title: Expression data from murine hematopoietic stem cells

city: Beijing

first: Wang

middle: meng

last: meng

address: No. 58 Jinghai Five Road

institute: Beijing Cnkingbio Biotechnology corporation

summary:
Long-term hematopoietic output is dependent on the hematopoietic stem cell (HSC) homeostasis which is maintained by a complex network of molecules. Among these, microRNAs (miRNAs) play crucial roles, while the underlying molecular basis have not been fully demonstrated. Here, we found that miR-21 is enriched in murine HSCs. Then, we generated a polyinosinic:polycytidylic acid (pIpC)-inducible mouse model (miR-21flox/flox:Mx1-Cre) to obtain a specific deletion of miR-21 in hematopoietic system. It was found that mice with conditional knockout of miR-21 exhibit an obvious perturbation of normal hematopoiesis.Further researches reveal that miR-21 deficiency affect HSC homeostasis and function.
We used microarrays to detail the global programme of gene expression, and identified distinct classes of up-regulated and down-regulated genes in murine HSCs after miR-21 conditional knockout.

overall_design: We have found that miR-21 deficiency affects the homeostasis and function of hematopoietic stem cells (HSCs). To explore the underlying molecular mechanisms, we sorted Lineage- c-Kit+ Sca1+ cells (LSKs) that are highly enriched with HSCs from the bone marrow of pIpC-injected miR-21 conditional knockout mice (miR-21flox/flox:Mx1-Cre+) and littermate control mice (miR-21flox/flox:Mx1-Cre-) by flow cytometry. Each group had three replicate samples. Then, these samples were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Mengjia

last: Hu

first: Yukai

last: Lu


title: TBC1D3 suppression of the Histone Lysine N-methyltransferase G9a promotes the generation of neural progenitors and cortical expansion [ChIP-seq]

status: Public on Feb 08 2021

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

country: China

institute: shanghaitech university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: we conducted chromotin Immunoprecipitation sequencing (ChIP-seq) using human cerebral organoids treated with TAT-Scrambled (Short for TAT-Scr) with the sequence of YGRKKRRQRRR-FRVRYWFQGCHSEDPWR and TAT-465-481, a special peoptide designed for inhibition of TBC1D3, with the sequence of YGRKKRRQRRR-EGPWFRHYDFRQSCWVR.

overall_design: Briefly, tissues were fixed in 1% formaldehyde to cross-link histone and non-histone protein to DNA for 10 to 20 minutes at room temperature and the crosslink was stopped by the addition of glycine. Then cells were lysated to release nucleus and micrococcal nuclease was used to digest chromatin into DNA/protein fragments.A part of the diluted chromatin in each group was transferred into a new microfuge tube to be saved as the input sample and H3K9me2 (Cell Signaling Technology, 4658s) was used as the immunoprecipitating antibody to be added into diluted chromatin mixture. Incubated IP samples at 4°C for overnight with rotation. Added ChIP-Grade Protein G Magnetic Beads to each IP reaction and incubated for 2h at 4°C with rotation and then the chromatin from antibody/Protein G magnetic beads was eluted and reversed. DNA in the chromatin mixture was purified and sequenced.

first: Qiongqiong

last: Hou

first: Zhen-Ge

last: Luo


title: S1PR3–G12-biased agonist ALESIA targets cancer metabolism and promotes glucose starvation [MCF-7 RNA-seq]

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

type: Expression profiling by high throughput sequencing

summary: Cancer tissues possess less glucose than surrounding normal tissue, because cancer cells predominantly produce energy by glycolysis than oxidative phosphorylation even in the presence of an adequate oxygen supply (Warburg effect). We found a novel compound ALESIA which causes apoptosis of malignant cells at a low glucose condition from an original phenotypic screening. Identified target molecule of ALESIA was Sphingosine-1-phosphate receptor 3 (S1PR3). Being different from the natural ligand, ALESIA selectively stimulated S1PR3-G12 coupling to S1PR3 without suppression by β-arrestin recruitment and continuously promoted NO synthesis. To reduce the enhanced oxidative stress, NAPDH production through pentose-phosphate pathway and resulting consumption of glucose were promoted in ALESIA-treated cells. ALESIA therefore accelerated glucose starvation of cancer cells and preferentially killed them both in vitro and in vivo.

overall_design: We analyzed polyA-tailed RNA profiles including transcribing RNAs in MCF-7 cells of ALESIA racemate treatment (n=3) and control (n=3) under normal culture condition using Ion-proton.

first: Masayasu

last: Toyomoto

first: Masatsugu

last: Denawa

last: Iida

first: Masatoshi

last: Hagiwara


title: A BAFF/APRIL axis regulates obesogenic-diet driven weight gain

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: To define the role of the BAFF/APRIL axis in the regulation of adipose tissue homeostasis through RNAseq.
Methods: Primary adipocytes were derived from pre-adipocyte precursors of inguinal white adipose from male C57BL/6 mice aged 6-8 weeks. Adipocytes were treated with rBAFF, rAPRIL, or multiple controls for 24 hours. mRNA profiles were generated for each condition, run in biological duplicates, using Illumina HiSeq2000 with single-end, 50bp reads.  Differential gene lists were generated by comparing BAFF and APRIL to controls using unpaired ttests.
Results:Following mapping an average of 30million reads across 10 samples to the mm10 mouse genome with annotations from UCSC, differential analysis identified genes involved in adipocyte pathways associated with lipid metabolism, lipolysis, and  inflammation.
Conclusion: BAFF and APRIL modulate modulate white adipocyte lipid handling.

overall_design: mRNA was obtained from inguinal adipose tissue obtained from male C57Bl/6 mice aged 6-8 weeks, following 24-hour treatment with rBAFF, rAPRIL, or multiple controls.

first: Senad

last: Divanovic

first: Calvin

last: Chan


title: SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior [RNA-Seq]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: We report gene expression data for zebrafish melanomas overexpressing human SATB2 and EGFP.

overall_design: RNA-seq was performed on three biological replicates of primary zebrafish melanoma tumors that were excized from MCR:EGFP (control) and MCR:SATB2 overexpressing Tg(BRAF V600E);p53-/-; mitf-/- zebrafish.

first: Ellen

last: van Rooijen

first: Song

last: Yang

first: Yi

last: Zhou

middle: I


title: SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior

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

overall_design: Refer to individual Series


title: SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior [ChIP-Seq]

summary: We report the distribution of human SATB2 in a primary zebrafish melanoma that overexpresses human SATB2, and H3K27Ac histone marks in zebrafish melanomas overexpressing either EGFP (control) or human SATB2.

overall_design: Examining SATB2 bound regions, and H3K27Ac-bound (super) enhancers in zebrafish melanomas

first: Eirini

last: Trompouki


title: Metoclopramide treatment blocks CD93-signaling mediated self-renewal of chronic myeloid leukemia stem cells

status: Public on Feb 07 2021

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary:
Purpose: The goal of this study was to compare the transcriptome of FACS-purified bone marrow BL/6 (WT) or CD93-/- (KO) LSKs and BL/6 (WT) or CD93-/- (KO) LSCs. We also compared the transcriptome of FACS-purified bone marrow LSCs isolated from BL/6 mice previously treated with MCP or Veh in vivo.
Methods: Transcriptomic analysis of CD93-proficient and deficient bone marrow LSKs and CML LSCs or CML LSCs upon treatment with MCP or Veh, were assessed in biological replicates using Illumina. qRT–PCR validation was performed using SYBR Green assays.
Results: We mapped around 30 million sequence reads per sample to the mouse genome (GRCm38 - mm10) and identified expressed transcripts in studied samples. RNA-seq data confirmed stable expression of known housekeeping genes. Differentially expressed genes among conditions were identified with a fold change ≥1.5 and FDR p-value <0.05.
Conclusions: Our study represents the first detailed transcriptome analysis of CD93-proficient and deficient bone marrow LSKs and LSCs isolated from BM of naïve and CML mice generated by RNA-seq. technology. Our results show that CD93-signaling triggers stem cell maintenance- and cell proliferation-promoting signaling pathways in CML LSCs. In addition, we showed transcriptome analysis of FACS-purified bone marrow LSCs isolated from BL/6 (WT) mice which were previously treated with MCP or Veh in vivo. Our results show that MCP treatment suppresses the stem cell maintenance- and cell proliferation-promoting signaling pathways in CML LSCs.

overall_design: mRNA of CD93-proficient and deficient LSKs and LSCs was isolated from BM of naïve and CML mice and profiled using Illumina. mRNA of FACS-purified bone marrow LSCs isolated from BL/6 (WT) mice treated with MCP or Veh in vivo and profiled using Illumina.

first: Carsten

last: Riether

first: Adrian

middle: F

last: Ochsenbein


title: Swapping the DNA binding domain of MeCP2 with that of MBD2 to abolish binding to non-CG methlyation results in RTT-like phenotypes in mice

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh


title: Gene expression analysis of extravillous trophoblast cells during the first-trimester

city: Tokyo

first: Manabu

last: Ogoyama

address: 1-1-5, Sendagi

department: Molecular Medicine and Anatomy

institute: Nippon Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: During early placentation, extravillous trophoblast (EVT) cell invasion into maternal decidua plays a crucial role in establishment of the successful pregnancy. However, little is known about the characteristic features of EVT-associated ncRNAs. The purpose of this study is to elucidate gene expression profile for both coding and non-coding genes (i.e., mRNAs, lncRNAs, and miRNAs) expressed in EVT cells isolated from the first-trimester human placenta by RNA sequencing analysis.
Methods: Human first trimester placental tissues (at gestational week 7, n=3) were obtained after legal abortions. EVT cells growing from explanted human chorionic villi were isolated. Minced chorionic villous tips were defined as first-trimester chorionic villous trophoblast (CVT) cells. Using total RNAs of these samples, mRNA/lncRNA-sequencing analysis was carried out on an Illumina MiSeq (San Diego, California, USA) using MiSeq v2 Reagent Kit 300cycle (cat. no. MS-102-2002; Illumina) and MiSeq v2 Reagent Kit 50cycle (cat. no. MS-102-2001; Illumina), respectively. The paired-end reads of 151 bp length for mRNA/lncRNA-sequencing and single reads of 26 bp length for miRNA-sequencing were obtained as fastq files which were imported into CLC genomics workbench (version 8.0.1; Qiagen, Venlo, Netherlands). Clean reads were aligned to the human genome sequence retrieved from the Ensembl database (Assembly GRCh38.p13, database version 82.38 and 101.38) and microRNA database miRbase (release 21), using CLC Genomics Workbench Map Reads to Reference tool. Normalization of gene expression data was performed by the TMM method of edgeR package. Statistically differentially expressed transcripts were conducted using edgeR. Genes that had a false discovery rate (FDR)-corrected p-value (q-value) of < 0.05 and an absolute log2 fold change (log FC) ≥ 1 were judged to be significantly differentially expressed (i.e., differentially expressed genes, DEGs).
Results: Five thousand ninty-two mRNAs , 422 lncRNAs and 400 miRNAs were found to be differentially expressed. One hundred differentially expressed genes (i.e., 10 mRNAs, 7 lncRNAs, and 83 miRNAs) that are located in the chromosome 14q32.2 region containing the eutherian-specific imprinted DLK1-DIO3 domain were significantly down-regulated in EVT cells. In terms of imprinted genes (http://www.geneimprint.com/site/genes-by-species), 68 genes were found to be differentially expressed; 71% of these genes were down-regulated in EVT cells. lncRNA H19 was a DEG (q = 1.29.E-09, log FC = 2.98) and the most highly expressed lncRNA (70.47%) in EVT cells.
Conclusions: The present research should be valuable for a resource for future ncRNA research in EVT cells.

overall_design: Comparison of gene expression level between EVT and CVT cells obtained from the first-trimester human placenta by RNA sequencing analysis (n=3).

first: Toshihiro

last: Takizawa

first: Takuji

last: Kosuge


title: Transcriptomic analysis of ethanol, DMSO, I-CBP112 and C646 treatment on mouse embryonic fibroblasts (MEFs) during direct cardiac reprogramming

status: Public on Feb 06 2021

city: Singapore

first: Choon Kiat

last: Lim

state: Singapore

address: 14 Medical Drive

department: Medicine

country: Singapore

institute: National University of Singapore

summary: Direct cardiac reprogramming represents an attractive way of reversing heart damage caused by myocardial infarction. Yet, it is still in pre-clinical stage mainly due to the lack of efficacy with current transdifferentiation protocols. Here, we describe that dimethyl sulfoxide (DMSO) is capable of augmenting direct cardiac reprogramming in vitro. Treatment of Gata4, Hand2, Mef2c and Tbx5 (GHMT) - transduced mouse embryonic fibroblasts (MEFs) with 1% DMSO induced ~5 fold increase in the percentage of Myh6-mCherry+ cells, and significantly increased the global expression of cardiac genes. Transcriptomic studies were carried out to explore the underlying mechanism of how DMSO may enhance cardiac transdifferentiation.

overall_design: RNA-seq was carried out on GHMT-transduced cells after 7 days of treatment with 0.1% ethanol, 1% DMSO, 5 uM I-CBP112 and 5 uM C646

first: Choon

middle: K

first: Motakis

last: Efthymios

first: Matias

last: Autio

first: Zenia

last: Tiang

first: Yiqing

last: Li

first: Roger

last: Yin


title: Transcriptomes of 1b Con1cc-infected cells

city: Guangzhou

first: jinqian

last: li

address: Sun Yat-sen University

institute: Sun Yat-sen University

summary: Huh7.5 cells were infected in duplicate with 1b Con1cc virus. At peak infection (>80% cells were HCV positive, day 7 post infection), total RNA was isolated using TRIzol LS reagent. Analysis of the transcriptomes of Huh7.5 cells disturbed by Con1cc infection. We found that in addition to activation of apoptosis and antiviral response in the cell, Con1cc infection also induced angiogenesis-related genes and disturbed cholesterol metabolism. This study provided experimental evidence towards the understanding of molecular mechanisms of HCV pathogenesis.

overall_design: mRNA profile of HCV genotype 1b virus (strain Con1cc) infection of Huh7.5 cells.

first: Jinqian

middle: P


title: mRNA transcriptome sequencing of colitis from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice after administered DSS and of colorectal tumors from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice after AOM/DSS colorectal tumor model treatment

city: WuHan

first: yang

last: wei

state: HuBei

address: 169#Donghu Nan road, Wuchang Disrict, Wuhan city

department: Medical Research Institute

institute: WuHan university

summary: Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice were administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days. The colons were flushed with PBS to clear feces and slit open longitudinally. The distal colon tissues (0.5 cm in length, about 0.5 cm away from the anus) were washed in PBS and homogenized in 2 ml TRIzol (Invitrogen). Colorectal tumors from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice were AOM/DSS colorectal tumor model. The colorectal tumors were flushed with PBS to clear feces and homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene). Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev). All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read. Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).

overall_design:
mRNA transcriptome sequencing of colitis from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice after administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days, mRNA transcriptome sequencing of colorectal tumors from Il1f5+/+, Il1f5-/-, Il1f9+/+ and Il1f9-/- mice after AOM/DSS colorectal tumor model treatment
Il1f5+/+(n=3), Il1f5-/-(n=3), Il1f9+/+(n=2) and Il1f9-/-(n=2) mice were used, respectively. Il1f5+/+(n=2), Il1f5-/-(n=2), Il1f9+/+(n=2) and Il1f9-/-(n=2) were used, respectively.

first: W

last: Yang

first: P

last: Wang

first: B

last: Zhong


title: Gene expression profiling of HUDEP-2 cells edited with either ZNF410 targeting or control sgRNA

status: Public on Feb 05 2021

first: Divya

last: Vinjamur

summary: RNA sequencing was performed of HUDEP-2 cells edited at either ZNF410 or AAVS1 (control locus) to measure gene expression changes due to loss of ZNF410 expression. CHD4 was the most significantly downregulated gene upon ZNF410 editing. We observed that ZNF410 binds to DNA upstream of the CHD4 gene. To test the requirement of ZNF410 binding for CHD4 expression we generated a HUDEP-2 clone in which this region of ZNF410 binding was deleted (CHD4 6.7 kb element deletion clone). We performed RNA-seq of CHD4 6.7 kb element deleted HUDEP-2 cells after either ZNF410 or AAVS1 (control locus) editing and only observed 2 differentially expressed genes after ZNF410 editing in CHD4 6.7 kb element deletion cells, consistent with our results that nearly all gene expression changes found after ZNF410 editing are due to changes in CHD4 expression.

overall_design: Four conditions are included in the study - HUDEP-2 cells edited with ZNF410 targeting sgRNA, HUDEP-2 cells edited with AAVS1 control sgRNA, CHD4_delta-6.7kb HUDEP-2 cells (clone C3-19) edited with ZNF410 targeting sgRNA and CHD4_delta-6.7kb HUDEP-2 cells (clone C3-19) edited with AAVS1 control sgRNA. 3 replicates were performed and analysed for each condition.

middle: S

first: Daniel

middle: E

last: Bauer


title: Whole-Body Senescent Cell Clearance Alleviates Age-Related Brain Inflammation and Cognitive Impairment in Mice

city: newberry

first: Shane

middle: A

last: Evans

state: Florida

address: 22806 West Newberry Road

department: Bio Med

institute: Brown University

summary: Cellular senescence is characterized by an irreversible cell cycle arrest and a pro-inflammatory senescence-associated secretory phenotype (SASP), which is a major contributor to aging and age-related diseases. Clearance of senescent cells has been shown to improve brain function in mouse models of neurodegenerative diseases. However, it is still unknown whether senescent cell clearance alleviates cognitive dysfunction during the aging process. To investigate this, we first conducted single-nuclei and single-cell RNA-seq in the hippocampus from young and aged mice. We observed an age-dependent increase in p16Ink4a senescent cells, which was more pronounced in microglia and oligodendrocyte progenitor cells and characterized by a SASP. We then aged INK-ATTAC mice, in which p16Ink4a-positive senescent cells can be genetically eliminated upon treatment with the drug AP20187 and treated them either with AP20187 or with the senolytic cocktail Dasatinib and Quercetin. We observed that both strategies resulted in a decrease in p16Ink4a exclusively in the microglial population, resulting in reduced microglial activation and reduced expression of SASP factors. Importantly, both approaches significantly improved cognitive function in aged mice. Our data provide proof-of-concept for senolytic interventions’ being a potential therapeutic avenue for alleviating age-associated cognitive impairment.

overall_design: Single Cell and Single Nucleus Droplet Based RNA-sequencing of hippocampus tissue of 4 month and 24 month old mice.

first: Mikolaj

last: Ogrodnik

first: Edward

last: Fielder

first: Patrick

last: Kruger

first: Stella

last: Victorelli

first: Hanna

last: Salmonowicz

first: Bettina

middle: M

last: Weigand

first: Ayush

middle: D

last: Patel

first: Tamar

last: Pirtskhalava

first: Christine

middle: L

last: Inman

first: Kurt

middle: O

last: Johnson

first: Stephanie

last: Dickinson

first: Azucena

last: Rocha

first: Marissa

middle: J

last: Schafer

first: Yi

last: Zhu

first: David

middle: B

last: Allison

first: Thomas

last: von Zglinicki

first: Nathan

last: LeBrasseur

last: Tchkonia

first: João

last: Passos

first: Nicola

last: Neretti

first: James

last: Kirkland

first: Diana

last: Jurk


title: Overexpressing low-density lipoprotein receptor reduces tau-associated neurodegeneration via apoE-dependent and independent mechanisms

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: APOE is the strongest genetic risk factor for late-onset Alzheimer’s disease. ApoE exacerbates tau-associated neurodegeneration by driving microglial activation. However, how apoE regulates microglial activation and whether targeting apoE is therapeutically beneficial in tauopathy is unclear. Here we show that overexpressing a low-density lipoprotein receptor (LDLR) transgene in P301S tau transgenic mice markedly reduces brain apoE and ameliorates tau pathology and neurodegeneration. ApoE specifically interacts with a high-molecular-weight tau species, and highly correlates with phospho-tau and insoluble tau levels. Microglial expression of the LDLR transgene reduces intracellular apoE and is associated with less microglial activation. snRNA-seq analysis of apoE-deficient or LDLR-overexpressing brains reveals that apoE deficiency drives microglial catabolism and increases the oligodendrocyte progenitor cell population. LDLR overexpression shares overlapping mechanisms, but uniquely upregulates microglial expression of specific ion channels and neurotransmitter receptors in tauopathy. A subset of disease-associated astrocytes with both neuroprotective and neurotoxic gene signatures is also identified.

overall_design:
7-8 biologically independent mouse hippocampi were pooled together as a single sample per genotype. Each sample was individually processed and sequenced. A total of 6 groups (genotypes) were analyzed.
Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse hippocampus through sucrose gradient and libraries were prepared using Chromium Single Cell 3′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.

first: Yang

last: Shi

first: Prabhakar

last: Andhey

first: Christina

last: Ising

first: Kairuo

last: Wang

first: Christoph

last: Schlaffner

first: Hendrik

last: Wesseling

first: Kaoru

last: Yamada

first: Wei

last: Qin

first: Melissa

last: Manis

first: Javier

middle: R

last: Serrano

first: Bruno

last: Benitez

first: Judith

last: Steen

first: Jason

last: Ulrich

last: Holtzman


title: Transcriptomic characteristics and impaired immune function of patients who retest positive for SARS-CoV-2 RNA

city: Hefei

first: Dongyao

state: Anhui

address: No.96, JinZhai Road Baohe District

institute: University of Science and Technology of China

summary: The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has gradually become a global public health crisis. Some patients who have recovered from COVID-19 subsequently tested positive again for SARS-CoV-2 after discharge (retesting-positive, RTP). However, the underlying mechanism is unknown. Here, 10 RTP patients, 6 convalescent patients, and 10 healthy controls were enrolled for analysis of the immunological characteristics of their peripheral blood mononuclear cells (PBMCs). We sought to comprehensively characterize the transcriptional changes in the three groups by transcriptome sequencing. Our findings provide insights into the impaired immune function and pathogenesis of RTP occurrence in COVID-19, which may contribute to the development of immunotherapy for RTP patients.

first: Dong

first: Min

last: Huang


title: Genome-wide ZNF410 binding sites identified by CUT&RUN in HUDEP-2, human CD34+ HSPCs and MEL cells.

first: Divya

last: Vinjamur

summary: We examined the chromatin occupancy of ZNF410 by conducting CUT&RUN. We used an HA antibody to probe for epitope tagged ZNF410 in HUDEP-2 cells. We used a ZNF410 antibody to probe for endogenous ZNF410 in HUDEP-2 cells, human CD34+ hematopoietic stem and progenitor cell (HSPC) derived erythroid precursors and mouse erythroleukemia (MEL) cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Genomic enrichment for ZNF410 binding was determined using IgG as the negative control.

first: Qiuming

last: Yao

first: Luca

last: Pinello

first: Daniel

last: Bauer


title: Expression data from human astrocytes (HA) under oxygen-glucose deprivation / reoxygenation

city: Urayasu

first: Yui

last: Yamane

state: Chiba

address: 2-1-1 Tomioka

institute: Juntendo University Urayasu Hospital

summary:
Ischemia lead to neuronal injury. Dexmedetomidine and astrocytes are likely to protect neuronal cells against ischemia-induced injury.
We used microarrays to examine the gene expression variation in astrocytes activated by oxygen-glucose deprivation and reoxygenation stress and identified distinct classes of genes up- and down-regulated by dexmedetomidine pretreatment.

overall_design: Human astrocytes were subjected to oxygen glucose deprivation and reoxygenation (OGD/R) stress for RNA extraction and hybridization on Affymetrix microarrays. To exam the preventive effect of DEX, cells were cultured with DEX for 1 hour, before OGD/R. Cells were washed by PBS and replaced with a glucose-free medium, set in a sealed container, filled with 95% N2 / 5% CO2, and incubated for 4 hours. The cells were then returned to air conditions, washed out and replaced with normal medium, and cells were incubated for a constant reoxygenation time. i.e., 0 h (HAC 0h and HAD 0h), 2 h (HAC 2h and HAD 2h), 6 h (HAC 6h and HAD 6h), 12 h (HAC 12h and HAD 12h), and 24 h (HAC 24h and HAD 24h)


title: Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing

city: CHAPEL HILL

first: Ann

middle: Lynette

last: Emery

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina At Chapel Hill

summary: Several prior reports have demonstrated that the epitranscriptomic addition of m6A to viral transcripts promotes the replication and pathogenicity of a wide range of viruses yet the underlying mechanism(s) causing this positive effect has remained unclear. It is known that m6A function is largely mediated by cellular m6A binding proteins or readers, however, how these m6A reader proteins contribute to the regulation of HIV-1 gene expression has remained controversial. Here, we confirm that m6A indeed enhances HIV-1 gene expression. We demonstrate that this effect is collectively mediated by the cytoplasmic reader YTHDF2, which increases HIV-1 transcript stability, and the nuclear m6A reader YTHDC1, which binds HIV-1 RNA at 7 distinct m6A methylated sites, regulating viral transcript alternative splicing.

overall_design: Splicing Assays run with 4 primer sets (1.8 KB, 4 KB, Random Reverse, Common K-mer) on 293T cell knockdowns of YTHDC1 using a control (siC) or YTHDC1 siRNA (siD); or overexpressed YTHDC1 (plusD).  Experiments were done in triplicate

first: Kevin

last: Tsai

first: Bryan

last: Cullen


title: Relative abundance of the integrant-derived viral RNAs in infected tissues harvested from chronic HBV carriers

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Five matching sets of non-malignant liver tissues and HCCs from individuals chronically infected with hepatitis B virus (HBV) were examined. The HBV genomic sequences were determined using overlapping PCR amplicons covering the entire viral genome. Four pairs of tissues were infected with HBV of genotype C, while one pair - with genotype B. HBV replication markers were found in all tissues. In majority of HCC samples, the levels of pre-genomic/pre-core RNA (pgRNA) and covalently closed circular DNA (cccDNA) were lower than those of liver tissue counterparts. Regardless of the presence of HBV replication markers, (i) integrant-derived HBV RNAs (id-RNAs) were found using RT-PCR analysis in all tissues, and were considerably abundant or predominant in 6/10 tissue samples (2 livers and 4 HCCs); (ii) the RNAs that were polyadenylated using cryptic HBV polyadenylation signal and therefore could be produced by HBV replication or derived from integrated HBV DNA were found in 5/10 samples (3 livers and 2 HCCs), and were considerably abundant species in 3/10 tissues (2 livers and 1 HCC); and (iii) cccDNA-transcribed RNAs polyadenylated near position 1931 were not abundant in 7/10 tissues (2 livers and 5 HCCs), and were predominant only in two livers. Subsequent RNA sequencing  analysis of selected liver/HCC samples also showed relative abundance of  id-RNAs in most of examined tissues. Our findings suggesting that id-RNAs could represent a significant source of HBV envelope proteins, which is independent of viral replication, are discussed in the context of possible contribution of id-RNAs to the HBV life cycle.

overall_design: We used the RNA sequencing approach to analyze the accumulation of HBV RNAs in matching liver/HCC tissue samples #3, #4, #7 and #8, which were collected from individuals chronically infected with HBV

first: Severin

last: Gudima

first: Natalia

last: Freitas

first: Tetyana

last: Lukash

first: Benjamin

last: Chappell

first: Betty

last: Slagle


title: Transcriptional profiling of mouse aorta after deletion of BMP9 and BMP10

city: Bad Nauheim

first: Thomas

last: Boettger

state: Hessen

address: Ludwigstr. 43

department: Cardiac Development

country: Germany

institute: MPI for Heart and Lung Research

summary:
Aorta was isolated from ANF-Cre positive/BMP10 loxP/loxP/BMP9-/- (BMP9/10 dKO) mice. ANF-Cre negative BMP10 loxP/loxP mice were used as controls.
Transcritional profiling was performed to understand the impact of BMP9/10 expression on aorta function.

overall_design: microarray profiling, genotype design


title: Stimulation of HUVEC by BMP9/10

summary: The experiment monitors the response of human umbilical vein endothelial cells to stimulation with BMP9 and BMP10

overall_design: Transcription profiling by array, compound treatment design


title: Androgen receptor Serine 81 phosphorylation is coupled to AR-mediated transactivation and co-sustained by CDK1 and CDK9 in prostate cancer

first: Shaoyong

last: Chen

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

summary: We examine total AR verus pSer81-phosphorylated AR chromatin-binding profiling in DHT-treated LNCaP cells to address the molecular functions of pS81 on the chromatin, and demonstrate that S81 phosphorylation can be mediated by both CDK1 and CDK9 at basal and androgen-stimulated levels.

overall_design: 2 total AR and 3 pSer81-AR samples based on DHT-treated LNCaP cells are subjected to ChIP-Seq analyses

first: Chen

last: Shaoyong

first: Liu

last: Xiaming

first: Liang

last: Jiaqian

first: Gao

last: Xintao


title: RNA-Seq identifies alternative splicing of CRBN induced by ILF3 KO

city: San Diego

first: Elizabeth

middle: Anne

last: Tindall

address: 10300 Campus Point Dr., Suite 100

institute: Bristol Myers Squibb

summary: We present a first-in-class GSPT1-selective CELMoD, CC-90009, which is currently in a phase 1 clinical trial for the treatment of relapsed or refractory (R/R) AML (CC-90009-AML-001; NCT02848001). Biochemical, structural and molecular characterization supports that CC-90009 coopts the CUL4-DDB1-CRBN-RBX1 (CRL4-CRBN) E3 ubiquitin ligase complex to selectively target GSPT1 for ubiquitination and proteasomal degradation, culminating in rapid induction of apoptosis and growth inhibition in AML cell lines and patient leukemic blasts. Knockout of ILF2/ILF3 decreased the production of full-length CRBN transcript via modulating CRBN mRNA alternative splicing, leading to significant downregulation of cereblon expression and hence diminished response to CC-90009.

overall_design: mRNA profiling on U937-Cas9 cells expressing sgNT or sgILF3 followed by differential exon usage analysis to predict alternative splicing


title: Time-series RNA-seq data of Geobacillus thermoglucosidasius DSM2542

city: Beijing

first: Junyang

last: Wang

address: 1 Beichen West Road, Chaoyang District, Beijing,

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: The present work aimed at discovering xylose-inducible and glucose-insensitive promoters from Geobacillus thermoglucosidasius DSM 2542. This strategy enabled the pathway from xylose metabolism to riboflavin production activated by xylose but not glucose, so that glucose was mainly used for cell growth while xylose was used for riboflavin production. By performing whole genome transcriptional analysis of G. thermoglucosidasius DSM 2542 with or without 1% xylose, 71 xylose-activated genes were identified which were controlled by 39 putative promoters. 3 experimentally validated xylose-inducible and glucose-insensitive promoters covering a broad range of transcriptional levels were used to activate the extra pathway from xylose metabolism to riboflavin production. Fermentation results showed the good performance of these promoters for riboflavin production improvement comparing to constitutive promoters. Therefore, our strategy could be applicable to the construction of cell factories that can efficiently use natural carbon sources with glucose and xylose components for the production of high-value chemicals.

overall_design: Transcriptional profiling of Geobacillus thermoglucosidasius DSM2542 at 3 different growth phases (exponential, transitional and stationary phase)

first: Yihua

first: Keqiang

last: Fan


title: RNA secondary structome of different cell lines

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

summary: we resolved the RNA secondary structure of human (HEK293,  HeLa, K562, HepG2, H9) and mouse (mES) cells based on optimized in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). we describe a deep discriminative neural network (PrismNet) that integrates big data of RBP binding and RNA secondary structure from matched living cells and accurately models the RNA sequence and structural preferences of protein-RNA interactions in vivo, enabling precise prediction of the perturbation effects of genetic variants.

overall_design: Libraries of 7 cell lines (human: HEK293, HeLa, K562, HepG2, H9 and mouse : mES) were constructed as the optimized icSHAPE protocol. The RNA structure in vivo was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) by the new protocol icSHAPE-pipe.

first: Qiangfeng

last: Zhang


title: The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

summary: We sought to validate the BDII/Han rat model as a model for diet-induced obesity in endometrial cancer (EC) and determine if transcriptomic changes induced by a high fat diet (HFD) in an EC rat model can be used to identify novel biomarkers in human EC. Nineteen BDII/Han rats were included. Group A (n = 7) were given ad lib access to a normal calorie, normal chow diet (NCD) while Group B (n = 12) were given ad lib access to a calorie rich HFD for 15 months. RNAseq was performed on endometrial tumours from both groups. The top-ranking differentially expressed genes (DEGs) were examined in the human EC using The Cancer Genome Atlas (TCGA) to assess if the BDII/Han rat model is an appropriate model for human obesity-induced carcinogenesis. Weight gain in HFD rats was double the weight gain of NCD rats (50 g vs. 25 g). The incidence of cancer was similar in both groups (4/7-57% vs. 4/12-33%; p = 0.37). All tumours were equivalent to a Stage 1A, Grade 2 human endometrioid carcinoma. A total of 368 DEGs were identified between the tumours in the HFD group compared to the NCD group. We identified two upstream regulators of the DEGs, mir-33 and Brd4, and a pathway analysis identified downstream enrichment of the colorectal cancer metastasis and ovarian cancer metastasis pathways. Top-ranking DEGs included Tex14, A2M, Hmgcs2, Adamts5, Pdk4, Crabp2, Capn12, Npw, Idi1 and Gpt. A2M expression was decreased in HFD tumours. Consistent with these findings, we found a significant negative correlation between A2M mRNA expression levels and BMI in the TCGA cohort (Spearman's Rho = -0.263, p < 0.001). A2M expression was associated with improved overall survival (HR = 0.45, 95% CI 0.23-0.9, p = 0.024). Crabp2 expression was increased in HFD tumours. In human EC, CRABP2 expression was associated with reduced overall survival (HR = 3.554, 95% CI 1.875-6.753, p < 0.001). Diet-induced obesity can alter EC transcriptomic profiles. The BDII/Han rat model is a suitable model of diet-induced obesity in endometrial cancer and can be used to identify clinically relevant biomarkers in human EC.

overall_design: n=67 samples, from n=24 animals, from tumour (n=32) and normal tissue (n=35), representing n=4 conditions based on Diet (high fat - HFD; normal chow - NC) and Intervention in HFD (n=3; No intervention - NO; Liraglutide - LIR; Diet Restriction - RES).

first: Michael

last: Wilkinson

first: Donal

last: Brennan

first: Carel

last: LeRoux


title: Smart-seq II Sequencing Analysis of Pdl1+  and Pdl1-  mammary gland basal  cell Transcriptomes

status: Public on Feb 04 2021

first: wang

middle: rui

last: rui

address: District fruit lake street

institute: WuHanUniversity

summary: Purpose:Smart  sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare gene expression of Pdl1+  and Pdl1-  mammary gland basal  cell analysis.Methods:Pdl1+  and Pdl1-  mammary gland basal  cell mRNA profiles of  wild-type (WT)  were generated by deep sequencing, in triplicate, using Illumina nova seq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Hisat2 as the mapping tool followed byDESeq R package. qRT–PCR validation was performed using TaqMan and SYBR Green assays.Results: Using an optimized data analysis workflow, RNA-seq data confirmed and validated with qRT–PCR.

overall_design: Pdl1+  and Pdl1-  mammary gland basal  cell  mRNA profiles of 8 weeks old wild type  mice

first: Ruirui

first: Fujing

last: Huang

first: Cheguo

last: Cai


title: RNA sequencing of the phase II PERFECT trial combining a PD-L1 inhibitor (atezolizumab) with neoadjuvant chemoradiotherapy in resectable esophageal adenocarcinoma patients.

city: Amsterdam

first: Tom

last: van den Ende

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: We performed bulk RNA sequencing of tumor biopsies from patients before treatment, on-treatment and in case a poor response was suspected from the resection specimen. At baseline we found in responding patients a higher six-gene IFNy score compared to non-responders. On-treatment non-responders showed either high expression of co-inhibitory checkpoints with a high number of cytotoxic lymphocytes or low expression and a low number of cytotoxic lymphocytes.

overall_design: RNA sequencing of esophageal tumor biopsies at baseline from patients, on-treatment (3rd week) and at resection.

first: Mark

last: Dings

first: Maarten

middle: F

last: Bijlsma


title: Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats (Histone acetylation dataset)

first: Hui

last: Li

address: 27th Taiping Road

institute: Beijing Key Laboratory of Neuropsychopharmacology

type: Genome variation profiling by genome tiling array

summary: Background: Methamphetamine (METH) is one of the most widely abused illicit substances worldwide; unfortunately, its addiction mechanism remains unclear. Based on accumulating evidence, changes in gene expression and chromatin modifications might be related to the persistent effects of METH on the brain. In the present study, we took advantage of METH-induced behavioral sensitization as an animal model that reflects some aspects of drug addiction and examined the changes in gene expression and histone acetylation in the prefrontal cortex (PFC) of adult rats. Methods: We conducted mRNA microarray and chromatin immunoprecipitation (ChIP) coupled to DNA microarray (ChIP-chip) analyses to screen and identify changes in transcript levels and histone acetylation patterns. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, were performed to analyze the differentially expressed genes. We then further identified alterations in ANP32A (acidic leucine-rich nuclear phosphoprotein-32A) and POU3F2 (POU domain, class 3, transcription factor 2) using qPCR and ChIP-PCR assays. Results: In the rat model of METH-induced behavioral sensitization, METH challenge caused 275 differentially expressed genes and a number of hyperacetylated genes (821 genes with H3 acetylation and 10 genes with H4 acetylation). Based on mRNA microarray and GO and KEGG enrichment analyses, 24 genes may be involved in METH-induced behavioral sensitization, and 7 were confirmed using qPCR. We further examined the alterations in the levels of the ANP32A and POU3F2 transcripts and histone acetylation at different periods of METH-induced behavioral sensitization. H4 hyperacetylation contributed to the increased levels of ANP32A mRNA and H3/H4 hyperacetylation contributed to the increased levels of POU3F2 mRNA induced by METH challenge-induced behavioral sensitization, but not by acute METH exposure. Conclusions: The present results revealed alterations in transcription and histone acetylation in the rat PFC by METH exposure and provided evidence that modifications of histone acetylation contributed to the alterations in gene expression caused by METH-induced behavioral sensitization.

overall_design: In order to whether the changes in gene expression occurring in response to METH-induced behavioral sensitization are related to histone acetylation in the PFC. Given the importance of the PFC in the development of METH abuse, we screened the alterations in gene expression and histone acetylation in the PFC following METH-induced behavioral sensitization and further investigated the contribution of histone acetylation to the expression of the candidate genes in the different phases of the behavior model.

first: Jing-An

last: Chen

first: Qian-Zhi

last: Ding

first: Guan-Yi

last: Lu

first: Ning

last: Wu

first: Rui-Bin

last: Su

first: Fei

first: Jin


title: RNA-seq and physiology analysis reveal new insights into gill response to acute hypoxia in Hybrid Yellow Catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂)

city: wuxi

first: Yi-Fan

last: Tao

state: jiangsu

address: 9 Shanshui East Road

institute: Freshwater Fisheries Research Center

summary: Hypoxia is an important environmental stressor in aquatic ecosystems, with increasingly impacts on global biodiversity. Yellow catfish is an economically important farmed fish in China, which has increased dramatically. We investigated the response of hybrid yellow catfish to hypoxia under experimental conditions and focused on the analysis of the differential expression patterns of specific genes associated with hypoxia response by RNA-seq and qPCR analysis. A total of 1556 genes were captured significantly differentially expressed, and were categorized into immune response and energy metabolism. Functional enrichment analysis revealed the NLR signaling pathway play pivotal roles in hypoxia tolerance and resistance. Our study provides important insights into the physiological acclimation, immune response and defense activity of  hybrid yellow catfish under hypoxia challenge.

overall_design: hypoxia (DO: 1.5 mg/L) groups and control stress (DO: 6.5 mg/L) groups under 96h hypoxia stress

first: Tao

last: Yi-Fan

first: Qiang

last: Jun

first: Dagoudo

last: Missinhoun

first: Zhu

last: Hao-Jun

first: Bao

last: Jing-Wen

first: Ma

last: Jun-Lei

first: Li

last: Ming-Xiao

first: Xu

last: Pao


title: The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology

city: Atlanta

first: Ken

last: Moberg

state: Georgia

address: 615 Michael Street

department: Cell Biology

institute: Emory University School of Medicine

summary: Nab2 encodes a polyadenosine RNA-binding protein (RBP) with broad roles in post-transcriptional regulation, including in RNA export, poly(A) tail length control, and mRNA splicing, and loss of its human ortholog ZC3H14 gives rise to a form of autosomal recessive intellectual disability. Understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part, because no comprehensive identification of metazoan-Nab2-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships likely remain unidentified. Here we present evidence that Drosophila melanogaster Nab2 interacts with the RBP Ataxin-2 (Atx2), a neuronal translational regulator, and implicate these proteins in coordinate regulation of neuronal morphology and adult viability. We then present the first high-throughput identifications of RNAs associating with Nab2 and Atx2 in Drosophila brain neurons using an RNA immunoprecipitation-sequencing (RIP-Seq) approach. Critically, the RNA interactomes of each RBP overlap. The identities of shared associated transcripts (e.g. drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g. Arpc2, tea, respectively) promise insight into the neuronal functions of and interactions between each RBP. Significantly, we find Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with only a fraction of all polyadenylated RNAs. These Nab2-associated RNAs are overrepresented for internal A-rich motifs, suggesting such sequences may partially mediate Nab2 target selection. Taken together, these data demonstrate 1)Nab2 opposingly regulates neuronal morphology and shares associated neuronal RNAs with Atx2 and 2)Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.

overall_design: Using an RNA immunoprecipitation-sequencing (RIP-Seq) approach on total RNA isolated from adult Drosophila melanogaster heads to identify RNAs associating with Nab2 and Atx2 in Drosophila brain neurons. RNA from twelve samples of 300 adult female Drosophila heads each was isolated via the immunoprecipitation and extraction protocols described herein, generating twelve pairs of IP and Input samples, or twenty-four samples in total. These samples were composed of four biological replicates each of elav>Gal4 alone (control samples), elav>Nab2-FLAG, and elav>Atx2-3xFLAG.

first: John

middle: C

last: Rounds

first: Kenneth

middle: H


title: Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats (mRNA dataset)

first: Hui

last: Li

first: Jing-An

first: Qian-Zhi

first: Guan-Yi


title: PolyA-selected RNA expression in whole brains of male BN-Lx/CubPrin and SHR/OlaIpcvPrin

city: Aurora

first: Laura

middle: Maren

last: Saba

state: CO

address: 12850 East Montview Blvd.

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary: As part of the PhenoGen Project (http://phenogen.org), RNA-Seq data has been collected from whole brain samples of two inbred strains that represent the parental strains from the HXB/BXH recombinant inbred panel, which is part of the Hybrid Rat Diversity Panel. Processed data were generated as part of manuscript, Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high throughput RNA sequencing and DNA sequence.

overall_design: RNA expression levels were examined in 6 male rat whole brain samples. Rats were from two inbred strains, BN-Lx/CubPrin and SHR/OlaIpcvPrin.

first: Boris

last: Tabakoff

first: Paula

last: Hoffman

first: Ryan

last: Lusk


title: Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats

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

overall_design: Refer to individual Series


title: Agilent SurePrint G3 Mouse GE V2.0 Microarray(8*60K,Design ID:074809)

city: shanghai

first: sun

middle: tong

last: xin

address: xinjunhuanlu

institute: oebiotech

summary: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). The sample labeling, microarray hybridization and washing were performed based on the manufacturer's standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).


title: Changes in epigenetic profiles throughout early childhood and their relationship to the response to  pneumococcal vaccination

city: Santiago de Compostela

first: Sara

last: Pischedda

state: A Coruña

address: Avenida da Choupana s/n

department: Instituto de Investigación Sanitaria de Santiago de Compostela

country: Spain

institute: Hospital Clinico Universitario de Santiago de Compostela

summary: Infinium Methylation 450 K was used to profile the epigenetic differences in 24 children between two timepoints: 12 months (baseline group) and 24 months and to elucidate the methylation differences between 12  high and 12  low PCV-13 booster vaccine responders, in order to identify pathways that show significant changes over time and those that are associated with a more robust immune response.

overall_design: DNA was extracted from blood clots collected from 24 participants at 12 and 24 months of age. The treated DNA was hybridized to the Illumina Infinium Methylation450K BeadChip

first: Pischedda

last: Sara

first: O'Connor

last: Daniel

first: Fairfax

last: Benjamin P

first: Salas

last: Antonio

first: Martinon-Torres

last: Federico

first: Pollard

last: Andres J

first: Trück

last: Johannes


title: Early life adversity promotes sex-specific resilience to opioid addiction-related phenotypes

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

summary: Early life stress that is not overwhelming can have an “inoculating” effect that promotes resilience in adulthood. However, the mechanisms underlying stress inoculation are unknown and animal models are lacking. Here we used the limited bedding and nesting (LBN) model of adversity to evaluate stress inoculation of addiction-related phenotypes. In LBN, pups from postnatal day 2–9 and their dams were exposed to a low resource environment. In adulthood, they were tested for addiction-like phenotypes and compared to rats raised in standard housing conditions.  High levels of impulsivity are associated with substance abuse, but LBN reduced impulsive choice compared to controls in males. LBN males also self-administered less morphine and had a lower breakpoint on a progressive ratio reinforcement schedule than controls. LBN had no effect on addiction-related behavior in females. The nucleus accumbens (NAc) mediates these behaviors, so we tested whether LBN altered NAc physiology in drug-naïve and morphine-exposed rats. LBN reduced sEPSC frequency in males, but not females. Only in males, LBN prevented a morphine-induced increased in the AMPA/NMDA ratio. RNA sequencing and genome-wide assessments of histone modifications were performed to delineate the molecular signature in the NAc associated with LBN-derived phenotypes. LBN produced sex-specific changes in transcription, including in genes related to glutamate transmission. Remodeling of unique histone marks may have contributed to these distinct transcriptional profiles. Collectively, these studies reveal that LBN causes a male-specific stress inoculation effect against addiction-related phenotypes. Identifying factors that promote resilience to addiction may reveal novel treatment options for patients.

overall_design: 20 total samples were analyzed including 4 male control, 5 male LBN, 5 female control, and 6 female LBN samples.

first: Evelyn

last: OrdoñesSanchez

first: Charlotte

last: Bavley

first: Andre

last: Deutschmann

first: Rachel

last: Carpenter

first: Drew

last: Peterson

first: Reza

last: Karbalaei

first: James

last: Flowers

first: Carleanne

last: Rogers

first: Miranda

last: Langrehr

first: Cory

last: Ardekani

first: Sydney

last: Famularo

first: Angela

last: Bongiovanni

first: Melissa

last: Knouse

first: Stan

last: Floresco

first: Benjamin

middle: A

last: Garcia

first: Lisa

last: Briand

middle: E

first: Debra

last: Bangasser


title: Efficient manipulation of gene dosage in human iPSCs using CRISPR/Cas9 nickases

city: Hong Kong

first: Nancy

middle: Y.

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

summary: The dysregulation of gene dosage due to duplication or haploinsufficiency is a major cause of autosomal dominant diseases such as Alzheimer’s disease. However, there is no rapid and efficient method for manipulating gene dosage in a human model system such as human induced pluripotent stem cells (iPSCs). Here, we describe a simple and precise method to simultaneously generate iPSC lines with different gene dosages using paired Cas9 nickases. We first generate a Cas9 nickase variant with broader protospacer-adjacent motif specificity to expand the targetability of double-nicking–mediated genome editing. As a proof-of-concept study, we examine the gene dosage effects on Alzheimer’s disease pathogenesis patient-derived iPSC line that carries three copies of APP (amyloid precursor protein). This method enables the rapid and simultaneous generation of iPSC lines with monoallelic, biallelic, or triallelic knockout of APP. The cortical neurons generated from isogenically corrected iPSCs exhibit gene dosage-dependent correction of disease-associated phenotypes of amyloid-beta secretion and Tau hyperphosphorylation. Thus, the rapid generation of iPSCs with different gene dosages using the method described herein can be a useful model system for investigating disease mechanisms and therapeutic development.

overall_design: RNA-sequencing of neurons derived from nondemented control (NDC), APP duplication (APP) and isogenically-corrected (Iso) iPSC lines

first: Tao

last: Ye

first: Yangyang

last: Duan

first: Hayley

middle: W

last: Tsang

first: He

last: Xu

first: Yuewen

last: Chen

first: Han

last: Cao

first: Yu

first: Amy

middle: K

last: Fu

middle: Y


title: Genome-wide DNA methylation analysis of a cohort of 41 patients affected by Oculo-auriculo-vertebral spectrum (OAVS).

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

summary: Oculo-auriculo-vertebral spectrum (OAVS; OMIM 164210) is a rare developmental disorder originating from abnormal development of the first and second branchial arch. The clinical phenotype is extremely heterogeneous with ear anomalies, hemifacial microsomia, ocular defects, and vertebral malformations being the main features. MYT1, AMIGO2 and ZYG11B gene variants having been reported in a few OAVS patients, but the etiology of the disease remains largely unknown. A multifactorial origin of the OAVS has been proposed, including the involvement of environmental or epigenetic mechanisms. To identify the epigenetic mechanisms contributing to OAVS, we evaluated the DNA-methylation profile of 41 affected patients by using a BeadChip 450K genome-wide approach. The analysis was first carried out at a group level by comparing the OAVS group methylation profile to the control group (n=48) revealing a slight epigenetic variation in a number of genes implicated in biological processes involving basic chromatin dynamics such as DNA packaging, chromatin assembly, protein-DNA organization, and gene silencing  in patients compared to controls . A subsequent analysis focused on searching for Stochastic Epigenetic Variations (SEV) in individual profiles identified an increased number of SEV in OAVS patients compared to controls. Although no recurrent deregulated enriched region was evidenced, isolated patients harboring suggestive epigenetic variations, including changes in imprinted domains, were identified. The recognition of a different DNA methylation pattern in OAVS patients and the identification of isolated patients with suggestive epigenetic variations provide consistent evidences for the contribution of epigenetic mechanisms to the etiology of this complex and heterogeneous disorder.

overall_design: Genome-wide DNA methylation analysis of a cohort of 41 OAVS patients using Illumina Human Methylation 450K Beadchips.

first: Valentina

last: Guida

first: Alessandro

last: De Luca

first: Davide

last: Gentilini


title: A distinct metabolic response characterizes sensitivity to EZH2 inhibition in multiple myeloma

city: Uppsala

first: Alba

last: Atienza-Párraga

state: Uppsala

address: Dag Hammarskjölds 20, Rudbecklaboratoriet-C11:3

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

type: Methylation profiling by genome tiling array

summary: Multiple myeloma (MM) is a heterogeneous haematological disease that remains clinically challenging. Increased activity of the epigenetic silencer EZH2 is a common feature in patients with poor prognosis. Previous findings have demonstrated that metabolic profiles can be sensitive markers for response to treatment in cancer. While EZH2 inhibition (EZH2i) has proven efficient in inducing cell death in a number of human MM cell lines, we hereby identified a subset of cell lines that despite a global loss of H3K27me3, remains viable after EZH2i. By coupling liquid chromatography-mass spectrometry with gene and miRNA expression profiling, we found that sensitivity to EZH2i correlated with distinct metabolic signatures resulting from a dysregulation of genes involved in methionine cycling. Specifically, EZH2i resulted in a miRNA-mediated downregulation of methionine cycling-associated genes in responsive cells. This induced metabolite accumulation and DNA damage, leading to G2 arrest and apoptosis. Altogether, we unveiled that sensitivity to EZH2i in human MM cell lines is associated with a specific metabolic and gene expression profile post-treatment.

overall_design: Bisulphite converted DNA from 2 multiple myeloma cell lines was hybridised to the Illumina Infinium MethylationEPIC Beadchip, in 3 replicates per cell line.

first: Patrick

last: Nylund

last: Atienza Párraga

first: Jakob

last: Haglöf

first: Elke

last: de Bruyne

first: Eline

last: Menu

first: Berta

last: Garrido-Zabala

first: Anqi

last: Ma

first: Jian

last: Jin

first: Fredrik

last: Öberg

first: Karin

last: Vanderkerken

first: Antonia

last: Kalushkova

first: Helena

last: Jernberg-Wiklund


title: Expression data from intestine samples of mice lacking intestinal Pcyt1a, which encodes an enzyme that regulates phosphatidylcholine synthesis.

city: Edmonton

first: René

middle: L

last: Jacobs

state: Alberta

address: Li Ka Shing Centre for Health Research

department: Agriculture, Food and Nutritional Science; Biochemistry

country: Canada

institute: University of Alberta

summary:
Phosphatidylcholine is a membrane lipid. To determine its role in the intestine, we deleted the gene that produces this lipid specificallly in intestinal epithelial cells and conducted expression analysis.
We used microarray analysis to determine changes in gene expression that occur in the absence of intestinal phosphatidylcholine synthesis.

overall_design: Mice lacking intestinal Pcyt1a and their Pcyt1a-positive controls were fasted overnight and re-fed a high fat diet. We then extracted RNA and hybridized to Affymetrix microarrays. Samples were collected from the geometric middle of the small intestine (jejunum).

first: Rene

first: John

middle: P

last: Kennelly


title: Substrate Identification Using a Chemical Genetics Approach Reveals a Role for PARP-7-Mediated MARylation in Controlling Microtubule Stability in Ovarian Cancer Cells

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: ADP-ribosylation (ADPRylation) is a regulatory posttranslational modification of proteins that results in the covalent attachment of ADP-ribose (ADPR) moieties on target proteins. PARP-7 (TiPARP) is a monoADPR transferase whose proteins substrates and biological activities are poorly understood. Here, we describe a chemical genetics approach that has allowed us to identify substrates of PARP-7 and explore their biological functions. We observed reduced levels of PARP7 mRNA in ovarian cancer patient samples versus normal tissue, but found nonetheless that PARP-7 is required for a number of cancer-related biological endpoints in ovarian cancer cells, including growth, migration, and invasion. Global gene expression and gene ontology analyses in ovarian cancer cells subjected to siRNA-mediated knockdown of PARP7 revealed an enrichment of genes encoding proteins with roles in cell-cell adhesion, cell cycle arrest, apoptosis, and gene regulation. To identify the ADPRylated substrates that underlie PARP-7-mediated ovarian cancer cell phenotypes, we developed an NAD+ analog-sensitive approach for PARP-7 comprising a PARP-7 NAD+ binding pocket mutant (S563G) paired with the NAD+ analog 8-Bu(3-yne)T-NAD+. When coupled with mass spectrometry, this approach allowed us to identify the PARP-7 ADP-ribosylated proteome in ovarian cancer cells, including components of the cell-cell adhesion and cytoskeleton organization machinery. Specifically, we found that PARP-7 monoADPRylates α-tubulin to promote microtubule instability, which may play a key role in the regulating ovarian cancer cell growth and motility. Collectively, our results point to an extensive PARP-7 ADP-ribosylated proteome with important roles in cancer-related cellular phenotypes.

overall_design: Using RNA-seq we evaluated the expression changes of mRNAs in OVCAR4 cells after siRNA mediated PARP7 knockdown.

first: Palavalli

last: Lavanya

first: Gibson

last: Bryan

first: Challa

last: Sridevi

first: Nandu

last: Tulip

first: Stokes

last: Mikayla

first: Huang

last: Dan

first: Lea

last: Jayanthi

first: Kraus

last: Lee


title: Human-specific transcriptome of ventral and dorsal midbrain dopamine neurons

status: Public on Feb 03 2021

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

summary: Neuronal loss in the substantia nigra pars compacta (SNpc) in Parkinson disease (PD) is not uniform, as dopamine neurons from the ventral tier are lost more rapidly than those of the dorsal tier. Identifying the intrinsic differences that account for this differential vulnerability may provide a key for developing new treatments for PD. Here, we compared the RNA-sequenced transcriptomes of ~100 laser captured microdissected SNpc neurons from each tier from 7 healthy controls. Expression levels of dopaminergic markers were similar across the tiers, whereas markers specific to the neighboring ventral tegmental area were virtually undetected. After accounting for unwanted sources of variation, we identified 106 differentially expressed genes (DEGs) between the SNpc tiers. The genes higher in the dorsal/resistant SNpc tier neurons displayed coordinated patterns of expression across the human brain, their protein products had more interactions than expected by chance, and they demonstrated evidence of functional convergence. No significant shared functionality was found for genes higher in the ventral/vulnerable SNpc tier. Surprisingly but importantly, none of the identified DEGs was among the familial PD genes or genome-wide associated loci. Finally, we found some DEGs in opposite tier orientation between human and analogous mouse populations. Our results highlight functional enrichments of vesicular trafficking, ion transport/homeostasis and oxidative stress genes showing higher expression in the resistant neurons of the SNpc dorsal tier. Furthermore, the comparison of gene expression variation in human and mouse SNpc populations strongly argues for the need of human-focused omics studies

overall_design: A total of 14 samples corresponding to the dorsal and ventral tiers of the SNpc of 7 healthy controls.  Each sample corresponds to ~100 laser captured microdissected SNpc neurons.

first: Ilaria

last: Poggiolini

first: Tobias

last: Ilmer

first: Richard

last: Wade-Martins

first: Caleb

last: Webber

first: Laura

last: Parkkinen


title: Expression data from intestine samples of mice lacking intestinal Pcyt1a, which encodes an enzyme that reguates phosphatidylcholine synthesis.

first: René

last: Jacobs

first: Rene


title: Single cell RNA-seq analyses of kidney repair and how maladaptive repair leads to kidney atrophy following ischemia/reperfusion injury

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

summary: To better understand the pathogenesis of AKI-to-CKD transition and specifically the mechanism of kidney atrophy, we compared the kidney response to an identical time of ischemic injury between mice subjected to unilateral ischemia/reperfusion (U-IRI) to induce atrophy and those subjected to unilateral IRI with contralateral nephrectomy (IRI/CL-NX) to induce adaptive repair. We performed single cell RNA-sequencing (scRNA-seq) analyses on day 14 after injury to identify major cell types in the kidney and the differential transcriptional response between the models in each cell type.

overall_design: Single cell mRNA profiling of kidneys from wild-type mice subjected to U-IRI or IRI/CL-NX

first: Xu

last: Leyuan

first: Lloyd

middle: G

last: Cantley


title: Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions as cells transit the cell cycle, but how remains unclear. Here, we use ChIP-seq in cell-cycle sorted cultured cells to define histone modification patterns through the cell cycle.

overall_design: We used cell-cycle sorting methods (fluorescence-activated cell sorting (FACS), centrifugal elutriation and mitotic shakeoff) in two cultured cell lines, HeLa and lymphoblastoid cells. We carried out ChIP-seq for histone modifications on chromatin from cells sorted into G1 phase, G2M phase or mitosis (HeLa only).

first: John

last: Halsall

first: Simon

last: Andrews

first: Charlotte

last: Rutledge

first: Gabriella

last: Ficz

first: Wolf

last: Reik

first: Bryan

middle: M

last: Turner


title: Expression data from mouse flow-sorted Kupffer cells

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

institute: University Health Network

summary: RNA was isolated from flow-sorted Kupffer cells under the two different conditions (tacrolimus and control) using RNeasy mini kit (Qiagen). Integrity of DNA and RNA was assessed by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). 500 nanograms of RNA were used for analysis with Affymetrix Mouse Gene 2.0 ST platform

overall_design: flow-sorted Kupffer cells isolated from mice 7 days after infected with S. aureus under the two different conditions: Tacrolimus only (1µg/g body weight), and Untreated

first: Mamatha

last: Bhat


title: Role of HLR1, an ancient light-harvesting protein of PSI, in light absorption and photoprotection in Nannochloropsis oceanica

city: Haikou

first: Yandu

last: Lu

state: China

address: State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology

department: College of Oceanology

institute: Hainan University

summary: We isolated a Nannochloropsis oceanica LHCR mutant, named hlr1, which exhibits a greater tolerance to high light (HL) stress compared to the wild type.Global gene expression of WT and the hlr1 mutant, as a function of time in dark incubation (DK) and under high irradiance was measured by mRNA-Seq

overall_design: Total RNA of the algal cells was prepared using an RNA miniprep kit (CWBIO) and the concentrations were measured using the NanoDrop 2000 spectrophotometer (Thermo). Libraries were constructed and then sequenced using the HiSeq 2500 (Illumina), which generated about 18 million read pairs per sample (ANNOROAD). Raw reads containing adapter, poly-N, and low-quality reads were filtered and the effective data were mapped with the Nannochloropsis reference genome using TopHat (version 2.0.12). After excluding the ribosomal RNA or transfer RNA, we estimated the abundance of the transcripts using RPKM (Reads per Kilo bases per Million reads) 62. The p values were adjusted using the Benjamini and Hochberg method 63. Corrected p value﹤0.05 and fold change more than two were set as the threshold for significant difference in expression. GO annotations of the data provided by our RNA-Seq analysis were performed using PANTHER (www.pantherdb.org/pathway/) 64. Three biologically independent sets of samples were prepared at each time point.

first: Qinhua

last: Gan

first: Masakazu

last: Iwai

first: Alessandra

last: Bellan

first: Adrien

last: Burlacot

first: Oliver

last: Dautermann

first: Thien

last: Crisanto

first: Gilles

last: Peltier

first: Tomas

last: Morosinotto

first: Anastasios

last: Melis

first: Krishna

last: Niyogi


title: Distinct transcriptomic profiles in the dorsal hippocampus and prelimbic cortex are transiently regulated following episodic learning

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: A fundamental, evolutionarily conserved biological mechanism required for long-term memory formation is rapid induction of gene transcription upon learning in relevant brain areas. For episodic types of memories, two regions undergoing this transcription are the dorsal hippocampus (dHC) and prelimbic (PL) cortex. Whether and to what extent these regions regulate similar or distinct transcriptomic profiles upon learning remains to be understood. Here, we used RNA sequencing in the dHC and PL cortex of male rats to profile their transcriptomes in untrained conditions (baseline) and at 1 hour and 6 days after inhibitory avoidance learning. We found that, out of 33,713 transcripts, over 14,000 were significantly expressed at baseline in both regions and approximately 3,000 were selectively enriched in each region. Gene Ontology biological pathway analyses indicated that commonly expressed pathways included synapse organization, regulation of membrane potential, and vesicle localization. The enriched pathways in the dHC were gliogenesis, axon development, and lipid modification, while in the PL cortex included vesicle localization and synaptic vesicle cycle. At 1 hour after learning, 135 transcripts changed significantly in the dHC and 478 in the PL cortex; of these, only 34 were shared. Biological pathways most significantly regulated by learning in the dHC were protein dephosphorylation, glycogen and glucan metabolism, while in the PL cortex were axon development and axonogenesis. The transcriptome profiles returned to baseline by 6 days after training. Thus, a significant portion of dHC and PL cortex transcriptomic profiles is divergent and their regulation upon learning is largely distinct and transient.

overall_design: Genome-wide RNAseq was conducted on 3 independent pools (replicates) of dorsal hippocampus (dHC) and prelimbic (PL) cortex extracts, each comprising 5 bilateral regions (5 individual animals), that were either: i) Untrained i.e., remained in home cage; ii) Trained in inhibitory avoidance and euthanized 1 hour after training; iii) Trained in inhibitory avoidance and euthanized 6 days after training.

first: Aaron

last: Katzman

first: Dana

last: Kapeller-Libermann

first: Xiaojing

last: Ye

first: Aristotelis

last: Tsirigos

first: Adriana

last: Heguy

first: Cristina

last: Alberini


title: Genome-wide identification and characterization of transfer RNA-derived small RNAs in Trichomonas vaginalis

city: Beijing

first: Zhensheng

last: Wang

address: Dongdan santiao

department: Microbiology and Parasitology

institute: Peking Union Medical College

summary: In this study, we performed deep sequencing and bioinformatics analyses of short RNAs from three strains of Trichomonas vaginalisto identify and characterize novel type of small RNAs. We detected a new type of small RNA from tranfer RNA known as tRFs and tRNA-halves.

overall_design: Trichomonas  vaginalis mall RNAs of 14–40 nt in length were extracted and purified from the total RNA of trophozoite staged parasites. Small RNA libraries were constructed and sequenced by  Illumina NextSeq 500 system.

first: Heng

first: Zenglei


title: Enhanced metabolic potentials and functional gene interactions of microbial stress response towards high elevation in freshwater lakes

city: Nanjing

first: Huabing

last: Li

address: East Beijing Road 73

institute: Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences

summary: Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in four lakes at low and high elevations of approximately 530 and 4,600 m a.s.l., respectively.

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: In this study, to investigate the influence of elevation  on microbial functional genes in aquatic environments, we focused on four shallow freshwater lakes at comparable elevations, two HELs (at 4,652 m and 4,608 m, respectively) and two LELs (at 530 m and 525 m, respectively), at Siguniang Mountain in Sichuan province, China. Six sampling sites were set in each lake. At each site, approximately 1 L of water was collected from surface waters (top 50 cm) for microbial Geochip analyses

first: Qinglong

last: Wu

first: Jin

last: Zeng


title: Analysis of chromatin accessibility in adult mouse pituitary using single-cell ATAC-seq

city: La Jolla

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

summary: To gain insight into patterns of chromatin accessibility in distinct cell subtypes of mouse pituitary, pituitaries from two adult mice were collected and subjected to single-cell ATAC-seq analysis using 10X Genomics platform

overall_design: Two adult pituitaries were dissected and processed indiviudally for single-cell ATAC-seq. Nuclei were isolated and diluted to achieve ~6000 individual nuclei for library construction. Libraries were sequenced to ~50% saturation. Analysis was done using Cell Ranger pipeline.

first: Jia

last: Shen

first: Qianlan

last: Xu

first: Dorota

last: Skowronska-Krawczyk


first: harini

last: ramalingam

state: Texas

address: 5323 Harry Hines Boulevard

department: IMN

institute: UTSW

summary: Purpose: Determine the differential m6A methylation pattern of Mettl3 between wildtype, Pkd1F/RC-KO and Pkd1F/RC-Mettl3-DKO mouse kidneys. Methods: m6A RNA IP using the Magna MeRIP™ m6A Kit (EMD Millipore, catalog #17-10499) was performed on P18 wildtype, Pkd1F/RC-KO and Pkd1F/RC-Mettl3-DKO mouse kidney samples. Two biological replicate samples from each genotype were sequenced. Each sample was a pool of 6 kidneys of the same genotype. The input samples were also sequenced to obtain mRNA profiles. Results: 133 mRNAs were found to be differentially hypermethylated in the Pkd1-KO kidneys compared to the control kidneys and differentially hypomethylated in the Pkd1-Mettl3-DKO kidneys compared to the Pkd1-KO kidneys. Two key pathogenic mRNAs namely, c-Myc and Avpr2 were identified and validated as Mettl3 targets. The mRNA transcript levels were unchanged between Pkd1-KO and Pkd1-Mettl3-DKO kidneys. Conclusion: Mettl3/m6A promotes translation of pathogenic mRNAs to mediate cystogenesis in mouse models of ADPKD.

overall_design: m6A methylation profile of P18 wildtype, Pkd1F/RC-KO and Pkd1F/RC-Mettl3-KO murine kidneys

first: Vishal

last: Patel

first: Harini

last: Ramalingam


title: NK cell transcriptomic study

city: Lyon

first: Antoine

last: Marçais

address: 21 avenue Tony Garnier

country: France

institute: Inserm

summary: Comparison of the transcripts expressed by NK cells from HBV infected patients compared to NK cells from healthy controls

overall_design: CD56+CD3neg cells were sorted from the PBMCs of 5 control healthy donors (VS) and 4 chronic hepatitis B patients (PA).

first: Anne-Laure

last: Mathieu

first: Marie

last: Marotel


title: Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules [ChIP-seq]

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Angiotensin-Converting Enzyme 2 (ACE2) binds SARS-CoV-2 spike protein and facilitates viral entry into the cell. ACE2 is expressed in the kidney and renal injury strongly impacts COVID-19 prognosis. In addition, a short, interferon-inducible isoform of ACE2, dACE2 was recently identified. Change in ACE2 expression has already been linked to several human nephropathies. However, these changes were not analyzed in context of dACE2 and regulation of ACE2 expression in the kidney remains unclear. Human primary Renal Proximal Tubule cells were used for all experiments. ChIP-seq analysis of histone modifications (H3K27ac, H3K4me3, K3K4me1), RNA polymerase loading and DNAse hypersensitive sites (DHS) were used to identify gene regulatory elements in the ACE2 locus. qRT-PCR was used to assess mRNA expression of ACE2, dACE2, TMPRSS2 and STAT1. RNA-seq was used to identify changes in global gene expression after cytokine treatment. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq profiles and RNA-seq mapping. qRT-PCR differentiating between ACE2 and dACE2 revealed that only dACE2 is interferon inducible. dACE2 mRNA was upregulated 300- and 600-fold by IFNα and IFNβ, respectively, while full length ACE2 was unchanged. Interferon stimulation also resulted in elevated STAT1 expression. JAK inhibitor ruxolitinib ablated both STAT1 and dACE2 expression after interferon treatment. RNA-seq analysis revealed approximately 1200 genes induced by IFNβ, largely innate immune response-related. We showed that human primary proximal tubules express ACE2 and its interferon-inducible short isoform, dACE2, from an intronic promoter. We also deliver new datasets identifying cytokine response genes in proximal tubule cells.

overall_design: ChIP-seq and RNA-seq was used to characterize ACE2 locus and gene expression profiles in cytokine stimulation.

first: Hye

first: Jakub

last: Jankowski


title: Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat

city: Urrbrae

first: Haipei

last: Liu

state: South Australia

address: PMB1 Waite Building, School AFW

country: Australia

institute: The University of Adelaide

summary: Water-deficit stress negatively affects wheat yield and quality. Abiotic stress on the parental plants during reproduction could have transgenerational effects on the progenies. Here we investigated the transgenerational influence of pre-anthesis water-deficit stress by detailed analysis of the yield components, grain quality traits, and physiological traits in durum wheat. Next-generation sequencing analysis profiled the small RNA-omics, mRNA transcriptomics, and mRNA degradomics in the progenies. Parental water-deficit stress had positive impacts on the progenies in certain traits like harvest index and protein content in given genotype. Small RNA-seq identified 1739 conserved and 774 novel microRNAs (miRNAs). Transcriptome-seq characterised the expression of 66,559 genes while degradome-seq profiled the miRNA-guided mRNA cleavage dynamics. Differentially expressed miRNAs and genes were identified, with significant regulatory patterns subject to trans- and inter- generational stress. Integrated analysis based on the three omics revealed the significant biological interactions between stress-responsive miRNA and targets, with possible contributions towards transgenerational stress tolerance via pathways such as hormone signalling and nutrient metabolism. Our study provides the first confirmation of the transgenerational effects of water-deficit stress in durum wheat. New insights gained on the molecular level indicate that key miRNA-mRNA modules are potential candidates in transgenerational stress improvement.

overall_design: Analysis of small RNA transcriptome, mRNA transcriptome and mRNA degradome in eight biological pools (four treatment groups by two tissue types)

first: Amanda

middle: J

last: Able

first: Jason


title: ChIP-seq analysis of HIF-1α capacity to bind the promoters of its target genes on wt vs. PARP-1 K.O. cells

city: Granada

first: Juan

middle: Manuel

last: Marti

address: Avda. del Conocimiento 17

institute: CSIC

summary: Comparison of the HIF-1α DNA binding profile after 4 hours of hypoxia 1% on HEK293T PARP-1 K.O. CELLS vs. HEK293T WT cells after 4 hours of hypoxia 1%.

overall_design: Examination of HIF-1α hypoxic-induced binding to the DNA in 2 cell types.

first: Alicia

last: Barroso del Jesus

first: Eduardo

last: Andrés León

first: Ángel

last: García Díaz

first: Javier

last: Oliver-Pozo

last: Martí


title: Genome-wide maps of FANCD2 binding sites in untreated and aphidicolin-treated HCT116 cells.

city: Villejuif

first: Valeria

last: Naim

address: 114 rue Edouard Vaillant

department: Genome Stability and Oncogenesis

institute: CNRS UMR8200 University Paris Sud, Gustave Roussy

summary: Analysis of FANCD2 targeted sequences and identification DNA motifs regulating transcription of large genes at common fragile sites.

overall_design: ChIP-seq analysis of FANCD2 peaks in untreated and aphidicolin-treated HCT116 cells using Active Motif Service

first: Philippe

last: Fernandes

first: Benoit

last: Miotto

first: Claude

last: Saint-Ruf

first: Viola

last: Nahse

first: Silvia

last: Ravera

first: Enrico

last: Cappelli


title: RNA Sequencing Analysis of MC38 tumors with Glutamate decarboxylase 1 Knockdown

status: Public on Feb 02 2021

city: Durham

first: De

last: Huang

state: NC

address: 308 Research Drive

institute: Duke university

summary: Various types of cancers, including colorectal cancer, have shown an unusual dependence on glutamine. Glutamine can undergo an alternate fate in neurons: conversion into a non-proteinogenic amino acid gamma-aminobutyric acid (GABA) by the glutamic acid decarboxylase (GAD), including two family members GAD1 and GAD2. Some studies have shown that GAD1 expression is dysregulated in certain cancer types, but the effect of GAD1 on the tumorigenic process remain largely unknown. Thus, we use mouse colon adenocarcinoma MC38 tumor samples to perform RNA-sequencing (RNA-seq) assay. The goal of this study is to investigate GAD1-mediated transcriptome changes within tumors.

overall_design: MC38 cells stably expressing GAD1 shRNAs (GAD1-shA and GAD1-shB) or non-targeting shRNA control (NTC) were subcutaneously injected into C57BL/6 mice. All the tumors were extracted 20 days after implantation. Total RNA was extracted from GAD1-shA GAD1-shB and NTC MC38 tumor samples (3 replicates per group) using an RNeasy kit (Qiagen) and dissolved in RNase-free water. RNA samples were sequenced on Illumina novaseq.

first: Xiao-Fan

last: Wang


title: MAPKAP kinase-2  Drives Expression of Angiogenic Factors by Tumor-Associated Macrophages in a Model of Inflammation-Induced Colon Cancer

first: Michael

middle: B

last: Yaffe

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: MK2 is essential for optimal macrophage differentiation into a pro-tumorigenic M2-like state.

overall_design: RNA-seq were performed on M0 and M2 polarized macrophages isolated from bone marrow of MK2 wild type and knock out mice.


title: Recurrent human papillomavirus-related head and neck cancer undergoes metabolic re-programming and is driven by oxidative phosphorylation

city: Pittsburgh

first: Umamaheswar

last: Duvvuri

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Human papillomavirus (HPV) infection drives the development of some head and neck cancer squamous cell carcinomas (HNSC). Although these tumors are sensitive to treatment, ~10% of patients fail therapy. However, the mechanisms that underlie treatment failure remain unclear. Here, we assessed the transcriptional profiles of 10 paired primary and subsequent recurrent HPV-related oropharyngeal squamous cell carcinomas (OPSCCs) using an exome-capture hybrid RNA sequencing assay. Principal componenent analysis using the expression data from the top 500 most variable genes revealed that 29.3% of the variance was aassociated with tumor status (i.e., primary vs recurrent tumor). Four of the primary/recurrent tumor pairs demonstrated greater clustering based on the patient of origin rather than the tumor status (primary vs recurrent). Additionally, two of the recurrences were distant, two were local, and the remaining six were regional. The recurrent tumors did not cluster necessairly based on site of recurrence. Unsupervised heirarchical clustering of the top 500 most variable genes revealed a correlation between recurrent tumors and metabolic gene expression while the primary tumors demonstrated increased expression in several immunologic related genes, mitogenic signaling, and epigenetic signaling genes. Using the PANTHER GO-Slim biological process pathway analysis, we identified enrichment of processes involved in biosynthesis, metabolism including oxidative phosphorylation, and Wnt signaling. Using gene set enrichment analysis, we observed enrichment in oxidative phosphorylation, fatty acid metabolism, and glutathione metabolism as well as MYC, P53-dependent DNA damage repair, and NRF2 pathway gene expression among the recurrent HPV-associated OPSCCs.

overall_design: A total of 24 samples were analyzed including 12 primary tumors and 12 recurrences. Quality control was performed on the raw reads. Of the original twelve sets of paired primary and recurrent tumors, gene expression data from two pairs were not included in the downstream analyses due to low quality. Counts were normalized using counts per million normalization.

first: Richard

last: Harbison

first: Avani

last: Vyas


title: Expression data from peripheral blood mononuclear cells(PBMCs) of patients with bronchial asthma and normal controls

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Bronchial asthma is a heterogeneous disease with distinct disease phenotypes and underlying pathophysiological mechanisms. LncRNAs involves in numerous functionally different biological and physiological processes. The aim of this study is to identify the differentially expressed lncRNAs and mRNAs in patients with asthma and to further explore the functions and interactions between lncRNAs and mRNAs.
Ten patients with asthma and 9 healthy controls were enrolled in this study. We used microarray analysis to identify lncRNA and mRNA expression in their PBMC.

overall_design: A total of 10 patients with bronchial asthma and 9 healthy controls participated in the study. Bronchial asthma was diagnosed according to the guidelines of Global Initiative for Asthma. We collected venous blood (6 ml) from each participant using an EDTA-anticoagulated tube. PBMCs were isolated via density gradient centrifugation.

first: Ting

last: Yang

first: Han

last: Cui


title: Effect of IMD-0354 on gene expression in melanoma A375 cells

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: The purpose of this RNAseq is to analyse the effect of compound IMD-0354 on gene expression in melanoma A375 cells. RNAseq analysis identified unfolded protein response, cell cycle and DNA damage pathways to be effected by IMD-0354.

overall_design: A375 cells were treated with different concentrations of IMD-034 for 24h and 48h. RNA were extracted and subjected to RNAseq

first: Yongmei

last: Feng

first: Gaurav

last: Pathria

first: Susanne

last: Heynen-Genel

last: Jackson

first: Jun

last: Yin

first: David

last: AScott

first: Ze’ev

last: ARonai


title: OBF1 and Oct factors control the germinal center transcriptional program (RNA-seq - mouse)

city: Basel

first: Shuang

last: Song

state: Basel

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: OBF1 is a specific coactivator of the POU family transcription factors OCT1 and OCT2. OBF1 and OCT2 are B cell-specific and indispensable for germinal center (GC) formation, but their mechanism of action is unclear. Here, we show by ChIP-seq that OBF1 extensively colocalizes with OCT1 and OCT2 and stabilizes their binding. We found that these factors also often colocalize with transcription factors of the ETS family, such as PU.1 and ETS1. Furthermore, we showed that OBF1, OCT2 and OCT1 bind widely to the promoters or enhancers of genes involved in GC formation, such as the master regulators Bcl6 and Foxo1. shRNA knockdown experiments demonstrated that OCT1, OCT2 and OBF1 are essential for proliferation of GC-derived lymphoma cell lines. OBF1 downregulation disrupts the GC transcriptional program: genes involved in GC maintenance -such as BCL6- are downregulated, while genes related to exit from the GC program are upregulated. Ectopic expression of BCL6 does not restore the proliferation of GC-derived Raji cells depleted of OBF1 unless IRF4 is also depleted, indicating that OBF1 controls a critical regulatory node in GC differentiation.

overall_design: RNA-seq of mouse PU1 KO and OBF1KO CD19+ B cells under LPS stimulation


title: The effect of Repeated Cross Fostering (RCF) on transcriptomic profiles of mouse Ventral Tegmental Areas across different sexes and strains

city: Rome

first: Luisa

last: Lo Iacono

address: via del fosso di Fiorano 64

department: behavioral neuroscience

institute: Fondazione Santa Lucia IRCCS

summary: Early life experiences affecting the attachment bond formation can result in maladaptive behaviors acting on developmental trajectories and programming adult brain functions in a sex-dependent manner. Repeated Cross Fostering (RCF) manipulation in mice is able to interfere with attachment bond formation in mice. Using males and females from two different inbred strains of mouse, known to respond very differently to the RCF, we analyzed the effect of RCF on  the ventral tegmental area (VTA)-transcriptome in a sex-specific manner. Through next-generation mRNA-Seq, we profiled VTA transcriptomes in RCF and control adult male and female mice from both backgrounds.

overall_design: Brain Ventral Tegmental Area mRNA profiles of adult RCF and control mice from 2 different backgrounds (C57 and DBA) and from both sexes (male and female) overall resulting in 8 experimental groups. We performed comparisons between RCF and control mice in 4 different conditions (C57 male, C57 female, DBA male and DBA female)

first: Rossella

last: Ventura

first: Carlo

last: Cifani

first: Marco

last: Pietrosanto

first: Manuela

last: Helmer-Citterich


title: Molecular mechanism of Atractylon in invasion and migration of hepatic cancer cells based on high-throughput sequencing

city: Shanghai

first: Yang

last: Cheng

address: No. 528 Zhangheng Road

department: Institute of liver diseas

institute: Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine

summary: The aim was to research molecular mechanism of Atractylon in inhibition of invasion and migration of hepatic cancer cells. High-throughput sequencing was used as the main solution.

overall_design: This research include two groups: Atractylon (HepG2 with Atractylon treatment) VS Control ( HepG2 without any treatment).High-throughput sequencing was used to compare the  expression of lncRNAs between the two groups. Differential expressed lncRNAs were analysed, and ceRNA network was constructed. Top significantly differential expressed lncRNAs were screened and verified by vitro and vivo experiment.

first: Jian

last: Ping

first: Jianjie

last: Chen

first: Yifei

last: Fu

first: Hui

last: Zhao

first: Jiahua

last: Xue


title: Atrx deletion impairs cGAS-STING signaling and increases response to radiation and oncolytic herpesvirus in soft tissue sarcoma

first: Warren

last: Floyd

state: North Carolina

address: 450 Research Drive, LSRC Bldg, Room B324

department: Pharmacology and Molecular Cancer Biology

institute: Duke University

summary: RNA sequencing of isogenic ATRX wild-type (WT) and ATRX knockout (KO) paired isogenic cell lines treated with either 1.)interferon stimulatory DNA (ISD) and harvested 24 hours after treatment, 2)4 Gy ionizing radiation and harvested 36 hours after treatment, or 3) untreated control. These experiments help determine the differential impact of ATRX mutational status on cGAS-STING and type-I interferon signaling in soft tissue sarcoma.

overall_design: RNA sequencing of ATRX WT and ATRX KO soft tissue sarcoma cell lines


title: OBF1 and Oct factors control the germinal center transcriptional program (RNA-seq - human)

overall_design: RNA-seq between ctrl and IRF4 overexpression Raji cells


title: OBF1 and Oct factors control the germinal center transcriptional program (ChIP-seq, CUT&RUN)

overall_design: mapping OBF1 and H3K27ac in GC-drived B lymphoma cell lines, primray murine and human germinal center B cells


title: Abdominal fat mRNA transcriptome of Muscovy duck

city: Hefei

first: Xingyong

state: Anhui

address: 130 Changjiangxilu

department: College of Animal Science and Technology

institute: Anhui Agricultural University

summary: Abdominal fat is considered negatively associated with egg production. Therefore, it is necessary to clarity the regulatory mechanism for the abdominal fat deposition of Muscovy duck.

overall_design: Three Muscovy duck from each stages (12, 35, and 66 weeks of age) were selected with normal body weight were euthanized for abdominal fat sampling.