples throughout the production process and the spaCBA-srtC1 gene locus was fully conserved and intact in all 31 samples examined. In addition, phenotypic expression of pili was demonstrated using immune-gold labelling EM. The images showed that pili production was preserved throughout the production process and that the number of pili were consistent in all batches. The present study extends the scope of previous findings to an industrial setting and shows that the region around the spaCBA-srtC1 cluster exhibits high stability in L. rhamnosus GG in an industrial production process.

overall_design: Genome sequencing of 37 Lactobacillus rhamnosus GG samples from Chr.Hansen

first: Marianne

last: Stage

first: Albin

last: Sandelin

first: Adam

last: Baker


title: E18.5 DRG: Identification of a sacral, visceral sensory transcriptome in embryonic and adult mice

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: Visceral sensory neurons encode distinct sensations from healthy organs and initiate pain states that are resistant to common analgesics. Transcriptome analysis is transforming our understanding of sensory neuron subtypes but has generally focused on somatic sensory neurons or the total population of neurons in which visceral neurons form the minority. Our aim was to define transcripts specifically expressed by sacral visceral sensory neurons, as a step towards understanding the unique biology of these neurons and potentially lead to identification of new analgesic targets for pelvic visceral pain. Our strategy was to identify genes differentially expressed between sacral dorsal root ganglia (DRG) that include somatic neurons and sacral visceral neurons, and adjacent lumbar DRG that comprise exclusively somatic sensory neurons. This was performed in male and female mice (adult and E18.5). By developing a method to restrict analyses to nociceptive Trpv1 neurons, a larger group of genes were detected as differentially expressed between spinal level. We identified many novel genes not previously been associated with pelvic visceral sensation or nociception. Limited sex differences were detected across the transcriptome of sensory ganglia, but more were revealed in sacral levels and especially in Trpv1 nociceptive neurons. These data will facilitate development of new tools to modify mature and developing sensory neurons and nociceptive pathways.

overall_design: Donor matched comparison of dorsal root ganglia from lumbar and sacral spine regions in E18.5 C57Bl6 mice

first: Casey

middle: A

last: Smith-Anttila

first: Elizabeth

last: Mason

first: Christine

last: Wells

first: Bruce

last: Aronow

first: Peregrine

middle: B

last: Osborne

first: Janet

middle: R

last: Keast


title: Identification of a sacral, visceral sensory transcriptome in embryonic and adult mice


title: TRPV1 DRG: Identification of a sacral, visceral sensory transcriptome in embryonic and adult mice

overall_design: Donor matched comparison of dorsal root ganglia from lumbar and sacral spine regions in adult Trpv1tm2Bbm mice


title: Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_SNP)

city: Uppsala

first: Yanara

last: Marincevic-Zuniga

address: Husargatan 3, BOX 1432, Biomedicinskt Centrum (BMC)

department: Medical Sciences

institute: Uppsala University

summary: We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.

overall_design: The Illumina HumanOmni2.5 Exome-8v1 SNP array was used to detect copy number changes in peditric ALL samples. LogR files  with the extension ".cn" are submitted to GEO and can be visualized in IGV. 450k methylation data for these ALL samples was submitted previously in GSE49031.

first: J

last: Nordlund

first: Y

first: A

middle: C

last: Syvänen


title: Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing

type: Genome variation profiling by genome tiling array

first: A-C


title: Analysis of pathways elicited by empty SV40 capsids (VLPs) in septic rats 6 hours post 2CLP operation

first: Ariella

last: Oppenheim

overall_design: Sprague-Dawley rats were randomly divided into 4 groups, each containing 3 replicates: Control rats that received vehicle (saline) only (VO), a second control, rats that received VLPs only (VLPs), and two groups of 2CLP-insulted rats, one that received vehicle only (2CLP+VO) and the second received VLPs (2CLP+VLP). VLPs were injected through the tail-vein at a dose of 0.3 mg/kg, on 3 consecutive days (0.1 mg/kg daily) prior to the insult. Lungs were harvested 6 hours post the 2CLP insult.

first: Orly

last: Ben-nun-Shaul

first: Sharona

last: Elgavish

first: Yuval

last: Nevo

first: Arieh

first: Hadar


title: Adult DRG: Identification of a sacral, visceral sensory transcriptome in embryonic and adult mice

first: Othmar

overall_design: Comparison of dorsal root ganglia from lumbar and sacral spine regions in adult C57Bl6 mice

first: Casey

first: Phil

last: Dexheimer


title: Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis

status: Public on Mar 01 2020

city: Salt Lake City

first: Katherine

last: Beebe

state: UT

address: 15 North 2030 East

department: Molecular Medicine

institute: University of Utah

type: Genome binding/occupancy profiling by high throughput sequencing


title: Microarray profiling of tomato provides an insight into the key transcription factors involved during fruit ripening and development

city: Jammu

first: Archana

last: Koul

state: J&K

address: University of Jammu

department: School of Biotechnology

country: India

institute: University of Jammu

summary: Tomato (Solanum lycopersicum) represents an established research model for studying fruit development and ripening processes which is genetically under tight control of various regulatory molecules. Elucidation of these regulatory mechanisms remains important to understand the production and accumulation of various metabolites, which ultimately determines the fruit quality. Therefore, it is essential to develop a platform that allows accurate identification and quantification of the gene transcript levels including transcription factors associated with ripening process. Microarray technology has become mainstream and preferred tool for studying the large number of targeted gene expression in a single run. In the present study, we have developed the microarray platform in the leaf and fruit tissues of four different accessions of tomato in order to check the expression levels of various genes and transcription factors involved in secondary metabolic pathways which directly or indirectly regulates the ripening process. A total of 42313 probes were used in 1 ×44k array of Agilent technology along with the custom design for many genes and transcription factors. A co-expression study revealed several transcription factors whose expression patterns strongly correlates with the genes involved in ethylene, carotenoid and flavonoid biosynthesis and accumulation. The above correlation was validated by generating expression networks using CytoScape v.3.1.1.  Real time PCR was also carried out for checking the expression profiles of transcription factors known to regulate the above three pathways. This study provides an insight into multiple events associated with transcription factors involved in secondary metabolism of tomato including maturation and ripening processes

overall_design: Gene expression profiles were generated and analysed in leaf and fruit tissues of  four different tomato accessions i.e AV, TM, SK and RJ. These accessions originated from different geographical areas of Jammu and Kashmir and showed different maturity progress and differential accumulation of carotenoids in their ripe fruit. AV accession was collected from RTGR, Hyderabad, TM was collected from Kashmir while as SK and RJ were collected from the Chatha and Rajouri regions of Jammu province.

first: Deepak

last: Sharma

first: Sanjana

last: Kaul

first: Manoj

last: Dhar


title: HOP family plays a major role in long term acquired thermotolerance in Arabidopsis affecting the HSR and protein QC

city: MADRID

first: M.

middle: MAR

last: CASTELLANO

address: Crta. de la Coruña, km 7,5

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA (CBGP)

summary: HOP is a family of cytosolic cochaperones whose molecular role in thermotolerance was quite unknown in eukaryotes and unexplored in plants. In this article, we describe that the three members of the HOP family display a different induction pattern under heat, being HOP3 highly regulated during the challenge and the attenuation period. Despite this tight HOP3 regulation, the analysis of the hop1 hop2 hop3 triple mutant demonstrates that the three AtHOP proteins act redundantly to promote long acquired thermotolerance in Arabidopsis. AtHOPs interact very strongly with HSP90 and part of the bulk of HOP shuttles from the cytoplasm to cytoplasmic foci and to the nucleus in response to heat. Consistent with this latter location, and with the formation of a HOP complex with HsfA1, RNAseq analyses demonstrate that HSR is altered in the hop1 hop2 hop3 triple mutant during the heat stress.In addition, this mutant displays an unusual high accumulation of insoluble and ubiquitinated proteins under heat. These data reveal that HOPs play a main role in two different aspects of the response to heat: the maintenance of protein homeostasis and the proper establishment of the HSR, affecting the plant capacity to acclimate to heat stress for long periods.

overall_design: 7 day old Arabidopsis seedlings from wt and hop1 hop2 hop3 triple mutant, grown under control conditions or challenged at 38ºC

first: Nuria

last: Fernández-Bautista

first: Lourdes

last: Fernández-Calvino

first: Alfonso

last: Muñoz

first: René

last: Toribio

first: H

middle: P

last: Mock

first: M

last: Castellano


title: Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing (ALL_450k)

first: Yanara

last: Marincevic-Zuniga

overall_design: The  Illumina Infinium HumanMethylation 450k BeadChip is based on the same biochemical principles as regular SNP genotyping arrays. Thus, the total raw fluorescence intensity from the 450k array can also be used to detect copy number variants in genomic DNA. We used the raw signal intensities from the 450k to assess copy number status of the ALL patient samples. LogR files  with the extension ".cn" are submitted to GEO and can be visualized in IGV. This is a re-analysis of 12 ALL samples previously submitted in GSE49031.

first: J

last: Nordlund

first: Y

first: A

last: Syvänen


title: GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment [RNA-Seq]

status: Public on Mar 10 2020

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

summary: The purpose of our study was to examine the role of GCN2 in the function of immunosuppressive cells such as tumor associated macrophages and MDSCs. We show that a myeloid lineage specific deletion of GCN2 results in a shift towards a more proinflammatory phenotype of tumor associated macrophages and MDSCs, thereby promoting anti-tumor immunity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We determined the expression pattern of tumor associated macrophages and MDSCs, impact of ATF4 and GCN2 silencing in M0, M1 and M2 polarized macrophages as well as ATF4 binding sites in M0 or M2 polarized bone marrow derived macrophages using RNA-Seq, scRNA-Seq and ChIP-Seq.

first: Marie

middle: J

last: Halaby

first: Kebria

last: Hezaveh

first: Tracy

last: McGaha


title: Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis [RNA-Seq d6]

first: Katherine

last: Beebe

summary: Metabolism and development must be closely coupled to meet the changing physiological needs of each stage in the life cycle. The molecular mechanisms that link these pathways, however, remain poorly understood. Here we show that the Drosophila Estrogen-Related Receptor (dERR) directs a transcriptional switch in mid-pupae that promotes glucose oxidation and lipogenesis in young adults. dERR mutant adults are viable but display reduced locomotor activity, susceptibility to starvation, elevated glucose and an almost complete lack of stored triglycerides. Molecular profiling by RNA-seq, ChIP-seq, and metabolomics revealed that glycolytic and pentose phosphate pathway genes are induced by dERR, and their reduced expression in mutants is accompanied by elevated glycolytic intermediates, reduced TCA cycle intermediates, and reduced levels of long chain fatty acids. Unexpectedly, we find that the central pathways of energy metabolism, including glycolysis, the tricarboxylic acid cycle, and electron transport chain, are coordinately induced at the transcriptional level in mid-pupae and maintained into adulthood, and this response is partially dependent on dERR, leading to the metabolic defects observed in mutants. Our data support the model that dERR contributes to a transcriptional switch during pupal development that establishes the metabolic state of the adult fly.

overall_design: Comparison of mRNA levels in 6 day old control and dERR mutant adults. n=3 replicates per treatment

first: Carl

middle: S

last: Thummel


title: Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis [ChIP-Seq]

overall_design: ChIP-seq comparison of enriched loci between ERR-FLAG tagged animals and controls.


title: Drosophila Estrogen-Related Receptor directs a transcriptional switch that supports adult glycolysis and lipogenesis [RNA-Seq timecourse]

overall_design: Time course comparison of mRNA levels in control and dERR mutant animals. n=3 replicates per condition (time_treatment)


title: ATAC-Seq for control and huntington's disease iPSC-derived medium spiny neuron-like cells

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

institute: MIT

summary: HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. Three control in triplicate, one control in duplicate,  one HD samples with CAG repeat length in typical adult onset range in triplicate and one in duplicate, and five HD samples with CAG repeat length in typical juvenile onset range in triplicate were differentiated as biological growth replicate (separate differentiations) into medium spiny neuron-like cells. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation using the strand specific Illumina TruSeq Total RNA protocol. Libraries were sequenced on the HiSeq 2500 using 100 cycles to obtain paired-end 100 reads at >50M reads per sample.

overall_design: ATAC-Seq profiles of control and HD patient IPSC-derived medium spiny neuron-like cells

first: Miriam

last: Adam

first: Ernest

last: Fraenkel


title: H3K4me3 ChIP-Seq profiles of control and huntington's disease iPSC-derived medium spiny neuron-like cells

overall_design: H3K4me3 ChIP-Seq profiles of control and HD patient IPSC-derived medium spiny neuron-like cells


title: Next Generation Sequencing Facilitates Quantitative Analysis of 231 and Pep-E3 cells' Transcriptomes in breast cancer

city: Beijing

first: Tingting

last: Zhang

address: Nanwei street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  231 and Pep-E3 breast cancer cells  by using NGS-derived breast cancer transcriptome profiling (RNA-seq).
Methods:  231 and Pep-E3 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions: Our study represents the first detailed analysis of 231 and Pep-E3  cells' transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Zhuowei

last: Hu

first: Ke

last: Li


title: Comparsion of transcriptome between slbp1 mutant and wildtype sibling

city: Kunigami kun

first: Nishtha

last: Ranawat

state: Okinawa

address: 1919-1 Tancha Onna son

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

summary: The neurogenic state at transcriptomic level in delayed-neurogenesis zebrafish mutant "slbp1" with wildtype sibling was compared using bulk RNA sequencing data from RNA obtained from head regions at 2dpf.

overall_design: Total RNA was extracted from slbp1 and wildtype sibling heads at 2dpf and sequenced.

first: Ranawat

last: Nishtha

first: Masai

last: Ichiro


title: Single cell RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

summary: HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. One control and one HD sample with CAG repeat length in typical adult onset range were differentiated into medium spiny neuron-like cells. Cells were dissociated into single cell suspension and single cell viability for each sample was determined (86.9% for control, 80.9% for HD). Cells were processed using 10x genomics single cell platform. Libraries were sequenced on the HiSeq 4000 using 100 cycles to obtain paired-end 100 reads at >50M reads per cell.  The estimated number of cells sampled was 5,070 (control) and 3,829 (HD) with an average number of reads per cell at 31,675 (control) and 41,939 (HDQ). After QC filtering, the data were aggregated using Cell Ranger and gene-by-cell expression matrices generated and used as input for Seurat and Scanpy.

overall_design: Single cell RNAseq profiles of control and HD patient iPSC-derived medium spiny neuron-like cells were generated with the 10x genomics platform and using the Illumina Hiseq 4000

middle: G

first: Jie

last: Wu

first: Leslie

last: Thompson


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT AHCY E14.1 cell  and T136A AHCY E14.1 cell

city: hang zhou

first: qiang

last: zhu

state: zhe jiang

address: yuhangtang road 866

institute: Zhe Jiang university

summary:
Purpose: To test the effect of AHCY O-GlcNAcylation on E14.1cell pluripotency and The goals of this study are to compare gene expression profiles of the WT AHCY rescue cells and the T136A AHCY rescue cells.
Method:Total RNA was Trizol-extracted and purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. cDNA was synthesized using random hexamer primer and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair A-tailing and adapter added were implemented. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Results:Significant alterations in gene expression levels were observed, with 1351 genes upregulated and 979 genes downregulated in the T136A AHCY rescue cells

overall_design: the mRNA profiles of WT AHCY E14.1 cells and  T136A AHCY E14.1 cells were generated by deep sequencing using Illumina GAIIx.

first: zhu

last: qiang


title: Total RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

summary: HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron (MSN)-like cells. Three control in triplicate, one control in duplicate,  one HD samples with CAG repeat length in typical adult onset range in triplicate and one in duplicate, and five HD samples with CAG repeat length in typical juvenile onset range in triplicate were differentiated as biological growth replicate (separate differentiations) into medium spiny neuron-like cells. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation using the strand specific Illumina TruSeq Total RNA protocol. Libraries were sequenced on the HiSeq 2500 using 100 cycles to obtain paired-end 100 reads at >50M reads per sample.

overall_design:
Total RNAseq profiles of control and HD patient iPSC-derived medium spiny neuron-like cells were generated by deep sequencing, in duplicate or triplicate, using Illumina Hiseq 2500

Rep 1/2/3/4 are all different human subjects except for the 18n2 and 18n6 samples which are the same person but 2 different iPSC clones. Thus, each Rep represents a different iPS cell line. Appended to the end of the title are _1/_2/_3 which represent different differentiations of those subjects' iPSCs and are separate RNA extractions. The rep number and appended differentation number are available in the 'source name' field on each sample page.


title: Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: The diverse bacterial communities that colonize the gastrointestinal tract play an essential role in maintaining immune homeostasis through the production of critical metabolites such as short chain fatty acids (SCFA), and this can be disrupted by antibiotic use. However, few studies have addressed the effects of specific antibiotics longitudinally on the microbiome and immunity. We evaluated the effects of four specific antibiotics; enrofloxacin, cephalexin, paromomycin, and clindamycin; in healthy female rhesus macaques. All antibiotics disrupted the microbiome, including reduced abundances of fermentative bacteria and increased abundances of potentially pathogenic bacteria, including Enterobacteriaceae in stool, and decreased Helicobacteraceae in the colon. This was associated with decreased SCFAs, indicating altered bacterial metabolism. Importantly, antibiotic use also substantially altered local immune responses, including increased neutrophils and Th17 cells in the colon. Furthermore, we observed increased soluble-CD14 in plasma, indicating microbial translocation. These data provide a longitudinal evaluation of antibiotic-induced changes to the composition and function of colonic bacterial communities, associated with specific alterations in mucosal and systemic immunity.

overall_design: 12 female rhesus macaques were treated with antibiotics (n=3/group) including: enrofloxacin (12 mg/kg, n=3, once daily, 9 days), cephalexin (30mg/kg, n=3, once daily, 9 days), paromomycin (25 mg/kg, n=3, twice daily, 9 days), or clindamycin (10 mg/kg, n=3, twice daily, 6 days). Total RNA was collected from biopsies of the colon before (42 and 21 days prior to treatment), during (day 3), and after (days 14, 28, 63 and 119 or 127) the antibiotic treatment for a total of 84 samples that were sequenced for comparing treatments longitudinally.

first: A

last: Zevin

first: R

last: Cheu

last: Gustin

first: J

last: Modesitt

first: T

last: Hensley-McBain

last: Manuzak

first: C

last: Miller

first: E

last: Coronado

last: Gott

first: B

last: Richardson

first: M

last: Fang

last: Cartwright

first: P

first: S

last: Wangari

last: Agricola

first: D

last: May

last: Smith

last: Gale

last: Smedley

first: N

last: Klatt


title: Identification of extracellular vesicle miRNA cargo

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

summary: Osteolineage cell-derived extracellular vesicles (EVs) play a regulatory role in hematopoiesis and have been shown to promote the ex vivo expansion of human hematopoietic stem and progenitor cells (HSPCs). Here, we demonstrate that EVs from different human osteolineage sources do not have the same HSPC expansion promoting potential. Comparison of stimulatory and non-stimulatory osteolineage EVs by next-generation sequencing and mass spectrometry analyses revealed distinct microRNA (miRNA) and protein signatures identifying EV-derived candidate regulators of ex vivo HSPC expansion. Accordingly, the treatment of umbilical cord blood-derived CD34+ HSPCs with stimulatory EVs altered HSPC transcriptome, including genes with known roles in cell proliferation. An integrative bioinformatics approach, which connects the HSPC gene expression data with the candidate cargo in stimulatory EVs, delineated the potentially targeted biological functions and pathways during hematopoietic cell expansion and development. In conclusion, our study gives novel insights into the complex biological role of EVs in osteolineage cell-HSPC crosstalk and promotes the utility of EVs and their cargo as therapeutic agents in regenerative medicine.

overall_design: Examination of the miRNA content of extracellular vesicles isolated from 2 different cell lines

first: Jess

last: Morhayim

first: Remco

last: Hoogenboezem

first: Eric

last: Bindels

last: Braakman


title: Next Generation Sequencing Facilitates Quantitative Analysis of CP5322-treated and Non-treated Transcriptomes in Kasumi-1 cells

last: Z

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: The goals of this study are designed to study the alteration of transcriptome profiling (RNA-seq) in CP5322-treated and non-treated cells. The drug was a herbal small molecular, which was designed as a HDAC inhibitor, called CP5322. TK1 was the group of CP5322-treated, and CK1 was the group of control.
Methods: The mRNA profiles of drug-treated and non-treated cells  were generated by next genenration sequencing, using Illumina platform. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated, which was called Raw Reads. And the low quality sequences and adaptor contamination were removed.Data processing was completed to obtain high-quality sequences (Clean Reads), and all subsequent analyses were based on Clean Reads.
Results: Using the data analysis workflow, we mapped about 46 million sequence reads per sample to the human genome (h19) and identified 23 thousand transcripts in the drug-treated and non-treated cells. And the mapping rate was about 97%. RNA-seq data showed a significant alteration when the Kasumi-1 cells were treated by drug.
Conclusions: The RNA-Seq data provided us a priori evidence for further research.

overall_design: The samples were designed as TK1 ( CP5322-treated group) and CK1 (non-treated group).The mRNA profiles of CP5322-treated and non-treated cells  were generated by next genenration sequencing, using Illumina platform.

first: Li

last: Yu

first: Juan

last: Zhang


title: Small RNA sequencing on affinity capture-purified tRNA-derived small RNAs (tsRNAs)

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

summary: During stress conditions, particular tRNAs are cleaved by stress-induced endonucleases resulting in distinct tRNA-derived small RNAs (tsRNAs). These small RNAs have been implicated in a wide array of mostly stress-related biological processes, however how exactly they exert their functions mechanistically is still largely unknown. Since parental tRNAs carry post-transcriptional modifications, stress-induced tsRNAs are likely modified, too. In order to use endogenously modified tsRNAs, we developed a biochemical pipeline for the production and purification of specific tsRNAs using a human cell culture system. Ectopic expression of Angiogenin combined with chromatography of small RNAs resulted in the production of endogenously modified 5’ tsRNAs on a preparative scale. Small RNA sequencing on purified tsRNAs was used to determine the identity and purity of the 5’ tsRNA preparations.

overall_design: HEK293 cells expressing human Angiogenin from an integrated via the Flp-In™-T-REx™ system were exposed to doxycycline for 48 hours, followed by chromatographic RNA purification for 5' tsRNA-GlyGCC and 5' tsRNA-GluCUC

first: Matthias

last: Schaefer

first: Aleksej

last: Drino


title: Sexual and asexual inheritance of epigenetic marks in Apple [BS-Seq]

city: BEAUCOUZE

first: Adrien

last: PERRIN

address: 42 Rue Georges Morel

country: France

institute: INRA - IRHS

type: Methylation profiling by high throughput sequencing

summary: In order to compare sexual and asexual multiplication in Malus domestica we performed bisulfite sequencing to study change in differentially methylated region

overall_design: We compare methylation of a Tree sample to Seedling in one hand and To Grafted plant in another end

first: Perrin

last: Adrien

first: Daccord

last: Nicolas

first: Roquis

last: David

first: Celton

last: Jean-Marc

first: Bucher

last: Etienne


title: Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny [MeDIP]

city: Madison

first: Bermans

last: Iskandar

state: WI

address: 600 Highland Ave, K4/832

department: Neurological Surgery

institute: University of Wisconsin

summary: Ancestral folate promotes neuronal regeneration in serial generations of progeny, eliciting transgenerational disruptions in DNA methylation.

overall_design: Methylated DNA immunoprecipitation (MeDIP) was performed on DNA extracted from 1cm segments of injured cervical spinal cord tissue of F3 male rats derived from an ancestral lineage adminstered folate, double distilled water, or trichostatin A (TSA).


title: Ancestral folate promotes neuronal regeneration in serial generations of progeny [RNA-seq]

summary: Folate supplementation in F0 mating rodents increases regeneration of injured spinal axons in vivo in at least 4 generations of  progeny (F1-F4) in the absence of interval folate administration to the progeny. Transmission of the enhanced regeneration phenotype to untreated progeny parallels axonal growth in neuron culture after in vivo folate administration to the F0 ancestors alone, in correlation with transformed patterns of genomic DNA methylation and gene expression in treated lineages. Enhanced axonal regeneration phenotypes are observed with diverse folate preparations and routes of administration, in outbred and inbred rodent strains, in distinct rodent genera, and are reversed in F4-F5 progeny by pretreatment with DNA demethylating agents prior to phenotyping. Uniform transmission of the phenotype to progeny suggests a non-Mendelian mechanism. The capacity of an essential nutritional co-factor to induce a beneficial transgenerational phenotype in untreated offspring carries broad implications for the diagnosis, prevention, and treatment of inborn and acquired disorders.

overall_design: Approximately 100 ng of total RNA from F3 generation spinal cord tissue of was used for sequence library construction following instructions of NuGen mRNA sample prep kit.


title: Ancestral folate promotes neuronal regeneration in serial generations of progeny

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

overall_design: Refer to individual Series


title: Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

city: Boston

first: Martha

middle: L.

last: Bulyk

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

summary: Systematic identification of factors that regulate human embryonic stem cell (hESC) differentiation can provide valuable insights into early development and disease. However, effective modulation of gene expression during differentiation has proven technically challenging. Here, we report the first described hESC lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers. We subsequently performed an unbiased, genome-wide CRISPRi screen targeting long non-coding RNAs during endoderm differentiation. From our screen, we identified known factors, as well as novel lncRNAs required for differentiation. Surprisingly, lncRNA expression was not predictive of enrichment scores, supporting the necessity for functional screening instead of relying on gene expression analysis. Further downstream analysis of two hits, RP11-222K16.2 and FOXD3-AS1, revealed two lncRNAs essential for differentiation and pluripotency, respectively. Taken together, the cell lines and screen methodology described herein can be adapted to discover novel regulators of differentiation into any lineage.

overall_design: We performed two experiments: (1) RNA-sequencing of three lineages (undifferentiated hESCs, endoderm, and mesoderm) and (2) a CRISPR interference screen aimed at assessing lncRNA loci in endoderm differentiation. For the RNA-seq, we provide the raw fastqs for each of the 2 replicates as well as the GENCODE v25 transcript abundances (as determined by kallisto). For the CRISPRi screen, we provide the raw fastqs for three populations: Day Zero input, FOXA2/SOX17 double positive endoderm cells, and FOXA2/SOX17 double negative undifferentiated cells, as well as the corresponding sgRNA counts for each population.

first: Jeffrey

last: Haswell

first: Kaia

last: Mattioli

first: Chiara

last: Gerhardinger

first: Philipp

last: Maass

first: Daniel

last: Foster

first: Paola

last: Fernandez

first: Xiaofeng

last: Wang

first: John

last: Rinn

first: Frank

last: Slack


title: Disruption of nonsense-mediated decay by the multifunctional long-distance movement protein of Pea enation mosaic virus 2

city: College Park

first: Jared

middle: Paul

last: May

state: MD

address: 4062 Campus Dr.

department: Cell Biology & Molecular Genetics

institute: University of Maryland

summary: Nonsense-mediated decay (NMD) is an RNA regulatory pathway that degrades both natural and faulty messenger RNAs with long 3’ untranslated regions. NMD targets diverse families of RNA viruses, forcing viruses to counteract the NMD pathway for successful amplification in host cells. Using a transcriptome-wide approach in the model plant Nicotiana benthamiana, We report that the Pea enation mosaic virus 2 long-distance movement protein, p26, protects a subset of natural cellular NMD-target transcripts, particularly those containing long, structured, GC-rich 3’ UTRs. Furthermore, RNA-seq revealed that the NMD pathway is highly dysfunctional during PEMV2 infection, with nearly half of NMD-targets increasing in abundance. Widespread changes in host transcriptomes are common during RNA virus infections and these results suggest that virus-mediated NMD-inhibition may be a major contributing factor.

overall_design: Identified differentially expressed transcripts in Nicotiana benthamiana in the presence of an NMD inhibitor, p26 over-expression, and PEMV2 infection

first: Anne

middle: E

last: Simon


title: The histone methyltransferase Setd8 alters the chromatin landscape and regulates the expression of key transcription factorsduring erythroid differentiation

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Avenue

department: Center for Pediatric Biomedical Research

institute: University of Rochester

summary: SETD8 is the sole methyltransferase capable of mono-methylating histone H4, lysine 20. SETD8 is highly expressed in erythroid cells and erythroid deletion of Setd8 is embryonic lethal by embryonic day 11.5 (E11.5) due to profound anemia, suggesting it has an erythroid-specific function. To gain insights into the function of SETD8 during erythroid differentiation, we performed ATAC-seq on sorted populations of E10.5 Setd8 null and control erythroblasts. Accessibility profiles were integrated with  expression changes and a mark of heterochromatin (H3K27me3) performed in wild type E10.5 erythroblasts to further understand the role of SETD8 in erythropoiesis.  Data integration identified regions of greater chromatin accessibility in Setd8 null cells that co-located with H3K27me3 in wild type E10.5 erythroblasts suggesting that these regions, and their associated genes, are repressed during normal erythropoiesis.  Pathway analysis of genes identified through data integration revealed stemness-related pathways. Among those genes were multiple transcriptional regulators active in multipotent progenitors but repressed during erythroid differentiation including Hhex, Hlx,  and Gata2. Consistent with a role for SETD8 in erythroid specification, SETD8 expression is upregulated upon erythroid commitment, and Setd8 disruption impairs erythroid colony forming ability. Taken together, our results suggest that Setd8 is important for the establishment of appropriate patterns of gene expression during erythroid differentiation.

overall_design: Biological replicates were generated for setd8-null(2) and setd8-control(3) embryos. Biological replicates were aggregated, sequencing depth normalized, and a continuous log2 ratio was computed to identify regions of differential accessiblity in the setd8-null compared to control.

first: Jacquelyn

last: Myers


title: Identification of transcripts regulated in the HN4 cells incubated with  NGF

city: Shanghai

first: Chengzhong

last: Lin

address: Zhizaoju road 639

department: Second Dental Clinic, Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, China

institute: Chengzhong Lin

summary: We performed RNA-Seq analysis to identify the transcripts that were differentially regulated in the HN4 cells after NGF incubation

overall_design: Examination of HN4 cells treated with or without NGF

first: Tong

last: Ji


title: DAP-Seq profiling of LHY2 shows night-length information is integrated to determine timing of poplar photoperiodic growth

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

summary: Daylength is a key indicator of seasonal information that determines major patterns of behavior in plants and animals. Photoperiodism has been described in plants for about 100 years, but the underlying molecular mechanisms of daylength perception and signal transduction in many systems are not well understood. In trees, photoperiod perception plays a major role in growth cessation during the autumn as well as activating the resumption of shoot growth in the spring, both processes controlled by FLOWERING LOCUS T2 (FT2) expression levels and critical for the survival of perennial plants over winter.  We find that night-length information is transmitted via the expression level of a poplar clock gene, LATE ELONGATED HYPOCOTYL 2 (LHY2), which controls FT2 expression.  Repression of FT2 is a function of the night extension and LHY2 expression level. We show that LHY2 is necessary and sufficient to activate night-length repressive signaling. We propose that the photoperiodic control of shoot growth in poplar involves a balance between FT2 activating and repressing pathways.

overall_design: DAP-seq: purified library DNA was incubated with recombinant PtaLHY2 Potri.014G106800 protein from Populus tremula x Populus alba genome.

first: Katja

last: Jaeger

first: Hui

last: Lan

first: Feng

last: Geng


title: Development of gene expression signatures using herbal drug ninjin'yoeito (NYT)

city: Fukuoka

first: Daisuke

last: Sugiyama

state: Fukioka

address: 3-1-1, Maidashi, Higasi-ku

department: Incubation Center for Advanced Medical Science (ICAMS)

institute: Kyushu university

summary: To identify hematopoietic genes regulated by NYT, microarray analysis was carried out to compare BM MNCs cultured with and without NYT for 11 days.

overall_design: BM MNCs cultured with NYT or negative controls were collected at day 11. Total RNA was extracted using RNeasy Plus Micro Kit (QIAGEN). RNA concentration was measured by NANODROP 2000c (Thermo Fisher Scientific). cRNA was amplified, labeled, and hybridized to an Agilent Whole Mouse GE 4 9 44K v2 Microarray (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. All hybridized microarrays were scanned using an Agilent scanner, and signals of all probes were analyzed using Feature Extraction Software (Agilent Technologies).


title: Genome-wide analysis of DNA methylation in maize inbred lines

city: St Paul

first: Nathan

last: Springer

state: MN

address: 140 Gortner

institute: University of Minnesota

summary: Analysis of whole genome bisulfite data for 3 maize inbred lines (B73, PH207, and W22) with data aligned to the corresponding genome for determination of methylation level (CG, CHG, and CHH) across 100bp windows of the maize genome.

overall_design: Whole genome bisulfite sequencing of 3 inbred maize lines including B73 (shoot, root, leaf), PH207 (shoot) and W22 (leaf)

first: Jaclyn

last: Noshay


title: Imprinting effects of UBE3A loss on synaptic gene networks and Wnt signaling pathways

city: Davis

first: Simon

middle: Jesse

last: Lopez

address: One Shields Ave

department: MMI

institute: UC Davis

summary: UBE3A encodes a E3 ubiquitin ligase whose loss from the maternal allele causes the neurodevelopmental disorder Angelman syndrome. Previous studies of UBE3A function have not examined full Ube3a deletion in mouse, the complexity of imprinted gene networks in brain, nor the molecular basis of systems-level cognitive dysfunctions in Angelman syndrome. We therefore utilized a systems biology approach to elucidate how UBE3A loss impacts the early postnatal brain in a novel CRISPR/Cas9 engineered rat Angelman model of a complete Ube3a deletion. Strand-specific transcriptome analysis of offspring from maternally or paternally inherited Ube3a deletions revealed the expected parental expression patterns of Ube3a sense and antisense transcripts by postnatal day 2 (P2) in hypothalamus and day 9 (P9) in cortex, compared to wild-type littermates. The dependency of genome-wide effects on parent-of-origin, Ube3a genotype, and time (P2, P9) was investigated through transcriptome (RNA-seq of cortex and hypothalamus) and methylome (whole genome bisulfite sequencing of hypothalamus). Weighted gene co-expression and co-methylation network analyses identified co-regulated networks in maternally inherited Ube3a deletion offspring enriched in postnatal developmental processes including Wnt signaling, synaptic regulation, neuronal and glial functions, epigenetic regulation, ubiquitin, circadian entrainment, and splicing. Furthermore, we showed that loss of the paternal Ube3a antisense transcript resulted in both unique and overlapping dysregulated gene pathways with maternal loss, predominantly at the level of differential methylation. Together, these results provide a holistic examination of the molecular impacts of UBE3A loss in brain, supporting the existence of interactive epigenetic networks between maternal and paternal transcripts at the Ube3a locus.

overall_design: Hypothalamus and cortex from P2 and P9 female rat pups in triplicate each with maternal and paternal-derived UBE3A deletion and litter-matched controls. RNA and DNA were extracted from the same sample in hypothalamus.

first: S

first: David

last: Segal

first: Janine

last: LaSalle


title: Deregulation of neuro-developmental genes and primary cilium cytoskeleton anomalies in iPSC retinal sheets from human syndromic ciliopathies

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

summary: We generated iPSCs from control and ciliopathy cases and differentiated them into polarized 3D-adherent retinal sheets that could recapitulate normal photoreceptor development and disease state, respectively.

overall_design: Retinal sheets mRNA profiles at dau 60 of differentiation from 4 Ctrl, 2 MKS and 1 BBS patient in duplicate, using Ion Torrent platform.

first: Roy

last: Hanna

first: Benjamin

last: Freedman

first: Anthony

last: Flamier

first: Elise

last: Héon

first: Andrea

last: Barabino


title: Codon and amino acid content regulate mRNA stability in mammalian cells

first: Jeff

last: Coller

department: Center for RNA Science and Therapeutics

summary: mRNA degradation is a critical aspect of gene expression which dictates mRNA steady-state levels in conjunction with transcription rate. Previous studies in other model organisms have demonstrated that enrichment of specific codons within the open reading frame (ORF) can influence mRNA stability, primarily by modulating translation elongation speed. Despite advancements in our understanding of mRNA stability regulation by microRNAs and 3'UTR-based factors in mammalian systems, the importance of other mRNA regions such as the ORF sequence on dictating cellular mRNA levels are incompletely understood. To characterize the effects of the coding sequence on mRNA decay in mammals, we analyzed mRNA stability in human and Chinese Hamster Ovary (Cricetulus griseus) cells by both global metabolic labeling and single-gene mRNA reporter transcription shutoffs. In agreement with previous studies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. Unexpectedly, we also found that amino acid content is a potent determinant of mRNA stability in humans and other mammalian species. Codon and amino acid effects on decay correlate with tRNA levels measured by tRNA-Seq or intracellular amino acid levels measured by HPLC, respectively. These results suggest that both tRNA and amino acid levels have complementary effects on regulation of mRNA stability in mammals, hinting at the possibility of dynamic control of mRNA levels via altered tRNA or amino acid levels.

sample_organism:
Homo sapiens
Cricetulus griseus

platform_organism:
Homo sapiens
Cricetulus griseus

overall_design: Metabolic labeling followed by RNA-seq of 10 time points to determine mRNA half lives in Chinese hamster ovary cells. In addition, tRNA sequencing replicates to determine tRNA levels in HeLa cells.

first: Megan

last: Forrest

first: Otis

last: Pinkard

first: Sophie

last: Martin

first: Thomas

last: Sweet

first: Daniel

last: Arango

first: Gavin

last: Hanson

first: Shalini

last: Oberdoerffer

first: Jeffery


title: Intratumoral heterogeneity and longitudinal changes in gene expression predict differential drug sensitivity in newly diagnosed and recurrent glioblastoma

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: We investigated longitudinal transcriptomic patterns associated with glioblastoma (GB) recurrence by integrative approach utilizing multisampling strategy, RNA sequencing and complementary investigations of tumor tissues and GB stem cells. In total, 128 tissue samples of 44 tumors including 23 first diagnosed, 19 recurrent and 2 secondary recurrent GBs were analyzed in parallel with 27 primary cultures of GB stem cells. We found that intratumoral transcriptomic heterogeneity is an intrinsic characteristic that is conserved in newly diagnosed and recurrent GBs and captured in GB stem cells. We revealed a high degree of concordance between GB tumor tissues and stem cells in the longitudinal transcriptomic changes associated with tumor recurrence. We used gene expression data to model the efficacy of 130 anti-cancer drugs. For the recurrent tumor tissues and isolated GB stem cells we showed dramatically reduced simulated sensitivities to the first line chemotherapeutic temozolomide. In turn, several therapeutics including immune checkpoint inhibitors were predicted to be more effective in the recurrence setting. Our results strongly suggest that the spectrum of potentially effective drugs may differ between newly diagnosed and recurrent glioblastomas and provides a transcriptional rationale for the lack of significant therapeutic benefit from temozolomide in patients with recurrent GB.

overall_design: Primary and recurrent GB tissues and GB-derived stem cells cultures were RNAseq-profiled. Gene expression values and molecular pathway activation scores were calculated for each sample. The efficacy of 130 anti-cancer drugs was modeled based on gene expression and molecular pathway activation data.

first: Kim

last: Ella

first: Sorokin

last: Maxim

first: Kantelhardt

last: Sven-Rainer

first: Bikar

last: Sven-Ernö

first: Giese

last: Alf

first: Buzdin

last: Anton


title: Human Embryonic Stem Cell-derived Expandable Hepatic Organoids  Enable Pathophysiological Model of Alcoholic Liver Injury

city: YiWu

first: wang

middle: chuan

last: wen

address: No. 288, Yang Cun road, Chou Jiang Street, Yiwu, Zhejiang

institute: AnnoGene

summary: We report the generation of human pluripotent-stem-cell-derived (hPSC), expandable hepatic organoids (hEHOs) using a newly established method that consists of subjecting hPSCs to a sequence of distinct wholly defined (serum-free, feeder free) media lineage restricting the cells to become determined hepatic stem cells followed by a process of shifting the cells from monolayer (2D) to organoid (3D ) cultures. The hEHOs stably keep phenotypic features of a bi-potent hepatic lineage that can differentiate into functional hepatocytes or cholangiocytes. The hEHOs can expand for over 20 passages enabling industrial scaling to amounts requisite for industry or clinical programs. The cells from culture are able to engraft rapidly into injured liver parenchyma of FRG mice following transplantation and to differentiate in vivo into mature hepatocytes. If implanted into the epididymis fat pads of immune-deficiency mice, they do not generate non-hepatic lineages nor teratomas. We further developed a derivative model by incorporating human fetal liver mesenchymal cells (hFLMCs) into the hEHOs, referred as hFLMC/hEHO, and used the organoids to model alcohol liver disease-associated pathophysiologic changes, such as oxidative stress generation, steatosis, inflammatory mediators release and fibrosis, following treatment with alcohol. Our work demonstrates that the hFLMC/hEHO provide a novel ex vivo pathophysiological model for studying alcohol liver disease as well as many other non-genetic liver diseases.

overall_design: evaluation of whole transcriptome of 7 cell types, each of them include 2 replication

first: Yunfang

last: Wang

first: Shuyong


title: mRNA expression profile in THP-1 macrophages treated with human serum extracellular vesicles

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
THP-1 macrophages were treated with EVs and stimulated with LPS, and then total RNA was extracted from cells. Extracted total RNAs were investigated by microarray analysis.
Increase and decrease of mRNA expression were investigated between EV-treated and non-treated THP-1 macrophages.

overall_design: THP-1 macrophages were cultured in medium with exosome free medium supplemented with or without EVs colllected from human sera, and then stimulated with mock or LPS for 2 hr. Total RNA extracted from each samples were subjected to the microarray analysis.

first: Hiroyuki

last: Oshiumi

first: Aika

last: Fugiwara


title: RNA-seq analysis of Arabidopsis treated with abscisic acid (ABA) and its derivatives

city: Wako-shi

first: Kazuko

last: Yoshida

state: Saitama

address: 2-1, Hirosawa

institute: RIKEN

summary: Transcriptome of chemical-treated plants were investigated for the evaluation of ABA derivatives.  Abscisic acid and its derivatives up-regulated mainly abiotic stress responsive genes.

overall_design: mRNA profiles of 7-day old wild type Arabidopsis seedlings treated with DMSO, ABA, and two ABA derivatives, in triplicate, using Illumina HiSeq.


title: Different Gene Expression Profile in Spontaneously Hypertensive Rats Treated with Songling Xuemaikang Capsule

city: Cheng Du

first: Ke

last: Xu

state: SiChuan

address: No.36, Shuxi Road

institute: Chengdu Kanghong Pharmaceutical Co. Ltd.

summary: To study in vivo action of Songling Xuemaikang Capsule (SXC), SHRs were orally administration with high- or low-dose of SXC for 28 days.Valsartan, an angiotensin receptor antagonist, is used as a positive control drug in this study and orally administrated for 28 days. The levels of AngII, Aldosterone in serum of SHRs from different groups were analyzed, and gene expression profiling were performed in the thoracic aortakidney of SHRs, using the Whole Rat Genome Oligonucleotide Microarray. The integrated causal network analysis is performed to understand the mechanism of antihypertensive effect of SXC. The results showed that expression of 706 unique genes (p<0.05) were changed (fold change >2.0) in SHRs at a dose of 472.5 mg/kg day SXC when compared with control rats, whereas the expression of 920 unique genes were changed (fold change>2.0) at a dose of 1417.5 mg/kg/day. Those genes are involved in lipid metabolism, complement system induced immune response, inflammation and vascular and endothelial dysfunction.

overall_design: SHRs were randomly divided into three groups : model group (n = 8), rats were orally administered with saline (7.5mL.kg-1) for 4 weeks; SXC low-dose group(n = 6), rats were orally administered with SXC (236.25 mg.kg-1) for 4 weeks; SXC high-dose group (n = 6), rats were orally administered with SXC (708.75 mg.kg-1) for 4 weeks; the positive group (n=8), rats were orally administered with valsartan (21.6mg.kg-1) for 4 weeks.

first: Litao

last: Liu


title: Differentially expressed genes in smooth muscle cells following miRNA-146a overexpression

city: Hannover

first: Daniel

last: Sedding

address: Carl-Neubergstr. 1

department: Cardiology

institute: Hannover Medical School

summary: We report that miRNA-146a exerts anti-proliferative effects on smooth muscle cells in vitro as well as in vivo. In order to obtain insights into potential target genes, we generated samples of SMC overexpressing miRNA-146a and RNA sequencing was performed by Novogene (Novogene Bioinformatics Technology, Beijing, China)

overall_design: Examination of differentially expressed genes following overexpression of miRNA-146a in smooth muscle cells


title: Differentially expressed genes in HUVEC following miRNA-146a overexpression

summary: We report that miRNA-146a exerts anti-proliferative effects on endothelial cells in vitro as well as in vivo. In order to obtain insights into potential target genes, we generated samples of HUVEC overexpressing miRNA-146a and RNA sequencing was performed by Novogene (Novogene Bioinformatics Technology, Beijing, China)

overall_design: Examination of differentially expressed genes following overexpression of miRNA-146a in HUVEC


title: Kidney-resident CD8 T cells downregulate IL-18R during maturation

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Using the expression of IL-18 receptor (CD218) as a surface marker, CD69+ kidney-resident CD8 T cells can be separated into two subsets. Transcriptional analysis suggests that IL-18R low subset represents the mature tissue-resident T cells

overall_design: 10000 congenically marked naïve P14 T cells were adoptively transferred into each sex-matched unmanipulated C57BL/6 mouse followed by LCMV Armstrong infection via an intraperitoneal route. 12 days after infection, lymphocytes were purified from the kidneys via enzymatic digestion and gradient centrifugation. Indicated P14 T cell subsets were FACS sorted from purified total kidney lymphocytes. Total RNA was extracted from freshly sorted cells. Kidneys from 10-15 recipient mice were pooled for each sorting.

first: Zhang

last: Nu

first: Zhao

last: Lai

first: Chaoyu

last: Ma

first: Yong

first: Erika

last: Demel

first: Xun

first: Shruti

last: Mishra

first: Qianjin

last: Lu

first: Wei

last: Liao


title: EBF1-mutant bone marrow stroma confers long-term changes in hematopoietic stem cell potential

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Crosstalk between mesenchymal stromal cells (MSCs) and hematopoietic stem and cells (HSCs) is essential for hematopoietic homeostasis and lineage output.  Ebf1-deficient MSCs have reduced mesenchymal lineage potential. Ebf1 deletion in Cxcl12-abundant reticular (CAR) cells and PDGFRα+Sca1+CD45-CD31-Lin- (PαS) cells in the bone marrow decreased the numbers of HSPCs and myeloid cells. EBF1 in the bone marrow niche regulates a transcriptional program that determines the functional interactions with HSCs and the long-term balance between the myeloid and lymphoid cell fates.

overall_design: Intact bones (femora and tibia) were chopped into small fragments and crushed in FACS buffer (PBS-2% FCS) using pestle and mortar. For the MSC cells isolation, the bone chips were digested with 0.3% collagenase type II and 0.02% DNase I at 37°C for 45 min with gentle shaking. After enzymatic digestion, the cells were filtered, washed with FACS buffer, and stained accordingly. CAR cells were identified as CD45-CD31-Lin-PDGFRα+Sca1-, PαS cells were identified as CD45-CD31-Lin-PDGFRα+ Sca1+. BD FACSAria Fusion was used for fluorescence-activated cell sorting.

first: Marta

last: Derecka

first: Rudolf

last: Grosschedl


title: Biomarkers in older ovarian cancer patients

city: Odense C

first: Sambavy

last: Nadaraja

address: Kløvervænget 8, Indgang 109

institute: Odense University Hospital

summary: Identification and validation of potential prognostic biomarkers in older ovarian cancer patients with high-grade serous adenocarcinoma (HGSC)

overall_design: Biomarker study with the purpose of identifying and validating biomarkers in patients with early disease progression of HGSC vs. patients with late.


title: Spermatogenomics: correlating testicular gene expression to human male infertility

city: Bangalore

first: Ruchi

last: Jain

state: Karnataka

address: C V Raman Road

department: Molecular Reproduction Development and Genetics

institute: Indian Institute of Science

summary: Analysis of differential testicular transcriptome in patients with different types of azoospermia.

overall_design: Total testicular RNA from 11 azoospermic patients and 1 pooled control testicular RNA sample was subjected to microarray analysis.

first: Arka

last: Baksi

first: Ravi

last: Manjithaya

first: S

last: Vasan

first: Paturu

last: Kondaiah

first: Rajan

last: Dighe


title: Alkylating Agent-Induced ER Stress Overcomes Microenvironmental Resistance to Lymphoma Therapy

city: Cambridge

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

summary: Compartment-specific resistance to cancer therapy remains poorly understood. We utilized orthotopic xenografts of human double-hit lymphoma (DHL) to interrogate responses across involved sites. We identified resistance to multiple chemotherapies and the anti-CD52 antibody Alemtuzumab within the bone marrow (BM) that depended on extensive lymphoma involvement and impaired antibody-dependent cellular phagocytosis. This resistance was overcome by high doses of alkylating agents, including cyclophosphamide (CTX), which exhibited >80-fold in vivo synergy with Alemtuzumab. CTX induced ER stress in BM DHL cells leading to ATF4- mediated paracrine secretion of VEGF-A and massive macrophage infiltration. Macrophages from DHL-engrafted, CTX-treated mice had increased phagocytic capacity for lymphoma cells that was reversed by VEGF-A blockade and required SYK phosphorylation. A subset of these macrophages, defined by surface CD36/FcgRIV and a distinct transcriptional state, were “super- phagocytic.” Together, our findings define a unique mechanism through which high-dose alkylating agents can overcome therapy-resistant niches by ER stress-induced activation of phagocytosis.

overall_design: Transcriptome profiling of double-hit lymphoma patient-derived xenograft (PDX) cells in immunodeficient mice and associated macrophages after treatment with vehicle (V), doxorubicin (D), alemtuzumab (A), cyclophosphamide (C) or a combination of alemtuzumab and cyclophosphamide (combo).

first: Chen

last: Lossos

first: Yunpeng

last: Liu

first: David

middle: M

last: Weinstock

middle: T


title: The role of NOXO1 in the mouse model of cigarette smoke-induced emphysema and pulmonary hypertension

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: NOXO1 KO mice seem to be protected from cigarette smoke-induced emphysema and pulmonary hypertension. Since the molecular mechanisms are not clear yet, this microarray experiment should help to identify the molecular differences in these KO mice compared to the wild-type (WT), figuring out how the protection occurs. Since we believe that vascular altertions could not only be responsible for vascular remodeling but also the trigger for emphysema development, we microdissected pre-capillary vessels from WT and KO mice, both controls and smoke-exposed. In addition, alveolar septa were microdissected to investigate the alveolar changes.

overall_design: Single-color hybridization of RNA from microdissected lung tissues from 40 mice in total. From each mouse, septa and vessels were used.  Four arrays were not analyzed because there was no signal.

first: Norbert

last: Weissmann

last: Seimetz

first: Mariola

last: Bednorz


title: Expression data from ATRA-treated LLC-PK1 cells

city: Detroit

first: Terrence

last: Monks

state: Michigan

address: 259 Mack Ave, Suite 5148

institute: Wayne State University

summary:
We have established a role for p-ERK in mediating ATRA cytoprotection against chemical-induced injury to LLC-PK1 renal proximal tubule epithelial cells. The present studies were conducted to assess downstream signaling from p-ERK in ATRA-mediated cytoprotection.
Gene expression profiling via microarray and ontology analyses indicated an upregulation of genes associated with cell proliferation and differentiation shortly after (0.5 and 1 hr) ATRA (25 μM) treatment. Target genes of these transcription factors associated with ribosome biogenesis, DNA replication, DNA repair, and the cell cycle were significantly increased by 4 hr.

overall_design: LLC-PK1 cells were cultured with ATRA for either 0, 0.5, 1, 4, 8, or 12 hr. Lysates were collected and total RNA was isolated and hybridized on Affymetrix microarrays. A total of 18 samples were analyzed, each sample in triplicate.

first: Jessica

last: Sapiro

first: Katherine

last: Gurdziel


title: RNA-Seq analyses with sorted ROSLow cells and ROSHigh cells

city: Taipei

first: Jeng-Fan

last: Lo

address: No. 155, Section 2, Li-Nong Street, Taipei, 11221, Taiwan

country: Taiwan

institute: National Yang-Ming University

summary: Recently, CICs were shown to be relatively resistant to therapy, perhaps due to increased expression of ROS defense genes. Additionally, in our previous study, the maintenance of low ROS levels within the HN-CICs was important for regulating stemness properties and conferring chemoresistance. Herein, we exploited RNA-Seq analyses with sorted ROSLow cells versus ROSHigh cells to obtain mechanistic insights into the role of the antioxidant defense system in CICs.

overall_design: 2 samples analyzed by high throughput sequencing

first: Ching-Wen

last: Chang


title: Global mapping of binding sites of Nrf2 in SAS and SAS sphere cells

summary: Cancer-initiating cells (CICs), a small subset of cancer cells, exploit the characteristics of self-renewal and differentiation to drive tumor growth. Previously, we enriched and identified head and neck CICs (HN-CICs) through sphere culture. Nrf2 played an important role in maintaining the characteristics of CICs; however, the identities of the Nrf2-regulated genes in CICs remain elusive. Therefore, we performed ChIP-Seq analyses of parental and sphere cells using an antibody against Nrf2.

overall_design: Genome binding profiling of Nrf2 by high throughput sequencing


title: Defining CBX7-dependent chromatin architecture with rapid small-molecule inhibition

city: Bethesda

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

summary: While the repressive roles of Polycomb complexes have been well-established with in vitro systems, it remains unclear how subtypes of these complexes function in living cells. Conditional alleles have enabled studies of Polycomb Repressive Complex 1 (PRC1), but the available timescales on which inducible deletion occurs is not sufficient to define its immediate regulatory targets. We have used rapid treatments with a new PRC1 inhibitor UNC4976, that functions as a chemical surrogate for H3K27me3 and engages chromodomain-containing subunit CBX7. This “histone prosthetic” inhibition strategy has enabled the discovery that hundreds of chromatin loop and contact domains are repressed by the chromodomain function of PRC1. Repressive chromatin architecture that is dependent specifically upon regulatory function of the PRC1 chromodomain is rapidly de-repressed with chemical inhibition within 4 hours. With Hi-C experiments after rapid drug treatment, and defining drug-sensitive chromatin by ChIP-seq before major transcriptional changes occur, we report canonical PRC1-dependent chromatin architecture in human T lymphocytes.

overall_design: Measuring effects of UNC4976 on CBX7 binding, gene expression, chromatin accessibility and chromatin interactions on human CD4 T cells by applying CBX7 ChIP-Seq, RNA-Seq, ATAC-Seq, HiC experiments in human CD4 T cells with treatment of UNC4976 for 4 hours.

first: Benjamin

middle: Z

last: Stanton

first: Binbin

last: Lai

first: Gang

last: Ren

first: Gangqing

last: Hu

first: Kelsey

middle: N

last: Lamb

first: Lindsey

middle: I

last: James

first: Gerald

last: Crabtree

first: Stephen

middle: V

last: Frye


title: Discovery of novel auxin-responsive genes of Arabidopsis using auxin inhibitors

city: Yokohama

first: Yukihisa

last: Shimada

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

institute: Yokohama City University

summary: To obtain more information on auxin-regulated gene expression, we treated Arabidopsis seedlings with auxin biosynthesis or signaling inhibitors, then performed DNA microarray analyses.

overall_design: Arabidopsis Col-0 seedlings were grown on 1/2MS agar medium containing 1% sucrose for 6 or 7 days. The seedlings were transferred into 1/2MS liquid medium containing 1% sucrose and grown with constatnt shaking for 1 day, and then treated with IAA and auxin inhibitors for 3 hours. Total RNA was extracted using RNeasy Plant mini Kit (QIAGEN).


title: Analysis of genes regulated by an Arabidopsis transcription factor, Dof3.2

summary: To obtain information on which genes are regulated by an Arabidopsis transcription factor Dof3.2, we treated Arabidopsis transgenic 35S::Dof3.2-GR seedlings with dexamethasone (DEX), then performed DNA microarray analyses. T3 homozygous Dof3.2-GR transgenic line was used.

overall_design: Arabidopsis transgenic 35S::Dof3.2-GR seedlings were grown on 1/2MS agar medium containing 1% sucrose and 50µg/ml kanamycin for 4 days. The seedlings were transferred into 1/2MS liquid medium containing 1% sucrose and grown with constatnt shaking for ４ day, and then treated with 10µM DEX for 3 hours. Total RNA was extracted using RNeasy Plant mini Kit (QIAGEN).


title: During development, the Sku5 mutant roots engage different genes than wild type WS roots, either on the ground or in spaceflight.

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: The wild type WS plants and the Sku5 mutant plants in the WS background were germinated on ISS or on the ground and the gene expression profiles in roots at 4 days or 8 days were established. The Sku5 gene (AT4G12420) codes for a multi-copper oxidase-like protein SKU5 protein that is involved in directed root tip growth. The Sku5 protein is glycosylated, GPI-anchored and localizes to the plasma membrane and the cell wall. The Sku5 gene is expressed most strongly in expanding tissues. The development of WS and Sku5 plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. However the development of Sku5 mutant plants also differs from WS at either age and in either environment, suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku5 roots in orbit engaged substantially more genes than the 4 days old WS roots in orbit but also more than the 4 days old Sku5 roots on the ground. Overall the 4 days old roots differentially expressed more genes in spaceflight relative to ground than the 8 days old roots of either genotype. Finally, the 4 days old Sku5 roots in orbit differ in 862 genes from the 8 days Sku5 roots in orbit while on the ground there is merely half of the number of genes differentially expressed between the 4 days and 8 days developmental stages of the Sku5 roots.

overall_design: APEX03-2 (Advanced Plant Experiment 03-2) also identified as TAGES-Isa (Transgenic Arabidopsis Gene Expression System—Intracellular Signaling Architecture) was launched on SpaceX mission CRS-5 on 10 January 2015. Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates and remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station). The plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS with the overhead LED lighting of the VPS. At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Upon return to Earth, the harvested material was used to compare the transcriptomes of each genotype and each age using RNAseq technology. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment. For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis.

first: Anna-Lisa

last: Paul

first: Agata

middle: K

last: Zupanska


title: Telomere dysfucntion activates YAP1 to drive tissue inflammation [ChIP-seq]

status: Public on Feb 29 2020

city: Houston

first: Deepavali

last: Chakravarti

state: TX

address: 1881East Rd

institute: MD Anderson Cancer Center

summary: Germline telomere maintenance defects provoke inflammatory disease via activated ATM/YAP1/IL-18 signaling in epithelial cells, providing novel therapies for inflammatory conditions associated with short telomeres.

overall_design: Telomere proficient intestinal epithelium (G0), which served as control, was compared to the telomere dysfunctional intestinal crypt epithelium (G3). Three samples from each group was pooled and ChIP-seq was performed.

first: Ronald

last: DePinho


title: CD11cHi monocyte-derived macrophages expressing CD38, CD14, and ABCA1 are the dominant niche for Mycobacterium tuberculosis

city: Shrewsbury

first: Jinhee

last: Lee

state: MA

address: 9 Deerfield Road

institute: Umass Med

summary: During tuberculosis, lung myeloid cells have two opposing roles: they are an intracellular niche occupied by Mycobacterium tuberculosis and they restrict bacterial replication. Lung myeloid cells from mice infected with yellow-fluorescent protein expressing M. tuberculosis mice were analyzed by flow cytometry and transcriptional profiling to identify the cell types infected and their response to infection. CD14, CD38, and Abca1 were expressed more highly by infected alveolar macrophages and CD11cHi monocyte-derived macrophages compared to uninfected cells. CD14, CD38, and Abca1 “triple positive” (TP) cells had incomparably high infection rates and bacterial loads, but also a strong interferon-γ signature and nitric oxide synthetase-2 production indicating recognition by T cells. Despite evidence of T cell recognition and appropriate activation, these TP+ macrophages became the dominant niche occupied by M. tuberculosis long-term. Defining this niche should help answer why M. tuberculosis resists elimination from activated macrophages even in the face of T cell immunity.

overall_design: There are two experiments for each myeloid cell subset, and each experiment has three to four replicates. Each replicate represents an individual mouse.

first: Samuel

last: Behar


title: Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure

city: Istanbul

first: Ceyhun

last: Bereketoglu

address: Goztepe

country: Turkey

institute: Marmara University

summary: We analyzed genome-wide transcriptional changes in the S. cerevisiae strain BY4742 upon exposure to NP to identify differentially expressed genes, biological processes, metabolic pathways, and cellular compartments affected by this compound. For these analyses, we focused on two NP exposure scenarios: (1) exposure to a low inhibitory concentration (resulting in <15% reduction in cell number), and (2) exposure to a high inhibitory concentration (resulting in >65% reduction in cell number).

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Yeast cells were exposed to nonylphenol (NP) at mid-exponential phase for 120 and 180 minutes and then were harvested for RNA extraction and hybridization on Affymetrix microarrays. We aimed to investigate the transcriptional profiles of Saccharomyces ceresivisae genome upon exposure to two different concentrations of NP.

first: Bulent

last: Mertoglu

first: Kazim

middle: Y

last: Arga

first: Serpil

last: Eraslan


title: Affymetrix  CytoScan array data for leukemia cell lines

city: Ibaraki

first: Fumio

last: Kasai

state: Osaka

address: Saito-Asagi 7-6-8

department: JCRB Cell Bank

institute: National Institute of Biomedical Innovation

summary: Genome reference profiles of 10 Kasumi leukemia cell lines

overall_design: Affymetrix CytoScan™ HD Arrays were performed according to the manufacturer's directions on DNA extracted from cell lines.


title: Sorting of Growth Plate Chondrocytes Allows the Isolation and Characterization of Cells of a Defined Differentiation Status

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

summary: Axial growth of long bones occurs through a coordinated process of growth plate chondrocyte proliferation and differentiation. This maturation of chondrocytes is reflected in a zonal change in gene expression and cell morphology from resting to proliferative, prehypertrophic, and hypertrophic chondrocytes of the growth plate followed by ossification. A major experimental limitation in understanding growth plate biology and pathophysiology is the lack of a robust technique to isolate cells from the different zones, particularly from small animals. Here, we report on a new strategy for separating distinct chondrocyte populations from mouse growth plates. By transcriptome profiling of microdissected zones of growth plates, we identified novel, zone-specific cell surface markers and used these for flow cytometry and immunomagnetic cell separation to quantify, enrich, and characterize chondrocytes populations with respect to their differentiation status. This approach provides a novel platform to study cartilage development and characterize mouse growth plate chondrocytes to reveal unique cellular phenotypes of the distinct subpopulations within the growth plate.

overall_design: The RNA from femoral growth plates of 14 days old swiss white mice was cryosectioned and microdisected. The resulting destinct growth plate zones were used for RNA isolation via the PicoPure RNA isolation kit (Arcturus Bioscience, Mountain View, CA) and amplified via the MessageAMP aRNA kit (Ambion, Austin, TX). For microarray analysis, 1.25 μg of aRNA originating from each growth plate zone was mixed with 250 ng of random hexamer primers (Roche Diagnostics, Basel, Switzerland), heated at 70 °C for 10 min, and snap-cooled on ice. The oligo/aRNA mix was then employed for complementary DNA (cDNA) synthesis at 42 °C for 2 h in a total reaction volume of 30 μl using 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.2 mM dTTP, 0.3 mM amino-allyl dUTP (aa-dUTP) (Amersham Biosciences, Uppsala, Sweden), 10 mM DTT, 1x first strand buffer, and 150 units of SuperScript II (Invitrogen, Carlsbad, CA). The RNA templates were hydrolyzed at 65 °C for 15 min after addition 10 μl of 1 M NaOH. The mixture was then neutralized with 25 μl 1 M HEPES buffer pH 7.0 and unincorporated aa-dUTP and free amines were removed by applying and spinning the mixture onto QIAquick purification columns (Qiagen, Hilden, Germany). The columns were washed and Cy3 or Cy5 monoreactive dyes (Amersham Biosciences, Uppsala, Sweden) were resuspended in 15 μl 0.1 NaHCO3 pH 9.0 and pipetted directly onto the columns. The coupling reaction was left in the dark for one h at room temperature. The reactions were eluted with 80 μl of H2O and then diluted with 400 μl of PB buffer. To remove uncoupled dyes the Cy3- and Cy5-labeled cDNA of one two-color hybridization experiment were loaded sequentially onto one fresh QIAquick column, washed, and eluted with 30 μl of H2O. The labeled cDNA targets were volume-reduced to 16.2 μl in a vacuum centrifuge and stored in the dark at 4 °C for up to 1 h. Microarray slides printed with the 44K whole-genome microarrays (G4122A, Agilent Technologies, Santa Clara, CA) were pre-hybridized with 10 mg/ml BSA, 25% formamide, 5× SSC, 0.1% SDS for 45 min at 42 °C, rinsed twice in distilled H2O, and then air-dried. The cDNA targets were diluted to a final volume of 60 μl with 30 μl 2x hybridization buffer (50% formamide, 5× SSC, 0.2% SDS), 5 μl mouse Cot1 DNA (5 μg/μl), 3.8 μl polyA (10 mg/ml), and 5 μl of salmon sperm DNA (10 mg/ml). The samples were heated to 100 °C for 2 min and pipetted onto the microarray slides. The slides were covered with a 60 × 25 mm plastic cover slip (Schleicher und Schuell, Kassel, Gemany) and hybridization was conducted in sealed humid chambers at 42 °C for 17 h. The slides were washed serially in 1× SSC/0.2% SDS and 0.1x SSC/0.2% SDS for 5 min each and twice in 0.1× SCC for 2 min, spun dry for 5 min at 1000 ×g, and stored under dark conditions. The arrays were then scanned at 10 μm resolution on an Agilent scanner and the features acquired with the Feature extraction software.

first: Danielle

last: Belluccio

first: John

last: Bateman


title: Inflammation favors the emergence of ETV6-RUNX1-positive pre-leukemic cells in a model of mesenchymal niche

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary: ETV6-RUNX1 (E/R) fusion gene, arising in utero from t(12;21), is the most frequent alteration in childhood acute lymphoblastic leukemia (ALL). Despite this, E/R is insufficient to overt disease since it generates a clinically silent pre-leukemic clone which contributes to hematopoiesis but fail to out-compete normal hematopoietic progenitors. Conversely, pre-leukemic cells show increased susceptibility to malignant transformation following additional genetic insults. Infections/inflammation are the most accredited triggers for mutations accumulation and progression in E/R+ pre-leukemic cells. However, how E/R and inflammation interact in promoting leukemia, both directly or through other cellular components in the bone marrow (BM) niche, is still poorly understood.  Here, we demonstrate that IL6/TNFα/ILβ pro-inflammatory cytokines cooperate with BM-MSC in promoting the emergence of E/R+ murine pro-B cells over their normal counterparts by differentially affecting their proliferation, survival and migration. Very interesting, E/R-expressing human CD34+IL7R+ progenitors, a candidate population for pre-leukemic initiation during development, were preserved within the inflamed niche compared to their normal counterparts. Finally, the extent of DNA damage and activation-induced cytidine deaminase (AID) expression increase within the inflamed niche in both cell type, potentially leading to transformation in the apoptosis-resistant pre-leukemic clone. Overall, our data provide new mechanistic insights in childhood ALL pathogenesis.

overall_design: Gene expression was measured on GeneChip Mouse 2.0 platform of cells derived from BaF3 cells with TEL_AML1 fusion trascript and from wild type BaF3 cells.

first: Silvia

last: Bresolin

first: Chiara

last: Palmi