title: Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation [RNA-seq]

first: Gang

last: Li

summary: TET-mediated oxidation of 5-mC participates in both passive and active DNA demethylation, which exerts a significant influence on diverse biological processes. Mass spectrometry has identified multiple phosphorylation sites of TET2. However, the functions of these phosphosites and their corresponding kinases are mostly unknown. Here we showed that AMP-activated protein kinase (AMPK) phosphorylates murine TET2 at the serine residue 97 (S97), enhances TET2 stability through promoting its binding to 14-3-3β. AMPK ablation resulted in decreased global 5-hmC levels at the myotube stages, severe differentiation defects of C2C12 cells and, significantly, total loss of expression of Pax7. Genome-wide analyses revealed increased DNA methylation at genic and enhancer regions of AMPK-null myoblasts and myotubes. Using CRISPR/Cas9 technology, we showed that a novel enhancer, which is hypermethylated in AMPK-null cells, regulates Pax7 expression. The phospho-mimicking mutant, TET2-S97E, could partly rescue the differentiation defect in AMPK ablated C2C12 cells. Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2.

overall_design: RNA sequencing of C2C12 cells with wildtype and AMPK knockout at day 0 and day 8 of differentiation. RNA sequencing of AMPK knockout C2C12 cells with WT and S97E mutation FLAGBirA-TET2 knockin (2 clones per condition). All experiments were conducted in duplicate.

first: Ting

last: Zhang

first: Xiaowen

last: Guan

first: Un-Lam

last: Choi

first: Jianming

last: Zeng


status: Public on Jun 04 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary:
CD4+ T cells depletion affects gene expression in hippocampus of mice raised in enriched environment
Enriched Environment Mice Hippocampi CD4+ T cells depleted or not (4 replicates)

first: J

last: Chabry

first: A

last: Petit

first: H

last: Zarif

last: Paquet

first: K

first: C

last: Heurteaux

last: Guyon


title: Screening Salinity Tolerance and Transcriptome Analysis in Rice (Oryza sativa L.)

status: Public on Jun 05 2019

city: Annamalainagar

first: Roshni

last: Mary

address: Annamalainagar

department: Department of Genetics and Plant Breeding

country: India

institute: Annamalai University

type: Expression profiling by high throughput sequencing

summary: Comparative transcriptome sequencing in leaf and root tissues of Control and Salt-treated Oryza sativa generated 52.2 and 17.29 million high-quality reads.

overall_design: mRNA sequencing for control and salinity treated samples at 6 dSm-1 of 14-days old seedlings of CARI Dhan 7 Rice variety by deep sequencing, using FastQC and Multi QC.

middle: M

last: Roshni

middle: R

last: Saravanan

first: M

last: Prakash

last: Harikrishnan


title: RNA sequence analysis of stable versus reversible EMT events and the resultant metastases

city: West Lafayette

first: Michael

middle: K.

last: Wendt

state: IN

address: 201 S. University Street

department: Department of Medicinal Chemistry and Molecular Pharmacology

country: USA

institute: Purdue University

summary: The ability of breast cancer cells to transiently transition between epithelial and mesenchymal states is critical to complete the metastatic process. In contrast, induction of epithelial-mesenchymal transition (EMT) through the acquisition of drug persistence is a more stable event. Herein, we utilize Her2 transformed human mammary epithelial (HMLE) cells to compare a reversible model of EMT induced by TGF-beta to a stable mesenchymal phenotype induced by chronic exposure to the ErbB kinase inhibitor, lapatinib. Indeed, only a TGF-beta cells capable of returning to an epithelial phenotype resulted in long bone metastasis (BM). These four cell populations were anylzed by RNA sequencing.

overall_design: The Her2 transformed HMLE cells are referred to as the parental (Par) cell line and serves as the control. These cells were treated with TGF-beta every three days for a period of 4 weeks to induce EMT (TGFB). Alternatively, the parental cells were treated with 1 micromolar of lapatinib every three days also for 4 weeks and a proliferative drug resistant population (LAPR) emerged. The TGF-beta treated cells were engrafted onto the mammary fatpad and resultant long bone metasases (BM) were isolated and subcluted ex-vivo.

first: Micahel

middle: K


title: The Glycan CA19-9 Promotes Pancreatitis and Pancreatic Cancer In Mice

city: Cold Spring Harbor

first: Dannielle

last: Engle

state: NY

address: 1 Bungtown Road, Cold Spring Harbor Laboratory

institute: Cold Spring Harbor Laboratory

summary: Gene expression changes in normal pancreatic ductal organoids were isolated from mice with inducible expression of the glycan, CA19-9.

overall_design: CA19-9 expression was induced with Doxycycline treatment for 0, 4, or 24 hours in organoids with the necessary alleles for CA19-9 expression (n = 3) or from organoids missing one of the requisite alleles (n = 2).

first: Sean

last: Whalen

first: David

last: Tuveson

first: Katherine

last: Pollard


title: Single cell sequencing analysis of the zebrafish pineal gland

city: Tel Aviv

first: Yoav

last: Gothilf

address: Sherman Building, room 405

country: Israel

institute: Tel Aviv University

summary: The purpose of this study was to genetically describe the different pineal cell types, and in particular the type of cells expressing the gene agrp2.  The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells, and that agrp2 is expressed in retinal-pigmented epithelium like cells.

overall_design: For each sample, twenty adult pineal glands were dissected and processed together.

first: Inbal

last: Shainer

first: Gregory

middle: D

last: Marquart

first: Harold

middle: A

last: Burgess


title: Illumina Sequencing of Wild Type, fip37L, cpsf30-3 and cpsf30-1 mutant plants

city: Perpignan

first: Thierry

last: Lagrange

address: 58 Avenue Paul Alduy

institute: CNRS

summary: The goals of this study are to compare gene readthrough transcription in various plant lines, including a Wild Type control, the fip37L, cpsf30-3 and cpsf30-1 mutant plants.

overall_design: Plant mRNA profiles of 9-day old WT, fip37L, cpsf30-3 and cpsf30-1 mutant plants were generated by deep sequencing, in duplicate using Illumina with single-end reads, 1x 75bp and 35-50x106 reads per library

last: LAGRANGE


title: Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex

city: Boston

first: Amanda

middle: Joy

last: Kedaigle

state: MA

address: 1325 Boylston St

department: Systems Biology - Molecular Innovation

institute: Decibel Therapeutics

summary: Stem cell-derived human brain organoids hold an unprecedented degree of promise as experimental models of the human brain. They are, however, plagued by poor reproducibility and high organoid-to-organoid variability. Here, we show that a human organoid model pre-patterned to form the dorsal forebrain and cultured for over six months can achieve reproducible generation of a rich diversity of cell types appropriate for the human cerebral cortex. Using single-cell RNA-sequencing of 166,242 cells isolated from 21 individual organoids, we find that 95% of the organoids generated a virtually indistinguishable compendium of cell types, through the same temporal trajectories, and with organoid-to-organoid variability that is comparable to that of individual endogenous brains. The data demonstrate that reproducible development of complex central nervous system (CNS) cellular diversity does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments.

overall_design:
Single cell RNA-sequencing from 21 individual organoids, after 3 or 6 months in culture. Batches of 3 organoids from each differentiation.
Position-sorted BAM files as created by CellRanger v.2.0.1 are supplied to SRA as raw data files. Each read has Chromium cellular and molecular barcodes information stored as TAG fields.

first: Silvia

last: Velasco

middle: J

last: Simmons

first: Allison

last: Nash

first: Marina

last: Rocha

first: Giorgia

last: Quadrato

first: Bruna

last: Paulsen

first: Lan

last: Nguyen

first: Xian

last: Adiconis

first: Aviv

last: Regev

first: Joshua

middle: Z

last: Levin

first: Paola

last: Arlotta


title: Genome-wide profiling of an enhancer-associated histone modification reveals the influence of asthma on the epigenome of the airway epithelium.

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Asthma is a chronic inflammatory disease of the airways driven by complex genetic-environmental interactions. Epigenomic mechanisms including histone modifications and DNA methylation are altered in key cell types of asthma. However, genome-wide studies of histone modifications in the airway epithelium of asthmatics have yet to be undertaken. We undertook genome-wide profiling of an enhancer (regulatory domain)-associated histone modification H3K27ac in bronchial epithelial cells (BECs) from asthmatic and healthy control individuals. We identified 49,903 (P<0.05) regions exhibiting differential H3K27ac enrichment in asthma and found they clustered predominately at genes associated with Th2-high asthma (e.g. CLCA1) and epithelial processes (e.g. EMT). We determined asthma had a dramatic influence on the enhancer landscape of BECs and identified asthma-associated Super-Enhancers encompassing genes encoding transcription factors (e.g. TP63) and enzymes involved in lipid metabolism (e.g. NOX4). We integrated published protein expression, epigenomic and transcriptomic datasets and identified epithelium-specific transcription factors associated with H3K27ac in asthma (e.g. TP73) and dynamic relationships between asthma-associated changes in H3K27ac, DNA methylation, genetic susceptibility and transcriptional profiles. Finally, using a CRISPR-based approach to recapitulate the H3K27ac landscape of asthma in vitro, we provide proof of principal that asthma-associated gene expression (e.g. SERPINB2) is driven in part by aberrant histone acetylation. This report identifies the influence of asthma on the epigenome of airway epithelium and provides evidence that aberrant epigenomic mechanisms exert functional consequences in key cell types of asthma, validating the combination of genome-wide and epigenome-editing approaches in identifying and deciphering the molecular mechanisms underlying asthma pathogenesis.

overall_design: H3K27ac Chip-Seq in primary bronchial epithelial cells from Healthy and Asthma volunteers.

first: Peter

last: McErlean

first: Audrey

last: Kelly

first: Jaideep

last: Dhariwal

first: Max

last: Kirtland

first: Julie

last: Watson

first: Ismael

last: Ranz

first: David

last: cousins

first: Roberto

last: Solari

first: Michael

last: Edwards

first: Sebastian

middle: L

last: Johnston


title: Profiling of RNA expression in soleus muscles from muscle-specific Gna13 knockout mice

city: Seoul

first: Sang Geon

last: Kim

state: Not required for this country

address: 1 Gwanak-ro, Gwanak-gu

department: College of pharmacy

country: South Korea

institute: Seoul National University

summary: Gna13 transmit extracellular signals from cell surface G protein-coupled receptors to intracellular effector molecules. We have characterized the Gna13-dependent regulatory network in muscle through transcriptional profiling of the mouse soleus in Gna13 muscle-specific knockout (Gna13 MKO) mice or wild-type littermates with floxed genotype (WT).

overall_design: We crossed Ckmm-Cre mice (Jackson laboratory #006475) with Gna13 flox/flox mice, which was provided from Dr. Offermanns S (Max Planc Institute). At 18 weeks of age, Gna13 flox/flox (WT) or Ckmm-Cre; Gna13 flox/flox (Gna13 MKO) mice were fasted overnight and sacrificed. Immediately after sacrifice, soleus muscles were snap-frozen and stored until RNA extraction (n=3 each). For the quality control, RNA purity and integrity were evaluated by OD 260/280 ratio, and analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA). The Affymetrix Whole transcript Expression array process was executed according to the manufacturer's protocol  (GeneChip Whole Transcript PLUS reagent Kit). cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit. Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC). We exported the result with gene level RMA analysis and perfomed the differentially expressed gene (DEG) analysis. The comparative analysis between test sample and control sample was carried out using LPE test and fold change in which the null hypothesis was that no difference exists among 2 groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

first: Ja

middle: H

last: Koo

first: Tae

first: Min

middle: S

last: Joo

first: Sang

middle: G


title: Mouse colon tumor samples with Apc, Kras, and Trp53 R270H or Tpr53 null mutations, and wild type controls.

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary: We treated the following 3 groups of 8-16 week old mice with tamoxifen: 1) CDX2P-CreERT2, Apc flox/+, Kras LSL-G12D/+, Trp53 flox/flox mice (n=6); 2) CDX2P-CreERT2, Apc flox/+, Kras LSL-G12D/+,Trp53 R270H/flox mice (n=6); 3) Wild-type control mice (n=3). The CDX2P-CreERT2 transgene expresses a tamoxifen (TAM)-regulated Cre protein (CreERT2) under control of human CDX2 regulatory sequences, allowing for TAM-inducible targeting of flox alleles in adult mouse terminal ileum, cecum, and colon epithelium. Treating the mice having CDX2P-CreERT2 transgene with tamoxifen permits the Cre recombinase to enter the cell nucleus and recombine the floxed alleles for Apc, Kras, and Trp53, resulting in deletion mutations in Apc and Trp53, and an activating, oncogenic mutation in Kras (G12D mutation). The Trp53 R270H allele carries a constitutive R270H mutation, which is the mouse equivalent of human TP53 R273H mutation. Laser capture microdissection was used to obtain adenocarcinoma tissue samples from the first two groups of mice and normal tissue from control mice.  RNA was purified and targets for Affymetrix arrays were synthesized from the mRNAs.  We used Affymetrix Mouse Gene 2.1 ST plate arrays, which hold 41345 probe-sets, but we largely analyzed just those 24562 probe-sets that were mapped to Entrez gene IDs.  Raw data was processed with the Robust Multi-array Average algorithm (RMA).  Data is log2-transformed transcript abundance estimates. We fit a one-way ANOVA model to the 3 groups of samples.  We supply a supplementary excel workbook that holds the same data as the data matrix file for those 24562 probe-sets, but also holds the probe-set annotation at the time we analyzed the data, and some simple statistical calculations, which selects subsets of the probe-sets as differentially expressed between pairs of groups. It also shows data and analysis from a separate experiment of RNA purified from organoids cultured from samples from 3 groups of mice similar to those here, as well as an extra group of mice with CDX2P-CreERT2 Apc flox/flox genotype.  It also joins a statistical summary of differences between 9 human tumors with TP53 missense mutations at codon 273 and 36 tumors with TP53 null mutations assayed with RNA-seq by the TCGA project. A separate supplementary file of the TCGA data is also provided. Consumers should consider obtaining more up-to-date probe-set annotation for the array platform.

overall_design: Laser capture microdissected mouse colon samples from 1) adenocarcinomas from 6 Apc fl/+, Kras LSL-G12D/+, Trp53 fl/fl mice, 2) adenocarcinomas from 6 Apc fl/+, Kras LSL-G12D/+, Trp53 R270H/fl mice,  3) normal colon tissue from three Wild type mice. Assayed on 15 Affymetrix Mouse Genome 2.1 ST arrays.

first: Ying

last: Feng

first: Jinyu

last: Tang

first: Megan

last: Green

first: Maranne

first: Naoya

last: Sakamoto

first: Jeffry

last: Lin

first: Kathleen

last: Cho

first: Eric

last: Fearon


title: ZIKV infection strongly induces antiviral immune responses in human NPCs

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiaotong University School of Medicine

summary: To investigate the cellular pathologies in human NPCs after ZIKV infection, we performed global transcriptome profiling of the FD, FV, and H&S organoids at 3 and 6 dpi.  We found 105 upregulated genes in the FD NPCs, 60 genes in the FV NPCs, and 168 genes in the H&S NPCs, with at least 1.5-fold differences found between ZIKV-infected groups and the control groups at 6 dpi. Among them, 28 genes overlapped in all three regional NPCs. These 28 common genes exclusively referred to the pathways associated with immune responses to viral infection, which could be clustered to the ISG family.

overall_design: Three regional organoids were infected with ZIKV at MOI=0.5 or mock infection, and total RNAs were extracted at 3 dpi or 6 dpi and used for global transcriptome analysis. RNA-seq libraries were generated from duplicated samples per condition using the Next Illumina Ultra RNA library prep kit (NEB) following manufacturer’s protocols. RNA concentration of library was measured using Qubit RNA Assay Kit in Qubit 2.0. The insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and then accurate quantification was performed with Taqman fluorescence probe of AB Step One Plus Real-Time PCR system and sequenced by an Illumina Hiseq 2500 platform.

first: Ling

last: Liu

first: Hexi

first: Yanhua

last: Du


title: Intestinal expression of ASBT determines the sclerosing cholangitis phenotype.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: Determine the impact of ASBT genotype on the onset and progression of liver disease, using RNA-sequencing to characterize the transcriptome of ASBT wildtype and knockout mice. We assess alterations at the gene and mechanistic-levels.
Methods: mRNA profiles were generated in 45-day-old ASBT WT and KO mice (BALB/cJ background).  Data were processed using the Tuxedo Pipeline, using the mm10 genome with annotations provided by Ensembl.
Results: We identified 1406 differentially expressed transcripts between knockout and wildtype mice, with ontologies heavily weighted toward fibrotic and inflammatory processes, with immune cell infiltration.
Conclusions:  Knockout of ASBT induces increased liver injury through exposure to elevated bile acids.

overall_design: We obtained caudate liver biopsies from mice aged 45 days following 2 weeks of high-fat breeder chow.  We generated mRNA profiles according to standard Illumina protocols.

first: R

first: A

middle: C

last: Arce-Clachar

last: Miethke


title: Human Ago2-HITS-CLIP

city: New York

first: Donghoon

last: Lee

address: 1399 Park Ave

department: Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: mRNA and microRNA profile of Endothelial cells (HUVEC and HUAEC) were generated by HITS-CLIP assay, in triplicate

first: Albertomaria

last: Moro

first: Mark

middle: B

last: Gerstein

first: Stefania

last: Nicoli


title: Paeonia lactiflora suppressed cancer-cachexia by downregulating muscular NF-κB signaling and muscle-specific E3 ubiquitin ligases in cancer-bearing mice.

first: Minwoo

last: Park

address: 25, Seonyu-ro 13-gil, youngdeungpo-gu

department: Research & Development

institute: ebiogen

summary: Paeonia lactiflora restored skeletal muscle function and mass in cancer-bearing mice, through the downregulations of muscular NF-kB signalling and muscle-specific E3 ubiquitin ligases. This study provides experimental evidence that Paeonia lactiflora can be a plausible candidate for a therapeutic agent for cancer cachexia.

overall_design: C57BL/6 mice (4 weeks old) were used to induce lung carcinoma by subcutaneous injection of 1 × 10^6 LLC cells in 100 μl of saline, and gastrocnemius muscle tissues were collected from the Normal and lung cancer mice model. RNA was extracted from the gastrocnemius muscle tissue of Normal mice, Control cancer-bearing mice and RP-treated cancer-bearing mice.

first: Yoosik

last: Yoon

first: Jaewoong

last: Jang


title: Pathologically distinct fibroblast subsets drive inflammation and tissue damage in arthritis

status: Public on Jun 03 2019

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: The identification of lymphocyte subsets with non-overlapping effector functions has been pivotal to the development of targeted therapies in immune mediated inflammatory diseases (IMIDs). Yet, despite their key role in disease, it remains unclear whether fibroblast subclasses with non-overlapping functions also exist and are responsible for the wide variety of tissue driven pathologies observed in IMIDs such as inflammation and damage . Here we identify and describe the biology of distinct subsets of fibroblasts responsible for mediating either inflammation or tissue damage in arthritis. We show that deletion of FAPa+ synovial cells suppressed both inflammation and bone erosions in murine models of resolving and persistent arthritis. Single cell transcriptional analysis identified two distinct fibroblast subsets: FAPa+ THY1+ immune effector fibroblasts located in the synovial sub-lining, and FAPa+ THY1- destructive fibroblasts restricted to the synovial lining. When adoptively transferred into the joint, FAPa+ THY1- fibroblasts selectively mediate bone and cartilage damage with little effect on inflammation whereas transfer of FAPa+ THY1+ fibroblasts  resulted in a more severe and persistent inflammatory arthritis, with minimal effect on bone and cartilage. Our findings describing anatomically discrete, functionally distinct fibroblast subsets with non-overlapping functions have important implications for cell based therapies aimed at modulating  inflammation and  tissue damage.

overall_design: Serum transfer inflammatory arthritis (STIA) was induced by intravenous injection of 100 µl of arthritogenic KRN serum (isolated from progeny of KRN mice (K/BxN) mice), into naive 8-week old C57BL/6 mice. From these mice, CD45-ve live synovial cells from hind limb joints were isolated and sort purified at day 9 (n=3 biological replicates, each comprised of cells from the joints of three animals) and captured with the 10X Genomics Chromium system.

first: Adam

middle: P

last: Croft

first: Kathrin

last: Jansen

first: Moustafa

last: Attar

middle: N

first: Christopher

last: Buckley


title: Genomic instability induced by chronic exposure of furfural in yeast

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Furfural is a potential mutagenic agent. To explore the global effect of furfural on genomic intergrity, chromosomal alterations in 14 furfural-treated isolates of JSC25-1 strain were determined  by whole genome SNP microarrays at a resolution about 1kb. Our results showed furfural exposure results in striking elevations of both mitotic recombination and aneuploidy events in yeast.

overall_design: The JSC25-derived isolates were plated on YPD plates containing 0.6 g/L furfural for 4 days at 30 degree. Single colonies were then picked and streaked on YPD plates. Such treatment procedure was carried out repeatly for 10 times. Finally, the genomic DNA of 14 independent isolates were extracted for SNP microarray analysis.

first: Lei

last: Qi

first: Dao-Qiong


title: Apc, Kras, and Trp53 mutations

first: Rork

last: Kuick

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

overall_design: Refer to individual Series


title: Organoids derived from mouse normal colon and tumor samples with Apc, Kras, and Trp53 mutations in several combinations.

summary: For organoid preparation, we first treated the following 4 groups of 8-12 week old mice with tamoxifen: 1) CDX2P-CreERT2, Apc flox/+, Kras LSL-G12D/+, Trp53 flox/flox mice (n=2); 2) CDX2P-CreERT2, Apc flox/+, Kras LSL-G12D/+,Trp53 R270H/flox mice (n=3); 3) CDX2P-CreERT2, Apc flox/flox mice (n=3); 4) Wild-type control mice (n=4). The CDX2P-CreERT2 transgene expresses a tamoxifen (TAM)-regulated Cre protein (CreERT2) under control of human CDX2 regulatory sequences, allowing for TAM-inducible targeting of flox alleles in adult mouse terminal ileum, cecum, and colon epithelium. Treating the mice having CDX2P-CreERT2 transgene with tamoxifen permits the Cre recombinase to enter the cell nucleus and recombine the floxed alleles for Apc, Kras, and Trp53, resulting in deletion mutations in Apc and Trp53, and an activating, oncogenic mutation in Kras (G12D mutation). The Trp53 R270H allele carries a constitutive R270H mutation, which is the mouse equivalent of human TP53 R273H mutation. Colon tumors were induced by TAM treatment in all the mice from the first three groups and organoids were derived from the tumors of each mouse. We also derived organoids from the normal colon epithelium in the 4th group of mice as controls. All organoids were generated and propagated using a slightly modified TMDU protocol as described in PMID:20872391. Organoids were cultured for 4 days and then harvested. RNA was purified from the organoids, and targets for Affymetrix arrays were synthesized from the mRNAs.  We used Affymetrix Mouse Gene 2.1 ST plate arrays, which hold 41345 probe-sets, but we largely analyzed just those 24562 probe-sets that were mapped to Entrez gene IDs.  Raw data was processed with the Robust Multi-array Average algorithm (RMA).  Data is log2-transformed transcript abundance estimates. We fit a one-way ANOVA model to the 4 groups of samples.  We supply a supplementary excel workbook that holds the same data as the data matrix file for those 24562 probe-sets, but also holds the probe-set annotation at the time we analyzed the data, and some simple statistical calculations, which selects subsets of the probe-sets as differentially expressed between pairs of groups. It also shows data and analysis from a separate experiment of RNA purified directly from 3 groups of mice with genotypes like those of the organoid data except that no group of mice with CDX2P-CreERT2 Apc flox/flox genotype were used.  It also joins a statistical summary of differences between 9 human tumors with TP53 missense mutations at codon 273 and 36 tumors with TP53 null mutations assayed with RNA-seq by the TCGA project. A separate supplementary file of the TCGA data is also provided. Consumers should consider obtaining more up-to-date probe-set annotation for the array platform.

overall_design: Organoids derived from colon tissue samples derived from 1) two Apc fl/+, Kras LSL-G12D/+, Trp53 fl/fl mice, 2) three Apc fl/+, Kras LSL-G12D/+, Trp53 R270H/fl mice,  3) three Apc fl/fl mice,and 4) four Wild type mice. Organoids derived from each mouse were assayed on separate arrays (12 arrays).

first: Ying

last: Feng

first: Jinyu

last: Tang

first: Megan

last: Green

first: Maranne

first: Naoya

last: Sakamoto

first: Jeffry

last: Lin

first: Kathleen

last: Cho

first: Eric

last: Fearon


title: Methylation analysis of STAT3 targets in gastric cancer cells

city: Chia-Yi

first: Yu Ming

last: Chuang

address: 168 University Road,Min Hsiung

department: Department of Biomedical Science

country: Taiwan

institute: National Chung Cheng University

type: Methylation profiling by genome tiling array

summary: To investigate the knockdown effect of STAT3 on DNA methylation on gastric cancer cells, genome wide DNA methylation profiling of AGS transfected with pLKO.1-puro-shGFP or shSTAT3 generated from Illumina Infinium MethylationEPIC.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChips

first: Michael

middle: W

last: Chan

first: Jian-Liang

last: Chou

first: Yu-Ming


title: E2F6-mediated ceRNA and epigenetic silencing of miR-193a promote cancer stemness and immunoevasion in ovarian cancer

summary: To investigate the knockdown effect of EZH2 and E2F6, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of EZH2 or E2F6 in CP70 ovarian cancer cells.

overall_design: CP70 ovarian cancer cells were infected with pLKO TRC005 (vector control) or pLKO TRC005 shE2F6 (treatment) or pLKO.1-puro shEZH2(treatment).

first: Chin

last: Li

first: Frank

last: Cheng


title: Gene expression in prostate cancer cells chronically exposed or not to pollutant Aldrin

city: Barcelona

first: Carmen

last: Bedia

state: Barcelona

address: Jordi Girona 18-26

department: Environmental Chemistry

country: Spain

institute: Institute of Environmental Assessment and Water Research (IDAEA-CSIC)

summary:
DU145 prostate cancer cells were exposed for 50 days to a very low and no-toxic concentration of Aldrin (1 mM).
We used microarrays to detect potential effects of Aldrin in gene expression under chronic exposure to Aldrin.

overall_design: DU145 cells were seeded in a 6-well plate at density of 2x10e5 per well in the presence of 1uM of Aldrin to a final volume of 2ml of supplemented RPMI (final concentration of DMSO 0.01%). Cells were cultured in standard conditions and diluted every 3 days. Cultures were treated after every passage to complete the 50-day treatment.

first: Núria

last: Dalmau


title: The constrained architecture of mammalian Hox gene clusters

city: Lausanne

first: Fabrice

last: Darbellay

address: Station 19

department: SV/ISREC

country: Switzerland

institute: EPFL


title: Identification of glucose-regulated lncRNAs in triple-negative breast cancer cells

city: Houston

first: Liuqing

last: Yang

state: Texas

address: 1515 Holcombe Blvd.

department: Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: To comprehensively identify the glucose-regulated lncRNAs, we have employed ArraryStar LncRNA Microarry discovery platform to detect lncRNA expression in glucose-starved and glucose-stimulated triple-negative breast cancer cells. Differentially expressed LncRNAs with statistical significance were identified through Volcano Plot filtering between two groups.

overall_design: Glucose-induced lncRNA expression in MDA-MB-231 cells was measured at 4 hours after exposure to 25 mM glucose. Three independent experiments were performed at each condition (- or + glucose) using different batch of cells for each experiment.

first: Qingsong

last: Hu

first: Chunlai

first: Shouyu

last: Wang

first: Yajuan

first: Yanyan

last: Zhang

first: Ke

last: Liang

first: Heidi

last: Hsiao

first: Tina

last: Nguyen

first: Jun

last: Yao

first: Peter

last: Park

first: Jeffrey

middle: R

last: Marks

first: Mien-Chie

last: Hung

first: Chunru


title: Expression data from human Circulating Tumor Cells (CTC) and HT-29 cells

status: Public on Jun 02 2019

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

institute: University Hospital of Montpellier, Inserm

summary:
Unraveling the yet unknown molecular mechanisms regulating the biology of metastasis-competent Circulating Tumor Cells (CTCs) is important for better understanding metastatic growth and disease relapses in patients with colon cancer. We investigated and compared the transcriptome profiles of the CTC line and of a cell line derived from a primary colon cancer to get some insight into the specific molecular mechanism of metastasis-competent CTCs.
We used microarrays to establish the molecular portrait of the metastasis-competent CTC and of HT-29 cells

overall_design: CTC line was isolated from the blood of a patient with colon cancer and the HT-29 line was derived from a primary colon cancer. Affymetrix Human Genome U133 Plus 2.0 DNA chips were performed to analyze the transcriptomes of CTC and HT29. The Affymetrix 3’ IVT express protocol was used to prepare cRNA (one-cycle amplification). The gene expression data were extracted using Affymetrix Expression Console software.

first: Catherine

last: Alix-Panabières

first: Laure

last: Cayrefourcq

first: Thibault

last: Mazard

first: Thierry

last: Maudelonde

first: Eric

last: Assenat


title: A transcriptome dataset revealing the molecular features of breast cancer stem cells

city: Wuxi

first: Xiaofeng

last: Dai

address: Lihu Ave 1800

institute: JiangnanUniversity

summary: Triple negative breast cancers lack targeted therapies with little side effects and contain higher percentage of cancer stem cells than the other breast cancer subtypes. Genes capturing the features of cancer stem cells of such diseases may serve as potential subtyping marker or therapeutic targets for triple negative breast cancer management. This data descriptor presents a set of transcriptome data from 3 cohorts of cancer stem cells as represented as CD44+/CD24-/low and 2 cohorts of non-cancer stem cells isolated from triple negative breast cancer cells, each having 3 replicates.

overall_design: 3 cohorts of cancer stem cells as represented as CD44+/CD24-/low and 2 cohorts of non-cancer stem cells isolated from triple negative breast cancer cells, each having 3 replicates are sequenced

first: Xiao

last: Chen

first: Shuo


title: Low-dose quercetin positively regulates mouse healthspan

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: we reported for the first time a geroprotective effect of low-dose quercetin alone that improved the healthspan of aged C57BL/6J male mice. Que-treated mice showed less hair loss, greater athletic endurance, enhanced diastolic function, and less muscle fibrosis, as well as alleviated cellular senescence in multiple tissues. Interestingly, these changes appear to be rarely associated with transcriptional alterations of protein-coding genes but are linked to heterochromatin stabilization and RTE silencing. Que treatment prevented L1 from hyperactivation, thereby inhibiting SASP.

overall_design: Transcriptome analysis of three tissues of mice upon long-term low-dose Que treatment.

first: Guanghui


title: Analysis of gene expression of PC3 human prostate cancer cells incubated with Polypurine reverse Hoogsteen hairpins (PPRH) against survivin

first: Carlos

last: Ciudad

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary:
We had previously shown the effect of PPRHs against the DNA coding for the antiapoptotic protein survivin in PC3 prostate cancer cells. Now, we explored the gene expression profile produced by 24 hours of incubation with specific PPRH against survivin (HpsPr-WT) and with a Watson-Crick PPRH negative control (HpsPr-WC).
PC3 cells were incubated with 100 nM of each PPRH for 24 hours. RNA was extracted and Affymetrix Clariom S exon microarray was performed to determine gene expression.

overall_design: The PC3 human prostate cancer cell line was used in the study. 9 samples are provided, which correspond to triplicates of 3 experimental conditions. The conditions were: control cells, cells incubated with 100 nM of HpsPr-WC (negative control PPRH) and cells treated with HpsPr-WT (specific PPRH against survivin). The platform used was:  Affymetrix.TranscriptomeChip.Clariom_S_Human_na36_hg38_2016-06-21. The associated list of probe set annotations is available on the foot of this record.

first: Veronica

last: Noe

first: Alex

last: Félix


title: Total RNA sequence under control and PD-L1 knockdown

city: Rochester

first: Zhenkun

last: Lou

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: Detect overall RNA level change under PD-L1 knockdown.

overall_design: The experiment is designed to determine the overall RNA level change between PD-L1 knockdown and control group. Briefly, we first infected MDA-MB-231 with either control  shRNA lentivirus or PD-L1 knockdown shRNA lentivirus. After PD-L1 knowdown efficiency has been confirmed, RNAs from each group were extracted and sequenced. The downregulated genes for RNA seq were then defined by counts>100, folds>1.5 and p<0.02.

first: Xinyi

last: Tu

first: Bo

last: Qin

first: Yong

last: Zhang

first: Cheng

first: Haidong

last: Dong

first: Robert

last: Mutter


title: To investigate whether recover DNMT3A expression permitted adult beta cell of βRapKO establishing proper transcriptome

status: Public on Jun 01 2019

first: Qicheng

last: Ni

address: 197 Ruijin 2nd Road

institute: Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Murine islets were isolated from 8-week-old WT and βRapKO mice and initially recovered in 1640 RPMI supplemented with 10% serum, 11.1mM glucose overnight. Then islets were transfected with Lenti-GFP or Lenti-Dnmt3a for 24 hours, following cultured in 1640 RPMI medium for 48 hours.Islets were harvested and stored in -80°C for preparation for RNA sequencing.

overall_design: Transcriptome of three groups: WT, βRapKO, βRapKO+LvDnmt3a

first: Qidi

last: Wang

first: Guang

last: Ning


title: Functional gene abundance of tundra soil microbial communities sampled at the EML Thaw Gradient site, AK in May 2004

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

summary: Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25 % and 5 %, while the community functional gene beta-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw related soil and plant changes, and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.

sample_organism:
Bacteria
Archaea
Eukaryota
Viruses
synthetic construct

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: A total of 107 soil samples were analyzed for functional genes of microbial communities. These samples were collected from a depth range of surface to permafrost from cores in a gradient of minimally, moderately, and extensively thawed locations. Please note that the *532.exp.ftr files recorded intensities of targeted spots, and *532.void.ftr files were intensities of the areas between two adjacent targeted spots, which were used as background intensity (noise) in the normalization step in GeoChip.

first: Mengting

middle: M

last: Yuan

first: Jin

first: Kai

last: Xue

first: Liyou

last: Wu

first: Ye

last: Deng

first: Jie

first: Lauren

last: Hale

first: Xishu

first: Zhili

last: He

first: Yunfeng

last: Yang

first: Joy

last: Van Nostrand

first: Edward

last: Schuur

first: Konstantinos

middle: T

last: Konstantinidis

first: C

last: Penton

first: James

last: Cole

last: Tiedje

first: Yiqi

last: Luo


title: RNA-seq analysis of liver transcriptomes from wild type and Ern1-LKO mice

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

summary:
This experiment was conducted to identify mRNA transcripts alteration in liver of Ern1 liver specific knockout mice. The following abstract from the submitted manuscript describes the major findings of this work.

The IRE1a-XBP1s axis regulates the COPII-mediated secretory program in response to nutrient availability. Lin Liu, Jie Cai, Xijun Liang, Qian Zhou, Huimin Wang, Chenyun Ding, Yuangang Zhu, Liwei Xiao, Tingting Fu, Zhisheng Xu, Jing Liu, Yujing Yin, Lei Fang, Bin Xue, Yan Wang, Aibin He, Yong Liu, Xiao-Wei Chen, and Zhenji Gan

The cytoplasmic coat protein complex-II (COPII) is an evolutionarily conserved machinery that is essential for efficient trafficking of protein and lipid cargos. How the COPII machinery is regulated to meet the metabolic demand in response to alterations of nutritional state remains largely unexplored, however. Here, we show that dynamic changes of COPII-mediated secretion parallel the activation of XBP1s, the critical transcription factor in handling cellular ER stress, in both live cells and mouse liver upon physiological fluctuations of nutrient availability. Using live-cell imaging approaches, we demonstrate that XBP1s is sufficient to promote COPII-dependent secretion, mediating the nutrient stimulatory effects. ChIP-seq and RNA-seq analyses reveal that nutritional signals induce dynamic XBP1s occupancy of promoters of COPII secretion-related genes, thereby driving COPII-directed secretory process. Liver-specific disruption of the IRE1a-XBP1s signaling branch results in diminished COPII-mediated secretion. Reactivation of XBP1s in mice lacking hepatic IRE1a restores COPII-mediated lipoprotein secretion, and reverses the fatty liver and hypolipidemia phenotypes. Thus, our results demonstrate a previously unappreciated mechanism in the metabolic control of liver protein and lipid secretion: the IRE1a-XBP1s axis functions as a nutrient-sensing regulatory nexus that integrates nutritional states and the COPII secretory program.

overall_design: Liver mRNA profiles of 8-week-old WT and Ern1-LKO mice were generated by deep sequencing, in replicate, using Illumina HiSeq 4000.

first: Qian

first: Xijun

last: Liang

first: Lin

last: Liu


title: scRNA-seq analysis of the dual expressors, B cells and T cells of a diabetes patient

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

summary: We identified a rare subset of autoreactive lymphocytes with a hybrid phenotype of T and B cells including coexpression of TCR and BCR and key lineage markers of both cell types (hereafter referred to as dual expressers or DEs).  To investigate the dual phenotype of DEs at single cell resolution, we examined their transcriptomes using single cell RNA sequencing (scRNA-seq). We sorted individual DEs, Bcon and Tcon cells from PBMCs of one type I diabetes patient and analyzed the transcriptomes  of 34 DEs,  20 Bcon , and 23 Tcon  using the plate-based SMART-seq2 protocol (Tirosh and Suva, 2018; Tirosh et al., 2016).  Our results show that DEs have uniquely expressed genes along with genes encoding lineage markers of T and B cells.

overall_design: Examination of the transcriptomes of three cell types, Des (Dual Expressors), Bcon (Conventional B) and Tcon (Conventional T) cells from the  PBMCs of one type I diabetes patient

first: Hamad

last: Abdel

last: Chunfa


title: Enhanced DNA repair and genomic stability identify a novel HIV related Diffuse Large B-cell Lymphoma subtype

city: Scottsdale

first: Alanna

last: Maguire

state: Arizona

address: 13400 East Shea Blvd

department: Research

type:
Other
Genome variation profiling by array


title: Ultra-low levels of CpG Island methylation control tissue-specific expression and hypermethylation in cancer.

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

type: Methylation profiling by high throughput sequencing

summary: We analyzed levels of 5-methyl cytosine CCCGGG target sites by sequential restriction digest by SmaI and XmaI enzymes, ligating Illumina adaptors to the restriction fragments and reading methylation-specific signatures at the ends of restriction fragments by paired ends Illumina high throughput sequencing.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of human genomic DNA from normal tissues. Genomic DNA spiked in with unmethylated, partially methylated and fully methylated standards was sequentially cut at CCCGGG sites with the methylation-sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5'CCGG overhangs), creating different end sequences that represented methylation status of the CCCGGG sites. These end sequences were analyzed by Illumina high throughput sequencing. Methylation status at individual CCCGGG sites across the genome was determined by counting the methylated reads with the CCGGG signature and unmethylated reads with the GGG signature at the beginnings of the sequencing reads after alignment to the human genome.

first: Priyanka

last: Maddiredi

first: Rodrigo

middle: V

last: Rodrigues

first: Yan

last: Zhang

first: Takahiro

last: Sato

first: Justin

last: Lee

first: Andrew

last: Magimaidas

first: Hanghang

middle: D

last: Kelly

first: Matteo

last: Cesaroni

first: Shinji

last: Maegawa

first: Woonbok

last: Chung

first: Shoghag

last: Panjarian

first: Judith

last: Garriga

first: Vinay

last: Puduvali

first: Gabriel

last: Malouf

first: Frank

last: Neumann

first: Yue

last: Lu

first: Jean-Pierre

last: Issa


title: LPS-induced gene expression changes in phraryngeal epithelial cells

city: Singapore

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

country: Singapore

institute: GIS

summary: Gram negative endotoxin Lypopolysaccharide (LPS) leads to a strong innate immune response through TLR4 signalling. This latter pathway activates cannonical NF-kB pathway, including its member RELA. Here, we want to investigate the gene expression response induced by LPS recognition.

overall_design: Treatment of FaDu cells with LPS and examination of gene expression response after stimulation compared to before by RNA-seq. Two biological replicates were analyzed for each condition.


title: Mapping of m6A and m5C on MLV with PA-antibody-seq

city: Durham

first: Bryan

last: Cullen

state: NC

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

summary: While it has been known for several years that viral RNAs are subject to the addition of several distinct covalent modifications to individual nucleotides, collectively referred to as epitranscriptomic modifications, the effect of these editing events on viral gene expression has been controversial. Here, we report the purification of murine leukemia virus (MLV) genomic RNA to homogeneity and show that this viral RNA contains levels of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and 2’O-methylated (Nm) ribonucleotides that are an order of magnitude higher than detected on bulk cellular mRNAs. Mapping of m6A and m5C residues on MLV transcripts identified multiple discrete editing sites and allowed the construction of MLV variants bearing silent mutations that removed a subset of these sites. Analysis of the replication potential of these mutants revealed a modest but significant attenuation in viral replication in 3T3 cells in culture. Consistent with a positive role for m6A and m5C in viral replication, we also demonstrate that overexpression of the key m6A reader protein YTHDF2 enhances MLV replication, while downregulation of the m5C writer NSUN2 inhibits MLV replication.

overall_design: In this GEO submission we include the PA-m6A-seq and PA-m5C-seq datasets for MLV in 3T3 cells

first: David

last: Courtney


title: Total RNA sequencing of prospective axial stem cell cultures derived from human pluripotant stem cells

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

summary: Here we describe a protocol for converting pluripotent stem cells to stable bi/multipotent stem cell populations with axial progenitor characteristics. To analyse the global transcriptome of the derived lines, we performed RNA-sequencing of 3 different axial stem cell lines

overall_design: total RNA sequencing of three stable cell lines at passage 9 and undifferentiated parental hESC line H9


title: Pro-infammatory Aorta-Gonad-Mesonephros-associated macrophages are involved in embryonic development of hematopoietic stem cells

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

institute: The University of Edinburgh

summary: Hematopoietic stem cells (HSC) are generated from specialized endothelial cells of the embryonic aorta. Previously, inflammatory factors have been implicated in regulating mouse HSC development, but it is unclear what cells in the embryonic aorta-gonad- mesonephros (AGM) microenvironment produce these factors. In the adult, macrophages play both pro- and anti-inflammatory roles. We sought to examine whether macrophages or other hematopoietic cells found in the embryo prior to HSC generation are involved in the AGM HSC-generative microenvironment. Our CyTOF results indicate two abundant myeloid cell types - mannose-receptor positive AGM- associated macrophages (AGM-aM) and mannose-receptor negative macrophages/progenitors. We show that the appearance of macrophages in the AGM is dependent on CX3CR1. AGM-aM express a pro-inflammatory signature, localize to the embryonic aorta and dynamically interact with nascent and emerging intra-aortic hematopoietic cells (IAHC). Importantly, upon macrophage depletion, no adult- repopulating HSCs are detected, thus implicating unique pro-inflammatory AGM- associated macrophages in regulating the embryonic development of HSCs.

overall_design: Mannose receptor negative and mannose receptor positive macrophages were extracted from 3 independent litters of E10.5 MacGreen embryos. Each sample was representative of 3-5 AGM. The AGM were dissected and dissociated by collagenese digestion and then mannose receptor negative and positive macrophages were extracted by FACS sorting.

first: Samanta

middle: A

last: Mariani


title: Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis

city: Cologne

first: Ali

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

summary: Liver myeloid leukocytes and their bone marrow precursors adapt a common and functionally relevant inflammatory signature during NAFLD progression.

overall_design: leukocytes from liver and bone marrow were isolated from ND and WD fed mice for single cell RNA sequencing analysis

first: Oliver

last: Krenkel

first: Jana

last: Hundertmark

first: Marlene

last: Kohlhepp

first: Tobias

last: Puengel

first: Tilman

last: Roth

first: Diogo

last: Branco

last: Mossanen

first: Tom

last: Luedde

first: Christian

last: Trautwein

first: Ivan

last: Costa

last: Tacke


title: From intracellular bacteria to differentiated bacteroids: transcriptome and metabolome analysis in Aeschynomene nodules using the Bradyrhizobium sp. ORS285 bclA mutant

city: Gif sur Yvette

first: Florian

last: Lamouche

address: 1, Avenue de la Terrasse

department: Institute of Integrative Biology of the Cell (I2BC)

institute: Centre national de la Recherche Scientifique (CNRS)

summary: During the legume-rhizobium symbiosis, free-living soil bacteria known as rhizobia trigger the formation of root nodules. The rhizobia infect these organs and adopt an intracellular lifestyle within the symbiotic nodule cells where they become nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this differentiation process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, Bradyrhizobium sp. ORS285 proceeds until the intracellular infection of nodule cells but the bacteria cannot differentiate into enlarged polyploid bacteroids and fix nitrogen. The nodule bacteria of the bclA mutant constitute thus an intermediate stage between the free-living soil bacteria and the intracellular nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the ORS285 wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules discriminated nodule-induced genes that are specific to differentiated and nitrogen-fixing bacteroids and others that are activated in the host microenvironment irrespective of bacterial differentiation and nitrogen fixation. These analyses demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but that are expressed to extremely elevated levels. The transcriptomes further highlighted the dynamics of oxygen and redox regulation of gene expression during nodule formation and we discovered that bclA represses the expression of non-ribosomal peptide synthetase gene clusters suggesting a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.

overall_design: 3 conditions with 3 replicates each for each condition are analyzed. Two nodule bacteria conditions are considered : one from A. indica nodules and from A. afraspera nodules, as well as a culture reference in rich medium

first: Peter

last: Mergaert

first: Benoit

last: Alunni


title: LPS-induced genome-wide RELA binding sites and H3K27ac changes in phraryngeal epithelial cells

first: Lisa

last: Borghini

summary: Gram negative endotoxin Lypopolysaccharide (LPS) leads to a strong innate immune response through TLR4 signalling. This latter pathway activates cannonical NF-kB pathway, including its member RELA. Here, we want to investigate the RELA response in terms of DNA binding as well as epigenetic changes induced by LPS recognition.

overall_design: Treatment of FaDu cells with LPS and examination of RELA genome-wide binding sites as well as H3K27ac mark by ChIP-seq before and after stimulation. One biological replicate was analyzed for each condition.


title: Transcriptome response to safener treatment in rice cell cultures

city: Egham

first: Gerhard

last: Leubner-Metzger

state: Surrey

address: Bourne Building 3-30

department: Biological Sciences

institute: Royal Holloway University of London

summary: Safeners are an important group of agrochemicals that can extend the selective use of existing herbicides into a wider range of cereals by protecting the crops from chemical injury.  The recently released aromatic sulphonamide safeners cyprosulfamide and metcamifen were tested for their ability to protect rice plants from the phytotoxicity caused by clodinafop-propargyl, a herbicide normally only used in wheat. Transcriptome studies in rice cultures demonstrated that whereas cyprosulfamide had a negligible effect on gene expression over a 4 h exposure, metcamifen perturbed the abundance of 590 transcripts.  Analysis of the inducible genes suggested that safening elicited similar gene families to those associated with specific biotic and abiotic stresses, notably those elicited by abscisic acid, salicylic acid and methyl-jasmonate.

overall_design: Changes in the transcriptome of rice cultures exposed to metcamifen (5 µM) or  cyprosulfamide (5 µM) were determined as compared with control cells treated with the carrier solvent DMSO.  Cultures were sampled at 0.5 h, 1.5 h and 4 h after dosing and subjected to RNA-seq analysis. Three biological replicates were sequenced for each sample for a total of 27 samples

first: Melissa

last: Brazier-Hicks

first: Anushka

last: Howell

first: Jonathan

last: Cohn

first: Tim

last: Hawkes

first: Gavin

last: Hall

first: Robert

last: Edwards


title: Gene expression analysis of human CD34+ ALL cells cultured with or without gabapentin

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: To clarify the global gene expression alteration in primary CD34+ ALL cells after BCAA metabolism inhibition, CD34+ AML cells were treated with or without gabapentin in vitro. After 9-12 hours of culture with or without gabapentin, FACS-purified CD34+ ALL cells were subjected to transcriptome analysis.

overall_design: To clarify how BCAA metabolism affect the gene expression of human CD34+ ALL cells, CD34+ ALL cells from 4 independent patients were treated with or without 40mM gabapentin, a specific BCAT1 inhibitor for 9-12 hours. After BCAA metabolism inhibition by gabapentin, CD34+ ALL cells were purified and total RNA was extracted from control and treated samples.

first: Koichi

last: Akashi


title: Kentucky assay: bourgeonal

city: Lexington

first: Timothy

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odorants is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or bourgeonal were subjected to microarray analysis using Clariom S arrays

first: William

last: Titlow


title: Kentucky assay: undecanal bourgeonal mixture

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or undecanal and bourgeonal mixture were subjected to microarray analysis using Clariom S arrays


title: The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

summary: Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin-remodeling coregulatory complex that physically associates with Pdx1, a diabetes-linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, were required to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed that these Swi/Snf deficient β cells lost the ability to produce insulin and other key metabolic genes, yet the expression levels of many essential islet-enriched transcription factors were unaffected. Swi/Snf was necessary for Pdx1 binding to the insulin enhancer, demonstrating the importance of this association in mediating chromatin accessibility. These results illustrate how fundamental the Pdx1:Swi/Snf coregulator complex is in the pancreas and we discuss how disrupting their association could influence Type 1 and Type 2 diabetes susceptibility.

overall_design: Comparison of TdTomato flow-sorted Swi/Snf-deficient islet β cells to those from TdTomato flow-sorted control islet β cells

first: Roland

last: Stein


title: PD-L1 binding RNAs: MDA-MB-231

first: Zhenkun

last: Lou

address: 200 1st St SW

summary: Analysis of PD-L1 binding RNAs using crosslinked RNA immunoprecipitation in MDA-MB-231.

overall_design: using PD-L1 antibody and its isotype IgG to perform RIP assay in MDA-MB-231. the PD-L1 binding RNAs were defined as RNAs that were at least 5-folds higher in the PD-L1 group compared to IgG.

first: Xinyi

last: Tu

first: Bo

last: Qin

first: Yong

last: Zhang

first: Cheng

first: Haidong

last: Dong

last: Mutter


title: De-differentiation by Adenovirus E1A Due to Inactivation of Hippo Pathway Effectors YAP and TAZ [ATAC-seq]

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

summary: Adenovirus-transformed cells have a de-differentiated phenotype. Eliminating E1A in transformed human embryonic kidney cells de-repressed ~2600 genes, generating a gene expression profile closely resembling mesenchymal stem cells (MSC). This was associated with a dramatic change in cell morphology from one with scant cytoplasm and a globular nucleus to one with increased cytoplasm, extensive actin stress fibers and actomyosin-dependent flattening against the substratum. E1A-induced histone hypoacetylation by p300/CBP at H3K27/18 was reversed. Most of the increase in H3K27/18ac was near TEAD transcription factors associated with their co-activators YAP and TAZ regulated by the Hippo pathway. E1A causes YAP/TAZ cytoplasmic sequestration. After eliminating E1A, YAP/TAZ were transported into nuclei where they associated with poised enhancers with DNA-bound TEAD4 and H3K4me1. This activation of YAP/TAZ required RHO-family GTPase signaling and caused histone acetylation by p300/CBP, chromatin remodeling, and cohesin loading to establish MSC-associated enhancers and then super-enhancers. Consistent results were also observed in rat embryo kidney cells, human fibroblasts and human respiratory tract epithelial cells. These results together with earlier studies suggest that YAP/TAZ function in a developmental check-point controlled by signaling from the actin cytoskeleton that prevents differentiation of a progenitor cell until it is in the correct cellular and tissue environment.

overall_design: Examination of YAP, H3K18ac, H3K27ac, H3K4me1, TEAD1, TEAD4, RAD21, chromatin accessibility and mRNA by ChIP-seq, ATAC-seq, and mRNA-seq

first: Nathan

last: Zemke

first: Arnold

last: Berk


title: Total RNA sequencing of a time course treatment of human embryonic stem cells with CHIR99021, recombinant Wnt3a, and a time course activation of constitutively active beta-catenin expression

first: Dmitry

last: Shaposhnikov

summary: Here we analysed the transcriptomic response of human embryonic stem cell line H9 to sustained activation of the canonical Wnt pathway by eiother treating cells with CHIR99021 or recombinant Wnt3a or inducing the overexpression of constitutively active beta-catenin mutant

overall_design: hESC cell line H9 was treated with 10 µM CHIR99021 or 240 ng/ml of rWnt3a. In parallel, H9 line with stable integration of doxycycline-regulatable deltaN90 mutant of beta-catenin was treated with 1 µg/ml of Doxycycline. Cells were collected at time points 0 hours (undifferentiated cells), 8 hours, 16 hours, 24 hours, 48 hours and 72 hours (additionally 96 and 120 hours for rWnt3a treatment) and subjected to total RNA sequencing using Illumina platform.


title: LPS-induced RELA binding, H3K27ac changes and gene expression in pharyngeal epithelial FaDu cells

first: Lisa

last: Borghini

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

overall_design: Refer to individual Series


title: Kentucky assay: isoamyl acetate

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or isoamyl acetate were subjected to microarray analysis using Clariom S arrays


title: RNA-Seq analysis sheds light on the breakdown of Tomato spotted wilt virus resistance in pepper at high temperature

city: Seoul

first: JOUNGHO

last: LEE

address: Gwanak-ro

institute: Seoul National University

summary: The Tsw gene conferring Tomato spotted wilt virus (TSWV) resistance in Capsicum chinense breaks down at high temperatures. Here, we performed RNA-Seq analysis under different temperature conditions to uncover the resistance breakdown mechanism using TSWV-resistant C. chinense ‘PI152225’ and susceptible ‘Habanero’. RNA-Seq analysis  revealed only a few differentially expressed genes (DEGs) at 1 dpi but 2,096 and 551 DEGs between plants at 25°C and 30°C at 5 dpi. At 5 dpi, there were more upregulated than downregulated DEGs at both temperatures. Gene ontology analysis revealed 30 enriched biological process terms and nine molecular function terms that were enriched among upregulated DEGs at 25°C. We performed KEGG analysis with 805 upregulated DEGs at both temperatures to explore the mechanism underlying resistance breakdown at high temperature.  The DEGs were mapped into 10 KEGG pathways. ACC oxidase genes in the ethylene biosynthesis pathway were differentially expressed upon pathogen challenge. Most DEGs from the biological process, molecular function, and cellular components categories involved in resistance responses were downregulated at 30°C. Finally, genes involved in abscisic acid-mediated stress signaling were differentially expressed at high temperature. These results shed light on host–virus interactions and temperature-dependent resistance mechanisms in pepper at the molecular level.

overall_design: mRNA profiles of 1 and 5 dpi mock- and TSWV-inoculated C. chinense 'PI152225' at 25℃ and 30℃ were generated by deep sequencing, in triplicate (except 1dpi mock-inoculated at 25℃), using Illumina HiSeq 2500 system.

first: Byoung-Choerl

last: Kang


title: Kentucky assay: undecanal

first: Timothy

last: McClintock

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or undecanal were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay: isoamyl acetate and whiskey lactone mixture

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or isoamyl acetate and whiskey lactone were subjected to microarray analysis

first: William

last: Titlow


title: Kentucky assay: whiskey lactone

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or whiskey lactone were subjected to microarray analysis


title: RNA-sequencing on  Nrn1-/- and Nrn1+/- OTII cells recovered from OVA-peptide induced anergy TCRa-/- host mice

city: Baltimore

first: Drew

last: Pardoll

state: Maryland

address: 1650 Orlean St.

department: Oncology

institute: Johns Hopkins Medical Institute

summary: Nrn1-/- and Nrn1+/- Thy1.1+ OTII cells were cotransferred with wt Treg cell into TCRa-/- hosts and subjected to soluble OVA peptide i.v. treatment for anergy induction on day 1, 4, and 7 post transfer. Nrn1-/- and Nrn1+/- Thy1.1+ OTII cells were recoverred by cell sorting 13 days after cell transferand subjected to RNA-Sequencing analysis

overall_design: Expression profiling by high throughput sequencing performed on Illumina HiSeq V2 Systems 75 cycles (1x75bp).

first: Hiroshi

last: Nishio

first: Hong

last: Yu


title: RNA-sequencing on sorted  Nrn1-/- and Nrn1+/- effector Treg and OTII cells


title: RNA-sequencing on sorted  Nrn1-/- and Nrn1+/- effector Treg cells

summary: Nrn1-/- and Nrn1+/- CD4+CD25+Cd62LlowCD44highFoxp3gfp+ were sorted from Nrn1-/- and Nrn1+/- mice on Foxp3DTRgfp background and subjected to RNASeq analysis

overall_design: Expression profiling by high throughput sequencing performed on Illumina HiSeq 75 cycles (1x75bp).


title: Comparing Gene Expression Profiling of ATO sensitive and Resistant cell lines

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: To further characerize the arsenic trioxide (ATO) resistance in acutepromyelocytic leukemia, we had made NB4 cell line (arsenic sensitive) to be resistant to arsenic by exposing them to increasing concentration till they are resistant to it and we named it NB4-EV-AsR1. We have also used another cell line (UF1) which is by default resistant to arsenic. Comparing the GEP will give us novel pathways that can contirbute to arseic trioxide.

overall_design:
Organism : Homo sapiens, Agilent's Human Gene Expression  8x60k Array (AMADID: 039494)
Contributor: Genotypic Technology Private Limited, Bangalore

first: Vikram

last: Mathews

first: Ezhilarasi

last: Chendamarai

first: Saravanan

last: Ganesan

first: Ansu

last: Alex


title: De novo assembled individual genome does not show advantage against standard reference genome: a demonstration of Chinese Han Population

city: Guangzhou

first: Zhibiao

last: Mai

state: Guangdong

address: Huang-Pu Avenue West 601

department: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering

institute: Jinan University

summary: We compared standard human reference genome GRCh38 and de novo assembled reference genome HX1 in precision medicine applications for specific ethnics. In order to quantify the HX1 misassembled genes and HX1-specific contigs, we performed RNA-seq and RNC-seq on hepatocellular carcinoma cell lines (MHCC97H, MHCCLM3 and MHCCLM6) which were derived from Chinese Han individuals. In which, RNC-seq datasets of MHCC97H and MHCCLM3 had been published. We found that a considerable fraction of HX1 misassembled genes was expressed in the Chinese Han samples. Furthermore, we found no HX1-specific contigs yielded more than 2.27 FPKM (minimun FPKM of 1 copy/cell transcript) in the Chinese Han sampels.

overall_design: RNA-seq of MHCC97H, MHCCLM3 and MHCCLM6. RNC-seq of MHCCLM6.

first: Mai

last: Zhibiao


title: RNA-Seq-based transcriptome profiling of primary interstitial cells of Cajal derived from the small intestine of Merino sheep in response to bovine viral diarrhea virus infection

city: Shihezi

first: Qiang

last: Fu

state: Xinjiang

address: Bei 4 Road

institute: Shihezi University

summary: Infections with bovine viral diarrhea virus (BVDV) contribute significantly to health-related economic losses in the beef and dairy industries and are widespread throughout the world. Severe acute BVDV infection is characterized by a gastrointestinal (GI) inflammatory response. The mechanism of inflammatory lesions caused by BVDV remains unknown. The interstitial cells of Cajal (ICC) network plays a pivotal role as a pacemaker in the generation of electrical slow waves for GI motility, and it is crucial for the reception of regulatory inputs from the enteric nervous system. The present study investigated whether ICC were a good model for studying GI inflammatory lesions caused by BVDV infection. Primary ICC were isolated from the duodenum of Merino sheep. The presence of BVDV was detected in ICC grown for five passages after BVDV infection, indicating that BVDV successfully replicated in ICC. After infection with BVDV strain TC, the cell proliferation proceeded slowly or declined. Morphological changes, including swelling, dissolution, and formation of vacuoles, of ICC were observed, pointing to quantitative, morphological and functional changes of ICC. Therefore, RNA sequencing (RNA-Seq) was performed to investigate differentially expressed genes (DEGs) in BVDV-infected ICC and to further explore the molecular mechanism of underlying quantitative, morphological and functional changes of ICC. Eight hundred six genes were differentially expressed upon BVDV infection, of which 538 genes were upregulated and 268 genes were downregulated. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the 806 DEGs were significantly enriched in 27 pathways, including cytokine-cytokine receptor interaction, interleukin (IL)-17 signaling, mitogen-activated protein kinase (MAPK) signaling pathway. Finally, 21 DEGs were randomly selected, and the relative repression levels of these genes were tested using the quantitative real-time PCR (qRT-PCR) to validate the RNA-Seq results. The results showed that the related expression levels of 21 DEGs were similar to RNA-Seq. This study is the first to establish a new infection model for investigating GI inflammatory lesions induced by BVDV infection.

overall_design: Transcriptome profiling of primary interstitial cells of Cajal derived from the small intestine of Merino sheep in response to bovine viral diarrhea virus infection generated by deep sequencing, in triplicate, using Illumina platform.

first: Shengnan

last: Li

first: Gang

last: Yao

first: Huijun

last: Shi


title: Genome transfer for the prevention of female infertility caused by maternal gene mutation

city: shanghai

first: Jin

last: Sun

department: life science and technology

institute: Tongji University

summary: Maternal gene plays crucial role in the regulation of oocyte maturation and preimplantation embryonic development and its mutation is an important cause of woman infertility

overall_design: WT MII oocyte, WT zygotes, Zar1-/- MII oocyte, Zar1-/- zygotes,WT 2 cell embryo,spindle transfer 2 cell embryo, polar body transfer 2 cell embryo and  pronuclear transfer 2 cell embryo are performed RNA sequencing.

first: Dandan

last: Bai

first: Yanping

last: Jia

first: Shaorong

last: Gao


title: Aryl hydrocarbon receptor dynamically regulates inflammatory and secretory gene pathways in decidual endometrial stromal cells

city: West Haven

first: Kalle

last: Rytkönen

state: CT

address: 840 West Campus Drive

department: EEB, Systems Biology institute

institute: Yale University

summary: We report sequencing of chromatin immunoprecipitated DNA (ChIP-Seq) of Aryl Hydrocarbon Receptor (AHR) targets from decidual stromal cells with kynurenine treatment and normal decidualization media

overall_design: We report Aryl Hydrocarbon Receptor (AHR) ChIP-Seq from decidual cells in normal decidualization media and after one hour 100 µM L-kynurenine treatment. We also sequenced ChIP input samples for each of the four experimental samples. Before kynurenine treatments endometrial stromal fibroblasts were in vitro decidulization with cAMP and progesterone (MPA) for 2 days.


title: PRSS8 Suppresses Colorectal Carcinogenesis and Metastasis.

city: Chicago

first: Wancai

last: Yang

state: IL

address: 840 South Wood Street

department: Pathology

institute: University of Illinois at Chicago

summary:
To study PRSS8 gene function.
We used microarrays to elucidate the underlying mechanisms of the PRSS8-mediated inhibition of tumor formation and metastasis.

overall_design: Human colon cancer HCT116 cells were transiently transfected with PRSS8 expression plasmids or the vector control and collected for gene profiling using the Affymetrix Platform.

first: Yongchen

last: Guo

first: Yonghua

last: Bao


title: Combined phosphoproteome and transcriptome analysis of the macrophage response to mycobacterial cord factor reveals a dichotomy of MINCLE-dependent and -independent signaling

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary: Immune sensing of Mycobacterium tuberculosis relies on recognition by macrophages. Mycobacterial cord factor, trehalose-6,6’-dimycolate (TDM), is the most abundant cell wall glycolipid and binds to the C-type lectin receptor (CLR) MINCLE. To explore the kinase signaling linking the TDM-MINCLE interaction to gene expression, we employed quantitative phosphoproteome analysis. TDM caused upregulation of 6.7% and suppressed 3.8% of the 14,000 phospho-sites identified on 3727 proteins. MINCLE-dependent phosphorylation was observed for canonical players of CLR signaling (e.g. PLCg, PKCd), and was enriched for PKCd and GSK3 kinase motifs. MINCLE-dependent activation of the PI3K-AKT-GSK3 pathway contributed to inflammatory gene expression and required the PI3K regulatory subunit p85a. Unexpectedly, a substantial fraction of TDM-induced phosphorylation was MINCLE-independent, a finding paralleled by transcriptome data. Bioinformatic analysis of both datasets concurred in the requirement for MINCLE for innate immune response pathways and processes. In contrast, MINCLE-independent phosphorylation and transcriptome responses were linked to cell cycle regulation. Collectively, our global analyses show substantial reprogramming of macrophages by TDM and reveal a dichotomy of MINCLE-dependent and -independent signaling linked to distinct biological responses.

overall_design: mRNA profiles from TDM stimulated and unstimulated wildtype and Mincle-/- BMDM were generated by RNASeq (8 samples, duplicates from independent experiments, for each sample RNA was pooled from biological replicates, controls: unstimulated BMDM and solvent controls)

first: Madlen

last: Hansen

first: Barbara

last: Killy

first: Christian

last: Büttner

first: Arif

last: Ekici

first: Roland

last: Lang


title: Next Generation Sequencing Analysis of control and siCHERP treated RKO cell Transcriptomes

first: Qianqian

last: Wang

address: yueyang road,number 320

institute: Chinese Academy of Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: We treated the RKO cells with siCHERP or control siRNA for 72 hours. Then we extracted the RNAs and performed the next generation sequencing. By comparing sequcing data from siCHERP and contron siRNA treated samples, we profiled the gene expression regulated by siRNA.

overall_design: RKO cells mRNA profiles of Control and siCHERP treated samples were generated by deep sequencing, using Illumina HiSeq 2000.


title: Assessment of Endocrine Disruption in the Shenandoah River Watershed – Transcriptome Data from Mobile Laboratory Fish Exposures and Other Experiments Conducted during 2016

city: Denver

first: David

last: Bertolatus

state: CO

address: Campus Box 171, PO BOX 173364

department: Integrative Biology

institute: University of Coloroado Denver

summary: Here, we employed integrated chemical and biological analyses to determine how environmental mixtures affected biological responses in watersheds with different landuse. Adult male fathead minnows (Pimephales promelas) were exposed to water from different locations within the Shenandoah River watershed (VA, USA) in 2014, 2015, and 2016. The exposure locations were chosen to capture unique landuse in surrounding watersheds, including agricultural, municipal, mixed-use, and forested sites. Gene expression profiles were measured in livers of male fish exposed for 7 days using Agilent 60K custom FHM microarrays.

overall_design: Independent statistical analyses were conducted for each year. In 2016, the upstream NFSRA site was used as the reference. Differentially expressed probes, relative to the NFSRA site,  were identified by one-way ANOVA followed by 0.05 FDR correction. In 2016, the sample sizes for microarray analysis were 8 at SHR and SFSR, 7 at NFSRB, 7 at NFSRW, and 5 at NFSRA.This study identified site-specific patterns of differentially expressed genes. SHR - Spring Hollow Run, SFSR - South Fork Shenandoah River, NFSRW - North Fork Shenandaoh River wastewater treatment plant, NFSRA - North Fork Shenandoah River above Spring Hollow Run, NFSRB - North Fork Shenandoah River below wastewater treatment plant effluent. For detailed site information see Barber, L.B.; et al. 2018. Assessment of endocrine disruption in the Shenandoah River watershed – Chemical and biological data from mobile laboratory fish exposures and other experiments conducted during 2014, 2015, and 2016. US Geol. Surv. Data Release. https://doi.org/10.5066/F7QF8S22)

first: D

first: C

middle: J

last: Martyniuk

first: L

last: Barber

first: A

last: Vajda


title: Comparison of oligodendrocyte mRNAs in normal and differentiated conditions in culture

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Oligodendrocyte mRNAs in control and differentiated conditions are compared.

overall_design: Oligodendrocyte mRNAs in control and differentiated conditions are isolated and compared.

first: Yuki

last: Miyamoto

first: Junji

last: Yamauchi


title: Aryl hydrocarbon receptor dynamically regulates immunological and secretory gene pathways in decidual endometrial stromal cells

first: Kalle

last: Rytkönen

summary: We report mRNA sequencing from decidual stromal cells after 24 hours and 6 days treatment with Aryl Hydrocarbon Receptor (AHR) activators 100 µM L-kynurenine or 10 nM TCDD  (2,3,7,8-Tetrachlorodibenzo-p-dioxin)

overall_design: We report mRNA sequencing from samples with 24 hours (n=3) or 6 days (n=2) treatment with Aryl Hydrocarbon Receptor (AHR) activators 100 µM L-kynurenine or 10 nM TCDD  (2,3,7,8-Tetrachlorodibenzo-p-dioxin) that was combined with AHR ChIP-Seq data. Before kynurenine and TCDD treatments endometrial stromal fibroblasts were in vitro decidulization with cAMP and progesterone (MPA) for 2 days. Media and activators were changed every 2 days. The 24 hours control (3 days of decidulization: GSM3138934, GSM3138935 and GSM3138936) and 6 days control (8 days of decidulization: GSM3138937 and GSM3138938) mRNA sequencing samples without AHR activators were submitted previously.

last: Rytkonen


title: ChipSeq Olineu after CRISPR knowkdown

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: This study investigates the distribution of three histone marks in Olineu cells with  or without  CRISPR-knockdown of PRMT5

overall_design: Chromatin immunoprecipitation of samples from Olineu cells after silencing with control (EGFP-CRISPR) or PRMT5 (PRMT5-CRISPR) knockdown

first: Jialiang

last: Liang

first: Yong-Hwee

last: Loh


title: Analysis of MGE Transcriptomes with or without Ctnnb1 knockout in human through RNA Sequencing

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

summary:
Purpose: Understand the cues that orchestrate the expansion or differentiation of medial ganglionic eminence (MGE) progenitors no matter in vivo or in vitro.
Methods: Total RNA from each sample was used to prepare the library. Then the libraries were sequenced at 50bp single read on an Illumina HiSeq 2500 platform. Sequencing reads from each sample were mapped to the human reference genomes (hg38 version) by using TopHat v2.1.1. The mapped reads were further analyzed by cufflinks v1.3.0 and the expression levels for each transcript were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM). For differential expression analysis, sequencing counts at the gene level were obtained using HTSeq v 0.9.1. R package DESeq2 was then used to identify differential expressed genes between different conditions.Statistically enriched functional categories of genes were identified using DAVID 6.8. PPI networks were constructed by using STRING v10.0 .
Results: Transcriptome profiling reveals that ablation of β-catenin in MGE cells leads to advanced neuronal differentiation, while activation of Wnt/β-catenin signaling keeps the MGE cells in an undifferentiated progenitor state.
Conclusions: Wnt signaling is a key player in governing self-renewal vs terminal differentiation of MGE progenitors both in vivo and in vitro.

overall_design: mRNA profiles of MGE cells with or without Ctnnb1 knockout were generated by RNA sequencing, using Illumina Hiseq 2500 platform.

first: Lin

last: Ma

first: Yanhua

last: Du


title: Assessment of Endocrine Disruption in the Shenandoah River Watershed – Transcriptome Data from Mobile Laboratory Fish Exposures and Other Experiments Conducted during 2015

overall_design:
Independent statistical analyses were conducted for each year, using a reference site (PCFH) as the comparison. Differentially expressed probes were identified by one-way ANOVA followed by FDR correction. This study identified site-specific patterns of differentially expressed genes.
----------------------------------
NFSRD - North Fork Shenandoah River above tributary near Woodstock, VA
NRWD - North River below WWTP near Mount Crawford, VA
NRWU - North River above WWTP near Mount Crawford, VA
PCFH - Passage Creek at fish hatchery at Waterlick, VA
SFSR - South Fork Shenandoah River above WWTP at Bentonville, VA

first: Chris

first: Larry

first: Alan


title: Assessment of Endocrine Disruption in the Shenandoah River Watershed – Transcriptome Data from Mobile Laboratory Fish Exposures and Other Experiments Conducted during 2014

first: David


title: Analysis of differential gene expression in the Streptococcus sanguinis SSA_0351 mutant

city: Richmond

first: Fadi

middle: Elias

last: El-Rami

state: VA

address: 521 N 11th Str, wood bldg, room 424

department: Microbiology & Immunology

institute: Virginia Commonwealth University

summary: Gene expression profile of the Streptococcus sanguinis SSA_0351 deletion mutant, ssx_0351, compared to the wild-type strain SK36

overall_design: Experiment: ssx_0351 mutant vs. wild-type SK36. Biological replicates (1-4) independently grown and prepared for each sample.

middle: E

last: El Rami

first: Ping

last: Xu


title: Role of miR-146a in mouse brain development: relevance for developmental brain disorders

city: Paris

first: Lam Son

last: Nguyen

state: IDF

address: 24 Bld du Montparnasse

department: Institute Imagine

institute: INSERM U1163

summary:
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. miRs are involved in a wide range of regulation networks, including those involved in brain development. We and other showed an upregulation of miR-146a in autism spectrum disorders, intellectual disability and epilepsy. Taking advantage of a mouse model constitutively inactivated for miR-146a, we investigated its functions during brain development using a combination of imaging, molecular, cell biology techniques and behavioral studies.
We demonstrated that loss of miR-146a causes time and region specific expression defects in the mouse brain. Pyramidal and interneurons are the most severely affected cell types with deregulated pathways reflecting different stages of neuronal differentiation and synaptic maturation. We showed that absence of miR-146a impairs the balance between proliferation and differentiation of neural progenitors. We observed no difference in neither brain weight nor total volume but an increased hemispheric asymmetry of hippocampal volume. Lastly, impaired associative memory was also observed.
Our results show that miR-146 is important for proper brain development and support the hypothesis that miR-146a deregulation may play a role in developmental brain disorders.

overall_design: We tested the neocortex at E14.5. For P30 and P6 stages, we tested the amygdala, hippocampus and sensoricortex. Each region was sampled at least 3 times (per genotype) from mice born to different moms.

first: Julien

last: Fregeac

first: Stéphanie

last: Moriceau

first: Olivier

last: Alibeu

first: Christine

last: Bole-Feysot

first: Noémie

last: Gadessaud

first: Sophie

last: Berissi

first: Nicolas

last: Cagnard

first: Patrick

last: Nitschke

first: Franck

last: Oury

first: Laurence

last: Colleaux

first: Lam


title: Assessment of Endocrine Disruption in the Shenandoah River Watershed – Transcriptome Data from Mobile Laboratory Fish Exposures and Other Experiments Conducted during 2014-2016

last: Bertolatus

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

overall_design: Refer to individual Series


title: FOXA1_ChIP from PDX model

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

summary: FOXA1 binding in human breast cancer cells in PDX mice after different treatments

overall_design: Mice given different treatment and tumor lump isolated and ChIP-Seq performed

first: Shixiong

last: Wang

first: Madhumonhan

last: Rao

first: Antoni

last: Hurtado


title: Loss-of-function due to MODY1/HNF4A mutation abrogates liver and pancreas differentiation from MODY1-hiPSCs

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

institute: IMCB, A*STAR

summary:
Purpose: To investigate the impact of MODY1/HNF4A mutation on foregut development using differentiated control and MODY1-hiPSCs
Methods: RNA-Seq was performed on foregut/hepato-pancreatic progenitors obtained on day 14 of the directed differentiation of hiPSCs from MODY1 patients (3 clones from iN904-1, 1 clone from iN904-2) and family controls (3 clones from iN904-7, 2 clones from iN904-13). Differential expression analysis, KEGG pathway and gene ontology analyses were carried out. qRT-PCR validation was also performed using SYBR Green assays.
Results: RNA-Seq and transcriptional analyses revealed that numerous foregut liver- and pancreas-related genes, including HNF4A, were downregulated in MODY1-hiPSC-derived hepato-pancreatic progenitors with a fold change ≥1.5 and p value <0.05, whereas hindgut HOX genes were upregulated. Altered expression of a number of genes were further confirmed with qRT-PCR.
Conclusions: The HNF4A loss-of-function mutation (p.Ile271fs) resulted in significantly reduced HNF4A expression or HNF4A haploinsufficiency, affecting the proper development of the foregut and its derivatives. This deficiency is propagated to both hepatic and pancreatic cell fates, and may account for β cell developmental defects and the progressive deterioration of β cell function in MODY1.

first: H

last: Ng

first: Joanita

last: Jasmen

first: Chang

last: Lim

first: Hwee

middle: H

last: Lau

first: Vidhya

last: Krishnan

first: Rohit

last: Kulkarni

first: Helge

last: Raeder

first: Ludovic

last: Vallier

first: Shawn

last: Hoon

first: Kee

middle: K


title: c-MYC drives neuroblastoma tumorigenesis and retinoic acid resistance in zebrafish [RNA-Seq]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Neuroblastoma is an often intractable tumor that accounts for 15% of childhood cancer deaths. In addition to MYCN amplification in 20% of tumors, 11% express high levels of c-MYC (MYC) protein. To study this newly defined subgroup, we have created a novel transgenic zebrafish model in which overexpression of MYC in the peripheral sympathetic nervous system drives early-onset neuroblastoma.

overall_design: RNA-seq was performed on MYC and MYCN driven neuroblastoma tumors to determine chromatin accesibility in these cells

first: Song

last: Yang

first: Yi

last: Zhou

middle: I

first: Mark

last: Zimmerman

first: Shuning

last: He

first: Adam

last: Durbin

first: A

last: Look

first: Amish

last: Khan

first: Xiaoling

last: Zhang

first: Shizhen

last: Zhu

first: Yu

last: Liu

first: Jinghui


title: Identification of miR-146a target genes in mouse monocyte subsets

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: To gain insight into the mechanisms underlying miR-146a-mediated modulation of Ly6Chigh monocyte function, we compared the expression profiles of Ly6Chigh and Ly6Clow monocytes in miR-146a+/+ (WT) versus miR-146a-/- (KO) conditions.

overall_design: Ly6Clow and Ly6Chigh monocyte subsets were isolated from spleen samples of miR-146a-/- mice or control littermates using a FACSAria sorter, and total RNA of each cell subsets were extracted using miRNeasy mini kit (Qiagen). The integrity of isolated and pooled RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and amount was checked with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The generation of biotinylated anti-sense cRNA was performed with 100 ng of total RNA using the Affymetrix IVT Express protocol (3' IVT Express 2010 technical manual P/N 702646 Rev8). Following fragmentation, 15 µg of the cRNA were hybridized for 16 h at 45 °C on GeneChip Mouse 430_2 arrays in the Affymetrix oven 645. GeneChips were washed and stained in the Affymetrix Fluidic station 450 with HWS kit. Chips were scanned using the Affymetrix GeneChip scanner 3000 7G, and the raw data were generated with the Affymetrix Expression Console software v 1.2.1. Raw data were analyzed with High Performance Chip Data Analysis (HPCDA) and database BioRetis using one vs. one chip analyses.

first: Meryem

last: Ammari

first: Isabelle

last: Duroux-Richard

first: Jessy

last: Presumey

first: Clara

last: Ponsolles

first: Gautier

last: Roussignol

first: Christine

last: Roubert

first: Virginie

last: Escriou

first: Karine

last: Toupet

first: Anne

middle: L

last: Mausset-Bonnefont

first: Philippe

last: Georgel

first: Ramzi

last: Nehmar

first: Leonie

middle: S

last: Taams

first: Joachim

last: Grün

first: Andreas

last: Grützkau

first: Thomas

last: Häupl

first: Yves

last: Pers

first: Christian

last: Jorgensen

first: Florence

last: Apparailly


title: Equine Embryonic Interzone and of Articular Cartilage Zones

city: Vienna

first: Florien

last: Jenner

address: Veterinärplatz 1

department: Equine Surgery

country: Austria

institute: University of Veterinary Medicine Vienna

summary: Cells from the superficial (AACS), middle (AACM) and deep (AACD)  adult articular cartilage zones and the intermediate (II) and outer (OI)  interzone layers and the transient embryonic cartilage of the long bone anlagen (EC) at gestational day 40 were separately collected using laser capture microdissection and microarray analysis was performed to confirm appropriate layer selection.

overall_design: Microarray gene expression analysis of ACCS, ACCM, ACCD, II, OI and EC (all n=1) was carried out by Miltenyi Biotech GmbH (Miltenyi Biotec, Bergisch-Gladbach, Germany). Briefly, RNA was amplified using SuperAmp (Agilent Technologies, Paolo Alto, CA, USA), a global PCR protocol using mRNA-derived cDNA, according to the manufacturer’s protocol. Yields of cDNA were measured with a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA). The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform. 250 ng of each of the cDNAs was labelled with Cyanine 3-CTP (Cy-3) and hybridized overnight (17 hours, 65°C) to an Agilent Whole Horse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Fluorescence signals of the hybridized microarrays were detected using Agilent’s Microarray Scanner System. The Agilent Feature Extraction Software was used to read out and process the microarray image files

first: Gerjo

last: van Osch

first: Rene

last: van Weeren

first: Pieter

last: Brama


title: Acquisition of stem cell properties in tumor-derived hepatocyte-like cells leads to metabolic reprogramming and chemoresistance

city: les mureaux

first: Karim

last: Fekir

address: 22 rue paul doumer

institute: Inserm

summary: Gene expression profile analysis allowed to identify a panel of genes and pathways characteristic of HepaRG Sphere-forming cells and HepaRG Side population

overall_design: Microarrays were conducted at day 10 for Sphere-forming cells and after cell sorting for Side population and compared to HepaRG at day 4 and 10 after differentiation. Four or three independent experiments were performed depending the experimental sample

first: Hélène

last: Dubois-Pot-Schneider

last: Corlu