title: Gene expression analysis of motor cortex between BERKO and wild type mouse

status: Public on Dec 01 2019

city: Huddinge

first: Ivan

last: Nalvarte

address: Hälsovägen 7C, NEO

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary:
Introduction: Male estrogen receptor beta (ERβ) knockout (BERKO) mice display anxiety and aggression linked to, among others, altered serotonergic signaling in the basolateral amygdala and dorsal raphe, impaired cortical radial glia migration and reduced GABAergic signaling. Effects on primary motor cortex (M1 cortex) and locomotor activity as a consequence of ERβ loss have not been investigated.
Objective: The aim of this study was to determine whether locomotor activity is altered as a consequence of the changes in the M1 cortex.
Methods: Locomotor activity of WT and BERKO male mice was evaluated using the open-field and rotarod tests. Molecular changes in the M1 cortex were analyzed by RNA-sequencing, electron microscopy, electrophysiology, and immunofluorescence techniques. In addition, we established oligodendrocyte cultures from WT and BERKO mouse embryonic stem cells to evaluate oligodendrocyte function.
Results: Locomotor profiling revealed that BERKO mice were more active than WT mice but had impaired motor coordination. Analysis of the M1 cortex pointed out differences in synapse function and myelination. There was a reduction in GABAergic signaling resulting in imbalanced excitatory and inhibitory neurotransmission, as well as a defective oligodendrocyte differentiation accompanied by myelin defects. The effects of loss of ERβ on oligodendrocyte differentiation was confirmed in vitro.
Conclusion: ERβ is an important regulator of GABAergic interneurons and oligodendrocyte differentiation, which impacts on adult M1 cortex function, and may be linked to increased locomotor activity and decreased motor coordination in BERKO mice.

overall_design: mRNA extracted from M1 cortex of 6 WT and 6 BERKO mice were multiplexed and sequenced using Illumina Hiseq 2000 in 3 lanes (2 samples from each cortex in 3 technical replicates). 1 BERKO sample was removed due to being an outlier.

first: Mukesh

last: Varshney

middle: Y

last: Yu

first: Shintaro

last: Katayama

first: Xin

last: Li

first: Tianyao

last: Liu

first: Wan

last: Wu

first: Virpi

last: Töhönen

first: Kareel

last: Krjutskov

first: Juha

last: Kere

first: Xiaotang

last: Fan

first: José

last: Inzunza

first: Jan

last: Gustafsson


title: Effect of ~ 25 days cortisol treatment on late gestation fetal biceps femoris

status: Public on Nov 01 2019

city: Gainesville

first: Maureen

last: Keller-Wood

state: Florida

address: 1225 Center Dr

department: Pharmacodynamics

country: USA

institute: University of Florida

summary: We have previously shown in sheep that 10 days of modest chronic increase in maternal cortisol result in fetal heart enlargement and Purkinje cell apoptosis. In subsequent studies in which we extended the duration of cortisol infusion (1mg/kg/d) to term, we found a dramatic incidence of stillbirth in the pregnancies with chronically increased cortisol and associated maternal hyperglycemia. In previous studies of the intraventricular septum from these fetuses we found significantly differentially regulated genes in the term fetuses (ie after ~25 days of cortisol) in pathways consistent with altered metabolism in the heart, particularly in mitochondria, associated with responses to hypoxia and to nutrient. Analysis of mitochondrial number by quantitative real-time PCR confirmed a significant decrease.  To investigate the effects on skeletal muscle, we extended the transcriptomic analyses to biceps femoralis.  Transcriptomic modelling revealed that pathways related to mitochondrial metabolism were downregulated, whereas pathways suggestive of positive regulation of  reactive oxygen species and activation of the apoptotic cascade were upregulated. Mitochondrial DNA (mt-DNA) and the protein levels of cytochrome C was significantly decreased in the biceps. RT- PCR validation of the pathways showed significant decrease in SLC2A4 mRNA levels, and a significant increase in PDK4, TXNIP, ANGPTL4 mRNA levels, consistent with reduced insulin sensitivity of the bicep muscles.  Comparison of the change in gene expression in biceps to that in cardiac intraventricular septum and left ventricle showed few  common genes with little overlap in specific metabolic or signaling pathways, despite reduction in mitochondria in both heart and biceps.   Our results suggest that glucocorticoid exposure affects nuclear genes important to mitochondrial activity and reactive oxygen  in both cardiac and skeletal muscle tissues in a tissue specific manner.

overall_design: Ewes carrying singleton sheep fetuses at 139-144d gestation (approximately term)  were used.  Ewes were either treated with  1 mg/kg/d of cortisol (Solu-Cortef) or vehicle atartign on day 115 of pregnancy and continuing until the time of necropsy for tissue collection  (n=7, cortisol; n=7  control ewes) .  Ewes were sacrificed  as soon as possible after the onset of labor.

first: Serene

last: Joseph

first: Elaine

last: Sumners

first: Andrew

last: Antolic

first: Charles

middle: E

last: Wood


title: Effect of ~ 25 days cortisol treatment on late gestation fetal

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

overall_design: Refer to individual Series


title: Effect of ~ 25 days cortisol treatment on late gestation fetal left ventricle

summary: We have previously shown in sheep that 10 days of modest chronic increase in maternal cortisol result in fetal heart enlargement and Purkinje cell apoptosis. In subsequent studies in which we extended the duration of cortisol infusion (1mg/kg/d) to term, we found a dramatic incidence of stillbirth in the pregnancies with chronically increased cortisol and associated maternal hyperglycemia. In previous studies of the intraventricular septum from these fetuses we found significantly differentially regulated genes in the term fetuses (ie after ~25 days of cortisol) in pathways consistent with altered metabolism in the heart, particularly in mitochondria, associated with responses to hypoxia and to nutrient. Analysis of mitochondrial number by quantitative real-time PCR confirmed a significant decrease.  We extended this investigation to the left ventricular free wall of these fetuses.le.  Fewer genes were differentially regulated in left ventricle in the near term fetuses.  In the LV of this cohort of fetuses, the nonredundant KEGG pathways represented by the DEG were insulin resistance and adipocytokine signaling pathway. GSEA analysis of the DEG in LV identified metabolic pathways as the nonredundant pathway altered.  Comparison of the change in gene expression in biceps to that in cardiac intraventricular septum and left ventricle showed few common genes with little overlap in specific metabolic or signaling pathways, despite effects on mitochondria and metabolism in both heart and biceps.   Our results suggest that glucocorticoid exposure affects nuclear genes important to mitochondrial activity and reactive oxygen  in both cardiac and skeletal muscle tissues in a tissue specific manner.

overall_design: Ewes carrying singleton sheep fetuses at 139-144d gestation (approximately term)  were used.  Ewes were either treated with 1 mg/kg/d of cortisol (Solu-Cortef) or vehicle starting on day 115 of pregnancy and continuing until the time of necropsy for tissue collection  (n=7, cortisol; n=7  control ewes) .  Ewes were sacrificed as soon as possible after the onset of labor.

middle: M

last: Richards


title: Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (RNA-seq)

status: Public on Nov 09 2019

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Expression profiling by high throughput sequencing

summary: Intronic RNAs are spliced from precursor-messenger RNAs and are usually subjected to degradation in eukaryotes. COLDAIR, a previously reported intronic long noncoding RNA (lncRNA), is produced from the first intron of a MADS-box gene, Flowering Locus C (FLC), which encodes a repressor of flowering time. Here we show that overexpression of a foreign COLDAIR sequence causes enhanced expression of FLC in trans, resulting in a late-flowering phenotype. In COLDAIR-overexpression lines, enhanced expression of FLC is correlated with up-regulation of the active histone mark H3K4me3 and down-regulation of the repressive histone mark H3K27me3. We demonstrate that overexpression of COLDAIR makes the corresponding FLC intronic region accessible to the histone H3K4 methyltransferase ATX1 but exclusive to the histone H3K27 methyltransferase CLF. Furthermore, we demonstrate that overexpression of intronic lncRNAs from many other MADS-box genes also activate the expression of their host genes in trans, suggesting that intronic lncRNAs act as enhancer RNAs in many MADS-box genes. Considering that MADS-box genes are highly conserved in multicellular eukaryotes, we suggest that involvement of intronic lncRNAs from MADS-box genes in gene activation may represent an evolutionarily conserved mechanism.

overall_design: Examination of the mRNA expression in Arabidopsis

first: Zhang-wei

first: Yin-na

last: Su

first: Xin-jian


title: Profiling of circular RNAs in gastric cancer tissues and adjacent normal tissues

city: chongqing

first: Mengmeng

last: Jie

address: No. 83, Xinqiao street

institute: Third Military Medical University Xinqiao Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To investigate the role and mechanism of circRNAs in gastric cancer.
Methods: RNA-seq of ribosomal RNA-depleted total RNA and qRT-PCR were performed to screen differential expressed circRNAs between paired gastric cancer tissues and adjacent normal tissues.
Results: A total of 57623 distinct circRNAs were identified in these samples, and 35120 of these circRNAs contained at least two independent back-spliced reads in at least two samples. Compared with circBase, we found that there were 29007 matched circRNAs and 28616 novel circRNAs in our study.

overall_design: Gastric circRNA profiles of paired gastric cancer tissues and adjacent normal tissues were generated by deep sequencing, using Illumina HiSeq Xten.

first: Shiming

last: Yang

first: Changjiang

last: Hu


title: A comprehensive analysis identified the key differentially expressed circular RNAs and methylation-related function in pheochromocytomas and paragangliomas

status: Public on Oct 29 2019

city: Changsha

first: Liang

last: Zhang

address: Departments of Urology, Xiangya Hospital, Central South University, Changsha, China

institute: Central South University

summary: Aim: To investigate the differentially expressed circular RNAs (circRNAs) and their potential functions in pheochromocytomas and paragangliomas (PCC/PGLs). Materials & Methods: We analyzed the expression levels of circRNAs through RNA sequencing in tumor and adjacent normal tissues from 7 PCC/PGL patients. Real-time qPCR was conducted to verify the key candidates identified in the sequencing data. GO and KEGG Pathway analyses were performed to predict the functions of these circRNAs. The circRNA-miRNA-mRNA coding-noncoding gene co-expression (CNC) networks were mapped to show the potential binding relationship between circRNAs and their targets in PCC/PGLs. Results: A total of 367 circRNAs were shown to have differential expression between tumor and normal samples. The top 3 histone methylation-related circRNAs (hsa_circ_0000567, hsa_circ_0002897, hsa_circ_0004473) and their target miRNAs were identified and validated. The top 5 mRNAs, 88 miRNAs, and 132 circRNAs related to the pathogenesis were utilized to map the CNC network, and we observed that the interactions of these candidates with their target miRNAs regulated the procedure of histone-methylation, and further controlled the pathogenesis of PCC/PGLs. Conclusions: Our study is the first to provide the whole profile of differentially expressed circRNAs in PCC/PGLs, and our data indicates that the altered circRNAs may control the pathogenesis of PCC/PGLs by regulating the histone-methylation processes and act as biomarkers.

overall_design: Pheochromocytoma and paraganglioma ceRNA profiles of 7 patients were generated by deep sequencing,using Illumina GAIIx.

first: Anze

last: Yu

first: Minghao

last: Li

first: Longfei

last: Liu


title: Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identified three classes of previously uncharacterized plant-specific SWR1 components: MBD9, TRA1a/1b and CHR11/17. We found that CHR11/17 were recruited to the SWR1 complex and facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.

overall_design: protein-DNA compelxes were extracted by antibody, and DNA were finally extracted and sequenced.

first: Yu-Xi

last: Luo

first: Xiao-Mei

last: Hou


title: Transcriptome Analysis of CircMRPS35 mediated mRNA expression profiles

summary: Purpose: To explore the mechanism of circMRPS35-mediated suppression of proliferation and invasion in gastric cancer. Methods: MGC-803 cells were transfected with control and SiRNA-circMRPS35, in triplicate. Total RNA was extracted using Trizol reagent.

overall_design: mRNA profiles of MGC-803 cells transfected with control and SiRNA-circMRPS35 were generated by deep sequencing, using IIIumina HiSeq X Ten.


title: Small RNA-Seq of human B cell lines

status: Public on Oct 26 2019

city: Ames

first: Walter

last: Moss

state: IA

address: Pammel Dr

institute: Iowa State University

summary: Small RNA-Seq study comparing Epstein-Barr virus (EBV) infected BJAB-B1 cells to isogenic, but uninfected, BJAB cells. The goal was to deduce differentially expressed small ncRNAs both micro and non-micro (up to 200 nt) between the two cell lines to gain insights into EBV-associated deregulation of host small ncRNAs.

overall_design: Small RNA-Seq was performed on total RNA extracted from BJAB and BJAB-B1 cells and size selected to be between 15-200 nt long.


title: Differential gene expression at shoot apices between Wild Type and vip3-1-null allele

status: Public on Oct 22 2019

city: Lyon

first: Christophe

last: TREHIN

address: 46, Allée d'Italie

department: Biology

country: France

institute: ENS Lyon

summary: The aim of this study was to evaluate gene expression defects at the shoot apical meristem and young flower meristems of the vip3-1 null allele. VIP3 belongs to polymerase II-associated factor 1 complex (Paf1c), which is involved in several RNA polymerase II-dependent transcriptional processes. Arabidopsis vip3 mutants exhibit phylotactic defects and strong floral indeterminacy phenotypes.

overall_design: Material for the RNA-seq was collected from the primary inflorescence of vip3-1 and Col-0 shoot apices (from plants grown in short day 21°C then continuous light 16°C conditions). Apices were dissected, by removing flower older than stage 4. Samples were collected into liquid nitrogen-cooled eppendorf tubes directly after dissection, each tube containing between 30 and 35 apices, 6 samples for each genotype. RNA extraction was performed using the PicoPure RNA Isolation kit Arcturus (ThermoFisher, KIT0204) with an on column DNAase treatment (Qiagen, catalog#79254). After elution, 2 samples were combined together, obtaining the final technical triplicates for each genotype. Isolated RNA was subjected to high throughput sequencing analyses to identify differentially expressed transcripts.

first: Kateryna

last: Fal


title: Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (stranded-RNA-seq)

overall_design: Examination of the RNA expression in Arabidopsis


title: Comprehensive analysis of the SWR1 complex reveals the coupling of H2A.Z deposition with nucleosome sliding in Arabidopsis [RNA-Seq]

overall_design: Extract the whole RNA for analysis


title: Dynamic 3D chromosomal landscapes in acute leukemia [WGS]

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

summary:
Background: Disruptions of 3D chromatin architecture can alter the activity of topologically associated domains (TADs), rewire enhancer-promoter interactions and thus significantly impact gene regulatory programs. Recently, such disruptions have been implicated in tumorigenesis, highlighting the need for a deeper understanding of their detailed role.
Methods: T-ALL primary samples and prototypical cell lines as well as healthy T cell samples were profiled by in-situ Hi-C, RNA-Seq, CTCF ChIP-Seq and suuported by matching WGS of three primary T-ALL samples. Data was subsequently integrated.
Results: Our studies showed that the genome of leukemia cells does not display global changes in TAD structures but presents local changes in selected TAD boundaries as well as alterations of intra-TAD activity which are associated with changes in gene expression of key oncogenes and tumor suppressors, strong correlation with CTCF-mediated insulation and enhancer activity. Finally, we showed that 3D interactions on selected loci can be partially corrected pharmacologically, potentially accounting for the anti-leukemogenic effects of these drugs.
Conclusions: Our studies underscore the need for further investigation of factors that rewire long range interactions especially during tumorigenesis, as they could be targets for pharmacological targeting.

overall_design:
Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) as well as healthy T cell counterparts from three different donors were collected.
Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft and when the tumor burden in pheripheral blood reached 80% the mice were the spleen was harvested and splenocytes were used for the Whole Genome Sequencing (WGS) analysis.

first: Palaniraja

last: Thandapani

first: Panagiotis

last: Ntziachristos

first: Ioannis

last: Aifantis

first: Aristotelis

last: Tsirigos


title: Gene expression analysis of different passages and subclones of the Huh7 cell line

status: Public on Nov 08 2019

city: Heidelberg

first: Marco

last: Binder

address: Im Neuenheimer Feld 280

department: F170 Virus-Associated Carcinogenesis

institute: German Cancer Research Center (DKFZ)

summary: Hepatitis C Virus (HCV) has a extremely narrow host cell tropism and robustly infects only very few cell lines, most importantly the human hepatoma cell line Huh7. This cell line was isolated from a 57-year old Japanese male with fulminant hepatitis. Different subclones and passages of the Huh7 cell line show up to 1000-fold differences in HCV replication efficiency (permissiveness). In this experiment, we sought to identify factors responsible for these differences by correlating gene expression from eight different uninfected Huh7 variants with their respective HCV permissiveness. HCV replication efficiency was determined using electroporation of a subgenomic luciferase reporter replicon (genotype 1b, "con1/ET") and measuring luciferase activity at 48h post transfection normalized to the input value at 4h p.t.. "Relative permissiveness" of cell lines corresponds to their replication efficiency, normalized to the efficiency in the lowest permissive cells (Huh7 p13 and p28).

overall_design: Gene expression data was collected from eight different, uninfected Huh7 variants; no treatment conditions.

first: Volker

last: Lohmann

first: Martin

last: Trippler


title: Allele-specific 4C-seq of rs2836411 located in the ERG gene in HUVEC and HASMCs

status: Public on Oct 11 2019

city: Dunedin

first: Judith

last: Marsman

state: Otago

address: 201 Great King Street

department: Surgical Sciences

country: New Zealand

institute: University of Otago

summary: Allele-specific circular chromosome conformation capture sequencing (4C-seq) using the single nucleotide polymorphism rs2836411 as a bait was performed in two cell types: human umibilical vein endothelial cells (HUVECs) and human aortic smooth muscle cells (HASMCs).

overall_design: 4C-seq was performed in HUVECs containing the C and T allele of rs2836411, and in HASMCs homozygous for the major allele (CC). For each cell line, two replicates and one control (omitting the first ligation step) library were prepared. The control for HASMCs was performed in a cell line homozygous for the minor alllele (TT).

first: Gregory

last: Gimenez

first: Robert

middle: C

last: Day

first: Julia

middle: A

last: Horsfield

middle: T

last: Jones


title: These are male and female mus musculus mRNA expression profiles from whole liver tissue of fatp2 knock-out and wildtype mice. .

city: Durham

first: Vincent

middle: Michael

last: Perez

state: NC

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

summary: Fatty acid transport protein 2 (FATP2) is highly expressed in liver, small intestine, and kidney where it functions in both the uptake of exogenous long chain fatty acids (LCFAs) and in the activation to CoA thioesters of very long chain fatty acids (VLCFAs). Here we address the phenotypic impacts of deleting FATP2 followed by an unbiased RNA-seq analysis of the liver transcriptome.  Wild type (C57BL/6J) and fatp2 null (fatp2-/-) mice (5 weeks old) were maintained on a standard chow diet for 6 weeks (11 weeks old). The male fatp2-/- mice had 258 differentially expressed genes (DEGs) and the female mice had a total of 91.  Of significance was the finding that most of the genes with increased expression in the fatp2-/- liver are regulated by the transcription factor peroxisome proliferator-activated receptor alpha (PPARα). Taken together, FATP2 has a broad impact on the expression of key lipid metabolic genes in the liver regulated by PPARα.

overall_design: For RNA-sequencing, we used 4 animals for each experimental group, and we had 4 experimental groups. The groups were - [1] wildtype c57bl6 male mice, [2] wildtype c57bl6 female mice, [3] fatp2 knock-out c57bl6 male mice, and [4] fatp2 knock-out c57bl6 female mice.

first: Jeff

last: Gabell

first: Mark

middle: R

last: Behrens

first: Concetta

last: DiRusso

first: Paul

middle: N

last: Black


title: FB5P-seq: FACS-based 5-prime end single-cell RNAseq for integrative analysis of transcriptome and antigen receptor repertoire in B and T cells

status: Public on Oct 06 2019

city: Marseille

first: Pierre

last: Milpied

address: Parc Scientifique de Luminy, case 906

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

summary: Single-cell RNA sequencing (scRNAseq) allows the identification, characterization, and quantification of cell types in a tissue. When focused on B and T cells of the adaptive immune system, scRNAseq carries the potential to track the clonal lineage of each analyzed cell through the unique rearranged sequence of its antigen receptor (BCR or TCR, respectively), and link it to the functional state inferred from transcriptome analysis. Here we introduce FB5Pseq, a FACS-based 5’-end scRNAseq method for cost-effective integrative analysis of transcriptome and paired BCR or TCR repertoire in phenotypically defined B and T cell subsets. We describe in details the experimental workflow and provide a robust bioinformatics pipeline for computing gene count matrices and reconstructing repertoire sequences from FB5Pseq data. We further present two applications of FB5Pseq for the analysis of human tonsil B cell subsets and peripheral blood antigen-specific CD4 T cells. We believe our novel integrative scRNAseq method will be a valuable option to study rare adaptive immune cell subsets in immunology research.

overall_design: This dataset contains data from B cell subsets sorted from two non-malignant human tonsil samples (Tonsil 1 and Tonsil 2), and C.alb-specific T cells sorted from human peripheral blood after in vitro peptide restimulation. Single-cells were FACS-sorted into several 96-well plates (Tonsil 1: 5 plates; Tonsil 2: 6 plates; T cells: 1 plate) and analyzed by 5'-end single-cell RNAseq following the FB5P-seq protocol. The three samples (Tonsil 1, Tonsil 2, T cells) were processed and sequenced in three separate experiments.

first: Chuang

last: Dong


title: Aortic Valve Tissue: Stenosis vs. Sclerosis

status: Public on Oct 08 2019

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

summary: We are looking at differential gene/protein expression in tissue from stenotic vs sclerotic human aortic valves in order to identify genetic predispositions for aortic valve disease, as well as novel targets for diagnostic and therapeutic strategies.

overall_design: Two-condition experiment, 3 stenotic vs 3 sclerotic human aortic valve samples

first: Alexander

middle: P

last: Kossar

first: Wanda

last: Anselmo

first: Juan

middle: B

last: Grau

first: Yichuan

last: Liu

first: Aeron

last: Small

first: Nancy

last: Rioux

first: Daniel

middle: J

last: Rader

last: Levy

first: Giovanni

last: Ferrari


title: Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 [ChIP-seq]

status: Public on Oct 04 2019

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

institute: Shenzhen University

summary: HOXB8 functions as a transcription factor, but its genomic targets remains unknown. Thus, we profiled HOXB8 binding loci across the genome using ChIP-seq.

overall_design: ChIP-seq was performed using a HOXB8 antibody (Abcam, cat# ab125727) in K562 cells. Input DNA was used as reference for peak calling.


title: Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1

overall_design: Refer to individual Series


title: Evaluation of the metabolic effects of insect meal from Tenebrio molitor L. in skeletal muscle of growing pigs by transcriptomics

status: Public on Oct 02 2019

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: The hypothesis was tested that insect meal (IM) as protein source influences intermediary metabolism of growing pigs. To test this, 5-week-old crossbreed pigs were randomly assigned to 3 groups of 10 pigs each with similar body weights (BW) and fed isonitrogenous diets either without (CON) or with 5 % IM (IM5) or 10 % IM (IM10) from Tenebrio molitor L. for 4 weeks and skeletal muscle was analyzed using transcriptomics.  Transcriptomics of skeletal muscle revealed a total of 198 transcripts differentially expressed between IM10 and CON.

overall_design: For microarray analysis, n = 6 RNA samples each of the group CON, group IM5 and group IM10 were used for hybridization to the Affymetrix GeneChip Porcine Gene 1.0 Sense Target array.

first: Sandra

last: Meyer

first: Denise

middle: K

last: Gessner

first: Klaus

last: Eder


title: RNA-seq from adipose and liver tissue in Fam13a knockout and wildtype mice on different diets

status: Public on Oct 01 2019

city: Stanford

first: Erik

last: Ingelsson

state: California

address: 300 Pasteur Drive

institute: Stanford University

summary: We performed RNA-sequencing of liver, visceral and subcutaneous adipose tissues from Fam13a KO/WT mice on high fat diet and chow. We observed genes in pathways relevant to adipose biology to be differentially expressed between WT and KO, and there to be a more pervasive effect of Fam13a KO on the transcriptome in SAT when compared to VAT.

overall_design: RNA-seq from 3 different tissue types in Fam13a KO an WT mice. Data available from males and females, on high fat diet and regular chow.

first: Joshua

last: Knowles


title: Gene expression in rhesus monkey vastus lateralis muscle in response to long-term calorie restriction

status: Public on Oct 15 2019

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

summary:
The effect of a long-term calorie restricted diet was evaluated in vastus lateralis muscle of rhesus monkeys
For biopsy collection, the animals were given buprenorphine (0.01-0.03 mg/kg, IM) in the morning immediately preceding all biopsies and again that afternoon

overall_design: At the time of tissue collection, control animals (27-30 years old) and CR animals (27-32 years old) had been subjected to CR for 18.5 years (n=5 control and n=8 CR monkeys per group);

middle: L


title: Circular RNA expression profiling in diabetic foot ulcers and human normal acute wounds

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

institute: Karolinska Institutet

summary: Circular RNA (circRNA) microarray analysis was performed to examine the expression profiles of circRNAs in diabetic foot ulcers (DFU) and in human excisional skin wounds 7 days after injury.

overall_design: The wound biopsies were divided into two groups: Control = normal day-7 wounds from healthy donors and Test = DFUs. Microarray analysis was performed using Arraystar human circRNA chip.

first: Aoxue

last: Wang

first: Maria-Alexandra

last: Toma


title: RNA-seq Analysis of Differential Gene Expression in Wild-type Versus FOXC2-deficient B16-F1 Melanomas

status: Public on Oct 25 2019

city: Hampden-Sydney

first: Kristian

last: Hargadon

state: VA

address: Brown Student Center, Box 837

institute: Hampden-Sydney College

summary: The FOXC2 transcription factor regulates a variety of developmental and biological processes in both embryonic and adult tissues.  Importantly, overexpression or dysregulation of FOXC2 is also associated with oncogenic activity in numerous cancer types, though the function of FOXC2 in the context of melanoma has not been previously investigated.  Therefore, the goal of this study was to assess FOXC2's regulation of gene expression in melanoma cells.  To this end, we employed CRISPR-Cas9 gene editing technology to disrupt the Foxc2 gene in B16-F1 melanoma, and we performed RNA-seq analysis to assess differential gene expression between the wild-type B16-F1 melanoma cell line and our novel FOXC2-deficient B16-F1ΔFOXC2 gene-edited variant cell line.

overall_design: B16-F1 or B16-F1ΔFOXC2 melanoma cells were cultured for 24 hours before isolating RNA for gene expression analysis using the Arraystar Inc. Illumina Hi-seq RNA-sequencing service.  Samples were run in replicates of five per group.  So that FOXC2's contribution to the induction or repression of gene expression in B16-F1 melanoma could be most easily assessed, B16-F1ΔFOXC2 melanoma cells lacking this transcription factor served as the reference sample.  Genes expressed at 1.5-fold higher or lower levels in B16-F1 (with a p value ≤ 0.05) were defined as genes exhibiting differential expression between the two tumors with statistical significance.


title: 16S rDNA  Amplicon Sequencing Analysis of Polystyrene Microplastic Exposed Zebrafish Intestine

city: Nanjing

first: Gu

last: Weiqing

address: Xianlin

institute: Nanjing University

summary: Microplastics (MPs) as widespread contamination pose high risk for aquatic organisms.Intestinal microbiotahas have high interaction with immune system of host body. In this study, intestinal microbiota of zebrafish after  Polystyrene (PS-MPs) exposure were characterized by 16S rDNA amplicon sequencing. We found that 100nm and 200μm PS-MPs exposure significantly increased diversity of intestinal microbiota and all the three sizes of PS-MPs increased abundance of pathogenic bacteria.

overall_design: Detection of intestine microbes were conducted in zebrafish followed treatment of MPs with different size (100nm, 5μm and 200μm). For each assay, three individual trials were taken.

first: Bing

last: Wu

first: Weiqing

last: Gu


title: Single Cell RNA Sequencing and Intestinal Microbial Analysis of Polystyrene Microplastic Exposed Zebrafish Intestine

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


title: Identification of YTHDF1 targeted m6A modified transcripts in lung cancer cells

status: Public on Sep 26 2019

city: guangzhou

first: Xingyang

last: Li

address: 195, dongfengxi road

department: Department of Temporomandibular Joint Surgery

institute: Affiliated Stomatology Hospital of Guangzhou Medical University

summary: In addition to perform the m6A-seq in A549 cells, we sequenced RNA obtained from the immuno-purified complex of YTHDF1 (RIP-seq) to reveal YTHDF1 bound mRNAs, 3,676 genes were shared (m6A-seq+RIP-seq) as high-confident targets of YTHDF1 , which were mapped to cell cycle and tumor (including lung cancer) related signaling pathways in the KEGG pathway database

overall_design: The transcriptome, m6A modified transcripts, and YTHDF1 binding transcripts were identified.

first: Zhixiang

last: Zuo

first: Yongbin

last: Chen


title: Candida albicans Cells: Control vs. BDSF (Cis-2-dodecenoic acid) treatment

status: Public on Sep 18 2019

first: Dongliang

last: Yang

state: Jiangsu

address: 9 wenyuan road, xianlin

department: Institute of Advanced Materials

institute: Nanjing University of Posts and Telecommunications

summary: Cis-2-dodecenoic acid (BDSF), a signalling molecule produced from burkholderia cenocepanic, can prevent C. albicans hyphal and biofilm formation. The mechanism of how BDSF controls C. albicans morphological switch is still unknown. To address this issue, we used DNA microarray method to investigate the changes in gene expression before and after BDSF treatment.  Further, screening a mutant library based on microarray data was carried out to find the mutants unresponding to BDSF.

overall_design: Two-condition experiment, control vs. BDSF treatment. Biological replicates: C1 and C2 are control group, B1 and B2 are BDSF treatment group. One replicate per array.

first: Lixing

last: Weng


title: High Resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells

status: Public on Sep 20 2019

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Department of Biological Science

institute: Florida State University

summary: DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116 as well as F1 sub-species hybrid mouse embryonic stem cells and their neural progenitor derivatives. Strong enrichment of nascent DNA in fine temporal windows reveals a remarkable degree of cell to cell conservation in replication timing and patterns of replication genome-wide. We identify 5 patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation were found throughout S phase and resolved to ~50kb precision. Temporal transition regions were resolved into segments of uni-directional replication punctuated with small zones of inefficient initiation. Small and large valleys of convergent replication were consistent with either termination or broadly distributed initiation, respectively. RT correlated with chromatin compartment across all cell types but correlations of initiation time to chromatin domain boundaries and histone marks were cell type specific. Haplotype phasing revealed previously unappreciated regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchrony was associated with large transcribed genes that resemble common fragile sites. Altogether, these data reveal a remarkably deterministic temporal choreography of DNA replication in mammalian cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 85 Samples

first: Peiyao

last: Zhao


title: RNA-Seq reveals novel mechanistic targets of withaferin A (WA) in prostate cancer cells

status: Public on Sep 17 2019

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: RNA-Seq analysis using WA-treated 22Rv1 human prostate cancer cells revealed upregulation and downregulation of 6993 and 6607 genes, respectively when compared to the vehicle-treated control. The pathways with significantly upregulated gene expression following WA treatment included mitogen-activated protein kinases, focal adhesion, endocytosis, and autophagy as revealed by KEGG and gene ontology analyses. WA treatment also resulted in downregulation of genes associated with metabolic pathways, oxidative phosphorylation, tricarboxylic acid cycle, cell cycle, and base excision repair. This study identifies novel mechanistic targets of WA in prostate cancer.

overall_design: Examination of altered genes expression in 22Rv1 human prostate cancer cell line after 16-h treatment with vehicle-treated control (n=3) or 2 µM of WA (n=3)


title: A post-processing algorithm for miRNA microarray data

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

summary:
One of the main disadvantages of using DNA microarrays for miRNA expression profiling is inability of adequate comparison of expression values across different miRNAs. This leads to a large amount of miRNAs with high scores which are actually not expressed in examined samples, i.e. false positives.
We propose a post-processing algorithm which performs scoring of miRNAs in the results of microarray analysis based on expression values, time of discovery of miRNA represented by MIMAT accession number and correlation level between the expressions of miRNA and corresponding pre-miRNA in considered samples. The algorithm was successfully validated by the comparison of the results of its application to miRNA microarray breast tumor samples with publicly available miRNA-seq breast tumor data.

overall_design: Results of microarray miRNA expression profiling should be post-processed in order to allow for inter-miRNA comparisons. In this work we propose a post- processing algorithm which assigns a score (number between 0 and 1) to each miRNA according to the degree of its reliability in analyzed samples.

first: Evgeny

last: Knyazev


title: Evaluation of the metabolic effects of insect meal from Tenebrio molitor L. in the liver of growing pigs by transcriptomics

first: Robert

last: Ringseis

summary: The hypothesis was tested that insect meal (IM) as protein source influences intermediary metabolism of growing pigs. To test this, 5-week-old crossbreed pigs were randomly assigned to 3 groups of 10 pigs each with similar body weights (BW) and fed isonitrogenous diets either without (CON) or with 5 % IM (IM5) or 10 % IM (IM10) from Tenebrio molitor L. for 4 weeks and liver was analyzed using transcriptomics.  Transcriptomics of the liver revealed a total of 166 transcripts differentially expressed between IM10 and CON.

first: Sandra

last: Meyer

first: Denise

last: Gessner

first: Klaus

last: Eder


title: Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 [RNA-seq]

first: Xing-sheng

last: Shu

summary: HOXB8 acts as a transcription facor, thus we knock down HOXB8 gene by doxycycline induced shRNA in colon cancer cells and profiled the change of transcriptome after knocking down HOXB8

overall_design: Two independent shRNAs targeting HOXB8 were stably transduced into HCT116 cells. The expression of these shRNAs is induced by the presence of doxycycline (dox). Therefore, the control group includes two independent repeats of two shRNAs respectively, while the HOXB8 knock-down group includes two independent repeats of two shRNAs treated with doxycline respectively.


title: The chromatin-bound proteome of the human malaria parasite, Plasmodium falciparum

status: Public on Sep 16 2019

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

state: CA

address: 3401 Watkins Drive, Genomics, Room 2126

department: Cell Biology

institute: University of California, Riverside

summary: P. falciparum chromatin is highly structured at the three-dimensional (3D) level, and this structure provides an epigenetic mechanism for gene expression regulation. To investigate how parasite nuclear architecture is being maintained and regulated, we undertook complementary computational and experimental approaches to identify and characterize chromatin-associated proteins (CAPs) in P. falciparum.

overall_design: Analysis of chromatin-associated proteins in Plasmodium falciparum during intraerythrocytic stages. In addition, SMC3 occupancy was explored and used to validate the findings from the Chromatin Enrichment for Proteomics (ChEP) methodology in P. falciparum.

first: Gayani

last: Batugedara

first: Anita

last: Saraf

first: Anthony

last: Cort

first: Steven

last: Abel

first: Jacques

last: Prudhomme

first: Laurence

last: Florens

first: Evelien

last: Bunnik

first: Karine

middle: G

last: Le Roch


title: Metabolite - sensing receptor Ffar2 regulates colonic group 3 innate lymphoid cells and gut immunity

city: MA

first: Sena

last: Bae

address: Boston

institute: Harvard T.H. Chan School of Public Health

summary: Group 3 innate lymphoid cells (ILC3s) sense environmental signals that are critical for gut homeostasis and host defense. However, the metabolite-sensing G-protein-coupled receptors that regulate colonic ILC3s remain poorly understood. We found that colonic ILC3s expressed Ffar2, a microbial metabolite-sensing receptor, and that Ffar2 agonism promoted ILC3 expansion and function. Deletion of Ffar2 in ILC3s decreased their in situ proliferation and ILC3-derived IL-22 production. This led to impaired gut epithelial function characterized by altered mucus-associated proteins and antimicrobial peptides and increased susceptibility to colonic injury and bacterial infection. Ffar2 increased IL-22+ CCR6+ ILC3s and influenced ILC3 abundance in colonic lymphoid tissues. Ffar2 agonism differentially activated AKT or ERK signaling and increased ILC3-derived IL-22 via an AKT and STAT3 axis. Our findings demonstrate that Ffar2 regulates colonic ILC3 proliferation and function in a cell-intrinsic manner and identifies an ILC3-receptor signaling pathway regulating gut inflammatory tone and pathogen defense.

overall_design:
Colonic ILC3s (CD45+Lin- CD90.2+ NK1.1- NKp46+/- KLRG1-) were sorted from Ffar2-/- mice and littermate control WT mice. Two independent RNA-seq experiments were performed. (i.e.  two biological replicates (sex-matched) for each group that contained RNA from pooled colonic ILC3s from 10 to 15 mice).

BioProject accession: PRJNA547949, SRA Study accession: SRP201015

Please note that the processed data files have been updated on Mar 12, 2020.

first: Chun

last: Eunyoung

first: Wendy

middle: S

last: Garrett


title: Experimental DNA demethylation associates with changes in phenotype and gene expression of tree seedlings

status: Public on Sep 28 2019

city: Los Angeles

first: Alayna

last: Mead

address: 4140 Terasaki Life Sciences Building 610 Charles E. Young Drive East

department: Ecology and Evolutionary Biology

institute: University of California, Los Angeles

summary: Epigenetic modifications, such as DNA methylation where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence the ability of plants to respond to changing environmental conditions. One approach to determining the association between DNA methylation, phenotypic variation, and gene expression, is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree species of Quercus lobata with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that foliar application of 5-azayctidine lead to a 3-6% absolute reduction and 6.1-43% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. We also show that the demethylation treatment had minimal impact on the soil microbiome. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings, and but no significant differences in fluctuating asymmetry (i.e., deviations from bilateral symmetry) of leaves compared to control seedlings. Finally, treated seedlings showed differential expression of a total of 23 genes relative to control seedlings, the majority of which were upregulated. Overall, this study provides evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings.

overall_design: 12 samples of leaf tissue from a single seedling were sequenced from two treatments (six control individuals and six individuals treated with 5-Azacytidine). Seedlings came from three maternal families. There were two seedlings per treatment/family combination.

first: Luke

last: Browne

first: Courtney

last: Horn

first: Kevin

last: Chang

first: Zeynep

last: Celikkol

first: Claudia

last: Henriquez

first: Feiyang

last: Ma

first: Eric

last: Beraut

first: Rachel

first: Victoria

last: Sork


title: Expression data from human kidney tubule epithelial cells

city: Pozzuoli

first: Diego

last: Carrella

state: NAPOLI

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

summary:
Methylmalonic acidemia (MMA) is one of the most common inherited metabolic disorders, due to deficiency of the mitochondrial methylmalonyl ̶ coenzyme A mutase (MUT). How MUT deficiency triggers mitochondrial alterations and cell damage remains unknown, preventing the development of disease-modifying therapies.
To assess the effect of MUT deficiency on gene expression we investigated the transcriptome of in kidney cells derived from healthy controls or patients with MMA who harbor inactivating mutations in MUT. Microarray data indicate that MUT deficiency induces a profound and global change in gene expression that may be in part responsible of cellular alterations observed in patient cells.

overall_design: Kidney cells were isolated from urine of either healthy controls or patients with MMA who harbor inactivating mutations in MUT. Confluent cells were sub–cultivated until 3rd passage and, subsequently, immortalized using pRSVneo vector containing SV40 DNA (pRNS1). Afterwards, immortalized kidney tubule epithelial cells were characterized for protein expression and enzyme activity. Total RNA was extracted from control and MMA cells to assess changes in gene expression with microarrays.

first: Alessandro

last: Luciani


title: A global transcriptome analysis of human epidermal keratinocytes upon knockdown of hsa_circ_0084443

first: Ning

last: Xu

summary:
Hsa_circ_0084443 expression level is down-regulated during normal skin wound healing and higher level of hsa_circ_0084443 was found in chronic non-healing diabetic foot ulcers compared to normal wounds. However, the biological function of hsa_circ_0084443 in epidermal keratinocytes during wound repair has not been studied.
To study the genes regulated by hsa_circ_0084443, we transfected siRNA targeting hsa_circ_0084443 diagnostic junction into human primary epidermal keratinocytes to knockdown hsa_circ_0084443 expression.
We performed a global transcriptome analysis of keratinocytes upon knockdown of hsa_circ_0084443 using Affymetrix arrays.

overall_design: Expression profiling of human primary epidermal keratinocytes transfected with 50 nM si-hsa_circ_0084443 or si-Control for 24 hours (biological triplicates in each group) was performed using Affymetrix GeneTitan system.

first: Maria-Alexandra

last: Toma


title: An Organoid Biobank for Childhood Kidney Cancers that Captures Disease and Tissue Heterogeneity

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: Kidney tumours are among the most common solid tumours in children, comprising several distinct subtypes differing in many aspects, including cell-of-origin, genetics, and pathology. Pre-clinical cell models capturing the disease heterogeneity are currently lacking. Here, we describe the first paediatric cancer organoid biobank. It contains tumour and matching normal kidney organoids from over 50 children with different subtypes of kidney cancer, including Wilms tumours, malignant rhabdoid tumours, renal cell carcinomas, and congenital mesoblastic nephromas. The malignant rhabdoid tumour organoids represent the first organoid model for tumours of non-epithelial origin. The tumour organoids retain key properties of native tumours, useful for revealing patient-specific drug vulnerabilities. We further demonstrate that organoid cultures derived from Wilms tumours consist of multiple different cell types, including epithelial, stromal and blastemal-like. Our organoid biobank captures the cellular heterogeneity of paediatric kidney tumours, providing a representative collection of well-characterized models for basic cancer research, drug-screening, and personalized medicine.

overall_design: 45 unique samples of human kidney tumors and tumor organoid cultures derived thereof were profiled using Illumina EPIC arrays.

first: Jarno

last: Drost

first: Marcel

last: Kool


title: Hippocampal DNA methylation alterations following prenatal ethanol exposure and maternal separation stress in 70 day-old mice

city: London

first: Shiva

last: Singh

state: ON

address: 1151 Richmond Street

country: Canada

institute: Western University

type: Methylation profiling by high throughput sequencing

summary: Fetal alcohol spectrum disorder (FASD) is a common developmental behavioral disorder caused by maternal drinking during pregnancy. Children born with FASD often face additional stress, particularly maternal separation that adds yet additional deficits. The mechanism associated with this phenomenon is not known. Using a mouse model, prenatal ethanol exposure and maternal separation stress have resulted in behavioral deficits and the combination of treatments results in more than additive effects. In addition, behavioral alterations are associated with changes in hippocampal gene expression that persist into adulthood. What initiates and maintains these changes remains to be established and forms the focus of this research. Specifically, MeDIP-Seq was used to assess how changes in promoter DNA methylation are affected by the combination of prenatal ethanol exposure and maternal separation stress with the potential to affect gene expression. The novel results show different sets of genes implicated by promoter DNA methylation affected by both treatments independently, and a relatively unique set of genes affected by the combination of treatments. Prenatal ethanol exposure leads to altered promoter DNA methylation at genes important for brain function and transcriptional regulation. Maternal separation stress leads to changes at genes important for histone methylation and immune response, and the combination of two treatments results in DNA methylation changes at genes important for neuronal migration and immune response. Our dual results on gene expression and DNA methylation from the same samples have allowed comparison of the two observations. There is minimal reciprocal overlap between changes in promoter DNA methylation and gene expression, although overlapping genes tend to be critical for brain development and function. These results suggest that epigenetic mechanisms beyond promoter DNA methylation must be involved in lasting gene expression alterations leading to behavioral deficits implicated in FASD.

overall_design: Hippocampal DNA methylation profiles of adult mice that had been prenatally exposed to ethanol and/or postnatal maternal separation stress as well as non-exposed controls were generated by MeDIP-Seq

first: Bonnie

last: Alberry


title: PRC2.1 and PRC2.2 synergize to co-ordinate H3K27 tri-methylation.

status: Public on Sep 11 2019

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Polycomb Repressive Complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2 and mediates mono-, di- and tri-methylation of Histone H3 at Lysine 27. While at least two subcomplexes exist, defined by their specific accessory proteins, termed PRC2.1 (Polycomb-like proteins 1-3, EPOP and PALI1/2) and PRC2.2 (AEBP2 and JARID2), little is known about their differential functions. Here, we show that PRC2.1 and PRC2.2 share the majority of target genes in mouse embryonic stem cells (ESCs). The loss of all three Polycomb-like proteins is sufficient to destabilise and evict PRC2.1 from chromatin, but also leads to reduced PRC2.2 and H3K27me3 at most Polycomb domains. However, the combined loss of PRC2.1 and PRC2.2 is necessary to completely remove H3K27me3 at broad Polycomb domains such as the Hox loci. Our data support a model in which the specific accessory proteins within PRC2.1 and PRC2.2 co-operate to direct and maintain H3K27me3, via both synergistic and independent mechanisms.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Quantitative ChIP-Rx analysis of Pcl1-3 WT EV, Pcl1-3 TKO EV and Pcl1-3/Jarid2 c12 QKO mouse embryonic stem cells. ChIPs include a 10% spike in of human chromatin (NT2 cell line). 25 samples are included.

first: Evan

last: Healy

first: Marlena

last: Mucha

first: Darren

last: Fitzpatrick

first: Eleanor

last: Glancy

last: Conway

first: Hannah

last: Neikes

first: Guido

last: Van Mierlo

first: Marijke

last: Baltissen

first: Yoko

last: Koseki

first: Michiel

last: Vermuelen

first: Haruhiko

first: Adrian

last: Bracken


title: TEAD1 and TEAD3 play redundant roles in human epidermal proliferation

city: San Diego

first: George

last: Sen

address: 9500 Gilman Drive

institute: UCSD

summary: TEAD1 is critical in maintaining human epidermis proliferation. It may function through its enhancer function.

overall_design: TEAD1 ChIP-seq in primary keratinocytes.

first: Jingting

last: Li


title: Myc regulation of ETC Biogenesis and mtDNA Replication

status: Public on Sep 01 2019

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: To investigate the important role of Myc in regulating mitochondrial respiration and DNA biogenesis during Drosophila oogenesis, we dissected ovaries with developmental stages from germarium to stage 10 egg chambers from 4-6 day-old w1118 and mycP0/P0 mutant flies. We purified and compared mRNA transcriptome profiles (RNA-seq) in triplicate. We found that the mRNA levels for about 75% components in ETC, heme metabolism, mtDNA replication and translation pathways are decreased in mycP0/P0 mutant. Interestingly, about 85.7% down-regulated mitochondrial genes have predicted Myc binding sites (E-box: CACGTG) in their regulatory regions. Considering that not all E-box are active, it is possible that mitochondrial biogenesis is also indirectly controlled by Myc through a secondary transcriptional regulation. We found that Myc also mediate expression of 48 TFs, 35 of which with predicted E-box in their regulatory regions. Hence, our results indicated that Myc is a master regulator of ETC biogenesis through mtDNA replication and ETC gene expression.

overall_design: Total mRNA were extracted from ovaries of w1118 and mycP0/P0 mutant flies. The mRNA profiles were generated in triplicate using Hiseq3000.

first: Zong-Heng

last: Wang

first: Hong

last: Xu


title: Expression of miRNA, lncRNA and mRNA in human lymphoblastoid TK6 cells under simulated microgravity after ionizing radiation

status: Public on Sep 06 2019

city: Beijing

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

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

summary: In space, multiple unique environmental factors, particularly microgravity and space radiation, pose constant threat to the astronaut’s health. To gain insight into the role of miRNAs and lncRNAs in response to radiation and microgravity, we analyzed RNA expression profiles in human lymphoblastoid TK6 cells incubated for 24 h in static condition or in rotating condition to stimulate microgravity in space after 2 Gy γ-ray irradiation. Expression of 14 lncRNAs and 17 mRNAs was found to be significantly down-regulated in the simulated microgravity condition. In contrast, irradiation up-regulated the expression of 55 lncRNAs and 56 mRNAs, while only one lncRNA, but no mRNA, was down-regulated. Furthermore, 2 miRNAs, 70 lncRNAs, and 87 mRNAs showed significantly altered expression under simulated microgravity after irradiation, and these changes were independently induced by irradiation and simulated microgravity. Together, our results indicate that simulated microgravity and irradiation additively and independently alter the expression of RNAs and their target genes in human lymphoblastoid cells.

overall_design: Human lymphoblastoid TK6 cells were incubated for 24 h in static condition without (Control) or with 2 Gy ionizing radiation (IR), rotating condition to simulate microgravity (MG) in space using Rotary Cell Culture Systems (Synthecon, Houston, TX, US), or rotating condition after ionizing radiation with γ-rays (MG + IR). Then total RNA were extracted for  hybridization on Affymetrix microarrays.

first: Hanjiang

last: Fu

first: Jie

last: Zhu

first: Xiaofei

last: Zheng


title: Linked optical and gene expression profiling of single cells at high throughput

status: Public on Sep 05 2019

city: San Francisco

first: Jesse

last: Zhang

department: BTS

institute: UCSF

summary: Single cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through gene expression alone. Linking sequencing with optical analysis has provided insight into the molecular basis behind cellular function, but current approaches have limited throughput. Here, we present a high throughput platform for linked optical and gene expression profiling of single cells. We demonstrate accurate fluorescence and gene expression measurements from thousands of cells in a single experiment and use the platform to characterize DNA and RNA changes in Jurkat cells through the cell-cycle. In addition to its scalability, our integration of microfluidics and array-based molecular biology holds promise for comprehensive multi-omics profiling of single cells.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: Linked flow cytometry and gene expression datasets from mouse and human cells stained with red and green live cell dyes,  Jurkat cells stained with a DNA-binding dye, and PBMCs labeled with antibodies against CD14 and CD16.

middle: Q

first: Adam

last: Abate


title: Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs

first: Darren

middle: John

last: Fitzpatrick

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

platform_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Laboratory Evolution Experiments Help Identify a Predominant Site of ΔrnhA-dnaA Constitutive Stable DNA Replication Initiation

status: Public on Sep 10 2019

city: Bengaluru

first: Aswin

middle: Sai narain

last: Seshasayee

state: Karnataka

address: GKVK campus Bellary road

department: Bioinformatics

country: India

institute: National Centre for Biological Sciences

summary: The study evaluated the effect of cSDR on gene expression by comparing the gene expression states in ΔrnhA-dnaA and evolved suppressor mutants

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA was extracted from E.coli populations grown in LB media at exponential phase of growth and RNA-sequencing using Illumina Hi-Seq 2500 platform, with two biological replicates for each sample.

first: Reshma

last: Veetil


title: Transition of breast cancer cells from luminal to basal-like phenotype engages a shift from genomic to non-genomic activities of ERα activity

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

summary: Estrogen receptor (ERα) is central in driving the development of hormone-dependent breast cancers. A major challenge in treating these cancers is to understand and struggle endocrine resistance. We have previously shown that the Megakaryoblastic Leukemia 1 (MKL1) protein, a master regulator of actin dynamic and cellular motile functions, directs down-regulation of ERα and hormonal escape of estrogen-responsive breast cancer cell lines. In the present study, we decipher the underlining mechanisms by tracking functional changes in ERα activity. We demonstrate through gene expression microarray analysis that the constitutive activation of MKL1 in ERα-positive MCF7 breast cancer cells induces a transition from a luminal to a basal-like phenotype and suppresses almost all regulations of gene expression by estrogen. Chromatin immunoprecipitation of DNA coupled to high-throughput sequencing (ChIP-Seq) shows a profound reprogramming in ERα cistrome associated with a massive loss of ERα binding sites (ERBSs) generally associated with lower ERα-binding activity. Novel ERBSs appear to be associated with EGF and RAS signaling pathways. ERα dynamic was further impacted by a displacement of its monomer/dimer equilibrium towards its monomer state, associated with a redistribution of the normally nuclear ERα protein to the entire cell volume. We next show that the combination of these remodeled dynamics of ERα alters its interactions with genomic and non-genomic partners. In particular, the formation of ERα/kinase complexes was promoted by the constitutive activation of MKL1. Hence, MKL1-induced transition of ER-positive breast cancer cells from luminal to basal-like phenotype shifts ERα activities from genomic to non-genomic function.

overall_design: Gene expression profiles of stably transfected MCF7 T-Rex sub-clones MCF7  MKL1 ΔN200 and MCF7 control cells was analyzed through microarray experiments after 4 hs of treatment with 10 nM of E2 or EtOH as vehicle control. Four independent RNA samples per condition (n=4) were randomly examined.

first: Charly

last: Jehanno

first: Denis

last: Habauzit

first: Stephane

last: Avner

first: Frederic

last: Percevault

first: Noureddine

last: Boujrad

first: Pascale

last: Le Goff

first: Monica

last: Marin

last: Michel

first: Raphaël

last: Métivier

first: Gilles

last: Flouriot


title: 4See: a flexible browser to explore 4C data

status: Public on Sep 14 2019

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

summary: For ease of visual inspection of 4C data we present 4See, a versatile and user-friendly browser. 4See allows 4C profiles from the same bait to be flexibly plotted together, allowing biological replicates to either be compared, or pooled for comparisons between different cell types or experimental conditions. 4C profiles can be integrated with gene tracks, linear epigenomic profiles and annotated regions of interest, such as called significant interactions, allowing rapid data exploration with limited computational resources or bioinformatics expertise.

overall_design: 4C-seq experiment on mouse ES cells before (two baits) and after (one bait) in vitro differentiation, and on CD4+/CD8+ double positive mouse thymocytes (two baits)


title: Expression data from ex vivo and cultured adipose-derived mesenchymal stromal cells (AdMSC)

status: Public on Aug 30 2019

city: Auckland

first: Hilary

last: Sheppard

address: Symonds St

institute: Auckland University

summary: The effect of standard tissue culture on AdMSC is not well defined, therefore we sought to analyse global gene changes when a defined ex vivo population of AdMSC was subjected to standard tissue culture conditions.

overall_design: A cocktail of antibodies and immunomagnetic beads were used to enrich for untouched ex vivo AdMSC from the stromal vascular fraction of adipose tissue. We used microarrays to detail the global changes in gene expression when these cells are freshly sorted and compared to when these cells are grown in standard tissue culture conditions for different time periods

middle: M


title: MicroRNA Expression Profiles Analysis in Sperm Reveals miR-191 is an Auspicious Omen of in Vitro Fertilization

city: Shanghai

first: Zhang

last: Tiancheng

address: Xietu Road NO.2140

institute: Shanghai institute of Planned Parenthood Research

summary:
Background: MicroRNAs(miRNAs) are a class of non-coding small RNAs, which play important roles in many physiological processes by regulating gene expression. Previously studies show that the expression level of total miRNAs increased during the progression of mouse embryonic development, and some miRNAs control the regulatory network in the development progression.
Results: In this study,the results showed that the sperm samples with high expression of miR-191 had higher fertilization rate (FR), blastocyst rate (EER) and high-quality embryo rate (HQER).
Conclusions: These findings suggest that higher miR-191-5p expression with better human early embryonic development, and indicate that the miR-191-5p could be a potential marker to access the quality of IVF.

overall_design: MicroRNA Expression Profiles of Sperm in Vitro Fertilization was generated by RNA-seq using HiSeq 2000

first: Hua

last: Xu

first: Xin

last: Wang

first: Zhikai

first: Jianhui

last: Li

first: Zhiming

first: Maohua

last: Miao

first: Guowu

last: Chen

first: Xiangdong

last: Lei

first: Jun

last: Wu

first: Huijuan

last: Shi

first: Ke

first: Tiancheng

last: Zhang

first: Xiaoxi

last: Sun


title: CT Irradiation Induced Changes of Gene Expression within Peripheral Blood Cells

status: Public on Aug 27 2019

city: Munich

first: Hanns Leonhard

last: Kaatsch

address: Neuherbergstraße 11

institute: Bundeswehr Institute of Radiobiology

summary: In this study, we describe a potential novel gene expression biomarker for early post-irradiation biodosimetry purposes in BARD1 and we portray the practicability of the established gene expression biomarkers AEN, FDXR and DDB2 after exposure to low dose radiation. Future in-vivo experiments and the inclusion of novel examination procedures present promising approaches to gain further insights into transcriptomic changes after low-level exposure in medical imaging.

overall_design: Analysis of RNA-Seq changes after CT-exposure in peripheral human blood cells

first: Hanns

first: Reinhard

last: Ullmann


title: An Aspergillus niger colony locally adapts its molecular responses to spatially separated substrates

status: Public on Aug 23 2019

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: Saprotrophic fungi, such as Aspergillus niger, grow as mycelial colonies that are often considered uniform entities. To test this uniformity, we analyzed pie-slice sections of a colony grown on spatially separated substrates (glucose, wheat bran, sugar beet pulp) using transcriptomics, proteomics and metabolomics. The colony tuned its response to the local carbon source composition. Plant biomass degrading CAZymes and intracellular carbon catabolic enzymes were more abundant in parts of the colony containing the corresponding sugars. For example a stronger pectinolytic response was observed in the part of the colony grown on the pectin-rich sugar beet pulp. Our results argue against a situation in which small molecules are transported efficiently through the colony  and favour high diversity within the fungal colony in natural biotopes, where the substrate is typically heterogeneous. It also demonstrates the high level of plasticity of A. niger in reponse to the composition of the prevailing lignocellulose.

overall_design: Aspergillus niger colony growing on a pie-slice culture with separated substrates in each section. Each of the three substrate sections on each plate were in turned divided into 3 compartments, each representing a unique configuration of neighboring compartments. Corresponding compartments on each plate were designated replicates of the same condition, e.g. samples P7-1, P11-1, and P14-1 are replicates for compartment 1.

first: Hugh

last: Mitchell

first: Meng

last: Markillie

first: Paul

last: Daly

first: Mao

last: Peng


title: Sov is required for genome-wide H3K9me3 deposition in Drosophila germ cells

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

summary: Sov was recently shown to play a role in heterochromatin formation in the Drosophila ovary. Here, we explored the effect of germline knockdown of Sov on the genome-wide levels of H3K9me3 by ChIP-seq

overall_design: Genome occupancy profiling by high throughput sequencing

first: Katalin

last: Fejes Tóth

first: Alexei

last: Aravin

first: Godneeva

last: Baira


title: STCH4/REIL2 confers cold stress tolerance in Arabidopsis by promoting rRNA processing and CBF protein translation

status: Public on Dec 03 2019

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: To understand the role of STCH4 in cold-responsive gene regulation

overall_design: 14-day-old wild-type and stch4-1 seedlings grown on 1/2 MS medium (1/2 × MS salts, 2% sucrose, 0.6% agar, pH 5.7) were treated without or with 4 ℃ for 4 or 24 hours for total RNA extraction.

first: Hasi

last: Yu

first: Xiangfeng

last: Kong

first: Huan

last: Huang

first: Wenwu

first: Junghoon

last: Park

first: Dae-Jin

last: Yun

first: Byeong-ha

last: Lee

first: Huazhong


title: Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

summary: Cryptococcus neoformans is an opportunistic environmental fungal pathogen that at its peak epidemic levels caused an estimated million cases of cryptococcal meningitis per year worldwide. This yeast can adapt to various external (trees, soil, and/or bird excreta) and internal environments (intracellular microenvironments of phagocytes and/or free-living in host tissues/fluids). The genetic basic for this adaptation is not fully characterized and primarily relies on a single reference C. neoformans strain.  To uncover genes important for yeast infection and disease progression we have compared the gene expression from multiple strains of different lineages (VNI and VNBI) and sources (environment and clinic) under diverse conditions. Here, we used RNA sequencing to assess the transcriptional profiles of seven C. neoformans isolates grown in five representative in vitro, environmental, and in vivo conditions. We characterized gene expression differences between isolates from two of the major lineages of this species, VNI and VNBI, between these conditions. Comparing isolates from these two lineages, we find that genes showing lineage specific expression are enriched in sub-telomeric regions and in lineage specific gene clusters. The major gene expression differences common in all conditions are involved in the utilization of different sugar and nitrogen sources. Comparing gene expression in macrophages and cerebrospinal fluid (CSF) also revealed several specific pathways down-regulated in CSF including lipid and carbohydrate metabolism, and valine, leucine and isoleucine degradation, which may reflect the usage of host nutrients during growth in the mammalian subarachnoid space compared to MP. In summary, our study provides the widest view to date of the transcriptome variation of C. neoformans across natural strains and provides insights into genes important for major in vitro and in vivo growth stages.

overall_design: RNA sequencing to assess the transcriptional profiles of seven C. neoformans isolates grown in five representative in vitro, environmental, and in vivo conditions. BioProject Accession: PRJNA167480

first: Chen-Hsin

first: Christopher

middle: A

last: Desjardins

first: Christina

last: Cuomo


title: Massively Parallel Reporter Assay for pluripotency factors in mESCs

city: St. Louis

first: Dana

last: King

state: Missouri

address: 4523 CLAYTON AVE, CB 8510

department: Department of Genetics

institute: Washington University

summary: A massively parallel reporter assay, MPRA, was conducted in mouse embryonic stem cells (mESC). Synthetic cis-regulatory elements comprised of binding sites for pluripotency transcription factors and genomic sequences with comparable binding sites configurations were used in the assay. Transcripts of dsRed were amplified via PCR from the end of the transcript to sequence 3' UTR barcodes.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design:
MPRA from RW.4 mESCs transfected with either Synthetic (SYN) element library or a Genomic ('GEN' or 'g') WT/MUT sequence library. Each unique sequence or element of interest is tagged with 8 unique 9bp barcodes (provided in the description field in each sample record). Each library also includes a basal control (basal promoter only) tagged with 112 unique 9bp barcodes. The original DNA plasmids that were used for transfections were sequenced to use for normalizating plasmid copy number for final expresson calculations. Tested SYN element and gWT/gMUT sequence names are included in processed data files.
These data are part of SRA submission SUB4287756 (SRP153192) and BioProject PRJNA480686.

first: Brett

last: Maricque

first: Barak

last: Cohen


title: The InsP7 phosphatase Siw14 regulates levels of inositol pyrophosphates and affects activity of general stress transcription factors Msn2 and Msn4

status: Public on Aug 08 2019

city: Tucson

first: Andrew

last: Capaldi

state: AZ

address: 1007 E Lowell St

department: MCB

institute: Univ of Arizona

summary: Cells missing the InsP7 phosphatase Siw14 were exposed to osmotic and oxidative stress and the transcriptional response compared to that in a wild-type strain.  The data show that the Siw14 delete strain has an elevated stress reponse in log growth conditions, but still mounts a robust response to acute stress.

overall_design: The study includes 5 experiments that measure the impact that the InsP7 phosphatase Siw14 has on the Environmental Stress Response (ESR) in budding yeast

first: Elizabeth

last: Steidle

first: Victoria

last: Morrissette

first: Kotaro

last: Fujimaki

first: Lucy

last: Chong

first: Adam

middle: C

last: Resnick

first: Ronda

last: Rolfes


title: Expression profile analysis of circular RNAs during embryonic lung development of C57BL/6 mice

status: Public on Aug 07 2019

city: Nanjing

first: mengjie

last: zhang

address: No. 72, Guang Zhou Road

institute: Children's Hospital Affiliated to Nanjing Medical University

summary:
Objectives: The contribution of circular RNAs (circRNAs) in the regulation of embryonic lung development is not yet clear. This study aims to uncover the differentially expressed circRNAs in mouse embryonic lung tissue.
Methods: High-throughput sequencing (HTS) was used to determine the cirRNA expression profiles at four time points of mouse embryonic lung tissue [embryonic (E) Day 14.5 (E14.5/S1), (E16.5/S2), (E18.5/S3), and newborn (N) Day 7.5 (N7.5/S4)]. CircRNAs that were significantly differential were subjected to bioinformatic analysis and functional prediction for their host genes. Finally, quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) was conducted to examine their levels.
Results: Dynamically expressed circRNAs in the mouse embryonic lung tissue were identified. After that, a total of 231 circRNAs differentially expressed between the three groups (S1 vs. S2, S1 vs. S3 and S1 vs. S4) in embryonic lung tissue (fold change ≥ 2.0; p < 0.05). These circRNAs were subjected to bioinformatic analysis to predict their potential biological functions. Finally, six circRNAs (circRNA3_Ttn, circRNA56_Galnt18, circRNA38_Alg12, circRNA42_Filip1l, circRNA43_Ptprm, and circRNA57_Ncoa3) that were further validated using qRT-PCR.
Conclusions: These findings illustrate the vital functions of circRNAs in mouse embryonic lung development. Combined with our results and previous researches, circRNAs may serve as potential miRNA sponges in the embryonic lung development. Our research is conducive to further explore the development of embryonic lungs, and the dynamic expressed circRNAs may be novel molecules that regulate mouse lung development.

overall_design: High-throughput sequencing was conducted assess the differentially expressed circRNAs in embryonic lung tissues divided into four different groups: pseudo glandular phase (S1), canalicular phase (S2), terminal sac phase (S3), and alveolar phase (S4) .

first: Meng-Jie

last: Zhang

first: Hong-jun

last: Miao


title: lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

status: Public on Sep 02 2019

city: Los Angeles

first: Wange

last: Lu

address: 1425 San Pablo Street, BCC 409

institute: University of Southern California

summary: Both three-dimensional chromatin architecture and long non-coding RNAs (lncRNAs) play essential roles in pluripotency maintenance.  However, whether lncRNAs are involved in organizing 3D chromatin structure remains largely unexplored.  Here, we identified 39 lncRNAs bound by Klf4, a pluripotency factor mediating long-range chromatin interactions.  Among these 39 Klf4-bound lncRNAs, we further investigated the function of 5430416N02Rik.  4C-seq and capture-C experiments revealed that the 5430416N02Rik promoter is a chromatin interaction hub, and 5430416N02Rik RNA functions to facilitate chromatin interactions with the 5430416N02Rik promoter.  Knockout of 5430416N02Rik reduces the proliferation rate of embryonic stem cells (ESCs).  Moreover, compared to deletion of the gene body alone, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and a more profound  impact on the transcriptome.  The reduced proliferation of 5430416N02Rik knockout ESCs is mainly due to the down-regulation of Mid1 transcription, the activation of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci.  In summary, our data demonstrated that lncRNA 5430416N02Rik maintains the proliferation of ESCs by activating the expression of Mid1 through its function of mediating chromatin interaction.

overall_design: We performed RIP-seq (5 conditions * 3 replicates), 4C-seq (2 replicates), capture-C-seq (2 conditions * 2 replicates), and RNA-seq (8 conditions * 3 replicates) to investigate the role of lncRNA 5430416N02Rik in proliferation and pluripotency of mouse embryonic stem cells through inter-chromosome interaction.

first: Zhao

last: Tong

first: Cai

last: Mingyang

first: Su

last: Guangsong

first: Liu

last: Man

first: An

last: Daniel

first: Moon

last: Byoungsan

first: Lyu

last: Guochang

first: Si

last: Yibo

first: Chen

last: Lingyi

first: Lu

last: Wange


title: Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells

status: Public on Aug 20 2019

city: Muang

first: Phongsakorn

last: Chuammitri

state: Chiang Mai

address: Cholprathan Road

department: Veterinary Biosciences

country: Thailand

institute: Chiang Mai Universtiy

summary: We utilized high-throughput small RNA-seq technology to investigate the altered miRNA profiling in miRNA libraries from uninfected (Control) and canine parvovirus type 2c (CPV-2c) infected Crandell Reese Feline Kidney (CRFK) cells. We identified five of known miRNAs (miR-222-5p, miR-365-2-5p, miR-1247-3p, miR-322-5p, and miR-361-3p) and 3 novel miRNAs (Novel 137, Novel 141, and Novel 102) by small RNA-seq with differentially expressed genes (DEGs) in the miRNA repertoire of CPV-infected cells over control. We further predicted the potential target genes of aforementioned miRNAs using sequence homology algorithms. Notably, the targets of miR-1247-3p exhibited a potential function associated with cellular defense and humoral response to CPV. We discovered 229 putative targets from a total of 38 enriched GO terms. We next constructed GO biological process network composed of 28 target genes of miR-1247-3p, of which, some genes, namely BCL6, DLL1, GATA3, IL6, LEF1, LFNG, and WNT1 were among the genes with obviously intersected in multiple GO terms. The miRNA-1247-3 and its cognate target genes suggested the great potential as novel therapeutic targets or diagnostic biomarkers of CPV or other related viruses.

overall_design: Two CRFK cells at 80% confluent were infected CPV-2c Laotian isolates (C22 and VTE034) and the other two were served as control by using PBS instead of viruses.

first: Chuammitri

last: Phongsakorn

first: Vannamahaxay

last: Soulasack

first: Sornpet

last: Benjaporn

first: Pringproa

last: Kidsadagon

first: Patchanee

last: Prapas


title: Dynamic 3D chromosomal landscapes in acute leukemia [HiChIP]

status: Public on Aug 04 2019

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

summary:
Background: Disruptions of 3D chromatin architecture can alter the activity of topologically associated domains (TADs), rewire enhancer-promoter interactions and thus significantly impact gene regulatory programs. Recently, such disruptions have been implicated in tumorigenesis, highlighting the need for a deeper understanding of their detailed role.
Methods: T-ALL primary samples and prototypical cell lines as well as healthy T cell counterparts were profiled by in-situ Hi-C, RNA-Seq and CTCF ChIP-Seq. Data was subsequently integrated.
Results: Our studies showed that the genome of leukemia cells does not display global changes in TAD structures but presents local changes in selected TAD boundaries as well as alterations of intra-TAD activity which are associated with changes in gene expression of key oncogenes and tumor suppressors, strong correlation with CTCF-mediated insulation and enhancer activity. Finally, we showed that 3D interactions on selected loci can be partially corrected pharmacologically, potentially accounting for the anti-leukemogenic effects of these drugs.
Conclusions: Our studies underscore the need for further investigation of factors that rewire long range interactions especially during tumorigenesis, as they could be targets for pharmacological targeting.

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) as well as healthy T cell counterparts from three different donors were collected.

first: Palaniraja

last: Thandapani

first: Panagiotis

last: Ntziachristos

first: Ioannis

last: Aifantis

first: Aristotelis

last: Tsirigos


title: DNA methylation analysis of HCT116 after knockdown and rescue of UHRF1

status: Public on Aug 14 2019

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Ave NE

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: In HCT116 colorectal cancer cells, UHRF1 was knocked down by shRNA (puromycin) while simultaneously transduced with wildtype or mutant UHRF1 (blasticidin) or NDI1 (- control) followed by dual antibiotic selection. DNA was analyzed 11 days after viral transduction.

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

first: Robert

last: Vaughan

first: Bradley

last: Dickson


title: Granulosa cells of ovarian antral follicles exhibit distinct follicle size-related processes

status: Public on Aug 15 2019

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

institute: Wageningen University

summary: Antral follicle size might be a valuable additive predictive marker for IVF outcome. However, while some studies show positive relations between follicle size and reproductive outcome, others have not been successful in establishing this relation. To better understand consequences of antral follicle size for reproductive outcome, we aimed to obtain insight in follicle size-related granulosa cell processes, as granulosa cells play an essential role in follicular development via the production of growth factors, steroids and metabolic intermediates, needed for follicular growth and oocyte development. Using pigs as a model, we compared gene and protein expression in granulosa cells of smaller and larger follicles in the healthy antral follicle pool at the start of the follicular phase of the estrous cycle. In sows, the early antral follicle pool is very heterogeneous when e.g. size and steroid content of the follicular fluid are considered. To which extent this variety contributes to the developmental competence of the follicles is not clear. Therefore, sows with high variation in antral follicle size (HighVAR) as well as sows with low variation in antral follicle size (LowVAR) were used. Granulosa cells of smaller antral follicles in the healthy antral follicle pool show increased cell proliferation, which was accompanied by a metabolic shift towards aerobic glycolysis (i.e. the Warburg effect), similar to other highly proliferating cells. High granulosa cell proliferation rates in smaller follicles might be regulated via increased granulosa cell expression of AR and EGFR which are activated in response to locally produced mitogens. While granulosa cells of smaller follicles in the pool were more proliferative, indicative of higher follicular growth, granulosa cells of larger follicles in the pool showed less proliferation and were more differentiated, as they showed a higher expression of follicular maturation marker IGF1 and ANGPT1. Our results imply that the inclusion of strict criteria of antral follicle size in IVF protocols might improve reproductive outcome.  In addition, we have granulosa cell gene expression of healthy follicles to unravel underlying mechanisms of differences in COC morphology. We compared gene expression in sows with low vs. high-COC-health and found a decreased expression of genes involved in ovarian steroidogenesis (e.g. CYP19A1, ADM, SPP1) and higher expression of genes involved in follicular atresia (e.g. GADD45A, INHBB) in sows with low-COC-health. Thereby we have identified several genes which may serve as markers for follicle developmental competence.

overall_design: A total of 29 multiparous Dutch Landrace sows (parity 3 to 5; Topigs Norsvin, Vught, the Netherlands) were used. The sows were fed a standard lactation diet (ca. 12.5MJ NE/kg, 154 g/kg CP, 9.3 g/kg lysine; Lacto Excellent, Agrifirm, Apeldoorn, The Netherlands). Within 24 hours after parturition, piglets were cross-fostered to ensure 13 suckling piglets per sow. The sows had a lactation period of 26.1±0.2 (25 to 27) days and weaned 13.0±0.9 piglets. The sows were slaughtered at the slaughterhouse by stunning and exsanguination within 2 hours after weaning. Follicle size, follicle health status and cumulus-oocyte complex (COC) morphology were determined. For each sow, the variation in follicle size of the 10 largest healthy follicles for each right ovary was determined, as well as the percentage healthy COCs.   The variation in follicle size was used to select a total of eight sows for further analysis; four sows with a large variation (SD) in follicle size of the 10 largest healthy follicles (HighVAR; 1.56±0.18 mm) and four sows with a small variation in follicle size (LowVAR; 0.54±0.16 mm).  For each sow, granulosa cells of the 3 largest (large follicles 1-3) and 3 smallest (small follicles 4-6) of the 10 largest healthy follicles were isolated and indiviudally hybridized on microarrays. Differences in gene expression between large and small follicles were determined, for both HighVAR and LowVAR sows. As an alternative approach, which will be described elsewhere, the percentage healthy COCs was used to group 4 of the previously mentioned sows as sows with Low-COChealth (% healthy COCs < 70%) and 4 sows with High-COChealth (% healthy COCs > 70%).  Granulosa cell gene expression profiles of sows with Low_COChealthy and high_COChealth were compared, by analysing 6 follicles for each sow (3 large follicles and 3 small follicles).

first: Natasja

last: Costermans

first: Katja

last: Teerds

first: Annelies

last: Bunschoten

first: Jaap

last: Keijer

first: Nicoline

last: Soede


title: Transient DNMT3L expression in mouse embryonic fibroblast (MEFs)

status: Public on Aug 02 2019

city: Taipei

first: Chih-Yun

last: Yu

address: Room 403, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: Global heterochromatin reduction, which is one of the hallmarks of aging cells, is associated with reduced transposable element repression and increased risk of chromatin instability. To ensure genomic integrity, the irreparable cells in a population exit permanently from the cell cycle, and this process is termed “senescence”. However, senescence only blocks the expansion of unwanted cells, and the aberrant chromatin of senescent cells remains unstable. Serendipitously, we found that the transient ectopic expression of a repressive epigenetic modulator, DNA methyltransferase 3-like (DNMT3L) was sufficient to delay the premature senescence progression of late-passage mouse embryonic fibroblasts (MEFs) associated with a tightened global chromatin structure. DNMT3L induces more repressive H3K9 methylation on endogenous retroviruses and downregulates the derepressed transposons in aging MEFs. In addition, we found that a pulse of ectopic DNMT3L resulted in the reestablishment of H3K27me3 on polycomb repressive complex 2 (PRC2)-target genes that were derepressed in old MEFs. We demonstrated that ectopic DNMT3L interacted with PRC2 in MEFs. Our data also suggested that ectopic DNMT3L might guide PRC2 to redress deregulated chromatin regions in aging cells. This study might lead to an epigenetic reinforcement strategy for overcoming aging-associated epimutation and senescence.

overall_design: Total 8 samples were included. 2 replicates for each condition. Young MEFs (P3), old MEFs (P5 and P6) and  MEFs prolonged-proliferation period after exogenous DNMT3L pulse (P20-30) contured in standard MEF culture condition or embryonic stem (ES) cell culture condition.

middle: Y

first: Tzu-Hao

last: Kao

first: Hung-Fu

last: Liao

first: Chia-Chun

last: Hou

first: Kai-Wei

last: Chang

first: Mong-Hsun

last: Tsai

first: Shau-Ping

last: Lin


title: Bacillus velezensis LG37: Transcriptome profiling and functional verification of GlnK and NmtA in ammonia (NH4+) assimilation

city: guangzhou

first: guangxin

last: liu

address: 501 Zhongkai Road, Haizhu District, Guangzhou

institute: zhongkai university of agriculture and engineering

summary: not provided; requested

overall_design: B. velezensis LG37 grown in a minimal medium containing 10 mmol/L NH4+-N (as treatment) and Gln-N (as control) and pelletized once reaching the late log phase (0.4 - 0.7 OD) samples were sequenced, each with three repetitions.

first: Guangxin

last: Liu

first: Li


title: Dynamic 3D chromosomal landscapes in acute leukemia

first: Andreas

last: Kloetgen

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

overall_design: Refer to individual Series


status: Public on Aug 01 2019

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Transcriptomic profiling of breast cancer cells incubated in vitro with surgical wound fluids from patients with breast cancer reveals similarities in the biological response induced by intraoperative radiation therapy and the radiation-induced bystander effect
In patients with breast cancer who undergo breast-conserving surgery (BCS), more than 90% of local recurrences occur in the same quadrant as the primary cancer. Surgical wound fluids (SWF) are believed to play a role in this process by inducing an inflammatory process in the scar tissue area. Despite strong clinical data demonstrating the benefits of intraoperative radiotherapy (IORT), the biological basis underlying this process remains poorly understood. Ionizing radiation (IR) directly affects cells by damaging DNA, thereby altering the cell phenotype. IR direct effects cancer cells and also influences unirradiated cells located nearby, a phenomenon known as the radiation-induced bystander effect (RIBE), significantly modifying the tumour microenvironment.
We hypothesized that SWF obtained from patients after breast-conserving surgery (BCS) and IORT would induce a radiobiological response (due to RIBE) in unirradiated cells, thereby modifying their phenotype.

overall_design: To confirm this hypothesis, breast cancer cells were incubated with SWF collected from patients after BCS 1) without IORT (WF group), 2) with IORT (RT-WF group), and 3) WF with conditioned medium from irradiated cells (WF+RIBE group) and then subjected to microarray analysis. We performed gene set enrichment analysis to determine  the biological processes present in these cells.

first: Katarzyna

last: Kulcenty

first: Igor

last: Piotrowski

first: Joanna

middle: P

last: Wroblewska

first: Karol

last: Jopek

first: Dawid

last: Murawa

first: Wiktoria

last: Suchorska


title: OMA1, DELE1 and HRI relay mitochondrial stress to the mammalian integrated stress response

status: Public on Jul 29 2019

city: San Francisco

first: Ruilin

last: Tian

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

summary: The goal of this study is to understand how mamalian cells respond to the mitochondial stress. Using Quant-seq, we identifed an integrated stress response signature in the cells with compromized mitochondria. Furthermore, using an unbiased CRISPRi genetic screen, we uncovered a novel signaling pathway, in which OMA1, DELE1 and HRI are three major players that relay the mitochondrial stress to the integated stress response. To further study the cellular response in the absence of this pathway, we again used Quant-seq to uncover alternative pathways that might play a role during the mitochondrial stress response.

overall_design: The Quant-seq experiments were performed using HEK293T cells with OMA1, DELE1, HRI KD via CRISPRi under both untreated or 1.25 ng/mL oligomycin (16hrs) treated conditions with 3 replicates for each sample. For WT type cells, 50 ug/mL Doxycyline treated and untreated cells were also included for Quant-seq experiments with 2 replicates.

first: Xiaoyan

last: Guo

first: Martin

last: Kampmann


title: Dynamic 3D chromosomal landscapes in acute leukemia [ChIP-Seq]

first: Palaniraja

last: Thandapani

first: Panagiotis

last: Ntziachristos

first: Ioannis

last: Aifantis

first: Aristotelis

last: Tsirigos


title: Dynamic gene expression in T-ALL following treatment and release of gamma-secretase inhibition [GRO-Seq]

summary: Gro-seq analysis following NOTCH1 inhibition and release gave an ovierview of the kinetics of NOTCH1 dependent transcriptional regulatiion

overall_design: NOTCH1-driven T-ALL cell line CUTLL1 was treated with gamma-secretase inhibitor (gSI) for 72 hours. Dynamic gene expression pattern was followed by GRO-Seq upon release of gSI after 0, 1, 2, 3, 4, 5, 6, 8 and 10 hours.

first: Thomas

last: Trimarchi