title: 10 Week Post Partical Pancreatectomy

first: Aref

last: Ebrahimi

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

summary: There are two groups of rats, Post 90%  Partial Pancreatectomy (PPX) and the Sham group.

overall_design: The goal of the study is investigate the effects of hyperglycemia on Islets cells using the partial pancreatectomy in rats. There are two groups of rats, Post 90%  Partial Pancreatectomy (n=10) and the Sham group (n=5). This experiment follows up the rats for 10 weeks post sham and PPX procedure. The differentially expressed genes are reported.

first: Susan

last: Bonner-Weir

first: Gordon

middle: C

last: Weir


title: 4 Week Post Partical Pancreatectomy

status: Public on Jun 26 2020

city: Boston

state: MA

country: USA

type: Expression profiling by high throughput sequencing

summary: There are two groups of rats, 1) Post 90% Partial Pancreatectomy (PPX) and the Sham Group.

overall_design: The goal of the study is investigate the effects of hyperglycemia on Islets cells using the partial pancreatectomy in rats. There are two groups of rats, Post 90% Partial Pancreatectomy (n=11) and the sham group (n=10). This experiment follows up the rats for 4 weeks post sham and PPX procedure. The differentially expressed genes are reported.

middle: G


title: Mouse colon organoids treated with inflammatory reagents.

status: Public on Jun 25 2020

city: Tokyo

first: Shuji

last: Hibiya

address: 1-5-45, Yushima, Bunkyo-ku

department: Gastroenterology and Hepatology

country: Japan

institute: Tokyo Medical and Dental University

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

overall_design: Refer to individual Series


title: Gene expression of mouse colon organoids after the removal of inflammatory reagents.

summary: Microarray analysis of mouse colon organoids after the removal of inflammatory reagents following long-term treatment with inflammatory reagents.

overall_design: 3 samples of the colonic organoids 12 weeks after the removal of inflammatory reagents following the 45-week treatment with inflammatory reagents, and that of untreated organoids, were compared.

first: Kiichiro

last: Tsuchiya


title: The Root-Knot Nematode Effector MiEFF18 Targets the Core Spliceosomal Protein SmD1 and Facilitates Giant Cell Formation

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

summary:
The goals of this study is understand the effect of the MiEFF18 nematode effector on alternative splicing.
Methods: PolyA RNA from WT, MiEFF18 overexpressor and smd1b mutant seedlings were sequenced using the illumina NextSeq500 sequencer, in triplicate. Total RNA was extracted from the roots of the three Arabidopsis lines (Col0, OE-MiEFF18#13.6 and smd1b) with TriZol (Invitrogen), according to the Invitrogen protocol. The RNA was treated with DNAse treatment (Ambion), and its quality and integrity were assessed with a Bioanalyzer (Agilent). Libraries were constructed with the Tru-Seq Stranded mRNA Sample Prep kit (Illumina®). Paired-end sequencing with 75-bp reads was performed on a NextSeq500 perform. A minimum of 30 million paired-end reads per sample was generated. RNA-seq preprocessing included the trimming of library adapters and quality controls with Trimmomatic. Paired-end reads with a Phred Quality Score Qscore > 20 and a read length > 30 bases were retained, and ribosomal RNA sequences were removed with SortMeRNA. Processed reads were aligned using Tophat2 with the following arguments: --max-multihits 1 -i 20 --min-segment-intron 20 --min-coverage-intron 20 --library-type fr-firststrand --microexon-search -I 1000 --max-segment-intron 1000 --max-coverage-intron 1000 --b2-very-sensitive.
Conclusions: MiEFF18 overexpression modifies the expression of genes important for the ontogenesis of giant cells, notably those involved in microtubule cytoskeleton reorganization and cell cycle regulation, strongly suggesting that MiEFF18-mediated SmD1 inactivation in plants leads to a loss of susceptibility to root-knot nematodes.

overall_design: mRNA profiles of PolyA RNA from WT, MiEFF18 overexpressor and smd1b mutant seedlings PolyA RNA from WT, MiEFF18 overexpressor and smd1b mutant seedlings

first: Bruno

last: Favery


title: Gene expression of mouse colon organoids treated with inflammatory reagents.

summary: Microarray analysis of mouse colon organoids after treatment with the mixture of inflammatory reagents.

overall_design: 3 samples for treatment with inflammatory reagents for 0, 12 and 60 weeks were compared by microarray analysis.


title: Comparison of microfludic and static culture of human intestinal organoids in normal and inflammatory conditions

city: Mechelen

first: Auste

last: Kanapeckaite

address: General De Wittelaan L11 A3

country: Belgium

institute: Galapagos NV

summary: Introduction: Inflammatory bowel disease (IBD) is a complex multi-factorial disease for which physiologically relevant in vitro models are lacking. Existing models are often a compromise between biological relevance and scalability. Here, we integrated intestinal epithelial cells (IEC) derived from human intestinal organoids from 3 different donors in a gut-on-a-chip platform to model the human intestine and key aspects of IBD. The goal of our transcriptomics experiment was to compare microfluidic-grown IEC to donor-paired HIO cultures in standard Matrigel droplets used for gut-on-a-chip seeding.     Methods: For the microfluidic gut-on-a-chip, IEC cells were seeded in the top channel of a 3-lane OrganoPlate on top of a Collagen I gel embedded in the middle channel. Cells were kept in HISC medium devoid of A83-01 for 2 days, before medium was switched back  to HISC medium. 6 days after seeding, cells were triggered with LPS 100ng/mL, IFN-γ 20ng/mL for 24 hours. RNA was isolated with TRI-reagent followed by a phenol-chloroform extraction. For the static Matrigel-grown HIO, RNA was isolated of confluent cultures with TRI-reagent followed by a phenol-chloroform extraction.     Library preparations, sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).    rRNA depletion was performed using Ribozero rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA sequencing library preparation used NEBNext Ultra RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (Applied Biosystems, Carlsbad, CA, USA).    The sequencing libraries were multiplexed and clustered on one lane of a flowcell and loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a HiSeq 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

overall_design: There are 9 samples (no replicates) from 3 different HIO donors. Each HIO donor is represented in 3 samples; microfluidic T- (untriggered), microfluidic (T+), Static/Matrigel

first: Claudia

last: Beaurivage

first: Cindy

last: Loomans

first: Kai

middle: S

last: Erdmann

first: Jan

last: Stallen

first: Richard

middle: J

last: Janssen


title: Gene expression profiling of drug-tolerant persister PC9 non-small cell lung cancer cells derived from osimertinib treatment

city: Beijing

first: Meng

last: Nie

address: Haidian  District

country: China

institute: Tsinghua  University

summary: Targeting drug tolerant persister (DTP) cells may present a therapeutic opportunity to eliminate residual surviving tumor cells and impede relapse. We sought to identify therapeutically exploitable vulnerabilities in DTP cells using the EGFR-mutant non-small cell lung cancer cell line PC9 as an experimental model. Here we provide RNAseq gene expression profiling data generated from parental PC9 cells compared to PC9 DTP cells generated from nine days of treatment with 2 uM osimertinib. These data can be used to identify genes and pathways which are upregulated in DTP cells, revealing potential therapeutic targets.

overall_design: two biological replicates of PC9 parental and DTP cells

last: Chen

first: Huanhuan

last: Pang

first: Zeping

last: Hu


title: Sequencing of RNA fragments immunoprecipitated by anti-Flag in CASC3 or MTDH overexpression breast cancer cells

city: Shantou

first: Jianzhen

last: Xu

address: No.22 Rd Xinling

institute: Shantou University Medical College

summary: RNA immunoprecipitated sequencings were conducted from CASC3 or MTDH overexpression breast cancer cells

overall_design: Breast cancer cells MD-MBA-231 was transfected with pEZ-93-CASC3 or pEZ-93-MTDH plasmids, which contain Flag sequence and over-express CASC3 or MTDH in cells. Bound complexes were pulled-down using an antibody against Flag. Then RNA immunoprecipitation (RIP) assays were performed with a Magna RIP Kit (Millipore). The RNA samples from RBP-OV and control cells were prepared and analyzed by the Agilent 2100 system. The library was conducted by the KAPA Stranded RNA-Seq Library Prep Kit (Illumina, USA), and sequenced on the Illumina NovaSeq 6000 using the NovaSeq 6000 S4 Reagent Kit (Illumina).

first: J


title: microRNA array data for forensically relevant body fluids samples

city: Chengdu

first: Weibo

last: Liang

state: Sichuan

address: Forensic Medicine Building, No.17, Renmin South Road Third Section

institute: Sichuan University

summary: Identifying the type and origin of biological samples left at a crime scene is crucial in forensic investigations as it can provide important clues for crime scene reconstruction and linkages between victim/perpetrator/scene. MicroRNAs (miRNAs) are considered to be more stable than mRNA due to their small size and protection by protein and have been demonstrated to be a viable tool for body fluid identification in forensic casework. To screen reliable body-fluid specific miRNAs, ten arrays were performed in five body fluids (peripheral blood, menstrual blood, saliva, semen and vaginal secretion). Two arrays were carried out for each body fluid: three samples for the first and the other two for the second (for menstrual blood, the second array detected three samples).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 26 samples: five peripheral blood, five vaginal secretion, five saliva, five semen and six menstrual blood were used in this study. Two arrays were carried out for each body fluid: three samples for the first and the other two or three for the second.

first: Lin

last: Zhang

first: Zhilong

last: Li


title: An activity-mediated transition in transcription in early postnatal neurons [10X]

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: The maturation of the mammalian brain occurs after birth, and this stage of neuronal development is frequently impaired in neurological disorders, such as autism and schizophrenia. However, the mechanisms that regulate postnatal brain maturation are poorly defined. By purifying neuronal subpopulations across brain development in mice, we identify a postnatal switch in the transcriptional regulatory circuits that operates in the maturing mammalian brain. We show that this developmental transition includes the formation of hundreds of cell-type-specific neuronal enhancers in the postnatal period that might in part be modulated by neuronal activity. Once selected, these enhancers are active throughout adulthood, suggesting that their formation in early life shapes neuronal identity and regulates mature brain function.

overall_design: RNA-seq from mouse neurons

first: Yael

last: Tsitohay

first: Michael

middle: E

last: Greenberg


title: An activity-mediated transition in transcription in early postnatal neurons [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC-seq from mouse neurons

first: Marty

last: Yang


title: An activity-mediated transition in transcription in early postnatal neurons [HiChIP]

overall_design: HiChIP from mouse neurons


title: An activity-mediated transition in transcription in early postnatal neurons [RNA-seq]


title: An activity-mediated transition in transcription in early postnatal neurons [BS-seq]

type: Methylation profiling by high throughput sequencing

overall_design: BS-seq from mouse neurons


title: An activity-mediated transition in transcription in early postnatal neurons


title: An activity-mediated transition in transcription in early postnatal neurons [ChIP-seq]

overall_design: ChIP-seq from mouse neurons


title: TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas [RNA-seq]

city: New York

first: Junfei Zhao

last: Zhao

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University

summary: We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in  epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes. We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in  epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes.

overall_design: We performed ChIP-seq (Chromatin immunoprecipitation and sequencing) for TOP2A and TOP2B to investigate its genomic localization in proneural glioma genotypes TS543 and BT142 and two mesenchymal glioma cell lines SNB19 and 0777A. To analyze the contribution of TOP2B on gene expression we treated cells with the TOP2 inhibitor ICRF193 10Um for 5hrs followed by RNA-seq. 20 TS543 samples (10 untreated; 10 treated), 12 BT142 samples (5 untreated; 7 treated) were included in the study.

first: Adam

middle: M

last: Sonabend

first: Junfei


title: An activity-mediated transition in transcription in early postnatal neurons [Cut&Run]

overall_design: CUT&RUN from mouse neurons

first: Christopher

last: Davis


title: Lophelia pertusa response to low pH

city: Philadelphia

first: Amanda

last: Glazier

state: PA

department: Biology

institute: Temple University

summary: RNA expression patterns of Lophelia pertusa to low pH are analyzed and presented to understand how the corals will respond to future environmental conditions

overall_design: Fragments from 3 genetically distinct colonies were maintained at 2 different pH regimes, 7.6 and 7.9, for 4 months. The colonies were sampled after 2, 4.5, and 8.5 weeks for RNA sequencing.

first: A

first: S

last: Herrera

last: Weinnig

first: M

last: Kurman

first: C

last: Gómez

first: E

last: Cordes


title: TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas [ATAC-seq]

summary: We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes. We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes.

overall_design:
We performed ChIP-seq (Chromatin immunoprecipitation and sequencing) for TOP2A and TOP2B to investigate its genomic localization in proneural glioma genotypes TS543 and BT142 and two mesenchymal glioma cell lines SNB19 and 0777A. To analyze the contribution of TOP2B on gene expression we treated cells with the TOP2 inhibitor ICRF193 10Um for 5hrs followed by RNA-seq. 20 TS543 samples (10 untreated; 10 treated), 12 BT142 samples (5 untreated; 7 treated) were included in the study.

This submission includes ATAC-seq samples.


title: Transcriptomic microRNA profiling of dendritic cells in response to gut microbiota secreted vesicles

city: Barcelona

first: Laura

last: Baldoma

address: Joan XXIII, 27-31

department: Bioquímica i Fisiologia

country: Spain

institute: Universitat de Barcelona

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular membrane vesicles (MVs) released by gut microbiota are key players in the communication with the host. Next-generation sequencing of small RNAs was used to quantify miRNA expression in monocyte-derived dendritic cells after 24 h-stimulation with MVs isolated from two E. coli intestinal isolates, the probiotic E. coli strain Nissle 1917 (EcN) and the commensal ECOR12. Analysis revealed miRNAs differentially expressed in response to MVs compared to immature control dendritic cells (log2fold-change > 0.7 and padj < 0.001). A common set of miRNAs was modulated by MVs from both strains (46 downregulated, 75 upregulated). In addition, these vesicles elicited differential expression of specific miRNAs depending on the producer strain (26 downregulated and 23 upregulated by EcN; 48 downregulated and 49 upregulated by ECOR12).

overall_design: A total of 9 samples were analyzed, from 3 experimental groups: unstimulated monocyte-derived dendritic cells, stimulated with EcN probiotic vesicles and incubated with vesicles from the commensal strain EcoR12.

last: Baldomà

first: Natalia

last: Díaz-Garrido

first: Josefa

last: Badia

first: Sarah

last: Bonnin


title: Shared upregulation and contrasting downregulation distinguish extremely desiccation tolerance from intolerant green algae

city: Woods Hole

first: Elena

last: Lopez Peredo

address: 7 MBL St

institute: Marine Biological Laboratory

sample_organism:
Enallax costatus
Flechtneria rotunda
Tetradesmus deserticola

overall_design: Refer to individual Series


title: Cancer cells educate natural killer cells to a metastasis-promoting cell state

city: Baltimore

first: Hildur

last: Knutsdottir

state: Maryland

address: 733 N Broadway

department: Biomedical Engineering

institute: Johns Hopkins University

summary: Gene expression comparisons revealed that healthy NK cells have an active NK cell molecular phenotype, whereas tumor-exposed (teNK) cells resemble resting NK cells. Receptor–ligand analysis between teNK cells and tumor cells revealed multiple potential targets.

overall_design: Gene expression from NK cells from tumor bearing mice, teNK,  compared to NK cells from healthy donor mice

first: Isaac

last: Chan

first: Gayathri

last: Ramakrishnan

first: Veena

last: Padmanaban

first: Manisha

last: Warrier

first: Juan

last: Ramirez

first: Matthew

last: Dunworth

first: Hao

last: Zhang

first: Elizabeth

last: Jaffee

first: Joel

last: Bader

first: Andrew

last: Ewald


title: Gene expression during desiccation and rehydration of the desert alga Acutodesmus deserticola

summary: A. deserticola suffers dramtic gene expression changes during water loss.

overall_design: Examination of gene exression changes using RNA-seq during five stages of desiccation, rehydration

middle: L

last: Peredo

first: Zoe

last: Cardon


title: Gene expression during desiccation and rehydration of the desert alga Flechtneria rotunda

summary: F. rotunda suffers dramatic gene expression changes during water loss.

overall_design: Examination of gene expression changes using RNA-seq during five stages of desiccation, rehydration.


title: Gene expression during desiccation and rehydration of the desert alga Enallax costatus

summary: E. costatus suffers dramtic gene expression changes during water loss.

overall_design: Examination of gene exression changes using RNA-seq during five stages of desiccation, rehydration.


title: Differenatiation of miRNA expression  in PBMCs (peripheral blood mononuclear cells)

city: Shanghai

first: Caiyan

address: 399, Wanyuan Road

institute: Children's Hospital of Fudan University

summary: To determine miRNA transcribed during the PBMCs, we have employed whole genome microarray expression profiling as a discovery platform to identify miRNA expression in PBMCs donated by T1DM (type 1 diabetes mellitus) patients and healthy volunteers.

overall_design: The changed miRNA expression in human PBMCs normal (Ctrl) or T1DM patients, respectively. Four persons  in each group (Normal, T1DM).

first: Yufeng

last: Zhou


title: Genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) upon DCP1A knockout

first: Eric

last: Aeby

state: Massachusetts

address: 185 Cambridge Street

department: Department of Molecular Biology and Department of Genetics

institute: Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School

summary: We analyzed the effect of DCP1A knockout on nascent transcripts population in undifferentiated mouse embryonic stem cells

overall_design: Two different DCP1A KO clones (C17 and J15) were compared to a parental cell line, independent biological replicates were performed for each cell line

first: Hungoo

last: Lee

first: Jeannie

middle: T


title: Transcriptome-wide analysis upon DCP1A knockout

summary: We analyzed the effect of DCP1A knockout on total RNA population in undifferentiated mouse embryonic stem cells


title: Expression data from EGF-stimulated A431 cells with or without Gefitinib treatment

status: Public on Jun 24 2020

city: Koto-ku

first: Harumi

last: Kagiwada

state: Tokyo

department: Cellular and Molecular Biotechnology Research Institute (CMB)

institute: National Istitute of Advanced Industrial Science And Technology (AIST)

summary:
Signals are transduced through multiple pathways, but it is difficult to check which pathways are responsible for each defined signal.
We used microarray to examine that the signal reached at the nucleus through pathways downstream EGFR.

overall_design: A431 cells were treated with three different conditions: control (No treatment), EGF-treatment, and both gefitinib and EGF-treatment.

first: Masashi

last: Kitazawa

first: Katsuhisa

last: Horimoto


title: Carbon catabolite repressor MoCreA is required for the asexual development and pathogenicity of the rice blast fungus

city: Fuzhou

first: Yonghe

last: Hong

state: --- Select a state ---

address: 15 shangxiadian road

department: College of Life Sciences

institute: Fujian Agriculture and Forestry University

summary: Comparative transcriptomic analysis demonstrates that MoCreA is a global regulator, and its disruption results in the extensive gene expression variations, including a large number of carbon metabolism enzymes, transcription factors and pathogenicity-related genes.

overall_design: Conduct a comparative transcriptomic analysis between wild type strain Ku80 andMoCreA deletion mutant ΔMocreA-2 using mycelia cultured in liquid CM medium

first: Zhenhui

last: Zhong

first: Jiandong

last: Bao

first: Xiaofeng

last: Chen


title: Development of gene expression during astrocyte differentiation from human embryonic stem cells

city: Daejeon

first: Jeongsu

last: B

address: Gwahak-ro

country: South Korea

institute: KRIBB

summary: To identify genes that affect astrocyte differentiation from human embryonic stem cells, we have employed whole genome microarray expression profiling. We efficiently derived astrocytes through neural progenitor cells from human embryonic stem cells using our developed differentiation method. The cells on day 21 and 28 of astrocyte differentiation were compared with neural progenitor cells.

overall_design: A total of three differentiation sets were statistically processed to select genes that increase and decrease during astrocyte differentiation. Astrocyte samples were sorted with astrocyte progenitor marker CD44.

last: Byun


title: PD-L1 lncRNA splice promotes lung adenocarcinoma proliferation and metastasis via enhancing c-Myc activity

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

summary: MicroArray analysis of mRNA in A549 cells overexpressed with PD-L1-lnc vector or control vector.

overall_design: Two samples are analyszed. A549 cells transfected with PD-L1-lnc vector or control vector.

first: Hongwei

last: Liang

first: Shuang

last: Qu


title: Heat-induced alternations in proteomic and transcriptomic profiles of spinach (Spinacia oleracea)

city: Suzhou

first: Yanfei

last: Bi

state: Jiangsu

address: Yulu NO.2

institute: Jiangsu Changshu National Agricultural Science and Technology Park Management Committee

summary: Spinach (Spinacia oleracea L.) is an economically important and globally consumed popular leafy vegetable that is heat-sensitive. Heat stress caused by global climate change is one of the primary deleterious elements limiting spinach production worldwide. Little work has been done to explore the heat-responsive mechanisms of spinach under high temperature-induced stress. In the present study, we used iTRAQ-based proteomic and transcriptomic approaches to investigate physiological, metabolic, and proteomic responses of spinach in response to day / night temperature of 35°C / 25°C compared to 20°C / 15°C for 4 days. A total of 3,543 differentially expressed genes (DEGs) were detected using transcriptome sequencing, of which 2,086 DEGs were downregulated and 1,457 were upregulated. The DEGs were mainly involved in superoxide dismutase activity, catalase, and peroxidase activity. A total of 3,246 differentially abundant proteins were detected using iTAQ-based quantitative proteomic approach, from which 567 differentially expressed proteins (DEPs) (277 upregulated and 290 downregulated) were identified. DEPs were mainly assigned to pathways related to metabolism, signal transduction, protein degradation, defense, and antioxidant. Four genes - superoxide dismutase (SOD, LOC110788339), catalase (CAT, LOC110790286), peroxidase (POD, LOC110775253), and heat shock protein (HSP, LOC110799288) - were validated using quantitative real-time PCR (qRT-PCR) to verify the proteomic and transcriptomic analyses, showing different transcriptional and translational expression levels. The findings of this study provide a fundamental understanding of the metabolic pathways and biological processes that control adaptation to heat stress in spinach, and provide novel insight into the development of heat-tolerant spinach.

overall_design: spinach in response to day / night temperature of 35°C / 25°C compared to 20°C / 15°C for 4 days，using transcriptome sequencing to find DEGs，expect to find some genes associated with resilience

first: Bin

last: Wei


title: Targeting Smyd3 by antisense oligonucleotides attenuates liver tumor growth

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira street

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

summary: We investigated whether pharamacological inhibition of Smyd3 by antisense oligonucleotides (ASOs) can influence diethylnitrosamine (DEN)-induced liver cancer development. Our phenotypic analyses, among others, included gene expression profiling.

overall_design: C57Bl6 mice received a single intraperitoneal injection of 25 mg/kg diethylnitrosamine at day 14 after birth. Livers were harvested at day 133 (P133) or day 260 (P260) after birth. After P133 the mice received intraperitoneally 50 mg/kg Control ASO or Smyd3-ASO twice a week, until P260, when sacrificed. Total RNAs were prepared by Nucleozol extraction and subjected to 3'Quant-Seq procedure.

first: Haroula

last: Kontaki

first: Marina

last: Koukaki

first: Maria

last: Vasilarou

first: Antonis

last: Giakountis

first: Elena

last: Deligianni

first: Youngsoo

last: Kim


title: miRNA Expression analysis from genomic form of Rhodopsin DNA Nanoparticles treated P23H Knock-in Heterozygous Mouse (P23H+/-)

city: Kanchipuram

first: Subramaniam

last: Sivakumar

state: TamilNadu

address: Enathur

department: Biochemistry

country: India

institute: Sri Sankara Arts and Science College

summary: Expression of miRNA analysis in mouse retinocytes was analysed using Next-generation sequencing (NGS) method in Rhodopsin DNA Nanoparticles treated P23H Knock-in Heterozygous Mouse (P23H+/-).

overall_design: Retinal miRNA profiles of 3 month old P23H+/- KI, Un-injected P23H+/- KI mouse, and P23H+/- KI mice treated with genomic constructs of human and mouse rhodopsin.

first: S

middle: P

last: Simna

first: Rajendra

last: Naryan

first: Min

last: Zheng

first: Sivakumar

last: Subramaniam

first: Zongchao

last: Han


title: Longitudinal RNA-Seq study of Nothobranchius furzeri fin biopsies

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Here, we performed a longitudinal study of genome-wide gene expression in the short-lived killifish Nothobranchius furzeri (MZM-0410 strain) and correlated variations in transcript abundance at two time points during early adult life with age at death.

overall_design: 114 animals (228 samples) were analyzed. Of each animal, two biological samples were taken by fin clipping at 10 and 20 weeks of age.

first: Mario

last: Baumgart

first: Marco

last: Groth


title: Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: To explore the underlying molecular and cellular mechanisms of increased efficacy of the combination therapy regimen, we employed a mouse model of lupus nephritis, MRL/lpr mice, and treated them with monotherapies of prednisone, mycophenolate mofetil, or tacrolimus, or with their combination. Consistent with previous clinical findings, combination therapy markedly improved renal outcome compared to the monotherapies in mice with lupus nephritis. Transcriptomic analysis of their kidneys revealed distinct molecular pathways that were differentially regulated in combination therapy versus monotherapies. Combination therapy not only provided additive immunosuppressive effects, but also induced gene expression and molecular pathways to confer enhanced renoprotection. Specifically, combination therapy inhibited TLR7 expression in the kidneys of mice with lupus nephritis; combination of tacrolimus and mycophenolate mofetil led to better stabilization of the podocyte actin cytoskeleton through the reciprocal regulation of RhoA and Rac1 activities. Combination therapy strongly suppressed the IL-6/Stat3 pathway. These findings were further validated in renal biopsy samples from patients with lupus nephritis before and after treatments with mycophenolate mofetil, tacrolimus or combination therapy. Thus, our study further supports the earlier clinical finding and further provides insights into the molecular basis for increased efficacy of combination therapy.

overall_design: transcriptomes of kidney cortices from healthy control and vehicle- and drug-treated LN mice (N 1⁄4 3 in each group).

first: Jia

last: Fu

first: Zichen

last: Wang

first: Zhihong

last: liu

first: Cijiang

last: He


title: Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [RNA-seq]

first: Xinyu

last: Cui

address: Siping road

institute: Tongji University

summary: Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodelingcomplexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. However, little is known about the biological functions of the two nuclear PfArp4 and PfArp6 proteins. Here, by Pfarp4 gene knockdown and comparative transcriptome analysis, we uncovered that PfArp4 correlated positively with the dynamic expression of eukaryotic genes. Genome-wide distribution analysis by ChIP-seq revealed that PfArp4 protein colocalized with the histone 2A variant H2A.Z and euchromatic marker H3K9ac in the intergenic regions. Inducible downregulation of PfArp4 resulted in the depletion of H2A.Z and lower H3K9ac level at the upstream regions of eukaryotic genes, thereby repressing the transcriptional abundances. Moreover, we found a significant enrichment of PfArp4 at the flanking sites of centromeres, which likely shapes the H2A.Z-enriched centromeric chromatin microenvironment as a boundary marker. PfArp4 depletion triggered loss of H2A.Z at the entire centromere regions, and arrested the blood-stage development probably through interference with the schizogony process. Finally, PfArp6 was detected as an interactor of PfArp4 in the nucleus. Taken together, our finding indicates that the nuclear PfArp4/6regulates the cell cycles through controlling H2A.Z deposition and centromere biology, which will contribute to understanding the complex epigenetic regulation of gene expression and development of the malaria parasites.

overall_design: Expression profiling by high throughput sequencing(RNA-seq) in the P. falciparum for wt ,wt_GlcN+,PfArp4 and PfArp4_GlcN+ parasites

first: Hui

last: Liu


title: WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations

city: Ithaca

first: Ian

middle: Michael

last: Rose

address: Ithaca, NY 14850

institute: Cornell University

summary: Many high-grade serous carcinomas (HGSCs) likely originate in the distal region of the Fallopian tube's epithelium (TE) before metastasizing to the ovary. Unfortunately, molecular mechanisms promoting malignancy in the distal TE are obfuscated, largely due to limited primary human TE gene expression data. Here we report an in depth bioinformatic characterization of 34 primary TE mRNA-seq samples. These samples were prepared from proximal and distal TE regions of 12 normal Fallopian tubes. Samples were segregated based on their aldehyde dehydrogenase (ALDH) activity. Distal cells form organoids with higher frequency and larger size during serial organoid formation assays when comparted to proximal cells. Consistent with enrichment for stem/progenitor cells, ALDH+ cells have greater WNT signaling. Comparative evaluation of proximal and distal TE cell population's shows heightened inflammatory signaling in distal differentiated (ALDH-) TE. Furthermore, comparisons of proximal and distal TE cell populations finds that the distal ALDH+ TE cells exhibit pronounced expression of gene sets characteristic of HGSC sub-types. Overall, our study indicates increased organoid forming capacity, WNT/inflammatory signaling, and HGSC signatures underlie differences between distal and proximal regions of the human TE. These findings provide the basis for further mechanistic studies of distal TE susceptibility to the malignant transformation.

overall_design: Primary human epithelial cells from proximal and distal Fallopian tube fragments were isolated by FACS before being used to construct 3ʹ mRNA-seq libraries with UMIs according to Lexogen’s QuantSeq protocol.  ALDH activity was used to enrich for stem or differentiated cells from each proximal or distal Fallopian tube fragment. In total 7 proximal EpCAM+/ALDH-, 9 proximal EpCAM+/ALDH+, 10 distal EpCAM+/ALDH-, 8 distal EpCAM+/ALDH+ samples were collected and sequenced. DESeq2 was used to identify differentially expressed genes between stem and differentiated cell enriched populations from the proximal and distal regions of the Fallopian tube.

first: Mallikarjun

last: Bidarimath

first: Alex

last: Webster

first: Andrew

middle: K

last: Godwin

first: Andrea

last: Flesken-Nikitin

first: Alexander

middle: Y

last: Nikitin


title: Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [Arp4/6 ChIP-seq]

summary: Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodeling complexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. However, little is known about the biological functions of the two nuclear PfArp4 and PfArp6 proteins. Here, by Pfarp4 gene knockdown and comparative transcriptome analysis, we uncovered that PfArp4 correlated positively with the dynamic expression of eukaryotic genes. Genome-wide distribution analysis by ChIP-seq revealed that PfArp4 protein colocalized with the histone 2A variant H2A.Z and euchromatic marker H3K9ac in the intergenic regions. Inducible downregulation of PfArp4 resulted in the depletion of H2A.Z and lower H3K9ac level at the upstream regions of eukaryotic genes, thereby repressing the transcriptional abundances. Moreover, we found a significant enrichment of PfArp4 at the flanking sites of centromeres, which likely shapes the H2A.Z-enriched centromeric chromatin microenvironment as a boundary marker. PfArp4 depletion triggered loss of H2A.Z at the entire centromere regions, and arrested the blood-stage development probably through interference with the schizogony process. Finally, PfArp6 was detected as an interactor of PfArp4 in the nucleus. Taken together, our finding indicates that the nuclear PfArp4/6regulates the cell cycles through controlling H2A.Z deposition and centromere biology, which will contribute to understanding the complex epigenetic regulation of gene expression and development of the malaria parasites.

overall_design: Genome-wide location analysis (ChIP-Seq) of  Arp4 and Arp6 in the P. falciparum.


title: Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [H2A.Z ChIP-seq]

overall_design: Genome-wide location analysis (ChIP-Seq) of  H2A.Z in the P. falciparum for  wt ,wt_GlcN+,PfArp4 and PfArp4_GlcN+ parasites


title: Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum

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

overall_design: Refer to individual Series


title: Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [H3K9ac ChIP-seq]

overall_design: Genome-wide location analysis (ChIP-Seq) of  H3K9ac in the P. falciparum for  wt ,wt_GlcN+,PfArp4 and PfArp4_GlcN+ parasites


title: Genome-wide expression analysis of Caenorhabditis briggsae SPR-4/IVP-1 and HTZ-1/IVP-2 mutants

city: Hamilton

first: Ish

last: Jain

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: The goal of this study is to identify differentially expressed genes in Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) and Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) mutant compare to AF16 wild-type (WT). Our study represents the first analysis of Cbr-spr-4/Cbr-ivp-1 and Cbr-htz-1/Cbr-ivp-2 transcriptomes in C. briggsae and facilitates investigations of Cbr-spr-4/Cbr-ivp-1 and Cbr-htz-1/Cbr-ivp-2 mediated processes

overall_design: Total RNA was extracted from synchronized L3 animals (representing AF16 wild-type isolate, Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) and Cbr-htz-1(gu167)/Cbr-ivp-2(gu167)), using standard TRIZOL methods. Animals were synchronized and staged by mounting the samples on slides and observing them under the Nomarski microscope. RNA was extracted just prior to the stage when vulval precursors (Pn.p cells) initiate division. At this stage, vulval cells are most responsive to Cbr-lin-3 levels. Three independent biological replicates were prepared from AF16, Cbr-spr-4(gu163) and Cbr-htz-1(gu167) strains for RNAseq, and the samples were processed, depleted for rRNA and sequenced using Illumina HiSeq platform by Genome Quebec. Differentially-expressed genes were called at a false discovery rate (FDR) of 0.05% using the DESeq package in R

first: Ayush

last: Ranawade


title: RNA Sequencing of C elegans control and mutant worms after 24 hour P.aeruginosa infection

city: Portland

first: Supender

last: Kaur

state: Oregon

address: 3181 SW Sam Jackson Park Road L220

department: Molecular Microbiology and Immuno

institute: Oregon health and science university

summary:
Purpose: After infection there was significant decrease in the lifespan of mutant animals . To decipher the mechanism responsible and the changes in the gene expression of mutant worms
Methods: Control and mutant worms were exposed at young adult stage to P.aeruginosa PA14 infection for 24 hours. Total RNA was extracted and RNA sequencing was done following standard protocols
Results:  Detailed analysis of the transcriptomic data show that  immune genes were significantly upregulated which have role in lifespan
Conclusions: This study showed the role of pathogenic infection in the life span modulation

overall_design: C. elegans RNA seq of young adults of control and mutant worms after 24 hour P.aeruginosa PA14 infection in triplicate, using Illumina platform

first: Alejandro

last: Aballay


title: Identification of functional variant enhancers associated with atrial fibrillation

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: STARR-seq analysis of human AF-associated loci in a rat inducible atrial cardiomyocyte cell line

overall_design: STARR-seq of AF associated loci and variants

first: Antoinette

middle: F

last: van Ouwerkerk

first: Karel

last: van Duijvenboden


title: Permissiveness to Form Pluripotent Stem Cells May Be an Evolutionaily Derived Chracteristic in Mus musculus

city: College Station

first: David

middle: William

last: Threadgill

address: Reynolds Medical Building 428

department: Department of Veterinary Pathobiology and Department of Molecular and Cellular Medicine

institute: Texas A&M University

summary: We developed and report on a novel new technique to reprogramm fobroblasts from two non-permissive mouse backgrounds into emrbyonic stem cell-like induced pluripotent stem cells

overall_design: Transcriptiomic comparision of iPSCs from derived from the non-permissive NOD and WSB mouse strains using 2iS reprogramming to true Emrbyonic Stem Cells and true Epiblast stem cells

first: Tiffany

middle: A

last: Garbutt

middle: W


title: MicroRNA expression profiles in pectoral muscle during pigeon(Columba livia) development

status: Public on Jun 23 2020

city: Chengdu

first: Xun

last: Wang

state: China

address: Huimin road 211#, Wenjiang district

institute: Sichuan agricultural university

summary: A comparative profile of miRNAs in pectoral muscle during pigeon development was performed by using high-throughput sequencing. We identified known pigeon miRNAs, novel miRNAs, and miRNAs that are conserved in other birds and mammals.Our results expanded the repertoire of pigeon miRNAs and may be of help in better understanding the mechanism of squab’s rapid development.

overall_design: we investigated miRNA expression profiles from pigeon skeletal muscle satellite cells during differentiation by using high-throughput sequencing technology.

first: Siyuan

last: Feng


title: Genome-Wide Profiling of Lesional and Non-Lesional Skin from Atopic Dermatitis, Psoriasis, and Contact Dermatitis Skin

city: South San Francisco

middle: Fong

last: Choy

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

overall_design: Agilent 2-color Whole Human Genome expression microarray analysis (Agilent, Santa Clara, Calif) using a common reference design with a Universal Human Reference control


title: A Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

summary: Single cell technologies hold promise for resolving complex early developmental phenotypes. Here we define a novel Hedgehog (Hh)-Fibroblast Growth Factor (FGF) signaling axis for the formation of anterior mesoderm lineages during gastrulation. Single-cell transcriptome analysis of Hh-deficient mesoderm revealed selective deficits in anterior mesoderm populations—culminating in defects to anterior embryonic structures including the pharyngeal arches, heart, and anterior somites. Transcriptional profiling of Hh-deficient mesoderm during gastrulation revealed disruptions to both transcriptional patterning of the mesoderm and FGF signaling for mesoderm migration. Mesoderm-specific Fgf4/Fgf8 double mutants recapitulated anterior mesoderm defects and Hh-dependent GLI transcription factors modulated enhancers at FGF gene loci.  Cellular migration defects during gastrulation induced by Hh pathway antagonism were mitigated by FGF4 protein. These findings implicate a multicomponent signaling hierarchy activated by Hh ligands from the embryonic node and executed by FGF signals in nascent mesoderm to control anterior mesoderm patterning.

overall_design: Comparing the cellular composition of Mesp1Cre sorted E8.25 mesoderm between Wt embryos and embryos expressing a dominant negative Hh pathway transcriptional repressor (Gli3R).

last: Guzzetta

first: Ivan

last: Moskowitz


title: Genome-wide analysis of whole transcriptome of isolated mouse islets of Langerhans

city: Aurora

first: Richard

last: Benninger

state: Colorado

address: 1775 Aurora Court, M20-4202V

department: Bioengineering

institute: University of Colorado Anschutz Medical Campus

summary: Diabetes results from insufficient insulin secretion as a result of dysfunction to β-cells within the islet of Langerhans. Elevated glucose causes β-cell membrane depolarization and action potential generation, voltage gated Ca2+ channel activation and oscillations in free-Ca2+ activity ([Ca2+]), triggering insulin release. Nuclear Factor of Activated T-cell (NFAT) is a transcription factor that is regulated by increases in [Ca2+] and calceineurin (CaN) activation. NFAT regulation links cell activity with gene transcription in many systems, and within the β-cell regulates proliferation and insulin granule biogenesis. However the link between the regulation of β-cell electrical activity and oscillatory [Ca2+], with NFAT activation and downstream transcription is poorly understood. In this study we test whether dynamic changes to β-cell electrical activity and [Ca2+] regulates NFAT activation and downstream transcription. In cell lines, mouse islets and human islets, including those with type2 diabetes, we applied both agonists/antagonists of ion channels together with optogenetics to modulate β-cell electrical activity. Both glucose-induced membrane depolarization and optogenetic-stimulation triggered NFAT activation, and increased transcription of NFAT targets and intermediate early genes (IEGs). Importantly only conditions in which slow sustained [Ca2+] oscillations were generated led to NFAT activation and downstream transcription. In contrast in human islets from donors with type2 diabetes NFAT activation by glucose was diminished, but rescued upon pharmacological stimulation of electrical activity. Thus, we gain insight into the specific patterns of electrical activity that regulate NFAT activation and gene transcription and how this is disrupted in diabetes.

overall_design: We report that there are a number of transcriptional gene changes in mouse islets under altered electrical activity

first: Jose

middle: G

last: Miranda

first: Wolfgang

last: Schleicher

last: Ramirez

first: Samantha

last: Landgrave


title: Gene expression signatures of healthy mouse skin after cold physical plasma treatment

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

institute: INP Greifswald

summary: The epidermal skin barrier plays an important role in health and diseases. It separates adjacent cells, regulates paracellular microfluidic processes and protects from environmental damage. Cold physical plasma is an emerging source for the spatially controlled generation of reactive oxygen and nitrogen species and can be directly delivered to the skin tissue in therapeutic approaches of wound healing. Using the kINPen argon plasma jet, we investigated barrier-modulating capacity utilizing healthy skin model in vivo (SKH1 hairless mice). Mice were exposed to 3 s/mm² or 20 s/mm² of plasma or were left untreated (0s/mm²) and compared to controls. Different clusters of genes were identified, including genes associated with tight (e.g. claudins), gap (e.g. connexins) and adherence junctional network (e.g. cadherins, catenins). Expression of selected targets was quantified by real-time PCR, and protein levels were validated with Western blot and immunohistological analysis. Moreover, plasma altered barrier permeability by untightening of stratum corneum (SC) in combination with increased oxygenation and perfusion of epidermal skin tissue.

overall_design: Mice were exposed to 3 s/mm² or 20 s/mm² of plasma or were left untreated (0 s/mm²) and compared to controls (n=9/group). After 24 h, the animals were euthanized by cervical dislocation and skin tissues were collected.

first: Grit

last: Liebelt

first: Thomas

last: von Woedtke


title: A two-step human culture system replicates intestinal monocyte maturation cascade: conversion of tissue-like inflammatory monocytes into macrophages

city: Montreal

first: Marika

last: Sarfati

state: Qc

address: 900 Rue St Denis

institute: CRCHUM

summary:
Monocyte maturation program into macrophages (MΦ) is well-defined in murine gut under homeostatic or inflammatory conditions. Obviously, in vivo tracking of monocytes in inflamed tissues remains difficult in humans. Furthermore, in vitro models fall short in generating the surrogates of transient extravasated tissue inflammatory monocytes. Here, we aimed to unravel environmental cues that replicate in vitro the human monocyte “waterfall” process by first generating tissue-like inflammatory monocytes, and then shifted them towards MΦ. Purified CD14+CD16- monocytes cultured with granulocyte-macrophage colony-stimulating factor (GM-CSF), IFNg and IL23 differentiated into CD14+CD163- cells displayed a monocyte-like morphology. The in vitro generated inflammatory CD14+CD163- cells (Infl mo-like), like the CD14+CD163- mo-like cells that accumulate in inflamed colon of Crohn’s disease patients, promoted IL-1β-dependent memory Th17 and Th17/Th1 responses. Next, in vitro generated Infl mo-like cells converted to functional CD163+ MΦ following exposure to TGFβ and IL10. Gene set enrichment analysis further revealed a shared molecular signature between converted CD163+ MΦ and MΦ detected in various inflamed non-lymphoid and lymphoid diseased tissues. Our findings propose a two-step in vitro culture that recapitulates human monocyte maturation cascade in inflamed tissue. Manipulating this process might open therapeutic avenues for chronic inflammatory disorders.
Classical CD14+CD16- human monocytes were sorted and cultured for 6 days with GM-CSF+IFNg+IL23, leading to the generation of CD163- d6 cells. Following the 6 days culture with GM-CSF+IFNg+IL23, TGFβ+IL10 were added for another 6 days. This gave rise to the CD163+ d12 and CD163- d12 populations. We used microarray (Clariom D, Affymetrix) to observe molecular differences in the 3 in vitro generated populations: (1) CD163- d6 (2) CD163+ d12 (3) CD163- d12.

overall_design: CD163- d6, CD163+ d12 and CD163- d12 populations were generated in vitro from 3 healthy donors. The populations were sorted for RNA extraction and hybridization on Affymetrix microarrays.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and nid1 knockout mutant Transcripts

city: seoul

first: Wonje

last: Lee

address: anam

institute: biosystems

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Arabidopsis mRNA profiles of 9-day-old wild-type (WT) and nid1 knockout mutant plants were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to Arabidopsis sample and identified 16,014 transcripts in the WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our  study represents the first detailed analysis of nid1 transcripts, 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  transcripts characterization would expedite genetic network analyses and  permit the dissection of complex biologic functions.

first: Hojoung

last: lee


title: Mouse brain transcriptome responses to inhaled nanoparticulate matter differed by sex and APOE in Nrf2-Nfkb interactions

city: San Diego

first: Amin

last: Haghani

address: 5510 Morehouse Dr

institute: Altos labs

summary: The neurotoxicity of air pollution is undefined for sex and APOE alleles. These major risk factors of Alzheimer’s disease (AD) were examined in mice given chronic exposure to nPM, a nano-sized subfraction of urban air pollution. In the cerebral cortex, female mice had two-fold more genes responding to nPM than males. Transcriptomic responses to nPM had sex-APOE interactions in AD-relevant pathways. Only APOE3 mice responded to nPM in genes related to Abeta deposition and clearance (Vav2, Vav3, S1009a). Other responding genes included axonal guidance, inflammation (AMPK, NFKB, APK/JNK signaling), and antioxidant signaling (NRF2, HIF1A). Genes downstream of NFKB and NRF2 responded in opposite directions to nPM. Nrf2 knockdown in microglia augmented NFKB responses to nPM, suggesting a critical role of NRF2 in air pollution neurotoxicity. These findings give a rationale for epidemiologic studies of air pollution to consider sex interactions with APOE alleles and other AD-risk genes.

overall_design: Young C57BL/6J and ApoE-targeted replacement mice (ApoE-TR) were exposed chronically to nPM.

first: Mafalda

last: Cacciottolo

first: Kevin

middle: R

last: Doty

first: Carla

last: D’agostina

first: Max

last: Thorwald

first: Nikoo

last: Safi

first: Arian

last: Saffari

first: Farimah

last: Shirmohammadi

first: Morgan

last: Levine

first: Constantinos

last: Sioutas

first: Terrence

middle: C

last: Town

first: Henry

last: Forman

first: Hongqiao

last: Zhang

first: Todd

last: Morgan

first: Caleb

last: Finch


title: The RNA-binding proteins Roquin-1 and Regnase-1 interact and cooperate to prevent autoimmunity

city: Planegg-Martinsried

first: Vigo

last: Heissmeyer

state: Bayern

address: Großhaderner Str. 9

department: Institute for Immunology

institute: Ludwig-Maximilians-Universität

summary:
This study aimed to analyze the transcriptomic changes occuring after knockout of alleles encoding for the RNA-binding proteins Roquin-1 and Roquin-2 (DKO), Regnase-1 (KO) or a combination of all three (TKO) in Th1 cells without or after restimulation with anti-CD3/28 antibodies.
Data analysis revealed that in unstimulated as well as restimulated T cells of all three knockout genotypes a number of genes is differentially expressed compared to WT cells, with the strongest deregulation seen in TKO cells. A comparison of gene expression changes of all three genotypes indicated that cooperativity of Roquin and Regnase-1 is the prevalent mode of target regulation.

overall_design: RNA Seq of WT, DKO, KO or TKO of CD4 T cells without or with restimulation with anti-CD3/28 for 1h, 2h, 4h

first: Gergely

last: Csaba


title: Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [mRNA]

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

summary: Septic shock is the most common cause of death in intensive care units. The aim of this study is to investigate the role of circular RNA (circRNA) and mRNA expression profiles and functional networks in aortic tissue of septic shock.

overall_design: Septic shock model in rats was established by intraperitoneal injection of lipopolysaccharide (LPS). High-throughput sequencing and bioinformatics analysis were performed on aortic tissue to identify differentially expressed mRNAs, which were validated by qRT-PCR. We performed bioinformatics analysis and constructed circRNA-mRNA and circRNA-miRNA-mRNA networks to investigate mechanisms related to biological functions and signaling pathways. Then, functional and pathway enrichment analyses were performed.

first: Muwen

last: Nie

first: Yechen

last: Han

first: Zhujun

last: Shen

first: Hongzhi

last: Xie


title: A Conditional Mouse Expressing a Tumor-derived Mutation in the NRF2 Transcription Factor Displays Hyperplasia of the Upper Gastrointestinal Tract and Decreased White Adipose Fat

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

summary: Activation of the nuclear factor (erythroid-derived 2)-like 2 (NFE2L2 or NRF2) transcription factor is a critical and evolutionarily conserved cellular response to oxidative stress, metabolic stress, and xenobiotic insult. Whereas NRF2 deficiency results in hypersensitivity to a variety of stressors, its aberrant activation contributes to several cancer types, most commonly squamous cell carcinomas of the oesophagus, oral cavity, bladder and lung. Between 10-35% of patients with squamous cell carcinomas display hyperactive NRF2 signaling, harboring activating mutations and copy number amplifications of the NFE2L2 oncogene or inactivating mutations or deletions of KEAP1 or CUL3, which co-complex to ubiquitylate and degrade NRF2 protein. To better understand the role of NRF2 in tumorigenesis and more broadly in development, we engineered the endogenous Nfe2l2 genomic locus to create a conditional mutant LSL-Nrf2E79Q mouse model. The NRF2E79Q mutant protein does not undergo KEAP1/CUL3-dependent degradation, resulting in its constitutive activity. The E79Q mutation is also one of the most commonly observed NRF2-activating mutations in human squamous cancers. Expression of NRF2E79Q protein in keratin 14 (Krt14)-positive murine tissues resulted in a stunted body axis, decreased weight, decreased adipocyte size, and hyperplasia of squamous cell tissues of the tongue, forestomach, and oesophagus. RNAseq profiling and follow-up validation studies of cultured Nrf2E79Q murine esophageal epithelial cells revealed known and novel NRF2-regulated transcriptional programs, including genes associated with squamous cell carcinoma (e.g. Myc), lipid and cellular metabolism (Hk2, Ppard), and growth factors (Areg, Bmp6, Vegfa). These data suggest that in addition to decreasing adipogenesis, KRT14 restricted NRF2 activation leads to hyperplasia of the oesophagus, forestomach and tongue, but notably is not sufficient to drive formation of squamous cell carcinoma.

overall_design: Transcriptional profiling of MDA-MB-231 cells treated with sgRNA targeting ADSL or control sgRNA

first: Michael

last: Major

first: Brittany

last: Bowman

first: Jeremy

last: Simon


title: Wnt/beta-catenin activated Ewing sarcoma cells promote the angiogenic switch

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Wnt/beta-catenin signaling is active in small subpopulations of Ewing sarcoma cells and these cells display a more metastatic phenotype, in part due to antagonism of EWS-FLI1-dependent transcriptional activity. Importantly, these beta-catenin-activated Ewing cells also alter secretion of extracellular matrix (ECM) proteins. We thus hypothesized that, in addition to cell autonomous mechanisms, Wnt/beta-catenin-active tumor cells might contribute to disease progression by altering the tumor microenvironment (TME). Activation of canonical Wnt signaling leads Ewing sarcoma cells to upregulate expression and secretion of pro-angiogenic ECM proteins, collectively termed the angiomatrix. Here we tested the role of Wnt-related TGF-beta signaling in angiomatrix induction by obtaining mRNA from Wnt3a-treated TC32 cells in the presence and absence of SB505124, a chemical inhibitor of TGF-beta receptor 1 (TGFBR1) and subjecting it to short read RNA-sequencing.

overall_design: Cultured TC32 Ewing sarcoma cells were treated with vehicle (control), Wnt (28 h), or both Wnt (28 h) and a TGF-beta signaling inhibitor (SB-505124, 24 h) prior to assay by RNA-seq, with three replicates per condition.

first: Allegra

last: Hawkins

first: Elisabeth

last: Pedersen

first: Wei

last: Jiang

first: Sydney

last: Treichel

first: Colin

last: Sperring

first: Jay

last: Read

first: Rajiv

last: Patel

first: Dafydd

last: Thomas

first: Rashmi

last: Chugh

first: Elizabeth

last: Lawlor


title: Genes differentially expressed in human AML cells after  treatment with a novel SirTi, MC2494.

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: Trascriptional profiling of human AML cells after SirT activity modulation

overall_design: Three different condition: MC2494 vs CTRL; EX527 vs CTRL; MC2494 vs EX527

first: Vincenzo

last: Carafa

first: Angela

last: Nebbioso


title: Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model

first: Jinghua

last: Yang

type:
Non-coding RNA profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Temperature shift under anaerobic conditions

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

institute: Research institute of Innovative Technology for the Earth (RITE)

summary: Cell proliferation is achieved by numerous enzyme reactions. Temperature governs the activity of each enzyme, which overall determines the optimal growth temperature. Synthesizing useful chemicals and fuels utilizes only part of the metabolic pathways, especially the central metabolic pathways such as glycolysis and TCA cycle to metabolize glucose. However, the optimal temperature for the activity of the central metabolic pathways is inconclusive whether it is correlated with the optimal temperature for cell proliferation. Here, we found that Corynebacterium glutamicum wild type increased the metabolic activity to consume glucose under anaerobic (oxygen deprived) conditions at 42.5ºC, in which the cell hardly grows under aerobic conditions. Glucose consumption rate was increased by 24% at 42.5ºC compared to that at the optimal growth temperature of 30.0ºC. Transcriptional analysis showed that gapX gene encoding glycelaldehydre-3-phosphate dehydrogenase, glucokinase gene, and a gene involved in glucose uptake were upregulated at 42.5ºC. Production of fermentative lactate was increased by 69% than that at 30.0ºC, whereas succinate production was decreased by 13%. In addition to several glycolytic enzymes, the activity of pyruvate kinase was increased with increasing the temperature, whereas the activity of phosphoenolpyruvate carboxylase in anapleotic pathway leading to succinate synthesis was decreased. However, a metabolically engineered succinate over-producing strain, in which lactate production was shut off and pyruvate carboxylase encoding gene in another anapleotic pathway was overexpressed, produced 34% higher succinate at 42.5ºC than that at 30.0ºC with increased glucose consumption. This study provides the evidence that the optimal reaction temperature for production of fermentative products can be set beyond upper limit of growth temperature in C. glutamicum, and hence it could be applicable for producing various chemicals and fuels in C. glutamicum under anaerobic conditions and non-growing cell reactions in other microorganisms.

overall_design: Comparison of gene expression profiles of the wild-type Corynebacterium glutamicum incubated at 30 °C and 42.5 °C under anaerobic conditions. Three independent experiments were performed.

first: Hikaru

last: Mizuno

first: Koichi

last: Toyoda

first: Kazuaki

last: Ninomiya

first: Kenji

last: Takahashi

first: Yota

last: Tsuge


title: The acute effects of chemotherapy and radiotherapy on peripheral blood epigenetic age in early stage breast cancer patients

city: Los Angeles

first: Mary

middle: Elizabeth

last: Sehl

address: 100 UCLA Medical Plaza, Suite 550

department: Medicine / Hematology-Oncology

institute: UCLA

summary:
Genome wide DNA methylation profiling of human blood samples. The Illumina Infinium EPIC DNA methylation Beadchip was used to obtain DNA methylation profiles
Survival has increased in early stage breast cancer (BC), and the late effects of cancer treatment can persist for decades.  The molecular mechanisms underlying acceleration of age-related diseases after chemotherapy and radiotherapy are poorly understood.  We examined epigenetic changes in peripheral blood in early stage BC patients undergoing either adjuvant radiotherapy, or adjuvant chemotherapy and radiotherapy.  DNA methylation experiments were performed on peripheral blood samples from women collected prior to and following completion of adjuvant therapy.  Methylation profiles were used to estimate three measures of epigenetic age acceleration - intrinsic, extrinsic, and phenotypic - as well as estimated cell counts.

overall_design: N=144 methylation arrays from women with breast cancer. Blood was drawn before treatment (time point 0, baseline) and after treatment. Some women were treated with radiation therapy.

first: Steve

last: Horvath

first: Julienne

last: Bower

first: Judith

last: Carroll


title: Two unequally redundant 'helper' immune receptor families mediate Arabidopsis intracellular 'sensor' immune receptor functions

status: Public on Jun 22 2020

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

institute: The University of North Carolina at Chapel Hill

summary: Investigate  the function of RNLs in transcriptional reprogramming during Pf0-1-induced PTI and ETI, using time-resolved transcriptomics. To do so we subjected Col-0, adr1 triple, nrg1.1 nrg1.2 and helperless mutants to infections with Pf0-EV (RNL-(in)dependent PTI), Pf0-AvrRps4 (fully RNL-dependent ETI + PTI), Pf0-AvrRpt2 (partial RNL-dependent ETI + PTI) or Pf0-AvrRpm1 (RNL-independent ETI + PTI).

overall_design: Time resolved transcriptomics (T0, 0.5h, 4h  and 8h) of 4 Arabidopsis thaliana genotypes (Col-0, nrg1.1 nrg1.2 , adr1 triple and helperless) infiltrated with 4 bacterial treatments (Pf0-EV (RNL-(in)dependent PTI), Pf0-AvrRps4 (fully RNL-dependent ETI + PTI), Pf0-AvrRpt2 (partial RNL-dependent ETI + PTI) or Pf0-AvrRpm1 (RNL-independent ETI + PTI))

last: Salas-Gonzalez

first: Pierre

last: Jacob


title: Development and Application of a Transcriptomic Signature of Bioactivation in an Advanced In Vitro Liver Model to Reduce Drug-induced Liver Injury Risk Early in the Pharmaceutical Pipeline

city: West Point

first: Alexei

last: Podtelezhnikov

state: PA

address: 770 Sumneytown Pike

department: Non-clinical Drug Safety

institute: Merck & Co., Inc.

summary: Translation of NRF1/NRF2 -mediated liver tissue biomarkers to an in vitro assay using an advanced micropatterned co-culture system (HEPATOPAC®) with primary hepatocytes from male Wistar-Hannover rats or humans

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Rat and human HEPATOPAC® cells and hepatocytes from various sources without treatment and rat and human HEPATOPAC cells dosed repeatedly with pharmaceuticals; total RNA extracted from frozen cells at various time points.

first: Wen

last: Kang

first: Keith

middle: Q

last: Tanis

first: Stephen

last: Paccione

first: Frank

middle: D

last: Sistare


title: Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide-induced rat septic shock model [circRNA]

first: Jinghua

last: Yang

overall_design: Septic shock model in rats was established by intraperitoneal injection of lipopolysaccharide (LPS). High-throughput sequencing and bioinformatics analysis were performed on aortic tissue to identify differentially expressed (DE)circRNAs, which were validated by qRT-PCR. We performed bioinformatics analysis and constructed circRNA-mRNA and circRNA-miRNA-mRNA networks to investigate mechanisms related to biological functions and signaling pathways. Then, functional and pathway enrichment analyses were performed.

first: Muwen

last: Nie

first: Yechen

last: Han

first: Zhujun

last: Shen

first: Hongzhi

last: Xie


title: Mouse retinal cell atlas: molecular identification of sixty-three amacrine cell types

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: Amacrine cells (ACs) are a diverse class of interneurons that modulate input from photoreceptors to retinal ganglion cells (RGCs), rendering each RGC type selectively sensitive to particular visual features, which are then relayed to the brain. While many AC types have been identified morphologically and physiologically, they have not been comprehensively classified or molecularly characterized. We used high-throughput single-cell RNA sequencing (scRNA-seq) to profile >32,000 ACs from mice of both sexes, and applied computational methods to identify 63 AC types. We identified molecular markers for each type, and used them to characterize the morphology of multiple types. We show that they include nearly all previously known AC types as well as many that had not been described. Consistent with previous studies, most of the AC types expressed markers for the canonical inhibitory neurotransmitters GABA or glycine, but several expressed neither or both. In addition, many expressed one or more neuropeptides, and two express glutamatergic markers. We also explored transcriptomic relationships among AC types and identified transcription factors expressed by individual or multiple closely related types. Noteworthy among these were Meis2 and Tcf4, expressed by most GABAergic and most glycinergic types, respectively. Together, these results provide a foundation for developmental and functional studies of ACs, as well as means for genetically accessing them. Along with previous molecular, physiological and morphological analyses, they establish the existence of at least 130 neuronal types and nearly 140 cell types in mouse retina.

overall_design: Amacrine cells from retina of P19 mouse was collected and transcriptomic analysis of single cells were performed.

first: Mallory

last: Laboulaye

first: Nicholas

middle: M

last: Tran

first: Irene

middle: E

last: Whitney

first: Inbal

last: Benhar

first: Joshua

last: Sanes


title: Application of a Rat Liver Drug Bioactivation Transcriptional Response Assay Early in Drug Development that informs Chemically Reactive Metabolite formation

summary: Transcriptional responses in rat liver following treatment with compounds with a range of in vitro covalent binding measurements

overall_design: Rats received repeted daily dosing of pharmaceuticals at doses and durations indicated. Approximately 24hrs after dosing, animals were sacrificed, livers removed, a section (~50-100mg) frozen on dry ice and stored at ~-80C until total RNA was isolated. Frozen liver was pulverized in Trizol reagent, extracted with Chloroform, and further purified using the RNEasy column RNA isolation procedure (Qiagen, Chatsworth, CA). 50 ng of each purified RNA sample was amplified and labeled using a custom automated version of the NuGEN Ovation WB protocol.  Hybridization to custom rat Affymetrix arrays (containing 43,686 probesets, GEO platform GPL28473), labeling and scanning were completed following the manufacturer's recommendations and profiles were normalized using robust multi-array average followed by ratio’ing to corresponding vehicle control samples within each study.

first: James

middle: J

last: Monroe


title: Cell atlas of the human fovea and peripheral retina

summary: Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral reti-na of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal gangli-on and non-neuronal cells. Nearly all types are shared between the two retinal re-gions, but there are notable differences in gene expression and proportions between foveal and peripheral cohorts of shared types. We then used the human retinal atlas to map expression of 636 genes implicated as causes of or risk factors for blinding dis-eases. Many are expressed in striking cell class-, type-, or region-specific patterns. Fi-nally, we compared gene expression signatures of cell types between human and the cynomolgus macaque monkey, Macaca fascicularis. We show that over 90% of human types correspond transcriptomically to those previously identified in macaque, and that expression of disease-related genes is largely conserved between the two species. These results validate the use of the macaque for modeling blinding disease, and pro-vide a foundation for investigating molecular mechanisms underlying visual pro-cessing.

overall_design: To generate a comprehensive cell atlas of human retina, we obtained eight retinas from seven genetically unrelated human donors with no clinical history of ocular disease. We dissected fovea (~1.5 mm diameter centered on the foveal pit, which was visible under a dissecting microscope) and peripheral samples (> 5 mm from the fovea) from whole retina, pooling peripheral pieces from all four quadrants. Foveal samples were dissociated into single cells, which were profiled without further processing using high-throughput droplet sequencing. For peripheral samples, in which rod photoreceptors and RGC comprise ~80% and <2 % of total cells respectively, we depleted rods using magnetic beads conjugated to anti-CD73 or enriched RGCs using anti-CD90-conjugated beads prior to collection , using protocols established in our study on macaque retina. Libraries were prepared from foveal and peripheral samples, and sequenced. Altogether, we obtained 84,982 high-quality transcriptomes, 55,736 from fovea and 29,246 from peripheral retina. The median number of unique transcripts captured per cell was 2,577 and the median number of genes detected was 1,308.

first: Yi-Rong

last: Peng

first: Tavé

last: van Zyl

first: Aviv

last: Regev

first: Karthik

last: Shekhar

first: Dejan

last: Juric


title: Gene expression profile of C. elegans biogenic amine synthesis mutants

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Rd

department: Genetics

institute: Waksman Institute / Rutgers University

summary: The goal of this study is to compare the RNA expression profile of wild-type C. elegans nematodes to mutants defective in the synthesis of the biogenic amine neurotransmitters dopamine, serotonin, tyramine, and octopamine in day 2 adults.

overall_design:
Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to release embryos.  Synchronized embryos were hatched on NGM plates and grown at 20°C until 48h after the L4 stage of development.  Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood (Gandhi, Santelli et al., 1980).  For each RNA-seq experimental replicate, populations were grown simultaneously under the same conditions.  Total RNA (typical amount of worms and mass amount of RNA) was isolated from animals using trizol (Invitrogen) combined with Bead Beater lysis in four biological replicates for each genotype, and an mRNA library (single-end, 75-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection (RUCDR).  Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run Mode, resulting in high quality sequence reads (FAST QC Phred score average of 40 out to the full 75 bp length).  Reads (30-40 million per genome and replicate) were mapped tp the C. elegans genome (WS245) and gene counts generated with STAR 2.5.1a.  From 93-95% of reads uniquely mapped to the genome.  Normalization and statistical analysis on gene counts were performed with EdgeR using generalized linear model functionality and tagwise dispersion estimates.  An MDS plot revealed the fourth replicate for each genotype was subject to a strong batch effect, so the fourth replicate samples were dropped, and all analysis re-run using only replicates one, two and three from each genotype. Likelihood ratio tests were conducted for each biogenic amine mutant relative to wild-type odIs77 in a pairwise fashion with a Benjamini and Hochberg correction.
Animals carry the odIs77 integrated transgene, which expresses both UbG76V-GFP and mRFP from the col-19 promoter

first: Kishore

last: Joshi


title: Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation

city: Marseille

first: Andrew

last: Saurin

address: Campus de Luminy

institute: IBDM / CNRS

summary: Autophagy is an essential cellular process that maintains homeostasis by recycling damaged organelles and nutrients during development and cellular stress. ZKSCAN3 is the sole identified master transcriptional repressor of autophagy in human cell lines. How ZKSCAN3 achieves autophagy repression at the mechanistic or organismal level however still remains to be elucidated. Furthermore, Zkscan3 knockout mice display no discernable autophagy-related phenotypes, suggesting that there may be substantial differences in the regulation of autophagy between normal tissues and tumor cell lines. Here, we demonstrate that vertebrate ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy repression. Expression of ZKSCAN3 in Drosophila prevents premature autophagy onset due to loss of M1BP function and conversely, M1BP expression in human cells can prevent starvation-induced autophagy due to loss of nuclear ZKSCAN3 function. In Drosophila ZKSCAN3 binds genome-wide to sequences targeted by M1BP and transcriptionally regulates the majority of M1BP-controlled genes, demonstrating the evolutionary conservation of the transcriptional repression of autophagy and allow the potential for transitioning the mechanisms, gene targets and plethora metabolic processes controlled by M1BP onto ZKSCAN3 and opens up Drosophila as a tool in studying the function of ZKSCAN3 in autophagy and tumourigenesis.

overall_design: Fat bodies from 3rd instar (L3) feeding (L3F) or wandering (L3W) Drosophila melanogaster larvae and total RNA prepared. For L3W versus L3F analyses, fat bodies from wild-type female fat bodies were used. For M1BP RNAi analyses, fat bodies from  male fat bodies with gonads removed were used (genotypes of cgGal4 crossed with either wild-type or MBP RNAi). For ZKSCAN3 analyses, fat bodies from  male fat bodies with gonads removed were used (genotypes of cgGal4 crossed with either wild-type or HA::ZKSCAN3). For M1BP RNAi/ZKSCAN3 analyses, fat bodies from  male fat bodies with gonads removed were used (genotypes of cgGal4 crossed with either wild-type or M1BP-RNAi;HA::ZKSCAN3). S2-DRSC Drosophila cells are stably transfected with HA-tagged vertebrate ZKSCAN3 or ZKSCAN4 (S2-DRSC:AbdA)and analysed for genomic binding of HA-ZKSCAN3 and ZKSCAN4

first: Marine

last: Barthez

first: Mathilde

last: Poplineau

first: Marwa

last: El-Refaey

first: Nathalie

last: Caruso

first: Yacine

last: Graba


title: CD8+ T-cells infiltrate Alzheimer’s disease brains and regulate neuronal- and synapse-related gene expression in APP-PS1 transgenic mice

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

summary: Neuroinflammation is a major contributor to disease progression in Alzheimer´s disease (AD) and is characterized by the activity of brain resident glial cells, in particular microglia cells. However, there is increasing evidence that peripheral immune cells infiltrate the brain at certain stages of AD progression and shape disease pathology. We recently identified CD8+ T-cells in the brain parenchyma of APP-PS1 transgenic mice being tightly associated with microglia as well as with neuronal structures. The functional role of CD8+ T-cells in the AD brain is however completely unexplored. Here, we demonstrate increased numbers of intra-parenchymal CD8+ T-cells in human AD post-mortem hippocampus, which was replicated in APP-PS1 mice. Also, aged WT mice show a remarkable infiltration of CD8+ T-cells, which was more pronounced and had an earlier onset in APP-PS1 mice. To address their functional relevance in AD, we successfully ablated the pool of CD8+ T-cells in the blood, spleen and brain from 12 months-old APP-PS1 and WT mice for a total of 4 weeks using an anti-CD8 antibody treatment. While the treatment at this time of disease stage did neither affect the cognitive outcome nor plaque pathology, RNAseq analysis of the hippocampal transcriptome from APP-PS1 mice lacking CD8+ T-cells revealed highly altered neuronal- and synapse-related gene expression including an up-regulation for neuronal immediate early genes (IEGs) such as the Activity Regulated Cytoskeleton Associated Protein (Arc) and the Neuronal PAS Domain Protein 4 (Npas4). Gene ontology enrichment analysis illustrated that the biological processes “regulation of neuronal synaptic plasticity” and the cellular components “postsynapses” were over-represented upon CD8+ T-cell ablation. Additionally, Kegg pathway analysis showed up-regulated pathways for “calcium signaling”, “long-term potentiation”, “glutamatergic synapse” and “axon guidance”. Therefore, we conclude that CD8+ T-cells infiltrate the aged and AD brain and that brain CD8+ T-cells might directly contribute to neuronal dysfunction in modulating synaptic plasticity. Further analysis will be essential to uncover the exact mechanism of how CD8+ T-cells modulate the neuronal landscape and thereby contribute to AD pathology.

overall_design: Two different strains were used: Ten APP Swedish PS1 dE9 (APP-PS1) mice and five wild type (WT) mice. Ten mice were treated with PBS (5 APP-PS1 and 5 WT) while 5 APP-PS1 were treated with an anti-CD8a antibody for four weeks

first: Michael

last: Unger


title: MAT2A as key regulator and therapeutic target in MLL leukemogenesis

city: Tuebingen

first: Corina

last: Schneidawind

address: Otfried-Mueller-Str. 10

department: Hematology and Oncology

institute: University Hospital Tuebingen

summary: Epigenetic dysregulation plays a pivotal role in MLL pathogenesis, therefore serving as suitable therapeutic point of attack. SAM is the universal methyl donor in human cells and is synthesized by MAT2A. MAT2A is already known to be deregulated in different cancer types. Here, we used our human CRISPR/Cas9-MLLr leukemia model, faithfully mimicking MLL patients’ pathology with indefinite growth potential in in vitro culture, to evaluate the unknown role of MAT2A as therapeutic target. Comparable to publicly available patient data, we detected MAT2A to be significantly overexpressed in our CRISPR/Cas9-MLLr model compared to healthy controls. By using non-MLLr and MLLr cell lines and our model, we detected an MLLr specific enhanced response to PF-9366, a new MAT2A inhibitor, by alteration of proliferation, viability, differentiation, apoptosis and cell cycling. Moreover, the combinational treatment of PF-9366 with chemotherapy or targeted therapies against the SAM-dependent methyltransferases DOT1L and PRMT5, revealed even more pronounced effects. In summary, we uncovered MAT2A as a key regulator in MLL leukemogenesis and its inhibition led to significant anti-leukemic effects. Therefore, our study paves the avenue for clinical application of PF-9366 to improve the treatment of poor prognosis MLLr leukemia.

overall_design: huCB CD34+ cells were engineered to bear endogenous MLL-AF4 translocations. Generated cells were treated with 15 µM of PF-9366 (Carbosynth) or DMSO for 4 days. RNA sequencing was performed using NextSeq mRNA Stranded Sequencing (Illumina) of two biological replicates comparing treated and non-treated cells.

first: Kathy-Ann

last: Secker


title: Transcriptomic analysis of masked birch caterpillars, Drepana arcuata (Lepidoptera: Drepanoidea),

city: ottawa

first: Chanchal

last: Yadav

address: 1125 colonel by drive

department: Biology

institute: Carleton University

summary: We assembled larval transcriptome of D. arcuata using RNA-seq data from both social and solitary instars, and then conducted differential gene expression analysis between the two behavioural instars. This revealed a large number of transcripts that were differential expressed between the two behavioral states,  including some transcripts coding for gene products that have been previously implicated in  social behaviour in other insects.

overall_design: Illumina NextSeq 500 150bp paired-end RNA seq data sequenced from social early (I,II) and solitary late instars (IV,V, followed by de novo transcriptome assembly (Trinity) that was used as reference to conduct differential gene expression analysis using RNA seq data from social early vs solitary late instars (RSEM, edgeR)

first: Myron

middle: L

last: Smith


title: Comprehensive analysis of circRNA expression profiles and circRNA-associated ceRNA networks in age-related changes of mouse thymus

city: Shenzhen

first: Wen

middle: Ting

last: Li

address: No,1120,LianHua Road,FuTian District

institute: Shenzhen PKU-HKUST Medical Center

summary: Our findings further expand the current knowledge regarding the biology of ceRNAs and their regulatory roles in thymic development and involution process. These newly discovered networks provide more ideas for further research about age-related thymic changes in the future.

overall_design: we used miRNA sequencing and LncRNA sequencing to detect several time points in mouse thymic development (2, 6 weeks old and 3 months old) to study the underlying biological mechanisms in the rapid development of the thymus after birth (from 2 weeks old to 6 weeks old) and the subsequent decline process (from 6 weeks old to 3 months old).

first: Wei

last: Zhang

first: Jun

last: Wan

first: Wenting

first: Nana

last: Ma


title: Unique gender-dependent serum microRNA profile in PLS3 osteoporosis  in PLS3 gene related osteoporosis

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

institute: TAmiRNA GmbH

summary: Plastin 3 (PLS3), encoded by PLS3, is a newly recognized regulator of bone metabolism and mutations in the encoding gene result in severe childhood-onset osteoporosis. Since an X chromosomal gene, PLS3 mutation-positive males are typically more severely affected while females portray normal to increased skeletal fragility. Despite the severe skeletal pathology, conventional metabolic bone markers tend to be normal and are thus insufficient in diagnosing or monitoring patients. Our study aimed to explore serum microRNA (miRNA) concentrations in subjects with defective PLS3 function to identify novel markers that could differentiate subjects according to mutation status and give insight into the molecular mechanisms by which PLS3 regulates skeletal health. We analyzed fasting serum samples for a custom-designed panel comprising 192 miRNAs in 15 mutation-positive (5 males, age range 8–76 years, median 41 years) and 14 mutation-negative (6 males, 8–69 years, 40 years) subjects from four Finnish families with different PLS3 mutations. We identified a unique miRNA expression profile in the mutation-positive subjects with seven   significantly up- or downregulated miRNAs (miR-93-3p, miR-532-3p, miR-133a-3p, miR-301b-3p, miR-181c-5p, miR-203a-3p, miR-590-3p; p-values 0.004–0.044).

first: Riikka

last: Mäkitie

first: Moritz

last: Weigl

first: Anders

last: Kämpe

first: Alice

last: Costantini

first: Johannes

last: Grillari

first: Outi


title: microRNA analysis of supernatants from stromal vascular fraction (SVF) cells derived from healthy controls and lipedema patients

summary:
SVF cells were isolated from liposuction material (hips, outer thigh) of  healthy controls and lipedema patients and seeded for the collection of cell supernatants after 24 hours. After several centrifugation steps, the supernatants were concentrated and enriched for small extracellular vesicles.
Total RNA was extracted from the concentrated supernatants and the small extracellular vesicles fraction. 187 miRNAs were analyzed using qPCR reaction (miRCURY SYBR® Green mastermix, Quiagen).

overall_design: microRNA analysis. Supernatants from SVF cells derived from 3 healthy controls and 3 lipedema patients were analyzed as indicated in the summary. Equal volume of extracted total RNA was used for qPCR.

first: Eleni

last: Priglinger

first: Karin

last: Strohmeier

first: Carolin

last: Lindner

first: Martin

last: Barsch

last: Sandhofer


title: Genome-wide binding of Rpb1  (the largest subunit of the RNA polymerase II) to the chromatin state in bud27∆ and wild-type mutant strains (ChIP-seq)

city: Jaén

first: Francisco

last: Navarro

state: Jaén

address: Campus Las Lagunillas s/n.

department: Experimental Biology

institute: Universidad de Jaén

summary: Comparison of the average normalised ChIP-seq signal over protein-coding genes in bud27∆ mutants strain and wild-type.

overall_design: 2 replicates for a wild-type BY4147 strain and bud27∆ strain. 2 Samples for Rpb1 chromatin immunoprecipitation and their corresponding 2 INPUTs

last: Navarro Gómez


title: Global analyisis to study the bud27∆ and WT treated with rapamycin regarding to WT [RNA-seq]

summary: RNA extraction for global analyisis and sequencing, to study the bud27∆ mutant and WT treated with rapamycin regarding to WT.

overall_design: 2 samples for each condition are analyzed. It means, 2 for bud27D mutant, 2 for a wild-type (WT) strain treated with rapamycin to block TOR pathway, and 2 for a wt strain without treatment, used as a control.


title: Genome-wide maps of Bud27 binding to the chromatin [ChIP-seq]

summary:
The goal of this study is to analyse genome-wide the binding profile of Bud27 prefoldin-like to the genes or other genomic regions in order to know which genes could be transcriptionally regulated by this protein and to elucidate the contribution of Bud27 to the transcription.
Average normalised ChIP-seq signal for Bud27 prefoldin-like binding in a S.cerevisiae wild-type strain.

overall_design: 2 replicates for a wild-type BY4147 strain containing a tap-tagged version of Bud7. 2 Samples for Bud27 chromatin immunoprecipitation and their corresponding 2 INPUTs


title: Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae

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

overall_design: Refer to individual Series


title: Expression of Human Lung Before and After Ex Vivo Lung Perfusion

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

institute: University Health Network

summary:
Ex vivo lung perfusion restores normothermia, ventilation and circulation to donor lungs, typically after a period of cold ischemia. This allows donor lungs to be evaluated prior to transplantation. We used
microarrays to study the biological response of human lungs to Ex Vivo Lung Perfusion. Samples were collected from donor lungs at Toronto General Hospital. Lungs were donation after brain death (DBD)

overall_design: Samples were collected at the end of cold ischemia (CIT1). Lungs were then placed on the EVLP circuit which was then followed by a second round of CIT prior to being transplanted. The second time point was collected at the end of the second round of cold ischemia (CIT2).

first: Aaron

last: Wong

first: Jonathan

last: Yeung

first: Gary

last: Bader

first: Claudia

last: Dos Santos

first: Xiaohui

last: Bai

first: Yubo

last: Wang

first: Shaf

last: Keshavjee

first: Mingyao

last: Liu


title: Expression of Human Lung Before and After Transplantation

summary:
Ischemia reperfusion induced injury contributes to poor lung transplant outcomes. We used microarrays to study the biological response of human lungs to the ischemia reperfusion process. Samples were
collected from lung transplant cases at Toronto General Hospital. Lungs were donation after brain death (DBD)

overall_design: Expression data from peripheral human lung biopsies at the end of cold ischemia and after two hours of reperfusion following transplantation


title: The functional diversity of stream microbes on mountainsides across Eurasia based on Geochip 4.0

city: Nanjing

first: Félix

last: Picazo

state: Jiangsu

address: 22#, 18, North Linshan Road, Qixia

department: Nanjing Institute of Geography and Limnology

institute: Chinese Academy of Sciences

summary: Understanding the biogeographical patterns and underlying drivers of microbial functional diversity is essential for anticipating climate change impacts on ecosystem functioning worldwide. However, this matter remains  scarcely addressed in freshwater ecosystems. Using the high-throughput gene array GeoChip 4.0, we show that functional gene alpha diversity and compositon differ across mountains, alpha diversity declines towards high elevations and compositional turnover increases with larger elevational distances. Both continental- and mountain-scale patterns were primarily driven by climatic variables.

platform_organism: Bacteria Archaea Fungi

overall_design: Fifty two biofilm samples along mountainsides were collected from one stream in Balggesvarri (Norway, 17 samples), one stream in Pyrenees (Spain, 17 samples) and one stream in Laojun (China, 18 samples), spanning an altitudinal range of 18-771 masl, 850-2500 masl and 1828-4045 masl, respectively

first: Jianjun