title: Cardamonin repel colitis and its associated colorectal cancer

city: Thycaud

first: Dr. Harikumar

last: B

state: Kerala

address: Poojappura

department: Cancer Research Program

institute: Rajiv Gandhi centre for Biotechnology

summary:
The effect of Cardamonin was checked on Dextran sulfate sodium and Azoxymethane (AOM) induced colon cancer in C57Bl/6 mice.
C57Bl/6 were given a single AOM (10mg/kg B.wt) intraperitonielly at day 0 and three bouts of 5% DSS at days 5-10, 25-30, 45-50. At day 140, the mice were sacrificed and colon was monitored for tumors. Cardamonin treatment (10mg/Kg B.wt, p.o) was started simulatenously for one group. For the second group it was started after 16 of first AOM injection. The study was terminated at 140 day. The RNA was ioslated uisng mirVANA kit from each samples followed miRNA analysis uisng affymetrix gene chip miRNA array 4.0

overall_design: 16 samples were analysed. The differential expression of miRNAs between groups were analysed.

first: S

last: James

first: J

last: Aparna

first: A

last: Paul

first: B

last: Manendra

first: M

last: Sabira

first: R

last: Girijadevi

first: Kuzhuvelil

last: Harikumar


title: Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer

status: Public on Apr 07 2021

city: New York

first: Nicholas

last: Brady

state: NY

address: 1188 York Ave

department: Pathology and Laboratory Medicine

country: USA

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions

status: Public on Apr 06 2021

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

summary: Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in E. coli for >2000 proteins over >60 growth conditions, including nutrient limitations, non-metabolic stresses and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.

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

overall_design: Three ribosome profiling datasets in E. coli (various strains: NCM3722, NQ1390, MG1655).

first: Ruedi

last: Aebersold

first: Amir

middle: B

last: Esfahani

first: Ben

last: Collins

first: Terry

last: Hwa

first: Gene-Wei

last: Li

first: Christina

last: Ludwig

first: Matteo

last: Mori

first: Hiroyuki

last: Okano

first: Alexander

last: Schmidt

first: Olga

last: Schubert

first: Zhongge

last: Zhang


title: Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ChIP-seq II]

status: Public on Apr 05 2021

city: Salt Lake City

first: Bradley

middle: R

last: Cairns

state: UT

address: 2000 Cir of Hope Dr

department: oncological Sciences

institute: Huntsman Cancer institute/HHMI

summary: Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps.  Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control.  We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. Prior to ZGA the zebrafish genome largely lacks physical structure, while after ZGA there are small domain-like structures detectable.  Lastly, we find initial chromatin architecture formation at super enhancers – and demonstrate that this formation is lost upon chemical inhibition of CBP/p300 activity (lowering histone H3K27ac), but not transcription inhibition. The experiments address fundamental mechanisms of initiation, how TADs are established and remodeled in vivo, and their effect on gene expression both during and after ZGA - a universal transition across animals - using the zebrafish model.

overall_design: Zebrafish sperm, and Embryos of 2.25, 4, 5.3 and 24 hours after fertilization were processed for Hi-C. ChIP-seq at 4hpf for RNA polymerase II, Rad21 (Cohesin) and ATAC-seq performed at 4hpf.

first: Candice

middle: L

last: Wike


title: Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ATAC-seq]

overall_design: Zebrafish sperm, and Embryos of 2.25, 4, 5.3 and 24 hours after fertilization were processed for Hi-C. ChIP-seq at 4hpf for RNA polymerase II and ATAC-seq performed at 4hpf.


title: Chromatin architecture transitions from zebrafish sperm through early embryogenesis [ChIP-seq]


title: IRS1 plays a dominant role in regulating pancreatic alpha cell function

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Inappropriate glucagon secretion deteriorates glycemic control in type 1 and type 2 diabetes. While insulin is known to regulate glucagon secretion via its receptor in alpha cells, the role of downstream proteins and signaling pathways underlying the actions of insulin are not fully defined.   Using in vivo (knockout) and in vitro (knockdown) studies targeting insulin receptor substrate (IRS) proteins, we compared the relative roles of   IRS1 versus IRS2 in regulating alpha cell function.   Alpha cell-specific IRS1 knock out (alpha IRS1KO) mice exhibit glucose intolerance and inappropriate glucagon suppression during glucose-tolerance tests. In contrast, alpha cell-specific IRS2 knock outs (alpha IRS2KO) manifest normal glucose tolerance and suppression of glucagon secretion after glucose administration. Alpha cell lines with stable knockdown of IRS1 (alpha IRS1KD) are unable to repress glucagon mRNA expression and exhibit reduction in phosphorylation of AKT. However, glucagon mRNA expression was suppressed in response to insulin stimulation in a stable IRS2 knock down alpha cell line (alpha IRS2KD). Alpha IRS1KD cells also display suppressed global protein translation including glucagon, impaired cytoplasmic Ca2+ response and mitochondrial function.  These data argue for IRS1 as a dominant regulator of pancreatic  alpha cell function.

overall_design: To identify candidate genes that are involved in the regulation of IRS1/2-mediated signaling in alpha cells, we performed gene expression microarray analysis of control, IRS1 knockdown (KD) or IRS2 KD alpha cells. Each group has three replicate samples.

first: Tomozumi

last: Takatani

first: Jun

last: Shirakawa

first: Kimitaka

last: Shibue

first: Rohit

middle: N

last: Kulkarni


title: RNA-seq profile of stimulated Tregs containing co-receptor signaling domain variant chimeric antigen receptors (CARs).

status: Public on Apr 03 2021

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

summary: Initial CAR therapies were designed and tested in conventional T cells, however several recent reports indicate that CAR Tregs may be effective in solid organ transplant or hematopoietic stem cell transplant. Since Tregs have different activation requirements, we sought to characterize the transcriptional profile of Tregs that were transduced with second-generation CARs containing various co-receptor signaling moieties to determine which bestows Tregs with the most desireable properties.

overall_design: Human Tregs/Tconv were transduced with second-generation chimeric antigen receptors (CARs) that contain various co-receptor signaling domains, then stimulated via CAR or T cell receptor.

first: Nicholas

middle: A

last: Dawson


title: Muscle and adipose transcriptome in a mouse model of cachexia induced by orthotopic pancreatic cancer, with and without tumor-derived interleukin-6 (IL-6)

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

summary: Pancreatic ductal adenocarcinoma (PDAC) causes involuntary wasting of adipose and muscle tissue, also known as cachexia. Cachexia is a major cause of cancer-related deaths, particularly among patients with PDAC. Here we profiled gene expression in adipose tissue and skeletal muscle in normal/sham control mice and in mice bearing orthotopic PDAC tumors.  PDAC tumors were initiated by intra-pancreatic injection of a cell line derived from the KPC (Kras-G12D;Trp-R172H;Pdx1::Cre) genetically engineered mouse model of pancreatic cancer, or by injection of the same cell line deleted for the IL6 gene using CRISPR/Cas9. KPC-IL6 knockout (ko) cells caused less adipose wasting and no muscle loss compared with KPC-wildtype (wt) cells.

overall_design: 8-week old C57BL6/J male mice were subjected to surgery without (sham) or with implantation of tumor cells by direct injection into the pancreas. All mice were kept until the KPC group demonstrated overt wasting, upon which time all mice were euthanized. mRNA was isolated from quadriceps muscles or from the epididymal fat pads for RNAseq. Muscle and fat samples came from separate sets of mice.

first: Joseph

middle: E

last: Rupert

first: Ashok

last: Narasimhan

first: Yunlong

last: Liu

first: Leonidas

middle: G

last: Koniaris


title: Superior production of heavy pamamycin derivatives using a bkdR null mutant of Streptomyces albus J1074/R2

status: Public on Apr 01 2021

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

summary:
Background: Pamamycins macrodiolides of polyketide origin which form a family of differently large homologues with molecular weights between 579 and 663. They offer promising biological activity against pathogenic fungi and gram-positive bacteria. Admittedly, production titers are still low and pamamycins are typically formed as crude mixture which mainly contains smaller derivatives. Therefore, strategies that enable a more efficient production of pamamycins with increased fractions of the rare large derivatives are highly desired. Here we took a systems biology approach, integrating transcription profiling by RNA sequencing and intracellular metabolite analysis to enhance pamamycin production in the heterologous host S. albus J1074/R2.
Results: Supplemented with L-valine, the recombinant pamamycin producer revealed a threefold increased pamamycin titer of about 3.5 mg L-1 and elevated fractions of larger derivatives: Pam 649 was strongly increased, and Pam 663 was newly formed. These beneficial effects were driven by increased availability of intracellular CoA esters, the building blocks for the polyketide, resulting from L-valine catabolism. Unfavorably, the presence of L-valine impaired growth of the strain, repressed genes of mannitol uptake and glycolysis, and suppressed pamamycin formation, despite the biosynthetic gene cluster was activated, restricting production to the post L-valine phase. A null mutant of the transcriptional regulator bkdR, controlling a branched-chain amino acid dehydrogenase complex, revealed decoupled pamamycin biosynthesis and accumulated the polyketide independent of the nutrient status. Supplemented with L-valine, the regulator mutant enabled the biosynthesis of pamamycin mixtures with up to 55% of the heavy derivatives Pam 635, Pam 649, and Pam 663, almost 20-fold more than the wild type.
Conclusions: Our findings open the door to provide rare heavy pamamycins at markedly increased efficiency and facilitate studies to assess their specific biological activities and explore this important polyketide further.

overall_design: Whole transcriptomes of a pamamycin production strain derived from two time points (growth and production phase), two treatments (+/- valine), and two strains (wildtype and Delta-bkdR) using 3 biological replicates each.

first: Lars

last: Gläser

first: Martin

last: Kuhl

first: Julian

last: Stegmüller

last: Rückert

first: Jörn

last: Kalinowski

first: Andriy

last: Luhetskyy

first: Christoph

last: Wittmann


title: Expression data from ovaries and adipose tissue in hyperandrogenized(DHT-treated) mice

status: Public on Apr 04 2021

city: Shenzhen

first: Li-Feng

last: Sun

address: University Town, Nanshan District

country: China

institute: Peking University Shenzhen Graduate School

summary:
Mice under chronic dihydrotestosterone (DHT) exposion represented reproductive and metabolic disorders, which were based on the dysfunction of ovaries and fat tissues.
We used microarrays to detail the global programme of gene expression and identified distinct difference in ovaries and gonadal fat pads between DHT-treated mice and control.

overall_design: 25-day-old C57BL/6J female mice were selected. Mice in the DHT group were implanted with silicone capsules containing 5 mg of DHT powder to mimic the hyperandrogenic state of PCOS patients. Control mice were implanted with empty capsules.The mice were euthanized ~60 days after implantation.Ovaries and gonadal fat pads were isolated from DHT-treated mice and control for RNA extraction and hybridization on Affymetrix microarrarys. We sought to obtain homogeneous populations of tissues from each group, DHT-treated mice and control, in order to increase the temporal resolution of expression profiles.n = 3 /treatment group

first: Ya-li

last: Yang

first: Mei-Yue

last: Wang

first: Hua-shan

last: Zhao

first: Tian-Xia

last: Xiao

first: Meng-Xia

last: Li

first: Bao-Bei

first: Chen

last: Huang

first: Pei-Gen

last: Ren

first: Jian

middle: V

last: Zhang


title: Transcriptomics analysis revealed reduction of Matrix Metallopeptidase 13 and promotion of chondrogenesis by Zeel T in primary human osteoarthritic chondrocytes

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

country: Belgium

institute: ULiege

summary:
Objectives: Zeel T (Ze14) is a multicomponent medicinal product. Initial preclinical data suggested a preventive effect on cartilage degradation. This study aimed to explore these effects further to better understand the mode of action of Ze14 on human osteoarthritic (OA) chondrocytes in vitro.
Methods: Primary chondrocytes were obtained from the knees of 10 OA patients and cultured in monolayers. The cultures were treated with 20 % or 10 % (v/v) Ze14 or placebo. For RNA-Seq, reads were generated with Illumina NextSeq5000 sequencer and aligned to the human reference genome (UCSC hg19). Differential expression analysis between Ze14 and placebo was performed in R using the DESeq2 package.
Results: In monolayer cultures, Ze14 20 % (v/v) significantly modified the expression of 13 genes in OA chondrocytes by at least 10 % with an adjusted p-value < 0.05 : EGR1, FOS, NR4A1, DUSP1, ZFP36, ZFP36L1, NFKBIZ and CCN1 were upregulated and ATF7IP, TXNIP, DEPP1, CLEC3A and MMP13 were downregulated after 24 h Ze14 treatment.
Conclusion: Ze14 significantly modified the expression of DUSP1, DEPP1, ZFP36/L1 and CLEC3A, which may reduce MMP13 expression and activation. Protein analysis confirmed that Ze14 significantly reduced the production of pro-MMP-13. As MMP-13 is involved in type II collagen degradation, Ze14 may limit cartilage degradation. Ze14 also promoted extracellular matrix formation arguably through CCN1 production, a growth factor well correlated with type II collagen and aggrecan production.

overall_design: RNA-Seq on primary human OA chondrocytes mRNA cultured in monolayer in the presence or not of 10-11M interleukin-1b and/or Zeel T (Ze14)

first: Kathrin

last: Hemmer

first: Natascha

last: Krömmelbein

first: Bernd

last: Seilheimer

first: Jean-Emile

last: Dubuc

first: Christophe

last: Antoine

first: Yves

last: Henrotin


title: Interaction of IL-26 and its novel receptor EphA3 regulates EGFR-TKI resistance in triple negative breast cancer cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: We investigated how IL-26 stimulation affected gene expression in E0771 cells by DNA microarray analysis.

overall_design: Mouse breast carcinoma cell line E0771 was treated with media as a control or IL-26 for 6 hr or 24 hr, and total RNA was isolated for a total of 4 samples.

first: T

last: Itoh

first: C

last: Morimoto

first: K

last: Ohnuma


title: Single cell hibernation cultures identify molecules dispensable for haematopoietic stem cell self-renewal

city: Cambridge

first: Daniel

last: Bode

email: db704@cam.ac.uk, 1danielbode@gmail.com

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary: Advances in the isolation and gene expression profiling of single haematopoietic stem cells (HSCs) have permitted in-depth resolution of their molecular program.  However, long-term HSCs (LT-HSCs) can only be isolated to near purity from adult mouse bone marrow, thereby precluding studies of their molecular program in different physiological states. Here, we describe a powerful 7-day culture system that removes single LT-HSCs from their native bone marrow microenvironment without compromising their functional potential. LT-HSCs are maintained as single cells and retain full HSC function compared to freshly isolated LT-HSCs with respect to divisional kinetics, colony forming cell potential (73.9%), and transplantation into primary (53%) and secondary (44%) recipients. Comparison of molecular profiles of single hibernating LT-HSCs to freshly isolated counterparts showed a high degree of similarity, but also identified key factors dispensable for LT-HSC function in transplantation assays including members of the AP1 complex (Jun, Fos, and Ncor2), Sult1a1 and Cish.

overall_design: We performed single-cell RNA-sequencing on LT-HSCs cultured in hibernating conditions for 7 days (n=106) and compared them to freshly isolated single LT-HSCs (n=165) and also to LT-HSCs stimulated with SCF for 16 hours (from both HSC+SCF (n=63) and hibHSC+SCF(n=127).

first: Caroline

last: Oedekoven

first: Miriam

last: Belmonte

first: Fiona

last: Hamey

first: Mairi

middle: S

last: Shepherd

first: James

last: Che

first: Craig

last: McDonald

first: Serena

last: Belluschi

first: Evangelia

last: Diamanti

first: Hugo

middle: P

last: Bastos

first: Katherine

last: Bridge

first: Berthold

last: Göttgens

first: Elisa

last: Laurenti

first: David

last: Kent


title: Environmental enrichment restores a young DNA methylation landscape in the aged mouse hippocampus [Experiment 1]

status: Public on Mar 31 2021

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that experiencing a stimulus-rich environment counteracted age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is known to control neuronal functions. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the rejuvenating effects of environmental enrichment at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.

overall_design: Mice of different ages were housed in standard housing conditions or in environmental enrichment. DNA methylation profiling was performed by Reduced Representation BIsulfite Sequencing on micro-dissected dentate gyrus tissue. Reduced representation bisulfite sequencing was performed on a total of 6 samples.

first: Sara

last: Zocher

first: Rupert

middle: W

last: Overall


title: Environmental enrichment restores a young DNA methylation landscape in the aged mouse hippocampus [Experiment 2]

overall_design: Mice of different ages were housed in standard housing conditions or in environmental enrichment. DNA methylation profiling was performed by Reduced Representation BIsulfite Sequencing on micro-dissected dentate gyrus tissue. Reduced representation bisulfite sequencing was performed on a total of 24 samples.


title: ATAC-Seq  of Wild Type pDC Transcriptomes  (CpG 0h, 2h)

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

summary:
Purpose: The goals of this study are to compare the pDC chromatin structure (ATAC-seq) at steady state and at 2h after CpG activation.
Methods: Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
Results: Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cut off of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Conclusions: Our study represents a detailed analysis of naive and activated pDC chromatin that analyzes the global murine TF reservoir as defined by Hu et al. in the AnimalTFdb (Hu et al. , 2019, Nucleic Acids Res 47, D33-D38). Our results show that pDC activation substantially altered the chromatin structure making it more or less accessible to specific TF families.

overall_design: Chromatin profiles of bone marrow-derived Flt3-L FACS purified pDCs from wild type mice that were left naïve or stimulated with TLR9 agonist CpG for 2h.

first: Shafaqat

last: Ali

first: Ritu

last: Mann-Nüttel


title: Murine deficiency of peroxisomal L-bifunctional protein (EHHADH) causes medium-chain 3-hydroxydicarboxylic aciduria and perturbs hepatic cholesterol homeostasis

status: Public on Apr 02 2021

first: Sander

middle: M

last: Houten

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Peroxisomes play an essential role in the β-oxidation of dicarboxylic acids (DCAs), which are metabolites formed upon ω-oxidation of fatty acids. The physiological functions of DCA metabolism remain largely unknown. In this study, we aimed to evaluate the biological role of DCA metabolism using mice deficient in the peroxisomal L-bifunctional protein (Ehhadh KO mice). We performed RNA-seq in WT and Ehhadh KO livers, treated with vehicle or L-aminocarnitine (L-AC), an inhibitor of mitochondrial fatty acid oxidation. We show that, in liver, Ehhadh KO mice have increased mRNA and protein expression of cholesterol biosynthesis enzymes with decreased (in females) or similar (in males) rate of cholesterol synthesis. We conclude that EHHADH plays an essential role in the metabolism of medium-chain DCAs and postulate that peroxisomal DCA β-oxidation is a regulator of hepatic cholesterol biosynthesis.

overall_design: 23 samples from mouse livers were analyzed distributed into 4 groups (WT+Veh; KO+Veh; WT+L-AC; KO+L-AC)

first: Pablo

last: Ranea-Robles

first: Carmen

last: Argmann


title: Environmental enrichment restores a young DNA methylation landscape in the aged mouse hippocampus [Experiment 3]

overall_design: Aged mice were housed in an enriched environment (ENR) or under standard housing conditions (STD) for three months. Young STD housed mice mice were used as controls. The dentate gyrus was micro-dissected and DNA methylation analyzed by RRBS.


title: Oxidized Lipids and CD36-Mediated Lipid Peroxidation in CD8 T Cells Suppress Anti-Tumor Immune Responses

city: La Jolla

first: Susan

last: Kaech

address: 10010 N Torrey Pines Rd

institute: Salk InstituteSalk Institute for Biological Studies

summary: T cell metabolic fitness plays a pivotal role in anti-tumor immunity and metabolic deregulation causes T cell dysfunction in cancer. We identify that CD36 limits anti-tumor CD8+ T cell effector functions through lipid peroxidation. In murine tumors, oxidized phospholipids (OxPLs) were highly abundant and CD8+ TILs increased uptake and accumulation of lipids and lipid peroxidation. Functionally ‘exhausted’ CD8+ TILs increased CD36 expression and CD36-deficient CD8+ TILs had more robust anti-tumor activity and cytokine production than wild-type cells. We further show that CD36 promotes uptake of oxidized low-density lipoproteins (OxLDL), induces lipid peroxidation in CD8+ TILs, and enhances p38 kinase phosphorylation. Moreover, we found that OxLDL inhibits CD8+ T cell functions in a CD36/p38-dependent manner. Furthermore, glutathione peroxidase 4 (GPX4) over-expression lowers lipid peroxidation and restores functionalities in CD8+ TILs. These results define a key role for an oxidized lipid-CD36-p38 axis in promoting intratumoral CD8+ T cell dysfunction.

overall_design: Single cell RNA sequencing was performed on Cd36+/+ WT or Cd36-/-  KO T cells (CD4+ T cells, CD8+ T cells ) FACS-sorted from B16 tumors (21 days post implantation).

first: Shihao

last: Xu

first: Ziyan


title: Skin and gut imprinted T helper cell subsets exhibit distinct functional phenotypes in CNS autoimmunity

city: Munich

first: Thomas

last: Korn

state: Bavaria

address: Ismaninger Str. 22

department: Neurology

institute: Technical University of Munich

summary: We developed an experimental framework to probe the idea that the site of priming in the systemic immune compartment is a determinant of T helper cell-induced immunopathology in remote organs. By site-specific in vivo labeling of antigen-specific T cells in inguinal (i) or gut draining mesenteric (m) lymph nodes, we show that i-T cells and m-T cells isolated from the inflamed central nervous system in a model for Multiple Sclerosis are distinct.

overall_design: We sorted i- and m-T cells (mD2REDCD4+CD44high) from lymph nodes and spleens of 2D2 x TH PhamT mice and performed RNAseq

first: Gildas

last: Lepennetier

last: Öllinger

first: Michael

last: Hiltensperger


title: Expression data of peritoneal macrophages from Wild-type mouse cultured in control or serine/glycine-depleted medium.

city: Nagoya

first: Kento

last: Kurita

state: Aichi

address: Furo-cho

department: Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine

institute: Nagoya University

summary:
Activation of signaling pathways downstream of Toll-like receptor 4 upregulate expression of genes related to serine metabolism. We cultured peritoneal macrophages in control or serine/glycine-depleted medium for 24 hr,  stimulated them with LPS (10 ng/ml) for 6 or 12 hr, and collected them to compare the gene expression.
Microarray analysis revealed that serine/glycine-depletion in peritoneal macrophages upregulates gene expression of enzymes for serine biosynthesis.

overall_design: We obtained primary peritoneal macrophages from 3% thioglycollate-treated mice 4 days after the injection, cultured them in control or serine/glycine-depleted medium for 24 hr, stimulated them with LPS (10 ng/ml) for 6 or 12 hr, and collected them for RNA extraction and hybridization on Affymetrix microarrays.

first: Ayaka

last: Ito

first: Takayoshi

last: Suganami


title: Dey_Huff_2021_Horizons_RNAseqData

city: Madison

first: Jack

last: Shireman

state: WI

address: 1500 Highland Ave

department: Neurological Surgery

institute: UW-Madison

summary: differential expression comparison between young adults, healthy age matched controls, and glioma, patients T-Cells and Tumor cells using RNA sequencing

overall_design: differential expression comparison between young adults (age 30), healthy age matched controls (average age 60), and glioma patients T-Cells and Tumor infiltrating T cells using RNA sequencing

first: Sheng

last: Liu

first: Jun

last: Wan

first: Mahua

last: Dey


title: Whole Transcriptome RNA-seq in Brain Tissue of Young and Old Peromyscus maniculatus and P. leucopus

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: Whole transcriptome RNA sequencing in brain tissue was generated to explore differences between young and old animals of two closely related species of deer mice (genus Peromyscus) that reportedly differ in their lifespans: P. leucopus that lives for up to 8 years and P. maniculatus that exhibits a lifespan of about 4 years.

sample_organism:
Peromyscus leucopus
Peromyscus maniculatus

overall_design: Brain mRNA profiles of young (n=6) and old (n=6) P. maniculatus and P. leucopus.

first: Soltanmohammadi

last: Elham

first: Zhang

last: Youwen

first: Ji

last: Hao

first: Kiaris

last: Hippokratis


title: Regulation of the DNA damage response and melanoma susceptibility by NCOA3

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

summary: NCOA3 has important roles in melanoma as a potential diagnostic and susceptibility marker, and as a target for therapy

overall_design: Anti NCOA3 shRNA vs control shRNA were stably transfected in C8161.9 cell lines to demonstrate differentially expressed genes in cDNA microarray run in duplicate.

first: David

last: De Semir

first: Mohammed

last: Kashani-Sabet


title: An iPSC-derived midbrain dopaminergic neuronal model of aromatic amino acid decarboxylase (AADC) deficiency gives insight into neurodevelopmental disease features

city: London

first: Manju

last: Kurian

address: Great Ormond Street Institute of Child Health, 30 Guilford Street

department: Developmental Neurosciences

institute: University College of London

summary: Aromatic L-amino acid decarboxylase (AADC) deficiency is a complex inherited neurological disorder of monoamine synthesis which results in dopamine and serotonin deficiency. Affected patients have severe cognitive and motor delay, recurrent oculogyric crises, a complex movement disorder and high risk of premature mortality. Standard pharmacological treatment provides limited clinical benefit. Promising gene therapy approaches are emerging, though may not be either suitable or easily accessible for all patients. In order to better characterize the underlying disease pathophysiology and guide precision therapies, we generated a patient-derived midbrain dopaminergic (mDA) neuronal model of AADC deficiency from induced pluripotent stem cells (iPSCs). The neuronal model recapitulates key disease features, including absent AADC enzyme activity and dysregulated dopamine metabolism. We observed developmental defects affecting synaptic maturation and neuronal electrical properties.

overall_design: Aged-matched healthy Control and 2 AADC deficiency patients iPSCs-derived midbrain dopaminergic neurons (3 biological replicates each).

first: Giada

last: Rossignoli


title: RNA-seq analysis of PR-expressing FTE cells (2D)

city: Minneapolis

first: Carol

last: Lange

state: MN

address: 2231 6th ST SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: FTE cells expressing the PRA or PRB isoforms or EV were treated with progestins and RNA-seq analyses performed

overall_design:
Cell lines were cultured in adherent conditions and treated with 10 nM R5020 for 6h prior to RNA isolation

contributor: Artificial Intelligene (AI, www.artificialintelligene.com)

first: Laura

last: Mauro


title: Ziziphus nummularia transcriptome analysis under drought

city: Bikaner

first: PN

last: Sivalingam

address: Beechwal

country: India

institute: ICAR - Central Institute for Arid Horticulture

summary: Ziziphus nummularia is well distributed in the Thar desert encompassing India and Pakistan. It survives in regions with an average annual rainfall lesser than 100 mm. Transcriptome profiling was done in Z. nummularia genotype CIAHZN-J under control and drought-stress at -0.3MPa.  Among the unique transcripts identified, 283 were found to be downregulated and 554 upregulated in comparison to control. The important down-regulated transcripts identified were: LRR receptor like serine/threonine protein kinases, oligo peptide transporter OPT family, myrcene synthase, LRR protein kinase family isoform1, ATP binding cassette transporter, phytochrome kinase, Pectin estrase inhibitor like-35, auxin efflux  facilitator isoform 1, multidrug resistance protein, pectin methyl esterase 3 and ABC transporter B family. Similarly some of the upregulated transcripts are: Raffinose synthase family protein, wall associated receptor kinase like, acyl transferase like protein, cadmium/zinc transporting ATPase 3 like, sucrose synthase 6-like, cytochrome P-450 like, phosphatase 2C family protein and TT12-2 MATE transporter. This study will be very useful to identify novel genes that may be involved in drought tolerance of Z. nummularia.

overall_design: Transcriptome analysis under normal and drought conditions.

first: Palaiyur

first: Dhurendra

last: Singh

first: Karun

last: Gurjar

first: Viswanathan

last: Satheesh


title: Activation of HERV-K(HML-2) limits cortical neuronal differentiation by modulating Neurotrophic Tyrosine Receptor Kinase 3 expression

status: Public on Mar 30 2021

city: Freising

first: Hengyuan

last: Liu

address: Maximus-von-Imhof Forum 3

department: TUM School of Life Sciences

summary: The biological function and disease association of human endogenous retroviral (HERV) elements remains largely elusive. We addressed the physiological role of HERV-K(HML-2) in neuronal differentiation by manipulating HERV-K(HML-2) expression levels. We used CRISPR engineering to activate or repress HERV-K(HML-2) and demonstrate that elevated HERV-K(HML-2) transcription is detrimental for development, functionality and growth of cortical neurons. Effects are cell-type specific, as dopaminergic neurons were unaffected. We further show that layer formation is altered during forebrain organoid formation following activation of HERV-K(HML-2) transcription. HERV-K(HML-2) transcriptional activation concurrently elevated Neurotrophic Tyrosine Receptor Kinase 3 (NTRK3) expression along with other neurodegeneration-related genes. Direct transcriptional activation of NTRK3 resembled the HERV-K(HML-2) activation phenotype. Intriguingly, reduction of NTRK3 levels in HERV-K(HML-2)-activated cortical neurons restored differentiated cortical neurons. Hence, our findings unravel a unique cell type-specific mechanism of HERV-K(HML-2) during cortical neuronal differentiation.

overall_design: We induced cortical neuronal differentiation in H9-CRISPRa-HERV-K(HML-2) as well as H9-CRISPRa-control cells and performed total RNA sequencing (RNAseq) at day 0, day 10, day 27, day 41 and day 60 of cortical neuronal differentiation.

first: Vidya

last: Nair

first: Gabriele

last: Ciceri

first: Johannes

last: Jungverdorben

first: Goar

last: Frishman

first: Jason

last: Tchieu

first: Gustav

middle: Y

last: Cederquist

first: Ina

last: Rothenaigner

first: Kenji

last: Schorpp

first: Lena

last: Klepper

first: Ryan

last: Walsh

first: Tae

last: Kim

first: Daniela

last: Cornacchia

first: Andreas

last: Ruepp

first: Jens

last: Mayer

first: Kamyar

last: Hadian

first: Dmitrij

first: Lorenz

last: Studer

first: Michelle

last: Vincendeau


title: The chaperonin GroESL supports the functions of the Z-ring regulators FtsA and FzlA

city: Stockholm

first: Kristina

last: Jonas

address: Svante Arrheniusväg 20 C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary: The highly conserved chaperonin GroESL performs a crucial role in protein folding, however the essential cellular pathways that rely on this chaperone are underexplored. Loss of GroESL leads to severe septation defects in diverse bacteria, suggesting the folding function of GroESL may be integrated with the bacterial cell cycle at the point of cell division. Here, we describe new connections between GroESL and the bacterial cell cycle using the model organism Caulobacter crescentus. Using a proteomics approach, we identify candidate GroESL client proteins that become insoluble or are degraded specifically when GroESL folding is insufficient, revealing several essential proteins that participate in cell division and peptidoglycan biosynthesis. We demonstrate that other cell cycle events such as DNA replication and chromosome segregation are able to continue when GroESL folding is insufficient. We further find that deficiency of two FtsZ-interacting proteins, the bacterial actin homologue FtsA and the constriction regulator FzlA, mediate the GroESL-dependent block in cell division. Our data show that sufficient GroESL is required to maintain normal dynamics of the FtsZ scaffold and divisome functionality in C. crescentus. In addition to supporting divisome function, we show that GroESL is required to maintain the flow of peptidoglycan precursors into the growing cell wall. Linking a chaperone to cell division may be a conserved way to coordinate environmental and internal cues that signal when it is safe to divide.

overall_design: RNA-sequencing was performed to determine gene expression changes induced by depletion of the chaperonin GroES-GroEL (GroESL). RNA abundance in cultures of a GroESL depletion strain (SG300) grown for four hours under depleting conditions was compared to the wild type control.

first: Kristen

last: Schroeder


title: RNA sequencing comparing interferon gamma-treated Wild-Type and STAT1-/- mouse breast cancer cell lines

city: Montréal

first: Claudia

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

summary: This study has identified a unique susceptibility that capitalizes on a cancer cell’s reliance on key metabolic pathways, not only to meet increased energetic demands, but also to maintain the critical balance between reactive oxygen species (ROS) and cellular antioxidant levels, necessary for cancer cell survival and growth. Specifically, we explored the use of phenformin, a metabolic drug that is being repurposed as a cancer treatment in clinical trials. We find that several breast cancer cell lines, across molecular subtypes, were sensitized to phenformin when combined with the pro-inflammatory cytokine, interferon-gamma (IFNγ), revealing a previously unidentified anti-tumor effect. Similarly, we find that an elevated inflammatory response (stimulated by PolyIC) synergizes with phenformin to attenuate tumor growth, in three different mouse models of breast cancer. Through inhibiting complex I of the electron transport chain, phenformin directly inhibits tumor growth by suppressing mitochondrial-dependent energy generation, and consequently increases levels of superoxide. Functionally, the mitochondrial ROS scavenger, MitoTempo, reverses the ability of, IFNγ and PolyIC to synergize with phenformin. Through RNA sequencing, by comparing Wild-Type and STAT1 KO cells,  we identify Nqo1 as a target gene that decreases upon IFNγ treatment in a STAT1 dependent manner. Nqo1 is a 2-electron reductase that is upregulated in many tumors and has important roles in ROS scavenging and cellular stress responses. In support, targeting Nqo1 either by shRNA-mediated gene silencing or through its bioactivatable inhibitor, β-lapachone, sensitized established human and mouse cell lines, cells from breast cancer patient-derived xenografts (PDX), and in vivo xenografted tumor growth to phenformin.

overall_design: Examination of interferon gamma regulated genes in Wild-Type and STAT1-/-  mouse breast cancer cell lines in response to interferon gamma treatment (1ng/ml) for 24 hours. Using two independent parental cell lines, MT4788 and MT864, and their WT and STAT-/- counterparts, with 3 replicates of each. For a total of 12 samples.

first: Steven

last: Hébert

first: Josie

last: Ursini-Siegel

first: Young

last: Im

first: Stephanie

last: Totten


title: low input RNA-sequencing of in vivo activated murine 2D2-WT and 2D2-HDAC1-cKO CD4+ T cells

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary: An analysis of 2D2-WT and 2D2-HDAC1-cKO mice indicates an important function of HDAC1 in regulating autoimmune diseases, in particular experimental autoimmune encephalomyelitis). The aim of this NGS experiment was to determine the transcirptome profile of in vivo activated 2D2-WT and 2D2-HDAC1-cKO CD4+ T cells in the absence of HDAC1 following MOG/CFA footpad immunization.

overall_design: mRNA expression profiles of in vivo activated 2D2-WT and 2D2-HDAC1-cKO CD4+ T cells were generated by low-input RNA sequencing. Naïve 2D2-WT or 2D2-HDAC1cKO CD4+ T cells (CD45.2+) were transferred (i.v.) into CD45.1+ recipient mice. 18 hours after transfer mice were footpad immunized with a 1:1 emulsion of 1 mg/ml CFA/MOG35-55 peptide. Draining (popliteal) lymph nodes were isolated 4 days later and single cell suspensions prepared. Two mice were pooled for one biological replicate and three biological replicates were generated for each genotype. 500 2D2+ CD4+ T cells CD45.2+ cells were sorted and subjected to low-input RNA sequencing.

first: Patricia

last: Hamminger


title: The 7SK/P-TEFb snRNP controls ultraviolet radiation-induced transcriptional reprogramming

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: Releasing promoter-proximally-paused RNA polymerase II (RNAPII) by the positive transcription elongation factor b (P-TEFb) is a central regulatory step of eukaryotic mRNA synthesis. The nuclear activity of P-TEFb is controlled mainly by the 7SK small nuclear RNP (snRNP) which sequesters active P-TEFb into inactive 7SK/P-TEFb snRNP. Here we demonstrate that under normal culture conditions, the lack of 7SK snRNP has only a minor impact on global RNAPII transcription and promoter-proximal pausing without detectable consequences on cell growth and proliferation. However, upon ultraviolet (UV) light-induced DNA damage, cells lacking 7SK have a defective transcriptional response and highly reduced viability. Both UV-induced release of ‘lesion-scanning’ polymerases and activation of key early responsive genes are compromised in the absence of 7SK. We show that proper induction of 7SK-dependent UV-responsive genes, namely efficient release of paused RNAPII and recruitment of key elongation factors, requires P-TEFb activity directly mobilized from the nucleoplasmic 7SK/P-TEFb snRNP.

overall_design: ChIRP-seq of 7SK in HAP1 and HAP1-7SK-KO cells -/+ 1h UV, mNET-seq of total pol II in HAP1 and HAP1-7SK-KO cells -/+ 1h, 2h, or 4h UV.

first: Cécilia

last: Studniarek

first: Pascal

last: Martin

first: Shona

last: Murphy

first: Tamás

last: Kiss

first: Sylvain

last: Egloff


title: RNA sequencing of SNRPA1 over-expression in MDA-MB-231 cells

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: We used RNA sequencing to compare SNRPA1 over-expression cells to mock-transfected (mCherry) controls.

overall_design: We over-expressed the SNRPA1 ORF in MDA-231 cells using the lentiviral construct pLX304. We then used RNA sequencing (smarter-seq pico v2) to compare SNRPA1 over-expression cells to mCherry-over expressing controls.

first: H

first: L

last: Fish

first: Bruce

last: Culbertson


title: Global promoter usage in the differentfractions of the cell during early zebrafish development

city: Birmingham

first: Sanjana

last: Pillay

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE-seq data revealed differences in promoter width within the same stage (Post-MZT) in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression.

overall_design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell, 256 Cell, 1000 Cell, Dome,  Shield and Prim-5 stages of development.

first: Aditi

last: Kanhere


title: Genome wide localization of RNAs during early zebrafish development

summary: We employed transcriptomics methods to examine RNAs from the nuclear and cytosolic fractions from zebrafish embryos at different stages of development. The RNA-seq revealed spatial and temporal regulation of lncRNA expression during zebrafish development.

overall_design: Localization of RNAs in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell, 256 Cell, 1000 Cell, Dome and Shield stages of development.


title: Trp53 mutation in Krt5-expressing basal cells facilitates the development of basal squamous-like invasive bladder cancer in the chemical carcinogenesis of mouse bladder

city: Kyoto

first: Takashi

last: Kobayashi

address: 54 Shogoinkawahara-cho, Sakyo-ku

department: Urology

institute: Kyoto University Graduate School of Medicine

summary: We investigated the genetic characteristics of the mouse tumors. First, we investigated whether mouse BBN-induced bladder cancers displayed distinct gene expression profiles according to the cell of origin or pre-induced Trp53 mutation. Gene expression profiles based on cDNA microarray data were analyzed using non-hierarchical clustering, which revealed that none of the mouse bladder tumors were differentially clustered based on the genotypes.

overall_design: Mice were given BBN for 24 weeks and urinary bladder was excised for RNA extraction.

first: Norihiko

last: Masuda


title: Pancreatic cancer prognosis is predicted by chromatin accessibility (Quantseq)

city: New York

first: Sagar

last: Chhangawala

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

summary: About 50% of resected pancreatic ductal adenocarcinoma (PDAC) recur within just one year following surgery. Prognostic molecular markers predicting rapid recurrence are currently unavailable. We hypothesized that epigenetic differences at the level of chromatin accessibility, potentially linked to distinct differentiation states, might distinguish rapidly recurrent from non-recurrent tumors.  Therefore, we interrogated genome-wide chromatin accessibility using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) on EpCAM+ PDAC malignant cells sorted from a cohort of 54 treatment-naïve resected tumors, in hopes of defining a tumor-intrinsic chromatin signature associated with recurrence. We discovered a signature of ~1000 loci that were differentially accessible between recurrent (disease free survival (DFS) < 1 year) and non-recurrent patients (DFS > 1 year).  Through transcription factor (TF) binding motif analysis using supervised learning, we identified candidate TFs whose accessible motifs were differentially associated with recurrence. Nuclear localization of two such TFs as selected by top hits, ZKSCAN1 and HNF1b, were assessed by both immunohistochemistry and immunofluorescence on the tissue microarrays (TMA) of 40 out of 54 patients.  Nuclear staining of HNF1b was strong in the non-recurrent and weak or absent in the recurrent patients but ZKSCAN1 was not significantly associated with recurrence. In an independent TMA of PDAC cohort (n=97) preselected for 52 long (OS 6 years)- and 45 short (OS 6 months)- term survivors, the number of nuclear positive cells for HNF1b was 52-fold higher in the long-term compared to the short-term survivors and that for ZKSCAN1 was 5.3-fold higher in the short-term compared to the long-term survivors. Altogether, these results provide novel prognostic molecular markers of early recurrence in PDAC and also suggest that the global epigenetic landscape is a prognostic feature in this disease.

overall_design:
54 PDAC primary tumor samples sequenced in duplicates
----------------------------------------------
*Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns

first: Steven

last: Leach

first: Christina

last: Leslie

first: Surajit

last: Dhara


title: Gene expression data of locally advanced rectal cancer patients by KRAS status

status: Public on Mar 29 2021

first: Julio

last: Garcia-Aguilar

department: Colorectal Surgery

institute: Memorial Sloan Kettering Cancer Center

summary:
Stromal and extracellular matrix related genes are downregulated in KRAS mutant rectal adenocarcinoma
We used Affymetrix U133 platform to profile the differences in the transcriptome of KRAS-wild-type and KRAS-mutant rectal cancer specimens

overall_design: RNA was extracted from 76 microsatellite stable pre-treatment biopsy samples from locally advanced rectal cancer patients accrued through the TIMING trial (ClinicalTrials.gov, number NCT00335816) and differential gene expression analysis was performed based on KRAS mutation status

first: Francisco

last: Sanchez-Vega


title: Pancreatic cancer prognosis is predicted by chromatin accessibility (ATAC-Seq)


title: Investigation of the transcriptional profile of stimulated HUMAN CRISPR/Cas9 MOCK and A2ARKO α-lewisY CAR T cells in the presence/absence of NECA

city: Melbourne

first: Paul

last: Beavis

state: Victoria

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Investigation of the transcriptional profile of sorted and stimulated CD8 and CD4 murine CRISPR/Cas9 MOCK and A2ARKO α-her2 CAR T cells in the presence/absence of NECA

overall_design: Following CRISPR/Cas9 mediated editing of T cells with either an A2AR sgRNA or a non-targeting control (MOCK), cells were transduced to express the anti-Her2 CAR. After 7 days culture in IL-2 (100 U/ml) and IL-7 (200 pg/ml), MOCK or A2AKO CAR T cells were stimulated with plate bound anti-myc Tag (anti-CAR) antibody in the presence or absence of NECA (1 µM) for 5 hours. CAR T cells were then sorted for CD8 and CD4 subsets by flow cytometry before being analyzed with 3' RNA-seq.

first: Lauren

last: Giuffrida

first: Kevin

last: Sek


title: RNA-seq of hydroxyurea treated Bacillus subtilis cells

city: Ann Arbor

first: Lyle

middle: A.

last: Simmons

state: MI

address: 1105 N. University Ave.

department: Molecular, Cellular, & Developmental Biology

institute: University of Michigan

summary: Hydroxyurea (HU) is thought to primarily target ribonucleotide reductase  (RNR), therefore inhibiting the conversion of rNTPs into dNTPs and slowing DNA replication. To understand how Bacillus subtilis responds to HU stress,  we performed RNA-seq and Tn-seq.

overall_design: We obtained transcriptomics following 1 and 2 hours of exposure to hydroxyurea compared to vehicle control from Bacillus subtilis cells.

first: Katherine

middle: J

last: Wozniak


title: FOXD1 Promotes Dedifferentiation and  Vemurafenib-resistance in Melanoma by Regulating the Expression of CTGF

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

institute: German Cancer Research Center

summary: Metastatic melanoma is the most aggressive skin cancer and associated with a poor prognosis. Targeted therapy is one of the most important treatments for patients with BRAFV600E-mutated advanced melanoma. However, the development of resistance to this treatment compromises its therapeutic success. Increasing evidence has indicated that NC-associated genes play important roles in tumor progress and drug resistance. Our previous study showed that FOXD1 is a neural crest (NC)-associated gene that has high expression levels both in NC cells and melanoma and that it could regulate melanoma migration and invasion. Here, we found that the FOXD1-CTGF axis  is important for melanoma resistance. The connective tissue growth factor (CTGF) was identified as a direct downstream factor of FOXD1 using microarray assay. In detail, when we compared the microarray data from FOXD1 OE and control groups, we found that the expression level of CTGF was also higher in FOXD1 OE cells (FC=1.97).

overall_design: total RNA isolated from FOXD1 silenced cell lines and its control cell lines, FOXD1 overepressed cell lines and its control cell lines.

first: Qian

last: Sun

first: Huizi

last: Wu


title: Whole genome sequencing of vehicle control and hydroxyurea treated Bacillus subtilis cells

summary: We obtained whole genome sequencing data as a measure of chromosome replication to see if HU inhibits replication compared to vehicle control.

overall_design: HU treatment


title: Gene expression analysis of WT, IFNAR KO, or STING KO bone marrow derived macrophages treated with IFNbeta and/or infected with live or heat killed Mycobacterium tuberculosis

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: The aim of this study was to identify the signaling pathways differentially engaged upon infection with either live or heat killed Mycobacterium tuberculosis in murine bone marrow derived macrophages. Based on preliminary data that type I IFN signaling dominates the transcriptional differences, we investigated what roles the type I IFN receptor IFNAR and the signaling molecule STING play during infection with either live or heat killed Mycobacterium tuberculosis in bone marrow derived macrophages. In WT and STING KO macrophages, IFNbeta treatment was added either by itself or in addition to both of the infection conditions to test whether the lack of IFNbeta induction in these cells accounted for any differences in transcriptional respones.added IFNbeta treatment either by itself or in addition to both of the infection conditions.

overall_design: Bone marrow derived macrophages from C57BL6/J (WT), B6.129S2-Ifnar1tm1Agt/Mmjax (IFNAR KO), or B6(Cg)-Sting1tm1.2Camb/J (STING KO) Mus musculus were differentiated for 6 days in MCSF and then re-plated before infection. Some conditions were treated with IFNbeta for 4 hours before infection and the rest were untreated. Within each treatment group, the cells were either mock infected or infected with live or heat killed Mycobacterium tuberculosis strain H37Rv (MOI 10) for either 4 or 24 hours. All conditions were done in biological duplicate (i.e. BMDM from different mice) for a total of 72 samples.

first: Gregory

last: Olson

first: Alan

last: Aderem


title: Regulation of B lymphocyte development by histone H2A deubiquitinase BAP1

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

institute: McGill University

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

overall_design: Refer to individual Series


title: Tn-seq of hydroxyurea treated Bacillus subtilis cells

summary:
Hydroxyurea (HU) is thought to primarily target ribonucleotide reductase  (RNR), therefore inhibiting the conversion of rNTPs into dNTPs and slowing DNA replication. To understand how Bacillus subtilis responds to HU stress,  we performed RNA-seq and Tn-seq.
We obtained genes with fitness defects following hydroxyurea treatment over 3 growth periods.

overall_design: A 120,000 insertion transposon library in PY79 was challened with vehicle control (water) or hydroxyurea for 3 growth periods to find genes important in HU-stress recovery


title: CRISPR/Cas9 mediated deletion of the adenosine A2AR enhances CAR T cell efficacy [NECA_RNA-seq]

summary: Investigation of the transcriptional profile of stimulated murine α-HER2 CAR T cells in the presence/absence of NECA and/or SCH58261

overall_design: Anti-Her2 CAR T cells were generated from WT mice and after 7 days culture in IL-2 (100 U/ml) and IL-7 (200 pg/ml), cells were stimulated with plate bound anti-myc Tag (anti-CAR) antibody in the presence or absence of NECA (1 µM) or SCH58261 (1 µM) for 8 hours. Cells were analyzed with 3' RNA-seq.


title: RNA-seq,Tn-seq, and whole genome sequencing of hydroxyurea treated Bacillus subtilis cells


title: Regulation of B lymphocyte development by histone H2A deubiquitinase BAP1 (BAP1_ChIP-Seq)

summary: BAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes, via deubiquitination of histone H2AK119ub and other substrates. BAP1 is an important tumour suppressor in human, expressed and functional across many cell-types and tissues, including those of the immune system. B lymphocytes are the mediators of humoral immune response, however the role of BAP1 in B cell development and physiology remains poorly understood. Here we characterize a mouse line with a selective deletion of BAP1 within the B cell lineage (Bap1fl/fl mb1-Cre) and establish a cell intrinsic role of BAP1 in the regulation of B cell development. We demonstrate a depletion of large pre-B cells, transitional B cells, and mature B cells in Bap1fl/fl mb1-Cre mice. We characterize broad transcriptional changes in BAP1-deficient pre-B cells, map BAP1 binding across the genome, and analyze the effects of BAP1-loss on histone H2AK119ub levels and distribution. Overall, our work establishes a cell intrinsic role of BAP1 in B lymphocyte development, and suggests its contribution to the regulation of the transcriptional programs of cell cycle progression, via the deubiquitination of histone H2AK119ub.

overall_design: To gain insight into the genomic regions directly regulated by BAP1 in B cells, we mapped BAP1 DNA binding sites by ChIP-Seq. The experiments were carried out in murine B cell precursor cell line Ba/F3 with and without triple-FLAG-tagged BAP1 expression.

first: HanChen

last: Wang

first: Yue

last: Liang

first: David

last: Langlais


title: Extended representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: DNA methylation of CpG dinucleotides impacts transcriptional activity and genome stability, and is altered in human disease. Whole genome and reduced-representation DNA methylation profiling methods have clarified biological roles of DNA methylation, but do not efficiently survey the vast numbers of noncoding regulatory elements in mammalian genomes.

overall_design: Here we present a novel extended representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design draws a balance between expanding coverage of regulatory elements and enriching for informative CpG dinucleotides. Barcoded DNA fragments are pooled prior to bisulfite conversion, allowing multiplex processing, improving consistency, and reducing cost and labor. Linear amplification of single stranded bisulfite-treated DNA enables library generation from fragmented and low input DNA samples. We further adapt the method for single-cell analysis, and apply it to evaluate methylation differences between cell types and individual cells in a population.

first: Sarah

last: Shareef

first: Bradley

last: Bernstein


title: CRISPR/Cas9 mediated deletion of the adenosine A2AR enhances CAR T cell efficacy

first: Paul

last: Beavis


city: Austin

first: Enamul

last: Huq

state: TX

address: Department of MBS, NHB 2.606, Stop A5000, 100 East 24th St.

institute: The University of Texas at Austin

summary: The mRNA expression profiles of the hypocotyl and root in WT and hy5 were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes were analyzed and compared within 22degC and 28degC and in different tissue type (hypocotyl vs root).

overall_design: Total twentiefour 24h 22degC and 28degC treated Arabidopsis samples were used. These include three replicates of following genotypes; Col-0 and hy5, with two tissue type; hypocotyl and root. Therefore, three replicates of following genotypes, tissue and conditions; Col-0 (hypocotyl-22degC), Col-0 (root-22degC), hy5 (hypocotyl-22degC), hy5 (root-22degC), Col-0 (hypocotyl-28degC), Col-0 (root-28degC), hy5 (hypocotyl-28degC), hy5 (root-28degC).

first: Sanghwa

last: Lee


title: CRISPR/Cas9 mediated deletion of the adenosine A2AR enhances CAR T cell efficacy [murine_CRISPR_A2AKO_RNA-seq]

summary: Investigation of the transcriptional profile of stimulated murine CRISPR/Cas9 MOCK and A2ARKO α-HER2 CAR T cells in the presence/absence of NECA

overall_design: Following CRISPR/Cas9 mediated editing of T cells with either an A2AR sgRNA or a non-targeting control (MOCK), cells were transduced to express the anti-Her2 CAR. After 7 days culture in IL-2 (100 U/ml) and IL-7 (200 pg/ml), MOCK or A2AKO CAR T cells were stimulated with plate bound anti-myc Tag (anti-CAR) antibody in the presence or absence of NECA (1 µM) for 8 hours. Cells were analyzed with 3' RNA-seq.

first: Lauren

last: Giuffrida

first: Kevin

last: Sek


title: Regulation of B lymphocyte development by histone H2A deubiquitinase BAP1 (Bap1KO_RNA-Seq)

overall_design: We performed RNA-Seq transcriptional profiling of FACS-sorted pre-B and immature B cells. Briefly, bone marrow cells were harvested from Bap1 fl/fl mb1-Cre, Bap1 fl/+ mb1-Cre, and Bap1fl/+ mice. The cells were sorted using FACS into pre-B and immature B cells, gating on B220+CD3-CD11b-NK1.1-CD11c-TER119-Gr1-, and IgM-IgD-CD19+CD43- for pre-B cells, and CD19+IgM+IgD- for immature B cells. RNA was isolated from the FACS-sorted cells using the MagMAX total RNA kit (Ambion, Life Technologies), and quality assessed using Bioanalyzer RNA Pico chips (Agilent). rRNA depletion and library preparation were performed using the SMARTer Stranded RNA-Seq kit (Takara Clontech). The libraries were sequenced on an Illumina HiSeq 4000 sequencer in paired-end 50bp configuration. Cells from multiple mice were pooled to achieve yields of >1.7ng of RNA per sample, and 3-4 independent samples were analyzed per genotype for each cell-type.

first: Yun

middle: H

last: Lin


title: Radiation-induced bystander effect impaired human hematopoietic stem cells by oxidative DNA damage

city: Tianjin

first: xiaowei

last: xie

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

summary: With the immunodeficient mouse model coupled with TBI and coculture system, we found that the radiation-induced bystander effect also occurred to human hematopoietic cells. The long-term hematopoietic reconstitution of bystander human HSCs was significantly decreased, and the colony-forming ability of bystander human hematopoietic progenitor cells was reduced. Further study found that the bystander human hematopoietic cells initiated enhanced DNA damage responses (DDRs), cell cycle arrest and p53-dependent apoptosis, mainly due to oxidative stress. Moreover, some antioxidants could mitigate this bystander effect with different efficacies both in vitro and in vivo.

overall_design: Human CB-CD34+ cells were cocultured with 10 Gy IR or NR human BM cells using a transwell system. After 17 hours of coculture, the CD34+ cells in the insert were collected for RNA-seq.

first: Linping

last: Hu

first: Xiuxiu

last: Yin

first: Tao

last: Cheng


title: Tumor progression in cholangiocarcinoma

city: Brussels

first: Frederic

last: Lemaigre

address: Avenue Hippocrate, 75

department: de Duve Institute

institute: UCLouvain

summary: Purpose:  The aim of this study is to investigate mechanisms driving tumor-promoting mechanisms in cholangiocarcinoma while focusing on transitions from normal cholangiocytes to precancer lesions and from precancer lesion to invasive carcinoma. An original mouse model of intrahepatic cholangiocarcinoma was developed, based on induction of a KrasG12D mutation in cholangiocytes combined with chronic inflammation.  RNA-Seq analyses compare the transcriptome of ductular proliferations, intraductal papillary neoplasm of the bile duct and intrahepatic cholangiocarcinoma. A gene cascade involving EGF, KrasG12D, Sox17 and Tns4 was identified to promote tumor progression.

overall_design: Ductular proliferations (Duct Prol), intraductal papillary neoplasm of the bile duct (IPNB) and intrahepatic cholangiocarcinoma (iCCA) were laser-capture microdissected from livers of mice expressing KrasG12D and affected with diet-induced cholangitis (n=3 for all lesions in 3 independent mice). These samples were subjected to RNAseq analysis and compared with FACS-purified control cholangiocytes (CTL).

first: Frédéric

first: Mickael

last: Di-Luoffo

first: Axelle

last: Loriot


title: CRISPR/Cas9 mediated deletion of the adenosine A2AR enhances CAR T cell efficacy [human_CRISPR_A2AKO_RNA-seq]

summary: Investigation of the transcriptional profile of stimulated HUMAN CRISPR/Cas9 MOCK and A2ARKO α-lewisY CAR T cells in the presence/absence of NECA

overall_design: Human anti-Lewis Y CAR T cells were generated from healthy donor peripheral blood mononuclear cells (PBMC) and then modified with CRISPR/Cas9 and a sgRNA targeting either human A2AR or a non-targeting control. CAR T cells were then cultured for another 6 days. MOCK or A2AKO CAR T cells were stimulated with plate bound anti-Lewis-Y idiotypic (anti-CAR) antibody in the presence or absence of NECA (10 µM) for 8 hours. Cells were analyzed with 3' RNA-seq.


title: Exposure with leukemia cell-derived exosomes to mouse HSPCs

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

institute: Kanazawa University

summary: Exosomes are extracellular vesicles that play crucial roles in intercullular communication. There is accumulating evidence that cancer cell-derived exosomes transfer malignant phenotypic trait to normal cells. Thus, we examined about the function of leukemia cell-derived exosomes on the normal hematopoietic stem/progenitor cells in this study.

overall_design: Mouse BM HSPCs were cocultured with exosomes isolated from normal or CML mouse spleen. Gene expression was determined at 24 hours after each treatment. There is single sample for each condition.

first: Naofumi

last: Mukaida


title: Pseudomonas syringae Virulence Regulatory Network construction

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas syringae, a Gram-negative plant pathogen, infects more than 50 crops with its type III secretion system (T3SS) and causes severe economic losses around the world. Although the mechanisms of virulence-associated regulators of P. syringae T3SS have been studied for decades, the crosstalk and network underlying these regulators are still elusive. Previously, we have individually studied a group of T3SS regulators, including AefR, HrpS, and RhpRS. In the present study, we found 4 new T3SS regulator genes (envZ, ompR, tsiS and phoQ) via transposon-mediated mutagenesis. Two-component systems EnvZ and TsiS natively regulate T3SS. In order to uncover the crosstalk between 16 virulence-associated regulators, (including AefR, AlgU, CvsR, GacA, HrpL, HrpR, HrpS, MgrA, OmpR, PhoP, PilR, PsrA, RhpR, RpoN, TsiR and Vfr) in P. syringae, we mapped an intricate network named PSVnet (Pseudomonas syringae Virulence Regulatory Network) by combining differentially expression genes in RNA-seq and binding loci in ChIP-seq of all regulators.

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

overall_design: ChIP-seq and RNA-seq for PSVnet

last: Deng


title: Control of limb initiation and antero-posterior patterning by cooperation between Meis and Tbx transcription factors [RNA-seq]

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Meis1 and Meis2 are highly similar homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Overexpression experiments have suggested an essential role for Meis factors in limb proximo-distal patterning; however, loss-of-function experiments supporting this notion have not been reported. Meis1 and Meis2 are coexpressed during limb development, first in the lateral plate mesoderm, before limb induction, and then they become restricted to a proximal domain of the growing limb bud. Here, we report that complete double conditional Meis1/2 inactivation in the lateral plate mesoderm leads to limb agenesis. Meis factors cooperate with Tbx factors in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles develop a complete PD set of limb skeletal elements, but show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior skeletal element specification reveals an early role of Meis factors in establishing the limb AP prepattern required for Shh activation at later stages. Our results uncover novel roles for Meis transcription factors in early limb development and identify their involvement in new molecular interaction networks that regulate organogenesis.

overall_design: Transcriptomic analysis comparing Meis1Ko;Meis2KO mutant limbs and WT limbs. RNA was isolated from the two hindlimbs E10 (30-31 somites approximately) of individual embryos. Six mutant and five WT embryos were used for analysis.

first: Delgado

last: Irene

first: Torres

last: Miguel


title: RNAseq and ATACseq of oyster hepatopancreas

status: Public on Mar 28 2021

city: Qingdao

first: Fei

last: Xu

address: 7 Nanhai Road

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: Hox and ParaHox genes encode transcription factors with conserved similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. We thus conducted experiments to show that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is also a direct target of Pdx in the Pacific oyster. We report that oyster has a diversity of insulin-related genes including one co-expressed with Pdx in the endodermal layer of oyster digestive tissue. Transcriptome analysis reveals functional similarity of this tissue to vertebrate pancreas. Using ATAC-seq we identify a Pdx homeodomain binding site upstream of the endodermally-expressed oyster insulin-related gene and using cell culture demonstrate that oyster Pdx acts as a transcriptional activator through this site. These data argue that a classic homeodomain-target gene interaction dates back to the base of Bilateria.

overall_design: RNAseq was conducted to identify hepatopancreas enriched genes. One biological replicate was conducted, while further confirmation was done with real-time qPCR on key genes. ATACseq was conducted to identify regulationary sites. Two biological replicates were conducted, while further cofirmation was done with dual luciferase assay on key genes.

first: Ferdinand

last: Marlétaz

first: Daria

last: Gavriouchkina

first: Tatjana

last: Sauka-Spengler

first: Peter

last: Holland


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and artificial sweeteners-stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

sample_organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and IncPα RP4 plasmid in response to 3 mg/L artificial sweeteners for 2 hours, bacteria and plasmid without dosing artificial sweeteners are the control group, in triplicate, using Illumina HiSeq 2500

first: Zhigang

last: Yu

first: Yue

last: Wang

first: Ji

last: Lu

first: Likai

last: Mao


title: Integration of central and peripheral neurons in human elongating multilineage organized (EMLO) gastruloids

status: Public on Mar 27 2021

city: Albany

first: Janet

last: Paluh

state: NY

address: CNSE, Nanofab East, 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

summary: Human stem cell technologies including self-assembling 3D tissue models provide unprecedented access to early neurodevelopment and are enabling fundamental insights into neuropathologies. Gastruloid models have yet to be used to investigate developing neuronal systems. Here we generate elongating multi-lineage-organized (EMLO) gastruloids with trunk identity that co-develop central and peripheral nervous system (CNS, PNS) correlates. We identify neural crest cells that differentiate to form peripheral neurons integrated with an upstream spinal cord region. This follows initial EMLO polarization events and is coordinated with primitive gut tube elongation and multicellular spatial reorganization. We evaluate EMLOs over a forty-day period, applying immunofluorescence of multi-lineage and functional biomarkers, including day 16 single-cell RNA-Seq, and use them to investigate the impact of mu opioid receptor modulation on neuronal activity. This comprehensive study demonstrates the first combined human CNS-PNS model of early organogenesis in the trunk to benefit biomedical research.

overall_design: 10x scRNA-Seq of day16 EMLO human hiPSC line H3.3.1

first: Zachary

middle: T

last: Olmsted


title: Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention

city: Boulder

first: Gabrijela

last: Dumbovic

state: Colorado

address: 3415 Colorado avenue

department: BioFrontiers

institute: University of Colorado

summary:
We performed poly(A) enriched RNA sequencing of HeLa, U-2 OS and mES cells.

This series includes two re-analyzed samples from mouse: GSM1032506 and GSM1032518 (denoted as iPS.A and iPS.B, respectively). The re-analyzed data for these samples are included in the file INCLUSION_LEVELS_FULL-Mm25.tab.gz.

This series includes three re-analyzed samples from human: GSM808734, GSM1023087 and GSM1023070 (denoted as iPS.A, iPS.B and iPS.C, respectively).  The re-analyzed data for these samples are included in the file INCLUSION_LEVELS_FULL-Hs23.tab.gz

overall_design: Analysis of intron retention in indicated cell lines.

first: Ulrich

last: Braunschweig

first: Christian

last: Much

first: Benjamin

last: Blencowe

first: John

last: Rinn


title: The miR-424(322)/503 gene cluster regulates pro- vs anti-inflammatory skin DC subset differentiation by modulating TGF-βsignaling

city: Memphis

first: Jiyang

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary: TGF-β family ligands are key regulators of dendritic cell (DC) differentiation and activation. Epidermal Langerhans cells (LCs) require TGF-β family signaling for their differentiation and canonical TGF-β1 signaling secures a non-activated LC state. LCs reportedly control skin inflammation and are replenished from peripheral blood monocytes, which also give rise to pro-inflammatory monocyte-derived DCs (moDCs). By studying mechanisms in inflammation, we previously screened LCs vs moDCs for differentially expressed miRNAs. miR-424/503 was the most strongly inversely regulated (moDCs > LCs). We found that miR-424/503 is induced during moDC differentiation and promotes moDC differentiation in human and mouse. Inversely, forced repression of miR-424 during moDC differentiation facilitated TGF-β1-dependent LC differentiation. Mechanistically, miR-424/503 deficiency in monocyte/DC precursors leads to the induction of TGF-β1-response genes critical for LC differentiation. Therefore, the miR-424/503 gene cluster plays a decisive role in anti-inflammatory LC vs pro-inflammatory moDC differentiation from monocytes.

overall_design: To decipher the role of miR-424(322/503), we performed RNA-seq for the bone marrow of WT and miR-424(322/503) KO mice at day 0 and day 2 after GM-CSF stimulation.

first: Victoria

last: Zyulina

first: Koon-Kiu

last: Yan

first: Jose

last: M. Silva

first: Herbert

last: Strobl


title: Glycolysis Promotes Phosphoinositide 3-Kinase Signaling In Support of T Helper 17 Cell-Mediated Autoimmunity

city: New York

first: Sagar

last: Chhangawala

address: 1300 York Ave.

institute: Weill Cornell Medical College

summary: T helper (Th) cell differentiation is driven by antigen and accessory signals that activate phosphoinositide 3-kinase (PI3K) to induce transcriptional and metabolic reprogramming including aerobic glycolysis (the Warburg effect).  Here, we show that ATP generated through glycolysis fuels PI3K signaling to promote pathogenic Th17 cell responses.  Mice with T cell-specific ablation of the glycolytic enzyme lactate dehydrogenase A (LDHA) were resistant to Th17 cell-mediated experimental autoimmune encephalomyelitis in association with defective T cell activation, migration, proliferation, and differentiation.  LDHA deficiency crippled the cellular redox balance and inhibited ATP production causing attenuated phosphoinositide (3,4,5)-trisphosphate generation, and diminished activation of the Akt kinase and phosphorylation of its transcription factor target Foxo1.  Th17 cell-specific expression of an Akt-insensitive Foxo1 mutant recapitulated the Th17 cell differentiation defects caused by LDHA deficiency.  Thus, PI3K signaling and glycolytic bioenergetics constitute a positive feedback regulatory circuit essential for Th17 cell-mediated autoimmunity.

overall_design: WT and LDHA-KO Th17 cells were subjected to RNA-Seq analysis. (2 samples in each group)

first: Ke

last: Xu

last: Yin

first: Min

last: Peng

first: Efstathios

last: Stamatiades

first: Amy

last: Shyu

first: Peng

last: Li

first: Xian

last: Zhang

first: Mytrang

last: Do

first: Kristelle

last: Capistrano

first: Chun

last: Chou

first: Christina

last: Leslie

first: Ming

middle: O


title: RNA-seq of Arabidopsis thaliana seedlings exposed to different communities of commensal bacteria [SSC]

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

summary: This study evaluates the transcriptome of Arabidopsis thaliana seedlings exposed to communities of suppressors (SynCom5-S1) and non-suppressors (SynCom5-NS1) of the plant immune system

overall_design: Arabidopsis seeds (wild-type Col-0) were germinated on Johnson medium and grown for 7 days in the vertical position. Plants were then transferred to media containing SynCom5-S1, SynCom5-NS1 (10E5 c.f.u / mL per strain), or no bacteria. Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). Seedlings were harvested twelve days after treatment. The experiment includes six biological replicates from two independent experiments.

first: Jeff

last: Dangl


title: RNA-seq of Arabidopsis thaliana roots exposed to the MAMP flg22 in the presence of a community of commensal bacteria [RST]

summary: This study evaluates the transcriptome of Arabidopsis thaliana roots exposed to the MAMP flg22 in the presence of a 35-member bacterial SynCom

overall_design: Arabidopsis seeds (wild-type Col-0) were germinated on Johnson medium and grown for 7 days in the vertical position. Plants were then transferred to media containing 1 uM flg22 or not in the presence of SynCom35 (10E5 c.f.u / mL per strain), heat-killed SynCom35 or no bacteria. Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). Roots were harvested one or twelve days after treatment. The experiment includes nine biological replicates from three independent experiments.


title: RNA-seq of Arabidopsis thaliana roots exposed to the MAMP flg22 in the presence of commensal bacteria

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

overall_design: Refer to individual Series


title: Genomic analysis of chromatin conformation and DNA damage distribution in ovarian cancer cell lines derived following acquired resistance to chemotherapy [ATAC-Seq]

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

institute: Imperial College London

summary: Changes in chromatin organization are associated with resistance to anti-cancer drugs, such as platinum-based chemotherapy used as the primary treatment of ovarian cancer. We have examined the genomic distribution of chromatin accessibility changes, and relationship to gene expression changes, occurring during acquisition of resistance in vivo of high grade serous ovarian cancer (HGSOC) patients and whether this associates with genomic DNA damage distribution. Using matched chemo-sensitive and chemo-resistant ovarian cell lines isolated from HGSOC patients before and following acquisition of clinical resistance to platinum-based chemotherapy, we have examined the relationship between chromatin accessibility by ATAC-seq, platinum-DNA adduct distribution by Pt-Exo-seq and gene expression by RNA-seq. We have correlated chromatin changes between the lines at gene promoters, CpG islands, enhancer sequences and other genomic regions with changes in gene expression and platinum-DNA adduct distribution. We observe chromatin conformation differences following acquisition of platinum-resistance, with the HGSOC resistant lines clustering together, separately from their respective sensitive counterparts. Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Super-enhancers, as defined by clusters of cis-regulatory elements, at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Genome-wide distribution of platinum adducts associates with the chromatin changes and distinguish sensitive from resistant lines. Regions incurring fewer platinum-adducts showed a significant reduction in accessibility the resistant HGSOC cell line PEO4 compared to the sensitive PEO1 counterpart. Surprisingly, regions showing increased damage in PEO4 had an even greater reduction in accessibility. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions. In cell lines derived from patients following acquisition of clinical resistance to platinum-based chemotherapy, chromatin changes at super-enhancers correlate with gene expression changes in DNA repair pathways known to influence platinum sensitivity. Although cisplatin is a relatively non-specific DNA damaging agent, there are consistent differences in distribution of adducts between the matched sensitive and resistant ovarian cell lines, which is independent of the overall level of adducts formed.

overall_design: Genetic, epigenetic and transcriptional profiling of ovarian cancer cells following cisplatinum treatment [ATAC-seq]

first: Robert

last: Brown

first: John

last: Gallon

first: Erick

last: Loomis

first: James

last: Flanagan


title: Genomic analysis of chromatin conformation and DNA damage distribution in ovarian cancer cell lines derived following acquired resistance to chemotherapy [RNA-Seq]

overall_design: Genetic, epigenetic and transcriptional profiling of ovarian cancer cells following cisplatinum treatment [RNA-seq]


title: Genomic analysis of chromatin conformation and DNA damage distribution in ovarian cancer cell lines derived following acquired resistance to chemotherapy


title: RNA-sequencing of Shox2 knockout and wildtype mouse embryonic stem cell-derived sinoatrial node-like cardiomyocytes

status: Public on Mar 26 2021

city: Heidelberg

first: Sandra

last: Hoffmann

address: Im Neuneheimer Feld 366

department: Human Molecular Genetics

institute: University of Heidelberg

summary: Differential RNA-seq-based expression profiling of Shox2+/+ and Shox2-/- ESC-derived sinoatrial node-like cardiomyocytes

overall_design: RNA profiles of 7+1 day old wild type (WT) and Shox2-/- ESC-derived sinoatrial node-like cardiomyocytes


title: Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

summary: Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos.

overall_design: mRNA-seq libraries were constructed for 8 plates of 93 samples isolated from globular stage wild type (Col-0) embryos


title: H3K27ac ChIP-seq from human glomeruli

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

summary: In order to understand the kidney compartment specific epigenetic feature of glomeruli, we isolated glomeruli from human kidney biopsy and performed H3K27ac ChIP seq.

overall_design: We dissected glomeruli from human puncture sample, and then process them with ChIP experiment.

first: Aiping

last: Duan

first: Hong

last: Wang


title: The conserved DNMT1-dependent methylation regions in human cells are vulnerable to to neurotoxicant rotenone exposure

city: Boston

first: Yanqiang

last: Li

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

summary: Rotenone is a known neurotoxicant with both human and experimental data linking it to sporadic Parkinson's disease. We used RNAseq to identify global changes in gene expression and to identify vulnerable regions responsible to the rotenone treatment. Our goal was to determine if rotenone exposure alters chromatin mediated gene regulation mechanisms. We first explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal development and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24 h. Indeed,14 genes adjacent to our identified regions were differentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes, HCN2 and NEFM, with potential to increase the risk of neurodegeneration. Both regions were significantly hypomethylated in response to rotenone.

overall_design: We used RNAseq with two controls (Control and DMSO vehicle) and two treatments (Rotenone treatment) to identify global changes in gene expression and to identify vulnerable regions of the genome responsible to the rotenone treatment.

first: Dana

last: Freeman

first: Zhibin


title: Effects of melatonin derivatives on gene expressions in human normal keratincytes

city: Birmingham

first: Andrzej

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

summary: The aim of this study was to test the effects of melatonin derivatives on gene expressions in human normal keratincytes.

overall_design: mRNAs were isolated from  normal human epidermal keratinocytes treated with10^-5 M melatonin, 6-hydroxymelatonin and AFMK. We utilized RNA-sequencing in order to compare changes in the gene expression profiles in human normal keratinocytes treated with melatonin and its derivatives in comparison to vehicle control. There are significant changes in gene expression profile in cells treated with melatonin and its metabolites in comparison to cells treated with of ethanol (0.1%) solvent. Analysis show up and down regulation of many genes with common or diverse pattern  for the compounds tested. The significance of the changes is analyzed using IPA and other bioinformatics tools.

first: Tae-Kang

last: Kim

first: Zorica

last: Janjetovic

first: Joanna

last: Stefan


title: Core TF Foxc1/2 reinforce differentiation of adult podocyte in glomeruli

summary: We identified Fox1 and Foxc2 core transcription factors in kidney glomeruli. To investigate their transcriptional regulatory roles in glomeruli, we performed ChIPseq of Foxc1 and Foxc2 in adult mouse kidney glomeruli. The genome wide distribution of Foxc1/2 binding sites revealed they regulated the differentiation and mature state of adult podocyte to maintain kidney homeostatis.

overall_design: Mouse kidney glomeruli were isolated by perfusion of magenetic beads and collection with MPC. ChIP-seq was performed with specific antibody.

first: Difei

last: Zhang

first: Yu

last: Pan


title: RNA-seq analysis of HCT116 human colon cancer cell line silenced ID4 expression

status: Public on Mar 25 2021

city: Hsinchu City

first: Cam-Thu

last: Ha

address: No. 101, Section 2, Guangfu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

summary: To investigate the function of ID4 in colon cancer cells, we collected total RNA from both HCT116-SC and HCT116-shID4 and examined mRNA expression profile, comprehensively.

overall_design: HCT116 cells were transduced with lentiviral particles encoding scramble control (SC) or shID4.

first: Yu-Ting

last: Chou


title: Allele-specific DNA methylation maps in monozygotic twins discordant for psychiatric disorders reveal that disease-associated switching at the EIPR1 regulatory loci modulates neural function

city: Guangzhou

first: Qiyang

state: Guangdong

address: 1838 Guangzhou Ave North

institute: Southern Medical University

summary: The non-Mendelian features of phenotypic variations within monozygotic twins are likely complicated by environmental modifiers of genetic effects that have yet to be elucidated. Here, we performed methylome and genome analyses of blood DNA from psychiatric disorder-discordant monozygotic twins to study how allele-specific methylation (ASM) mediates phenotypic variations. We identified that thousands of genetic variants with ASM imbalances exhibit phenotypic variation-associated switching at regulatory loci. These ASMs have plausible causal associations with psychiatric disorders through effects on interactions between transcription factors, DNA methylations, and other epigenomic markers and then contribute to dysregulated gene expression, which eventually increases disease susceptibility. Moreover, we also experimentally validated the model that the rs4854158 alternative C allele at an ASM switching regulatory locus of EIPR1 encoding endosome-associated recycling protein interacting protein 1, is associated with demethylation and higher RNA expression and shows lower TF binding affinities in unaffected controls. An epigenetic ASM switching induces C allele hypermethylation and then recruits repressive Polycomb repressive complex 2 (PRC2), reinforces trimethylation of lysine 27 on histone 3 and inhibits its transcriptional activity, thus leading to downregulation of EIPR1 in SCZ. Moreover, disruption of rs4854158 induces gain of EIPR1 function and promotes neural development and vesicle trafficking. Our study provides a powerful framework for identifying regulatory risk variants and contributes to our understanding of the interplay between genetic and epigenetic variants in mediating psychiatric disorder susceptibility.

overall_design: Examination of the expression of WT and rs4854158KO in SK-N-SH cell before and after RA treatment.

first: Zhongju

first: Cunyou

last: Zhao