title: Dynamic regulation of chromatin accessibility and transcription factors underlies distinct organ identity and function

status: Public on Mar 27 2022

city: Charlottesville

first: Hongpan

last: Zhang

state: VA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

summary: After gut tube closure, different regional domains develop into uniquely functional organs. Our single cell analysis demonstrates that chromatin accessibility predicts lineage fate decisions, reflecting the transcriptional profiles of individual cells. Combining with bulk analyses, we have generated a comprehensive map of epigenetic changes over developmental time, revealing how chromatin accessibility and transcription factor (TF) binding cooperate to control organ identity and differentiation. Loss of the foregut and hindgut lineage-specific TFs, Sox2 and Cdx2, leads to the acquisition of accessibility profiles similar to neighbouring organs, while Sox2 overexpression in early development induces a loss of intestinal identity and pancreatic transformation into foregut fate precursors. Moreover, ectopic expression of Sox2 in normal adult and cancer intestinal and pancreatic tissues leads to lineage alterations, demonstrating its critical role in homeostasis and cancer. Together, these studies define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and disease.

overall_design: We profiled genome-wide chromatin accessibility profile in single cell resolution (scATAC from 10x genomics) in mouse gut endoderm at E9.5. Bulk ATAC-seq and RNA-seq were also generated in mouse gut endoderm at E13.5. Each dataset has two replicates.

first: Smith

last: Ryan

first: Sheng'en

last: Hu

first: Yung

last: Theodora


title: Metformin regulated genes in human prostate cancer cells

status: Public on Feb 10 2022

city: Nashville

first: LaMonica

middle: V

last: Stewart

state: TN

address: 1005 DB Todd JR BLVD

department: School of Graduate Studies and Research (SOGSR)

country: USA

institute: Meharry Medical College

type: Expression profiling by high throughput sequencing

summary: The biguanide metformin has been shown to not only reduce circulating glucose levels but also suppress in vitro and in vivo growth of prostate cancer.  However, the mechanisms underlying the anti-tumor effects of metformin in advanced prostate cancers are not fully understood. The goal of the present study was to define the signaling pathways regulated by metformin in androgen-receptor (AR) positive, castration-resistant prostate cancers.  Our group used RNA sequencing (RNA-seq) to examine genes regulated by metformin within the C4-2 human prostate cancer cell line. Western blot analysis and quantitative RT-PCR were used to confirm alterations in gene expression and further explore regulation of protein expression by metformin.  Data from the RNA-seq analysis revealed that metformin alters the expression of genes products involved in metabolic pathways, the spliceosome, RNA transport, and protein processing within the endoplasmic reticulum.  Gene products involved in ErbB, insulin, mTOR, TGF-, MAPK, and Wnt signaling pathways are also regulated by metformin. A subset of metformin-regulated gene products were genes known to be direct transcriptional targets of p53 or AR.  Together, our results suggest metformin regulates multiple pathways linked to tumor growth and progression within advanced prostate cancer cells.

overall_design: C4-2 cells were plated in 10 cm dishes at a density of ~ 750,000 million cells/dish in T medium (80% DMEM low glucose medium, 20% Hams’ F12 medium, 5% heat inactivated FBS, 1% penicillin/streptomycin, 0.244 μg/ml d-biotin, 25 μg/ml adenine hemisulfate, 5 μg/ml insulin and 5 μg/ml apotransferrin) and allowed to attach for two days.  The cells were then treated for 24 hours with either PBS vehicle or 5 mM metformin. Total RNA was extracted from treated cells using the Trizol reagent and further purified using the Qiagen RNeasy Mini kit.  Each RNA sample (three replicates per treatment group) was validated for RNA integrity using an Agilent 2100 Bioanalyzer.   RNA-sequencing (RNA-seq), including library preparation, was conducted at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core facility.  A standardized TruSeq mRNA protocol was used for library preparation, followed by sequence runs on an Illumina HiSeq 2500 utilizing a 50-bp RNA-Seq protocol.

first: Siddarth

last: Pratap

first: Ayorinde

last: Cooley


title: E0771 mouse mammary tumor RNA-seq gene expression profiling: impact of time course of metronomic cyclophosphamide treatment of triple negative breast cancer tumors implanted in female C57/BL6N mice

status: Public on Mar 17 2022

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: RNA-seq analysis of polyA-selected RNA isolated from frozen tumor tissue excised from adult female C57/BL6N mice implanted with E0771 tumors in the mammary fat pad. Mice were treated with cyclophosphamide given on a metronomic schedule (treatment at 130 mg/kg per injection, or PBS (vehicle control)) (lab experiment # TD229). Tumor tissue was collected and used for RNAseq analysis at the following time points: day 1, day 2, day 3, day 6, and day 12, with cyclophosphamide treatments given on day 0, and then again on day 6 in the case of the day 12 time point. These tumor RNA samples were part of a study where we investigated the role of type-I interferon signaling in mouse models of breast cancer [Vergato et al, Canc Res Communic].

overall_design: Tumor-derived RNA-seq libraries were prepared for n=2-3 independent pools for tumor-extracted RNA for each condition tested, with each pool comprised of RNA isolated from n=2-3 independent biological replicate tumors.

first: Cameron

last: Vergato

middle: J


title: Transciptional profile of pericytes and stromal cells in bleomycin lung injury

status: Public on Feb 28 2022

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

summary: We previously showed that pericyte-like cells derived from the FoxD1-lineage contribute to myofibroblasts following bleomycin-induced lung injury. However, their functional significance in lung fibrosis remains unknown. In this study, we used a model of lung pericyte-like cell ablation to test the hypothesis that pericyte-like cell ablation attenuates lung fibrosis in bleomycin-induced lung injury. Methods: Lung fibrosis was induced by intratracheal instillation of bleomycin. To ablate pericyte-like cells in the lung, diphtheria toxin (DT) was administered to Foxd1-Cre;Rosa26-iDTR mice at two different phases of bleomycin-induced lung injury. For early ablation, we co-administered bleomycin with DT and harvested mice at days 7 and 21. To test the effect of ablation after acute injury, we delivered DT 7 days after bleomycin administration. We assessed fibrosis by lung hydroxyproline content and semiquantitative analysis of picrosirius red-staining. We performed bronchoalveolar lavage to determine cell count and differential.  We also interrogated genome-wide mRNA expression at day 7 post injury in whole lung RNA. We focused on the following cell populations for the transcriptional profiling experiments: FoxD1-derived+/Coll-GFP– pericytes (Peri), FoxD1-derived+/Coll-GFP+ pericytes (PeriFibro), and FoxD1-derived–/Coll-GFP+ stromal fibroblasts (Fibro).Results: Compared to DT-insensitive littermates where pericyte-like cells were not ablated, DT-sensitive animals exhibited no difference in fibrosis at day 21 both in the early and late pericyte ablation models. However, early ablation of pericytes reduced acute lung inflammation, as indicated by decreased inflammatory cells. Our data confirm a role for pericytes in regulating pulmonary inflammation in early lung injury.

overall_design: Total RNA from Peri, Peri_Fibro, and Fibro cells from bleomycin injured and control mice were hybridized to Illumina MouseWG-6 v2.0 microarrays.

middle: A

first: Chi

middle: F

last: Hung


title: Profiling the Panc1 pancreatic cancer cell line following Gemcitabine treatment using single cell RNA sequencing

status: Public on Mar 21 2022

city: Chicago

first: Elizaveta

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: Pancreatic ductal adenocarcinoma (PDAC) often presents at late clinical stages, and most patients are managed solely through palliative chemotherapy. With no approved treatment modalities for patients who progress on broad-spectrum chemotherapy, we set to identify druggable targets to prevent or reverse resistance to the first line anti-neoplastic Gemcitabine. In our first experiment, we used the well-established Panc1 cell line as an in vitro model of PDAC. Panc1 cells were incubated with a tolerable dose of Gemcitabine in vitro, and examined alterations in gene expression via single cell RNA sequencing. In our subsequent studies, we incubated Panc1 cells with increasing doses of Gemcitabine for several passages, until viable in approximately 10x the known IC50 value. These cells were designated Panc1-GR. Based on our observations in the prior experiment, Panc1-GR cells were compared to those treated with wither the Calmodulin inhibitor W-7, Calcium chelator BAPTA-AM, or the calcium channel blocker Amlodipine. Through these efforts, we hope to better understand the mechanisms of Gemcitabine resistance in PDAC, as well as introduce new therapeutic strategies to reverse drug resistant phenotypes in the clinic.

overall_design: Examining gemcitabine resistance in pancreatic cancer using single cell RNA-seq

first: Ajay

last: Rana

first: Daniel

middle: R

last: Principe

first: Alexandre

last: Aissa

first: Abul

middle: B

last: Islam


title: RNA-Seq quantitative analysis of the regulation of platelet-derived extracellular vesicles on NPC cells transcriptomes

status: Public on Feb 23 2022

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

country: China

institute: Sun Yat-sen university

summary: Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor with a high metastatic feature and invasive nature. The survival rate of NPC patients is still very low due to the high incidence of distant metastasis. Platelets are versatile blood cells and mediate the distant metastasis of tumor cells via the blood circulation. However, the role and underlying mechanism of platelets responsible for the NPC cells hematogenous metastasis are not well understood. In our study, we found that platelet-derived EVs of NPC patients (P-EVs) induced the metastasis and mesenchymal-epithelial transition process in NPC cells.  To shed light on the mechanism underlying P-EVs-induced NPC metastasis and MET process, we performed high throughput RNA-Seq analyses to reveal the differentially expressed genes in NPC cells treated with or without P-EVs. We observed that there was a significant overlap in the expression of integrins that were altered in 6-10B and 5-8F upon P-EVs treatment. Of these, integrin β3 (ITGB3) exhibited the most obvious upregulation.

overall_design: Examination of P-EVs treated 6-10B and 5-8F cells and untreated 6-10B and 5-8F control group

first: Qing


title: Next Generation Sequencing of Transcriptomes of human cells expressing the human gene LY6S which is the TransMap and phylogeneticlly predicted homolog to murine Ly6a also known as T-cell Activating Protein, Sca1, Stem Cell Antigen-1, Ly6A2/E1 [U87]

status: Public on Mar 15 2022

city: Tel-Aviv

middle: H

last: Wreschner

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: We discovered a new human gene, LY6S, coding for an LY6-like protein. TransMap and phylogenetic studies reveal that LY6S is the homolog of the murine Ly6a gene known as Ly6A.2/Ly6E.1, Sca1 (Stem Cell Antigen-1) and TAP (T-cell activating protein) which codes for a cell-surface protein used extensively as a hematopoietic stem cell marker. LY6S is interferon-inducible and codes for both GPI-linked membrane and secreted proteins. The LY6S cell-surface protein, contains only 9 cysteines distinguishing it from all other LY6-like proteins that have 10 consensus cysteine residues.  LY6S is most highly expressed in cells of the human spleen that constitute a unique spleen cell lineage. Expression of the GPI-linked LY6S protein in various human cell lines leads to profound changes in cell morphology and cell growth, neither of which are affected by expression of the secreted LY6S protein. RNA-Seq analyses presented here show distinct shifts in patterns of gene expression, particularly of genes coding for inflammatory and immune response proteins, were associated with these changes. Our findings reveal the presence of a previously non-annotated human gene, LY6S, which is the Ly6a homolog and that codes for proteins expressed in  spleen cells representing a new cell lineage, are associated with a florid inflammatory phenotype and  regulate immune responses and cell growth.

overall_design: mRNA profiles of human U87 glioblastoma cells that were stably transfected with either control pQCXIP expression vector or with the same vector coding for the GPI-linked, cell membrane located human LY6-iso1 protein  were generated by deep sequencing, in triplicate.

first: Avital

last: Sarusi-Portuguez


title: Next Generation Sequencing of Transcriptomes of human cells expressing the human gene LY6S which is the TransMap and phylogeneticlly predicted homolog to murine Ly6a also known as T-cell Activating Protein, Sca1, Stem Cell Antigen-1, Ly6A2/E1

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

overall_design: Refer to individual Series


title: Expression data from HepaRG human progenitor hepatic cells treated with different sources of Vitamin E and wheat germ oil.

status: Public on Jan 30 2022

city: Sansepolcro

first: Jacopo

last: Lucci

state: Arezzo

address: Loc. Aboca, 20

country: Italy

institute: Bios-Therapy, Physiological Systems For Health S.p.A

summary:
According with the hepatic protection role of Vitamin E (VE), clinical guidelines of gastroenterology societies are now supporting the administration of VE as first line treatment of Non-Alcoholic SteatoHepatitis (NASH).
We used microarrays to detail the transcriptional response obtained by pre-administration to HepaRG cell line of different sources of VE (WGO-VE, nVE and sVE) followed by exposure to oleic acid (OA) to induce conditions of steatosis

overall_design: We compared transcriptional response of OA-treated HepaRG for 48 hours with transcriptional response of HepaRG pre-treated with different sources of VE for 24 hrs and subsequent 48 hours of treatment with OA.

first: Angela

last: Guerrini

first: Tiziana

last: Frammartino


title: Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions

status: Public on Jan 29 2022

city: Madison

first: Vania

last: Pankievicz

state: WI

address: 1550 Linder Dr.

department: Bacteriology

institute: University of Wiscosin - Madison

summary: Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure.

overall_design: Sierra Mixe and B73 maize growing in a high ceiling room (14/10h light/dark cycles and 25/17º C and 85%/90% relative humidity) were subject to rain events twice a week to trigger mucilage production. Stage 1 Sierra Mixe aerial roots, stage 2 Sierra Mixe aerial roots, and stage 1 B73 aerial roots were collected before a rain event and then 2 and 24 hours after a rain event.

first: Vânia

middle: C

last: Silva Pankievicz

first: Pierre

middle: M

last: Delaux

first: Hayley

last: Hirsch

first: Shanmugam

last: Rajasekar

first: Valentina

last: Infante

first: Pablo

last: Zamora

first: Dhileepkumar

last: Jayaraman

first: Claudia

middle: I

last: Calderon

first: Alan

last: Bennett

first: Jean

last: Ané


title: Antigen presentation by type 3 innate lymphoid cells directs the differentiation of gut microbiota-specific regulatory T cells

city: New York

first: Peter

last: Smibert

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: The mutualistic relationship of gut-resident microbiota and cells of the host immune system promotes homeostasis that ensures maintenance of the microbial community and of a poised, but largely non-aggressive, immune cell compartment1,2. Consequences of disturbing this balance, by environmental or genetic factors, include proximal inflammatory conditions, like Crohn’s disease, and systemic illnesses, both metabolic and autoimmune.  One of the means by which this equilibrium is achieved is through induction of both effector and suppressor or regulatory arms of the adaptive immune system. In mice, Helicobacter species induce regulatory (iTreg) and follicular helper (Tfh) T cells in the colon-draining mesenteric lymph nodes under homeostatic conditions, but can instead induce inflammatory Th17 cells and colitis when iTreg cells are compromised3,4. How Helicobacter hepaticus and other gut bacteria direct T cells to adopt distinct functions remains poorly understood. It could involve targeting a common antigen presenting cell (APC) by distinct microbial products, endowing it with specialized functions, or targeting APCs with pre-determined features suited to directing appropriate T cell differentiation programs. Here, we investigated which cells and molecular components are required to convey the microbial instruction for the iTreg differentiation program. We found that antigen presentation by cells expressing RORgt, rather than by classical dendritic cells, was both required and sufficient for iTreg induction. The MHC class II antigen presentation machinery, chemokine receptor CCR7, and av integrin, which activates TGF-β, were necessary in RORgt+ cells, likely type 3 innate lymphoid cells (ILC3), for iTreg cell differentiation. In the absence of any of these, instead of iTreg cells there was expansion of H. hepaticus-specific pathogenic Th17 cells, which were induced by other APCs that did not require CCR7. Our results illustrate the ability of microbiota to exploit specialized functions of distinct innate immune system cells, targeting them to achieve the desired composition of equipoised T cells, thus maintaining tolerance.

overall_design: CITE-seq and cell hashing of C1 MLN of tdTomato-ONΔCD11c or tdTomato-ONΔRORɣt;zbtb46-eGFP  mice that were colonized with Helicobacter for 7 days.

first: Stephanie

last: Hao

first: Ranit

last: Kedmi


title: Increased expression of p53 with APR-246 (eprenetapopt) reprograms tumor-associated macrophages to promote the efficacy of immune checkpoint blockade

status: Public on Feb 11 2022

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Expression of genes in sorted CD4, CD8 and non-T CD45 cells isolated from TME of B16 tumors in wildtype B6, APR-246 treated wildtype B6 and Super p53 mice.

overall_design: mice bearing B16 tumors were implanted in super p53 or WT mice. WT mice were treated with vehicle or APR-246 starting day 7 for 6 days and single cell suspensions of the tumors were obtained and antibody stained for CD45, CD8. CD4 and live/dead. CD45+ CD8+, CD45+CD8+ and CD45+CD4-CD8- sorted and RNA was extracted with the PAXgene RNA kit and purified in accordance with the manufacturer’s protocols. RNA was assessed with the Agilent BioAnalyzer for quantity and quality.

first: Arnab

last: Ghosh

first: Taha

last: Mergoub


title: Monocyte and macrophage lipid accumulation results in downregulated type-I interferon responses

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC


title: Single-cell RNA sequencing reveals a role for reactive oxygen species and peroxiredoxins in fatty-acid-induced rat ß-cell proliferation

status: Public on Jan 21 2022

city: Montréal

first: Alexis

last: Vivoli

state: Québec

address: 900 rue St denis

country: Canada

institute: Centre de recherche du centre hospitalié de l'université de montréal (CRCHUM)

summary: The functional mass of insulin-secreting pancreatic β cells expands to maintain glucose homeostasis in the face of nutrient excess, in part via replication of existing β cells. To decipher the underlying molecular mechanisms, we assessed β-cell proliferation in isolated rat islets exposed to glucose and oleate or palmitate for 48 h and analyzed the transcriptional response by single-cell RNA sequencing. Unsupervised clustering of pooled β cells identified subpopulations, including proliferating β cells. β-cell proliferation increased in response to oleate but not palmitate. Both fatty acids enhanced the expression of genes involved energy metabolism and mitochondrial activity. Comparison of proliferating vs. non-proliferating β cells and pseudotime ordering suggested the involvement of reactive oxygen species (ROS) and peroxiredoxin signaling. Accordingly, the antioxidant N-acetyl cysteine and the peroxiredoxin inhibitor Conoidin A both blocked oleate-induced β-cell proliferation. Our data reveal a key role for ROS signaling in β-cell proliferation in response to nutrients.

overall_design: Isolated rat pancreatic islets were treated for 48h in the presence of 16,7mM glucose (VEH; 4 replicates), 16,7mM glucose + 0.5mM palmitate (PAL; 3 biological replicates) or oleate (OL; 4 biological replicates) prior single cell RNA-sequencing

first: Julien

last: Ghislain

first: Ali

last: Filali-Mouhim

first: Robert

last: Sladek

first: Vincent

last: Poitout


title: Co-ordinated humoral and cell-mediated immune responses drive class-switched antibody production and improved patient survival in endometrial cancer

status: Public on Jan 20 2022

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: NOT PROVIDED; REQUESTED

overall_design: mRNA profiles of KLE cell lines with and without PIGR transduction

first: Gunjan

last: Mandal

first: Xiaoqing

last: Yu

first: Jose

last: Conejo-Garcia


title: Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [polyA_RNA]

first: Yong

last: Peng

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

summary: We introduce m6A Selective Allyl Chemical labeling and Sequencing (m6A-SAC-Seq), a novel method for transcriptome-wide quantitative mapping of m6A at single-nucleotide resolution. The m6A-SAC-Seq employs a dimethyltransferase to selectively label m6A followed by introducing mutations with reverse transcriptase during sequencing. We identified the widespread distributions of m6A and quantitated their fractions in the transcriptome of HeLa, HEK293, HepG2, and human CD34+ hematopoietic stem/progenitor cells (HSPCs).

overall_design: The RNA is treated with recombinant MjDim1 enzyme with allylic-SAM cofactor under optimized conditions to selectively convert m6A residues to a6m6A, followed by adding I2 to convert am6A to EA. Reverse transcription induces mutations at EA sites, enabling identification of the sites labeled with a6m6A.

first: Lulu

last: Hu

first: Shun

last: Liu

first: Ruiqi

last: Ge

first: Rui

last: Su

first: Chamara

last: Senevirathne

first: Bryan

middle: T

last: Harada

first: Qing

last: Dai

first: Jiangbo

last: Wei

first: Lisheng

last: Zhang

first: Ziyang

first: Liangzhi

last: Luo

first: Huanyu

last: Wang

first: Yuru

first: Mingkui

first: Mengjie

last: Chen

first: Jianjun

first: Chuan

last: He


title: Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [shRNA RNA-seq]

status: Public on Jan 27 2022

first: Yong

first: Lulu

last: Hao


title: Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution

status: Public on Jan 19 2022


title: Genome-wide transcriptional response of bone marrow derived macrophages (BMDM) to tunicamycin (TM).

status: Public on Jan 25 2022

city: Atlanta

first: Svetlana

last: Atasheva

state: Georgia

address: 1760 Haygood Dr

department: Pediatrics

institute: Emory University

summary: We analyzed global genome-wide transcriptional response of bone marrow derived macrophages (BMDM) to tunicamycin (TM). This analysis demonstrated that TM treatment changed the expression of 1,426 genes in WT BMDM and 1,075 genes in 4KO BMDM ( Casp1-/-Casp8-/-Casp11-/-Ripk3-/- ) (2-fold cut-off, p<0.05). Among differentially-expressed genes, all downregulated 759 genes were downregulated to similar levels in both WT and 4KO BMDM after TM treatment. However, 667 genes activated by TM treatment were globally upregulated to significantly higher levels in WT, compared to 4KO BMDM which is consistent with previous findings of a muted macrophage responses to triggers in cells lacking CASP8. Next we used gene set enrichment analysis to annotate pathways deregulated by TM in BMDM and compared down-regulated and upregulated gene sets in BMDM to their expression in liver resident Mf, Kupffer cells, at homeostatic conditions in vivo. The most prominently down-regulated pathways in BMDM after TM treatment were cell cycle, DNA replication, and metabolism pathways (normalized enrichment score (NES) =-8.5, -7.9, -7.1, respectively, FDR<1e-4,). Importantly, the gene sets constituting downregulated pathways in TM-treated BMDM were highly expressed in KC in vivo at homeostatic levels (NES= 8.7, 10.5, 6.6 , FDR<1e-4), suggesting the lack of phenotypic similarity between TM-treated BMDM and KC for this set of pathways. However, this same analysis showed that the most prominently enriched pathways in BMDM after TM treatment were pathways related to innate and adaptive immune signaling, cytokine signaling and mitogen-activated protein kinase signaling (NES =8.7, 6.4, 6.9, 3.2, respectively , FDR<1e-4). The gene set enrichment analysis for this set of genes demonstrated that in KC at homeostatic conditions, these same genes are also highly enriched (NES=12.6,  9.8, 7.1, 4.5 , FDR<1e-4), suggesting that for upregulated gene sets, TM treatment drives BMDM in vitro to transcriptomic phenotype similar to that observed in KC in vivo at homeostatic conditions.

overall_design: Bone marrow cells were harvested from femurs of  mice (pooled cells from three mice were used for each genotype) . Marrow cells were re-suspended in DMEM media supplemented with 10% FBS (Life Technologies, Carlsbad, CA), 1×pencillin/ streptomycin (Life Technologies, Carlsbad, CA) and 40ng/ml of macrophage colony–stimulating factor, mouse M-CSF (R&D, Minneapolis, MN). After 6 days differentiation, bone marrow derived macrophages (BMDM) were retrieved and plated on FBS pre-treated 4-well glass bottom slides (Thermo Fisher Scientific Inc, Suwanee, GA) at 2-2.2× 105 cell/well. One day later, culture media were changed with phenol-red free DMEM with 20ng/ml of M-CSF in the presence of DMSO (control) or 0.5µg/ml of tunicamycin (Sigma) for 6 hrs. For each genotype four replicate samples were  analyzed. Kupffer cells were isolated from five C57Bl6 mice and submitted for RNA-sequencing independently.

first: Dmitry

last: Shayakhmetov


title: RNA sequencing/Gene expression studies of mTORC1 signaling in myeloma

status: Public on Feb 07 2022

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: We determined that mTORC1 is a predominant target of RAS-dependent signaling in multiple myeloma.  We sought to obtain a gene signature of mTORC1 activity in myeloma cells by examining changes in gene expression by RNA seq following treatment with the mTORC1 inhibitor everolimus at 100 nM

overall_design: RNA sequencing to determine gene expression in XG2 and SKMM1 multiple myeloma cells treated with control (DMSO) versus 100 nM everolimus for 3 and 8 hours.

first: Ryan

last: Young


title: Microglia P2Y6 receptor signaling regulates a broad range of innate immune responses after TLR engagement

status: Public on Feb 04 2022

city: Rijswijk

first: Raissa

last: Timmerman

address: Lange Kleiweg 161

department: Alternatives

institute: Biomedical Primate Research Centre

summary: We analyzed the transcriptomes of adult primary rhesus macaque microglia that were exposed to 10 µg/mL uLPS, in the absence or presence of 5 µM P2RY6 antagonist MRS2578

overall_design: Primary microglia cultured in medium containing serum for 8 days. At day 7, microglia were exposed to 5 µM P2RY6 antagonist (MRS2578) 1hr prior to exposure to uLPS (10 µg/mL), or exposed to uLPS alone.

first: Jeffrey

last: Bajramovic


title: Durum wheat meristem transcriptome

status: Public on Jan 10 2022

city: Fort Collins

first: Carl

last: VanGessel

state: CO

address: Colorado State University

institute: Colorado State University

summary: For characterizing the predominant transcriptional profiles associated with spike development progression, and to identify core regulatory candidate genes.

overall_design: Tetraploid Triticum turgidum L. subsp. durum (Desf.) var. Kronos. Approximately 20 apices were combined for each biological replicate of samples harvested at stages W1.0 (shoot apical meristem, SAM) and W2.0 (early double ridge, EDR) and approximately 12 apices for samples harvested at stages W3.0 (double ridge, DR), W3.25 (lemma primordia, LP) and W3.5 (terminal spikelet, TS) (Waddington et al., 1983). Four biological replicates were harvested at each timepoint.

first: Stephen

last: Pearce


title: mRNA sequencing of control and resolvase-deficient ex vivo-stimulated B cells

status: Public on Feb 01 2022

last: Smolkin

address: 408 E 69th St

institute: MSKCC

summary: Our RNA-seq analysis comparing control, Gen1-knockout, Mus81-knockout, and Gen1-Mus81-double knockout activated B cells showed that the control and Gen1-KO B lymphocytes resemble each other transcriptomically whereas differential gene expression (DGE) analysis comparing Mus81-KO to control cells identified 8 genes with a minimum of 2-fold upregulation in Mus81-KO cells. Between Gen1-KO and Mus81-KO cells, the transcript level of only 4 genes, including Mus81 were differentially altered. DGE analysis of control versus DKO cells, on the contrary, revealed that 279 genes were upregulated by at least twofold (log2 fold change 1; FDR <0.05) and 167 genes were downregulated by a minimum of log2 fold change of –0.3 in the DKO B cells (corresponding to a 19% de-enrichment relative to control cells).

overall_design: mRNA-seq profiles of control, Gen1-KO, Mus81-KO, and Gen1-Mus81-DKO splenic B cells stimulated with lipopolysaccharide (30 ug/mL) and interleukin-4 (25 ng/mL) for 48 hours.

first: Keith Conrad

last: Fernandez

first: Jayanta

last: Chaudhuri


title: Circadian disruption enhances HSF1 signaling and tumorigenesis in Kras-driven lung cancer

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

summary: Disrupted circadian rhythmicity is a prominent feature of modern society and has been designated as a probable carcinogen by the World Health Organization. However, the biological mechanisms that connect circadian disruption and cancer risk remain largely undefined.  We demonstrate that exposure to chronic circadian disruption (chronic jetlag, CJL) increases tumor formation in a mouse model of KRAS-driven lung cancer. Molecular characterization of tumors and tumor-bearing lung tissues revealed that CJL enhances the expression of heat shock factor 1 (HSF1) target genes. Consistently, exposure to CJL disrupted the highly rhythmic nuclear trafficking of HSF1 in the lung, resulting in an enhanced accumulation of HSF1 in the nucleus. HSF1 has been shown to promote tumorigenesis in other systems, and we find that pharmacological inhibition of HSF1 reduces the growth of KRAS-mutant human lung cancer cells. These findings implicate HSF1 as a molecular link between circadian disruption and enhanced tumorigenesis.

overall_design: To identify mechanisms potentially underlying the pro-tumorigenic effect of CJL in K mice, we compared the transcriptional programs in tumors and total lung from K mice housed in normal or CJL conditions. Up to 12 individual tumors were collected from each animal at either ZT9 or ZT21 and the remaining lung tissue was also collected for subsequent analyses. We sequenced RNA prepared from 3 tumors per animal and two mice per time point and lighting condition

first: Marie

last: Pariollaud

first: Michael

last: . Bollong

first: Katja

last: Lamia


title: Single Cell RNA sequencing of BRONJ disease control and HMDP-treated mouse gingiva

status: Public on Jan 08 2022

city: Los Angeles

first: Takeru

last: Kondo

address: 10824 Lindbrook Dr. #304

institute: UCLA School of Dentistry

summary: Purpose: The goal of this study was to characterize the gingival oral barrier immunity of bisphosphonate-related osteonecrosis of the jaw (BRONJ) and HMDP-treated BRONJ mouse maxilla. Method: Mouse BRONJ was induced by Zoledronate IV injection and maxillary left first molar extraction. HMDP-DNV was topically applied to the BRONJ lesion 2 times. Mouse palatal gingiva was harvested 2 weeks after tooth extraction. Gingival cells were harvested and subjected to 10X Genomix scRNA-seq. Cell Ranger processed data were analysed.

overall_design: BRONJ disease gingival oral barrier immune cells were compared with HMDP-DNV-treated BRONJ gingival oral barrier immune cells.

first: Ichiro

last: Nishimura


title: Gene expression profiles from the cardiac tissue of HIPK2-knockout and Wild Type (WT) mice

status: Public on Jan 01 2022

city: Shanghai

first: Qiulian

last: Zhou

address: Nanchen Road

department: Institute of Cardiovascular Sciences

institute: Shanghai University

summary: We use Affymetrix Gene Chip Array to screen the targets of HIPK2 in heart. Total RNA was extracted from 8-week-old HIPK2-knockout and Wild Type (WT) mice.

overall_design: C57BL/6 HIPK2-/- mice were generated in Beijing Viewsolid Bioteh Co. Ltd (Beijing, China) by embryo injection of CRISPRs targeting the second exon (guide RNA sequences: AAGTTCCAACTGGGACATGACTGGGT) of the mouse Hipk2 gene. Frameshift mutations (56bp deletion: TGGGTACGGCTCCCACAGCAAAGTGTACAGCCAGAGCAAGAACATACCACCTTCTC) were identified and crossed with C57BL/6 WT mice for colony expansion and subsequent experiments. Tail biopsies of HIPK2-/- mice were analyzed by genomic PCR (forward primer 5’- TTCAGAGTGGAAGAACAATC -3’ and reverse primer 5’- TTGGTAGGTGTCAAGGAG -3’).

first: Junjie

last: Xiao


title: Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [Ribo-minus_RNA]

first: Yong

last: Peng

first: Lulu

last: Hu

first: Shun

last: Liu

first: Ruiqi

last: Ge

first: Rui

last: Su

first: Chamara

last: Senevirathne

first: Bryan

last: Harada

first: Qing

last: Dai

first: Jiangbo

last: Wei

first: Lisheng

last: Zhang

first: Ziyang

last: Hao

first: Liangzhi

last: Luo

first: Huanyu

last: Wang

first: Yuru

first: Mingkui

first: Mengjie

last: Chen

first: Jianjun

first: Chuan

last: He


title: Pronounced specificity of the TET enzyme catalytic domain guides cellular function

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary: Epigenetic memory in the form of cytosine methylation is essential for vertebrate development and the formation of cellular identity. Active removal of DNA methylation by the action of the TET hydroxylase family helps enable developmental potency, both in vivo and during creation of induced pluripotent stem cells. Despite this, little is known about how TET proteins are targeted to DNA. We report that mammalian TET enzymes show strong preference (>200 fold) for oxidising certain CG-containing hexamers in vitro, and during global methylation reprogramming in cultured cells and during embryogenesis. These preferred sequences, and also the most poorly targeted motifs, constitute recognition sites for developmental transcription factors whose binding activity is sensitive to DNA methylation. X-ray structural analysis and molecular dynamics simulations suggest that TET proteins use indirect readout to sense the sequence context flanking CG sites. These results are significant for understanding epigenetic reprogramming during development and the biological role TET enzymes play in modulating epigenetic memory.

overall_design: An ESC line with TET1-3 genetically inactivated (TET-TKO) was rescued using an inducible PiggyBAC transposon based vector containing the catalytic domain from mouse TET3 induced by doxicycline and transcriptionally linked to an mCherry reporter gene. Cells without doxycicline treatment were used as control. Wild-type V6.5 hybrid embryonic stem cells (i.e. C57BL/6 X 129/sv cross) were treated with decitabine (5-aza-2’-deoxycytidine). Genome-wide bisulfite sequencing was used to uncover the rate at which DNA demethylation occurred in these samples.

first: Timothy

last: Hore

first: Claudia

last: Davies

first: Rosie

last: Glanfield


title: Mice Lacking MBNL1 and MBNL2 Exhibit Sudden Cardiac Death and Molecular Signatures Recapitulating Myotonic Dystrophy

city: Gainesville

first: Eric

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: Myotonic dystrophy (dystrophia myotonica, DM) is caused by expansions of CTG (type 1; DM1) or CCTG (type 2; DM2) repeats in the non-coding regions of the DMPK and CNBP genes, and patients with DM1 or DM2 often suffer from sudden cardiac death due to lethal arrhythmia. Specific molecular changes that underlie DM cardiac pathology have been linked to repeat-associated depletion of Muscleblind-like (MBNL) 1 and 2 proteins and upregulation of CUGBP Elav-like family member 1. Aims: We aim to create an Mbnl KO mouse model recapitulating DM cardiogenic death not under anesthesia, since none of the DM mouse models have reached this goal. Besides, it is unclear whether dysfunction of cardiomyocytes, among other cell types in the heart, can solely drive phenotypes. Methods and Results: We generated Myh6-Cre DKO (Mbnl1-/-; Mbnl2cond/cond; Myh6-Cre+/-) mice that completely eliminate Mbnl1/2 expression in cardiomyocytes. In this model, we found increased myocardial fibrosis, dilated cardiomyopathy and various arrhythmias. Importantly, we observed spontaneous lethal arrhythmic events in the context of shortened lifespan. RNA sequencing (RNA-seq) revealed mis-splicing events involving sarcomeric structure, mitochondrial dynamics and vesicular trafficking that mimics DM hearts. Gene expression changes were also noted by RNA-seq, and confirmed by qPCR. Notably, immunoblotting revealed a nearly 6-fold increase of Calsequestrin 1 and 50% reduction of epidermal growth factor proteins. Conclusion: These results showed that complete elimination of MBNL1/2 in mouse cardiomyocytes is sufficient to elicit a full spectrum of DM cardiac phenotypes including cardiac-related sudden death, and therefore these mice could serve as a useful model for studying DM heart pathogenesis and related translational research.

overall_design: Myh6-Cre DKO (Mbnl1-/-; Mbnl2cond/cond; Myh6-Cre+/-) mice were generated that lack Mbnl1 and Mbnl2 expression in cardiomyocytes. Hearts were harvested from 3-6 month old mice and subjected to RNA-seq. Strand-specific paired-end RNA sequencing of total RNA was performed using the NEBNext Ultra II Directional Library Prep Kit. Libraries were pooled and sequenced on an Illumina NextSeq 500 v2 instrument using 2x75 paired end reads.

first: Lee

last: Kuang-Yung

first: Seah

last: Carol

first: Li

last: Ching

first: Chen

last: Yu-Fu

last: Chwen-Yu

first: Wu

last: Ching-I

first: Liao

last: Po-Cheng

first: Shyu

last: Yu-Chiau

first: Olafson

last: Hailey

first: McKee

last: Kendra

first: Wang

last: Eric T

first: Yeh

last: Chi-Hsiao

last: Chao-Hung


title: DNA methylation analysis of hypertensive, pre-hypertensiveand healthy control samples

city: Xi’an

first: Congxia

last: Bai

state: Shanxi

address: 127 Changle West Rd

department: Clinical Laboratory Medicine

institute: xijing hospital

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of  hypertensive, pre-hypertensive, and healthy control samples. The Illumina Infinium 450k Human DNA methylation Beadchip  was used to obtain DNA methylation profiles. Samples included 44 hypertensive samples, 44 pre-hypertensive samples, and 44 healthy controls.

overall_design: Bisulphite converted DNA from the 132 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Ming

last: Su

first: Yaohua

last: Zhang

first: Yahui

last: Lin

first: Jingzhou

last: Chen

first: Hao

last: Li


title: RIP-seq of Ythdf3 in MEFs with or without nutrient starvation

status: Public on Dec 30 2021

city: Guangzhou

first: Weichao

last: Hao

state: Guangdong

address: No.1838 Guangzhou Avenue North, Baiyun District

institute: Southern Medical University

summary: The variation of mRNA targets of mouse YTH N6-methyladenosine RNA binding protein 3 (Ythdf3) during nutrient starvation was determined by RNA immunoprecipitation and sequencing (RIP-seq).

overall_design: RIP-seq in MEFs with or without nutrient starvation

first: Meijuan

last: Dian

first: Jiahong

last: Wang


title: MeRIP-seq of mRNAs in MEFs with or without nutrient starvation

summary: To investigate the dynamic m6A modification during starvation-induced autophagy, we performed MeRIP-seq in MEFs with or without nutrient deprivation and identified the variations of m6A modification on mRNAs. Briefly, the total polyadenylated mRNAs in MEFs cultured with or without nutrient-deprived medium for 2 hours were isolated using RNAiso plus reagent (Takara) followed Dynabeads mRNA Purification Kit (Invitrogen). The m6A RNA immunoprecipitation was performed using GenSeq m6A RNA IP Kit. NEBNext Ultra II Directional RNA Library Prep Kit (NEB) was used for library generation. Each experiment was conducted in two biological replicates. Methylated sites on peaks were identified by MACS2 peak-calling software (Zhang et al., 2008). Differentially methylated sites were identified by diffReps (Shen et al., 2013) with default setting.

overall_design: m6A modification profiles of RNA in MEFs with or without nutrient starvation


title: Genome-wide binding patterns of the Plastid-encoded polymerase in Arabidopsis

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Plastids are endosymbiotic organelles containing their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplasts DNA using ptChIP-seq. We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex pattern of binding to DNA with preferential association at genes encoding rRNA, tRNA and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with the levels of RNA accumulation, which allowed estimating the quantitative contribution of transcription to RNA accumulation.

overall_design: The data consists of 2 or 3 replicates of ptChIP from pTAC12-HA or RpoB protein in Arabidopsis thaliana Col-0 wild type, sig2-2 or sig6-1 genotypes from 4 or 14 days-old plants. Different formaldehyde cross-linking treatment lengths were tested. Input or no antibody controls were included. Additionally 14 days-old plants TSS RNA-seq data in Col-0 plants were generated and 3 replicates are included

first: V

first: Andrzej

last: Wierzbicki


title: Transcriptome analysis for vorinostat-treated choriocarcinoma cells

status: Public on Dec 25 2021

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

summary: Choriocarcinoma is one of the rare gynecological malignancies with aggressive behavior. Vorinostat is an approved HDAC inhibitor, and HDACs play important roles in regulating gene expression and modulating various cellular processes. Here, the human choriocarcinoma cell lines (JAR and JEG-3) were treated with 1 μM vorinostat or DMSO for 48 h. Then, total RNA was extracted, and transcriptome analysis was performed.

overall_design: RNA sequencing for vorinostat-treated choriocarcinoma cells

first: Eri

last: Watanabe

first: Akira

last: Yokoi


title: Paired-end Sequencing of Transcriptomes of human cells expressing the human gene LY6S

status: Public on Jan 11 2022

city: Tel-Aviv

first: Daniel

last: Wreschner

address: Ramat Aviv

institute: Tel Aviv University

summary: We discovered a new human gene, LY6S, coding for an LY6-like protein. TransMap and phylogenetic studies reveal that LY6S is the homolog of the murine Ly6a gene known as Ly6A.2/Ly6E.1, Sca1 (Stem Cell Antigen-1) and TAP (T-cell activating protein) which codes for a cell-surface protein used extensively as a hematopoietic stem cell marker. LY6S is interferon-inducible and codes for both GPI-linked membrane and secreted proteins. The LY6S cell-surface protein, contains only 9 cysteines distinguishing it from all other LY6-like proteins that have 10 consensus cysteine residues.  LY6S is most highly expressed in cells of the human spleen that constitute a unique spleen cell lineage. Expression of the GPI-linked LY6S protein in various human cell lines leads to profound changes in cell morphology and cell growth, neither of which are affected by expression of the secreted LY6S protein. RNA-Seq analyses presented here show distinct shifts in patterns of gene expression, particularly of genes coding for inflammatory and immune response proteins, were associated with these changes. Our findings reveal the presence of a previously non-annotated human gene, LY6S, which is the Ly6a homolog and that codes for proteins expressed in  spleen cells representing a new cell lineage, are associated with a florid inflammatory phenotype and  regulate immune responses and cell growth.

overall_design: mRNA profiles of human U87 glioblastoma cells that were stably transfected with either control pQCXIP expression vector or with the same vector coding for the GPI-linked, cell membrane located human LY6-iso1 protein  were generated by deep sequencing, in triplicate, ??using Illumina GAIIx??.

first: Avital

last: Sarusi-Portuguez


title: Genome-wide mapping of N4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing

status: Public on Dec 15 2021

city: Wuhan

first: Jun

last: Xiong

state: Hubei

department: Chemistry

institute: Wuhan university

summary: N 4-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. In the 4mC-AMD-seq method, cytosine and 5-methylcytosine (5mC) are deaminated by APOBEC3A (A3A) protein to generate uracil and thymine, both of which are read as thymine in sequencing, while 4mC is resistant to deamination and therefore read as cytosine. Thus, the readouts of cytosines from sequencing could manifest the original 4mC sites in genomes. With the 4mC-AMD-seq method, we achieved the genome-wide mapping of 4mC in Deinococcus radiodurans (D. radiodurans). In addition, we confirmed that 4mC, but not 5mC, was the major modification in the D. radiodurans genome. We identified 1586 4mC sites in the genome of D. radiodurans, among which 564 sites were located in the CCGCGG motif. The average methylation levels in the CCGCGG motif and non-CCGCGG sequence were 70.0% and 22.8%, respectively. We envision that the 4mC-AMD-seq method will facilitate the investigation of 4mC functions, including the 4mC-involved R-M systems, in uncharacterized but potentially useful strains.

overall_design: Single-base resolution mapping of N4-methylcytosine in Deinococcus radiodurans.

first: Bifeng

last: Yuan


title: Multiscale profiling of enzyme activity in cancer [Bulk-seq]

status: Public on Dec 20 2021

city: Cambridge

first: Sangeeta

middle: N

last: Bhatia

state: MA

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary:
Purpose: The goal of this study was to use enzyme activity as a proxy for profiling tumor progression and treatment response in an autochthonous mouse model of Alk-mutant non-small-cell lung cancer (NSCLC). The Eml4-Alk model was originally described in Maddalo et al., Nature 2014. This dataset describes bulk RNA-seq profiling of cells from Eml4-Alk lungs following administration of a protease-activatable probe, QZ1, and sorting single cells based on signal from this probe.
Methods: Eml4-Alk mice were anesthetized, and QZ1-(PEG2K) was administered intravenously via tail vein injection. Lungs were excised two hours later, separated into lobes, tumors were microdissected, and single cell suspensions were prepared. FACS sorting was performed on a FACSAria II (BD). Flow cytometry data was analyzed by the FlowJo software (Treestar). At least 100,000 cells from each of the QZ1+ and QZ1- compartments were collected into RPMI-1640 + 2% heat-inactivated FBS and pelleted via centrifugation at 1800 rpm for 5 minutes. Cell pellets were lysed in Trizol (ThermoFisher), and RNA was extracted using RNEasy Mini Kits (Qiagen), and bulk RNA sequencing was performed. Libraries were prepared using the Clontech SMARTer Stranded Total RNAseq Kit (Clontech), precleaned, and sequenced using an Illumina NextSeq500 on an Illumina NextSeq flow cell.
Results: Feature counting was performed on BAM files using the Rsubread package. Differential expression analysis on QZ1+ vs QZ1- cells was performed using the DESeq2 package in R. GSEA was performed using GenePattern, and results were visualized using the clusterProfiler R package.
Conclusions: This study demonstrates a method for activity-based cell sorting that can be coupled to downstream phenotypic characterization via RNA-seq.

overall_design: Bulk RNA-seq profiles of cells from lungs of Eml4-Alk (EA) tumor-bearing mice administered with the protease-activatable probe QZ1. n=4 biological replicates for each of QZ1+ and QZ1- conditions.

first: Ava

middle: P

last: Soleimany

first: Jesse

middle: D

last: Kirkpatrick

first: Cathy

middle: S

first: Alex

first: Susan

last: Su

first: Santiago

last: Naranjo

first: Qian

last: Zhong

first: Christina

last: Cabana

first: Tyler

last: Jacks


title: Dissection of corticotroph transcriptome in a mouse model of glucocorticoid-induced suppression of the HPA axis

status: Public on Jan 03 2022

city: Edinburgh

first: Thomas

middle: James Gray

last: Chambers

address: Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: The effect on the transcriptome of dexamethasone (0.4mg/kg) treatment, and recovery 1 and 4 weeks following withdrawal was examined in corticotrophs FACS isolated from POMC-GFP mice. We show dexamethasone has persistent effects on the corticotroph transcriptome, some lasting up to 4 weeks.

overall_design: Male mice , n = 9 were expsoed to dexamethasone in drinking water for 4 weeks. Animals were collected after cessation of dexamethaonse treatment and 1 and 4 weeks later. A control group of mice received only standard drinking water. Corticotrophs were FACS isolated from pools of 3 pituitaries. Total RNA was extracted for RNA-seq.

first: Nicola

last: Romanò

first: Peter

last: Duncan

first: Heather

last: McClafferty

first: Oscar

last: Nolan

first: Qinghui

last: Ding

first: Natalie

middle: Z

last: Homer

first: Paul

last: Le Tissier

first: Brian

last: Walker

first: Michael

last: Shipston


title: The investigation of OVOL2 regulated gene

status: Public on Dec 07 2021

city: Beijing

first: Lihua

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

summary: To investigate the  OVOL2-regulated gene with MCF7 wild-type and knock-out cells.

overall_design:
OVOL2 knock-out cells MCF7 cells
Breast cancer tissue of 69 aged female


title: FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression [ATAC-seq]

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We used single cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) to generate chromatin accessibility profiles of mouse splenic regulatory T cells from B6 mice.

overall_design: Splenic regulatory T cells (CD4+, TCRβ+, FoxP3-IRES-GFP+) and T conventional cells (CD4+, TCRβ+, FoxP3-IRES-GFP-) were sorted from 6-8 week old B6 FoxP3-IRES-GFP mice into DMEM + 2% FCS, then resuspended in PBS + 0.04% BSA.   Nuclei isolation, transposition, GEM generation, and library construction targeting capture of ~12000 cells (75% Tregs, 25% Tconv) were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics). Libraries were pooled and sequenced on an Illumina NovaSeq to a final median depth of approximately 30,000 reads per cell (~80% saturation).

first: Kaitavjeet

last: Chowdhary

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: A mechanistic framework for cardiometabolic and coronary artery disease

status: Public on Nov 19 2021

first: Simon

last: Koplev

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

department: Cambridge Stem Cell Institute

institute: University of Cambridge

summary: RNA-seq data of livers from mice injected with endocrine candidates identified in the STARNET study

overall_design: Recombinantly expressed endocrine candidates injected at 1 μg/g body weight at regimen of 3 times with 1 day intervals

first: Johan

middle: L

last: Björkegren

first: Marcus

last: Seldin


title: Multiscale profiling of enzyme activity in cancer

first: Sangeeta

last: Bhatia

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

overall_design: Refer to individual Series


title: Multiscale profiling of enzyme activity in cancer [scRNA-seq]

summary:
Purpose: The goal of this study was to use enzyme activity as a proxy for profiling tumor progression and treatment response in an autochthonous mouse model of Alk-mutant non-small-cell lung cancer (NSCLC). The Eml4-Alk model was originally described in Maddalo et al., Nature 2014. Single-cell transcriptomic profiling of the Eml4-Alk NSCLC model was performed for unbiased discovery of the phenotypic landscape of Eml4-Alk and wild type mice.
Methods: Single cell suspensions were prepared from excised lungs of Eml4-Alk and sex- and age-matched healthy, wild type C57/Bl6J mice. Suspensions were pooled from n=3 mice per condition, and then were enriched for cell viability and depleted for CD45+ cells. Single cells were processed using the 10X Genomics Single Cell 3’ platform using the Chromium Single Cell 3’ Library & Gel Bead Kit V2 kit (10X Genomics), per manufacturer’s protocol. Approximately 10,000 cells were loaded onto each channel and partitioned into Gel Beads in Emulsion (GEMs) in the 10x Chromium instrument. Following lysis of the captured cells, the released RNA was barcoded through reverse transcription in individual GEMs, and complementary DNA was generated and amplified. Libraries were constructed using a Single Cell 3’ Library and Gel Bead kit. The libraries were sequenced using an Illumina NovaSeq6000 sequencer on an Illumina NovaSeq SP flow cell.
Results: Gene expression matrices were generated for each sample by the Cell Ranger (v.3.0.2) Pipeline coupled with mouse reference version GRCm38. The output filtered gene expression matrices were analyzed by Python software (v.3.9.0) with the scanpy package (v.1.7.2). For final analysis, genes expressed in at least three cells in the data and cells with > 200 genes detected were selected for further analyses, and low quality cells were removed based on number of total counts and percentage of mitochondrial genes expressed.
Conclusions: This study provides the first (to the best of our knowledge) single-cell RNA-seq dataset of the Eml4-Alk autochthonous model of NSCLC.

overall_design: Lung single-cell RNA profiles of sex- and age-matched wild type (WT) and Eml4-Alk (EA) mice. One sample for each of WT and Eml4-Alk (EA), with each sample representing a pooled sample of n=3 individual mice.

first: Ava

last: Soleimany

first: Jesse

last: Kirkpatrick

first: Cathy

last: Wang

first: Alex

first: Susan

last: Su

first: Santiago

last: Naranjo

first: Qian

last: Zhong

first: Christina

last: Cabana

first: Tyler

last: Jacks


title: scGOF-Seq using ND islets

status: Public on Nov 11 2021

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

institute: University of Arizona

summary: Type 2 diabetes is associated with defective insulin secretion and reduced β-cell mass. Available treatments provide a temporary reprieve, but secondary failure rates are high, making insulin supplementation necessary. Reversibility of b-cell failure is a key translational question. Here, we reverse-engineered and interrogated pancreatic islet-specific regulatory networks to discover T2D-specific subpopulations characterized by metabolic-inflexibility and endocrine-progenitor/stem cell features. Single-cell gain- and loss-of-function and glucose-induced Ca++ flux analyses of top candidate MR in islet cells validated transcription factor BACH2 and associated epigenetic effectors as a key driver of T2D cell states. BACH2 knockout in T2D islets reversed cellular features of the disease, restoring a non-diabetic phenotype. BACH2-immunoreactive islet cells increased ~4-fold in diabetic patients, confirming the algorithmic prediction of clinically relevant subpopulations. Treatment with a BACH inhibitor lowered glycemia and increased plasma insulin levels in diabetic mice, and restored insulin secretion in diabetic mice and human islets. The findings suggest that T2D-specific populations of failing b-cells can be reversed and indicate pathways for pharmacological intervention, including via BACH2 inhibition.

overall_design: Adenovirus encoding candidate TF with its corresponding guide-barcode was infected in human nondiabetic islets which are subjected to scRNA-seq.

first: Jinsook

last: Son

first: Andrea

last: Califano

first: Domenico

last: Accili


title: Genome-wide miCLIP-Seq reveals methylation targets and RNA interactome of human NOP2/NSUN1

status: Public on Nov 15 2021

city: Houston

first: Catherine

last: Denicourt

state: TX

address: 6431 Fannin St

department: Integrative Biology & Pharmacology

institute: The University of Texas HSC Houston

type: Non-coding RNA profiling by high throughput sequencing

summary: 5-Methylcytosine (m5C) is a base modification broadly found on a variety on coding and non-coding RNAs in the human transcriptome. In eukaryotes m5C is catalyzed by enzymes of the NOL1/NOP2/SUN domain (NSUN) family, which is composed of seven members in humans (NSUN1-7). NOP2/NSUN1, a member of this family, has been mostly characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C at position C2870 of the 25S rRNA. Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer for decades, its functions remain poorly characterized. To better define the roles of NOP2/NSUN1 in human cells, we used an adapted genome-wide methylation of individual-nucleotide-resolution crosslinking and immunoprecipitation-sequencing (miCLIP-seq) approach to identify its RNA methylation targets. Our analysis revealed that vault RNA 1.2 (vtRNA1.2) and 28S rRNA are NOP2/NSUN1-specific methylated targets. In addition, NOP2/NSUN1 predominantly binds to rRNA, followed by C/D box snoRNA, and other ncRNAs. Together, our data provided a genome-wide spectrum of NOP2/NSUN1 binding RNA and methylated target RNA for understanding the function of human NOP2/NSUN1.

overall_design: miCLIP-Seq for wildtype NOP2/NSUN1 and C459A mutant NOP2/NSUN1 exogenously expressed in HEK-293T cells. Experiment are done in biological duplicates. Each biological replicate has a IP sample and a control size-matched input (SMInput) sample. Eight samples are included for this experiment.

first: Han

last: Liao

first: Anushri

last: Gaur

first: Hunter

last: McConie

first: Amirtha

last: Shekar

first: Karen

first: Jeffrey

last: Chang

first: Ghislain

last: Breton


title: Single-cell RNA-seq analysis of WT and Furin KO TECs

status: Public on Jan 15 2022

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

summary: To assess the effect of Furin ablation on TEC development and heterogeneity, we detected the transcriptional profiles of 2-week-old WT and Furin KO TECs using single-cell RNA-seq. Employing an unsupervised graph-based clustering strategy, 20 clusters of TECs and 5 clusters of non-TEC contaminants were identified. After removing contaminants, 4301 WT TECs and 4086 Furin KO TECs were obtained. UMAP visualization revealed that the proportion of mTECs decreased significantly and the proportion of cTECs increased significantly in TEC-specific Furin knockout mice in comparison with WT mice. Further analysis showed that Furin ablation did not affect the proportion of mTEC I, II and III subsets, but reduced the proportion of mTEC IV subsets markedly.

overall_design: Compare the transcriptional profiles of 2-week-old WT and Furin KO TECs using single-cell RNA-seq

first: Zhanfeng

last: Liang


title: Systems-wide Analysis Revealed Shared and Unique Responses to Moderate and Acute High Temperatures in the Green Alga Chlamydomonas reinhardtii

city: St. Louis

first: Ru

state: Missouri

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

summary: Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35oC) and acute (40oC) high temperatures and subsequent recovery at 25oC. We identified transcripts/proteins with unique differential regulation at 35oC, uncovering previously overlooked novel elements in response to moderate high temperature. Heat at 35oC increased transcripts/proteins involved in gluconeogensis/glyoxylate-cycle for carbon uptake, promoted growth, and increased starch accumulation. Heat at 40oC inhibited growth, resulting in carbon uptake over usage and increased starch accumulation. Heat at 35oC transiently arrested the cell cycle followed by partial synchronization while 40oC inhibited DNA replication and arrested the cell cycle. Both high temperatures induced photoprotection, while 40oC decreased photosynthetic efficiencies, distorted thylakoid/pyrenoid ultrastructure, and affected the carbon concentrating mechanism. We demonstrated increased transcript/protein correlation during heat, which decreased during recovery, suggesting reduced post-transcriptional regulation during heat may help coordinate heat tolerance activities efficiently. During recovery after both treatments, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops.

overall_design: Transcriptomic time-course analysis of wild-type Chlamydomonas reinhardtii cells exposed to 24-hours of moderate (35C) or acute (40C) high temperature, followed by a 48-hour recovery at 25C.

first: Ningning

first: Erin

last: Mattoon

first: Will

last: MicHargue

first: Benedikt

last: Venn

first: David

last: Zimmer

first: Kresti

last: Pecani

first: Jooyeon

last: Jeong

first: Cheyenne

last: Anderson

first: Chen

last: Chen

last: Berry

first: Ming

last: Xia

first: Shin-Cheng

last: Tzeng

first: Eric

last: Becker

first: Leila

last: Pazouki

first: Bradley

last: Evans

first: Fred

last: Cross

first: Jianlin

last: Cheng

first: Kirk

middle: J

last: Czymmek

first: Michael

last: Schroda

first: Timo

last: Mühlhaus


title: RNA-Seq analysis of Wild Type and lrpap1-/- zebrafish eyes at three month

status: Public on Nov 02 2021

first: Jiali

last: Li

address: 253 Gongye Middle Avenue

institute: Zhujiang Hosptial

summary: Zebrafish is a good model organism for studying eye diseases, but there is a lack of transcriptome information, especially as it related to myopia. The aim of this study was to compare transcriptome differences between lrpap1-/- mutant and wild-type zebrafish eyeballs. Eye tissue mRNA profiles of three-month-old wild-type (WT) and low-density lipoprotein receptor-related protein-associated protein 1 knockout (lrpap1-/-) zebrafishes were generated by deep sequencing using Illumina HiSeq2500. RNA-seq reads were aligned to the zebrafish genome(Ensembl, GRCz11) using HISAT2, TPM was used to further normalize gene expression counts between all samples. Differentially expressed genes (DEG) were determined by DESeq2, which was based on the Negative Binomial Generalize Linear Model. Finally, there are 1661 differentially expressed genes between the mutant and the wild-type zebrafish eyeballs using the criterion of p-value <0.05 and ׀Log (Fold Change)|>1 ,among which 1209 genes are up-regulated, and 452 genes are down-regulated in the mutants. Our study shows the first detailed analysis of zebrafish eyes transcriptomes by RNA-seq technology. The transcriptome information provided in this study may help to reveal the molecular mechanism of genetic myopia.

overall_design: mRNA profiles of three-month-old wild type (WT) and lrpap1-/- zebrafish eyes.

first: Shanshan

last: Liu

first: Ting


title: Next Generation Sequencing to study Thalidomide mechanism in Cutaneous Lupus

city: Barcelona

first: Cristina

last: Sole Marce

address: Pg Vall Hebron 119-129

country: Spain

institute: Vall Hebron Institute Research

summary:
Thalidomide has been shown to be effective in patients with refractory cutaneous lupus erythematosus (CLE). However, its use is still limited by its potential severe side-effects. We conducted an RNA-sequencing study using CLE skin biopsies before and after thalidomide treatment to discover its mechanism of action.
Methods: Total mRNA from skin biopsies from 10 CLE patient have been processed by RNA-seq in duplicate using Illumina Hiseq 2000 sequencing platform version 3. Application was stranded mRNA-Seq, paired-end and read length was 75bp.  The sequence reads that passed quality filters were analyzed at the transcript isoform level using STAR program, RSEM program and DESeq2. Mapping was done with STAR (version 2.5.2a), quantification by RSEM (1.2.28) and differential analysis by DESeq.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to human genome (hs37d5). Average un-mapped was between 11,40-7,05 %, average unique was 80.48-76,62% and average alignment insert size was 170,00-155,00 in the 20 samples.
Conclusions: Plausibles mechanisms of action for thalidomide in lupus cutaneous were discovered using this study; however, in vitro and in vivo experiments would be performed to demostrate them.

overall_design: Total skin mRNA profiles pre and post-treatment of thalidomide (3weeks between them).

first: Cortés-Hernández

last: Josefina

first: Solé

last: Cristina


title: Circulating microRNA signatures that predict liver fibrosis progression in HIV-1/HCV co-infected patients

status: Public on Nov 08 2021

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: The lack of available biomarkers to diagnose and predict different stages of liver disease with a non-invasive strategy is currently one of the main challenges that clinicians are facing. Recent evidence indicates that the plasma levels of specific microRNAs (miRNAs) may be significantly altered in patients with liver injury, including human immunodeficiency virus type 1 (HIV-1) infected patients. Large-scale deep sequencing analysis of small RNA expression was performed on plasma samples from 46 HIV-1/hepatitis C virus (HCV) co-infected patients that did not exhibit liver fibrosis at the time of sampling. A total of 1065 different miRNAs were identified. After a mean of 10.3 years, 26 of the former patients developed liver fibrosis (stage F2-4) and 20 remained without signs of liver fibrosis (stage F0-1). We identified a signature of seven miRNAs, 100-5p, 192-5p, 99a-5p, 122-5p, 125b-2-3p, 1246 and 194-5p, that highly correlated with patients progressing to liver fibrosis. These seven miRNAs detected liver fibrosis progression with an area under curve (AUC) of 0.910-0.806. The two miRNAs, 100-5p and 192-5p, displaying the best AUC values, yielded both a sensitivity of 88% and a specificity of 85% for liver fibrosis progression. Our results demonstrate the predictive potential of circulating levels of miRNAs to foresee liver fibrosis progression even before liver fibrosis or significant clinical differences such as liver transaminases or platelets are detectable. Thus, our study might help in predicting the progression of liver injury in HIV-1-infected patients.

overall_design: In total 67 plasma derived small RNA samples were analyzed: 21 from healthy reference and 46 from virally co-infected individuals with different liver fibrosis progression status. There were two patient groups based on fibrotic progression levels among co-infected individuals:  20 non-progressors and 26 progressors. Differential miRNA expression was assesed between the different groups under study. All samples were controlled for hemolysis using a qPCR based test taking only samples with miR-451/miR-23a ratios with ΔCt<7 (range −0.04 to 6.3; average 3.53). Design efforts were made to randomize all subgroups to be equally represented in the library preparation and size selection steps to be able to correct for possible batch effects.  Size selection was performed in pools of 24 libraries, and 3 sets of 2 library pools were merged into 3 superpools of 48 samples each for Illumina sequencing. The experiment was performed in the context of a larger sample set including a total of 144 samples (a subset described in a previous study by Franco et al, Antiviral Res 2018 Jul;155:106-114. PMID: 29807039, GEO GSE141522 which included the same healthy control samples).The final results of this work are from a different subsetusing a different analysis pipeline.

first: Sandra

last: Franco

first: Daniela

last: Buccione

last: Tural

first: Miguel

middle: A

last: Martinez


title: DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and plant development

status: Public on Jan 16 2022

city: Shanghai

first: Li

last: He

address: No. 3888 Chenhua Road

department: Shanghai Center for Plant Stress Biology

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS)

summary: A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, the relevance of this epigenetic mark for genome-wide gene regulation and plant development is unclear. Here, we knocked out all five known DNA methyltransferases in Arabidopsis, generating DNA methylation-free plants. This quintuple mutant exhibits a suite of unique and extreme developmental defects, unequivocally demonstrating that DNA methylation is essential for normal plant development. We show that CG methylation or non-CG methylation alone or jointly control multiple biological processes, including pavement cell shape, endoreduplication, cell death, flowering, trichome morphology, vasculature and meristem development, and root cell fate determination. Moreover, we found that DNA methylation has a strong dose-dependent effect in the regulation of gene expression and the repression of transposable element movement. Thus, our results demonstrate crucial roles of DNA methylation in orchestrating plant development and provide new insights into the function of this epigenetic mark in regulating gene expression in higher eukaryotes.

overall_design: We performed strand-specific RNA sequencing, whole-genome bisulfite sequencing, and DNA sequencing

first: Huan

last: Huang

first: Jian-Kang

last: Zhu


title: High throughput sequencing of Vero, A549, CaCO2, and HRT18 cells infected with SARS-CoV2

status: Public on Dec 09 2021

city: Cheongju

first: Jiyeong

last: Noh

address: Chungdae-ro 1

country: South Korea

institute: Chungbuk National University

summary:
Purpose: The goals of this study are to monitor the evolution pattern of SARS-CoV2 in depending host cells by viral transcriptome sequencing analysis of Vero, A549, Caco2, and HRT18 cells infected with SARS-CoV2.
Methods: SARS-CoV-2 isolate was passaged 4 time on Vero cells  and used to extract RNA for the high-throughput sequencing.  The 8×104 PFU of SARS-CoV2 stocks passaged on vero cells were inoculated to the monolayer of A549, CaCO2, and HRT-18 cell lines in 75T flask  for 1hour at 37℃ in a 5% CO2 incubator with gentle shaking of 15 minutes interval.  After that, the infected cells were washed two times with DPBS and incubated with the fresh maintenance medium for 3 days.  The virus inoculation was performed in triplicate for each cell lines.  In case of the first passage, the infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing.  The cultured cell supernatant of the virus-infected A549, CaCO2, and HRT18 cells was centrifuged at 3,000g for 10min to use for the next passage, and stored at -80℃.  The serial passage of SARS-CoV-2 on A549, CaCO2, and HRT18 cell lines were continued to passage 12 and the cultured cell supernatant of the infected cells in passage 12 was centrifuged at 3,000g for 10 min, and used to extract RNA for the high-throughput sequencing. The RNA samples were sequenced with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing. The raw reads were trimmed with BBDuk and mapped the isolate SARS-CoV-2/human/KOR/KCDC03-NCCP43326/2020 (Genebank accession number. MW466791) with Bowtie 2 using Geneious program 2021.2.2
Result: Using SNP analysis workflow, our result showed the sequence variations pattern of SARS-CoV2 depending on host cell (A549, CaCO2, and HRT18 cell lines) and it was confirmed that a relatively large number of SNPs were commonly observed in spike protein. Some SNPs affect amino acid changes, and a common pattern of amino acid changes was observed the genomic sequence of SARS-CoV2 passaged  in A549, CaCO2 and HRT18 cells.
Conclusion: In this study, we tried to monitor the SARS-CoV-2 (GenBank accession No. MW466791 in 2020, Korea) evolution pattern in different host cells using high throughput sequencing analysis, and compare the selected mutations by each host cells with natural mutations found in currently circulating SARS-CoV-2 variants.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: Monitor of mutation pattern of SARS-CoV2 transcript depending on host cells by high throghput sequencing analysis

first: Hoyin

last: Chung

first: Bon-Sang

last: Koo

first: Jungjoo

last: Hong

first: Hye Kwon

last: Kim


title: Growth-limiting drought stress induces time-of-day dependent transcriptome and physiological responses in hybrid poplar

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

institute: University of Manitoba

summary: Episodic drought stress negatively impacts the health of long-lived trees. Understanding the genetic and molecular mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. Here we aim to establish standardized drought stress protocols for transcriptome studies in poplar trees, to determine how hybrid poplars respond to prolonged and uniform exposure to drought; to determine if the responses to moderate and more severe growth-limiting drought stresses were qualitatively or quantitatively different; and, to determine how response to drought changes throughout the day. We established hybrid poplar trees (Populus x ’Okanese’) from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish three soil water contents reflecting well-watered, moderate, and severe growth-limiting drought conditions. Plants were rewatered as needed for three weeks to maintain the soil water conditions. The mild and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates and global transcriptomic changes. Notably, the time of day of sampling was strongest signal in the transcriptome data and it quantitatively and qualitatively affected drought responsive changes in gene expression. These analyses emphasize the complex nature of drought regulation in long-lived trees.

overall_design: Examination of 3 water deficit treatments of Okanese poplar seedling leaves at 2 times of day; includes 18 samples: 3 replicates each of 3 treatments at 2 timepoints

first: Sean

last: Robertson

first: Solihu

middle: K

last: Sakariyahu

first: Ayooluwa

last: Bolaji

first: Mark

middle: F

last: Belmonte


title: Chronic adolescent exposure to Δ-9-tetrahydrocannabinol in mice leads to long-term changes in gene expression networks in the brain

status: Public on Dec 06 2021

city: La Jolla

first: Hai-Ri

last: Li

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary:
Background: Adolescent cannabis use leads to long-lasting behavioral changes involving cognitive and reward processes. However, the underlying molecular mechanisms are not well understood. To address this limitation, we performed gene network analyses using transcriptomic data from mice exposed during adolescence to Δ-9-tetrahydrocannabinol (THC), the major psychoactive component of cannabis.
Methods: We injected vehicle or THC in female and male mice during the entire adolescence period. Two weeks following the last exposure, we measured recognition memory, social interaction and anxiety-related behaviors. We generated 120 RNA-seq datasets from 5 brain regions for each mouse. We performed differential gene expression analysis and constructed co-expression networks to identify THC-induced transcriptional alterations at the level of individual genes, gene networks, biological pathways, and cellular specificity. Further, we integrated THC-correlated gene networks with human traits from genome-wide association studies and performed key driver analysis to identify potential regulators of disorder-associated networks.
Results: THC impaired cognitive behaviors of mice, with memory being more impacted in females, which coincided with larger transcriptional alterations in the female brain. Gene network analyses identified brain region-, cell type- and sex- specific co-expressed genes (“modules”) dysregulated by THC. THC-induced memory deficits in females were correlated with disruption of gene networks involved in endocannabinoid signaling and inflammation. Additional THC-correlated modules in both sexes involved converging pathways related to dopamine signaling and addiction processes. Moreover, the connectivity map of THC-correlated modules uncovered intra- and inter-region molecular circuitries influenced by THC. Further, modules altered by THC treatment were enriched in genes relevant for human cognition and schizophrenia.
Conclusions: These findings provide novel insights concerning the genes, cell types, and pathways underlying persistent behavioral deficits induced by adolescent exposure to THC in a sex-specific manner, and highlight the connection between adolescent cannabis use and neuropsychiatric disorders in humans.

overall_design: mRNA profiles of mice 2 weeks after adolescent chronic THC administration or vehicle in the amygdala, nucleus accumbens, prefrontal cortex, dorsolateral striatum and ventral tegmental area.

first: Francesca

last: Telese

first: Xia

last: Yang

first: Yanning

last: Zuo

first: Attilio

last: Iemolo

first: Hairi

first: Patricia

last: Montilla-Perez


title: Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index

first: Harry

last: MacKay

address: 1100 Bates Ave

institute: Baylor College of Medicine

summary: Developmental epigenetic study of DNA methylation in arcuate nucleus neurons and glia.

overall_design: Genome-wide bisulfite-seq and RNA-seq in FANS-sorted neural (NeuN+) and glial (NeuN-) nuclei from the mouse arcuate nucleus of the hypothalamus at postnatal days 12 and 35

first: Chathura

last: Gunasekara

first: Hari

last: Yalamanchili

first: Kit-Yi

last: Yam

first: Dollada

last: Srisai

first: Yumei

first: Rui

last: Chen

first: Cristian

last: Coarfa

first: Robert

last: Waterland


title: The transcriptome data of didymin against acute hepatic injury

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the protective mechanisms of didymin on acute liver injury,mice were intragastrically administrated with the equal volume of saline or didymin once per day for two weeks.after that,except the normal group, mice were injected with LPS (50 μg/kg) and D-Gal (800 mg/kg) intraperitoneally to induce ALI; Finally, the transcriptomic analysis was performed to acquire the differently expressed genes amog these groups, trying to figure out the potential targets, which regulated by didymin.

overall_design: the mice were randomly divided into several groups: the Bifendate treatment group,the model group and didymin-treated groups injected with LPS (50 μg/kg) and D-Gal (800 mg/kg) to induce ALI, followed by various agents.

first: Lijun

last: Pang

first: Zhongwen

last: Feng

first: Yushen

last: Huang

first: Wuchang

last: Zhu


title: Perturb-Seq using T2D islets

first: Hongxu

last: Ding

overall_design: Adenovirus encoding CAS9_gRNAs targetting candidate TF with its corresponding DNA guide-barcode was infected in human T2D islets which are subjected to scRNA-seq.

first: Jinsook

last: Son

first: Andrea

last: Califano

first: Domenico

last: Accili


title: Comparative chemical-genomic profiling of plant-based hydrolysate toxins enables predictive assessment of responses to complex mixtures

status: Public on Nov 01 2021

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Many toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation, requiring mitigation strategies including strain engineering. To identify mechanisms of toxicity and targets for genetic engineering, we used a chemical genomics approach with a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates, to explore shared and divergent gene requirements across inhibitors. Relationships in chemical-genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions are beneficial for surviving some toxins but detrimental for others.  As a proof of principle, we used the gene-deletion responses to single inhibitors to successfully predict strains whose fitness was improved in complex inhibitor mixes found in synthetic hydrolysates. We discuss the implications for strain engineering and the potential of this rich dataset for identifying engineering targets.

overall_design: We conducted a chemical genomics experiment using a barcode-sequencing approach with a gene-deletion library of S. cerevisiae under anaerobic conditions, and quantified knockout strains growth, in triplicates, in cultures without (control) and with each of 45 inhibitory chemicals individually, including solvents used in pre-treatment, toxins generated during hydrolysis of plant material, and biofuel products that are stressful to cells at high levels.

first: Trey

last: Sato

first: Michael

last: Place

first: Lisa

last: Liu

first: Derek

last: Debrauske

first: Megan

last: Young

first: Kaitlin

last: Fisher

first: Chris

last: Hittinger

first: Elena

last: Vanacloig-Pedros


title: mRNA sequencing of mouse melanoma xenografts with micro-domain sAC expression

status: Public on Oct 11 2021

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Transcriptome sequencing of mouse melanoma xenografts containing micro-domain localized sAC under control of doxycycline.

overall_design: Replicate experiments of murine melanoma xenografts controlling for doxycycline induced expression of sAC in nuclear, cytoplasmic, or mitochondrial micro-domains.


title: Longitudinal RNA sequencing of skin and DRG neurons in mice with paclitaxel-induced peripheral neuropathy

status: Public on Oct 12 2021

city: Coral Gables

first: Sandra

last: Rieger

address: 5151 San Amaro Drive

department: Biology

institute: University of Miami

summary: Paclitaxel-induced peripheral neuropathy is a significant problem, which afflicts up to 70% of chemotherapy patients. Therapeutic interventions are currently unavailable due to an incomplete understanding of the underlying mechanisms. We previously discovered a major target in the skin, MMP-13, which underlies the development of paclitaxel-induced peripheral neuropathy in zebrafish and rodents. To better understand gene expression changes in sensory neurons and target tissue prior to and during the progression of neuropathy, we performed longitudinal RNA sequencing of mouse skin and dorsal root ganglion (DRG) neurons. Samples were harvested at time points associated with behavioural responses following injection of mice for 7 days either with vehicle or paclitaxel. The responses were categorized into pain onset (day 4 of paclitaxel injection), maxima (d7), beginning of pain resolution (d11) and recovery phase (d23). This dataset will be useful to understand changes in gene regulation in both neurons and skin, which can aid in the discovery of therapeutic interventions.

overall_design: Paclitaxel or vehicle was administered on days 0, 2, 4 & 6 and samples were isolated from 4 mice at each of 4 different timepoints corresponding to pain onset, peak response, pain resolution, and recovery. [n = 16 per treatment]

first: Anthony

last: Cirrincione

first: Cassandra

last: Thorburn

first: Benjamin

last: Harrison


title: mRNA sequencing of mouse melanoma cells  with micro-domain sAC expression

summary: Transcriptome sequencing of mouse melanoma cell lines containing micro-domain localized sAC under control of doxycycline.

overall_design: Replicate experiments controlling for doxycycline induced expression of sAC in nuclear, cytoplasmic, or mitochondrial micro-domains.


title: The effect of 5-ASA on colitis-associated carcinogenesis

status: Public on Oct 10 2021

city: Philadelphia

first: Mariana

last: Franco Fragoso

state: PA

address: 333 Cottman Avenue

department: Cancer Prevention and Control

institute: Fox Chase Cancer Center

summary:
The impact of the antiinflammatory agent 5-aminosalicylic acid (5-ASA) on the risk for colitis-associated colorectal cancer remains controversial. The chemopreventive activity of 5-ASA was evaluated in the Swiss Webster model of azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced colitis-associated neoplasia. Mice were injected with AOM (7.4 mg/kg i.p.) and randomized to receive either vehicle or 5-ASA (75mg/kg) for the remainder of the study.
DSS treatment began at 9 weeks of age and continued for 3 cycles. At the time of sacrifice (18 weeks of age), the entire colon and rectum were processed for histopathologic examination and microarray profiling. For information regarding the histopathological analysis, refer to Clapper ML, Gary MA, Coudry RA, Litwin S, Chang WC, Devarajan K, Lubet RA, Cooper HS. 5-aminosalicylic acid inhibits colitis-associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium-induced colitis. Inflamm Bowel Dis. 2008 Oct;14(10):1341-7. doi: 10.1002/ibd.20489. PMID: 18452197.

overall_design: Mice were injected with AOM (7.4 mg/kg i.p.) and randomized to receive either vehicle or 5-ASA (75 mg/kg) for the remainder of the study. DSS treatment began at 9 weeks of age and continued for 3 cycles. At the time of sacrifice (18 weeks of age), the entire colon and rectum were processed for histopathologic examination.

last: Fragoso

first: Geysson

last: Fernandez

last: Vanderveer

first: Harry

last: Cooper

last: Slifker

first: Margie

last: Clapper


title: miRNA profiling of colitis-associated dysplasia in animals submitted to the AOM/DSS model

status: Public on Oct 09 2021

summary:
The impact of the antiinflammatory agent 5-aminosalicylic acid (5-ASA) on the risk for colitis-associated colorectal cancer remains controversial. The chemopreventive activity of 5-ASA was evaluated in the Swiss Webster model of azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced colitis-associated neoplasia. Mice were injected with AOM (7.4 mg/kg i.p.) and randomized to receive either vehicle or 5-ASA (75mg/kg) for the remainder of the study. Only untreated animals were used in this array.
DSS treatment began at 9 weeks of age and continued for 3 cycles. At the time of sacrifice (18 weeks of age), the entire colon and rectum were processed for histopathologic examination and microarray profiling. For information regarding the histopathological analysis, refer to Clapper ML, Gary MA, Coudry RA, Litwin S, Chang WC, Devarajan K, Lubet RA, Cooper HS. 5-aminosalicylic acid inhibits colitis-associated colorectal dysplasias in the mouse model of azoxymethane/dextran sulfate sodium-induced colitis. Inflamm Bowel Dis. 2008 Oct;14(10):1341-7. doi: 10.1002/ibd.20489. PMID: 18452197.


title: ATAC-seq for human dermal fibroblasts (HDF) after vemurafenib or DMSO treatment

status: Public on Dec 11 2021

city: Freiburg

first: Eyleen

last: Corrales

address: Breisacherstr. 153

department: Medizinische Fakultät

country: Germany

institute: Institut für Medizinische Bioinformatik und Systemmedizin

summary:
Background: Vemurafenib (PLX4032) is one of the most frequently used treatments for late-stage melanoma patients with the BRAFV600E mutation; however, acquired resistance to the drug remains as a major challenge. It remains to be determined whether off-target effects of the vemurafenib on normal stroma components could reshape the tumor microenvironment in a way that contributes to cancer progression and drug resistance.
Methods: By using temporary-resolved RNA- and ATAC-seq, we studied the early molecular changes induced by vemurafenib in human dermal fibroblast (HDF), a main stromal component in melanoma and other tumors with high prevalence of BRAFV600 mutations.
Results: Transcriptomics analyses revealed a stepwise up-regulation of proliferation signatures, together with a down-regulation of autophagy and proteolytic processes. The gene expression changes in HDF strongly correlated in an inverse way with those in BRAFV600E mutant malignant melanoma (MaMel) cell lines, consistent with the observation of a paradoxical effect of vemurafenib, leading to hyperphosphorylation of MEK1/2 and ERK1/2. The transcriptional changes in HDF were not strongly determined by alterations in chromatin accessibility; rather, an already permissive chromatin landscape seemed to facilitate the early accessibility to MAPK/ERK-regulated transcription factor binding sites. Combinatorial treatment with the MEK inhibitor trametinib did not preclude the paradoxical activation of MAPK/ERK signaling in HDF. When administered together, vemurafenib partially compensated the reduction in cell viability and proliferation induced by trametinib. These paradoxical changes were restrained by using the third generation BRAF inhibitor PLX8394, a so-called paradox breaker compound. However, the advantageous effects on HDF during combination therapies were also lost.
Conclusion: Vemurafenib induces paradoxical changes on HDF, which are allowed by a permissive chromatin landscape. These changes might provide an advantage during combination therapies, by compensating the toxicity induced in stromal cells by less specific MAPK/ERK inhibitors. Our results highlight the relevance of evaluating the effects of the drugs on non-transformed stromal components, carefully considering the implications of their administration either as mono- or combination therapies.

overall_design:
Human dermal fibroblasts (HDF) and patient derived malignant melanoma cell lines (MaMel) treated  with vemurafenib, or an analog volume of vehicle (DMSO) for different durations.
Please note that each processed data file was generated from both replicates and is linked to the corresponding *rep1 records.

first: Patrick

last: Metzger

first: Melanie

last: Boerries


title: A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation

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

overall_design: Refer to individual Series


title: Gene expression in human corneal epithelial cells (hCECs) with different post-mortem intervals and cultivated in monoculture or used for human tissue‐engineered corneas (hTECs)

status: Public on Oct 08 2021

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

institute: CUO-Recherche

summary:
In this study, we evaluated the effects of the post-mortem interval, defined as the number of days elapsed between the death of a donor and the isolation of hCECs, on the properties of hCECs.
Using gene profiling, we compared the mRNA profiles of passage 1 hCECs (10 populations) cultivated in moculture with different post-mortem intervals and passage 2 hCECs (6 populations) with different post-mortem intervals from hTECs.

overall_design: Ten hCECs populations (passage 1) with different post-mortem intervals cultivated in monoculutre and six hCECs populations (passage 2) with different post-mortem intervals from hTECs are analyzed by gene profiling

first: Pascale

last: Desjardins

first: Christelle

last: Gross

first: Sergio

last: Cortez Ghio

first: Camille

last: Couture

first: Lucie

last: Germain

first: Sylvain

last: Guérin