title: Transcriptional profiling of the mid-proliferative phase eutopic endometrial samples from women with endometriosis

first: Geetanjali

last: Sachdeva

summary:
Purpose- To identify the pathways and processes that are dysregulated in the eutopic endometrium of women with endometriosis
Methods- RNA sequencing was used to detect and quantify  the transcripts encoded by the whole genome in the eutopic endometrium.  Mid-proliferative phase eutopic endometrial samples from women with (n=4) and without endometriosis (n=3) were processed for RNA sequencing and the data were compared to identify the transcripts displaying differential abundance in women with endometriosis, compared to those without endometriosis (controls)

overall_design: Total RNA isolated from mid-proliferative phase eutopic endometrial samples from women with (n=4) and without endometriosis (n=3) were enriched for messenger RNA (mRNA) using poly (A) selection. Strand-specific libraries were synthesised, adapter ligated, amplified and sequenced to obtain paired-end reads using Illumina Next Seq 500 platform. The data were analysed using the Tuxedo pipeline to  detect differentially abundant transcripts in the endometrial samples from women with endometriosis, compared to those without endometriosis. This was followed by annotation for the pathways and processes enriched by the differentially expressed transcripts in endometrial samples from women with endometriosis.

first: Kashmira

last: Bane

first: Junita

last: Desouza

first: Diksha

last: Shetty

first: Prakash

last: Choudhary

first: Shalaka

last: Kadam

first: Rajendra

last: Katkam

first: Gwendolyn

last: Fernandez

first: Raj

last: Sawant

first: Uddhavraj

last: Dudhedia

first: Neeta

last: Warty

first: Anahita

last: Chauhan

first: Uddhav

last: Chaudhari

first: Rahul

last: Gajbhiye


title: Epigenomic profiling of hair follicle stem cells identifies PRDM16 as a regulator of sebaceous gland homeostasis [RNA-seq]

status: Public on Mar 26 2021

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

country: Germany

institute: University of Cologne (UoC), Germany

type: Expression profiling by high throughput sequencing

summary: The epidermis consists of different compartments such as the hair follicle (HF), sebaceous gland (SG) and interfollicular epidermis (IFE), each containing distinct stem cell (SC) populations.  However, with the exception of the SCs residing within the HF bulge, other epidermal SC populations remain poorly characterized at the molecular level.  Here we used an epigenomic strategy that combines H3K27me3 ChIP-seq and RNA-seq profiling to identify major regulators of HFSC located outside the bulge. When applied to the bulk of HFSC isolated from mouse skin our approach identified both previously known and potentially novel non-bulge HFSC regulators. Among the latter, we found that PRDM16 was preferentially expressed within the Junctional Zone (JZ). To investigate PRDM16 function within the JZ SCs, we generated an epidermal-specific Prdm16 Knock-out mouse model (K14-Cre-Prdm16fl/fl). Notably, although these K14-Cre-Prdm16fl/fl mice did not show any major skin or hair abnormalities, the homeostasis of the SG was clearly compromised. Namely, PRDM16 deficient mice displayed enlarged SGs and excessive sebum production, thus resembling some of the features associated with certain human conditions (i.e. acne, sebaceous hyperplasia). Overall, our study provides a list of putative novel regulators of HFSC outside the bulge and identifies PRDM16 as a major regulator of SG homeostasis.

overall_design: Transcriptional profiles in Αlpha6+/Sca1- cells isolated from back skin of P56 mice using RNA-seq.

first: Rizwan

last: Rehimi

first: Alvaro

last: Rada-Iglesias


title: Mechanism of melatonin regulating the interaction between radish and Alternaria alternata

status: Public on Mar 28 2021

city: guizhou

first: xia

last: ming

address: china guizhou huaxi

country: China

institute: guizhoudaxue

summary:
Purpose:In this study, we observed the effect of exogenous melatonin on the proliferation and pathogenicity of Alternaria alternata, judged the biological function of melatonin on Alternaria alternata, and found the key genes of melatonin regulating Alternaria alternata traits at the transcription level by RNA SEQ, and preliminarily revealed its mechanism of action.
Methods:SNA medium with melatonin concentration of 50, 100, 500, 1000 and 1500 μ m was prepared and 30 ml plate was made. Take sterilized circular filter paper with a diameter of 1 cm, add 100 UL 50 CFU / cm3 spore suspension, transfer to SNA medium center, and culture upside down for 7 days
Results:In this study, 20 metabolic pathways with the most significant KEGG enrichment were selected from the four control groups by P value analysis (Fig. 9). In 500 μ m vs control group, DEGs were mainly enriched in ribosome, glyoxylic acid and dicarboxylic acid metabolism pathways. In 1500 μ m vs control group, the metabolic pathways such as glyoxylic acid and dicarboxylic acid metabolism, valine, leucine and isoleucine degradation, ketone body synthesis and degradation, terpenoid main chain biosynthesis were the most significant; in 500 μ m vs 1500 μ m, DEGs were mainly enriched in eukaryotic ribosome biosynthesis and RNA polymerase pathway; 500 μ m vs 1500 μ M Compared with the control treatment, DEGs were significantly enriched among the three groups, and the pathways were rich, such as amino acid metabolism, glyoxylic acid and dicarboxylic acid metabolism, valine, leucine and isoleucine degradation, glyceride metabolism, glycolysis / gluconeogenesis, ABC transporter and so on.
Conclusions:Nine DEGs related to the development and pathogenesis of streptozospora were obtained by transcriptional sequencing. The results showed that melatonin involved aflatoxin biosynthesis (sld1 and sld2, s-adenosine-l-methionine dependent methyltransferase synthesis), MAPK signal pathway (GLP), linoleic acid metabolism (HP1), heme peroxidase synthesis ）The results showed that the metabolism of selenium (THR), protein processing in endoplasmic reticulum (KHP, 30kda heat shock protein synthesis), glycolysis / glycometagenesis (PPL), and synthesis of non reductive poly ketoacetase (NPS) and heme peroxidase (HP2) were also studied. Among them, THR is related to proliferation regulation [49], sld1, sld2, NPs and ppl are related to pathogenicity , GLP is related to colony growth and pathogenicity, KHP is related to stress , HP1 and HP2 are related to antioxidant activity .

overall_design: The colony of Alternaria alternata treated with 0, 500 and 1500 μ m melatonin was used as experimental material

first: Xia

last: Ming

first: Li

middle: J

last: Wei


title: Single cell sequencing of e13 Embryonic Thymuses

city: Dallas

first: Nicolai

middle: S

last: van Oers

state: TX

address: NA2.200, 6000 Harry Hines Blvd

department: Immunology

country: USA

institute: UT Southwestern Medical Center

summary:
Purpose: To identify and compare all the cell subsets present in Normal and 22q11.2 DS Hypoplastic thymus
We have identified 17 distinct cell clusters in normal e13 embronic thymus.
While both normal and 22q11.2 DS Hypoplastic thymus have same number of cell clusters, the trancriptome pattern varies significantly between them.
Our scRNA sequencing results provide mesenchymal cells driven thymus hypoplasticity in 22q11.2 DS thymus.

overall_design: scRNA seq is performed using e13 embryonic thymuses from control, Tbx1neo2/neo2 and Foxn11089/1089 thymuses

first: Pratibha

last: Bhalla

first: Ashwani

last: Kumar


title: Prefrontal cortical transcriptome analysis of Cyfip2 mutant mice

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

country: South Korea

institute: Korea University College of Medicine

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

overall_design: Refer to individual Series


title: Prefrontal cortical transcriptome analysis of Cyfip2 mutant mice (jouvenile mouse)

summary: CYFIP2 is a component of the WAVE regulatory complex which regulates actin polymerization and branching in diverse cellular compartments. Recent molecular genetic studies identified mutations of CYFIP2 in patients with intellectual disability and seizures, suggesting that CYFIP2 may have some roles in brain development and function. To understand its functions in vivo at the molecular level, we performed RNA-seq analysis in juvenile Cyfip2 mutant mice.

overall_design: Prefrontal cortical transcriptome of postnatal day 28 wild-type and Cyfip2 mutant mice.

first: Yinhua

last: Zhang

first: Hyojin

last: Kang


title: Transcriptional programming of human epidermis during wound repair and in pressure ulcer at single-cell resolution

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

summary: Pressure ulcer (PU) is a chronic non-healing wound caused by continuous pressure of the bodyweight to the skin, which is often seen in spinal cord injury patients and in the bedridden elderly population. In spite of high mortality, the pathophysiology of PU remains poorly understood. We performed single-cell transcriptomic analysis of epidermal cells from PU wound-edges, and compared them with epidermal cells from the intact skin and normal acute wounds (AW) of healthy donors. We identified four keratinocyte clusters, one melanocyte cluster, and one immune cell cluster, and the cellular heterogeneity and gene expression were altered in PU. Our findings provided a high-resolution map of human PU and AW, which are likely to yield new areas for exploration of the pathophysiology of chronic wounds and development of wound therapy.

overall_design: In total, 1170 cells with three cell types from nine patients.

middle: X

last: Landén

first: Qiaolin

last: Deng

first: Dongqing

last: Li

first: Shangli

last: Cheng


title: Detection of circRNA biomarker for Acute Myocardial Infarction based on system biological analysis of RNA Expression

city: Harbin

first: Wen

last: Yang

address: No.23 youzheng road,nangang district

institute: The First Affiliated Hospital of Harbin Medical University

summary: A series of system biological analysis are performed on RNA expression to find new effective circRNA biomarkers for AMI. Firstly, the expression level of circRNA in blood samples of patients with AMI and those with mild coronary stenosis are compared to reveal circRNAs which are involved in AMI. Then, circRNAs which are significant expressed abnormally in the blood samples of patients with AMI are selected from those circRNAs.

overall_design: Abnormal expression of circRNAs often affects the occurrence and development of diseases. In order to discover the circRNA related to acute myocardial infarction (AMI), the expression levels of circRNAs in blood samples of patients with AMI are firstly analyzed and compared with the expression levels of circRNAs in patients with mild coronary artery stenosis to find abnormally expressed (up-regulated or down-regulated) circRNAs.

first: Weimin


title: Effects of the HDACi SAHA on IgH transcription in B-cell splenocytes and effect of deletion of two cis-transcriptional enhancer on IgH transcription in femoral B-cells.

status: Public on Mar 27 2021

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: B-cell development is spatially and temporally regulated with the Ig heavy chain (IgH) locus as a conductor. Starting with the first steps of B-cell development, IgH DNA remodeling constantly occurs under the control of several cis-regulatory elements scattered all along the IgH locus. Their individual genomic deletion had partial or no effect on B-cell development. In this study we investigate the effect of the dual deletion of 5’Eµ and 3’RR enhancer on IgH transcription. Numerous B-cell lymphomas feature translocations linking oncogenes with the IgH locus and epigenetic drugs such as histone deacetylase inhibitors (HDACi) have been approved to treat some of them. In this study we investigated IgH locus transcription in B-cell splenocytes stimùulated with LPS and the HDACi SAHA.

overall_design: Femoral B-cells from 5’Eµ/3’RR-deficient mice and RAG2-deficient mice were recovered. RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer’s instructions. Two pooled RNAs (each with mice samples) were obtained for the two genotypes. CD43- splenocytes were obtained from wt mice after 48h of in vitro stimulation (1x10^6 cells/ml in RPMI 1640 with 10% FCS) with 5µg/ml LPS ± 200 ng/ml SAHA. RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer’s instructions. Two pooled RNAs (each with three samples) were obtained for each stimulatory condition. There are two replicates per condition.

first: Nour

last: Ghazzaui

first: Melissa

last: Ferrad

first: Hussein

last: Issaoui

first: Yves

last: Denizot


title: HDAC inhibitors and IgH locus transcription. Mini 3'RR and IgH locus transcription

summary: Numerous B-cell lymphomas feature translocations linking oncogenes with the IgH locus and epigenetic drugs such as histone deacetylase inhibitors (HDACi) have been approved to treat some of them. In this study we investigated IgH locus transcription in B-cell splenocytes stimulated with LPS and the HDACi SAHA. B-cell development is spatially and temporally regulated with the 3'RR enhancer of the IgH locus as a conductor. 3'RR is composed of 4 enhancer elements with a palindromic structure of great significance. We investigated the role of this palindrome with KOKI mice where the 30Kb structure of the 3'RR has been deleted of its palindromic structure.

overall_design: Femoral B-cells from KOKI mice (in a RAG2-deficient and RAG2/gamma c-deficient background) and RAG2/gamma c -deficient mice were recovered. RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer’s instructions. Two pooled RNAs (each with 3 mice samples) were obtained for the three genotypes. CD43- splenocytes were obtained from KOKI mice and stimulated 2 days (1x10^6 cells/ml in RPMI 1640 with 10% FCS) with 5µg/ml LPS. RNA was extracted using miRNeasy kit from QIAGEN, according to the manufacturer’s instructions. CD43- splenocytes were obtained from wt mice and stimulated 2 days (1x10^6 cells/ml in RPMI 1640 with 10% FCS) with 5µg/ml LPS ± 200 ng/ml SAHA. RNA was extracted using miRNeasy kit from QIAGEN. There are two replicates per condition.

first: Sandrine

last: Le Noir


title: Transcriptional regulation of cell division and cytokinin response in Arabidopsis shoot apical meristem [RNA-seq]

city: Cambridge

first: Weibing

state: Select...

address: 47 Bateman Street, Cambridge

country: United Kingdom

institute: Sainsbury Laboratory  University of Cambridge

summary: In plants, the phytohormone cytokinin plays a major role in promoting cell division. However, the molecular mechanisms underlying cytokinin stimulated cell proliferation remain poorly understood. Here we show that, in the meristems of Arabidopsis thaliana, two transcriptional factors, MYB3R1 and MYB3R4, are master regulators of mitotic cell cycle gene expression and cytokinin response.

overall_design: RNA-seq was carried out using dissected inflorescence meristems.

first: Elliot

middle: M

last: Meyerowitz

first: Sandra

last: Cortijo


title: H3K27me3 is dispensable for early differentiation but required to maintain differentiated cell identity

city: Boston

first: Manashree

last: Damle

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb repressive complex 2 (PRC2) catalyzes trimethylation of histone H3 on lysine 27 and is required for normal development of complex eukaryotes. The requirement for H3K27me3 in various aspects of mammalian differentiation is not clear. Though associated with repressed genes, the modification is not sufficient to induce gene repression, and in some instances is not required. To examine the role of the modification in mammalian differentiation, we blocked trimethylation of H3K27 with both a small molecule inhibitor, GSK343, and by introducing a point mutation into EZH2, the catalytic subunit of PRC2. We found that cells with substantively decreased H3K27 tri-methylation were able to differentiate, which contrasts with EZH2 null cells. Different PRC2 targets had varied requirements for K27me3 in repressive regulation with a subset that maintained normal levels of repression in the absence of methylation. The primary cellular phenotype where H3K27 tri-methylation was blocked was the inability of the altered cells to maintain a differentiated state when challenged. This phenotype depended upon H3K27me3 deposition both in embryonic stem cells and in the first four days of differentiation. H3K27 tri-methylation therefore was not necessary for formation of differentiated cell states but was required to maintain a stable differentiated state.

overall_design: RNA-seq and Cut&Run analysis of GSK343-treated, EZH2-mutant or WT ESC or differentiated embryoid bodies.

first: Sara

last: Miller

first: Robert

middle: E

last: Kingston


title: RNA-Seq of FBXO44 knockdown in MDA-MB-231

city: San Diego

first: Jia

middle: Zack

last: Shen

state: California

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Targeting FBXO44 or SUV39H1 transcriptionally reactivates repetitive elements, triggering RIG-I-MDA5-MAVS and cGAS-STING  antiviral defense responses and IFN signaling, specifically in cancer cells

overall_design: RNA-Seq analysis of control and FBXO44 knockdown MDA-MB-231 cells

middle: Z


title: ChIP-Seq of FBXO44 and H3K9me3 in MDA-MB-231

summary: FBXO44 bound H3K9me3-modified nucleosomes at the replication fork and recruited the H3K9me3 methyltransferase SUV39H1 for repetitive element silencing post-DNA replication

overall_design:
1) ChIP-Seq analysis of FBXO44 and H3K9me3 in MDA-MB-231 cells.
2) ChIP-Seq analysis of H3K9me3 in Control and FBXO44 knockdown groups of MDA-MB-231 cells.


title: Repeat RNAs associate with replication forks and post-replicative DNA

city: Copenhagen

first: Helene

middle: Maria

last: Gylling

address: Ole maaløes vej 5

department: SUND/BRIC

country: Denmark

institute: University of Copenhagen


title: ETS1 and ETS2

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina


title: Epigenomic profiling of hair follicle stem cells identifies PRDM16 as a regulator of sebaceous gland homeostasis.

first: Giuliano

last: Crispatzu


title: Endothelial Poldip2 Regulates Sepsis-induced Lung Injury via Rho Pathway Activation

city: ATLANTA

first: Elena

last: Dolmatova

state: GA

address: 100 Woodruff cir NE #1013 # 1013

institute: Emory University

summary: We report the effect of Poldip2 knock-down on gene expression in human pulmonary endothelial cells with and without TNF-alpha challenge.

overall_design: Human lung microvascular endothelial cells treated with siControl + PBS, siControl+ TNF-alpha, siPlodip2 + PBS, or siPoldip2 + TNF-alpha.

first: Kathy

last: Griendling


title: Repeat RNAs associate with replication forks and post-replicative DNA [long]

summary: Non-coding RNA has a proven ability to direct and regulate chromatin modifications by acting as scaffolds between DNA and histone-modifying complexes. However, it is unknown if ncRNA plays any role in DNA replication and epigenome maintenance, including histone eviction and re-instalment of histone-modifications after genome duplication. Isolation of nascent chromatin has identified a large number of RNA-binding proteins in addition to unknown components of the replication and epigenetic maintenance machinery.  Here, we isolated and characterized long and short RNAs associated with nascent chromatin at active replication forks and track RNA composition during chromatin maturation across the cell cycle. Shortly after fork passage, GA-rich-, Alpha repeats and TERRA RNA are associated with replicated DNA. These repeat RNAs arise from loci undergoing replication, suggesting an interaction in cis. Post-replication during chromatin maturation, and even after mitosis in G1, the repeats remain enriched on DNA. This argues that specific types of repeat RNAs are transcribed shortly after DNA replication and stably associates with their loci of origin throughout cell cycle. Our rich data set provides a resource to understand how repeat RNAs and their engagement with chromatin are regulated with respect to DNA replication and across the cell cycle.

overall_design: Cells were synchronized, released and harvested at 3 different time points (0, 2 and 10h) measured from 3 hours post cell release into S-phase.An Input sample was taken at t=0 and every sample was produced in biological quadruplicates. 3/4 of samples were labeled with biotin dUTP (b-dUTP) each of which was harvested at different time points and 1 sample was harvested at t=0 and used for Histone3 pull-down.

first: Cristina

last: Gonzalez-Aguilera

first: Dominik

last: Kaczorowski

first: Martin

middle: A

last: Smith

first: Anja

last: Groth

first: Anders

middle: H

last: Lund


title: Epigenomic profiling of hair follicle stem cells identifies PRDM16 as a regulator of sebaceous gland homeostasis [ChIP-seq]

overall_design: Genome-wide binding profiles for H3K27me3 and H3K4me3 were generated in Αlpha6+/Sca1- cells isolated from back skin of P56 mice using ChIP-seq.

first: Rizwan

last: Rehimi

first: Alvaro

last: Rada-Iglesias


title: Chronic perinatal hypoxia delays cardiac maturation in a mouse model for cyanotic congenital heart disease

city: Washington

first: Nikki

middle: Gillum

last: Posnack

state: Please select a region, state or province.

address: 111 Michigan Ave, NW

institute: Childrens National Hospital

summary:
Whole heart RNA isolated from mice in hypoxic vs normoxic environment
Microarray analysis for changes in global gene expression

overall_design: RNA isolated from mice at P8 or P30, normoxic vs hypoxic environment. Clariom arrays were only run on samples with RIN >6

middle: G


title: Heterogeneity of  hematopoietic progenitors in adult mouse liver

city: Hefei

first: Hui

last: Peng

address: 443 Huangshan Road

institute: University of Science and Technology of China

summary: To investigate whether liver-resident ILC1s could develop from local hematopoietic progenitors, we analyzed the phenotypic properties of liver CD45+Lin- progenitors. We found that the adult mouse liver contained Lin-Sca-1+Mac-1+ (LSM) hematopoietic progenitors derived from the fetal liver. This population included Lin-CD122+CD49a+ progenitors that could generate liver ILC1s but not conventional NK (cNK) cells. By performing single-cell RNA seq, we show the heterogeneous composition of these hematopoietic progenitors.

overall_design: Purified liver LSM cells and Lin-CD122+CD49a+ cells from adult WT mice were stained with 0.4% Trypan blue to check their viability, and processed for scRNA-seq (10X Genomics).


title: Re-oxidation of cytosolic NADH is a major contributor to the high oxygen requirements of the thermotolerant yeast Ogataea parapolymorpha in oxygen-limited cultures

city: Delft

first: Raúl

middle: Antonio

last: Ortiz-Merino

address: van der Maasweg 9

department: Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Analysis of gene expression changes in O. parapolymorpha in response to oxygen-limitation

overall_design:
8 samples (comprising 4 pairwise comparisons), two biological replicates per sample.
In addition, we re-analyzed (mapped and counted) 4 samples S590, S591, S614 and S615 of project PRJNA589876, GEO: GSE140480. Corresponding sample accessions are GSM4162762, GSM4162763, GSM4162764, GSM4162765.

first: Wijb

last: Dekker

first: Raul


title: Profiling the immune response to Mycobacterium tuberculosis Beijing family infection: A perspective from the transcriptome

status: Public on Mar 25 2021

city: Cuernavaca

first: Gamaliel

last: Lopez

state: Morelos

address: Ave. Universidad s/n, Chamilpa

department: Genómica Evolutiva

country: Mexico

institute: Centro de Ciencias Genómicas

summary: Tuberculosis continues as an important public health problem. Particularly considering  Beijing-family strains of Mycobacterium tuberculosis, which have been associated  with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most  prevalent Beijing strain in Colombia. The pathogenic mechanism and immune  response against this pathogen is unknown. Thus, we compared the course of  pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain  323. The disease course was different among infected animals with Classical-Beijing  and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection  (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with  Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis.  Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day14 dpi), and  late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected  mice with Classical-Beijing showed several over-expressed genes, associated with a  pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines,  both biomarkers of disease severity. Contrary, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-  suppression, including Nkiras, Dleu2 and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory  response. In summary, both Beijing strains induced a non-protective immune response  which induced extensive tissue damage, BL strain induced rapidly extensive  pneumonia and death, whereas Classical-Beijing strain produced slower extensive  pneumonia later associated with extensive necrosis.

overall_design: In this study, the progressive pulmonary TB model in BALB/c mice were used; groups of 50 male animals per group were anaesthetized with sevoflurane (100 uL per mice) and infected by intratracheal inoculation with 250.000 bacteria/100uL of each strain. At day 1, 3, 7, 14, 21, 28 and 60 (with surviving mice) after infection groups of six mice were euthanized by exsanguination under anesthesia with pentobarbital. Left lungs lobes and spleens were removed for CFU processing and histopathology. Here, higher virulence of Beijing like strain was characterized by earlier and higher mortality, higher pulmonary bacillary loads with extensive tissue damage (pneumonia). In contrast, classical Beijing 391 strain induced slower disease progression, allowing animals live up to day 60, however at this day the pulmonary histology showed necrotic areas, but with lower bacillary burdens than the animals infected with Beijing Like

first: María

middle: I

last: Cerezo-Cortés

first: Juan

last: Rodríguez-Castillo

last: López-Leal

first: Martha

last: Murcia

first: Rogelio

last: Hernández-Pando


title: RNA-seq analysis of HeLa cell lines

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

summary: We perfomed RNA-seq analysis using HPV18-postive HeLa cells for HPV integration and expression analyses

overall_design: Examination of HPV integration and expression in HeLa cell lines

first: Lulu

last: Yu

first: Alexei

last: Lobanov

first: Vladimir

last: Majerciak


title: Transcriptional regulation of cell division and cytokinin response in Arabidopsis shoot apical meristem

first: Weibing

last: Yang

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

overall_design: Refer to individual Series


title: mRNA expression profile of diesel exhaust particle treated human Wharton’s jelly-derived mesenchymal stem cells

first: Hyun Sung Park

last: Park

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea, 200 Dong 4204 Ho

department: College of Agriculture and Life Science

institute: Seoul National University

summary: We performed RNA sequencing to identify differentially expressed gene patterns between WJ-MSC treated with or without 5 µg/mL of DEP.

overall_design: Diesel exhaust particles exposure in hWJ-MSCs

first: Hyun

first: Joong

middle: W

last: Lee

first: Kyung

middle: R


title: RNA-seq analysis in breast cancer cell lines BT549 WT and SF3A3 5'UTR DSL3 edited.

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

institute: Lund University

summary: Splicing is a central RNA-based process commonly altered in human cancers; however, how the splicing machinery is co-opted during tumorigenesis remains largely unresolved. Here we identify the splice factor SF3A3 at the nexus of an oncogenic translation program that rewires splicing to promote tumorigenesis. Our results suggest that key spliceosomal networks centered on the essential core U2-associated factor, SF3A3, are exquisitely controlled at the translation level during oncogenic stress. Upon oncogene activation, SF3A3 translation is rapidly enabled via a conserved internal stem-loop structure embedded in the transcript 5’ untranslated region (UTR). Uncoupled SF3A3 translation leads to alternative splicing of several mRNAs involved in mitochondrial dynamics, and induces a metabolic switch that fuels cancer initiation properties in MYC-driven breast tumorigenesis in vivo. Finally, we compelling show that SF3A3 is post-transcriptionally altered and predicts for poor prognosis in aggressive triple negative breast cancers. Together, these findings unveil a highly dynamic regulatory network that interfaces mRNA splicing and translation to orchestrate cancer gene expression networks.

overall_design: 2 sets of samples including wild-type (WT)  and CRISPR/CAS9 edited SF3A3 5'UTR (DSL3) were included in the study. Each sample was prepared in the biologically indpendent, matched triplicates.

first: Maciej

last: Ciesla

last: Ngoc

first: Cristian

last: Bellodi


title: Targeted DMS probing of SF3A3 5' UTR

summary: To delineate the native structure of SF3A3 5'UTR, RNA was harvested from IMR90 human fibroblasts. Using specific primers and DMS-MaPSeq pipeline, we validated individual base pairing probabilities within the endogenous 5'UTR of SF3A3 (samples described as 'in vivo' transcribed). DMS-MaP-Seq  is based on the principle that DMS is highly reactive to solvent-accessible, unpaired adenine (A) and cytosine (C) residues, but remains inert toward base-paired A and C engaged in Watson-Crick interactions (Rouskin et al., 2014). Using this methodology, we identify stable stem-loop structure (SL3) positioned within SF3A3 5'UTR. To further validate the functional importance of SL3, the structural point mutant (SF3A3 5'UTR mut: A55C and U95A) and rescue (SF3A3 5'UTR res: A55C and U95A and rescuing point mutations G61U and U100G) sequences of SF3A3 5'UTR were cloned into the reporter plasmid. For the validation of these mutate-and-rescue constructs, plasmids were in vitro transcribed and either used directly (samples described as 'in vitro')  for DMS-MaP-Seq probing.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: 2 replicates for IMR90 RNA (2 specific primers for SF3A3 5'UTR) and 3 experiments for SF3A3 5'UTR WT, SF3A3 5'UTR mut, SF3A3 5'UTR res cloned into the plasmids

first: Danny

last: Incarnato


title: Transcriptional regulation of cell division and cytokinin response in Arabidopsis shoot apical meristem [ChIP-seq]

overall_design: ChIP-seq was carried out using dissected inflorescence meristems.

first: Elliot

last: Meyerowitz

first: Sandra

last: Cortijo


title: Neuroanatomy and Behaviour in Mice with a Haploinsufficiency of AT-Rich Interactive Domain 1B (ARID1B) Throughout Development

status: Public on Mar 24 2021

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

summary: Background - One of the causal mechanisms underlying neurodevelopmental disorders (NDDs) is chromatin modification, and the genes that regulate chromatin. AT-Rich Interactive Domain 1B (ARID1B), a chromatin modifier, has been shown to be reduced in autism spectrum disorder (ASD) and to affect rare and inherited genetic variation in a broad set of NDDs. Methods - A novel preclinical mouse model of Arid1b deficiency was created and validated to characterize and define neuroanatomical, behavioural and tran¬scriptional phenotypes. Neuroanatomy was assessed ex vivo in adult animals and in vivo longitudinally from birth to adulthood. Behavioural testing was also performed throughout development and tested all aspects of motor, learning, sociability, repetitive behaviours, seizure susceptibility and general milestones delays. Results – We validated decreased Arid1b mRNA and protein in Arid1b+/- mice, with signatures of increased axonal and synaptic gene expression and decreased transcriptional regulator and RNA processing expression in adult Arid1b+/- cerebellum. During neonatal development, Arid1b+/- mice exhibited robust impairments in ultrasonic vocalizations (USVs) and metrics of developmental growth. In addition, a striking sex dependence was observed throughout development; males had an early emergence of this neuroanatomical phenotype at postnatal day 7, whereas females had a delayed emergence around postnatal day 40. Behaviourally, as adults, Arid1b+/- mice showed low motor skills in open field exploration and normal three chambered approach. Arid1b+/- mice had learning and memory deficits in novel object recognition but not in visual discrimination and reversal touchscreen tasks. Social interactions in the male-female social dyad with USVs revealed social deficits on some but not all parameters. No repetitive behaviours were observed. Brains of adult Arid1b+/- mice had a smaller cerebellum and a larger hippocampus and corpus callosum. These results stand in contrast to previously reported data highlighting losses in corpus callosum volume in mice. Limitations – The behaviour and neuroimaging analyses were done on separate cohorts of mice, which did not allow a direct correlation between the imaging and behavioural findings, and the transcriptomic analyses was exploratory, with no validation of altered expression beyond Arid1b. Conclusions – This study represents a full validation and investigation of a novel model of Arid1b+/- haploinsufficiency throughout development and highlights the importance of examining both sexes throughout development in NDDs.

overall_design: Characterization of differential gene expression changes with heterozygous Arid1b knockout.

first: Jacob

last: Ellegood

first: Stela

middle: P

last: Petkova

first: Adrienne

last: Kinman

first: Lily

last: Qiu

first: Anna

last: Adhikari

first: A

last: Wade

first: Darren

last: Fernandes

first: Zsuzsa

last: Lindenmaier

first: Amie

last: Creighton

first: Lauryl

last: Nutter

first: Jill

middle: L

last: Silverman

first: Jason

last: Lerch


title: Unexpected variability of allelic imbalance estimates from RNA sequencing

first: Saumya

last: Gupta

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: RNA sequencing and other experimental methods producing large amounts of data are increasingly dominant in molecular biology. However, the noise properties of these techniques are not fully appreciated. We assessed how reproducible are the measurements of allele-specific expression between replicate RNA-seq experiments from the same RNA sample. Surprisingly, estimates of allelic imbalance (AI) varied between technical replicates up to 8-fold higher than expected from commonly applied noise models. We show that AI overdispersion substantially varies between replicates and experimental series, appears to arise during the construction of sequencing libraries, and can be measured by comparing technical replicates. We demonstrate that compensation for AI overdispersion greatly reduces technical variation and enables reliable differential analysis of allele-specific expression across samples and across experiments. Conversely, not taking AI overdispersion into account can lead to a substantial number of false positives in analysis of allele-specific gene expression.

overall_design: RNA-seq was performed in mouse kidney tissue samples and immortalised B cell line, Abl.1 and Abl.2 clonal cell lines of 129xCastF1 background [1,2]. Libraries (with replicates) were sequenced and data was analyzed. [1] Zwemer, L.M., Zak, A., Thompson, B.R., Kirby, A., Daly, M.J., Chess, A., and Gimelbrant, A.A. (2012). Autosomal monoallelic expression in the mouse. Genome Biol. 13, R10. [2] Nag, A., Savova, V., Fung, H.-L., Miron, A., Yuan, G.-C., Zhang, K., Gimelbrant, A.A., and Gingeras, T. (2013). Chromatin signature of widespread monoallelic expression. eLife 2, e01256.

first: Asya

last: Mendelevich

first: Svetlana

last: Vinogradova

first: Alexander

last: Gimelbrant


title: Chronic intermittent hypoxia enhances pathological tau seeding, propagation, and accumulation, and exacerbates Alzheimer’s-like memory and synaptic plasticity deficits and molecular signatures

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Obstructive sleep apnea (OSA), characterized by sleep fragmentation and chronic intermittenthypoxia (CIH), is a risk factor for Alzheimer’s disease (AD) progression. Recent epidemiologicalstudies point to CIH as the best predictor of developing cognitive decline and AD in elderly withOSA. However, the precise underlying mechanism(s) remain unknown. The present study wasundertaken to evaluate the effect of CIH on pathological human tau seeding, propagation, andaccumulation, cognition, synaptic plasticity, neuronal network excitability, and gene expressionprofiles in a P301S human mutant tau mouse model of AD and related tauopathies. We exposed 4-4.5-month-old, male, P301S and WT mice to an 8-week CIH protocol (6 min cycle:21% O 2 to 8% O 2 to 21% O 2 , 80 cycles per 8 h during daytime), and assessed its effect on taupathology and various AD-related phenotypic and molecular signatures. Age- and gender-matched P301S and WT mice were reared in normoxia (21% O 2 ) as experimental controls. CIH significantly enhanced pathological human tau seeding and spread across connected brain circuitry in P301S mice; it also increased phospho-tau load. CIH also exacerbated memory and synaptic plasticity deficits in P301S mice. However, CIH had no effect on seizure susceptibility and network hyperexcitability in these mice. Finally, CIH exacerbated AD-related pathogenic molecular signaling in P301S mice. CIH-induced increase in pathologic human tau seeding and spread and exacerbation of other AD- related impairments provide new insights into the role of CIH and OSA in AD pathogenesis.

overall_design: RNA-seq of WT Normoxia, WT Hypoxia, P301S Normoxia and P301S Hypoxia mice samples

first: Syed

middle: F

last: Kazim

first: Abhijeet

last: Sharma

first: Sivaprakasam

last: Saroja

first: Ana

last: Pereira


title: Repeat RNAs associate with replication forks and post-replicative DNA [short]

first: Helene

last: Gylling

overall_design: Cells were synchronized, released and harvested at 3 different time points (0, 2 and 10h) measured from 3 hours post cell release into S-phase. Input samples were taken at each time-point and every sample was produced in biological triplicates. 3/4 of samples were labeled with biotin dUTP (b-dUTP) each of which was harvested at different time points and 1 sample was harvested at t=0 and used for Histone3 and Streptavedin pull-down.

middle: M

first: Cristina

last: Gonzalez-Aguilera

first: Dominik

last: Kaczorowski

first: Martin

last: Smith

first: Anja

last: Groth

first: Anders

last: Lund


title: Skin and blood expression data from psoriasis patients treated with secukinumab

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM


title: MyD88/IL-1R axis sustains immunosuppressive function of TAMs by regulating PD-1 expression in melanoma

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Macrophages are critical mediators of tissue homeostasis, cell proliferation, angiogenesis and tumor metastasis. The presence of TAMs is generally associated with tumor-promoting immunosuppressive function in solid tumors. These macrophages are widely acknowledged as one of the central suppressive populations within tumors, blocking effective T-cell responses. In the present study, we examined the transcriptional landscape of adaptor molecules downstream of TLRs in human cancers and found that higher expression of MYD88 is very well correlated with the tumor progression. In addition, we also found that mouse MyD88 but not TRIF, is essential for tumor progression and angiogenesis in melanoma. Interestingly, MyD88 is critical to maintain the immunosuppressive phenotype of TAMs in the tumors. Moreover, we found that interleukin-1 receptor (IL-1R)-Myd88 axis regulates programmed cell death (PD)-1 expression on TAMs by promoting the recruitment of phospho-NF-κB p65 to the CR-C region of the Pdcd1 promoter. Using myeloid-cell specific MyD88 mutant mice, we also showed that MyD88 expression in myeloid cells alone is sufficient to drive the melanoma progression. Thus, IL-1R/MyD88 axis maintains the immunosuppressive function of tumor-tissue macrophages to promote tumor growth by regulating PD-1/PD-L1 expression

overall_design: We used microarrays to compare the global transcription profiles of tumor-associated macrophages (TAMs) from WT and MyD88-null mice after engraftment of B16-F10 melanoma cells

first: Tartey

last: Sarang

first: Peter

last: Vogel

first: Kannaganti

last: Thirumala-Devi


title: Blood expression data from psoriasis patients treated with secukinumab

summary:
Psoriasis is a common chronic inflammatory skin disease where IκBζ is known to play an important role by mediating IL-17A-driven effects. However, the molecular mechanism by which IL-17A regulates IκBζ expression is not known.
We assessed global gene expression my microarray analysis to explore the molecular transformation in blood samples from psoriatic patients during anti-IL-17A (secukinumab) treatment.

overall_design: Blood samples were taken from psoriatic patients before secukinumab treatment (day 0) and at day 4, 14, 42 and 84 during secukinumab treatment. PBMCs were isolated from the blood and RNA extracted and used for microarray analysis.

first: Claus

last: Johansen

first: Trine

last: Bertelsen

first: Lars

last: Iversen


title: Screen a novel biomarker in DLBCL by using microarray analysis

city: Suzhou

first: Zhuang

last: Wenzhuo

state: Jiangsu

address: Ren Ai Road 199

institute: Soochow University

summary: Diffuse large B-cell lymphoma (DLBCL) represents the most common subtype of malignant lymphoma and is heterogeneous with respect to morphology, biology, and clinical presentation.However, a robust prognostic factor based on cell biology of DLBCL has not yet been determined.To find the biomarker which may associate with clinical outcome in patients with DLBCL, microarray analysis was performed to screen a novel biomarker.

overall_design: 6 DLBCL samples from patients of various ages were selected for RNA extraction and hybridization on Affymetrix HTA2.0 Array.

first: Wenzhuo

last: Zhuang

first: Bingzong

last: Li


title: Transcriptomic analysis for understanding differential gene expression upon FKBP5 knockdown

city: Kolkata

first: Abhishake

last: Lahiri

address: 4, Raja S. C. Mullick Road

country: India

institute: CSIR-Indian Institute of Chemical Biology

summary: To investigate differentially expressed genes in HEK293T cells upon FKBP5 knockdown (n =2, reported in this study) and control scramble (n=2) (reported earlier Yadav et al., Cell Reports 2019, NCBI Genbank SRA accession no. PRJNA512165) using total RNA extracted from HEK293T cells and analysed by RNA-seq.

overall_design: We created stable FKBP5 knockdown cells using specific shRNAs. Total RNA were extracted from these cells and used for downstream RNA-Seq analyses.

first: Debabrata

last: Biswas


title: HMGB1 and Alu-siRNA inhibit the growth of human lung tumor cells

city: Bangkok

first: Warayupa

last: Thompat

address: Praram 4

country: Thailand

institute: Chulalongkorn University

summary: We performed expression profiling using microarray technology. The expression profiling identified genes or mechanism potentially regulating the proliferation of human lung cancer cells by BoxA of HMGB1 and Alu-siRNA transfection. The RNAs of our experiment were hybridized with Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®).

overall_design: Two type of human lung cancer cell lines (H1650 and H1975) and embryonic kidney cell line (HEK-293) were transfected with BoxA of HMGB1 and siRNA-Alu, plasmid control and mock were represented internal control. The cells were harvested after transfection for 4 hour.

first: Apiwat

last: Mutirangura


title: Gene expression profile in E2F1 and E2F2 deficient mice treated with the procarcinogen agent diethylnitrosamine and fed a high fat diet

city: Leioa

first: Patricia

last: Aspichueta

address: Barrio Sarriena s/n

department: Physiology

country: Spain

institute: University of the Basque Country UPV/EHU

summary: To investigate mechanism involved in the development of NAFLD-driven hepatocarcinoma (HCC), we used genome microarray expression profiling. The aim was to identify genes which upregulation could be controlled by E2F1 and/or E2F2 in NAFLD -driven HCC. For that, HCC was induced in wild type (WT), E2f1 knockout mice (E2f1-/-) and E2f2 knockout mice (E2f2-/-) by administration of the procarcinogenic agent diethylnitrosamine (DEN) combined with a feeding of high fat diet (HFD) for 32 weeks.The microarray results were then validated by RT-qPCR. For that, the expression of the selected genes (some overexpressed, some downregulated and others with no change) was measured in the same RNA samples by real time PCR. The results were clustered in pathways with the Reactome Database.

overall_design: The differential gene expression associated to HCC development was measured in livers of WT,  E2f1-/- mice, and E2f2-/- mice treated with DEN and fed a HFD. An n of 4 mice was used in each group

first: Daniela

last: Mestre

first: Beatriz

last: Gómez

first: Igor

last: Aurrekoetxea

first: Diego

last: Saénz de Urturi

first: Maitane

last: Núñez-García

first: Juan

last: Rodríguez-García

first: Francisco

last: González-Romero

first: Larraitz

last: Fernández-Ares

first: Xabier

last: Buqué

first: Ainhoa

last: Iglesias

first: Irantzu

last: Bernales

first: Ana

last: Zubiaga


title: RNA-seq analysis of BT549 cells based on SIK2 knockdown

city: Chang Sha

first: zhuoxian

last: rong

state: Hu Nan

address: Xiangya road 87th

institute: central south universty

summary:
Purpose: Analysis of the regulatory network involved in SIK2 in breast cancer cells activated by the Wnt/β-catenin pathway.
Methods: mRNA profiles of BT549-shSIK2 and BT549-Scrambled group that Wnt3a treated for 2 hours were generated by deep sequencing,  using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets.
Results: We identified 1709 differential genes, of which 1147 were up-regulated and 562 were down-regulated. In GO enrichment analysis, the biological process is mainly in the cell ions homeostasis, the cell components are mainly enriched on the cell surface, and the molecular function is mainly in the transmembrane signaling receptor activity. KEGG analysis shows that differential genes are enriched in Axon guidance and Nicotinate and nicotinamide metabolism pathways.
Conclusion: Based on RNA-seq analysis, the regulatory network involved in SIK2 in breast cancer response to Wnt signaling is depicted.

first: Zhuoxian

last: Rong

first: Yuezhen

last: Deng

first: Xinxin

last: Ren

first: Lunquan

last: Sun


title: MicroRNA profiling of retinoic acid-induced myogenic tongue abnormalities in fetal mice

city: Dalian

first: Bo

last: Liu

address: 9 Western Section, Lvshun South Street

institute: Dalian Medical University

summary: In this study present here, we established RA-induced tongue abnormal mice model,  muscle samples acquired from the tongue body and genioglossus of fetuses on E15.5 was used to get differently expressed miRNA in RA-induced group, then validated by qRT-PCR, futher analysis was conducted by bioinformatics method.

overall_design: 6 samples, 3 RA-treated and 3 controls

first: Jing

last: Xiao

first: Wei

last: Cong


title: Transcriptional silencing of ALDH2 confers a dependency on Fanconi anemia proteins in acute myeloid leukemia

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: With domain focused CRISPR screen, we revealed Fanconi anemia (FA) proteins UBE2T (an E2) and FANCL (an E3) as unique dependencies in AML. We demonstrate that these dependencies are due to a synthetic lethal interaction between FA proteins and Aldehyde Dehydrogenase 2 (ALDH2), which function in parallel pathways to counteract the genotoxic effects of endogenous aldehydes. We provide evidence that DNA hypermethylation and transcriptional silencing of ALDH2 occur in a recurrent manner in human AML patient samples, which is sufficient to confer FA pathway dependency in this disease. Taken together, our study suggests that targeting of the ubiquitination reaction catalyzed by FA proteins can eliminate ALDH2-deficient AML.

overall_design: Gene expression profiling upon CRISPR knockout or cDNA overexpression

first: Zhaolin

last: Yang

middle: S

first: Christopher

last: Vakoc


title: Next generation sequencing to assess prenatal exposure to aerosols of paraquat and TiO2 nanoparticles on the gene expression of the developing brain

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

institute: IGFL-ENS

summary: Nanopesticides (NPe) are innovative pesticides involving engineered nanomaterials (ENM) to increase the efficiency of plant protection products. However, no toxicological data is available on their inhalation toxicity and the potential cocktail effects between pesticide active substances and ENM. In particular, the neurodevelopmental toxicity of prenatal repeated exposures has not been specifically evaluated. To this end, C57Bl/6j gestating mice were exposed to aerosols in an ad hoc whole-body exposure chamber. Exposures consisted in low repeated doses of the paraquat herbicide (PQ), and/or TiO2 nanoparticles (nTiO2). The monitoring of aerosol characteristics, in addition to their prior metrological characterization, enabled a precise estimation of the exposure doses received by animals, which can be extrapolated to the recommended exposure limit proposed by health agencies. We used RNA-seq to assess the gene expression in pups striatum at post-natal stage, in order to highlight possible neurodevelopmental alterations. This sensitive method revealed that both PQ and nTiO2 aerosols had a significant effect on the gene expression of the offspring, highlighting dysregulations of oligodendrocyte differentiation and neuronal maturation. Exposure to the nTiO2 aerosol modulated notably the regulation of neurotransmitters pathway being possibly indirect consequences of a minor change in the neuroinflammation state. No synergy was found between the PQ + nTiO2. Instead, the neurodevelopmental effects were surprisingly lower than the one measured for each substance separately.

overall_design: Exposure of C57Bl/6J gestating mice to aerosols and assessment of the pups striatum transcriptome at post-natal stage to highlight possible neurodevelopmental alterations

first: Quentin

last: Hamdaoui

last: Zekri

first: Frédéric

last: Flamant


title: Cepba dependent gene expression in hematopoietic progenitors from mice treated with interleukin-1

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: We analyzed gene expression in Cebpa+/+ or CebpaΔ/Δ  multipotent progenitors (MPP3) from mice treated with or without interleukin-1-beta.

overall_design: We competitively transplanted sorted hematopoeitic progenitor cells from donor Cebpa+/+ or CebpaΔ/Δ mice with C57BL/6 (CD45.2) competitor bone marrow into congenic Boy/J recipient mice. We isolated both donor and competitor-derived multipotent progenitors (MPP3) from recipient mice. Recipient mice were treated +/- interleukin-1-beta for 20 days, MPP3 sorted, RNA isolated, and RNA sequencing (RNA-seq) performed.

first: Kelly

last: Higa

first: Eric

last: Pietras

first: James

last: DeGregori


title: Analysis of Wild Type, H-NS KO and cover mutated H-NS Transcriptomes

city: Tianjin

first: Hanyang

last: Dong

state: Tianjin

address: Tianjin Medical university

institute: Tianjin Medical university,China

summary: The goals of this study are to compare the difference transcriptome of Wild Type, H-NS KO and cover mutated H-NS by RNA-seq

overall_design: Retinal mRNA profiles of Wild Type, H-NS KO and cover mutated


title: Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants [ChIP-Seq]

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

institute: University of Edinburgh

summary: Point mutations within the histone H3.3 are frequent in aggressive childhood brain tumours known as paediatric high-grade gliomas (pHGGs). Intriguingly, different mutations arise in discrete anatomical regions: H3.3-G34R within the forebrain and H3.3-K27M preferentially within the hindbrain. The reasons for this contrasting aetiology are unknown. By engineering human foetal neural stem cell cultures from distinct regions, we demonstrate here that cell-intrinsic regional identity provides differential responsiveness to each mutant that mirrors the origins of pHGGs. Focusing on H3.3-G34R, we find that the oncohistone supports proliferation of forebrain cells, while inducing a cytostatic response in the hindbrain. Mechanistically, H3.3-G34R does not impose widespread transcriptional or epigenetic changes, but impairs recruitment of ZMYND11, a transcriptional repressor of highly expressed genes. We therefore propose that H3.3-G34R promotes tumorigenesis by stabilising the expression of key progenitor genes and, thus, locking initiating forebrain cells into their preexisting immature state.

overall_design: Mapping genome-wide distribtuition of H3K4me3, H3HK27me3, H3K36me3, H3.3-G34R (endogenous) and V5-H3.3 (wild-type and G34R-mutant, ectopically expressed) in the H3F3A G34R-mutant paeditric glioblastoma cells (Parental pGBM002 and H3F3A-G34R CRISPR ablated pair)

first: Raul

middle: B

last: Bressan

first: Benjamin

first: Steven

last: Pollard


title: Single cell RNA-sequencing (scRNA-seq) of the human hematopoietic stem cell compartment (CD34+CD38-CD45RA-)

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: To identify a trajectory of human hematopoietic stem cell (HSC) activation we performed scRNAseq of CD34+CD38—CD45RA—cells from G-CSF-mobilized peripheral blood from 3 donors. We show that INKA1 and CDK6/PAK4 expressing single cells segregate across alternative states of quiescence.

overall_design:
Single cell gene expression profiling of RNA from human HSC was performed by flow cytometry-based single cell deposition of CD34+CD38—CD45RA—cells from G-CSF-mobilized peripheral blood from 3 individual donors and 1 bone marrow donor in concert with single cell index-sorting (signals indexed: CD34, CD38, CD45RA, CD90, CD49f) and followed by SMARTseq2  based protocol.

>>>Submitter states that raw data will be submitted to EGA due to data access requirements.<<<

first: Kerstin

last: Kaufmann

first: Efthymia

last: Papalexi

first: Andy

last: Zeng

first: Rahul

last: Satija

first: John

middle: E

last: Dick


title: Effect of Notch1 on gene expression profiles of mouse decidua on E7.5 of first and subsequent pregnancies

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

summary:
Decidualization is one of the most important processes during female reproduction, decidualization was regulated differently in first and subsequent pregnancies
Notch1 affects decidualization of mouse uterine stromal cells, but the mechanisum under is still unclear

overall_design: Decidua tissues of mouse uterine endometrium were collected on E7.5 of 1st or 4th pregnancy, from both Notch1 uterine specific knockout (PgrCre/+Notch1f/f) and control (Pgr+/+Notch1f/f) mouse


title: MBNL1 and RBFOX1 co-regulate alternative splicing events transcriptome-wide through a conserved buffering mechanism

city: Gainesville

first: Joseph

middle: Anthony

last: Ellis

state: FL

address: 1200 Newell Drive, ARB R3-234

institute: University of Florida

summary: Alternative splicing (AS) is an important component of RNA processing controlled by cis- and trans-acting component. Here we investigate modes and mechanisms of AS co-regulation by MBNL1 and RBFOX1. We generated two cell models (human and mouse) whereby the expression of both RBPs can be independently modulated and utilize these cell lines to perform RNAseq and transcriptome wide alternative splicing analysis. Categorization of alternative splicing outcomes of the impacts of RBFOX1 expression on MBNL1 splicing revealed a common co-regulatory mode whereby RBFOX1 buffers MBNL1 dose-dependent splicing regulation by reducing the total range of exon inclusion induced. Overall, our studies define a conserved co-regulatory mechanism through which RBFOX1 and MBNL1 can fine-tune and provide redundancy for AS outcomes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Analysis of alternative splicing changes in the presence or absence of MBNL1 and RBFOX1 in human embyonic kidney and mouse embryonic fibroblasts

middle: A

first: Ryan

last: Meng

first: Jared

last: Richardson


title: Next Generation Sequencing Analysis of Wild Type and SESAME Transcriptomes II

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: The purpose is to analyze the effect of SESAME complex on gene transcription

overall_design: The mRNA profiles of control, serine treatment, wild type (WT), CK2, YBL574, H3T11A mutant were generated by deep sequencing, in duplicate. Technical replicates were made by producing another library from the same RNA extraction.

first: Shanshan

last: Li


title: Next Generation Sequencing Analysis of Wild Type and SESAME Transcriptomes I

overall_design: The mRNA profiles of wild type (WT),  acs2-ts, sam1, ser33, shm2, pyk1, were generated by deep sequencing, in duplicate.  Technical replicates were made by producing another library from the same RNA extraction.


title: Monocyte Heterogeneity and Distinct Monocyte Subsets in Kawasaki Disease Revealed by scRNA-seq

city: Hangzhou

first: Fangqi

last: Gong

address: Binsheng Road

institute: Children's Hospital, Zhejiang University School of Medicine

summary: Kawasaki disease (KD) is characterized by a disorder of immune response, and its etiology remains unknown. Monocyte is an important member of body's innate immune system, however its role in KD is still elusive due to its ambiguous heterogeneity and complex functions. Here, scRNA-seq was performed to reveal monocytes heterogeneity in healthy and KD infants. Circulating monocytes were separated from peripheral blood and scRNA-seq was used to transcriptionally profile the monocytes in both healthy and KD infants. Four monocyte subsets are identified in infants, in which three clusters are mainly CD14+CD16- monocytes and one cluster is mainly CD14-CD16+ monocytes. The four monocyte subsets possess different biological functions and represent a relatively linear differentiation. CD14+ monocyte subsets in KD are distinct from that of healthy infants, including one subset expressing FOLR3, S100A12 and IL1R2 and the other expressing MT-TN specifically. Moreover, the CD14+ monocyte subsets in KD are poorly differentiated, and their functions mainly involve neutrophil activation. In conclusion, a relatively comprehensive map of circulating monocyte subsets was plotted for the first time in healthy infants. CD14+ monocyte subsets that are distinct from healthy infants were revealed in KD, which may serve as a target for KD treatment in the future.

overall_design: scRNA-Seq of enriched monocytes in 2 healthy infants and 2 KD infants

first: Zhimin

last: Geng


title: B2 and B3 Raf-like protein kinases activate SnRK2s and are essential for abscisic acid signaling

city: Shanghai

first: Xiaolei

last: Liu

address: Chenhua Road 3888

institute: Chinese Academy of Sciences

summary: m9 was identified to function in ABA signaling pathway and we applied RNAseq assay to identify ABA induced and repressed genes in m9

overall_design: mRNA profiles of 12-day old m9 and wild type arabidopsis seedlings with or without ABA treatment were generated by deep sequencing, in triplicate.

first: Pengcheng

last: Wang


title: CUL4B ChIP-sequencing in non-treated  MDA-MB-231 cells

city: Beijing

first: Yan

address: No. 10, Xitoutiao, You An Men, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: Capital Medical University

summary: Cullin 4B (CUL4B) is a scaffold protein of the CUL4B-Ring E3 ligase (CRL4B) complex. Here, we found that CRL4B interacted with transcriptional corepressor complexes. Our results supporting CUL4B as a potential target of cancer therapy.

overall_design: Examination of CUL4B target genes in MDA-MB-231 cell line.

first: Wei

last: Huang


title: Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Despite recent improvements in management of idiopathic pulmonary arterial hypertension, mortality remains high. Understanding the alterations in the transcriptome–phenotype of the key lung cells involved could provide insight into the drivers of pathogenesis. In this study, we examined differential gene expression of cell types implicated in idiopathic pulmonary arterial hypertension from lung explants of patients with idiopathic pulmonary arterial hypertension compared to control lungs. After tissue digestion, we analyzed all cells from three idiopathic pulmonary arterial hypertension and six control lungs using droplet-based single cell RNA-sequencing. After dimensional reduction by t-stochastic neighbor embedding, we compared the transcriptomes of endothelial cells, pericyte/smooth muscle cells, fibroblasts, and macrophage clusters, examining differential gene expression and pathways implicated by analysis of Gene Ontology Enrichment. We found that endothelial cells and pericyte/smooth muscle cells had the most differentially expressed gene profile compared to other cell types. Top differentially upregulated genes in endothelial cells included novel genes: ROBO4, APCDD1, NDST1, MMRN2, NOTCH4, and DOCK6, as well as previously reported genes: ENG, ORAI2, TFDP1, KDR, AMOTL2, PDGFB, FGFR1, EDN1, and NOTCH1. Several transcription factors were also found to be upregulated in idiopathic pulmonary arterial hypertension endothelial cells including SOX18, STRA13, LYL1, and ELK, which have known roles in regulating endothelial cell phenotype. In particular, SOX18 was implicated through bioinformatics analyses in regulating the idiopathic pulmonary arterial hypertension endothelial cell transcriptome. Furthermore, idiopathic pulmonary arterial hypertension endothelial cells upregulated expression of FAM60A and HDAC7, potentially affecting epigenetic changes in idiopathic pulmonary arterial hypertension endothelial cells. Pericyte/smooth muscle cells expressed genes implicated in regulation of cellular apoptosis and extracellular matrix organization, and several ligands for genes showing increased expression in endothelial cells. In conclusion, our study represents the first detailed look at the transcriptomic landscape across idiopathic pulmonary arterial hypertension lung cells and provides robust insight into alterations that occur in vivo in idiopathic pulmonary arterial hypertension lungs.

overall_design:
This study utilized the 10X Genomics platform and single cell RNA-Seq 3PrimeV1 and 3PrimeV2 chemistries. The gene expression of the lung tissue of patients with idiopathic pulmonary arterial hypertension (IPAH) was compared to healthy donor control lung tissue.  Single-cell suspensions from three IPAH patient lungs were prepared and subsequently loaded into the Chromium Single cell controller (10x Genomics). Single cell RNA-seq libraries were generated from the IPAH lung suspension and, following  sequencing, these were then compared to already published normal control data.
*** For the control samples, raw data are unavailable due to patient privacy concerns.

first: Didem

last: Saygin

first: Humberto

last: Bittar

first: Eleanor

last: Valenzi

last: Sembrat

first: Stephen

middle: Y

last: Chan

first: Mauricio

last: Rojas

first: Robert

last: Lafyatis


city: Linhai

first: Xuejiao

last: Chen

address: chichen

institute: Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University

summary:
Potocki-Shaffer syndrome (PSS) is a rare contiguous gene deletion syndrome marked by haploinsufficiency of genes in chromosomal region 11p11.2p12. Approximately 50 cases of PSS have been reported; however, a syndrome with a PSS-like clinical phenotype caused by 11p11.12p12 duplication has not yet been reported. We first report the 11p11.12p12 duplication in a family with intellectual disability and craniofacial anomalies.
11p11.12p12 duplication syndrome was identified by karyotype analysis. Next-generation sequencing (NGS) analysis clarified the location of the chromosomal variations, which was confirmed by chromosome microarray analysis (CMA). Whole-exome sequencing (WES) was performed to exclude single nucleotide variations (SNVs). The raw data of NGS analysis and WES have been submitted to SRA, the accession number is PRJNA713823.

overall_design:
Karyotype analysis was performed in 6 main members of the family to identify the 11p11.12p12 duplication syndrome genetic aetiology. 11 members of the family underwent next-generation sequencing analysis, which was also performed in 7270 pregnant women to detect chromosomal microdeletions and microduplications for prenatal diagnosis. CMA was used to confirm the location of the chromosomal variations in the family and detect chromosomal microdeletions and microduplications in 2906 pregnant women for prenatal diagnosis. Whole-exome sequencing (WES) was performed to exclude single nucleotide variations (SNVs).
In order to be scientifically rigorous and avoid methodological differences, we used chromosome microarray analysis to confirm the the chromosomal variation sites of two samples with clinical phenotypes in the family.

first: Meizhen

last: Dai


title: Hepatic fat accumulation regulates somatic growth through lipid-based energy metabolism in tadpoles of wood frog (Rana omeimontis)

city: Chengdu

first: Liming

last: Chang

state: Sichuan

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

institute: Chengdu Institute of Biology

summary: In this part, we compared the transcriptional profiles before and after hepatic fat accumulation.

overall_design: Comparative transcriptomics of the liver at different physiological status.

first: Chang

last: Liming

first: Zhu

last: Wei

first: Wang

last: Bin

first: Jiang

last: Jianping

first: Zhao

last: Tian

last: Chunlin

first: Shu

last: Guocheng

last: Xungang

first: Xie

last: Feng

first: Li

last: Cheng


title: Epigenetic variability among saffron crocus (Crocus sativus L.) accessions characterised by different phenotypes

city: Piacenza

first: Marcello

last: Del Corvo

address: Via Emilia Parmense, 84

department: Institute of Zootechnics, Faculty of Agricultural, Food and Environmental Sciences

country: Italy

institute: Università Cattolica del S. Cuore

type: Genome variation profiling by high throughput sequencing

summary: This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.

overall_design: Epigenetic profiles of five accessions of saffron crocus, showing differences in tepal pigmentation, yield of saffron and flowering time.

first: Matteo

last: Busconi

first: Elisabeth

last: Wischnitzki

first: Licia

last: Colli

first: Giovanna

last: Soffritti

first: Lorenzo

last: Stagnati

first: Silvia

last: Fluch

first: Eva

last: Sehr

first: Marcelino

last: de los Mozos Pascual

first: José

last: Fernández


title: CircSPI1 functions as an oncogene through antagonizing SPI1 and interacting with microRNAs in acute myeloid leukemia

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

institute: SHANGH RUIJIN HOSPITAL

summary: Background: Strict control of PU.1, encoded by SPI1, is importmant for myeloid development, and inhibition of PU.1 expression and activity, even moderate, can lead to acute myeloid leukemia (AML). Much effort has focused on regulatory elements at the SPI1 locus on controlling PU.1. Discovery of circular RNAs (circRNAs), a novel class of noncoding regulators, has raised additional questions regarding their impacts on PU.1 and the development of AML. Methods: We used the pan-cancer circRNA compendium MiOncoCirc to investigate the existence and expression pattern of circSPI1s. We designed short hairpin RNAs (shRNAs) targeting the back-spliced site to silence circSPI1 and then performed CCK8 proliferation assay, flow cytometry analysis and Wright-Giemsa stain to explore the function of circSPI1. We performed RNA-sequencing with and without circSPI1 knockdown, western bloting and luciferase assay to explore the potential mechanisms. We utilized machine learning techniques and integrated bioinformatic analysis to evaluate the prognostic value of circSPI1 for AML, based on TCGA and BeatAML cohorts. Results: We found that circSPI1, the circular RNA derived from the SPI1 gene (encoding PU.1), was highly expressed in AML than that in normal counterparts. Functional experiements showed circSPI1 acted as an oncogene, as evidenced by the observation that circSPI1 knockdown induced myeloid differentiation and apoptosis of AML cells. This was different from the parental gene SPI1 that is generally low expressed in AML and functions as a tumor suppressor. Mechanistic investigations revealed that circSPI1 exerted multiple regulatory roles in AML progression. On one hand, circSPI1 contributed to the orchestrated differentiation of AML cells by antagonizing SPI1 expression. On the other hand, circSPI1 was involved in proliferation and apoptosis by interacting with microRNAs miR-1307-3p, miR-382-5p and miR-767-5p, which was uncoupled with SPI1. Finally, circSPI1-regulated genes were associated with the clinical outcome of AML patients, implicating the clinical significance of circSPI1 in AML. Conclusions: We demonstrate that highly expressed circSPI1 acts as an oncogene in  AML, through both antognizing PU.1 expression and binding to microRNAs that is independent to PU.1. Our data provide new insight into complex SPI1 gene regulation now involving cicrSPI1 as well as the independent role of cicrRNA in AML.

overall_design: Expression profiling of NB4 cells before and after circSPI1 knockdown using RNA-seq.

last: Kankan

first: Waang

last: Xiaoling

first: Jin

last: Peng


title: RNA-Seq analysis EIF5A2 knockdown effect on ovarian cancer cells

city: Jinan

first: Kun

last: Wang

address: WenHua west road 107

institute: Shandong University qilu hospital

summary: Eukaryotic initiation factor 5A2 (EIF5A2) acts as a candidate oncogene and is located on human chromosome 3q26, a region frequently amplified in several tumors. Accumulating evidence shows that EIF5A2 plays important roles in enhancing anchorage-independent growth, xenograft tumour growth, increasing cancer cell metastasis and promoting treatment resistance through multiple pathways. Here, we showed that EIF5A2 knockdown reduced the expression of KLF4, which could partially rescue stem-like properties abolished by EIF5A2 knockdown or strengthened by EIF5A2 overexpression, through the transcription factor E2F1, which directly bind to KLF4 promoter.

overall_design: Si-EIF5A2 or NC were transfected into SKOV3 cells (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: W

last: Kun

first: Y

last: Xingsheng


title: Expression profiles of circularRNAs and microRNAs in PK-15 cells infected by PrV-II

first: Haimin

last: Li

state: zhejiang

address: yuhangtang Road

department: College of Animal Science

institute: Zhejiang University

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) and microRNAs (miRNAs) participate in regulating many biological processes. However, their roles in PrV-II pathogenicity are largely unknown. Here, we analyzed the expression profile of circRNAs and miRNAs in the PrV-DX, a wild-type (WT) strain of PRV-II, and its attenuated gE-TK- PRV-DX infected cells by high-throughput sequencing.

overall_design: Expression profiles of circRNAs and miRNAs in  PRV-DX, gE-TK-PRV-DX or MOCK infected PK-15 cells were generated by deep sequencing, in duplicates, using Illumina Hiseq 4000.

first: Yulan

first: Jiyong

last: Zhou


title: Transcriptomic changes driven by oncogenic kinases

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: Transcriptomic changes were compared by RNA-seq in human mammary epithelial cells (HMECs) with or without ectopic expression of oncogenic kinase HER2, PI3KCA(mut), or SHP(mut).

overall_design: RNA seq were performed in four engineered cell lines: HMEC-DD-pBABE, HMED-DD-pbabe-HER2; HMEC-DD-PI3KCA(H1047R), and HMEC-DD-SHP2(E76A). Three independent experiments were performed In each cell line.

first: E

last: Hazard

first: Qi


title: Gene expression profile of MDA-MB-231 breast cancer cells with BRCA1 pseudogene (BRCA1P1) knockout (KO)

city: Chicago

first: Yoo-Jeong

last: Han

state: IL

address: 900E. 57th street

institute: University of Chicago

summary: Analysis of genes influenced by knockout of BRCA1P1 in MDA-MB-231 cells using CRISPR-Cas9

overall_design: Total RNA obtained from MDA-MB-231 cells with wild type or BRCA1P1-KO

first: Olufunmilayo

last: Olopade


title: Gene expression profile of breast cancer cells depleted for BRCA1 pseudogene (BRCA1P1)

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

overall_design: Refer to individual Series


title: Genome-wide maps of Dnmt1-dependent DNA methylome in adipocytes

city: Seoul

first: Yoon Jeong

last: Park

address: San 56-1, Sillim-Dong, Gwanak-Gu

institute: Seoul National University

type: Methylation profiling by high throughput sequencing

summary: White adipose tissue (WAT) is a key regulator of systemic energy metabolism, and impaired WAT plasticity characterized by enlargement of preexisting adipocytes associates with WAT dysfunction, obesity and metabolic complications. However, the mechanisms that retain proper adipose tissue plasticity required for metabolic fitness are unclear. Here, we comprehensively showed that adipocyte-specific DNA methylation, manifested in enhancers and CTCF sites, directs distal enhancer-mediated transcriptomic features required to conserve metabolic functions of white adipocytes. Particularly, genetic ablation of adipocyte Dnmt1, the major methylation writer, led to increased adiposity characterized by increased adipocyte hypertrophy along with reduced expansion of adipocyte precursors (APs). These effects of Dnmt1 deficiency provoked systemic hyperlipidemia and impaired energy metabolism both in lean and obese mice. Mechanistically, Dnmt1 deficiency abrogated mitochondrial bioenergetics by inhibiting mitochondrial fission and promoted aberrant lipid metabolism in adipocytes, rendering adipocyte hypertrophy and WAT dysfunction. Dnmt1-dependent DNA methylation prevented aberrant CTCF binding and, in turn, sustained the proper chromosome architecture to permit interactions between enhancer and dynamin-related protein gene Drp1 in adipocytes. Also, adipose DNMT1 expression inversely correlated with adiposity and markers of metabolic health, but positively correlated with AP-specific markers in obese human subjects. Thus, these findings support strategies utilizing Dnmt1 action on mitochondrial bioenergetics in adipocytes to combat obesity and related metabolic pathology.

overall_design: DNA methylation profiles of primary adipocytes from wild type (WT) and adipocyte-specific Dnmt1 knockout (Dnmt1 AKO) mice. Expression profiling by high throughput sequencing of primary adipocytes from WT mice.

first: Jae-Bum

last: Kim


title: A genome-wide exploration of the targets of the transcription factors FOXL2 and ESR2 unveils their implication in cell migration, invasion and adhesion [ChIP-Seq]

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

institute: CNRS/Université Paris Cité

summary: To explore what FOXL2-dependent changes of gene expression observed in our RNA-seq data were directly related to FOXL2 binding, we performed ChIP-seq analysis in FOXL2-expressing granulosa cells (two data points). To explore the potential co-regulation between FOXL2 and ESR2 of several targets, we knocked-down Esr2 in granulosa cells and performed a ChIP-seq under the same conditions as those previously described for FOXL2.

overall_design: We performed ChIP-seq analysis in FOXL2-expressing granulosa cells (two data points).

first: Laëtitia

last: Herman

first: Anne

first: Reiner

last: Veitia


title: The subcellular redistribution of NLRC5 promotes angiogenesis via interacting with STAT3 in endothelial cells

first: Yefei

last: Shi

address: 1239 Siping Road

institute: Tongji University School of Medicine

summary: We investigated the role of NLRC5 in the endothelial cells (ECs) and in-vivo angiogenesis. The results showed that the deficiency of NLRC5 decreased angiogenesis in vitro and vivo.And the subcellular redistribution of NLRC5 was regulated by VEGFA-165. RNA-seq and Co-IP indicated the potential relationship of NLRC5 and STAT3. ChIP assay determined that the mRNA expression of  angiopoietin-2 (Ang2) and cyclin D1 (CCND1) were orchestrated by the interaction of NLRC5 and STAT3.

overall_design: RNA sequencing was performed after the following treatments: human umbilical vein endothelial cells were transfected with siRNA (siNLRC5 or negative control, 50 nM) for 48 h. After starvation for 12 h, VEGFA-165 (50 ng/mL) was used to stimulate HUVECs for 12 h.

first: Xu

last: Xu

first: Peipei

last: Luan

first: Wenxin

last: Kou

first: Bo

first: Ming

last: Zhai

first: Shuangjie

last: You

first: Qing

last: Yu

first: Jianghui

last: Zhuang

first: Weixia

last: Jian

first: Mark

last: Feinberg

first: Wenhui


title: A genome-wide exploration of the targets of the transcription factors FOXL2 and ESR2 unveils their implication in cell migration, invasion and adhesion [RNA-Seq]

summary: We depleted Foxl2 or Esr2 in murine primary granulosa cells and assessed the molecular consequences at the transcrit levels. We show that FOXL2 is involved in a large number of regulatory actions essential for the maintenance of cell fate of granulosa cells. We confirm that FOXL2 and ESR2 modulate, directly of through a coherent feed-forward loop, an important number of common targets.

overall_design: Single Read 75pb runs, on an Illumina NextSeq500 instrument, using NextSeq 500 High Output 75 cycles kits

last: HERMAN

last: TODESCHINI

last: VEITIA


title: A genome-wide exploration of the targets of the transcription factors FOXL2 and ESR2 unveils their implication in cell migration, invasion and adhesion


title: Transcriptome characterization of human periodontal ligament cell clones (DMEM medium)

city: Campinas

first: Luciana

middle: Souto

last: Mofatto

state: Sao Paulo

address: R. Carl Von Linaeus

department: Genetics, Evolution and Bioagents

country: Brazil

institute: Institute of Biology - University of Campinas

summary: we isolated single-cell-derived clones and evaluated their potential to differentiation into osteo/cementoblastic (O/C) phenotype (C-O clones) or fibroblastic phenotype (C-F clones) in vitro, and evaluated the transcriptomic profile of the groups of clones in standard medium cultivation (without O/C induction medium), using next-generation sequencing technology (RNA-seq).

overall_design: 2 clones of each phenotype [osteo/cementoblastic (O/C) phenotype (C-O clones) or fibroblastic phenotype (C-F clones)] were compared

first: Miki

middle: T

last: Saito

first: Francisco

middle: H

last: Nociti-Jr

first: Karina

middle: G

last: Silvério


title: Arabidopsis thaliana KO1 and KO3 deletion lines of the selective autophagy receptor AtNBR1 - roots and shoots

status: Public on Mar 23 2021

city: Warsaw

first: Agnieszka

last: Sirko

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

summary:
We used the CRISPR/Cas9 technique to construct nbr1-KO lines (KO1 and KO3) in order to test the effects of AtNBR1 depletion. Reduced expression of several ABA-up regulated genes were observed in shoots of the two KO lines.
Grant number: 2014/15/B/NZ3/04854
Grant funding source: National Science Centre (Poland)
Grantee Name: Agnieszka Sirko
Grant title: Upstream regulators and cellular targets of the selective autophagy cargo receptor AtNBR1 in different phases of sulfur deficiency in plants.

overall_design: Plant material for transcript profiling was grown in Araponic boxes (16 plants/box) kept in short day conditions (22 °C 8h day/18 °C 16h night) for about 4 weeks, with weekly changes of the 0.5 x Hoagland medium. Individual plants were divided into shoot and root tissue and frozen in liquid nitrogen. Portions of plant material, drawn from at least 3 plants, were homogenised in TRI Reagent (Molecular Research Centre), and genomic DNA was removed with a RapidOut DNA removal kit (ThermoScientific) and total RNAs were separately isolated from shoots and roots. We looked for effects of the NBR1 gene deletion in the KO1 and KO3 lines compared to the the wild type plants (Col-0). These effects were investigated in roots and shoots separately. Totally, 36 samples of RNA were prepared (18 grown on low sulphate and 18 grown on media with standard concentrations of sulphate). After Principal Component Analysis one normal sulphate sample was rejected and remaining 35 series accepted.

first: Leszek

middle: J

last: Tarnowski

last: Gromadka

first: Jerzy

last: Brzywczy


title: RNA-seq of UV irradiated human epidermal melanocytes from neonatal foreskin, HEMn-DP2.

city: Philadelphia

first: Sarah

last: Alp

address: 3307 N Broad Street

department: Fels Institute

institute: Temple University

summary: UVR is the principal risk factor for melanoma development. While the role of UVR in DNA mutagenesis is incontrovertible, it remains controversial what role UVR-induced mutations play in melanoma genesis. To better understand how UVR is contributing to melanoma development, we investigated the non-mutational effect of UVR on the epigenome, specifically DNA methylation.  Aberrant DNA methylation changes are a hallmark in melanoma; however, there are few reports on the effects of UVR on DNA methylation. We exposed melanocytes to UVR and cultured them for one-month to detect hertible and stable changes in DNA methylation. We found both hyper and hypo methylated sites after UVR exposure. While many of these changes occured outside of promoters and areas of active gene expression, there were changes in promoter DNA methylation changes that correlated with changes in gene expression.  These changes also correlated with those found in melanoma and UVR sensitive sites were prognostic of patient overall survival. Our work shows for the first time UVR induced DNA methylation changes in melanocytes and may be another way in which UVR contributes to melanoma development.

overall_design: Melanocyte cells were UV irradiated with a broad band UVR spectrum ( UVA & UVB) for a total dos of 175 J/m2. Cells were cultured for one month before performing reduced representation bisulfite sequencing (RRBS). Genomic DNA was digested by MspI restriction enzyme, which recgonizes the CCGG sequence, and then subjected to bisulfite converstion. Methylated cytosines within CpG sites are protected from sodium bisulfite conversion and remain unchanged. Unmethylated cyotosines undergo a reaction with sodium bisulfite resulting in a base change from cytosine to uracil. This base change allows for the detection of methylated versus unmethylated CpG sites through high throughput sequencing.

last: Preston-Alp

first: Jaroslav

last: Jelinek

first: Jean-Pierre

last: Issa

first: M

middle: R

last: Zaidi


title: RNAseq in WT and Dnmt3a KO HSCs naive and after 1-month of infection with M. avium

city: Houston

first: Katherine

middle: Y.

last: King

state: Texas

address: 1102 Bates Ave., Ste.1150

department: Pediatrics and Infectious diseases

institute: Baylor College of Medicine

summary: 5000-10000 HSCs (KL CD150+ CD48- CD34-) were sorted into lysis buffer from the pools of naive or 1-month infected WT or Dnmt3a-/- mice (n=10-12 per group). RNA was isolated with the NucleoSpin ® RNA Plus XS kit (Macherey Nagel). RNA-seq libraries were prepared by using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio Usa). Illumina NovaSeq SP was used for sequencing with a paired-end sequencing length of 10bp. FASTQ files were preprocessed using HTS stream (https://github.com/ibest/HTStream) and the clean FASTQ file were aligned using STAR. Differential expression (DE) analysis of gene expression was performed using Limma-Voom. False discovery rate (FDR)<0.05 was considered statistically significant. We performed gene ontology analysis for differentially expressed genes with q value <0.05.

overall_design: WT and Dnmt3a-/- HSCs extracted after 1 month of infection with M. avium or PBS (naïve)

first: Daniel

last: Hormaechea Agulla

first: Bailee

last: Kain

first: Roman

last: Jaksik

first: Pawel

last: Kus


title: mRNA expression quantitative Analysis of NB4 and Kasumi-1 treated with OGP46 compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in NB4 and Kasumi-1 cell lines treated with OGP46

overall_design:
There are 12 samples. There are 6 samples  for NB4 cell line ( control and OGP46-treated). There are 6 samples  for Kasumi-1 cell line ( control and OGP46-treated),
*** Raw files were not submitted to GEO because they were lost and thus not available ***

first: Min

last: Zhao


title: miRNA Array of Transformed FTSECs [OCV versus CV & FAC versus UNT]

city: Tampa

first: Meera

last: Nanjundan

state: Florida

address: 4202 East Fowler Avenue, ISA2015

institute: University of South Florida

summary:
We implementing a transcriptomic approach to identify global miRNA alterations in chronic iron exposed FTSECs.
Chronic iron exposure in fallopian tube secretory epithelial cells (FTSECs) leads to alterations in oncogene expression and functional changes reminescent of early changes in ovarian cancer development (serous epithelial high grade ovarian tumors).

overall_design: Cell type Comparison Design: FT194 cells Untreated versus FT194 cells FAC-treated & FT194 cells CV-infected (control virus) versus FT194 cells OCV-infected (Oncogenic Cocktail)

first: Stephanie

last: Rockfield

first: Ravneet

last: Chhabra


title: Suppression of the NTS-CPS1 regulatory axis by AFF1 in lung adenocarcinoma cells

city: Nanjing

first: Xiaoxu

last: Liu

state: Jiangsu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

summary: Up-regulation of the neuropeptide NTS in a subgroup of lung cancers has been linked to poor prognosis. However, the regulatory pathway centered on NTS in lung cancer remains unclear. Here we identified the NTS specific enhancer in lung adenocarcinoma cells. The AF4/FMR2 (AFF) family protein AFF1 occupies the NTS enhancer and inhibits NTS transcription. Clustering analysis of lung adenocarcinoma gene expression data demonstrated that NTS is highly positively correlated with the expression of the oncogenic factor CPS1. Detailed analyses demonstrated that NTS antagonizes the IL6 pathway in regulating CPS1. Thus, our analyses revealed a novel NTS centered regulatory axis, consisting of AFF1 as a master transcription suppressor and IL6 as an antagonist in lung adenocarcinoma cells.

overall_design:
AFF1 ChIP sample.
RNA-seq in control and AFF1 knockdown A549 cells were performed in duplicates.

first: Chengqi

last: Lin


title: The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo

city: London

first: Clara

last: Collart

state: london

address: 1 Midland road

department: developmental biology

institute: Crick

summary:
Background
Vasculogenesis in amniotes is often viewed as two spatially and temporally distinct processes, occurring in the yolk sac and in the embryo. However, the spatial origins of the cells that form the primary intra-embryonic vasculature remain uncertain. In particular, do they obtain their haemato-endothelial cell fate in situ, or do they migrate from elsewhere? Recently developed imaging techniques, together with new Tal1 and existing Flk1 reporter mouse lines, have allowed us to investigate this question directly, by visualising cell trajectories live and in three dimensions.
Results
We describe the pathways that cells follow to form the primary embryonic circulatory system in the mouse embryo. In particular, we show that Tal1-positive cells migrate from within the yolk sac, at its distal border, to contribute to the endocardium, dorsal aortae and head vasculature. Other Tal1 positive cells, similarly activated within the yolk sac, contribute to the yolk sac vasculature.  Using single-cell transcriptomics and our imaging, we identify VEGF and Apela as potential chemo-attractants that may regulate the migration into the embryo. The dorsal aortae and head vasculature are known sites of secondary haematopoiesis; given the common origins that we observe, we investigate whether this is also the case for the endocardium. We discover cells budding from the wall of the endocardium with high Tal1 expression and diminished Flk1 expression, indicative of an endothelial to haematopoietic transition.
Conclusions
In contrast to the view that the yolk sac and embryonic circulatory systems form by two separate processes, our results indicate that Tal1-positive cells from the yolk sac contribute to both vascular systems. It may be that initial Tal1 activation in these cells is through a common mechanism.

overall_design: Two parts of 25 mouse embryos between E7.25 and E7.5 were cut and analysed by single cell transcriptomics to compare gene expression in the endoderm of both parts.

first: Amelia

last: Edwards

first: Gavin

last: Kelly


title: Myofibroblast de-differentiation proceeds via distinct transcriptomic and phenotypic transitions

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan


title: Genome-wide transcriptome analysis between WT and OsGRP3 overexpressing (or knock-down) rice

city: Pyeongchang

first: Jun Sung

last: Seo

state: Gangwon

address: Pyeongchangdaero 1447

department: Company-affiliated research institute

institute: LaSemilla Co. Ltd.

summary:
Purpose: The goals of this study are to find putative target transcript regulated by OsGRP3 by comparing rice transcriptome between wild-type and OsGRP3 overexpressing (or Knock-down) plants.
Methods: Total RNAs were extracted from the leaf tissues of OsGRP3OE, OsGRP3KD, and non-transgenic (NT) plants using the RNeasy plant mini kit (Qiagen, USA) according to the manufacturer’s instruction. cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (v2) (Macrogen, Korea). Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome, differentially expressed genes (DEGs) were selected using a cut-off change of at least 2-fold change and Student’s t-test (P < 0.05). The selected DEGs were grouped by hierarchical clustering analysis (Complete Linkage).
Results: A cutoff change of at least two-fold was used to isolate up- and down-regulated genes by OsGRP3. The analysis revealed that OsGRP3OX plants contained 195 up-regulated and 190 down-regulated genes compared with WT plants. Among the 195 up-regulated transcripts, 45 genes belonged to the gene ontology (GO) category of response to abiotic and/or biotic stress and defense. The majority of these genes were categorized into defense- and stress-related genes and interestingly many PR genes were up-regulated. This high frequency of defense- and stress-related genes affected by OsGRP3 overexpression suggests that OsGRP3 is closely associated with biotic and abiotic stress responses. We then isolated genes showing opposite expression patterns between OsGRP3OX and OsGRP3KD plants as candidate genes directly regulated by OsGRP3. Through these criteria, we finally isolated 15 genes as target candidates in the OsGRP3-mediated drought tolerance pathway. Interestingly, six genes showing a positive correlation with the expression level of OsGRP3 were associated with plant stress responses. The list included four PR genes, LATE EMBRYOGENESIS ABUNDANT PROTEIN 17 (LEA17), and EXOCYST SUBUNIT EXO70 FAMILY PROTEIN FX1 (FX1). On the other hand, eight genes showing negative correlation with OsGRP3 expression level included PEROXIDASE 1 (POX11), METALLOTHIONEIN 1d (MT1d), CAROTENOID 9, 10-CLEAVAGE DIOXYGENASE 1 (CCD1), 4,5-DOPA DIOXYGENASE EXTRADIOL-LIKE PROTEIN (DOPA), LEUCINE-RICH REPEAT DOMAIN CONTAINING PROTEIN (LRR), LIPOXYGENASE (LOX) and S-ADENOSYLMETHOININE SYNTHETASE 1 (SAM1) that were mainly associated with plant metabolic regulations.
Conclusions: OsGRP3 positively affects the expression of stress-responsive genes and negatively affected the expression of metabolic pathway genes.

overall_design: mRNA profiles of 4-week-old wild type (WT) and OsGRP3 OX (or KD) rice

first: Ju-Kon

last: Kim