title: ChIP-Seq for Rhesus monkey placenta

status: Public on Jul 31 2021

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

country: USA

institute: National Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We generated ChIP-Seq (H3K4me1, H3K4me3 and H3K27ac) data for term Rhesus monkey placenta. Together with RNA-Seq and epigenomic data generated for placentas of human and mouse, we aim to understand the evolution of gene expression and regulatory elements among the placentas of different mammalian species.

first: Ming-an

first: Gernot

last: Wolf

first: Todd

last: Macfarlan


title: The effect of over expression of long non-coding RNA (ENSG00000233262) transcriptome changes in patient-derived human-induced pluripotent stem cells (IPSCs)

city: Shreveport

first: Tarek Magdy

last: Mohamed

state: LA

address: 1501 Kings Highway, BRI F3-15/22

department: Pathology

institute: LSU Health Shreveport

type: Expression profiling by high throughput sequencing

summary: We investigate the transcriptome changes in IPSC overexpressing ENSG00000233262 as compared to wilt-type IPSCs using an unbiased approach

overall_design: Patient–derived isogenic IPSCs was trasduced with lentiviral plasmid that over-expresseses ENSG00000233262 cDNA to generated ISO-NODICR that was then compared to wild-type isogenic IPSC (ISO).

first: Tarek

last: Magdy

first: Paul

last: Burridge


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB [RNA-Seq 5]

city: Toronto

first: Laura

last: Garcia Prat

address: 101 College street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: We show that lysosomes are antagonistically controlled by TFEB and MYC to balance catabolic and anabolic processes required for activating LT-HSC and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway for membrane receptor degradation limits LT-HSC metabolic and mitogenic activation; this promotes quiescence and self-renewal and governs erythroid-myeloid commitment. By contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism to drive LT-HSC activation. Collectively, our study identifies lysosomes as a central regulatory hub for proper and coordinated stem cell fate determination.

overall_design:
Short-term hematopoietic stem cells (ST-HSC) were sorted from human cord blood and cultured overnight before transduction with lentivirus to overexpress GP91 (CTRL) or TFEB. Three days later, BFP+ transduced cells were sorted for RNA extraction and sequencing.
Authors state that raw data will be uploaded to the EGA database.

last: Garcia-Prat


title: Gestational diabetes exposure induces an altered cardiac transcriptome that is associated with impaired cardiac function in the rat offspring

city: Winnipeg

first: Dr. Vernon

last: Dolinsky

state: Manitoba

address: 601 John Buhler Research Centre, 715 McDermot Avenue

department: Department of Pharmacology and Therapeutics

institute: University of Manitoba

summary: Gestational diabetes mellitus (GDM) is the most common complication of pregnancy. Children of mothers with GDM are at an increased risk for the development of cardiometabolic disease later in life, though the mechanisms responsible for this observation are unknown. We propose that an altered cardiac transcriptome, programmed in utero, may be a contributing mechanism to cardiometabolic disease development and hypothesize that the hearts of offspring exposed to GDM will exhibit altered gene expression pathways. The purpose of this project will be to study alterations in the cardiac transcriptome of young adult rat offspring after exposure to GDM to investigate the mechanisms responsible for the developmental origins of cardiovascular disease.

overall_design: To induce gestational diabetes mellitus (GDM) female Sprague-Dawley rats were fed a high fat and sucrose (HFS) diet prior to mating, throughout pregnancy and lactation. Lean control females received a low fat (LF) diet. Offspring were randomly assigned to HFS or LF diets after weaning at 3-weeks of age. Cardiac tissue was collected from the four groups of young-adult rat offspring at 3-months of age (n=6 Lean-LF, n=6 Lean-HFS, n=6 GDM-LF and n=6 GDM-HFS) for biochemical and gene expression (RNA-seq) analysis.

first: Stephanie

last: Kereliuk

first: Prasoon

last: Agarwal

first: Vern


title: Transcriptional characterization of cardiac tissue  of rat pups with pulmonary banding

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Expression analysis of cardiac tissue of rat pups with and without pulmonary banding

overall_design: RNA-seq on rat tissue

first: Guido

last: Bossers

first: Karel

last: van Duijvenboden

first: Phil

last: Barnett

first: Marie

last: Günthel


title: ExplorATE test data: a pipeline to explore active transposable elements from RNAseq data without a reference genome

status: Public on Jul 30 2021

city: Puerto Madryn

first: Martin

middle: Miguel

last: Femenias

state: Chubut

address: Bv. Almte Brown 2915

country: Argentina

institute: IPEEC-CENPAT-CONICET

summary: Transposable elements (TEs) are ubiquitous in genomes. Many of these TEs remain active and are an important fraction of the transcriptomes with potential effects on the host genomes. The functional impact of TEs is well known for model organisms, however, in transcriptomes analysis of non-model organisms, this information is ignored due to the difficulty in identifying and quantifying TEs. Here we develop ExplorATE, a pipeline that allows the identification and quantification of active TEs in non-model organisms that can be easily implemented within the R environment. Based on simulated data, we show that our pipeline accurately identifies and quantifies TEs, over-performing the commonly used tools in model organisms. We show the implementation of ExplorATE using real data for RNA-seq samples from different tissues (liver, ovary, and brain) of Liolaemus parthenos, the only parthenogenetic lizard known to date in the entire clade Iguanidae (pleurodonta). Our results show that a significant fraction of the transcriptome contains repeats, however many of these are co-expressed with genes. The implementation of our pipeline in real data allowed the identification of the most abundant transposon families in each tissue. The ERV2, CR1, and SINE3 families were particularly abundant in the liver. A test data set is provided in the ExplorATE package.

overall_design: The goal is to test the pipeline and evaluate the expression profiles of active transposable elements with real data. For this, three samples of different tissues (brain, ovary, and liver) from the South American parthenogenetic lizard Liolaemus parthenos are analyzed and compared.

middle: M

first: Juan

middle: C

last: Santos

first: Jack

middle: W

last: Sites Jr

first: Mariana

last: Morando


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB [RNA-Seq 2]

overall_design:
Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors overexpressing an shRNA against Renilla (shCTRL) or TFEB (shTFEB). Six days later, mCherry+ transduced cells were sorted for RNA extraction and sequencing.
Authors state that raw data will be uploaded to the EGA database.


title: Identification of altered blood microRNAs  in a rat model of Parkinson’s disease by Custom "Brain Specific miRNA" Open Array Real-time PCRpanel

city: Raebareli

first: SANJAY

last: YADAV

state: UTTAR PRADESH

address: All India Institute of Medical Sciences Dalmau Road, Munshiganj,

country: India

institute: AIIMS RAEBARLI

summary: 12 week male wistar rats were exposed with rotenone (2.5mg/kg b.wt.) and control rats exposed with vehicle (corn oil)  intraperetonially for two months. Animals were sacrifised at the end of the experiment and blood was isolated and stored at -80°C in RNALater until further analysis.RNA (including small RNAs) was extracted by Ribopure Blood RNA Isolation Kit by Thermo Fisher as suggested protocol by manufacturer. A custom Taqman OpenArray panel was used to profile the miRNAs expression.

overall_design: RNA isolated from control and rotenone exposed group blood samples were quantified and perfomed reverse transcription reaction using custom primer pool for cDNA synthesis. Further preamplification of CDNA sample was also performed using preamplification primer pool. The preamplification products then diluted in TE buffer and mixed with Taqman Open Array universal master mix and run the Open array.

first: Sanjeev

middle: K

last: Yadav

first: Anuj

last: Pandey

first: Sana

last: Sarkar

first: Smriti

middle: S

first: Devendra

last: Parmar

first: Sanjay


title: Tubuloside B alleviates inflammation of murine macrophages

city: Shenzhen

first: Jie

last: Yao

address: Luohu district

country: China

institute: Shenzhen People’s Hospital

summary: Purpose: Studies in mice have indicated that Tubuloside B has therapeutic potentials in various models of inflammatory diseases. We set out to analyze how Tubuloside B regulates transcription in LPS+IFN-γ-stimulated macrophages.  Methods: RNA-seq was performed with two repetitions in RAW264.7 followed by treatment with Tubuloside B and LPS as well as IFN-γ.  Conclusions: Tubuloside B inhibits the production of pro-inflammatory cytokines in activated macrophages.

overall_design: RNA-seq was performed with two repetitions in RAW264.7 followed by treatment with Tubuloside B and 10 ng/ml LPS as well as 20 ng/ml IFN-γ for 24 h. The gene expression profile was studied by RNA sequencing.

first: Xiaobin

last: Zeng

first: Lingyun

last: Xiao

first: Chenyan

last: Shi


title: Gene expression patterns of a Rhodopseudomonas palustris ΔregSR strain under photoheterotrophic growth conditions

city: Saint Paul

first: Kathryn

middle: R

last: Fixen

state: Minnesota

address: 1479 Gortner Ave. RM140

department: Plant and Microbial Biology

institute: University of Minnesota

summary: The redox-sensing two-component signal transduction system, RegSR, in Rhodopseudomonas palustris has been shown to regulate an uptake hydrogenase in response to varying cellular redox states; however, its role is still largely undefined. Here, we used RNA sequencing to compare gene expression patterns in wild type R. palustris strain CGA010 to a ΔregSR derivative, CGA2023, under varying metabolic conditions. Growth conditions were chosen to utilize the different metabolic capabilites of R. palustris and, thus, present a variety of different redox challenges to the cell.

overall_design: Total RNA from two replicates of each strain was submitted for seven different growth conditions for a total of 28 samples. Cultures were provided with either high-light or low-light intensities in either nitrogen-fixing or non-nitrogen-fixing conditions. Carbon sources with varying redox states were provided including acetate, malate, and succinate as well as the aromatic compound benzoate.

first: Nicholas

last: Haas


title: Transcriptome analysis of normal oral cells and oral cancer cells treated with elemental diet (ED) Elental®

city: Ube

first: Koji

last: Harada

address: 1-1-1 minami-kogushi

department: Oral & maxillofacial surgery

country: Japan

institute: Yamaguchi university

summary:
Purpose: Previously, we have reported the effectiveness of elemental diet (ED) Elental® against radiotherapy- or chemoradiotherapy- induced oral mucositis (Support Care Cancer 2016, Mol Clin Oncol 2019). However, administration of additional nutrition or ED in oral cancer patients might also provide extra nutrition for cancer cells, which could result in cancer development. At present, it is still unclear whether the beneficial effect of ED can be expected to surpass its possible harmful effect on oral cancer treatment. In the present study, we tried to clarify whether Elental® has different effects on human oral keratinocyte (HOK) cells compared to oral squamous cell carcinoma (OSCC) cells (HSC2).
Method: Gene expression profiles of HOK cells and HSC2 cells treated with Elental® were generated by deep sequencing.
Results: Whole transcriptome analysis data suggested that Elental® helped in the proliferation and survival of HOK through the induction of ERK. Moreover, Elental® added stress to HSC2 through the induction of endoplasmic reticulum stress response marker, BiP. Our results showed that Elental® might add stress to HSC2, and provide growth stimulation to HOK.
Conclusion: Whole transcriptome analysis showed different gene expression profile between HOK cells and HSC2 cells treated with Elental®, suggesting that effects of Elental® might differ between normal oral cells and oral cancer cells.

overall_design: Gene expression profiles of HOK cells and HSC2 cells treated with elental for 0 hr, 0.5 hr, 3 hr and 12 hr.

first: Tarannum

last: Ferdous

first: Kenji

last: Watanabe

first: Yoichi

last: Mizukami

first: Katsuaki

last: Mishima


title: Niraparib treatment of metastatic melanoma in vivo

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

summary: Twenty four NSG mice (3 groups, 8 mice/group) were injected subcutaneoulsy with melanoma PDX cells (MM425X). When tumors reached 100mm3, daily i.p. injections of 25mg/kg niraparib were administred to the tumor bearing mice for 30 days. The treatment resulted in significant anti-tumor effects against MM425X. To determine the transcriptomic profiles altered following niraparib treatment, RNA-Seq was performed in MM-425 tumors from three mice treated with niraparib compared with three mice treated with vehicle. To that end, 3 tumors/group (vehicle vs Niraparib treated) were harvested for RNA extraction.  RNA extraction from flash-frozen tissue samples was performed as previously described (Olsson et al., 2016, Salomonis et al., 2010, Soroceanu et al., 2013). Total RNA was extracted from PDX tumor tissues using the RNeasy tissue kit (Qiagen) after tissue disruption using ruptor disposable probes and the concentration measured by Qubit RNA HS Assay Kit (ThermoFisher Scientific). RNA-Seq was performed from ~500ng of total RNA processed using TruSeq polyA selection, at a target depth of 40 million paired-end, stranded reads on an Illumina 2500

overall_design: 6 samples were anlyzed, 3 from vehicle treated mice and 3 from mice treated with Niraparib

first: Kevin

middle: B

last: Kim

first: Mohammed

last: Kashani-Sabet

first: Nathan

last: Salomonis

first: Liliana

last: Soroceanu


title: Whole genome expression profiling based on paraffin embedded tissue of a large DLBCL cohort

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

summary: Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 1311 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.

overall_design: Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies of 1311 diagnosed DLBCL using the Illumina Whole-Genome DASL HT version 4 array

middle: A

first: Sharron

middle: L

last: Barrens


title: High-throughput sequencing of mLST8-knockout H1299 cells reconstituted with mLST8-wild type and mLST8-E303D mutant .

city: Shanghai

first: Yingji

last: Chen

address: 2005 Songhu Road

department: School of Life Science

institute: Fudan University

summary: we performed the RNA-sequencing to compare the transcriptome of mLST8 KO H1299 cells reconstituted with mLST8-WT or mLST8-E303D mutant.

overall_design: A total of six samples, of which three WT samples are the control group, and the 303 sample is the experimental group


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB [RNA-Seq 3]

first: Laura

last: Garcia Prat

overall_design:
Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentivirus to overexpress GP91 (CTRL) or TFEB. Three days later, BFP+ transduced cells were sorted for RNA extraction and sequencing.
Authors state that raw data will be uploaded to the EGA database.

last: Garcia-Prat


title: Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [Hi-C]

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Hi-C analysis of Aire+/+ and Aire-/- mTECs

overall_design: CD45-Ly51loMHCIIhi mTECs were FACS sorted and in situ Hi-C was perfomed.

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB [RNA-Seq 1]

overall_design:
Long-term hematopoietic stem cells (LT-HSC) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors (empty E CTRL or MYC). Six days after transduction, BFP+ transduced cells were sorted for RNA extraction and sequencing
Authors state that raw data will be uploaded to the EGA database.


title: Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [CUT&Tag]

summary: NIPBL and IgG CUT&Tag in Aire+/+ mTECs

overall_design: CD45-Ly51loMHCIIhi mTECs were FACS sorted and CUT&Tag was perfomed.


title: Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [RNA-seq]

summary: RNA-seq analysis of Aire+/+ and Aire-/- mTECs with or without deletion of STAG2 (SA-2).

overall_design: CD45-Ly51loMHCIIhi mTECs were FACS sorted and low input RNA-seq was perfomed.


title: Reduced basal insulin secretion from islets isolated from tafazzin deficient mice is associated with reduced mitochondrial function

first: Dr. Vernon

last: Dolinsky

summary: Tafazzin is a transacylase which causes the content and molecular structure of cardiolipin (CL) to be altered in the inner mitochondrial membrane. The enzymatic machinery responsible for oxidative respiration are localized to the inner mitochondrial membrane and require CL for activity. As a result, tafazzin is critical for maintaining mitochondrial function. In beta-cells, which are the insulin secreting cells in pancreatic islets, mitochondrial function is linked to insulin secretion. We previously established that tafazzin knock-down mice were lean and maintained insulin sensitivity compared to the obese insulin resistant control litter mates. However, it was unknown whether tafazzin deficiency also influenced insulin secretion in the establishment of the lean phenotype. Using X week-old mice, we ascertained that the number of beta-cells was similar between genotypes. Ex vivo insulin secretion under low glucose conditions was reduced (52%) from islets isolated from tafazzin knock-down mice. Consistent with this tafazzin knock-down mice exhibited reduced fasting insulin plasma insulin levels. Measurement of mitochondrial oxygen consumption revealed that basal oxygen consumption was reduced (58%) in islets from tafazzin-deficient animals. The addition of etomoxir, an inhibitor of mitochondrial fatty acid translocation, significantly elevated basal mitochondrial respiration (5-fold) in islets from tafazzin knockdown mice, indicating a significant fatty acid-mediated inhibitory effect. In contrast, etomoxir lacked any measurable effect on control wild-type islets. The altered mitochondrial function identified in taffazin knock-down islets was not associated with reduced CL content or elevated oxyCL species.  Our experiments indicate that tafazzin plays a key role in regulating normal islet beta-cell function.

overall_design: RNA-Seq was performed to compare the transcriptome of Tafazzin-knockdown mouse islets to non-transgenic control islets. Islets were isolated from male mice at 3-4 months of age. Approximately 300 Islets were used for each sample that were pooled from 2-3 mice to provide sufficient RNA for analysis.

last: Cole

first: Prasoon

last: Agarwal

first: Mario

last: Fonseca

first: Vernon


title: Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Osteochondroma Explants Nontreated or Treated with Selective Agonist of Retionic acid Nuclear Receptor  Gamma (RARg) II

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

summary:
Purpose: Next-generation sequencing (NGS) has used to detect alterations in cellular pathways by various drugs. The goal of this study is to identify alteration of gene expression in human osteochondromas in response to identify nontreated or RARg agonist-treated osteochondorma transcriptome profiling (RNA-seq)  and to evaluate the actions of RARg agonists on osteochondromas.
Methods: Osteochondroma mRNA profiles of untreated or RARg agonist treated (4 days) osteochondroma explants were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results and Conclusions: Our study represents the  detailed analysis of human osteochondromas, with biologic replicates, generated by RNA-seq technology.   We conclude that RNA-seq based transcriptome revealed that RARg agonists acts on human osteochondromas and altered various types of  biological functions.

overall_design: Osteochondroma explant mRNA profiles without or with RARg agonist treatment

first: Enmoto-Iwamoto

last: Motomi

first: Iwamoto

last: Masahiro

first: Yuka

last: Imamura


title: RNA-seq of Tipranavir-treated primary tumor-derived human gastric cancer stem cells (GCSCs)

first: Jixian

last: Xiong

state: Guangdong

address: Xueyuan Ave 1066

institute: Shenzhen University

summary: We performed RNA-seq analysis of human gastric cancer stem cell treated with or without Tipranavir to elucidate the effect of Tipranavir on GCSCs, and find Tipranavir's potential targets in GCSCs.

overall_design: Fresh isolated, primary tumor-derived GCSC cells were treated with or without Tipranavir for 24 h, and then were collected for TRIzol lysed for RNA extraction. 6 RNAseq samples across 2 conditions:Control (n=3) and Tipranavir (n=3)


title: A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination

city: Innsbruck

first: Univ.-Prof. Dr. Andreas

last: Mayer

address: Innrain 80/82

department: Institute for Genomics and RNomics

country: Austria

institute: Biocenter, Medical University Innsbruck


title: Stem cell fate choices are regulated through antagonistic control of lysosomes by MYC and TFEB [RNA-Seq 4]

summary: We show that lysosomes are antagonistically controlled by TFEB and MYC to balance catabolic and anabolic processes required for activating LT-HSC and guiding their lineage fate. TFEB-mediated induction of the endolysosomal pathway for membrane receptor degradation limits LT-HSC metabolic and mitogenic activation; this promotes quiescence and self-renewal and governs erythroid-myeloid commitment. By contrast, MYC engages biosynthetic processes while repressing lysosomal catabolism to drive LT-HSC activation. Collectively, our study identifies lysosomes as a central regulatory hub for proper and coordinated stem cell fate determination.

overall_design:
Megakaryocyte-erythrocyte progenitors (MEP) were sorted from human cord blood and cultured overnight before transduction with lentiviral vectors overexpressing GP91 (CTRL) or TFEB (TFEBWT). Six days later, BFP+ transduced cells were sorted for RNA extraction and sequencing.
Authors state that raw data will be uploaded to the EGA database.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Osteochondroma Explants Nontreated or Treated with Selective Agonist of Retionic acid Nuclear Receptor Gamma (RARg)


title: Transcriptome analysis of AIMP1 overexpression (OE) or knockdown (KD) or cells treatedwith AIMP1 protein compared with wildtype (WT) cells in multiple myeloma

city: Nanjing

first: Rong

middle: Fang

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in multiple myeloma cells when AIMP1 overexpressed, knockdowned or treated with AIMP1 protein.

overall_design: Examination of  ten cell types

first: Rongfang


title: Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on super-enhancers [ChIP-seq]

summary: ChIP-seq for proteins involved in Aire's functioning in Aire+/+ and Aire-/- mTECs

overall_design: CD45-Ly51loMHCIIhi mTECs were FACS sorted and ChIP-seq was perfomed.


title: Transcriptional changes over time in exploring cultures of Streptomyces venezuelae

city: Hamilton

first: Evan

last: Shepherdson

state: Ontario

address: 1280 Main St W

institute: McMaster University

summary: We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.

overall_design: Streptomyces venezuelae mRNA profiles from two media conditions at three growth timepoints; two replicates each. Changes in gene expression compared using DeSeq2

first: Marie

last: Elliot

first: Yordan

last: Stoyanov


title: Single-cell RNA-seq of control and Sendai virus-infected mouse lungs [1wk/7wk timepoint]

city: Houston

first: Margo

middle: Patricia

last: Cain

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

summary: The Sendai virus infection model induces global changes involving multiple lung cell types. At 1 week post-infection, there is acute damage to the lung.  At 2 weeks post-infection, when the virus had been largely cleared and the lung is undergoing repair, proliferation of endothelial cells and alveolar type 2 (AT2) cells is observed, as well as aberrant appearance Trp63/Sox2-expressing basal-like cells reminiscent of pods or lineage-negative epithelial progenitors observed upon severe H1N1 virus infection.  At 7 weeks post-infection, the lung has been largely repaired, though the Trp63/Sox2-expressing basal-like cells remain.

overall_design: FACS-purified control or virus infected whole murine lung epithelial, endothelial, mesenchymal, and immune cells were mixed together in similar proportions and processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics).  The samples GSM4293527 and GSM4293528 from GSE144678 are also included in this study.

middle: P

first: Jichao

last: Chen

first: Belinda

middle: J

last: Hernandez


title: A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination [NET-seq]

summary: In this study, we reveal that BRD4 underlies a general 5'-elongation checkpoint that primes transcribing RNA polymerase II for 3'-RNA processing and transcription termination. BRD4-specific degradation impairs Pol II pause release, induces massive readthrough transcription, and RNA cleavage defects. Acute loss of BRD4 disrupts the recruitment of 3'-RNA processing factors.

overall_design: SI-NET-seq measurements for indicated time points upon DMSO (control), dTAG7 (BRD4 degradation) and dBET6 (pan-BET degradation) treatment in MOLT4 and K562 dTAG-BRD4 cells (two biological replicate measurements for each condition).

first: Mirjam

last: Arnold

first: Annkatrin

last: Bressin

first: Olga

last: Jasnovidova

first: David

last: Meierhofer

first: Andreas


title: A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination [ChIP-seq]

overall_design: ChIP-Rx measurements for Pol II, Pol II Ser2-P, SPT5, PAF1, FIP1, CPSF73 and CstF64 upon DMSO (control) and dTAG7 (BRD4 degradation) treatment in K562 dTAG-BRD4 cells (two biological replicate measurements and matched input controls for each condition).


title: A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination [nascONT-seq]

overall_design: nascONT-seq of K562 cells treated with DMSO (control) or dBET6


title: Gene expression signatures for gata4/5/6 knocking down in zebrafish

first: Wenshuang

last: Jia

address: NO.129 Jiangjun Road

institute: Nanjing University

summary: Zebrafish gata4/5/6 are known to lie on the apex of the regulatory hierarchy in primitive myelopoiesis. However, little is known about the roles of microRNAs in this process. Performing microarray analysis on the expression changes of microRNAs in the gata4/5/6 knockdown embryos, we found that miR-210-5p is a novel regulator in zebrafish primitive myelopoiesis. To uncover the target genes of miR-210-5p to mediate its role in inhibiting zebrafish primitive myelopoiesis, we performed microarray analysis to identify differentially expressed genes in gata4/5/6 knockdown embryos.

overall_design:
The embryos microinjected with control MO or gata5/6 MOs at 1-cell stage were collected at 14 hpf for analyzing the gene expression changes affected by knocking down gata4/5/6.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO, or 7.5 ng control MO per embryo.  2 replicates of gata5/6 knockdown embryos and 3 replicates of control embryos were analyzed.

Please note that as it is reported that morpholinos against gata5 and gata6 also lead to a loss of gata4 expression in zebrafish (PMID 17869240),  a combination microinjection of gata5 and gata6 morpholinos was used for knocking down all the three genes.

first: Qingshun

last: Zhao


title: Isoform- and mutation- specific roles of Wilms Tumor 1 in acute myeloid leukemia maintenance (ATAC-Seq)

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Acute myeloid leukemia (AML) is caused by recurrent mutations in members of the gene regulatory and signalling machinery subverting hematopoietic differentiation. We previously showed that each AML sub-type displays a different gene regulatory network with specific transcription factor families playing distinct roles in maintaining the leukemic phenotype. Here we show that the transcription factor WT1 forms a major node in the gene regulatory networks of multiple AML sub-types. It is frequently mutated and up-regulated in AML and its expression is pedictive for relapse. The WT1 protein exists as different isoforms which we show here to harbor differential chromatin binding and contrasting biological activity, including directing differential splicing. For two main AML subtypes we demonstrate that WT1 responds to oncogenic signaling and is part of a signaling-responsive transcription factor hub that controls AML growth. WT1 therefore plays a central and wide-spread role in AML biology.

overall_design: ATAC sequencing data were used to study WT1 in t(8;21) AML

first: Sandeep

last: Potluri

first: Paulynn

last: Chin

first: Dan

last: Coleman

first: Anna

last: Pickin

first: Shogo

last: Moriya

first: Naohiko

last: Seki

first: Olaf

last: Heidenreich

first: Peter

middle: N

last: Cockerill

first: Constanze

last: Bonifer


title: High SOX9 promotes glioma stem cell activity through a regulatory loop involving STAT3 and PML

status: Public on Jul 29 2021

city: Donsotia-San Sebastian

first: charles

last: lawrie

address: Paseo Mikeletegi, 83- planta 3

department: Oncology

country: Spain

institute: Biodonostia Research Institute

summary: shRNA silencing of SOX9 in GNS166 glioblastoma cell line in three batches along with vector only control

overall_design: Cells were infected with lentiviral particles harboring the pLKO.1-sh-hSOX9-1 plasmid or pLKO.1 puro empty vector for 48hours before harversting for RNA

first: Charles

last: Lawrie

first: Ander

last: Matheu


title: Isoform- and mutation- specific roles of Wilms Tumor 1 in acute myeloid leukemia maintenance (ChIP-Seq)

overall_design: ChIP sequencing of WT1, EGR1 and ETO transcription factors are used to study WT1 in t(8;21) AML


title: iRPE scRNA

city: Bethesda

first: David

last: McGaughey

address: 10 Center Dr

department: NEI

institute: NIH

summary: iPSC based RPE samples matured in transwell and sequenced with 10xv2

overall_design: iPSC based RPE samples

first: Robert

last: Hufnagel

first: Temesgen

last: Fufa


title: Isoform- and mutation- specific roles of Wilms Tumor 1 in acute myeloid leukemia maintenance (DNAse I hypersensitivity)

overall_design: DNAseI sequencing data were used to study WT1 in t(8;21) AML


title: mTOR-dependent translation amplifies microglia priming in ageing

city: Bonn

first: Melania

last: Capasso

address: Venusberg-Campus 1, Gebaeude 99

country: Germany

institute: DZNE e.V.

summary: Microglia maintain homeostasis in the brain. However, with age, they become primed and respond more strongly to inflammatory stimuli. We show here that microglia from aged mice upregulated mammalian target of rapamycin (mTOR) complex 1 signaling regulating translation, as well as cytokine protein levels. Genetic ablation of mTOR signaling showed a dual, yet contrasting effect on microglia priming: it caused an NF-kB-dependent upregulation of priming genes at mRNA level; however, mice displayed reduced cytokine protein levels, diminished microglia activation and milder sickness behavior. The effect on translation was dependent on reduced phosphorylation of 4EBP1 and increased 4EBP1 expression, resulting in decreased binding of EIF4E to EIF4G. Similar changes were present in aged human microglia and in damage-associated microglia, indicating upregulation of mTOR-dependent translation is an essential step licensing microglia priming in ageing and neurodegeneration.

overall_design: Examination of gene expression profiles in microglia over age in wild-type C57BL/6J mice.

first: Lily

last: Keane

first: Ignazio

last: Antignano

first: Sean-Patrick

last: Riechers

first: Raphael

last: Zollinger

first: Anaelle

last: Dumas

first: Nina

last: Offermann

first: Maria

middle: E

last: Bernis

first: Jenny

last: Russ

first: Frederike

last: Grälmann

first: Patrick

last: McCormick

first: Julia

last: Esser

first: Dario

last: Tejera

first: Ai

last: Nagano

first: Jun

last: Wang

first: Claude

last: Chelala

first: Yvonne

last: Biederbick

first: Annett

last: Halle

first: Paolo

last: Salomoni

first: Michael

middle: T

last: Heneka


title: Next-generation sequencing analysis of molecular subtypes of gastric cancer

city: Beijing

first: Yilin

last: Lin

address: 38 Xueyuan Road

institute: peking university

summary: Increasing evidence has clarified that the tumor microenvironment (TME) is closely related to the prognosis and therapeutic efficacy of gastric cancer (GC). However, there is no reliable TME evaluation system used to accurately predict the prognosis and therapeutic efficacy of gastric cancer. In this study, immune cell enrichment analysis was used to construct an immune microenvironment score (IMS).We further demonstrated that IMS may be used as an indicator to predict the efficacy of immunotherapy in patients with GC.

overall_design: 30 fresh tissue samples for gastric cancer

first: Zhanlong

last: Shen


title: PIF4 / 5 is required for heat stress-induced leaf senescence

first: Lei

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

summary: Functional analysis of PIF4 and PIF5 in response to heat stress in Arabidopsis.

overall_design: We analyzed the transcriptomic profile of Col-0 and pif4-2 pif5-3 double mutant using 3-week-old plants. Two biological replicates were performed with the materials were treated at 42°C for 5 hours, and after 3 days of recovery growth, the 3rd and 4th rosette leaves which began to turn yellow at the edge were collected.

last: Li

first: Yuanyuan

last: Zhang


title: Isoform- and mutation- specific roles of Wilms Tumor 1 in acute myeloid leukemia maintenance

first: Salam

last: Assi

overall_design: Refer to individual Series


title: Trancriptome profiling of murine lung after pneumococcal respiratory infection, antibiotic administation, and treatment with immunostimulants

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: The study aimed at defining the transcriptional responses of the respiratory tract after respiratory infection with Streptococcus pneumoniae, treatment with antibiotic and administration of immunostimulatory molecules. For this purpose, mice were infected by intranasal route with S. pneumoniae. After 12h, animals were treated by orogastric administration of amoxicillin and either intraperitoneal injection of monophosphoryl lipid A or intranasal instillation of flagellin FliC∆174-400. Whole lungs were then sampled at selected times for microarray analyses.

overall_design: Animals were maintained in individually ventilated cages and handled in a vertical laminar flow cabinet (class II A2, ESCO, Hatboro, PA). Experiments complied with current national, institutional and European regulations and ethical guidelines (Animal facility agreement C59-350009, Institut Pasteur de Lille; Protocol 2015121722429127). Six-to-eight weeks old female BALB/cJRj mice were used for all in vivo experiments. Mice were first anesthetized by intraperitoneal injection of 1.25 mg ketamine plus 0.25 mg xylazine in 250 μl PBS, then infected intranasally with 30µL of a PBS suspension containing 2-4106 S. pneumoniae serotype 1 (clinical isolate E1586). All treatments described were administered 12h post-infection. Amoxicillin trihydrate (AMX) was prepared in a stock solution of 1.75 mg/mL in sterile water, then adjusted to a final dose of 10µg/mouse before intragastric administration by oral gavage at a volume of 200µL. Monophosphoryl lipid A (MPLA) from S. minnesota R595 (Re) (Innaxon UK) in sterile distilled water at a concentration of 1 mg/L was adjusted to the dose of 50µg in sterile PBS and administered by intraperitoneal injection at a volume of 200µL. Alternatively, the recombinant flagellins FliC∆174-400 (2.5 µg in 30 μl PBS) or PBS alone were administrated intranasally under light anesthesia by inhalation of isoflurane. Mock animals received only amoxicillin.

first: J

middle: C

last: Sirard


title: KAP1-mediated epigenetic suppression in anti-RNA viral responses by direct targeting RIG-I and MDA5

status: Public on Jul 28 2021

city: Jinan

first: Li

last: Qi

address: School of Basic Medical Science,Shandong University,Wenhua West Road,No 44,Jinan City,Shandong 250000,China

department: School of Basic Medical Science

institute: Shandong University

summary: Retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs), including RIG-I (encoded by Ddx58) and MDA5 (melanoma-differentiation-associated gene 5, encoded by Ifih1), are crucial for initiating antiviral responses. Endogenous retroviral elements (ERVs) are transposable elements derived from exogenous retrovirus that integrated into the genome. KRAB-associated protein 1 (KAP1) is a master epigenetic suppressor of ERVs, and thereby protects cells from detrimental genome instability. Increased ERV transcripts are sensed by RLRs and trigger innate immune signaling. However, whether KAP1 could directly control RLRs activity remain unclear. Here we show that KAP1 attenuates RNA viral infection induced type I IFNs and facilitates viral replication by inhibiting RIG-I/MDA5 expression in primary peritoneal macrophages of C57BL/6J mice. Kap1 deficiency increased IFN-β expression and inhibited VSV replication in C57BL/6J mice in vivo. Mechanistically, KAP1 binds to the promoter regions of Ddx58 and Ifih1, and promotes the establishment of repressive histone marks in primary peritoneal macrophages of C57BL/6J mice. Concordantly, KAP1 suppresses the expression of RIG-I and MDA5 at transcriptional level in primary peritoneal macrophages of C57BL/6J mice. Our results establish that KAP1 epigenetically suppresses host antiviral responses by direct targeting RIG-1 and MDA5, and thus facilitates the immune escape of RNA viruses.

overall_design: Examination of KAP1 bound genes in primary peritoneal macrophages.

first: Qin

last: Ying

first: Wang

last: Wenwen

first: Zhao

last: Chunyuan


title: Single cell ATAC-seq study of Lung epithelial cells with Il33 KO cells

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: 660 S. Euclid Avenue

department: Department of Developmental Biology, Washington University School of Medicine

institute: Washington University in St Louis

summary: Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here we identify a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaces normal airspaces in a mouse model of progressive post-viral lung disease due to Sendai virus. Single-cell and lineage-tracing technologies identify a distinct subset of basal epithelial stem cells (basal- ESCs) that extend into gas-exchange tissue to form long-term bronchiolar-alveolar remodeling regions. Moreover, this cell subset is selectively expanded by crossing a cell growth and survival checkpoint linked to the nuclear-localized alarmin IL-33 that is independent of IL-33-receptor signaling and instead connected to autocrine chromatin accessibility. This mechanism creates an activated stem-progenitor cell lineage with potential for physiological or pathological function. Thus, conditional loss of Il33 gene function in basal epithelial cells disrupts homeostasis of the epithelial barrier at skin and gut sites but also markedly attenuates post-viral disease in the lung based on down-regulation of remodeling and inflammation. We thereby identify a basal-ESC strategy to deploy innate-immune machinery that appears to overshoot the primordial goal of self- defense. The findings reveal new targets to stratify and correct chronic and often deadly post-viral disease.

overall_design: This dataset consists of 2 10x Genomics scATAC-seq libraries, including WT sample and Il33KO sample.

first: Kangyun

last: Wu

first: Kenji

last: Kamimoto

first: Yong

first: Kuangying

last: Yang

first: Shamus

last: Keeler

first: Benjamin

last: Gerovac

first: Eugene

last: Agapov

first: Stephen

last: Austin

first: Jennifer

last: Yantis

first: Kelly

last: Gissy

first: Derek

last: Byers

last: Alexander-Brett

first: Christy

middle: M

last: Hoffmann

first: Matthew

last: Wallace

last: Hughes

first: Erika

last: Crouch

last: Holtzman


title: Isoform- and mutation- specific roles of Wilms Tumor 1 in acute myeloid leukemia maintenance (RNA-Seq)

first: Salam

last: Assi

overall_design: RNA sequencing data were used to study WT1 in t(8;21) AML

first: Sandeep

last: Potluri

first: Paulynn

last: Chin

first: Dan

last: Coleman

first: Anna

last: Pickin

first: Shogo

last: Moriya

first: Naohiko

last: Seki

first: Olaf

last: Heidenreich

first: Peter

last: Cockerill

first: Constanze

last: Bonifer


title: RNA-seq profiling of Tetep (resistant)  and HP2216 (susceptible) rice lines at 0, 48, 72, and 96 hours post infection after M. oryzae inoculation in panicle

city: New Delhi

first: Amolkumar

middle: U.

last: Solanke

state: Delhi

address: Pusa Campus

department: Rice Genetics

institute: National Institute for Plant Biotechnology

summary:
Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of rice panicle tissue from resistant and suceptible lines at different time intervals infected with M.oryzae.  The results were validated using Semi-quantitative PCR.
Methods: Panicles from resistant and suceptible rice lines were inoculated with suspension having double distill water, Tween-20 without spores for 0 hour and same suspension with spores was used to inoculate for 48, 72 and 96 hour samples. After collection, samples were frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). RNA libraries were prepared for sequencing using standard Illumina protocols.
Results: Differential Expressed Genes were identified, comparing transcriptome of Control 0 hour vs 48, 72 and 96 hour post infection. Where we get 1070, 2383 and 1080 total significant genes at 48, 72, and 96 hour post infection respectively in HP2216. And, 1564, 1433 and 2263 total significant genes at 48, 72, and 96 hour post infection respectively in Tetep.

overall_design: mRNA was isolated from M.oryzae infected panicle of Tetep (resistant) and HP2216 (Susceptible) rice lines, at 0, 48,72 and 96 hours post infection. After that, mRNA profile was generated by RNA-Seq, in duplicates, using Illumina HiSeq 2000

first: Vishesh

last: Kumar

first: Priyanka

last: Jain

first: Suresh

first: Jyotika

last: Bhati

first: Dwijesh

last: Mishra

first: Krishna

middle: K

last: Chaturvedi

first: Malik

middle: Z

last: Abdin

first: Tilak

last: Sharma

first: Amitha

last: Sevanthi

middle: U


title: Distribution of Holliday Junctions and Repair Forks during Escherichia coli DNA Double-Strand Break Repair

city: BETHESDA

first: Benura

last: Azeroglu

state: Maryland

address: National Cancer Institute, NIH, Building 37, Room 1108 37 Convent Drive

summary: Here, we correlated and compared two different steps of the Double-Strand Break Repair pathway: RecA loading and Holliday junction formation

overall_design: Examination of RecA binding during double-strand break repair in Escherichia coli

first: Tahirah

last: Yasmin

first: Charlotte

last: Cockram

first: David

last: Leach


title: Gene expression profiling in BEAS-2B cells treated with organic extracts from particulate matter produced by gasoline (E0) or gasoline-ethanol blend (E15)

city: Prague

first: Helena

last: Líbalová

address: Videnska 1083

department: Department of Nanotoxicology and Molecular Epidemiology

country: Czech Republic

institute: Institute of Experimental Medicine CAS

summary: The aim of this study was to perform comparative analysis of global gene expression changes in lung BEAS-2B cells in response to treatment with extracts of particulate matter produced by conventional gasoline (E0) or biogasoline (E15) differing in the content of organic compounds, particularly PAHs. To examine the toxicity, we monitored genome-wide gene expression changes in human lung BEAS-2B cells, exposed for 4h and 24h to a subtoxic dose of each PM extract. After 4h exposure, numerous dysregulated genes and processes such as oxidative stress, lipid and steroid metabolism, PPARα signaling and immune response, were found to be common for both extract treatments. Twenty four hour exposure resulted in more distinctive gene expression patterns. Although several common modulated processes indicating the metabolism of PAHs and activation of aryl hydrocarbon receptor (AhR) were identified, E15 specifically dysregulated a variety of other genes and pathways related to cancer promotion and progression, possibly due to the increased PAH content in PM organic extract.

overall_design: Organic compound mixtures were extracted from particulate matter (PM) generated by a conventional gasoline engine fueled with neat gasoline (E0), or gasoline-ethanol blend (15% ethanol, v/v). The cells were treated with the subtoxic dose (50 μg PM/ml) of E0 or E15 extract and the duration of the exposure was 4h or 24h. Control cells were exposed with the extract from blank non-exposed filters.

last: Libalova

first: Jan

last: Topinka

first: Pavel

last: Rössner


title: Effects of different fat source diets on the transcriptome of brain, liver and spleen in Yangze sturgeon

city: Chengdu

first: hu

last: chen

state: Sichuan

address: 211 huimin road

institute: sichuan agriculture university

summary: Nutrition is an important part of the protection process of Yangze sturgeon. This study tested the transcriptome levels of brain, liver and spleen after feeding different fat source diets to Yangze sturgeon.

overall_design: We used RNA sequencing to detect  transcriptome levels of brain, liver and spleen after feeding different fat source diets to Yangze sturgeon.

first: Hu

last: Chen

first: Zhiqing

last: Li


title: FTO regulated genes in bladder cancer cell

city: Fuzhou

first: Zhihua

last: Zhou

address: 312 Xihong Road

institute: Menchao Hepatobiliary Hospital of Fujian Medical University

summary: To investigate the global genes regulated by FTO high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between  253Jcells transfected with control siRNA or FTO siRNA.

overall_design: RNA-seq was performed in 253J cells after control siRNA or FTO siRNA transfection


title: Steady-state and IL-1{alpha}-induced gene expression in wild-type and p38{alpha}-knockout HaCaT keratinocytes

city: Charlestown

first: JIn Mo

last: Park

state: Massachusetts

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital, Harvard Medical School

summary: Keratinocytes, the epithelial cells of the skin, reprogram their gene expression and produce immune effector molecules when exposed to environmental and endogenous triggers of inflammation. It remains unclear how keratinocytes process physiologic signals generated during skin irritation and switch from a homeostatic to an inflammatory state. This gene expression analysis shows that the stress-activated protein kinase p38{alpha} is crucial for keratinocytes to prompt changes in their transcriptome upon cytokine stimulation.

overall_design: Comparison of steady-state and IL-1{alpha}-induced gene expression in wild-type and p38{alpha}-knockout HaCaT keratinocytes

first: Toshim

last: Yoshida

first: Kathryn

middle: R

last: Hillette


title: Transcriptomic analysis of Organs Following Stem Cell Therapy for Dengue (Denv 2) Infection

city: Chennai

first: Suresh

middle: Kumar

last: Subbiah

address: 173, Agaram Main Rd, Selaiyur, Chennai, Tamil Nadu 600073, India

institute: Bharath university

summary:
Dengue virus can infect and cause systemic damage in many organs, resulting in organ failure. Here, we present a novel report showing a tailored stem cell-based therapy which can aid in viral clearance and rescue liver and blood vessels cells from further damage during dengue infection by administering combination of hematopoietic stem cells, endothelial progenitor cells and dental pulp stem cells in a dengue virus-infected BALB/c mouse model. To analyze the molecular level changes induced by DENV infection and stem cell treatment in dengue-infected mice, RNA sequencing (RNA-seq) using MiSeq next-generation sequencing was employed in this study. Transcriptomics analysis was performed comparing gene expression patterns in different experimental groups.
Methods: Liver mRNA profiles of 21-day-old healthy, Dengue virus infected, and dengue infected plus stem cells treated BALB/C mice were generated by sequencing, in triplicate, using Illumina Miseq V3 150. The sequence reads that passed quality filters were assembled and analyzed using Tuxedo software. The results were analyzed using Cuffdiff to identify differentially expressed genes and transcripts. The relative expression of genes was determined based on FPKM (total fragments per kilobase of exon per million mapped reads) values
Results: After analysis, it was found that 59 genes were significantly up-regulated in the DVI group, and in the DVI-SCT group, 47 of the genes were successfully corrected to the level similar to that of control group, while the remaining genes showed down-regulation
Conclusion: In the recent years, the incidence of dengue has continued to increase, but there is currently no rapid and effective treatment available. This study demonstrates stem cell therapy as a promising management to reduce the global burden of dengue.

overall_design: Liver and blood vessels mRNA profiles of 21-day-old healthy, Dengue virus infected, and dengue infected plus stem cells treated BALB/C mice were generated by sequencing, in triplicate, using Illumina Miseq V3 150.

first: Kumar

middle: S

last: Suresh

first: Pooi

last: Mok

first: Sakina

last: Syed


title: Mouse neutrophil maturity analysis in homeostasis, acute-inflammation and cancer

city: Glagow

first: John

last: Mackey

address: Switchback Rd, Bearsden

institute: CRUK Beatson Institute

summary:
Purpose: Identification of neutrophils at different stages of maturation and their phenotypic and functional differences remain unknown. The goal of this study was to confirm maturation status of Ly6GIntermediate, Ly6GHigh and Ly6G+ neutrophils, the consistency of this means of identication in disease, and identify functional differences.
Methods: Ly6G+, Ly6GIntermediate and Ly6GHigh neutrophil populations were isolated by FACS into individual cell populations from PBS controls, acute-LPS inflammation and pancreatic adenocarcinoma (PDAC) bearing mouse tissues (metastatic KPC, non-metastatic KPflC and WT controls). RNA-Sequencing was performed on bulk isolated populations
Results: We identified Ly6GIntermediate as bona-fide immature neutrophils and analysis of Ly6G expression level as a consistently accurate marker of identifying neutrophil maturity. Gene expression was influenced by maturation stage, tissue of isolation, developmental niche and pathology. Function associated expression differences were maintained between Ly6GIntermediate and Ly6GHigh neutrophils throughout tissues and pathology.

overall_design: Ly6G+, Ly6GIntermediate and Ly6GHigh neutrophil populations from PBS, LPS, and PDAC mouse models (metastatic KPC, non-metastatic KPflC and WT controls) were isolated from the peripheral blood, bone marrow and spleen

middle: B

last: Gilroy

first: William

last: Clarke

first: Leo

last: Carlin


title: Desiccating stress triggers conjunctival monocyte to macrophage cascade - Implications for Sjögren Syndrome keratoconjunctivitis Desiccation induced monocyte cascade

city: Houston

first: Jahan

last: Alam

address: One Baylor Plaza, MS: BCM-706,  Room C 505D,, MS: BCM-706,  Room C 505D,

department: Ophthalmology

institute: Baylor College of Medicine, Ocular-surface Center Lab

summary: Lacrimal gland secretory dysfunction in Sjögren syndrome (SS) causes ocular surface desiccation that is associated with increased cytokine expression and number of antigen-presenting cells (APCs) in the conjunctiva. This study evaluated the hypothesis that desiccating stress (DS) alters the percentage and gene expression of myeloid cell populations in the conjunctiva.

overall_design: Flow cytometry evaluated myeloid cell populations in conjunctivae obtained from non-stressed eyes and those exposed to DS for 5 days. CD11b+ myeloid lineage cells were gated on monocyte (Ly6C), macrophage (CD64, MHCII) and DC (CD11c) lineage markers. NanoString immune arrays were performed on sorted MHCII+ and MHCII- monocyte/macrophage cell populations.

first: Jehan

first: Cintia

last: de Paiva

first: Stephen

last: Pflugfelder


title: Circulating miRNome of Trachemys scripta after elective gonadectomy

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

type: Non-coding RNA profiling by high throughput sequencing

summary: Pain management is an important issue in veterinary medicine, requiring biomarkers with high sensitivity and specificity for the timely and effective treatment. Emerging evidence suggests that miRNAs are promising pain-related markers. The aims were to profile the circulating miRNA signature in plasma of turtles (Trachemys scripta) and point out potential candidate biomarkers of pain. Plasma of female turtles underwent surgical gonadectomy were collected 24h pre-surgery, and 2.5h and 36 h post-surgery. The expression of miRNAs was profiled by Next Generation Sequencing and the dysregulated miRNAs were validated using RT-qPCR. The diagnostic value of miRNAs was calculated by ROC curves.

overall_design: Plasma from eight female turtles, undergoing to surgical gonadectomy, were collected at 24h pre-surgery, 2.5h and 36 h post-surgery .

first: Edoardo

last: Bardi

first: Stefano

last: Brizzola

first: Giuliano

last: Ravasio

last: Romussi

first: Paola

last: Dall’Ara

first: Valentina

last: Zamarian

first: Maddalena

last: Arigoni

first: Cristina

last: Lecchi


title: Expression data from limbic system in mouse brain treated with or without rosemary extract (RE)

city: Tsukuba

first: Kazunori

last: Sasaki

address: 1-1-1 Tennodai

institute: AIST

summary:
Most significantly affected GOs by TST stress include Cellular localization, transport and migration such as Cellular macromolecule localization (GO:0070727), Intracellular transport (GO:0046907) and Intracellular protein transport (GO:0006886), metabolic processes such as Small molecule metabolic process (GO:0044281), Cellular amide metabolic process (GO:0043603) and Lipid metabolic process (GO:0006629), neuronal cell population differentiation and proliferation such as Neurogenesis (GO:0022008), Neuron differentiation (GO:0030182), Glial cell differentiation (GO:0010001), Central nervous system development (GO:0007417), Astrocyte differentiation (GO:0048708) and Gliogenesis (GO:0042063), and cell signaling such as G-protein-coupled receptor signaling pathway (GO:0007186), Negative regulation of signaling (GO:0023057), Positive regulation of signaling (GO:0023056), Response to endogenous stimulus (GO:0009719) and Regulation of intracellular signal transduction (GO:1902531). Peptide metabolic process (GO:0006518), Peptidyl amino acid modification (GO:0018193), Regulation of steroid biosynthetic process (GO:0050810) were also significantly enriched in the TST stress-induced mice brain.
Top significantly enriched Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways by the stress response related DEGs between high-dose RE vs TST include mitogen-activated protein kinase (MAPK) signaling pathway, Chemokine signaling pathway, Neurotrophin signaling pathway, Cytokine-cytokine receptor interaction, GnRH signaling pathway, ErbB signaling pathway, Toll-like receptor signaling pathway, T cell receptor signaling pathway, B cell receptor signaling pathway, vascular endothelial growth factor (VEGF) signaling pathway, Long-term depression, NOD-like receptor signaling pathway, Insulin signaling pathway, Jak-STAT signaling pathway, Apoptosis, and mTOR signaling pathway.

overall_design: Microarray analysis was performed on RNA samples extracted from the TST-induced mice brains (limbic region): control, low-dose RE, and high-dose RE groups. Clariom S assay system (Thermo Fisher, Japan) was used on duplicate RNA samples of each group.  In accordance with the procedure, complementary DNA (cDNA) for microarray was generated using the GeneChip WT Plus Reagent kit (Thermo Fisher Science, Japan). Samples were hybridized using Clariom S GeneChip microarray kit (Thermo Fisher Science, Japan). After washing and staining, images were captured, and then CEL data were generated using the GeneChip Scanner 3000 (Thermo Fisher Science, Japan). The raw CEL data were normalized using the transcriptome analysis console (TAC) software ver.4.0.1 following the robust multichip average (RMA) algorithm (Thermo Fisher Scientific, Japan).  Genes with fold changes (FC) > 1.2 (in linear space) and a p-value < 0.05 (one-way between-subjects ANOVA) were considered as differentially expressed genes (DEGs) and were included for gene ontology (GO) analysis. For GO and pathway analyses, we used online data mining tools: Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8. [24,25]  and the Molecular Signatures Database (MSigDB, v7.1) of Gene Set Enrichment Analysis (GSEA) software [26,27]. Heat map was generated using an online visualization software Morpheus. Hallmark gene set is defined as ‘gene sets that summarize and represent specific well-defined biological states or processes and display coherent expression’. The hallmark gene sets have reduced noise and redundancy and they provide a better delineated biological space for GSEA [26]. FDR q-value refers to the false discovery rate analog of hypergeometric p-value followed by Benjamini and Hochberg correction for multiple hypothesis testing. The ‘Fold Enrichment’ score is predefined as the magnitude of enrichment (DAVID) and is computed as the ratio of the two proportions. Microarray data are deposited in the Gene Expression Omnibus (GEO) [28] under Accession Number:


title: Assessing the immune profile of primary tumours upon combination of Anakinra with Doxorubicin+Zoledronic acid for the treatment of breast cancer bone metastasis in vivo

city: Sheffield

first: Penelope

last: Ottewell

address: Beech Hill road

department: Oncology and Metabolism

institute: University of Sheffield

summary: Genetic profile of immune cells was characterised in primary breast tumours upon treatment with Anakinra, Dox+Zol, Anakinra+Dox+Zol

overall_design: A syngeneic orthotopic model was used to study spontaneous breast cancer metastasis to bone. Mouse mammary tumour cells were injected into 6-8 week-old C57BL/6J female mice via intra-ductal injection. Mice were randomised after tumour cell injection to Placebo (P), Anakinra (A), Doxorubicin and Zoledronic Acid (Dox and Zol) and Anakinra in combination with Dox and Zol (ADZ). RNA was isolated from primary tumours and the immune profile assessed using the NanoString nCounter™ panCancer Immune profiling panel (NanoString Technologies).

first: Claudia

last: Tulotta

middle: D


title: Transcriptome characterization of organoids derived from healthy and irreversibly damaged NASH patient liver

city: Philadelphia

first: Tobias

last: Raabe

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Background and Aims: Nonalcoholic steatohepatitis (NASH) will soon become the leading cause of liver transplantation in the US and is  also associated with increased COVID-19 mortality. Currently, there are no FDA approved drugs available that slow NASH progression or address NASH liver involvement in COVID-19. Since animal models cannot fully recapitulate human NASH, we hypothesized that stem cells isolated directly from end-stage NASH patient liver may address current knowledge gaps in human NASH pathology.  Approach and Results: We devised methods allowing derivation, proliferation, hepatic differentiation and extensive characterization of bipotent ductal organoids from irreversibly damaged NASH patient liver. The transcriptomes of organoids derived from NASH liver, but not healthy liver show significant upregulation of pro-inflammatory and cytochrome p450-related pathways, as well as of known liver fibrosis and tumor markers, with the degree of upregulation being NASH patient-specific.

overall_design: Hepatically differentiated organoids from 3 healthy livers (FDD,FLD,MLD) and 8 diseased livers (NASH1-6, AC and CF) were subjected to RNA seq. In addition liver samples correponding to NASH5 and NASH6 organoids were also squenced


title: Next generation sequencing of mRNA in control human schwannoma cells (HEI-193) and human schwannoma cells exposed to electromagnetic field (EMF)

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

institute: Università degli studi di Milano

summary: Hearing loss (HL) is the most common sensory disorder in the world population. One common cause of hearing loss is the presence of vestibular schwannoma (VS) a benign tumor of the VIII cranial nerve, arising from Schwann cells (SCs) transformation. In the last decade, an increasing incidence of VSs may be ascribed to the exposure to electromagnetic field (EMF), which may be considered a pathogenic cause of VS development and HL. In this paper, we explore the possible molecular mechanisms underlying the biologic changes of human SCs and/or their oncogenic transformation following EMF exposure. We investigated, by NGS technology RNA-Seq transcriptomic analysis, the genomic profile and the differential display of HL-related genes following chronic EMF. We found that cell proliferation in parallel with intracellular signaling and metabolic pathways, mostly related to translation and mitochondrial activity were modified by chronic EMF exposure. Importantly, the expression of some HL-related genes, such as NEFL, TPRN, OTOGL, GJB2 and REST appeared regulated chronic EMF.

overall_design: In conclusion, we suggest that, at a preclinical stage, EMF exposure might promote the transformation of the VS cells versus an HL phenotype.

first: Valerio

last: Magnaghi

first: Matteo

last: Audano


title: Androgen-mediated events during BMSC-to-adipocyte transition

first: Robert

middle: L

last: Satcher

state: TX

address: 1515 Holcombe

department: Orthopaedic Oncology

institute: MD Anderson Cancer Center

summary: DHT inhibits adipogenesis on M2-10B4 cells

overall_design: Three biological triplicates were analyzed for each of 4 conditions (culture of M2-10B4 cells with/without adipogenic medium and with/without DHT 10 nM) for 9 days

first: Tianhong

last: Pan

first: Yu-Chen

last: Lee

first: Sue-Hwa

last: Lin


title: Transcriptome analysis of a drug combination in two patient-derived xenograft (PDX) tumors of pancreatic cancer

city: Birmingham

first: Karina

last: Yoon

address: 1670 University Blvd VH241

institute: University of Alabama at Birmingham

summary: We report that eight gene products were downregulated in PA4 and PA16 PDX models by BET inhibitor JQ1 + gemcitabine, compared to vehicle controls.

overall_design: We sought to determine the efficacy of the BET inhibitor JQ1 + gemcitabine in preclinical models of PDAC, and to identify gene products that may contribute to the efficacy of this combination. We used RNA-seq to identify gene products whose expression was inhibited by JQ1 + gemcitabine, compared to controls.

first: Aubrey

last: Miller

first: Dongquan

last: Chen

middle: J


title: Lockdown, caregiving, and antiviral gene regulation in macaques

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Previous research has linked perceived social isolation (loneliness) to reduced antiviral immunity, but the immunologic effects of the objective social isolation imposed by pandemic “shelter in place” (SIP) policies is unknown.  We assessed the immunologic impact of SIP by relocating 21 adult male rhesus macaques from 2000 sq-m field cage communities of 70-132 other macaques to 2 wks of individual housing in indoor shelters.  SIP was associated with down-regulation of Type I interferon (IFN) antiviral gene expression.  This effect emerged within the first 48 hrs of SIP, persisted for at least 2 wks, and abated within 4 wks of return to social housing.  A subsequent round of SIP in the presence of a novel juvenile macaque abrogated this effect. These results identify a significant adverse effect of SIP social isolation on antiviral immune regulation in circulating immune cells and they suggest a potential behavioral strategy for ameliorating such effects by promoting pro-social engagement during SIP.

overall_design: Peripheral blood mononuclear cell mRNA profiles of adult male rhesus macaques at baseline, day 2, day 8, and day 13 of individual SIP housing, and parallel time points from a subsequent SIP round accompanied by an unrelated juvenile macaque.


title: Pax7 pioneer factor action requires both paired and homeo DNA binding domains.

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

institute: IRCM

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

overall_design: Refer to individual Series


title: Pax7 pioneer factor action requires both paired and homeo DNA binding domains [Mnase-seq]

summary: The pioneer transcription factor Pax7 contains two DNA binding domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 showed that each DBD binds a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed sites for both paired and homeo domains. The present work investigated the implication of the DBDs in pioneer action. We show that the composite sequence is a higher affinity binding site and that efficient binding to this site involves both DBDs of the same Pax7 molecule. This binding is not sensitive to cytosine methylation of the DNA sites consistent with pioneer action within nucleosomal heterochromatin. Introduction of single amino acid mutations in either paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites.

overall_design:
MNase in AtT-20 cells expressing empty vector and Pax7
Micrococcal nuclease assay followed by high throughput sequencing (MNase-seq)

first: Alexandre

last: Mayran

first: Yves

last: Gauthier

first: Jacques

last: Drouin


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome

city: Exeter

first: Lorna

last: Harries

address: RILD Building, Barrack Road,

department: Exeter Medical School

institute: University of Exeter

summary:
Transcriptome analysis of partially fragmented RNA from EndoC BH1 human beta cells sorted by FACs
Global gene expression profiling has shown great promise in identifying altered cell differentiation status from cultured cells. However, FACs sorting cells using internal markers causes the RNA to be partially fragmented. Clariom D pico arrays are able to utilise partially fragmented RNA to provide exon level definition to determine changes in both total gene expression and splicing.

overall_design: A somatostatin-positive cell population was induced in stressed clonal human EndoC Bh1 beta cells and was isolated using FACs. A transcriptomic characterisation of somatostatin positive cells was then carried out. Potential candidate effector genes were assessed by targetted gene knockdown.

first: Nicola

last: Jeffery


title: The human monocyte model BLaER1 exhibits an epigenetic GPI anchor defect that impairs TLR4 signaling

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital, University of Bonn

summary: We show that the human monocyte model BLaER1 contains GPI-anchor-deficient cells, which lack CD14 surface expression when differentiated to monocytes, resulting in diminished LPS/TLR4 responsiveness. We found that this GPI anchor defect is caused by epigenetic silencing of the PIGH gene, leading to a random distribution of intact and PIGH-deficient clones after single-cell cloning.

overall_design: Comparison of mRNA expression profiles of 3 undifferentiated GPI-positive and 4 undifferentiated GPI-negative BLaER1 monoclonal cell lines

first: Julia

last: Wegner

first: Thomas

last: Zillinger

last: Schlee-Guimaraes

first: Eva

last: Bartok

first: Martin

last: Schlee


title: Pax7 pioneer factor action requires both paired and homeo DNA binding domains [ChIP-seq]

overall_design:
ChIPseq in AtT-20 cells expressing Pax7 WT and DNA binding mutants (G43A, R56L and S264E)
ChIP assay followed by high throughput sequencing (ChIP-seq)

first: Audrey

last: Pelletier


title: Development of an Androgen Receptor Inhibitor Targeting the N-Terminal Domain of Androgen Receptor for Treatment of Castration Resistant Prostate Cancer

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

summary: Prostate cancer patients undergoing androgen deprivation therapy almost invariably develop castration-resistant prostate cancer. Resistance occurs when mutations in the androgen receptor (AR) render anti-androgen drugs ineffective or when constitutively active splice variants lacking the androgen binding domain entirely (e.g. ARV7) is expressed. In this study, we are reporting the discovery of novel AR-NTD covalent inhibitor 1‐chloro‐3‐[(5‐([(2S)‐3‐chloro‐2‐hydroxypropyl]amino)naphthalen‐1‐yl)amino]propan‐2‐ol (VPC-220010) targeting the AR-N-terminal Domain (AR-NTD). VPC-220010 inhibits AR-mediated transcription of full length and truncated variant ARV7, downregulates AR response genes, and selectively reduces the growth of both full-length AR- and truncated AR-dependent prostate cancer cell lines. We show that VPC-220010 disrupts interactions between AR and its known coactivators and interactors, such as CHD4, FOXA1, ZMIZ1, and several SWI/SNF complex proteins. Taken together, our data suggest that VPC-220010 is a promising small molecule AR-NTD inhibitor for the treatment of CRPC.

overall_design: Polyadenylated RNA profiles of LNCaP cells treated with dihydrotestosterone (DHT) plus either DMSO (Control), Enzalutamide, or VPC-220010, in three biological replicates, obtained using BGISeq500 platform.

first: Ayse-Derya

first: Nathan

last: Lack


title: Revealing the target of PASMC from PAH patients and mechanism

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

institute: University of Macau

summary: The goal of this study is to identify the target of PAH in PASMC from donor control and PAH patients by transcriptome profiling (RNA-seq) and the mechanism from transcriptome profiling (RNA-seq) and histone modification (ChIPseq)

overall_design: mRNA profiles of PASMC from 12 PAH patients and nine donor controls, ALDH1A3 target genes in three PAH PASMC by RNAseq and ALDH1A3 target histone mark H3k37ac regulated genes by ChIPseq in three PAH PASMC with or without ALDH1A3 siRNA

first: Dan

last: Li

first: Marlene

last: Rabinovitch


title: Transcriptomic effects of nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) deletion on human AML cells

first: Rebecca

last: Murdaugh

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Through integration of whole genome CRISPR screening and pan-cancer genetic dependency mapping, we identified nicotinamide phosphoribosyltransferase (NAMPT) and nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) as acute myeloid leukemia (AML) dependencies governing NAD+ biosynthesis. While both NAMPT and NMNAT1 were required for AML, we found that the presence of NAD+ precursors bypassed the dependence of AML on NAMPT, but not NMNAT1, pointing to NMNAT1 as a gatekeeper of NAD+ biosynthesis. We provide evidence that reduced nuclear NAD+ upon deletion of NMNAT1 activated p53, which is due to attenuated deacetylation by SIRT6/7 in AML cells. Our findings reveal that NAD+ is a critical metabolic foundation for AML, and NMNAT1 is a novel therapeutic target for this disease.

overall_design: Gene expression profiling upon CRISPR knockout

first: Xiangguo

last: Shi

first: Kevin

last: Hoegenauer

first: Daisuke

last: Nakada


title: RORα is critical for mTORC1 activity in T cell-mediated colitis [16S rRNA-seq]

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Inflammatory bowel disease (IBD) is multi-factorial chronic intestinal inflammation driven by pathogenic T cells. The mechanisms underlying colitis pathogenicity and anti-TNF therapy resistance are not fully understood. Here we demonstrate that RORα is highly expressed in active UC patients, particularly in those non-responsive to anti-TNF treatment. Rorα deficient CD4+ T cells could not induce severe gut inflammation in a T cell transfer colitis model. Mechanistically, RORα regulated T cell infiltration in colon by promoting T cell migration and inhibiting T cell apoptosis. Meanwhile, genome-wide occupancy and transcriptome analysis revealed that RORα promoted mTORC1 activation. mTORC1 signaling, also hyperactivated in active UC patients, was necessary for T cell-mediated colitis.

overall_design: 16S rRNA-seq of gut microbiota isolated from cecum of WT and  Rorα KO mice.

first: Xinxin

last: Chi

first: Wei

last: Jin

first: Xue

last: Bai

first: Xiaohong

last: Zhao

first: Jing

first: Jiaqi

first: Qinli

last: Sun

first: Bing

last: Su

first: Xiaohu

last: Wang

first: Xuexian

last: O Yang


title: RORα is critical for mTORC1 activity in T cell-mediated colitis [RNA-seq]

overall_design: RNA-seq of WT and Rorα KO in vitro cultured Th17 cells and CD4+ T cells isolated from colon tissues of colitis model.


title: RORα is critical for mTORC1 activity in T cell-mediated colitis [ChIP-seq]

overall_design: We constructed RORα-HA-ires-RFP expressing plasmid, and performed ChIP-seq using transfected in vitro cultured Th17 cells.


title: Uniacial Cyclic Stretching Promotes Chromatin Accessibility of Gene Loci Associated with Mesenchymal Stem Cells Morphogenesis and Osteogenesis

city: Hefei

first: Ran

last: Zhang

address: No.96 Jinzhai road

institute: University of Science and Technology of China

summary: Our results showed that UCS induced cell reorientation and actin fibers realignment, and in turn caused nuclear reorientation and deformation. Furthermore, UCS promoted the expression of osteogenic and chondrogenic marker genes. Based on assay for transposase accessible chromatin with high throughput sequencing (ATAC-seq), gene loci with up-regulated chromatin accessibility under UCS were found associate with regulation of cell morphogenesis, ossification, and osteogenic differentiation signaling pathways. These findings demonstrated UCS increased the openness of gene loci associated with cell morphogenesis and osteogenesis as well as the corresponding transcription activities. Moreover, our findings also connect the changes in chromatin accessibility with cell reorientation, nuclear reorientation and deformation.

overall_design: Examination of  different chromatin accessbility in mesenchymal stem cells with or without uniacial cyclic stretching

first: Duo

first: Haiyi

last: Liang


title: Reprogramming mRNA expression in response to defect in RNA polymerase III assembly in the yeast Saccharomyces cerevisiae

city: Warsaw

first: Izabela

last: Rudzińska

address: Pawińskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: Interplay between nuclear RNA polymerases is key to growth control. Here, we explored the ways in which mRNA transcription by polymerase II (Pol II) is influenced by a defect in the biogenesis of Pol III. We used the cold-sensitive yeast mutant rpc128-1007, which prevents assembly of the Pol III complex and consequently leads to low tRNA levels. mRNA upregulation in rpc128-1007 cells was generally stronger and involved more genes than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the de-repression of general control transcription factor Gcn4. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. We also investigated the ways in which the reprogramming of Pol II genes is influenced by the rpc128-1007 suppressors RBS1 and PRT1, which encode the Pol III assembly factor and the subunit of translation initiation factor eIF3, respectively. Both of the suppressor genes countered the effects of rpc128-1007 on the expression of Gcn4-dependent genes and the effects of PRT1 were stronger than the effects of RBS1. Additionally, Rbs1 modulates Gcn4 activity in a manner that depends on of the Pho85 cyclin Pcl5. We have shown that the downregulation of Pcl5 protein levels by Rbs1 overproduction leads to a Gcn4 response that is likely related to the stabilization of Gcn4 protein. Altogether, our data contribute to the regulatory network which links transcription of different RNA classes

overall_design: mRNA analysis in mutant rpc128-1007 and suppressors strains [RBS1], [RBS1-R3H], [PRT1] compared to isogenic wt strain

last: Rudzinska

first: Małgorzata

last: Cieśla

first: Tomasz

middle: W

last: Turowski

first: Alicja

last: Armatowska

first: Ewa

last: Leśniewska

first: Magdalena

last: Boguta


title: Gene expression levels of evolved thermotolerant yeast and its parent under fermentation condition

city: Wuxi

first: Nai-Xin

last: Lin

address: lihu avenue

institute: Jiangnan University

summary: Purpose: To explore the differentially expressed genes and pathways in the thermotolerant mutant compare to wildtype. To figure out the contribution of these genes and pathways to high protein expression ability in the mutant. Method: the samples were collected from the 60h fermentation culture. The fermentation medium was BMGY/BMMY with 1%(v/v) methanol as inducer. the cultivation condition was set under 28℃ and 37℃. Results: after data analysis, we found genes related to oxidative stress response were important.

overall_design: Examination of 3 groups of sample under fermentation condition.

first: Yan

last: Xu

first: Xiao-Wei

last: Yu


title: Genome wide chromatin accessibility analysis reveals a role for CREB in retinal ganglion cells axon growth decline in development and regeneration after optic nerve injury [ATAC-seq]

city: St. Louis

first: Guoyan

last: Zhao

state: MO

address: 660 South Euclid Ave.

department: Genetics & Neurology

institute: Washington University

summary: CNS neurons lose their ability to grow and regenerate axons during development. This is the case for Retinal Ganglion Cells (RGCs) in the retina, which transmit visual information to the brain via axons projecting into the optic nerve.  RGCs are unable to regenerate their axon after injury,  and start a degeneration process that leads to cell death and loss of vision. To identifying molecular mechanisms that increase regeneration of RGC and may offer new treatment strategies for patients with glaucoma or other types of optic neuropathies, we  focused on the identification of transcription factors and chromatin accessible sites that are enriched in RGC during developmental stages, in which axon growth capacity is robust. We find that stage-specific gene expression changes are correlated with temporal changes in promoter chromatin accessibility. We also find that Creb binding motifs are enriched in the differentially opened regions of the chromatin at embryonic developmental stage. Overexpression of active Creb promotes axon regeneration after optic nerve injury. Our results provide a map of the chromatin accessibility during RGC development and highlights that manipulating TF associated with developmental stages can stimulate axon growth in adulthood.

overall_design: For embryonic E21 day and postnatal P11 Retinal Ganglion Cell were isolated by immunopanning. After isolation, 300,000 RGCs were centrifugued and resuspended in Neurobasal/B27+ medium and 10% DMSO, to quick frozen at -80 °C. Samples were processed by UCSD Center of Epigenomic Technologies using their proprietary assay for Transposase-Accessible Chromatin coupled with high-throughput sequencing (ATAC-seq).

first: Wolfgang

last: Pita-Thomas

first: Tassia

last: Mangetti Goncalves

first: Valeria

last: Cavalli


title: Differential lncRNA expression profile and function analysis in primary Sjogren’s syndrome

city: Hangzhou

first: xiaochan

last: chen

address: No.88 Jiefang Road

institute: The second Affliated Hospital of Zhejiang University School of Medicine

summary: Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease characterized by abnormal immune cell activation. This study aimed to investigate differentially expressed long non-coding RNA (lncRNA) in peripheral blood mononuclear cells (PBMCs) in patients with pSS to identify lncRNAs that affect pSS pathogenesis. Transcriptome sequencing detected 38096 lncRNAs and 50869 mRNAs in PBMCs from patients with pSS and healthy individuals. The differentially expressed mRNAs underwent functional enrichment analysis. A protein interaction relationship (PPI) and ceRNA network was constructed. LncRNA expression in patients with pSS and controls was determined using RT-PCR. 1180 lncRNAs and 640 mRNAs were differentially expressed in pSS patients (fold change > 2 in healthy persons). The PPI network was constructed with 640 mRNAs and a ceRNA network with four key lncRNAs (GABPB1-AS1, PSMA3-AS1, LINC00847 and SNHG1). A co-expression relationship was found between GABPB1-AS1 and several upregulated mRNAs (IFI44, IFI44L, IFI6, and EPSTI1). RT-PCR revealed that GABPB1-AS1 and PSMA3-AS1 were significantly upregulated 3.0- and 1.4-fold in the pSS group, respectively. In patients with pSS, the GABPB1-AS1 expression level was positively correlated with B cell and IgG levels. GABPB1-AS1 expression levels are positively correlated with B cell levels and may be involved in the pathogenesis of pSS.

overall_design: Transcriptome sequencing of PBMC from 4 pSS patients and 4 healthy controls

first: Xiaochan

last: Chen

first: Qi

last: Cheng

last: Du

first: Lei

last: Liu

first: Huaxiang

last: Wu


title: Genome wide chromatin accessibility analysis reveals a role for CREB in retinal ganglion cells axon growth decline in development and regeneration after optic nerve injury


title: Genome wide chromatin accessibility analysis reveals a role for CREB in retinal ganglion cells axon growth decline in development and regeneration after optic nerve injury [RNA-seq]

overall_design: For embryonic E21 day and postnatal P11 Retinal Ganglion Cell were isolated by immunopanning. RNA from 700,000 to 1.25 million RGCs per sample was isolated using the Qiagen RNAeasy kit from Qiagen. RNA was analyzed using Bioanalyzer obtaining RIN numbers >9.5 in all samples. Libraries were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.


title: CD276 is an important player in macrophage recruitment into the tumor and an upstream regulator for PAI-1

city: Biberach (Riss)

first: Sibel

last: Durlanik

address: Birkendorferstr. 65

department: Cancer Immunology & Immune Modulation

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: 70-100% of colorectal, prostate, ovarian, pancreatic and breast cancer specimens show expression of CD276 (B7-H3), a potential immune checkpoint family member. Several studies have shown that high CD276 expression in cancer cells correlates with a poor clinical prognosis. This has been associated with the presence of lower tumor infiltrating leukocytes. Among those, tumor-associated macrophages can comprise up to 50% of the tumor mass and are thought to support tumor growth through various mechanisms. However, a lack of information on CD276 function and interaction partner(s) impedes rigorous evaluation of CD276 as a therapeutic target in oncology. Therefore, we aimed to understand the relevance of CD276 in tumor-macrophage interaction by employing a 3D spheroid coculture system with human cells. Our data show a role for tumor-expressed CD276 on the macrophage recruitment into the tumor spheroid, and also in regulation of the extracellular matrix modulator PAI-1. Furthermore, our experiments focusing on macrophage-expressed CD276 suggest that the antibody-dependent CD276 engagement triggers predominantly inhibitory signaling networks in human macrophages.

overall_design: bulk RNA-Seq analysis of HCT116-WT and HCT116-CD276KO (5 replicates each).

first: Katrin

last: Fundel-Clemens

first: Coralie

last: Viollet

first: Heinrich

last: Huber

first: Martin

last: Lenter

first: Kerstin

last: Kitt

first: Stefan

last: Pflanz


city: Wuhan

first: Xiaojian

last: Cao

state: Hubei

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

summary: Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells 3 d.p.i

overall_design: Raw 264.7 cells and bEnd.3 cells were infected with M.tb (MOI=10) for 6 h at 37°C in 5% CO2. Infected cells were lysed with 30 mL of GTC buffer at day 3 postinfection and centrifuged for 20 min at 5,000 g to pellet bacteria. The bacterial pellets were resuspended in 1 mL of GTC and centrifuged for 2 min at 15,000 g. The bacterial pellets were disturbed in 1mL of Trizol reagent by vortex for 10 min. Total RNAs were extracted as described above. rRNA was removed under the guidelines of Ribo-Zero rRNA Removal Kit (Illumina). The mRNAs were reverse-transcripted to cDNA and converted into double-stranded cDNA molecules. Following end-repair and dA-tailing, the paried-end sequencing adaptors were ligated to the ends of the cDNA fragments, and then subjected to library amplification and purification. The purified libraries were validated and quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies) and sequenced with Hi-Seq 10× instrument

first: Xi

first: Yingying

last: Lei


title: Next Generation Sequencing  Analysis of Wild Type and Chd8-/- LSK in Transcriptomes, Chromatin accessibility and chromatin state mapping

city: Cincinnati

first: Zhaowei

last: Tu

address: 3333 Burnet Ave

institute: Cincinnati Children's Medical Center

summary: Next-generation sequencing (NGS) has been used for study the transcriptomic and genomic change after Chd8 dletion. The goals of this study are to compare NGS-derived LSK transcriptome profiling (RNA-seq), ATAC and H3K4me3 and H3K27me3 Cut&Run data to find downstream targets of CHD8 and its impact on chromatin state.

overall_design: LSK cells were sorted by flow at 6 days after CHD8 deletion induction, then preceed to RNA extraction, Tn5 Transposase digestion and H3K4me3, H3K27me3 Cut&Run assay.

first: Yi

last: Zheng


title: Factor Xa and factor IIa inhibitors differentially regulate inflammation in myocardial ischemia reperfusion injury [19-0267 RNA-seq]

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: While thrombin is the key protease in regard to thrombus formation, other coagulation proteases, such as fXa or activated protein C (aPC), independently modulate intracellular signaling via partially disjunct receptors. Hence, we postulate that inhibition of fXa or fIIa conveys different effects in myocardial ischemia-reperfusion injury (IRI) in regard to inflammation despite comparable anticoagulant efficacy.

overall_design: Wild-type mice (C57BL/6, age 8-10 weeks) received fXai (3 mg/kg) or fIIai (10 mg/kg) for 7 days prior to myocardial IRI surgery. Myocardial ischemia reperfusion was induced by LAD ligation for 90 min followed by 24 h of reperfusion. Drugs treatment was reinitiated 2 h post-surgery and continued for 24 h. Mice were sacrificed at the end of study period and heart samples including infarcted part were isolated and RNAseq was performed.

first: K

last: Shahzad

first: I

last: Berend

first: R


title: Factor Xa and factor IIa inhibitors differentially regulate inflammation in myocardial ischemia reperfusion injury [20-0174 RNA-seq]

overall_design: Wild-type mice (C57BL/6, age 8-10 weeks) received fXai (Rivaroxaban; 3 mg/kg) or fIIai (Dabigatran; 10 mg/kg) for 7 days.  Mice were sacrificed at the end of study period and heart samples including infarcted part were isolated and RNAseq was performed.


title: Gene expression data of MKN45 xenograft tumors treated with anti-VEGFR2 and anti-VEGF-A antibodies

city: Tokyo

first: Tetsuo

last: Mashima

address: 3-8-31, Ariake,Koto-ku

institute: JFCR

summary: The vascular endothelial growth factor (VEGF) /VEGF receptor (VEGFR) axis is an essential regulator of angiogenesis and important therapeutic target in cancer. However, the efficacy of combination treatment with an anti-VEGFR2 antibody and anti-VEGFR-A antibody on tumor progression is not clear. In this study, we examined the anti-tumor effect of the combination treatment using BALB/c-nu/nu mouse xenograft model subcutaneously injected with human gastric cancer MKN45 cells. In this model, we evaluated intra-tumor molecular changes after the combination treatment by cDNA microarray analysis.

overall_design: BALB/c nude mice were subcutaneously injected with human gastric cancer MKN45 cells. When the tumor reached 100-200 mm3, the mice were treated with vehicle, anti-VEGFR2 antibody, anti-VEGF-A antibody, or the two antibodies together (Dual). Xenograft tumor tissues were collected at day 14 after the start of treatment, and then gene expression data were obtained.

first: Takeru

last: Wakatsuki

first: Hiroyuki

last: Seimiya

first: Kensei

last: Yamaguchi


title: RORα is critical for mTORC1 activity in T cell-mediated colitis.

first: Chen

last: Dong

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

overall_design: Refer to individual Series


title: RNA-sequencing results of MDA-MB-231 with/without OGFOD1

city: Seoul

first: Han-Teo

last: Lee

address: Daehakro 103, Jongro

department: College of Medicine

country: South Korea

institute: Hong-Duk Youn

summary: Recently, high levels of OGFOD1 has been reported in variety of cancers. Despite of the significances, the precise mechanism is poor understood. In order to find how OGFOD1 affects the cancer development, we conducted RNA-sequencing in MDA-MB-231. OGFOD1 was knocked out using CRISPR/Cas9 system. Total mRNA was isolated from parental and OGFOD1-knockout (OGFOD1Δ/Δ) MDA-MB-231 cells. Isolated RNA was used to prepare an mRNA sequencing library using TruSeq Stranded mRNA sample preparation kit. All the samples were sequenced on Illumina NextSeq 500 Sequencer with a 75 bp paired-end High Output kit.

overall_design: mRNA profiles of parantel and OGFOD1 KO MDA-MB-231 cells.

first: Il-Hwan

first: Jae-Hwan

last: Kim

first: Hong-Duk

last: Youn


title: Pax7 pioneer factor action requires both paired and homeo DNA binding domains [ATAC-seq]

city: Montreal

first: Amandine

last: Bemmo

address: 110 Avenue des Pins

institute: IRCM

summary: The pioneer transcription factor Pax7 contains two DNA binding domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 showed that each DBD binds a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed sites for both paired and homeo domains. The present work investigated the implication of the DBDs in pioneer action. We show that the composite sequence is a higher affinity binding site and that efficient binding to this site involves both DBDs of the same Pax7 molecule. This binding is not sensitive to cytosine methylation of the DNA sites consistent with pioneer action within nucleosomal heterochromatin. Introduction of single amino acid mutations in either paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites.

overall_design:
ATAC-seq in AtT-20 cells expressing Pax7 DNA binding mutants (G43A, R56L and S264E)
Transposase assay followed by high throughput sequencing (ATAC-seq)

first: Alexandre

last: Mayran

first: Audrey

last: Pelletier

first: Jacques

last: Drouin