title: Effect of Sesaminol on brown adipose tissue of mice

status: Public on Jul 31 2020

city: Mysore

first: Ram

last: Rajasekharan

state: Karnataka

address: Cheluvamba Mansion

country: India

institute: Central Food Technological Research Institute (CSIR-CFTRI)

type: Expression profiling by high throughput sequencing

summary: Energy expenditure via brown fat activation and induction of thermogenic program in white fat is associated with weight loss and metabolic benefits. In the current study, we investigated the effect of a small molecule, Sesaminol (SML) on brown fat activity and energy expenditure

overall_design: 8-12 weeks old C57BL6/J mice were treated with 5mg/kg BW, SML intraperiotoneally along with a high fat challenge for 10 days. Control and SML treated brown adipose tissues were subjected to RNA-seq to study global gene expression patterns.

first: Sona

last: Rajakumari

first: Anusha

last: Jahagirdar


title: RNA-seq of Bacillus subtilis WT W168 treated with the SynAnt 49 (BDTL049) (4 µg ml-1) compared to untreated control

city: Dresden

first: Thorsten

last: Mascher

address: Zellescherweg 20b

country: Germany

institute: TU Dresden

summary: To obtain global cellular response of Bacillus subtilis WT W168 when treated with SynAnt 49 (BDTL049) we performed RNA-seq experiments. For this, we added 4 µg ml-1 SynAnt 49 to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Examination of SynAnt 49 (BDTL049) induced Bacillus subtilis WT cells compared to non-induced Bacillus subtilis WT cells

Please note that [1] the 'tm5_2_05_*_no_treatment' raw data (i.e. GSM4485628- GSM4485630 in GSE148903) was re-analyzed for the current study (as reference sample data) and duplicated sample records were created for the convenient retrieval of the complete raw data from SRA [2] the counts*.txt  files both contain the counts of the reference (TM5_2_05_1-3) compared to AmpB (TM5_2_23_1-3; GSE148903), BDTL049 (TM5_2_24_1-3; current study) and some Streptomyces supernatants (TM5_2_25_1-3;  submission in preparation). These analysis were pooled in the respective files to increase the reproducibility of the DESeq2 analysis.

first: Ainhoa

last: Revilla-Guarinos

first: Philipp

middle: F

last: Popp


title: Unraveling lineage specific transcription factors involved in the reprogramming of Neuroblastoma from self-renewal to differentiation state

status: Public on Jul 29 2020

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Temporal regulation of super enhancer (SE) driven lineage specific transcription factors (TFs), underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify critical SEs driving TF regulators of NB, we utilized NB cells in which retinoid (RA) induces growth arrest and differentiation. H3K27ac ChIP-seq paired with RNA-seq over a time course of RA treatment revealed that SEs moving in a coordinated manner with four distinct temporal patterns (clusters).  SEs that decreased with RA linked to 24 TFs involved in stem cell differentiation (MYCN, GATA3, SOX11). Three other TF SE clusters had sequential waves of activation at 2, 4 and 8 days of RA treatment and involved TFs regulating neural development (GATA2 and SOX4).  Our study has identified candidate oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.

overall_design: Neuroblastoma cell lines were used for H3K27ac ChIP-seq (2 lines) with MYCN amplification, over time course (2 days, 4 days, 8 days), with each time point having both retinoic acid and ethanol.

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Mapping of hydrogen sulfide molecular targets in human keratinocytes

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

summary: In the present paper, we report on the pan-genomics and pan-proteomics analysis of cultured epithelial sheets of human keratinocyte progenitors. Our results notably show that NaHS stimulates the secretion of specific pro-inflammatory cytokines and promotes the synthesis of molecules involved in antioxidative mechanisms

overall_design: RNA-seq analysis was performed on epidermal sheets generated in vitro from human samples. NaHS was applied at 0.25 mM for 24h than cells were lysed using RLT lysis. The cells were stored at -80°C until use. The analysis was performed on 10 donors: 5 treated vs 5 controls

first: Olivia

last: Gross-Amat

first: Marine

last: Guillen

first: Jean-Pascal

last: Gimeno

first: Michel

last: Salzet

first: Nicolas

last: Lebonvallet

first: Laurent

last: Misery

first: Céline

last: Auxenfans

first: Serge

last: Nataf


title: Gene Expression Profiling in high-grade serous ovarian cancer mouse models

status: Public on Jul 30 2020

city: Indianapolis

first: Jaeyeon

last: Kim

state: IN

address: 635 Barnhill Drive, MS4053

department: Department of Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

overall_design: mRNA profiles of wild type (WT), DKO (Dicer Pten conditional KO) mice and TKO (p53 Dicer Pten conditional KO) were generated by RNA sequencing, in triplicate, using Illumina NextSeq500.

first: Eunyoung

last: Park


title: The role of TCF7L2 rs290487 variant in hepatic glucose metabolism: an integrated analysis of clinical and multi-omics data

city: hangzhou

first: ZHANG

last: XUEYOU

address: road 17th,laozheda

country: China

institute: Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, China

summary: TCF7L2 rs290487 C allele increases diabetic risk in Chinese, however the mechanism remains unclear. We herein evaluated the role of rs290487 variant in hepatic glucose homeostasis by integrating clinical and multi-omics data (ChIP-seq, ATAC-seq, RNA-seq, and metabolomics) from CRISPR/Cas9 edited PLC-PRF-5 cell lines (C/C vs. C/T). In clinical cohort, C/C genotype was associated with higher insulin resistance index and higher incidence of hepatogenous diabetes as compared to C/T heterozygote and T/T homozygote genotypes. In liver cell lines, C/C-cells had enhanced glucose production and lower TCF7L2 mRNA and protein levels than C/T-cells. Moreover, C/C-cells presented specific binding affinity of TCF7L2 with genes involving glucose metabolism (e.g., PFKP and PPARGC1A), increased expression of gluconeogenetic genes with specific chromatin openness (e.g., PPARGC1A and HNF4A), and deregulation of metabolites (e.g., β-D-Fructose 2,6-bisphosphate). In addition, diabetic status (high glucose and insulin) had a more potent effect on TCF7L2 expression than the genetic variant, indicating a significant role of environmental factors on gene expression and disease progression. This study provides a novel mechanism underlying the association between TCF7L2 rs290487 polymorphism and hepatic regulation of glucose homeostasis.

first: Qi

last: Ling

first: Xueyou

last: Zhang

first: Haitao

last: Huang

first: Xinyi

last: Zhao

first: Baohong

last: Wang

first: Fengqin

last: Dong

first: Panpan

last: Ye


title: Primordial Germ Cell Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: Previously the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 13 (E13) primordial germ cells. The DMRs between the control versus vinclozolin lineage samples were determined for this stage.

overall_design: The experimental design involved the development of F3 generation control and vinclozolin lineage male rats to isolate the primordial germ cell (PGC) stage for epigenetic analysis. The F0 generation gestating female rats at 90 days of age were transiently exposed to vinclozolin or a vehicle control during embryonic days 8–14 when the PGCs were migrating to colonize the indifferent gonad and during the early stages of gonadal sex determination. The F1 generation offspring were obtained and at 90 days of age were bred within the control and vinclozolin lineages, respectively, to generate the F2 generation (grand offspring) which were then bred at 90 days of age to obtain the F3 generation for each control and vinclozolin lineage. No cousin or sibling breedings were used to avoid any inbreeding artifacts. Only the F0 generation gestating females were transiently exposed to vinclozolin, which also directly exposed the F1 generation fetus and the germline within the F1 generation fetus that will generate the F2 generation. Therefore, the transgenerational F3 generation is the first generation not directly exposed and was used to study the developmental origins of the sperm epimutations. The F3 generation control and vinclozolin lineage male rats were aged to the embryonic day 13 (E13) fetal stage for PGC cell isolation. Two pools each from different individual sets of animals were obtained from 5-6 males per pool for the E16 stage. Therefore, 3-7 different males were used in each of the three different pools analyzed for both the control and vinclozolin lineages. The DNA was isolated from each pool for subsequent epigenetic analysis.

first: Eric

last: Nilsson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck

first: Millissia

last: Ben Maamar

first: John

middle: R

last: McCarrey


title: hCyfip1 overexpression in the basolateral amygdala of mice

city: Los Angeles

first: Aaron

last: Gordon

state: CA

address: Gonda Building, 695 Charles E. Young Drive South

department: Neurology

institute: UCLA

summary: CYFIP1, a protein that interacts with FMRP and regulates protein synthesis and actin dynamics, is over-expressed in Dup15q syndrome as well as autism spectrum disorder (ASD). While CYFIP1 heterozygosity has been rigorously studied due to its loss in 15q11.2 deletion, Prader-Willi and Angelman syndrome, the effects of CYFIP1 over-expression, as is observed in patients with CYFIP1 duplication are less well understood. Here, we developed a mouse model of human CYFIP1 overexpression (CYFIP1 OE) to study the effects of excess CYFIP1 on rodent behavior and biological pathways. Extensive behavioral testing of CYFIP1 OE mice reveals no changes in the core behaviors related to ASD: social interactions and repetitive behaviors. However, we did observe mild learning deficits and an exaggerated fear response. Using RNA sequencing of the basolateral amygdala, a region associated with fear response, we observed changes in pathways related to cytoskeletal regulation, oligodendrocytes and myelination. We also identified GABA-A subunit composition changes in BLA neurons which are part of the fear conditioning neuronal circuit. Overall, this research identifies the behavioral and molecular consequences of CYFIP1 overexpression and how they contribute to the variable phenotype seen in Dup15q syndrome and in ASD patients with excess CYFIP1.

overall_design: Quant seq from the BLA of 16 controls and 15 hCYFIP1 over-expressing mice.

middle: H

last: Geschwind


title: Transcriptional response to single amino acid starvation in HEK293T cells

city: Vienna

first: Vitaly

last: Sedlyarov

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: Research Center for Molecular Medicine

summary: We analyzed gene expression profiles in response to starvation of single amino acids in HEK293T cells.

overall_design: 62 samples; 3 biological replicates for amino acid starvation conditions and 2 biological replicates for vitamins starvation

first: Manuele

last: Rebsamen

first: Stefania

last: Scorzoni

first: Giulio

last: Superti-Furga


title: Assessment of transcriptomic and apical responses of Daphnia magna exposed to a  3 polyethylene microplastic in a 21-day chronic study

city: apex

first: Lyle

last: Burgoon

state: nc

address: 216 kelly west dr

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

summary: There is global concern regarding the fate and effects of microplastics in the environment, particularly in aquatic systems. In this study, ethylene acrylic acid copolymer particles were evaluated in a chronic toxicity study with the aquatic invertebrate, Daphnia magna. The study design included a natural particle control treatment (i.e., silica) in order to discern any potential physical effects of a particlefrom intrinsic toxicity of the test material. In addition to the standard endpoints of survival, growth, and reproduction, the transcriptomic profile of control and ethylene acrylic acid copolymer-exposed D. magna were evaluated at the termination of the 21-day toxicity study. No significant effects on D. magna growth, survival, or reproduction were observed in the study in comparison to both particle and untreated control groups. Significant transcriptomic alterations were induced in the highest treatment level of 2.3 x 1012 particles of the ethylene acrylic acid copolymer/ L in key pathways linked to central metabolism and energy reserves, oxidative stress, as well as ovulation and molting indicating a global transcriptomic response pattern. To put the results in perspective is challenging at this time, since, to date, microplastic environmental monitoring approaches have not been equipped to detect particles in the nano size range. However, the results of this study indicate that ethylene acrylic acid copolymer microplastics in the upper nano-size range are not expected to adversely affect D. magna growth, survival, or reproductive outcomes at concentrations up to 1012 particles/L.

overall_design: There are 5 samples exposed to vehicle control, and 5 samples each are exposed to one of either 2.3x10^11 particles/L of ethylene acrylic acid copolymer (nanolow), 2.3x10^12 particles/L of ethylene acrylic acid copolymer (nanohigh) or 2.3x10^12 fumed silica.

first: Katherine

last: Coady

middle: W

last: Davis

first: Claire

last: Doskey


title: Multi-omics Analyses Reveal Molecular Mechanisms of Potassium Deprivation Adaption in Wheat (Triticum aestivum L.)

city: Baoding

first: KE

last: XU

state: Hebei

institute: Hebei agricultural university

summary: This study evaluated the level of genetic variation among 543 wheat associations differing in K-deficiency tolerance at seedling and adult plant stages. Two of the 543 wheat associations, i.e. KN9204 and BN207, were identified as extreme K-deficiency tolerant and sensitive cultivars, respectively. We further conducted transcriptomic and metabolomics analyses using the roots of KN9204 and BN207 under normal or K-deficient conditions.Integrated analysis of gene expression and metabolite profiles revealed that dramatically more genes including those involved in ion homeostasis, cellular reactive oxygen species (ROS) homeostasis and glutamine synthetase pathways were induced in KN9204 as compared with BN207 under K-deficient conditions, which might indicate their unique roles in regulating plant K-starvation tolerance. These findings provided a better understanding of molecular responses of root adaptive strategies to K deprivation in wheat.

overall_design: Root mRNA profiles of Kenong 9204 and Bainong 207 treated with normal potassium and low potassium for 14 days

first: Yong

last: Zhao

first: Ruo

middle: X

last: Sun

first: Hao

middle: D

last: Liu

first: Ke

last: Xu


title: Transcriptomic profile of primary culture of skeletal muscle cells isolated from semitendinosus muscle of bulls of different performance

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

summary: The goal was to examine and compare the transcriptomic profiles of  primary muscle cell cultures (80% confluence) isolated from skeletal muscle (m. semitendinosus) derived from bulls belonging to different breeds and showing different levels of performance.

overall_design: Comparison of transcriptomic profiles of proliferating muscle cell cultures isolated from skeletal muscle (m. semitendinosus) from beef breed (Limousin - LIM and Hereford - HER) vs. dairy breed (Holstein Friesian - HF) - used as a control. Each comaprison was performed in four biological repetitions.

first: Anna

last: Ciecierska


title: Urinary exosomal small non-coding RNA expression of prostate cancer patients

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: Small non-coding RNA profiling of urine exosomal total RNA from patients with or without prostate cancer were performed using Affymetrix GeneChip miRNA  4.0 to identify small non-coding RNA profile that can be used for prostate cancer diagnosis.

overall_design: Changes in small non-coding RNA expression in prostate cancer patients were deteremined by comparing the small non-coding RNA expression to the positive or negative results of core-needle biopsy of patients suspicious of prostate cancer.

first: Winnie

last: Wang

first: Martin

last: Tenniswood


title: Lsh/HELLS is required for B lymphocyte development and immunoglobulin class switch recombination

city: Frederick

first: Scott

last: Durum

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

summary: We report here high-throughput sequencing analyses of class switch recombination junctions in Lsh deficient B cells with reduced capacity of class switch recombination compared to control B cells.

overall_design: Examination of  genomic localization of junctions and junction patterns among purified B cells derived from conditional  Lsh-/- vav (KO) or control  (CTRL) mice

first: Kathrin

last: Muegge

first: Yafeng

last: He

first: Jianke

last: Ren

first: Richard

last: Finney


title: Comparison of cortisol metrics and total RNA profiles from Healthy Individuals

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: The study seeks to identify transcripts whose expression levels are significantly correlated with bedtime and awakening cortisol levels in healthy individuals.

overall_design: Expression levels of transcripts were determined by RNA-Seq from total RNA extracted from blood following 30 consecutive days of bedtime and awakening saliva sampling. Bedtime and awakening cortisol levels from the saliva samples were determined by radioimmunoassay. Both cortisol and transcript levels were compared by linear regression.

last: Lee

first: Gary

last: Wand


title: In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis [RNAseq/Riboseq]

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Translation is a fundamental biological process, which defines every aspect of cell physiology. Dysregulation of protein synthesis is associated with the diseases, such as ribosomopathies, diabetes, and cancer. To examine translation dysregulation in vivo, we employed RNA interference to knockdown m-subunit of the translation initiation factor eIF3 exclusively in mouse liver. We observed an increase in the number of monosomes and multiple signs of impaired translation. We further characterized the early cellular response using transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses. The major response of hepatocytes to eIF3m deficiency was associated with the changes in mRNA expression, with almost no effect on translation efficiency for particular mRNAs. The transcription changes fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins, dephosphorylation of eIF2α, and inhibition of rRNA processing) and cell metabolism (lipid, amino acid, nucleic acid, and drug metabolism). Overall, this work uncovers a new mode of regulation of protein synthesis mediated by the inhibition of translation initiation. It also highlights advantages of RNAi-based in vivo approach for studying regulatory network associated with essential factors involved in mammalian translation.

overall_design:
RNAseq/Riboseq experiment of Eif3m knockdown in mouse livers at day 9 (3 replicates) and day 13 (2 replicates).

Please note that GSM3327719-GSM3327724 sample raw data (in GSE118394) have been re-analyzed in the currect study and therefore, duplicated sample records (GSM3402655-GSM3402660) have been created for the convenient retrieval of the complete raw data from SRA.

first: Elena

middle: M

last: Smekalova

first: Maxim

last: Gerashchenko

first: Patrick

last: O'Connor

middle: A

first: Roman

middle: L

last: Bogorad

first: Kevin

last: Kauffman

last: Fefilova

first: Timofei

last: Zatsepin

first: Vadim

middle: N

last: Gladyshev

first: Pavel

last: Baranov

first: Daniel

middle: G

last: Anderson

first: Victor

last: Koteliansky


title: MKL1 global knockout effect on transcriptome of bone marrow derived macropahges

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: The goal of this project is to determine the critical genes and pathways regulated by MKL1 in bone marrow differentiated macrophages in mice.

overall_design: We isolated bone marrow cells from Mkl1+/+, Apoe-/- and Mkl1-/-, Apoe-/- male mice (6 months old) challenged with Ang II for 7 days. We then differentiated these cells  for 7 days before total RNA was isolated for RNA-seq analysis.  Two batchs of samples were included in the assay. First batch of samples were sample 1,2,5,6; second batch of samples were 3,4,7,8. We  do comparision seprately for each batch.

first: Xiaochun

last: Long

first: Ping

last: Gao


title: Transcriptional response of Emiliania huxleyi CCMP2090 exposed to the bacterial signaling molecule 2-heptyl-4-quinolone

city: Haverford

first: Jamie

middle: William

last: Becker

state: PA

address: 370 Lancaster Ave

department: Biology

institute: Haverford College

summary: In order to determine how the bacterial quorum-sensing precursor molecule 2-heptyl-4-quinolone (HHQ) induces cellular senescence in populations of some eukaryotic marine phytoplankton, we examined the transcriptional response of Emiliania huxleyi CCMP2090 to HHQ exposure.  Quadruplicate batch cultures were treated with HHQ at three concentrations (1, 10 and 100 ng/ml) and compared to a vehicle control after 24 and 72 hours of exposure.  The majority of gene expression changes occurred after 24 hr of exposure in the 10 and 100 ng/ml treatments and many of these changes persisted for 72 hr in the 100 ng/ml treatment.  RNAseq analysis revealed that HHQ exposure impacts many aspects of Emiliania huxleyi metabolism including: chlorophyll biosynthesis and light harvesting, vitamin biosynthesis, vesicle trafficking, and general signals related to energy production.  Changes in genes involved in intraphase cell cycle check points implicate DNA damage as the primary driver of HHQ-induced cellular senescence.

overall_design: At 2 timepoints, samples from 4 biological replicate axenic Emiliania huxleyi cultures exposed to either 1, 10, or 100 ng/ml of 2-heptyl-4-quinolone (HHQ) are compared to 4 biological replicates exposed to a vehicle control.

first: Kristen

last: Whalen

first: Elizabeth

last: Harvey


title: In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis

first: Charles

last: Whittaker

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

overall_design: Refer to individual Series


title: RNA-seq of mouse small intestine samples from different Fecal Microbiota Transplantation treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: The aim of this project was to explore the role of gut microbiota in the development of small intestine. The gut microbiota from different groups was used to treat the mice for 1 or 2 weeks. Then the small intestine samples were collected. The RNA was used for the RNA-seq analysis to search the role of gut microbiota in the development of small intestine. Groups: IMA100 mean gut microbiota from Alginate oligosaccharide 100mg/kg treated mice; IMA10 mean gut microbiota from Alginate oligosaccharide 10mg/kg treated mice; IMC mean gut microbiota from control group mice (dosed with water); Sa mean dosed with saline (no gut microbiota). "1" mean dosed for 1 week, "2" means dosed for 2 weeks.

overall_design: RNA-seq of mouse small intestine samples from Fecal Microbiota Transplantation different groups treated with gut microbiota from different treatments.

first: Yanni

last: Feng

first: Hongfu

last: Zhang


title: A copper activated protease regulates photosynthetic soluble electron carriers in cyanobacteria

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

country: Spain

institute: CBGP-Universidad Politecnica de Madrid

summary: identifying genes under PetRP regulatory system in Synechocystis

overall_design: Copper treated petR-

first: Raquel

last: García-Cañas

first: Joaquin

first: Francisco

middle: J

last: Florencio

first: Luis

last: López-Maury


title: Cocaine induces paradigm-specific changes to the transcriptome within the Ventral Tegmental Area

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: We found that cocaine alters distinct sets of VTA genes within each exposure paradigm. Using behavioral measures from cocaine self-administering mice, we also found several genes whose expression patterns corelate with cocaine intake. In addition to overall gene expression levels, we identified several predicted upstream regulators of cocaine-induced transcription shared across all paradigms. Although distinct gene sets were altered across cocaine exposure paradigms, we found, from Gene Ontology (GO) term analysis, that biological processes important for energy regulation and synaptic plasticity were affected across all cocaine paradigms. Our analyses demonstrate that transcriptional changes within the VTA depend on the route and context of cocaine exposure, and highlight several affected biological processes by cocaine. Overall, these findings provide a unique resource of gene expression data for future studies examining novel cocaine gene targets that regulate drug-associated behaviors.

overall_design: We employed genome-wide RNA-sequencing to analyze transcriptional profiles within the VTA from male mice that underwent one of four commonly used paradigms: acute home cage injections of cocaine, chronic home cage injections of cocaine, cocaine-conditioning, or intravenous-self administration of cocaine

first: R

last: Campbell

first: S

last: Beardwood

first: A

last: López

first: L

last: Pham

last: Keiser

first: J

last: Childs

first: D

middle: P

last: Matheos

first: P

last: Baldi

first: M

last: Wood


title: Effect of HDL enriched with Serum Amyloid A1 (HDL+SAA1) on Gene Expression by Classical CD14+/CD16- Human Peripheral Blood Monocytes from Asthmatics

city: Bethesda

first: Mehdi

last: Pirooznia

summary: IL-6 and PTGS2 were the most highly expressed mRNA transcripts in Classical CD14+/CD16- Monocytes from Asthmatic Subjects in response to treatment with HDL+SAA1

overall_design: Analysis of mRNA expression by Classical CD14+/CD16- monocytes from asthmatic subjects treated with HDL+SAA1

first: Xianglan

last: Yao

first: Stewart

last: Levine


title: Next generation sequencing to reveal the transcriptome of a DUX4 inducible FSHD model

city: Utrecht

first: Niels

last: Geijsen

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Hubrecht institute

summary: Bulk RNA sequencing was performed on a CML derived cell line, which contains an TET-ON inducible system for DUX4 inducible expression (DIE). Due to the unconventional cellular background used for the generation of an inducible FSHD cell line, bulk RNA seq was performed to determine if, and otherwise to what extend, this cellular background inteferes with  the transcriptional program DUX4 is known to activate in muscle cells.

overall_design: The transcriptomes of induced DIE cells were compared to uninduced or DIE cells, to identify differentially expressed genes or pathways that change upon DUX4 induction. Induced and uninduced DIE cells in which the DUX4 transgene was knocked-out (DIE_KO) served as controls. Samples were sequenced using Illumina Nextseq 500, 2x75 kit, high output. Four technical replicates per samples were send for sequencing.

first: Ator

last: Ashoti

first: Judith

last: Vivié

first: Menno

last: Creyghton

first: Mirna

last: Baak


title: Impaired estrogen signaling underlies regulatory T cell loss-of-function in the chronically-inflamed intestine

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: The goal of this study was to identify differences in intestinal regulatory T cell gene expression in male and female mice lacking ESR2 (estrogen receptor beta), compared to those expressing ESR2.

overall_design: Sequencing of regulatory T cells from male versus female SAMP mice expressing or lacking global expression of ESR2.

first: W

last: Goodman

last: Bedoyan

first: H

last: Havran

first: B

last: Richardson

first: T

last: Pizarro


title: Analysis of Transcriptome in hematopoietic stem cells after radiation injury with treatment of EGF or saline

first: John

last: Chute

address: 615 Charles E Young Drive South OHRC 545

institute: University of California, Los Angeles (UCLA)

summary:
Purpose: This study is designed to understand whether Epidermal Growth Factor treatment alters the transcriptome of hematopoietic stem cells after radiation injury
Method: RNA was extracted from C57BL/6J mice at six weeks post 500cGy total body radiation and Epidermal Growth Factor or saline subcutaneous treatment. Libraries for RNA-Seq were prepared with Clontech kit. The data was sequenced on NextSeq500 for a paired-end 75bp read run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program. The Partek flow and Ingenuity Pathway Analysis (IPA) were used for bioinformatics methods and data analysis, respectively. The reads were mapped to the latest UCSC transcript set using STAR - 2.7.2a and GRCm38.97.

overall_design: mRNA profiles of C57BL/6J mice at six weeks post 500cGy total body radiation and Epidermal Growth Factor or saline subcutaneous treatment were sequenced, in five replicates, using Illumina NextSeq500.

first: Tiancheng

last: Fang


title: Inhibition of miR-21 regulates mutant KRAS effector pathways and intercepts pancreatic ductal adenocarcinoma development [miRNA]

city: Baltimore

first: Jacquelyn

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

summary: We identified miR-21 and miR-224 as cell-specific and compartment-specific regulators in PanINs and PDA.  miR-21 is overexpressed in tumor epithelial cells of premalignant ducts, while miR-224 is overexpressed in cancer-associated fibroblasts in PDA stroma.  Inhibition of miR-21 reverted pro-tumorigenic functionalities to baseline levels.  Overexpression of miR-224 induced activated phenotypes in normal fibroblasts.  miR-21 inhibition downregulated MAPK, mTOR and actin cytoskeleton pathways downstream of KRAS activation in tumor cells.  In vivo miR-21 inhibition improved survival in established PDA, while early systemic miR-21 inhibition intercepted premalignant progression.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: TaqMan OpenArray Rodent MicroRNA Panel.  We conducted a comprehensive miRNA profiling study of multiple PanIN stages and PDA using KPC mice.  We performed microdissections on increasing grades of PanINs from sections of KPC pancreata followed by a miRNA microarray analysis utilizing the Taqman OpenArray platform to quantify the levels of 750 known murine miRNAs.

first: Elizabeth

last: Jaffee


title: Gene expression profiling of mouse liver cells treated with or without MET/CAT and SB transposase

city: Guangzhou

first: Xiongjun

last: Wang

address: 230 Wai Huan Xi Road

institute: Guangzhou University

summary: mice were induced with  MET/CAT and SB for 0, 2 or 7 weeks , then mRNA were extracted for high-throughput sequencing

overall_design: 0, 2 and 7 weeks treatment,in duplicate

first: Hongwen

last: Zhu


title: Inhibition of miR-21 regulates mutant KRAS effector pathways and intercepts pancreatic ductal adenocarcinoma development

overall_design: 8 samples composed of 2 replicates of 4 conditions


title: In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis (mRNA-seq)

first: Charles

last: Whittaker

overall_design: RNAseq experiment comparing 3 replicates of Eif3m knockdown mouse livers with 3 replicates of control mouse livers at day 9 and 3 replicates of Eif3m knockdown mouse livers with 3 replicates of control mouse livers at day 13.

first: Elena

last: Smekalova

first: Maxim

last: Gerashchenko

first: Patrick

last: O'Connor

first: Roman

last: Bogorad

first: Kevin

last: Kauffman

first: Anna

last: Fefilova

first: Timofei

last: Zatsepin

first: Vadim

last: Gladyshev

first: Pavel

last: Baranov

first: Daniel

last: Anderson

first: Victor

last: Koteliansky


title: Ahr-Foxp3-RORγt Axis Controls Gut Homing of CD4+ T Cells by Regulating GPR15

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

summary: The orphan chemoattractant receptor GPR15 is important for homing T lymphocytes to the large intestine, thereby maintaining intestinal immune homeostasis. However, the molecular mechanisms underlying the regulation of GPR15 expression remain elusive. Here we show a central role of the aryl hydrocarbon receptor (Ahr) in promoting GPR15 expression both in mice and human, thus gut homing of T lymphocytes. Mechanistically, Ahr directly binds to open chromatin regions of the Gpr15 locus to enhance its expression. Ahr transcriptional activity in directing GPR15 expression was modulated by two transcription factors, Foxp3 and RORγt, both of which are expressed preferentially by gut Tregs in vivo. Specifically, Foxp3 interacted with Ahr and enhanced Ahr DNA binding at the Gpr15 locus, thereby promoting GPR15 expression. In contrast, RORγt plays an inhibitory role at least in part by competing with Ahr binding to the Gpr15 locus. Our findings thus demonstrate a key role for Ahr in regulating Treg intestinal homing under the steady state and during inflammation, and the importance of Ahr-RORγt-Foxp3 axis in regulating gut homing receptor GPR15 expression by lymphocytes.

overall_design: ChIP-seq (2 replicates)  analysis of in vitro differentiated Th17 and iTreg from Ahr KO and wild type mice.

first: Lifeng

last: Xiong

first: Joseph

last: Dean

first: John

last: Bostick


title: Inter-species genetic regulation of longevity: Δhns E. coli activate C. elegans DAF-16 in distinct ways from IIS

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We confirmed that the life span of C. elegans feeding hns mutant E. coli was increased. hns mutant E. coli was found to regulate lifespan of C. elegans through daf-16 activation in C. elegans. It is well known that daf-16 is the transcription factor of the insulin/IGF-1 signaling pathway and it is known to regulate downstream genes such as longevity, stress response, and dauer diapause regulation genes. Thus, we performed Next Generation Sequencing(NGS) to investigate the downstream genes regulated by daf-16 in C. elegans that are activated by hns mutant E. coli. N2 wild type worms and daf-16 mutant worms were fed with BW25113 wild type E. coli and hns mutant E. coli, respectively, and then NGS was performed by harvesting the worms and purifying the RNA. We investigated how the downstream genes of daf-16 of C. elegans, which is regulated by hns mutant E. coli, differs from the downstream genes of daf-16 of C. elegans, which is regulated by the insulin/IGF-1 signaling pathway. To do this, we carried out the analysis including two previous studied papers that analyzed the daf-16 downstream genes related to the insulin/IGF-1 signaling pathway. Surprisingly, only 6 genes were up-regulated in all three experiments and 288 genes were found to be dependent on daf-16 and hns mutant E. coli. This study indicated that hns mutant E. coli regulate daf-16 distinct from insulin/IGF-1 signaling pathway on C. elegans.

overall_design: Whole body mRNA profiles of young adult wild type and daf-16 mutant feeding BW25113 control E. coli or hns mutant E. coli were generated NGS in duplicate.

first: Min-gi

last: Shin

first: Jae-woong

last: Lee

first: Eun-soo

last: Kwon

first: Jong-hwan

first: Seon-young


title: In vivo RNAi mediated knockdown of translation initiation factor eIF3m is associated with alterations in ribosome biogenesis (rRNA-seq)

first: Charles

last: Whittaker

overall_design: Total RNAseq experiment comparing 3 replicates of Eif3m knockdown Hepa1c1c7 cells with 3 replicates of control Hepa1c1c7 cells (in vitro samples) and Eif3m knockdown mouse livers with 3 replicates of control mouse livers (in vivo).

first: Elena

last: Smekalova

first: Maxim

last: Gerashchenko

first: Patrick

last: O'Connor

first: Roman

first: Kevin


title: M1hot tumour associated macrophages are positively associated with tissue-resident memory T cell responses and survival outcomes in human lung cancer (single cells).

city: Southampton

first: Eva

last: Garrido-Martin

address: University Road

country: United Kingdom

institute: University of Southampton

summary: Tumour-associated macrophages (TAMs) are classified as M1 (“anti-tumour”) and M2 (“pro-tumour”), but their balance has not yet been accurately established in human cancer tissue. Here, we present bulk and single-cell transcriptomic data from human TAMs isolated from lung cancer compared with autologous non-tumour involved lung tissue macrophages (N-TAM). TAMs have a profoundly different transcriptomic profile from N-TAMs and displayed a broad M2 pro-tumour signature that was homogeneous across all the lung cancer patients studied. However, in some tumours, we found TAM populations that simultaneously displayed strong M1 gene expression pattern. These M1hot TAMs appeared to contribute to effective anti-tumour immunity via expression of T cell chemo-attractants (CXCL9, 10 and 11). We found that M1hot TAMs expressed low levels of FABP3, 4 and 5, take up less fatty acids and showed “metabolic generosity” to tissue resident memory T cells (TRM) by allowing them access to this essential nutrient resource that is required for their maintenance. Importantly, tumours harbouring M1hot TAMs were highly enriched for TRM cells and were also associated with improved overall survival outcomes. Our findings suggest that immunotherapeutic approaches aimed at inducing the expression of M1hot program in TAMs rather than generically eliminating all TAMs are likely to be beneficial.

overall_design: mRNA profiles of Tumour Associated Macrophages isolated from human lung cancer and macrophages from paired lung were generated by 10x genomics, using Illumina HiSeq 2500.

first: Tilman

last: Sanchez-Elsner

first: James

last: Clarke

first: Pandurangan

last: Vijayanand

first: Christian

last: Ottensmeier


title: M1hot tumour associated macrophages are positively associated with tissue-resident memory T cell responses and survival outcomes in human lung cancer


title: WDR68 is essential for the PRC1-AUTS2 complex activating role and for stem cell differentiation

city: Hershey

first: Qiang

last: Wang

address: 700 HMC Crescent Road

department: Department of Biochemistry & Molecular Biology

institute: Penn State College of Medicine

summary: Recent studies on Polycomb repressive complexes (PRC) reveal a surprising role in transcriptional activation, yet the underlying mechanism remains poorly understood. We previously identified a type 1 PRC (PRC1) that contains Autism Susceptibility Candidate 2 (AUTS2), which positively regulates transcription of neuronal genes. However, the mechanism by which the PRC1-AUTS2 complex influences neurodevelopment is unclear. Here we demonstrate that WDR68 is not only an integral component of the PRC1-AUTS2 complex, it is required for PRC1-AUTS2-mediated transcription activation. Furthermore, deletion of Wdr68 in mouse embryonic stem cells leads to defects in neuronal differentiation without affecting self-renewal. Through transcriptomic analysis, we found that many genes responsible for neuronal differentiation are down-regulated in Wdr68 deficient neural progenitors. These genes include several that are targeted by the PRC1-AUTS2 complex. In summary, our studies uncovered a previously unknown but essential component of the active PRC1 complex and evidence of its role in regulating the expression of genes that may be important for neuronal differentiation.

overall_design: RNA-seq analysis for ESC and NPC of wildtype E14 cells and Wdr68 knockout cells, all samples are sequenced in duplicates

first: Zhonghua

last: Gao


title: M1hot tumour associated macrophages are positively associated with tissue-resident memory T cell responses and survival outcomes in human lung cancer (bulk).

overall_design: mRNA profiles of Tumour Associated Macrophages isolated from human lung cancer and macrophages from paired lung were generated by deep sequencing, using Illumina HiSeq 2500.


title: Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

status: Public on Jul 28 2020

city: Tel Aviv

first: Tamir

last: Tuller

address: Ramat Aviv

department: Biomedical Engineering

country: Israel

institute: Tel Aviv University

summary:
The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 Signalosome exhibit a number of diverse pleiotropic phenotypes.  Total or partial loss of COP9 Signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results: We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function mutants of the COP9 Signalosome. Our results indicate that the COP9 Signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. In addition, our analyses suggest that COP9 Signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes.  These results suggest that the COP9 Signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 Signalosome conservation among eukaryotes may also suggest that COP9 Signalosome regulates methylation not only in plants but also in other eukaryotes, including humans.
We report the application of Bisulfite-sequencing  to compare methylation of two CSN mutants with their corresponding wild types: a non-lethal  csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype

overall_design: Examination of 2 different histone modifications in 2 cell types.

first: Tuller

last: Tamir

first: Diament

last: Alon

first: Avital

last: Yahalom

first: Assaf

last: Zemach

first: Shimshi

last: Atar

first: Daniel

last: Chamovitz


title: Increased long noncoding RNA maternally expressed gene 3 contributes to podocyte injury induced by high glucose through regulation of mitochondrial fission

city: Zhuhai

first: qiongxia

last: deng

state: Guangdong

address: 52 Meihua Dong Lu, Xiangzhou District, Zhuhai city, Guangdong Province, China

department: 1.	Division of nephrology, Department of medicine

institute: Fifth affiliated hospital Sun Yat-Sen University

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

summary: Excessive mitochondrial fission plays a key role in podocyte injury in diabetic kidney disease (DKD), and long noncoding RNAs (lncRNAs) are important in the development and progression of DKD. However, lncRNA regulation of mitochondrial fission in podocytes is poorly understood. Here, we want to identify how lncRNA changes in human podocytes cultured with high glucose.

overall_design: Differentiated human podocytes were treated with normal glucose (NG, 5.5 mmol/l) and high glucose (HG, 30 mmol/l) medium for 72 h. All experiments were performed in triplicate. Analysis for expression of lncRNA was carried out using a microarray (Arraystar Human lncRNA microarray v3; Agilent Technology, Santa Clara, USA).

first: Cheng

first: Qiongxia

last: Deng


title: Genome-wide DNA methylation analysis of lung carcinoma II

status: Public on Jul 27 2020

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

type: Methylation profiling by genome tiling array

summary:
Complements GSE56044 with 36 additional samples belonging to the large-cell carcinoma (LCC) and large-cell neuroendocrine (LCNEC) histologies. LCC classification is according to WHO 2004 guidelines.
Genomic DNA from 36 lung cancer samples was treated with bisulfite and hybridized to Illumina methylation 450K arrays using standard protocols. Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes. Both raw intensity values, signal detection p-values and the final normalized data are included for each sample.

overall_design: Genome-wide DNA methylation analysis of 36 lung carcinomas using Illumina Human Methylation 450K v1.0 Beadchips.

first: Mattias

last: Aine


title: A zebrafish model of Granulin deficiency reveals essential roles in myeloid cell differentiation

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: Granulin (GRN) is a pleiotropic protein involved in inflammation, wound healing, neurodegenerative disease, and tumorigenesis. These roles in human health have prompted research efforts to utilize Granulin in the treatment of rheumatoid arthritis, frontotemporal dementia, and to enhance wound healing. How granulin contributes to each of these diverse biological functions, however, remains largely unknown. Here, we have uncovered a new role for granulin during myeloid cell differentiation. Using a zebrafish model of granulin deficiency, we reveal that myeloid progenitors are unable to terminally differentiate into neutrophils and macrophages in the absence of granulin a (grna), and fail to express the myeloid genes cebpa, rgs2, lyz, mpx, mpeg1, mfap4, and apoeb. Pathology studies in combination with RNA-sequencing show that in addition to facilitating myeloid cell differentiation, granulin actively inhibits the erythroid program. Moreover, grna deficient myeloid progenitors are incapable of triggering a myelopoiesis emergency response, resulting in decreased recruitment of macrophages to the wound and therefore abnormal healing showing aberrant collagen depositions. Mechanistically, we have performed CUT&RUN for the first time in zebrafish, and identified that Pu.1 directly binds grna enhancers, triggering its expression. Similarly, mammalian granulin is also upregulated in myeloid cells, and its expression is controlled by the myeloid transcription factors PU.1 and IRF8, demonstrating a conserved regulatory mechanism among the zebrafish and mammalian genes. Altogether, our findings uncover a previously unrecognized role for granulin during myeloid cell differentiation, opening a new field of study that will help elucidate how granulin impacts inflammation, wound healing, tumor progression, and neurodegenerative disease.

overall_design: Adult grna-/- and grna+/+ control fish (three fish per condition) were subjected to cardiocentesis and kidney dissection as described here. RNA was isolated with RNeasy (Qiagen) following the manufacturer instructions. Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 75 basepair (bp) single reads (SR75) to a depth of approximately 20 million reads per sample on an Illumina HiSeq 4000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

first: Clyde

last: Campbell

first: Oksana

last: Fursova

first: Xiaoyi

last: Cheng

first: Elizabeth

last: Snella

first: Abbigail

last: McCune

first: Liangdao

last: Li

first: Barbara

last: Solchenberger

first: Bettina

last: Schmid

first: Mark

last: Morton

first: David

last: Traver

first: Raquel

last: Espín-Palazón


title: Characterization of mature Tregs in the thymus

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

institute: Weizmann Institute of Science

summary:
Using Foxp3.RFP Rag.GFP reporter mice,
mature Tregs in the thymus were characterized by performing RNA sequencing on Rag.GFP– and Rag.GFP+ Tregs that were isolated from the thymus and Tregs isolated from the spleen

overall_design: mRNA profiles of Rag.GFP- (mature)Tregs from thymus, Rag.GFP+(recently developed) Tregs from thymus and Tregs from spleen were generated by MARSeq Method

first: Cristina

last: Peligero-Cruz


title: IL18 signaling promotes homing of mature Tregs into the thymus

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

overall_design: Refer to individual Series


title: Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

first: Tamir

last: Tuller


title: Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

summary:
The COP9 signalosome (CSN) is a highly conserved complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. Mutations in each of the CSN subunits exhibits diverse pleiotropic phenotypes
We used microarrays to compare gene expression of two CSN mutants with their corresponding wild types: a non-lethal  csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype

overall_design: Light grown seedlings of the two wild types and two mutants were selected for RNA extraction and hybridization on Affymetrix microarrays

first: Tuller

last: Tamir

first: Diament

last: Alon

first: Avital

last: Yahalom

first: Assaf

last: Zemach

first: Shimshi

last: Atar

first: Daniel

last: Chamovitz


title: In-Vitro Identification and In-Vivo Confirmation of DNA Methylation Biomarkers for Urothelial Cancer

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: DNA-methylation targets specific for urothelial cancer (UC) were identified by genome-wide methylation difference analysis of human urothelial (RT4, J82, 5637), prostate (LNCAP, DU-145, PC3) and renal (RCC-KP, CAKI-2, CAL-54) cancer cell lines with their respective primary epithelial cells

overall_design: Factorial design based on disease and tissue type

first: Christina

middle: U

last: Köhler

first: Heiko

last: Käfferlein

first: Lang

last: Kerstin

first: Plöttner

last: Sabine

first: Roghmann

last: Florian

first: Noldus

last: Joachim

first: Tannapfel

last: Andrea

first: Tam

last: Yu Chun

first: Brüning

last: Thomas


title: Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development (bulk)

city: Ramat Gan

first: Tomer

last: Kalisky

address: Max and Anna Webb

department: Electrical Engineering

institute: Bar Ilan University

summary: Kidney development is a complex process involving multiple interacting and transforming cell types. These cell types were recently characterized using the Drop-seq single-cell technology for measuring gene expression from many thousands of individual cells. However, many genes can also be alternatively spliced and this creates an additional layer of cellular heterogeneity that cannot be measured with the Drop-seq technology. This study describes the use of full transcript length single-cell RNA sequencing to characterize alternative splicing in the developing mouse fetal kidney; in particular, the identification of genes that are alternatively spliced during the transition from mesenchymal to epithelial cell states, as well as their splicing regulators. These results improve our understanding of the molecular mechanisms involved in kidney development.

overall_design: We performed “bulk” RNA sequencing on three replicates of sorted Six2-high and Six2-low cell fractions from the kidneys of E18.5 mouse embryos using the INCPM-Genomics in-house protocol for mRNA sequencing,  which is compatible with Illumina's TrueSeq RNA sequencing protocol (with a few improvements).

first: Nissim

last: Ben-Haim


title: PRMT5 promotes cancer cell migration and invasion through the E2F pathway

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

summary: We identified distinct sets of genes under the control of PRMT5 and E2F1. Some of the most highly regulated genes, such as cortactin/CTTN, influenced cell migration, invasion and adherence. We characterised the functional role of the cortactin/CTTN gene, which enabled PRMT5 through E2F1 to promote cellular migration and invasion, whilst decreasing cellular adherence. Most significantly, there was a striking coincidence between the expression of PRMT5 and E2F1 in certain human tumours, and elevated levels of PRMT5, E2F1 and cortactin/CTTN correlated with poor prognosis disease. Our results suggest a causal relationship between PRMT5, E2F1 and the migration and invasion of cancer cells, thereby highlighting an important pathway that contributes to the cancer biology of tumour cells.

overall_design: Examination of expresion profile of colorectal cancer wild type and E2F1 knockdown HCT116 cells treated with PRMT5 inhibitor

first: Wojciech

last: Barczak

first: Li

last: Jin

first: Simon

last: Carr

first: Shonagh

last: Munro

first: Anastasia

last: Samsonova

first: Nicholas

last: La Thangue


title: Transcriptomic analysis of shCtrl and shCTCL  organoids by bulk RNA-seq

city: Shanghai

first: Minyi

last: Ou

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210

institute: ShanghaiTech University

summary: To explore the mechanism for the role of CTCLduring cortical development, we compaired the transcriptomes of shCtrl and shCTCL  organoids by bulk sequencing

overall_design: Stable line of shCtrl and shCTCL were generated by transfecting Human ES line H9 with lentivirus. Then, ES cells were processed organoid  culture protocal. At day30, RNA  from 2-4 organoids of each group were purified with the HiPure Total RNA Mini Kit. Raw reads were mapped to the hg19 reference using Hisat2 software, then transcripts were measured with StringTie/prepDE.py and differentially expressed genes were identified using R  package Ballgown.

first: Min-Yi

first: Xiang-Chun

last: Ju

first: Qi

last: Xiao


title: Ribosomal profiling of WT and mORF4/NBDY KO hearts [WT_vs_mORF4-NBDYKO_RNAseq]

city: Utrecht

first: Eva

last: van Rooij

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Left ventricles from the hearts of adult WT and mORR4/NBDY KO mice were obtained.

overall_design: Left ventricles of 4 hearts from wt mice and 4 heart from mORF4/NBDY KO mice were harvested. From each left ventricle the total RNA was isolated using Trizol.

first: Bas

last: Molenaar

first: Sebastiaan

last: van Kampen

first: Alexandre

last: Bossu

last: van Heesch

first: Jorge

last: Ruiz-Orera

first: Benedikt

last: Obermayer

first: Kamila

last: Kutz

first: Marta

last: Vigil-Garcia

first: Jantine

last: Monshouwer-Kloots

first: Mauro

last: Giacca

first: Norbert

last: Hubner

first: Toon

last: van Veen

first: Teun

last: de Boer


title: A Multimodal Study of Wild Tomato Species Introgressions Unravels the Genetic Basis of Transcriptome and Metabolome Variation in Important Fruit Traits

first: Jedrzej Jakub Szymanski

middle: Jakub

last: Szymanski

address: 234 Herzl Street, POB 26

summary: Here, we report RNAseq data from a Solanum lycopersicum-pennellii introgression population (IL) and a backcross introgression population (BIL), to establish the genetic basis of gene expression and chemical variation accompanying transfer of wild species-associated fruit traits. Transcriptome analysis of these lines resulted in the identification of genomic loci significantly linked with levels of hundreds of transcripts and metabolites. These associations occurred in functionally coherent hotspots that represent coordinated perturbation of metabolic pathways and ripening-related processes. We demonstrated the efficacy of our approach by discovering yet undisclosed components of the renowned Solanum alkaloids pathway and moreover, showing that fruit fungal resistance is associated with changes in the ripening regulatory network.

sample_organism: Solanum lycopersicum x Solanum pennellii

overall_design: 523 lines of IL and BIL population with introgression mapping provided in associated manuscript (Szymanski et al. 2020). Samples were collected in field conditions and skin tissue in a breaker stage of fruit ripening (~44 days post-anthesis) has been manually separated for further analysis.


title: IL18 signaling controls the CCR6-CCL20-dependent migration axis used by IL18R+ Tregs to enter the thymus

first: Jakub

last: Abramson

summary: We identified transcriptional changes in Tregs in response to IL18 stimulation, including upregulation of CCR6

overall_design: mRNA profiles of Tregs cultured in presence of CD3/CD28 activating beads together with increasing doses of IL18, were generated by MARSeq Method.

first: Cristina

last: Peligero-Cruz


title: Reversal of synaptic and behavioral deficits in a 16p11.2 duplication  mouse model via restoration of the GABA synapse regulator Npas4

city: Buffalo

first: Fengwei

last: Yang

address: 955 Main St

institute: University at Buffalo

summary: The human 16p11.2 gene locus is a hot spot for copy number variations, which predispose carriers to a range of neuropsychiatric phenotypes. Microduplications of 16p11.2 are associated with autism spectrum disorder (ASD), intellectual disability (ID), and schizophrenia (SZ). Despite the debilitating nature of 16p11.2 duplications, the underlying molecular mechanisms remain poorly understood. Here we performed a comprehensive behavioral characterization of 16p11.2 duplication mice (16p11.2dp/+) and identified social and cognitive deficits reminiscent of ASD and ID phenotypes. 16p11.2dp/+ mice did not exhibit the SZ-related sensorimotor gating deficits, psychostimulant-induced hypersensitivity, or motor impairment. Electrophysiological recordings of 16p11.2dp/+ mice found deficient GABAergic synaptic transmission and elevated neuronal excitability in the prefrontal cortex (PFC), a brain region critical for social and cognitive functions. RNA-sequencing identified genome-wide transcriptional aberrance in the PFC of 16p11.2dp/+ mice, including downregulation of the GABA synapse regulator Npas4. Restoring Npas4 expression in PFC of 16p11.2dp/+ mice ameliorated the social and cognitive deficits and reversed GABAergic synaptic impairment and neuronal hyperexcitability. These findings suggest that prefrontal cortical GABAergic synaptic circuitry and Npas4 are strongly implicated in 16p11.2 duplication pathology, and may represent potential targets for therapeutic intervention in ASD.

overall_design:
This study was designed to characterize mice carrying 16p11.2 duplication behaviorally, biochemically, transcriptionally, and electrophysiologically. RNA-sequencing was performed in prefrontal cortex in order to characterize the transcriptional profile associated with this copy number variation.
These animals were originally generated on a hybrid C57BL/6N:129Sv background before being backcrossed 10 generations onto C57BL/6 inbred strain and maintained on C57BL/6 genetic background.

first: Benjamin

last: Rein

first: Tao

last: Tan

first: Wei

last: Wang

first: Jamal

last: Williams

first: Freddy

last: Zhang

first: Alea

last: Mills

first: Zhen

last: Yan


title: RNA sequencing of maize FDL1 mutants

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

summary: In higher plants, the outer surface of the aerial parts is covered by the cuticle, a complex lipid layer that constitutes a barrier against damages caused by environmental factors and provides protection against non-stomatal water loss. We show in this study that cuticle deposition, during the juvenile phase of in maize (Zea mays) plant development, and cuticle-dependent leaf permeability are controlled by the MYB transcription factor ZmMYB94/FUSED LEAVES1(ZmFDL1).  Transcriptome analysis allowed the identification of a set of maize candidate genes involved in lipid metabolism and the definition of a proposed pathway for cuticle biosynthesis in maize. Lack of ZmFDL1 affects the expression activities of genes located in different modules of the pathway and correspondence between gene transcriptional variations and biochemical defects will be discussed.

overall_design: RNAseq of WT and mutants. 3 biological replicates for each condition

first: Giulia

last: Castorina

first: Frédéric

last: Domergue

first: Massimo

last: Zillo

first: Martina

last: Persico

first: Valentina

last: Ricciardi

first: David

middle: S

last: Horner

first: Gabriella

last: Consonni


title: Microglia require CD4 T cells to complete the fetal to adult transition

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

institute: The Babraham Institute

summary: The blood brain barrier has long been thought to isolate the brain from the adaptive immune system. While CD4 T cells have been reported in the central nervous system, their presence in the healthy brain remains controversial, and their function at this site unknown. Here we have used a combination of imaging, single cell and surgical approaches to identify a unique CD69+ CD4 T cell population in both the mouse and human brain, which is distinct from circulating CD4 T cells. The brain-resident population was derived through in situ differentiation from activated circulatory cells, and was shaped by interaction with the gut microbiome and self-antigen in the brain. Single cell sequencing revealed that in the absence of murine CD4 T cells, resident microglia remained suspended between a fetal and adult state. This maturation defect resulted in excess immature neuronal synapses and behavioral abnormalities in the adult mouse. These results illuminate a role for CD4 T cells in the basic developmental processes of the brain, and a potential interconnected dynamic between the evolution of the immunological and neurological systems.

overall_design: Quantification and characterisation of the brain CD4 T cell population in two wild type mice and one MHC class II-deficient mouse with a near-complete absence of CD4 T cells


title: Seminal fluid components alone stimulate post-mating changes in honey bee queens (Apis mellifera)

city: Davis

first: Laura

last: Brutscher

address: One Shields Avenue

department: Entomology and Nematology

institute: University of California, Davis

summary: Honey bee queens undergo dramatic behavioral (e.g., reduced sexual receptivity), physiological (e.g., ovary activation, ovulation, and modulation of pheromone production) and molecular changes after they complete mating. To elucidate how queen post-mating changes are influenced by seminal fluid, a non-spermatozoa-containing component of semen, we injected queens with semen or seminal fluid alone. We assessed queen sexual receptivity, ovary development, worker retinue response (which is influenced by queen pheromone production), and transcriptional changes in queen abdominal fat body and brain tissues. Injection with either seminal fluid or semen resulted in decreased sexual receptivity, increased attractiveness of queens to workers, and altered expression of several genes that are also regulated in naturally mated queens. The post-mating and transcriptional changes of queens receiving seminal fluid were not significantly different from queens treated with seminal fluid, suggesting that components in seminal fluid, such as seminal fluid proteins, are largely responsible for stimulating post-mating changes in queens.

overall_design: 38 samples total were analyzed. These samples comprised 20 fat body RNAseq libraries and 18 brain RNAseq libraries from 20 queens. Queens were injected in the abdomen with Hayes solution (fat body n=5;brain n=5 ), semen (fat body n=5;brain n=5),  or seminal fluid ((fat body n=5;brain n=3), or were not treated at all (controls, fat body n=5;brain n=5).

first: William

last: Cameron Jasper

first: Christina

last: Grozinger

first: Elina

last: Nino


title: Characterization of mature IL18R- and IL18R+ Tregs in the thymus

first: Jakub

last: Abramson

summary: Using Foxp3.RFP Rag.GFP reporter mice, we characterized  differences between the IL18R- and the IL18R+ mature Treg populations in the thymus

overall_design: mRNA profiles of different Treg populations of the thymus was generated by MARSeq Method. These include: Rag.GFP+(recently developed) Tregs, Rag.GFP- (mature)IL18R- Tregs and  Rag.GFP- (mature)IL18R+ Tregs

first: Cristina

last: Peligero-Cruz


title: A Highly Phenotyped Open Access Repository of Alpha-1 Antitrypsin Deficiency Pluripotent Stem Cells

city: Boston

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We profiled the global transcriptomes of 10 featured AATD-patient specific iPSC that underwent directed differentiation towards a hepatic and lung lineage. We used digital gene expression (DGE), a platform for high-fidelity RNA sequencing, and in addition to differentiated iPSC-derived cell types mentioned above (iHeps and iPSC-Lung progenitors), we also collected RNA from undifferentiated iPSCs and from a panel of primary adult human hepatocytes (PHH) for comparison.

overall_design: For digital gene expression (DGE) the concentrations of all samples were normalized and sent to the Broad Institute for library construction and sequencing. Reads were then aligned to the ENSEMBL human reference genome. The count matrix was filtered and normalized to facilitate linear model fitting and differential expression testing. A liver enrichment score was derived by identifying differentially expressed genes between PHH and undifferentiated iPSCs.

first: Joseph

last: Kaserman

first: Andrew

last: Wilson


title: Dynamics and transcriptomic driver landscape of metastatic osteosarcoma

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

summary: We report MAPK7-MMP9 signalling axis in metastatic osteosarcoma

overall_design: RNA seq experiment was designed to capture mRNA at several stages of cancer progression in primary tumours, CTCs and metastatic tumours

first: Darrell

last: Green

last: Fraser


title: Single-cell RNA sequencing reveals mRNA splice isoform switching during kidney development

first: Tomer

last: Kalisky

overall_design: We performed single cell RNA sequencing on 576 individual cells from the kidneys of E18.5 mouse embryos using the Smartseq2 protocol for sequencing full transcript lengths

first: Nissim

last: Ben-Haim


title: mRNA sequencing time course of C. elegans samples at time point 1 hours until time point 24 hours at 25 degree [blmp-1(tm548) mutant]

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

summary:
We find gene expression oscillations which arise after a time lag of around 5 hours.
Molecular oscillators can organize gene expression during development both temporally and spatially. In C. elegans, oscillations occur for ~25% of the transcriptome to control molting and potentially other developmental processes. The underlying mechanisms and organization of the oscillator remain unknown. We investigated the transcription factor BLMP-1, orthologous to mammalian PRDM1, as a rhythmically accumulating transcription factor that is required for robust rhythmic development, molting, and animal viability. We have sequenced synchronously growing populations of wild-type and blmp-1(tm548) mutant animals in a time course from 1 – 24 hours after plating with an hourly resolution.

overall_design:
Examination of gene expression profiles of blmp-1(tm548) mutant animals over time (1-24 hours after plating L1 arrested C. elegans larvae) using high throughput mRNA sequencing.

Please note that the processed data file (of total 48 data columns) contains the control sample data (represented in GSE141514)


title: Expression data of human mesenchymal stromal cells isolated from bone marrow of ML-DS, AMKL patients and HD

city: Essen

first: Theresa

last: Hack

address: Hufelandstraße 55

department: Children's clinic 3

institute: University Hospital Essen

summary:
Bone marrow fibrosis (BMF) is a rare complication in acute leukemia. In pediatrics, it predominantly occurs in acute megakaryoblastic leukemia (AMKL) and here especially in patients with trisomy 21, called myeloid leukemia in Down syndrome (ML-DS). Defects in mesenchymal stromal cells (MSCs) and cytokines specifically released by the myeloid blasts are the main drivers of fibrosis in the bone marrow niche (BMN). In order to determine which factors are necessary/sufficient for the BMF, we first established MSCs from pediatric patients with AMKL and ML-DS. Healthy donor (HD) control MSCs were established from children and adolescents ≤18 years of age. Steady-state analyses of the MSCs revealed that patient-derived MSCs exhibited decreased adipogenic differentiation potential, enrichment of proliferation-associated genes and upregulation of the oncofetal protein IF2B3. TGFB1 exposure in vitro promoted early profibrotic changes in all three MSC entities. To study BMF induction for longer periods of time, we created an in vivo humanized artificial BMN in immunodeficient mice. Injection of AMKL blasts as producers of TGFB1 specifically induced fibrosis grade I/II in a dose-dependent fashion, thus strongly suggesting TGFB1 excess to be sufficient for BMF. Our in vivo BMF model will be instrumental to specifically prevent the BMF and to identify potentially druggable target genes.
We used microarrays to obtain a global overview of the differences between undifferentiated ML-DS- and AMKL-MSC compared to HD-MSC

overall_design: Isolated and expanded MSC were cultured until a density of 80-90% followed by RNA extraction and hybridization on Affymetrix microarrays. We performed a gene expression profile of MSC from 8 ML-DS, 5 AMKL patients and 5 HD.

first: Markus

last: Schneider

first: Mareike

last: Rasche

first: Ludger

last: Klein-Hitpass


first: Adrian

last: Liston

overall_design: single cell RNA-seq of CD4+ cells from human brain and PBMC


title: Next generation sequencing of FFPE human colon cancer samples for validation of ColoType consensus molecular subtype (CMS) assay

city: Notre Dame

first: Steven

last: Buechler

state: IN

address: 102B Crowley Hall

department: Appl. Comp. Math & Statistics

institute: University of Notre Dame

summary:
Purpose: To validate the novel ColoType assay for computing consensus molecular subtypes of colon cancer tumor samples
Method: Whole-genome RNA-sequencing of colon cancer samples from formalin-fixed paraffin-embedded (FFPE) provided data for consensus molecular subtyping samples using multiple independent methods, including the novel ColoType method. A custom Illumina AmpliSeq library was also used to implement ColoType on these samples by targeted RNA-sequencing.
Results: Multiple independent methods for computing CMS subtypes for FFPE colon cancer samples have widespread agreement with ColoType assay.

overall_design: Whole-transcriptome profiles of mRNA extracted from FFPE human colon cancer samples


title: Arachidonic acid promotes intestinal regeneration by activating Wnt signaling

city: Beijing

first: Qingyu

last: Wang

address: Qinghua East Road No.17

department: College of Food Science and Nutritional Engineering

institute: China Agricultural University

summary: We identify arachidonic acid (AA), as a direct proliferation promoter of intestinal epithelial cells, facilitating small intestinal regeneration. In the transcriptomes, it shows that AA treatment upregulated proliferation-related genes including Wnt signaling target genes, while downregulated differentiation-related genes including enterocyte, goblet cell, Paneth cell, enteroendocrine cell, and tuft cell markers. Additionally, AA could also upregulate stem cell-associated genes which have been highly expressed three days after 12Gy IR injury (e.g. Clu, Lamc2, Anxa1, Areg, and Ly6d). The study shows that AA treatment can be considered a potential therapy for irradiation injury repair and tissue regeneration.

overall_design: Organoids isolated from mouse small intestine were treated with arachidonic acid for three days followed by passage. The mRNA profiles were generated by deep sequencing using Illumina NovaSeq 6000 platform.


title: Gene expression profilings in human embryonic stem cell-derived cardiomyocytes in vivo and in vitro

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

summary: RNA sequencing of human embryonic stem cell-derived cardiomyocytes

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: There are 16 RNA-sequencing samples

first: Yuji

last: Shiba


title: mRNA sequencing time course of C. elegans samples at time point 1 hours until time point 24 hours at 25 degrees [N2 control]

summary: We find gene expression oscillations which arise after a time lag of around 5 hours.

overall_design: Examination of gene expression profiles over time (1-24 hours after plating L1 arrested C. elegans larvae) using high throughput mRNA sequencing.


title: 8-oxoG RNA IP data set 2: Air pollution mixture derived from the reaction of 100 ppb acrolein, 97 ppb methacrolein, 44 ppb alpha-pinene and 100 ppb O3 for 1.5 h

city: Austin

first: Lydia

last: Contreras

state: TX

address: 200 E. Dean Keeton St Stop C0400

department: McKetta Department of Chemical Engineering

institute: University of Texas at Austin

summary: While environmental agents such as air pollution have been shown to be causative to diseases, yet limited knowledge exist on their mechanism of action. Here we used RNA-sequencing in combination with specific immunoprecipitation of 8-oxo-7,8-dihydroguanosine (8-oxoG) to identify transcripts accumulating oxidation after exposure to air pollution (derived from the reaction of  acrolein, methacrolein, alpha-pinene and ozone) in bronchial epithelial BEAS-2B cells. Results from this analysis suggest a functional role of the 8-oxoG modified transcripts after air pollution exposure in pathways that are central regulators of cell metabolism, growth, proliferation and maintenance of cellular structure. This study highlights a critical role for a RNA epitranscriptomics modification that can be used to further characterize biological responses to external stressors once considered indistinguishable.

overall_design: 8-oxoG was measured from rRNA depleted RNA in BEAS-2B cells exposed to air pollution mixtures (derived from the reaction of 100 ppb acrolein, 97 ppb methacrolein, 44 ppb alpha-pinene and 100 ppb O3) and clean air for 1.5 hours. Two biological replicates are available from control input, and two biological replicates for IP 8-oxoG RNA.

first: Juan

middle: C

last: Gonzalez-Rivera

first: Kevin

last: Baldridge

first: Dongyu

first: Kananben

middle: H

last: Patel

first: Jamie

last: Chuvalo-Abraham

first: Lea

last: Hildebrandt Ruiz


title: The transcription factor BCL6 controls early development of innate-like T cells (ATAC-seq)

city: Vari

first: Mihalis

last: Verykokakis

address: 34, Fleming street

country: Greece

institute: BSCR Alexander Fleming

summary: Innate T cells, including invariant natural killer T (iNKT) and mucosal-associated innate T (MAIT) cells, are a heterogeneous T lymphocyte population with effector properties pre-programmed during their thymic differentiation. How this program is initiated is currently unclear. Here, we show that the transcription factor BCL6 is transiently expressed in iNKT cells upon exit from positive selection and is required for their proper development beyond stage 0. Notably, development of MAIT cells is also impaired in Bcl6-deficient mice. We found that BCL6 regulates the expression of genes that are associated with the innate T cell lineage, including PLZF and its targets. BCL6 contributes to a chromatin accessibility landscape that is permissive for the expression of development-related genes and inhibitory for genes associated with naïve T cell programs. Our results reveal novel functions for BCL6 and indicate that this transcription factor controls the inception of innate T cell lineage programming.

overall_design: Tetramer+TCRb+CD24+CD44- (Stage 0, ST0) and Tetr+TCRb+CD24-CD44- (ST1) cells from the thymi of 4-7 pooled WT and CDCre;Bcl6F/F (Bcl6KO) mice were sorted and RNA was extracted for RNA-seq analysis. Similar populations were sorted and cells were porcessed for ATAC-seq. Mature NKT (mNKT) cells were sorted as Tetramer+TCRb+CD24-CD44+NK1.1+, followed by ATAC-seq.

first: Barbara

last: Kee


title: The transcription factor BCL6 controls early development of innate-like T cells

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

overall_design: Refer to individual Series


title: Analysis of lacking Nα-terminal acetylation of proteins by NatA and NatB in Saccharomyces cerevisiae on mRNA levels and protein synthesis

city: Heidelberg

first: Ulrike

middle: Anne

last: Friedrich

address: Im Neuenheimer Feld 282

department: ZMBH

country: Germany

institute: Heidelberg University

summary: N-terminal (Nt)-acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt-acetyltransferases (Nat) with differing specificities. Nt-acetylation has been implicated in protein quality control but its broad biological significance remains elusive. We investigated the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome and translatome profiling by using mRNA sequencing and ribosome profiling. The results are combined with global proteome, aggregome and stabilome datasets. To analyze previously proposed physiolocal roles of NatA and NatB in yeast cells on protein stability and interaction specific growth conditions such as different growth media and heat stress are used in addition to physiological growth.

overall_design: mRNA sequencing and ribosome profiling of generated yeast strains lacking the N-terminal acetyltransferase complex catalytic subunit Naa10 (for NatA) or Naa20 (for NatB) in wild-type background or hmlΔ background under different growth conditions (as indicated), each sample is prepared in replicates and wild-type yeast strain is used as reference (also in replicates)

first: Mostafa

last: Zedan

first: Bernd

last: Hessling

first: Kai

last: Fenzl

first: Ludovic

last: Gillet

first: Joseph

last: Barry

first: Michael

last: Knop

first: Günter

last: Kramer

last: Bukau


title: FXR isoform selective effects on hepatoma cell line HepG2

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

institute: University of Innsbruck

summary: The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids that regulates bile acid metabolism, glucose and cholesterol homeostasis. FXR is expressed as four isoforms (α1-4), and their relative abundance is tissue specific. Human livers express predominantly FXR isoforms α1 and α2. From mouse studies we know that the FXR agonist obeticholic acid (OCA) regulates expression of many genes in the liver. However,  there is currently no data on the effects of OCA on FXR isoform selective gene regulation.  This is particularly relevant since the relative FXR isoform amounts in the liver are regulated by general bioenergetic cues (Correia JC et al. 2015). In this study we investigate the effect of variations in FXR isoforms α1 or α2 expression on HepG2 cell lines response to treatment with OCA.

overall_design: HepG2 cells were transduced with FXR isoforms α1 or α2, or GFP using lentiviral vectors (pLV IRES PuroR). After selection, the cells were treated with the FXR agonist Obeticholic acid for 8 hours before lysis. RNA was extracted and prepared for sequencing analysis.

first: Jose

first: Saskia

middle: W

last: van Mil


title: State transitions of a developmental oscillator

first: Helge

last: Grosshans


title: Effect of miRNA-30e-5p on innate immunity during viral infection.

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

summary: Comparative transcriptomic analysis of A549 cell after overexpression of miRNA-30e-5p revealed that miRNA-30e-5p elevate innate immune responses by targeting the negative regulators of innate immune signalling.

overall_design: We transfected A549 cells with either miR-NC1 or miR-30e mimic or mock, cells were then mock infected or infected with Newcastle Disease Virus (NDV) infection, total RNA was isolated and whole transcriptomic sequencing was done.

first: Richa

last: Mishra


title: Time-resolved transcriptome analysis under sulfur starvation stress in the green microalga Chromochloris zofingiensis

city: Shenzhen

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

institute: Shenzhen University

summary: Chromochloris zofingiensis has been proposed as a potential producer of lipids and the high-value carotenoid astaxanthin. Previous studies have demonstrated that TAG (triacylglycerol) and astaxanthin accumulated in a well-coordinated manner in response to different stresses in C. zofingiensis. The integrated production of lipids with co-products emerges as a new research direction and is proposed to be a promising approach toward offsetting the algal biodiesel production cost. Therefore, it is suggested C. zofingiensis can serve as research models for the integrated production. Sulfur starvation stress simultaneously induced TAG and astaxanthin accumulation in C. zofingiensis. To understand the mechanism underlying TAG and astaxanthin accumulation induced by sulfur starvation stress, we applied time-resolved high-throughput mRNA sequencing in C. zofingiensis.

overall_design: Chromochloris zofingiensis cells in exponential phase were harvested by centrifugation at 5000 rpm for 5 min and washed twice. Then cells (initial cell density at 0.5 g/L) were re-inoculated in modified Kuhl medium in which MgSO4 was replaced with MgCl2 for sulfur starvation stress. Cells were collected for RNA isolation at 0 h and 6, 12, 24, 48 h after re-inoculation. After 48 h of sulfur starvation, cells were re-inoculation into fresh kuhl medium for sulfur replenishment and samples were collected after 12 h. Three biological replicates of algal cultures were carried out. In total, 18 samples were collected for mRNA-seq.


title: Effect of NOTCH-γ-secretase inhibitor LY3039478 therapy on patient derived xenograft (PDX) mouse model of intrahepatic cholangiocarcinoma

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary:
Intrahepatic Cholangiocarcinoma (iCCA) is a deadly disease with rising incidence and few treatment options. Recently, aberrant Notch signaling was reported in iCCA carcinogenesis. Specifically, altered expression and/or activation of the receptors Notch1/2 suggests a role for Notch pathway overactivation during iCCA formation and progression. In this study, we examined the effects of Notch inhibition by γ-secretase inhibitor, LY3039478 in human iCCA cell lines and in an excellent patient derived-xenograft (PDX) model. Expression of several Notch pathway components, including NICD, Hes1, and DLL4, were reduced after GSI treatment. Moreover, LY3039478 inhibits cell migration and invasion while in GSI-treated mice, tumor growth was delayed compared to vehicle and chemotherapy. These results support the notion that Notch inhibition by GSI may reduce in vivo tumorigenesis. In addition, GSI reduces in PDX model VEGFA and MMP13 involved in capillary tube formation and tumor progression. Here, we therefore show a link between the efficacy of Notch inhibition and the tumor microenvironment through LY3039478 that slows tumor progression compared to control mice blocking angiogenesis via MMP13 downregulation.
We used microarray technology to understand the molecular mechanisms affected by LY3039478. Cholangiocarcinoma PDX model was employed in this analysis.

overall_design: Expression profiling of patient-derived xenografts (PDX) from patients with intrahepatic cholangiocarcinoma after and before LY3039478 treatment. Moreover, we also analyzed the of the original tumor mass and PDX tissue comparing them to the surrounding normal mass of patient.

first: Serena

last: Mancarella

first: Gianluigi

last: Giannelli


city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

institute: wannan medical college

summary:
Long non-coding RNAs (lncRNAs) play key roles in various biological processes. However, the roles of lncRNAs in macrophage polarization remain largely unexplored. Our study have found that lncRNA AK085865 play a vital role in macrophage polarization and specific bind to ILF2 protein and further influence the miRNA processing process.
The miRNA expression profiles in the BMDM of C57BL/6J wild type and lncRNA AK085865 knock-out mice were obtained using microarray analysis. Based on the threshold of fold-change ≥2.0 and a p-value ≤ 0.05, we screened a total of 24 miRNAs, of which 11 were upregulated and 13 were downregulated in KO compared to that in WT BMDMs.This study provides new insights into the role of lncRNA AK085865 regulating miRNAs expression in the mice BMDMs.

overall_design: Total RNA was prepared from bone marrow-derived macrophages of wild-type C57BL/6J and lncRNA AK085865 knock-out mice  (n=2 replicates per condition originating from different mice)

first: Kun

last: Lv


title: Combining RNA-Sequencing with immunoprecipitation of 8-oxo-7,8-dihydroguanosine (8-oxoG) facilitates discovery of cellular effects associated with lung cell exposure to air pollution

first: Lydia

last: Contreras

country: USA


title: FXR isoform selective transcriptional activation in mouse liver organoids

summary: The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids that regulates metabolic processes. FXR is expressed as four isoforms (α1-4), and their relative abundance is specific to tissue and bio-energetic conditions (Correia JC et al. 2015). Depending on the FXR isoform expressed, there is a degree of selectivity in target-genes activation. In this dataset, we defined FXR-isoforms selective effects on transcription in mouse liver organoids after treatment with the FXR agonist Obeticholic acid(OCA). By linking the DNA binding profiles of the FXR isoforms with their transcriptional output, we concluded that differential DNA binding plays a defining role in FXR-isoform target gene selectivity.

overall_design: FXR -/- mouse liver organoids were transduced with mouse FXR isoforms α1, α2, α3, α4 or H2b-NeonGreen(ko) using lentiviral vectors (pLV IRES PuroR). After selection, the organoids were differentiated into the hepatocyte lineage before treatment with OCA


title: mRNA sequencing time course of C. elegans samples at time point 0 hours until time point 15 hours at 25 degree.

overall_design: Examination of gene expression profiles over time (0-15 hours after plating L1 arrested C. elegans larvae) using high throughput mRNA sequencing.

first: Gert-Jan

last: Hendriks


title: HES1 and HES4 have both unique and overlapping roles as downstream mediators of Notch-dependent hematopoietic lineage decisions in human

city: Ghent

first: Matthias

last: De Decker

address: Corneel Heymanslaan 10

department: Diagnostic Sciences

country: Belgium

institute: Ghent University

summary: In both mouse and human, Notch1 activation is the main initial driver to induce T-cell development in hematopoietic progenitor cells. The initiation of this developmental process coincides with Notch1-dependent repression of differentiation towards other hematopoietic lineages. Although well described in mice, the role of the individual Notch1 target genes during these hematopoietic developmental choices is still unclear in human. Here, we investigated the functional capacity of the Notch1 target genes HES1 and HES4 to modulate human Notch1-dependent hematopoietic lineage decisions. Using well-established in vitro cocultures and RNA sequencing, we show that HES1 acts as a repressor of differentiation by maintaining a quiescent stem cell signature in CD34+ hematopoietic progenitor cells. While HES4 can also inhibit NK and myeloid development like HES1, it acts differently on the T- versus B-cell lineage choice. Surprisingly, HES4 is not capable of repressing B-cell development, the most sensitive hematopoietic lineage with respect to Notch-mediated repression. In contrast to HES1, HES4 promotes initiation of early T-cell development. Overall, we show that the Notch1 target genes HES1 and HES4 display both unique and overlapping functions downstream of Notch during human hematopoietic lineage decisions.

overall_design: Three independent CB CD34+Lin- samples, from three independent donors, were transduced with a control-, HES1- or HES4-expressing construct and cultured for one day on OP9-GFP or OP9-DLL1 before extracting RNA and sequencing.

first: Tom

last: Taghon


title: mRNA-seq time course of C. elegans sampled from 5h until 48h at 25 degrees

summary: We find 3739 'high-confidence oscillating' genes. These genes peak 4 times during larval development, but cease in adulthood

overall_design: examination of gene expression profiles over time, 5h-48h after plating L1 arrested larvae at 25 degrees, using high throughput mRNA sequencing

first: Yannick

last: Hauser


title: Derivation and Characterization of a UCP1 Reporter Human ES Cell Line

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Interest in human brown fat as a novel therapeutic target to tackle the growing obesity and diabetes epidemic has increased dramatically in recent years. While much insight into brown fat biology has been gained from murine cell lines and models, few resources are available to study human brown fat in-vitro. In this study, we detail the derivation and characterization of a novel human ES UCP1 reporter cell line that marks UCP1 positive adipocytes in-vitro. We targeted a mCherry reporter to the UCP1 stop codon via CRISPR-Cas9 and demonstrated that when differentiated to brown adipocytes, reporter cells express UCP1, display high mitochondrial content and multi-locular lipid morphology, and exhibit functional properties such as lipolysis in the presence of isoproterenol and forskolin. Isolation and purification of mCherry positive cells demonstrated elevated expression of brown fat marker genes and a high similarity to isolated human brown fat versus white fat via RNA-seq. This reporter cell line thus presents new opportunities to study human brown fat biology by enabling future work to understand early human brown fat development, performing disease modeling, and enabling drug screening applications.

overall_design: RNA-seq was performed on isolated mCherry positive and negative cells in duplicate.

first: Suranjit

last: Mukherjee


title: 8-oxoG RNA IP data set 1: Air pollution mixture derived from the reaction of 790 ppb acrolein, 670 ppb methacrolein, and 4 ppm O3 for 1.5 h

summary: While environmental agents such as air pollution have been shown to be causative to diseases, yet limited knowledge exist on their mechanism of action. Here we used RNA-sequencing in combination with specific immunoprecipitation of 8-oxo-7,8-dihydroguanosine (8-oxoG) to identify transcripts accumulating oxidation after exposure to air pollution (derived from the reaction of 790 ppb acrolein, 670 ppb methacrolein, and 4 ppm ozone) in bronchial epithelial BEAS-2B cells. Results from this analysis suggest a functional role of the 8-oxoG modified transcripts after air pollution exposure in pathways that are central regulators of cell metabolism, growth, proliferation and maintenance of cellular structure. This study highlights a critical role for a RNA epitranscriptomics modification that can be used to further characterize biological responses to external stressors once considered indistinguishable.

overall_design: 8-oxoG was measured from rRNA depleted RNA in BEAS-2B cells exposed to air pollution mixtures (derived from the reaction of 790 ppb acrolein, 670 ppb methacrolein, and 4 ppm ozone) and clean air for 1.5 hours. 3 biological replicates are available from control input, and two biological replicates for IP 8-oxoG RNA.

first: Juan

last: Gonzalez-Rivera

first: Kevin

last: Baldridge

first: Dongyu

last: Wang

first: Jamie

last: Chuvalo-Abraham

first: Lea

last: Hildebrandt Ruiz


title: mRNA-seq time course of C. elegans sampled at and after release from dauer starvation at 25 degrees

first: Helge

last: Grosshans

summary:
We find that the 'high-confidence oscillating' genes initiate oscillations similarly as after release from L1 dauer.
We performed high-throughput RNA sequencing on worms that were synchronously released from the dauer stage by refeeding on OP50. In particular, we investigate oscillatory gene expression as described in Hendriks et al., 2014 (doi: 10.1016/j.molcel.2013.12.013) and observe the re-initiation of oscillatory gene expression from stable expression with a time delay upon dauer exit. Experimental observation of the transitions between non-oscillatory and oscillatory states during the first 5 hours after dauer exit reveals that the oscillatory gene expression is arrested in a specific oscillator phase, similar to the observation we make in animals released from L1 arrest (see Meeuse et al., 2020, doi: https://doi.org/10.1101/755421).

overall_design: Examination of gene expression profiles over time at 25 degrees, using high throughput mRNA sequencing. The "RNAseq_N2_dauer" sample was combined with the samples GSM1277134 - GSM1277155 (in GSE52861) and all samples were mapped to C. elegans genome (ce10) using the qAlign function (splicedAlignment=TRUE) from the QuasR package in R followed by counting the reads using qCount() from the QuasR package in R. A pseudocount of 8 was added and then the counts were log2-transformed. For the pairwise correlation analysis described in XX we used the mean normalized gene expression of the "oscillating" gene set using pearson correlation.

first: Florian

last: Aeschimann


title: Microarray-based gene expression on human aortic valves

status: Public on Jul 26 2020

first: Dong

last: Han

address: 28 Fuxing street

country: China

institute: China PLA general hospital

summary: Calcified aortic valve leaflets (CAVs) were explanted from patients with severe aortic valve stenosis undergoing aortic valve replacement at the Department of Cardiovascular Surgery, Union Hospital, affiliated to Tongji Medical College. Control non-calcified aortic valves with normal echocardiographic analyses were obtained during heart transplant procedures. RNA was extracted from valve leaflets and gene expression evaluated using the Arraystar Human mRNA Array. This study aimed to perform the expression analysis of mRNA on human aortic valves.

overall_design: Whole-genome gene expression was performed in 6 human aortic valves.

first: Yongjun