title: Emergence of a high-plasticity cell state during lung cancer evolution, single-cell RNAseq

status: Public on Jul 24 2020

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

summary: Tumor evolution from a single cell into a malignant, heterogeneous tissue remains poorly understood. Here, we profiled single-cell transcriptomes of genetically engineered mouse lung tumors at seven stages, from atypical adenomatous hyperplasia to adenocarcinoma. The diversity of transcriptional states increased over time and was reproducible across tumors and mice. Cancer cells progressively adopted alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). Accordingly, HPCS cells prospectively isolated from mouse tumors and human patient-derived xenografts displayed high capacity for differentiation and proliferation. The HPCS program was associated with poor survival across human cancers and demonstrated chemoresistance in mice. Our study reveals a central principle underpinning intra-tumoral heterogeneity and motivates therapeutic targeting of the HPCS.

overall_design: Single-cell RNAseq by 10x of advanced (30week) mouse lung tumors, comparing response to cisplatin at 72h of treatment.

first: Nemanja

last: Marjanovic

first: Jason

last: Chan

first: David

last: Canner

first: Katherine

last: Wu

first: Marianna

last: Trakala

first: Griffin

last: Hartmann

first: Olivia

last: Smith

first: Jonathan

last: Kim

first: Kelly

middle: V

last: Evans

first: Anna

last: Hudson

first: Orr

last: Ashenberg

first: Caroline

middle: B

last: Porter

first: Alborz

last: Bejnood

first: Ayshwarya

last: Subramanian

first: Kenneth

last: Pitter

first: Yan

last: Yan

first: Toni

last: Delroy

first: Devan

middle: R

last: Phillips

first: Nisargbhai

last: Shah

first: Ojasvi

last: Chaudhary

first: Alexander

last: Tsankov

first: Travis

last: Hollmann

first: Natasha

last: Rekhtman

last: Massion

first: John

last: Poirier

first: Linas

last: Mazutis

first: Ruifang

last: Li

first: JooHyeon

last: Lee

first: Angelika

last: Amon

first: Charles

last: Rudin

first: Tyler

last: Jacks

first: Aviv

last: Regev

first: Tuomas

last: Tammela


title: Emergence of a high-plasticity cell state during lung cancer evolution, single-cell RNAseq tigit

city: Jerusalem

first: Matan

last: Hofree

country: Israel

type: Expression profiling by high throughput sequencing

overall_design: Single-cell RNAseq by 10x of mouse lung tumors and orthotropic allotransplant tumros, sorted for expression of Tigit.

first: Nemanja

middle: D

last: Marjanovic

first: Jason

middle: E

last: Chan

first: David

last: Canner

first: Katherine

last: Wu

first: Marianna

last: Trakala

first: Griffin

middle: G

last: Hartmann

first: Olivia

last: Smith

first: Jonathan

last: Kim

first: Kelly

last: Evans

first: Anna

last: Hudson

first: Orr

last: Ashenberg

first: Caroline

last: Porter

first: Alborz

last: Bejnood

first: Ayshwarya

last: Subramanian

first: Kenneth

last: Pitter

first: Yan

last: Yan

last: Delroy

first: Pierre

middle: P

middle: T

middle: M


title: Defective axon guidance links H3K4 deregulation to neurodevelopment disorder

status: Public on Jul 27 2020

city: København

first: Steffen

last: Abay-Nørgaard

state: København

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA sequencing (mRNAs) of N2 and two set-2 mutant  set-2(tm1630) and set-2(zr2012) during mid-embryogenesis

overall_design: Examination of the effect on the transcriptional landscape when removing set-2 a H3K4 methyltransferase. Three samples pr. genotype.  Sample name with prefix 2 was run in a seperate experiment

first: Lisa

last: Salcini

last: Noergaard


title: AutoRELACS: Automated Generation And Analysis of Ultra-parallel ChIP-seq

status: Public on Jul 28 2020

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We present AutoRELACS, an automated implementation of the RELACS protocol using the Biomek i7 automated workstation (Beckman&Coulter). We test the performance of AutoRELACS by assessing 1) the scalability of the chromatin barcode integration step, 2) the quality of the generated data in comparison to the benchmark set by the manual protocol, and 3) the sensitivity of the automated method when working with low (≤ 25.000 cells/sample) and very low (≤ 5.000 cells/sample) cell numbers.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: 1) First, we test the effciency of automated barcode integration. We barcode 60 batches of S2 cells and we sequence only the input chromatin. 2) To test the overall quality of AutoRELACS in comparison to the manual protocol, we barcode the chromatin of 28 batches of S2 cells using custom RELACS adaptors and we pool them together using Biomek i7 automated workstation. The chromatin is used to generate genome-wide profiles for H3K4me3, H3K27ac and H3K27me3. 3) To test the sensitivity of the automated RELACS protocol, we profile the same three histone marks using 4 batches of HepG2 cells. We distribute the barcoded cells into two poolings. The Low pool contained a total of 300,000 cells, while the Very Low pool contained a total of 60,000 cells (see Fig 3a of publication for details).

first: Laura

last: Arrigoni

first: Francesco

last: Ferrari

first: Juliane

last: Weller

first: Chiara

last: Bella

first: Ulrike

last: Boenish


title: Transcriptome of E. coli during Long-Term Stationary Phase

city: Carson

first: Karin

middle: E.

last: Kram

state: California

address: 1000 E. Victoria St.

department: Biology

country: USA

institute: California State University Dominguez Hills

summary: Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we begin to unravel the cells’ responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program, and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold-shock. By competing cells missing these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment, and lead to identification of novel functions of proteins.

overall_design: Analysis of 3 replicates of the transcriptome of E. coli at 6 time points throughout the life cycle. Post inoculation: 4 hours (log phase), 8 hours (late-log phase), 24 hours (stationary phase), 72 hours (death phase), 144 hours (long-term stationary phase), 192 hours (long-term stationary phase)

first: Autumn

middle: L

last: Henderson

first: Steven

last: Finkel


title: Emergence of a high-plasticity cell state during lung cancer evolution, ATACseq

first: Matan

last: Hofree

overall_design: Bulk ATACseq of mouse lung tumor cells sorted by expression of Tigit.

first: Nemanja

last: Marjanovic

first: Jason

last: Chan

first: David

last: Canner

first: Katherine

last: Wu

first: Marianna

last: Trakala

first: Griffin

last: Hartmann

first: Olivia

last: Smith

first: Jonathan

last: Kim

first: Kelly

last: Evans

first: Anna

last: Hudson

first: Orr

last: Ashenberg

first: Caroline

last: Porter

last: Bejnood

first: Toni

first: Devan

last: Phillips

first: Nisargbhai

last: Shah

first: Ojasvi

last: Chaudhary

first: Alexander

last: Tsankov

first: Travis

last: Hollmann

first: Natasha

last: Rekhtman

last: Massion

first: John

last: Poirier

first: Linas

last: Mazutis

first: Ruifang

last: Li

first: JooHyeon

last: Lee

first: Angelika

last: Amon

first: Charles

last: Rudin

first: Tyler

last: Jacks

first: Aviv

last: Regev

first: Tuomas

last: Tammela


title: Response of cv. Rywal, and two transgenic lines NahG-Rywal and shRBOHD to PVYN-Wilga infection

city: Ljubljana

first: Maja

last: Križnik

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: RNA-Seq of mock and PVYN-Wilga inoculated samples to study the transcriptional response of potato to viral infection in the cell death zone (pool A) and surrounding tissue (pool B) in different genetic backgrounds. Potato cv. Rywal reacts to the virus by hypersensitive response (HR), where spot necroses that limit the virus at the site of virus entry are formed. NahG-Rywal plants, compromised in salicylic acid accumulation, develop necrotic lesions that do not limit viral spread and show delayed defense response. shRBOHD plant with silenced RBOHD gene are not able to arrest the virus spread.

overall_design: For RNA-seq, early visible lesions were sampled from PVYN-Wilga-inoculated leaves of Rywal, NahG-Rywal and shRBOHD-Rywal plants. 30 tissue sections of the lesion (A) and its immediate surrounding (B) were collected and pooled separately (pool A, pool B). For mock (control samples), cca 300 leaf sections were pooled together. Samples were collected from second bottom inoculated leaves from three plants (three biological replicates).

first: Tjaša

last: Lukan

first: Maruša

last: Pompe-Novak

first: Špela

last: Baebler


title: Emergence of a high-plasticity cell state during lung cancer evolution, single-cell ATACseq

first: Matan

last: Hofree

overall_design: Single cell ATACseq by 10x of mouse lung tumor cells sorted by expression of Tigit.

first: Nemanja

last: Marjanovic

first: Jason

last: Chan

first: David

last: Canner

first: Katherine

last: Wu

first: Marianna

last: Trakala

first: Griffin

last: Hartmann

first: Olivia

last: Smith

first: Jonathan

last: Kim

first: Kelly

last: Evans

first: Anna

last: Hudson

first: Orr

last: Ashenberg

first: Caroline

last: Porter

first: Alborz

last: Bejnood

first: Ayshwarya

last: Subramanian

first: Kenneth

last: Pitter

first: Yan

last: Yan

first: Toni

last: Delroy

first: Devan

last: Phillips

first: Nisargbhai

last: Shah

first: Ojasvi

last: Chaudhary

last: Tsankov

first: Pierre


title: Near-infrared-emitting nanoparticles activate collagen synthesis via TGFβ signaling

status: Public on Jul 25 2020

city: SEONGNAM

first: JAEHWI

last: SONG

address: SEONGNAM-DAERO 1342

department: LIFE SCIENCE

country: South Korea

institute: GACHON UNIVERSITY

summary: We describe the novel synthesis Ag2S nanoparticles (NPs) by using a sonochemical method and reveal the effects of NIR irradiation on the enhancement of the production of collagen through NIR-emitting Ag2S NPs. We also synthesized Li-doped Ag2S NPs that exhibited significantly increased emission intensity because of their enhanced absorption ability in the UV - NIR region.

overall_design: Examination of 2 different type nanoparticles in human keratinocyte cells


title: Emergence of a high-plasticity cell state during lung cancer evolution, single-cell DNA

first: Matan

last: Hofree

overall_design: Single-cell DNA of mouse lung tumor cells. Cells from the same tumors also underwent single-cell RNAseq by SmartSeq2 (included in GSE154989).

first: Nemanja

last: Marjanovic

first: Jason

last: Chan

first: David

last: Canner

first: Katherine

last: Wu

first: Marianna

last: Trakala

first: Griffin

last: Hartmann

first: Alexander

first: Travis

last: Hollmann

first: Natasha

last: Rekhtman

last: Massion

first: John

last: Poirier

first: Linas

last: Mazutis

first: Ruifang

last: Li

first: JooHyeon

last: Lee

first: Angelika

last: Amon

first: Charles

last: Rudin

first: Tyler

last: Jacks

first: Aviv

last: Regev

first: Tuomas

last: Tammela


title: Microarray analysis of salivary gland CD4+ T cells

city: Oklahoma City

first: A. Darise

last: Farris

state: OK

address: 825 NE 13th Street, MS 24

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

summary: Whole human genome arrays were used to assess the transcriptome differences in CD3+CD4+CD45RA- memory T cells isolated and sorted from minor salivary gland biopsy tissue of individuals who met 2002 American European Consensus Group classification criteria for primary Sjogren’s syndrome (SS) and subjects who did not meet criteria for SS, lacked focal lymphocytic sialoadenitis, lacked anti-Ro antibodies, lacked anti-La antibodies, but who had subjective symptoms of dryness (non-SS, sicca controls).

overall_design: Samples from 17 pSS and 15 non-SS subjects were hybridized to Agilent Whole Human Genome 8x60K microarrays in three batches (Batch 1: 2 pSS, 3 non-SS; Batch 2: 6 pSS, 5 non-SS; Batch 3: 9 pSS, 7 non-SS).  All data were pooled to assess potential batch effects by principal components analysis and gene expression data were quality control checked using the arrayQualityMetrics R package. Batch effects were equalized via ComBat analysis (‘Surrogate Variable Analysis’ R package Ver 3.8.0; manual specification of batches).

first: A


title: Gene expression fluctuation in Abatacept treated Rheumatoid Arthritis patients between baseline and 6 months

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

summary: The objective of this study was to identify response-specific gene expression fluctuations in  methotrexate /abatacept (Aba) treated rheumatoid arthritis patients : responders (R) VS no-responders (NR). Nineteen RA patients were received Abatacept. The drug efficacy was evaluated with the DAS28 score after 6 months of treatment according to the EULAR response criteria. Among 19 Aba RA patients, 14 were R and 5 were classified as NR.  A blood sample was carried out in patients both at baseline (just before the first injection of ABA) and at 6 months in PaxGene tubes.

overall_design: Two color experiments : 6 months(Cy5)/baseline (Cy3).


title: Gsta4 restricts apoptosis in differentiating adult oligodendrocytes via Fas/Casp8/Bid-axis during homeostasis and remyelination

status: Public on Jul 23 2020

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Arrest of oligodendrocyte (OL) differentiation and remyelination following myelin damage in Multiple Sclerosis (MS) are associated with disease progression but the underlying mechanism are elusive. We show that Glutathione S-transferase 4α (Gsta4) is highly expressed during adult OL differentiation and that its loss prevents differentiation into myelinating OLs. Also, Gsta4 appeared to be a novel target for Clemastine, in clinical trial for MS. Over-expression of Gsta4 reduced the expression of Fas and activity along the mitochondria-associated Casp8/Bid-axis in adult pre-OLs from the corpus callosum, together promoting enhanced pre-OL survival during differentiation. The Gsta4-mediated input on apoptosis during adult OL differentiation was further verified in the LPC and EAE model, where Casp8 were reduced in pre-OLs with high Gsta4 expression in an immune response-independent fashion. Our results place Gsta4 as a key regulator of intrinsic mechanisms beneficial for OL differentiation and remyelination, and as a possible target for future MS therapies.

overall_design: GSTA4 transgenenic mice compared with WT at D0, D10 and D15 of EAE. P9560_104 was run on 2 lanes and was demultiplexed using an index-

first: Karl

last: Carlström


title: Expresion and methylation analysis of adult somatic cell lines, five days after OSK, AOX15 and AO9 overxpression and derived iPSC using the different combinations

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

type: Methylation profiling by genome tiling array

summary: Methods of reprogramming somatic cells to an induced pluripotent state (iPSC) have enabled the direct modeling of human disease and ultimately promise to revolutionize regenerative medicine. iPSCs offer an invaluable source of patient-specific pluripotent stem cells for disease modeling, drug screening, toxicology tests and importantly for regenerative medicine, and already have been employed to unmask novel insights into human diseases. While iPSCs can be consistently generated through overexpression of the four Yamanaka Factors OCT4, SOX2, KLF4 and c-MYC (OSKM), reprogrammed cells present worrisome differences with embryonic stem cells in transcriptional and epigenetic profiles, as well as developmental potential and difficulties in cell culturing. A thorough mechanistic understanding of the reprogramming process is critical to overcoming these barriers to the clinical use of iPSC. We have recently published a novel factor combination based on molecules specifically enriched in the metaphase II human oocyte. We have shown that just the overexpression of histone-remodeling chaperone ASF1A and OCT4 in hADFs previously exposed to the oocyte-specific paracrine growth factor GDF9 can reprogram hADFs into pluripotent cells (AO9-iPSCs). Our study contributes to the understanding of the molecular pathways governing somatic cell reprogramming. Here we want to go deeper in the reprogramming mechanisms by understanding the importance of somatic cell origin, and analyzing (and establishing comparison with) the transcriptional and epigenetic characteristics of AO9-iPSCs. As the intrinsic histone chaperone activity of ASF1A and our data indicate, these cells could be closer to the embryonic pluripotent state, with less epigenetic memory, better culture properties and differentiation potential.

overall_design: Three-four biological replicates (from different healthy adult donors: 01,02,03,04) were used for analysis, factor overexpression and iPSC reprogramming

first: Lidia

last: Lopez-Caraballo

last: Martorell-Marugán

first: Pedro

last: Carmona-Sáez

first: Elena

last: Gonzalez-Munoz


title: Comparative  microRNA Transcriptome  in Domestic Goats  Reveals Adaptation to High Altitude

city: Chengdu

first: Siyuan

last: Feng

state: Sichuan

address: Huiming Road #211, Wenjiang District

department: College of Animal Science and Technology

country: China

institute: Sichuan Agriculcural University

summary: High-altitude adaptation is a representative example of vertebrates getting adapted to harsh and extreme environments. To investigate the miRNA expression alterations of goats that were induced by high altitude stress, we performed comparative miRNA transcriptome analysis on six hypoxia-sensitive tissues (heart, kidney, liver, lung, skeletal muscle and spleen) in two indigenous goat populations from distinct altitudes (600 m and 3000 m). We obtained the expression of 1391 mature miRNAs and identified 138 differentially expressed miRNAs between altitudes. Combined with tissue specificity analysis, we illustrated alterations of expression levels between altitudes and among tissues, which suggested the coexisting tissue-specific and tissue-conserved mechanism for hypoxia adaptation. Notably, the interplay between DE miRNA and DE target genes strongly indicated post-transcriptional regulation in HIF-1 signaling pathway, insulin signaling pathway and p53 signaling pathway, which might play a significant role in high altitude adaptation in domestic goats. These results provide insights into the complicated miRNA expression pattern and regulatory mechanism of high altitude adaptation in domestic goats.

overall_design: Six organs (heart,liver,spleen,lung,kidney and muscle) miRNA profiles of high- and their low-altitude goat were generated by deep sequencing,in triplicate using Illumina Hiseq2500 .

first: Jideng

last: Ma

first: Keren

last: Long

first: Jinwei

last: Qiu

first: Wanling

first: Yan

first: Long

last: Jin

first: Xun

last: Wang

first: Anan

last: Jiang

first: Lingyan

last: Liu

first: Weihang

last: Xiao

first: Xuewei

first: Qianzi

last: Tang

first: Mingzhou


title: Landscape of Cohesin-Mediated Chromatin Loops in the Human Genome (ChIP-Seq)

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

summary: Physical interactions between distal regulatory elements in the genome play a key role in regulating gene expression, yet the extent to which these interactions vary between cell types and contribute to cell type-specific gene expression patterns remains unclear. To address this question we have mapped cohesin-bound chromatin loops in 24 diverse human cell types at high resolution using the chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing approach. We combined a total of ~9.6 billion reads across all samples to generate a compendium of 124,830 loops, the most extensive resource currently available. We find that 39% of all chromatin loops vary across cell types, and such changes are effective at grouping cell types based on their tissue of origin, indicating commonalities in three-dimensional (3D) genome architecture amongst related cell types. In contrast, different cell types derived from the same individual show markedly different patterns of interactions indicating that the observed differences are mainly caused by epigenetic changes. Variation in chromatin loops correlates with changes in gene expression, especially for long-range contacts linking cell type-specific enhancers to promoters; moreover, genes contained within the same loop show coordinated co-expression changes in expression across cell types. We further find that loops specific to either blood or embryonic cell lines harbor distinct sets of genes relevant to cell type-specific function, and are enriched for lineage determining transcription factors, indicating a possible mechanism for the assembly of variable loops. Finally, we demonstrate that genetic variants identified in GWAS are enriched in variable loops in disease relevant cell types. Our results provide important insights in how changes in 3D chromatin organization potentially regulate cell type-specific functions.

overall_design: To identify chromatin loops which vary in interaction frequency across cell lines we mapped cohesin (RAD21)-mediated loops in 24 different cell lines. These cell lines span both primary and cancer cell lines from a variety of tissues, and more over span all three germ layers. We further generated RNA -Seq,,  Histone -ChIPP-Seq  (H3K27ac)  and ATAC-Seq data to study the interplay between looping, enhancer activity, and gene expression.

first: Rohith

last: Srivas

first: Damek

last: Spacek

first: Maya

last: Kasowski

first: Marian

last: Velasco

first: Nasa

last: Sinnott-Armstrong

first: Peyton

last: Greenside

first: Anil

last: Narasimha

first: Qing

first: Benjamin

last: Geller

first: Akshay

last: Sanghi

first: Michael

last: Kulik

first: Silin

last: Sa

first: Marlene

last: Rabinovitch

first: Anshul

last: Kundaje

first: Stephen

last: Dalton

first: Judith

last: Zaugg

last: Snyder


title: Bach1-silenced and control C2C12 cells before and after inducing differentiation

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

country: Japan

institute: Tohoku university school of medicine

summary: To investigate the Bach1 function in proliferation and differentiation of myogenic cells, we performed DNA microarray analysis using C2C12 cells with silencing of Bach1 and control cells before and after inducing differentiation.

overall_design: Differentiation induced gene expression in siRNA-transfected C2C12 cells was measured at day 0 and day 2 after replacing in the DMEM with 2% horse serum (HS) when the cells reached confluence.

first: Katsushi

last: Suzuki

first: Kyoko

last: Ochiai

first: Kazuhiko

last: Igarashi


title: Comparative analysis of the different Streptomyces bingchenggensis strains by RNA-seq

city: Beijing

first: pinjiao

last: jin

address: No. 2 Yuanmingyuan West Road

department: Institute of Plant Protection

institute: Chinese Academy of Agricultural Sciences

summary: Streptomyces bingchenggensis is a soil bacterium that produces milbemycins. Milbemycins are commercially insecticidal and acaricidal antibiotics in agriculture, owing to their advantages such as high efficiency and safety for human and animal. To obtain genes valuable for further improvement of titer, we have compared two strains（the parental strain and high-yielding strain）by whole genome microarray expression profiling as a discovery platform. In Streptomyces bingchenggensis, there are abundant transporters, which are responsible for transporting various substrates. In the result, some sugar transporter genes showed significant gene expression.

overall_design: 6 time points were designed at 18,48,72,96,144,and 192 hours in two strains. The samples were collected at each time point named W1,W2,W3,W4,W5,W6,H1,H2,H3,H4,H5,and H6.

first: Y

last: Zhang

first: H

last: He

first: P

last: Jin

first: S

last: Li

first: W

last: Xiang

first: L

last: Chu

first: Z

last: Dong


title: Landscape of Cohesin-Mediated Chromatin Loops in the Human Genome (ATAC-seq)

first: Fabian

last: Grubert

overall_design: To identify chromatin loops which vary in interaction frequency across cell lines we mapped cohesin (RAD21)-mediated loops in 24 different cell lines. These cell lines span both primary and cancer cell lines from a variety of tissues, and more over span all three germ layers. We further generated RNA -Seq,,  Histone -ChIPP-Seq  (H3K27ac)  and ATAC-Seq data to study the interplay between looping, enhancer activity, and gene expression. To identify chromatin loops which vary in interaction frequency across cell lines we mapped cohesin (RAD21)-mediated loops in 24 different cell lines. These cell lines span both primary and cancer cell lines from a variety of tissues, and more over span all three germ layers. We further generated RNA -Seq,  Histone -ChIP-Seq  (H3K27ac)  and ATAC-Seq data to study the interplay between looping, enhancer activity, and gene expression.

first: Rohith

last: Srivas

first: Damek

last: Spacek

first: Maya

last: Kasowski

first: Marian

last: Ruiz Velasco

first: Nasa

last: Sinnott-Armstrong

first: Peyton

last: Greenside

first: Anil

last: Narasimha

first: Qing

last: Liu

first: Benjamin

last: Geller

first: Akshay

last: Sanghi

first: Michael

last: Kulik

first: Silin

last: Sa

last: Rabinovitch


title: A1-Reactive Astrocytes and a loss of TREM2 are associated to an early state of pathology in a mouse model of Cerebral Amyloid Angiopathy

status: Public on Jul 22 2020

city: Indianapolis

first: Cristian

last: Lasagna-Reeves

state: IN

address: 320 West 15th Street

department: Anatomy & Cell Biology

institute: Indiana University School of Medicine

summary: In this study, we dissect in detail the glial and immune responses associated to early stages of CAA. To do so, RNAseq gene expression analysis were performed in a mouse model for Familial Danish Dementia (FDD), a neurodegenerative disease characterized by the accumulation of Danish amyloid (ADan) in the vasculature. Findings observed in this CAA mouse model were complemented with primary culture assays.

overall_design: RNAseq of 3 replicates of WT (control) and Tg-FDD

middle: A


title: Aberrant AKT Activation Drives Ganglioneuroma and Can Be Therapeutically Targeted by mTOR Inhibitors

city: Hangzhou

first: Ting

last: Tao

state: Zhejiang

address: 3333 Binsheng Road

institute: Children's Hospital, Zhejiang University School of Medicine

summary: Peripheral sympathetic nervous system tumors are the most common extra-cranial pediatric tumors in children and include neuroblastoma, ganglioneuroma and intermixed ganglioneuroblastoma. Ganglioneuroma can be induced by activating mutations of the RET proto-oncogene or activated Ras in murine models, but the etiology and molecular pathogenesis of this disease is unknown for the majority of human ganglioneuromas. Surgery is the only effective therapy for ganglioneuroma which can be challenging due to tumor location and compression of surrounding structures. Thus, there is great potential benefit to the definition of presurgical therapies that can reduce the size and extent of these tumors, and therefore limit morbidity. We found high levels of phosphorylated AKT in most of human ganglioneuromas, but only in a small portion of human poorly differentiated neuroblastomas (p<0.0001, Fisher’s exact test). As a result, we created zebrafish transgenic for constitutively activated myr-Akt2 in the sympathetic nervous system. These zebrafish were found to develop benign ganglioneuroma without progression to neuroblastoma. Zebrafish tumors displayed high expression of phosphorylated Akt and the downstream Akt targets, phosphorylated mTOR, S6 and EIF4EBP1. Histopathological and comparative genomic analyses revealed that zebrafish ganglioneuroma highly resembles human ganglioneuroma. Inhibition of the downstream AKT target, mTOR, using clinically available inhibitors effectively reduced tumor burden in zebrafish embryos transplanted with primary ganglioneuroma. Our results implicate activated and phosphorylated AKT as a tumorigenic driver in ganglioneuroma, and propose inhibition of the AKT-target kinase mTOR as an ideal candidate to treat patients with ganglioneuroma.

overall_design: RNA-Seq for zebrafish tumor cells from MYCN and myrAKT transgenic fish

first: Hui

last: Shi

first: Adam

last: Durbin

first: Meng

last: Wang

first: Antonio

last: Perez-Atayde

first: Wendy

last: London

first: Alejandro

last: Gutierrez

first: Bernardo

last: Lemos

first: A

last: Look


title: Bulk RNA-sequencing and Single-cell RNA-sequencing of adult mice intestinal stromal cells and lacteal LECs with PDGFRb-specific deletion of LATS1/2 [scRNA-seq]

city: Daejeon

first: Hyunsoo

last: Cho

address: Yuseonggu

institute: IBS/KAIST

summary: To investigate the effect of Hippo-YAP signaling in insterinal stromal cells and lacteal LECs, we performed bulk and single-cell RNA-sequencing by using intestinal stromal cells isolated from mice PDGFRb-specific deletion of LATS1/2

overall_design: PDGFRb+ intestinal stromal cells were isolated from mice with indicated genotype in adult and mRNA profiles were generated

first: Gou-Young

last: Koh

first: Seon-Pyo

last: Hong

first: Myung-Jin

last: Yang


title: Primary Human Airway Epithelial Cultures infected with SARS-CoV-2

status: Public on Jul 21 2020

city: Atlanta

first: Mehul

middle: Shamal

last: Suthar

state: GA

address: 954 Gatewood Road, Office 2022

institute: Emory University

summary: We performed RNAseq analysis on primary human airway epithelial cultures either mock infected (PBS) or infected with SARS-CoV-2. Transcriptional profiling studies found that infected pHAE cells had a molecular signature dominated by pro-inflammatory cytokines and chemokine induction, including IL-6, TNFα, CXCL8, and identified NF-κB and ATF4 as key drivers of this pro-inflammatory cytokine response. Surprisingly, we observed a lack of a type I or III interferon (IFN) response to SARS-CoV-2 infection

overall_design: pHAE cultures were infected apically with SARS-CoV-2 (MOI= 0.25) for 48 hours, at which point mock and SARS-CoV-2 infected (n=3) samples were harvested for bulk RNA-Seq analysis.

first: Abigail

last: Vanderheiden

first: Philipp

last: Ralfs

first: Tatiana

last: Chirkova

first: Amit

last: Upadhyay

first: Matthew

last: Zimmerman

first: Shamika

last: Danzy

first: Kathryn

last: Pellegrini

first: Candela

last: Manfredi

first: Eric

last: Sorscher

last: Mainou

first: Jenna

last: Lobby

first: Jacob

last: Kohlmeier

first: Anice

last: Lowen

first: Pei-Yong

first: Vineet

last: Menachery

first: Larry

last: Anderson

first: Arash

last: Grakoui

first: Steven

last: Bosinger

middle: S


title: Bulk RNA-sequencing and Single-cell RNA-sequencing of adult mice intestinal stromal cells and lacteal LECs with PDGFRb-specific deletion of LATS1/2 [scRNA-seq 2]

first: Hyunsoo

last: Cho

first: Gou

last: Koh

first: S

last: Hong

first: M

last: Yang

first: H


title: Bulk RNA-sequencing and Single-cell RNA-sequencing of adult mice intestinal stromal cells and lacteal LECs with PDGFRb-specific deletion of LATS1/2

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

overall_design: Refer to individual Series


title: The role of transcriptional factor brachyury on cell cycle regulation in non-small cell lung cancer [ChIP-Seq]

city: wuxi

first: ming

last: chen

address: zhongshan road

institute: nanjing medical university

summary:
Purpose:Lung cancer is the leading cause of cancer-related death, and non-small cell lung cancer (NSCLC) accounts for almost 80-85% of all lung cancer cases.The transcriptional factor brachyury has been verified to promote tumor cells migrate, invade and metastasis in various types of tumors, whereas divergent roles of brachyury on cell proliferation have been reported in several types of tumor cells. In this study, we attempted to explore the effect of brachyury on the cell cycle progression and proliferation capability of NSCLC cells.
Methods: Firstly, we performed RNA-sequence and ChIP-sequence to explore underlying downstream pathways regulated by brachyury. Cell proliferation and colony formation assays were utilized to detect the effect of brachyury on the proliferation ability of two types of lung NSCLC cells: H460 and Calu-1, which represent different brachyury expression levels. Following Cell cycle and cell apoptosis assays were used to investigate the mechanism by which brachyury promotes NSCLC grow and progression.
Results: RNA-sequence and ChIP-sequence (ChIP-seq) showed that one of the vital downstream pathways regulated by brachyury involves in cell cycle progression. Through cell proliferation assays and colony formation assays, we found that inhibition of brachyury could decrease the capability of proliferation in H460 cells. We also found that brachyury overexpression could prevent the transition from G0/G1 to S phase in Calu-1 cells, and brachyury knockdown could decrease the transition of G2/M phase in H460 cells. The cell apoptosis assays showed that inhibition of brachyury could promote apoptosis in H460 cells.
Conclusion: In this study we demonstrate that brachyury and downstream target genes together involve in tumor cell cycle regulation by inducing accelerated transition through G2/M, promote tumor cell proliferation and inhibit apoptosis in lung NSCLC H460 cells. Targeting brachyury expression could be developed into a promising avenue for the prevention of lung cancer progression.

overall_design: Pericardial RNA profiles of three test and three control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Jingyi

last: Xu

first: Ming

last: Chen

first: Yinghui

last: Wu

first: Hong

last: Zhang

first: Jundong

last: Zhou

first: Donglai

last: Wang

first: Tianming

last: Zou

first: Jun

last: Shen


title: The role of transcriptional factor brachyury on cell cycle regulation in non-small cell lung cancer [RNA-Seq]


title: The analysis of gene expression profile in rabbit retinal vein occlusion model.

city: Fukui city

first: Takuma

last: Neo

state: Fukui

address: 3-9-1, Bunkyo

institute: Fukui university

summary:
The rabbit retinal vein occlusion (RVO) model is one of the experimental systems that mimic retinal ischemic diseases. This model is widely used as an evaluation system for various surgical procedures.
We focused on the gene expression profiles of the rabbit RVO model and considered about the validity as an ischemic model.

overall_design: To analyze the ischemia-induced gene expression change, we performed microarray using RVO sample and untreated control sample.

first: Makoto

last: Gozawa

first: Yoshihiro

last: Takamura

first: Masaru

last: Inatani

first: Masaya

last: Oki


title: Single-cell RNA-seq of PBMCs from severe COVID-19 patients

city: Hefei

first: Bin

last: Li

address: NO. 96 Jinzhai Road

institute: University of Science and Technology of China

summary: We profiled the single-cell transcriptomes of 13,289 peripheral blood mononuclear cells isolated at three longitudinal stages from two severe COVID-19 patients treated with Tocilizumab. The raw sequencing data can be obtained from the Genome Sequence Archive for Human (GSA-Human) at https://bigd.big.ac.cn/gsa-human/browse/HRA000172 .

overall_design: We generated single-cell transcriptome library following the instructions of single-cell 3’ solution v2 reagent kit (10x Genomics). Briefly, after thawing, washing and countin cells, we loaded the cell suspensions onto a chromium single-cell chip along with patitioning oil, reverse transcription (RT) reagents, and a collection of gel beads that contain 3,500,000 unique 10X Barcodes. After generation of single-cell gel bead-in-emulsions (GEMs), RT was performed using a C1000 TouchTM Thermal Cycler (Bio-Rad). The amplified cDNA were purified with SPRIselect beads (Beckman Coulter).

first: Kun

last: Qu

first: Chuang

last: Guo

last: Lin


title: Tousled-like kinase activity is required for transcriptional silencing and suppression of innate immune signaling [HeLa ATAC-Seq]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: The Tousled like kinases 1 and 2 (TLK1/2) control histone deposition through the ASF1 histone chaperones and are regulated by the DNA damage response. Depletion of TLK activity caused replication stress, increased chromosomal instability and cell arrest or death. Here, we show that stalled forks in TLK depleted cells are processed by BLM, SAMHD1 and the MRE11 nuclease to generate ssDNA and activate checkpoint signaling. TLK depletion also impaired heterochromatin maintenance, inducing features of alternative lengthening of telomeres and increasing spurious expression of other repetitive elements, associated with impaired deposition of the histone variant H3.3. TLK depletion culminated in a BLM-dependent, STING-mediated innate immune response. In many human cancers, TLK1/2 expression correlated with signatures of chromosomal instability and anti-correlated with STING and innate and adaptive immune response signatures. Together, our results show that TLK activity protects replication forks from active processing, contributes to chromatin silencing and suppresses innate immune responses, suggesting that TLK amplification may protect chromosomally unstable cancers from immune detection.

overall_design: Human HeLa LT WT and TLK1-knockout cells were transfected in biological duplicate with siRNAs (siCont, siTLK2) to address the effect of TLK loss on chromatin accessibility. 48 hours post-transfection cells were collected by trypsinization and 75000 cells were subsequently used for nuclei preparation.

first: Sandra

last: Segura-Bayona

last: Stephan-Otto Attolini

first: Travis

middle: H

last: Stracker


title: Tousled-like kinase activity is required for transcriptional silencing and suppression of innate immune signaling [ChIP-Seq]

overall_design: Human U-2-OS cells were transfected in biological duplicate with siRNAs (siCont, siTLK1+2) to address the effect of TLK loss on histone H3.3 occupancy. Nuclear extracts were isolated 48h after siRNA transfection.


title: Bulk RNA-sequencing and Single-cell RNA-sequencing of adult mice intestinal stromal cells and lacteal LECs with PDGFRb-specific deletion of LATS1/2 [RNA-seq]

first: Hyunsoo

last: Cho

summary: To investigate the effect of Hippo-YAP signaling in insterinal stromal cells and lacteal LECs, we performed RNA-sequencing by using intestinal stromal cells isolated from mice PDGFRb-specific deletion of LATS1/2

overall_design: PDGFRb+ intestinal stromal cells were isolated from mice with indicated genotype in adult and mRNA profiles were generated by deep sequencing, using Illumina NextSeq 500

first: Gou-Young

last: Koh

first: Seon-Pyo

last: Hong

first: Myung-Jin

last: Yang


title: The role of transcriptional factor brachyury on cell cycle regulation in non-small cell lung cancer

first: ming

last: chen


title: Tousled-like kinase activity is required for transcriptional silencing and suppression of innate immune signaling [RNA-Seq]

overall_design: Human U-2-OS cells were transfected in biological duplicate with siRNAs (siCont, siTLK1, siTLK2, siTLK1+2) to address the effect of TLK loss on transcriptional regulation. RNA was isolated 48h after siRNA transfection. To avoid limiting our analysis in mRNA polyA+, we performed enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) species


title: Genome-wide identification and characterization of Gibberellin Metabolic and Signal Transduction (GA MST) pathway mediating seed and berry development (SBD) in Grape (Vitis vinifera L.)

status: Public on Jul 20 2020

city: Nanjing

first: Wenran

last: Wang

address: Weigang

institute: Nanjing Agricultural University

summary:
Background: Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine.
Results: In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed.
Conclusions: Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.

overall_design: Detected GA Metabolic and Signal Transduction pathway gene expression profiles during grape seed and berry development

first: Chen


title: Emergence of a high-plasticity cell state during lung cancer evolution

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

institute: The Hebrew University of Jerusalem

relation:
SuperSeries of: GSE154965
SuperSeries of: GSE154966
SuperSeries of: GSE154970
SuperSeries of: GSE154977
SuperSeries of: GSE154978
SuperSeries of: GSE154989


title: ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression [ChIP-seq]

first: Ting

last: Tao

summary: Gene mutations in components of SWI/SNF chromatin-remodeling complexes are found in approximately 20% of all human cancers, with ARID1A being the most frequently mutated subunit. In neuroblastoma, sequence alterations of ARID1A were identified in 6% of primary tumors and cell lines, and this gene is hemizygously deleted in at least 87% of cases with chromosome 1p deletion, which almost always accompanies MYCN gene amplification and is the most common deletions in high-risk subtypes of this tumor. However, the role of ARID1A haploinsufficiency in neuroblastoma pathogenesis and the mechanisms involved remain unclear. Here, we show that disruption of ARID1A homologs in a zebrafish model accelerates the onset and increases the penetrance of MYCN-driven neuroblastoma by increasing cell proliferation in the sympathoadrenal lineage. Depletion of ARID1A in human NGP neuroblastoma cells promoted the adrenergic-to-mesenchymal transition with changes in enhancer-mediated gene expression due to alterations in the genomic occupancies of two distinct SWI/SNF assemblies, BAF and PBAF. Our findings indicate that ARID1A is a haploinsufficient tumor suppressor in MYCN-driven neuroblastoma, whose depletion enhances tumor development and promotes the emergence of the more drug resistant mesenchymal cell state.

overall_design: ChIP-Seq for SS18, ARID2, BRG1, H3K4Me3 and H3K27Ac in  control and two ARID1A mutant NGP cells

first: Hui

last: Shi

first: Brian

middle: J

last: Abraham

first: Adam

last: Durbin

first: Mark

middle: W

last: Zimmerman

first: Cigall

last: Kadoch

first: A

last: Look


title: ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression


title: Tousled-like kinase activity is required for transcriptional silencing and suppression of innate immune signaling

first: Camille

last: Stephan Otto Attolini


title: Schwann Cell Tn5Prime

city: Ann Arbor

first: Elizabeth

last: Fogarty

state: MI

address: 1105 N. University Ave

institute: University of Michigan

summary: Here we provide sequencing data derived from our efforts to identify SOX10-regulated promoters in Schwann cells genome-wide. We assess the activity of SOX10-bound promoters using Tn5Prime to identify and quantify transcription start sites in adult peripheral nerve, in differentiating primary Schwann cells, and upon ablation of SOX10 in vitro. Tn5Prime libraries were prepared essentially as described by Cole and colleagues (NAR, 2018). Analyses focused on transcription start sites associated with H3K4me3 and SOX10 ChIP-Seq peaks from sciatic nerve (ChIP-Seq data derived from previously published datasets).

overall_design: Samples include two libraries derived from independent adult rat sciatic nerves (age 6-9 months), three libraries each from control- and CPT-cAMP-treated rat primary Schwann cells, two libraries from unmodified immortalized rat myelinating Schwann (S16) cells, and four libraries each derived from independent clonal ΔSOX10 S16 cell lines. Each library was prepared from an independent RNA isolation.

first: Anthony

last: Antonellis


title: Epigenetic regulation of gonadal and brain aromatase expression in a cichlid fish with environmental sex determination

city: Portland

first: Suzy

middle: CP

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

institute: Reed College

type: Methylation profiling by high throughput sequencing

summary: We examined the methylation state of upstream intergenic regions associated with two aromatase genes (cyp19a1A and cyp19a1B) in P. pulcher, a cichlid fish with pH-based sex and male morph determination. Methylation levels in fry head and trunk and adult brain and gonad samples were assessed with a bisulfite amplicon sequencing assay and sequence data was processed through two pipelines to determine % methylation of individual CpG sites and abundance of specific patterns of methylated and unmethylated CpGs (i.e., epialleles).

sample_organism:
Pelvicachromis pulcher
blank sample

platform_organism:
Pelvicachromis pulcher
blank sample

overall_design: Illumina-based bisulfite amplicon sequencing of four amplicons (two upstream of cyp19a1A and two upstream of cyp19a1B) to assess methylation state of CpGs in these regions

first: Rose

last: Driscoll

first: Cynthia

middle: F

last: O'Rourke

first: Joshua

last: Faber-Hammond

first: Peter

last: Hurd

middle: C


title: ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression [RNA-seq]

overall_design: RNA-Seq for control and two ARID1A mutant NGP cells

middle: D


title: Distinct bacterial pathways influence the efficacy of antibiotics against Mycobacterium tuberculosis

status: Public on Jul 18 2020

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

summary: Understanding how M. tuberculosis survives during antibiotic treatment is necessary to rationally devise more effective tuberculosis chemotherapy regimens. Using genome-wide mutant fitness profiling and the mouse model of TB, we identified genes that alter antibiotic efficacy specifically in the infection environment.

overall_design: TnSeq was performed in mice treated with antibiotics over a time-course. Mutant abundance was compared pretreatment and posttreatment.

first: Michelle

last: Bellerose

first: Megan

middle: K

last: Proulx

first: Clare

last: Smith

first: Thomas

middle: R

last: Ioerger

first: Christopher

last: Sassetti


title: Expression Profile of Isolated Endothelial cells in Human Keloids: A microarray analysis

city: Tokyo

first: noriko

middle: muto

last: matsumoto

address: 1-1-5 Sendagi, Bunkyo-ku

department: Department of Plastic, Reconstructive and Regenerative Surgery

institute: Nippon Medical School

summary: Endothelial cells (ECs) are one of the major inductive cells in inflammation and keloid formation.The aim of this study was to identify gene expression patters of endothelial cells from keloid patients (KECs) comparing endothelial cells from normal patients (NECs).

overall_design: Immediately after the skin tissue excision, we performed CD31 positive ECs isolation. Keloid and normal skin tissue were gently minced with a GentleMACS Octo Dissociator with Heaters®. EC purification was performed using negative depletion with Anti-CD45 MicroBeads and Anti-Fibroblast for negative selection, and Anti-CD31-PE and Anti-PE Microbeads were used for positive selection for the CD31 positive EC by magnetic labeling with MicroBeads in MACS LS columns®. The purity of ECs as measured by flow cytometry was more than 85%. After the RNA extraction, Agilent Gene expression analysis was performed compared ECs isolated from keloid skin tissue (KECs) with ECs from normal skin tissue (NECs).Total RNA of KECs from 5 patients and NECs from 6 patients were analyzed.

first: Noriko

last: Matusumoto


title: Tousled-like kinase activity is required for transcriptional silencing and suppression of innate immune signaling [U2OS ATAC-Seq]

overall_design: Human U-2-OS cells were transfected in biological duplicate with siRNAs (siCont, siTLK1, siTLK2, siTLK1+2) to address the effect of TLK loss on chromatin accessibility. 48 hours post-transfection cells were collected by trypsinization and 50000 cells were subsequently used for nuclei preparation.

first: Sandra

last: Segura-Bayona

last: Stephan-Otto Attolini

first: Travis

last: Stracker


title: Zonation of pancreatic acinar cells in diabetic mice

status: Public on Jul 17 2020

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

institute: Weizmann Institute

summary: We sequenced AR42J cell exposed to CCK or insulin in different concentrations. This enable us to uncover the possible effect of the different hormones on acinar cells in pathlogy.

overall_design: mRNA profiles from AR42J cell line exposed to 5 different concentrations of CCK or insulin (in triplicates) and their untreated controls were sequenced in an Illumina NextSeq.

first: Adi

last: Egozi

last: Bahar Halpern

first: Lydia

last: Farack

first: Hagar

last: Rotem

first: Shalev

last: Itzkovitz


title: Transcriptome profiling of wildtype and E2A knockout embryonic stem cells and Neural progenitor cells

status: Public on Jul 16 2020

first: Yang

last: Li

address: Xueyuan Road 38,Haidian District

institute: Peking University

summary:
Background:  E2A, encoded by the TCF3 gene locus, belongs to the E protein transcription factor family, which also includes HEB (TCF12) and E2-2 (TCF4), has been suggested to play an important role in leukemogenesis. However, far less is known about the function of E2A in cell-fate regulation of hESCs. Therefore,  further understanding of E2A in self-renewal and differentiation of embryonic stem cells may be influenced.
Methods: The mRNA profiles of wildtype and E2A knockout embryonic stem cells were generated by RNA-seq technique, in triplicate for each group, using IIIumina Hiseq 2500.
Results: A comprehensive human transcriptome map of wild type and E2A knockout embryonic stem cells was provided. Function enrichment, network characteristics and disease association of the differentially expressed genes were analyzed.
Conclusion: The dataset could serve as a baseline resource for investigating the potential effects and mechanism of E2A in embryonic stem cells.

overall_design: The mRNA profiles of wildtype and E2A knockout embryonic stem cells in neural induction period were generated by RNA-seq technique, in triplicate for each group, using llumina HiSeq 2500.

first: Yi

last: Siqi

first: Huang

last: Xiaotian

first: Zhou

last: Yuan

first: Li

last: Yang


title: Using bone marrow stromal cells as micro-environmental sensors identifies IL-6 and TGFa signalling as regulators of declining erythropoiesis and lymphopoiesis during hematopoietic ageing

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

overall_design: Refer to individual Series


title: Basophils prime group 2 innate lymphoid cells for neuropeptide-mediated inhibition

city: Newark

first: Juan

middle: C.

last: Inclan Rico

state: New Jersey

address: 205 South Orange Avenue, Rutgers Cancer Institute of New Jersey at University Hospital

department: Medicine/CII

institute: Rutgers New Jersey Medical School


title: Transcriptome profiling of wildtype and E2A knockout embryonic stem cells

city: Beijing

overall_design: The mRNA profiles of wildtype and E2A knockout embryonic stem cells were generated by RNA-seq technique, in triplicate for each group, using llumina HiSeq 2500.


title: Emergence of a high-plasticity cell state during lung cancer evolution, single-cell RNAseq timecourse

first: Matan

last: Hofree

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

summary: Tumor evolution from a single cell into a malignant, heterogeneous tissue remains poorly understood. Here, we profiled single-cell transcriptomes of genetically engineered mouse lung tumors at seven stages, from atypical adenomatous hyperplasia to adenocarcinoma. The diversity of transcriptional states increased over time and was reproducible across tumors and mice. Cancer cells progressively adopted alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). Accordingly, HPCS cells prospectively isolated from mouse tumors and human patient-derived xenografts displayed high capacity for differentiation and proliferation. The HPCS program was associated with poor survival across human cancers and demonstrated chemoresistance in mice. Our study reveals a central principle underpinning intra-tumoral heterogeneity and motivates therapeutic targeting of the HPCS.

overall_design: Single cell RNAseq by SmartSeq2 of mouse lung tumor cells across different disease progression time-points.

first: Nemanja

last: Marjanovic

first: Jason

last: Chan

first: David

last: Canner

first: Katherine

last: Wu

first: Marianna

last: Trakala

first: Griffin

middle: G

last: Hartmann

first: Olivia

last: Smith

first: Jonathan

last: Kim

first: Kelly

middle: V

last: Evans

first: Anna

last: Hudson

first: Orr

last: Ashenberg

first: Caroline

middle: B

last: Porter

first: Alborz

last: Bejnood

first: Ayshwarya

last: Subramanian

first: Kenneth

last: Pitter

first: Yan

last: Yan

first: Toni

last: Delroy

first: Devan

last: Phillips

first: Nisargbhai

last: Shah

first: Ojasvi

last: Chaudhary

first: Alexander

last: Tsankov

last: Hollmann

first: Natasha

last: Rekhtman

first: Pierre

middle: P

last: Massion

first: John

middle: T

last: Poirier

first: Linas

last: Mazutis

first: Ruifang

first: JooHyeon

last: Lee

first: Angelika

last: Amon

first: Charles

middle: M

last: Rudin

first: Tyler

last: Jacks

first: Aviv

last: Regev

first: Tuomas

last: Tammela


title: Metabolomic and Transcriptomic Signatures of Prenatal Excessive Methionine in Mice Support Nature Rather than Nurture in the Pathogenesis and Therapy of Schizophrenia

status: Public on Jul 15 2020

city: Irvine, CA

first: Amal

last: Alachkar

address: 355 Med Surge II

institute: University of California Irvine

summary: Abstract: The imbalance of prenatal micronutrients may perturb one-carbon (C1) metabolism and increase the risk for neuropsychiatric disorders. Prenatal excessive methionine (MET) produces in mice behavioral phenotypes reminiscent of human schizophrenia. Whether in-utero programming or early life caregiving mediate these effects is, however, unknown. Here, we show that the behavioral deficits of MET are independent of the early life mother-infant interaction. We also show that MET produces in early life profound changes in the brain C1 pathway components as well as glutamate transmission, mitochondrial function, and lipid metabolism. Bioinformatics analysis integrating metabolomics and transcriptomic data reveal dysregulations of glutamate transmission and lipid metabolism, and identify perturbed pathways of methylation and redox reactions. Our transcriptomics Linkage analysis of MET mice and schizophrenia subjects reveals master genes involved in inflammation and myelination. Finally, we identify potential metabolites as early biomarkers for neurodevelopmental defects and suggest new therapeutic targets for schizophrenia.

overall_design: Saline pup brain and Methionine pup brain

first: Siwei

last: Chen

first: Wedad

last: Alhassen

first: Ryan

last: Yoshimura

first: Angele

last: De Silva

first: Geoffrey

last: Abbott

last: Baldi


title: TMBIM6/BI-1 contributes to cancer progression through assembly with mTORC2 and AKT activation

city: Jeonju

first: Hyun-Kyoung

last: Kim

address: 567 Baekje-daero, Deokjin-gu

department: Department of Pharmacology

institute: Jeonbuk National University

summary:
Transmembrane B cell lymphoma 2-associated X protein inhibitor motif-containing (TMBIM) 6, a Ca2+ channel-like protein, is highly upregulated in several cancer types. Here, we show that TMBIM6 is closely associated with survival in patients with cervical, breast, lung, and prostate cancer. TMBIM6 deletion or knockdown suppressed primary tumor growth. Further, mTORC2 activation was up-regulated by TMBIM6 and stimulated glycolysis, protein synthesis, and the expression of lipid synthesis genes and glycosylated proteins. Moreover, ER-leaky Ca2+ from TMBIM6, a unique characteristic, was shown to affect mTORC2 assembly and its association with ribosomes. In addition, we identified that BIA compound, a suggestive TMBIM6 antagonist, prevented TMBIM6 binding to mTORC2, decreased mTORC2 activity, and also regulated TMBIM6-leaky Ca2+, further suppressing tumor formation and progression in cancer xenograft models. This previously unknown signaling cascade in which mTORC2 activity is enhanced via the interaction with TMBIM6 provides effective therapeutic targets for various malignancies.
We used microarrays to detail the global of gene expression and identified that most of the differentially expressed genes related to apoptotic process, migration, proliferation, and metabolic pathways were decreased in TMBIM6 KO HT1080 cells

overall_design: Transcriptome profiling of TMBIM6 wild type and knock out HT1080 cells using Affymetrix GeneChip Human Gene 2.0 ST oligonucleotide Array. Two replicates of cells for each cell type were performed.

first: Han-Jung

last: chae


title: IL6/STAT3 co-opts ER/FOXA1 regulatory elements to drive metastasis in breast cancer (ChIP-Seq)

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: Interleukin 6 (IL6) signaling has been associated with an aggressive and metastatic phenotype in multiple solid tumors including breast cancer, but its mechanism of action in mediating tumor progression and treatment response is not clear. By exploiting a clinically relevant intraductal xenograft model of estrogen receptor positive (ER+) breast cancer, we demonstrate that IL6 increases both primary tumor growth and distant metastases. By integrating pre-clinical models and clinical specimens, we show that signal transducer and activator of transcription 3 (STAT3) mediates IL6-induced activation of a metastatic gene program from enhancer-elements shared with ER and its pioneer factor FOXA1. Although IL6 activated STAT3 and ER/FOXA1 share cis-regulatory regions, STAT3 drives transcription independent of ER and FOXA1 function, and the IL6/STAT3 gene program is not influenced by ER-targeted therapies, decoupling these two important pathways. This demonstrates that ER/FOXA1 and IL6/STAT3 are two parallel, but independent actionable pathways controlling breast cancer progression.

overall_design:
ChIP-seq in breast cancer cell lines in response to IL6 and in clinical samples.
ChIP-sequencing on ER on T47D cells with FOXA1 siRNA with or without IL6

first: Rasmus

last: Siersbaek

first: Igor

last: Chernukin

middle: S


title: Genome-wide maps of chromatin state in wild type and E2A knockout neural progenitor cells

first: Yang

last: Li

summary:
Background:  E2A, encoded by the TCF3 gene locus, belongs to the E protein transcription factor family, which also includes HEB (TCF12) and E2-2 (TCF4), has been suggested to play an important role in leukemogenesis. However, far less is known about the function of E2A in cell-fate regulation of hESCs. Therefore,  further understanding of E2A in self-renewal and differentiation of embryonic stem cells may be influenced. In the study, we demonstrated E2A knockout exhibited blocked neural differentiation, which is tightly related to histone modification H3K4me3 and H3K27me3.
Methods: The genomic DNA of H3K4me3 and H3K27me3 binding peaks in wild type and E2A knockout neural progenitor cells were generated by ChIP-seq technique using  IIIumina Hiseq 2500.
Results: A comprehensive human chromatin state of H3K4me3 and H3K27me3 in wild type and E2A knockout neural progenitor cells was provided. Function enrichment, network characteristics and disease association of the binding peaks were analyzed.
Conclusion: The dataset could serve as a baseline resource for investigating the potential effects and mechanism of H3K4me3/H3K27me3/E2A complex in neural differentiation period of embryonic stem cells

overall_design: Examination of 2 different histone modifications in Neural progenitor cells.

first: Yi

last: Siqi

first: Huang

last: Xiaotian

first: Zhou

last: Yuan

first: Li

last: Yang


title: Expansion of human iPSC derived ureteric bud organoids with repeated branching potential

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: We report a new method to generate UB organoids that possess epithelial polarity and tubular lumen and repeat branching morphogenesis. We also succeeded in monitoring UB tip cells by utilizing the ability of tip cells to uptake very-low-density lipoprotein, cryopreserving UB progenitor cells and expanding UB tip cells that can reconstitute the organoids and differentiate into collecting duct progenitors. Moreover, we successfully reproduced some phenotypes of multicystic dysplastic kidney (MCDK) using the UB organoids.

overall_design: Dissecting cell types in UB organoid that induced from human iPS cells by single cell RNA sequencing.

first: Shin-Ichi

last: Mae

first: Makoto

last: Ryosaka

first: Satoko

last: Sakamoto

first: Kyoko

last: Matsuse

first: Aya

last: Nozaki

first: Maiko

last: Igami

first: Ryotaro

last: Kabai

first: Kenji

last: Osafune


title: Effect of dmPGE2 radioprotection on hematopoietic stem cell (HSC) gene expression 1 h and 24 h after lethal irradiation

city: Indianapolis

first: Andrea

middle: Marie

last: Patterson

address: 980 W. Walnut St.

department: Medicine

institute: Indiana University School of Medicine

summary: DmPGE2 predominantly interferes with IR-induced p53-downstream apoptotic gene expression at 1 h, and suppresses IR-induced cell cycle gene expression at 24 h.

overall_design: Fgd5 mice (C57BL/6 background with ZsGreen fluorescent HSC) were treated with dmPGE2 or vehicle (8 mice/group) 30 min prior to irradiation at the 50% lethal dose of 8.53 Gy. Non-irradiated control groups were also treated with dmPGE2 or vehicle (7-8 mice/group). At 1 h and 24 h post-irradiation, alongside treated non-irradiated controls, bone marrow cells were extracted and HSC sorted for RNA sequencing by SLAM-LSK(wide) gating and Fgd5/ZsGreen fluorescence as described.

first: Louis

last: Pelus


title: Tumor-associated neutrophils actively immunosuppress T cell responses and promote cutaneous squamous cell carcinoma development

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: We profiled the transcriptomes of sorted neutrophils from precancerous and tumors in a DMBA/PMA cutenous squamous cell carcinoma, as well as the healthy adjacent tissue.

overall_design: Papillomas, tumors and skin from DMBA/PMA-treated mice were enzymatically treated and neutrophils sorted by flow cytometry to reach >98% purity. mRNA was extracted and cRNA synthesized and hybridized to SurePrint G3 Mouse GE 8x60K microarrays (Agilent Technologies).

first: Veronique

last: Braud

first: Alexandra

last: Popa

first: Fabienne

last: Anjuère

first: Franck

last: Bihl

first: Carmelo

last: Luci


title: Me31B interaction with Kdo in stage 14 oocytes

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

summary: Study of the interaction between Me31B and UBC-E2H (Kdo) in stage 14 Drosophila oocytes as part of a study of RNA-binding proteins during the maternal-to-zygotic transition

overall_design: RNA immunoprecipitation sequencing was performed for ME31B in stage 14 oocytes

first: Michael

last: Zavortink

first: Lauren

middle: N

last: Rutt

first: Svetlana

last: Dzitoyeva

first: Chloe

last: Barrington

first: Danielle

middle: Y

last: Bilodeau

first: Xiao

middle: L

last: Chen

first: Miranda

last: Wang


title: Regulatory networks in prenatal porcine skeletal muscle development under nutrient restriction

status: Public on Jul 14 2020

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We generated transcriptome profiles of skeletal muscles from Largewhite pigs at 35, 55, and 90 days of gestation (dg), using high-throughput deep sequencing methods. A large number of differentially expressed (DE) genes and miRNAs were identified between stages and dietary treatments. Interestingly, reduced maternal calorie supply led to significant changes in mRNA and miRNA expression patterns. Down-regulation of critical genes and miRNAs associated with increased cell growth and myoblast differentiation at certain stages was found to be responsible for repressed myofiber formation in calorie-restricted pigs. Moreover, an integrative analysis of the miRNA and mRNA using sequence-based target prediction and negative correlation of miRNA-mRNA profiles identified a number of novel miRNA-mRNA interactions that are potentially involved in prenatal myogenesis regulation. Importantly, some critical miRNA-mRNA interactions were validated. And we first proposed a miRNA-TF-mRNA regulatory loop, which significantly increased the number of biologically relevant targets of miRNAs and introduced new mechanisms underlying the nutrient-modulated myogenesis.

overall_design: Sows were fed with a normal or calorie-restricted diet during the gestation

first: He

last: Jun

first: Chen

last: Daiwen


title: Inhibiting YAP1 in hepatoblastoma drives therapeutic differentiation of tumor cells to functional hepatocyte-like cells

first: Tomas

middle: Christopher

last: Rodriguez

address: 55 N Lake Ave, AS5-2005

department: RNA Therapeutic Institute

summary: Despite advances in surgical care and chemotherapeutic regimens, the five-year survival rate for Stage IV Hepatoblastoma (HB), the predominant pediatric liver tumor, remains at 27%. YAP1 and β-Catenin co-activation occur in 80% of children’s HB; however, a lack of conditional genetic models precludes exploration of tumor maintenance and therapeutic targets. Thus, the clinical need for a targeted therapy remains unmet. Given the predominance of YAP1 and β-catenin activation in children’s tumors, we sought to evaluate YAP1 as a therapeutic target in HB. We engineered the first conditional murine model of HB using hydrodynamic injection to deliver transposon plasmids encoding inducible YAP1S127A, constitutive β-CateninDelN90, and a luciferase reporter to murine liver. Tumor regression was evaluated using in vivo bioluminescent imaging, and tumor landscape characterized using RNA sequencing, ATAC sequencing and DNA foot-printing. Here we show that YAP1 inhibition mediates >90% tumor regression with survival for 230+ days in mice. Mechanistically, YAP1 inhibition induces a cell fate switch driving therapeutic differentiation of HB tumors into Ki-67 negative “hbHep cells” with hepatocyte-like morphology and mature hepatocyte gene expression.

overall_design:
RNA-seq performed on YAP1on tumors, YAP1off D6 liver, hbHeps D114+, and FAH DeltaExon5 mouse liver

ATAC-seq performed on YAP1on tumors, YAP1off {D14,D33,D64} hb Heps, and mouse liver.

Mouse strains purchased from Jax laboratories include:
B6.Cg-Gt(ROSA)26Sortm1.1(CAG-rtTA3)Slowe/LdowJ (Strain#029627),
B6N.FVB(Cg)-Tg(CAG-rtTA3)4288Slowe/J (Strain #016532),
FVB/NJ (Strain #001800).
FAH-/- (deltaExon5) mice were a gift from Dr. Markus Grompe (Oregon Health & Science University).

middle: C

first: Jordan

last: Smith


title: Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers (PCHiC)

status: Public on Jul 13 2020

first: Michiel

middle: Johannes

last: Thiecke

state: Cambridgeshire

address: Babraham Hall

department: Nuclear dynamics

institute: Babraham research institute

summary: It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows that steady-state transcription of only a minority of genes is affected by depletion of architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics of chromosomal contacts of all human gene promoters upon rapid architectural protein degradation. We show that promoter contacts lost in these conditions tend to be long-range, with at least one interaction partner localising in the vicinity of topologically associated domain (TAD) boundaries. In contrast, many shorter-range chromosomal contacts, particularly those that connect active promoters with each other and with active enhancers remain unaffected by cohesin and CTCF depletion. We demonstrate that the effects of cohesin depletion on nascent transcription can be explained by changes in the connectivity of their enhancers. Jointly, these results provide a mechanistic explanation to the limited, but consistent effects of cohesin and CTCF on steady-state transcription and point towards the existence of alternative enhancer-promoter pairing mechanisms that are independent of these proteins.

overall_design: PCHiC was performed on HeLa kyoto cells in which SCC1 and separately CTCF were raplidly and selectively depleted using an Auxin inducible degron. Additionally, PCHiC was performed on synchronised cells in G1, G2 and Mitosis. Lastly, PCHiC was performed on triple RNAi inhibited cells for WAPL, PDS5A and PDS5B

first: Gordana

last: Wutz

first: Stefan

last: Schoenfelder


title: Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers

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


title: Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt

city: Irvine

first: Amber

middle: Nicole

last: Habowski

state: CA

address: 240 Sprague Hall

department: MMG

institute: University of California, Irvine

summary:
Abstract: The intestinal epithelium is replaced weekly by non-quiescent stem cells with kinetics that rely on a rapid loss of stemness and choice for secretory or absorptive lineage differentiation. To determine how the cellular transcriptome and proteome changes during these transitions, we developed a new cell sorting method to purify stem cells, secretory and absorptive progenitor cells, and mature, differentiated cells. Transcriptome analyses revealed that as stem cells transition to the progenitor stage, alternative mRNA splicing and polyadenylation dominate changes in the transcriptome. In contrast, as progenitors differentiate into mature cell types, alterations in gene expression and mRNA levels drive the changes. RNA processing targets mRNAs encoding regulators of cell cycle, RNA regulators, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, carrier-assisted mass spectrometry of sorted cell populations detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.

Sorting Protocol: To create a high-resolution profile of colon crypt stem cells and their daughter cells we developed a new flow sorting protocol using freshly dissected, wild-type C57Bl/6N mouse colons and antibodies to validated intestinal cell surface markers including Cd44. Upon discovery that Cd44 is highly sensitive to TrypLE, and other commonly used proteases, we developed a dissociation protocol that uses only EDTA and mechanical force. This change enabled a 10-fold greater range of Cd44 antigen surface expression and therefore higher resolution for cell sorting. Using additional commonly used cell surface markers, six cryptal populations were purified. A previously validated intestinal stem cell signature of Cd44 high, Cd24 low, and cKit negative was used to identify and isolate an abundant fraction of stem cells, a cell population that directly overlapped with Lgr5-EGFP+ cells from Lgr5-EGFP-IRES-creERT2 mice, confirming their stem cell identity. In addition to the stem cell population, five additional Epcam positive populations were collected, and the biological replicate samples of the six populations were processed for bulk RNA-seq. The clearly identified populations are stem cells, two distinct populations of progenitor cells (absorptive and secretory), and three mature, differentiated populations (enterocytes, Tuft cells and Enteroendocrine (EEC) cells). Thus, the new protocol for crypt isolation and the greater range of Cd44 surface expression it preserves, enables a significant improvement in the resolution and sorting of stem cells away from their daughter cells and differentiated progeny.  Specifically, it is now possible to distinguish stem cells from Absorptive Progenitor cells (AbsPro; Cd44Med) and from mature Enterocytes (Ent; Cd44Low/-) because of the higher resolution of Cd44 surface expression. Secretory progenitors are identified as SecPDG as this population contains a majority of Secretory Progenitors and Deep Crypt Secretory cells, with a possible minor contribution of Goblet cells, a cell type that is largely missing in this procedure. Finally, preserved Cd44 expression (and cKit expression) enabled resolution of two rare Epcam+/Cd24high populations identified as Tuft cells and Enteroendocrine cells (EEC), mature cell types from the secretory lineage (EEC are predominantly Enterochromaffin; Tuft, comprise both Tuft-1 and Tuft-2 subtypes).

overall_design: Bulk RNA-seq + Proteomics (LC-MS) of flow sorted wildtype mouse colon crypt epithelial cell types (Stem, AbsPro, SecPDG, Tuft, Ent, EEC).

first: Habowski

last: Amber

first: Waterman

last: Marian


title: Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers (SLAM-Seq)

overall_design: SLAM-seq was performed on HeLa kyoto cells in which SCC1 was raplidly and selectively depleted using an Auxin inducible degron and on control cells (without Auxin)

first: Matthias

last: Muhar


title: RNAseq and ribosome profiling of yeast cells grown under glucose restriction condition.

status: Public on Jul 10 2020

city: San Francisco

first: Hao

last: Li

department: Biochemistry and Biophysics

institute: UCSF

summary: We investigate the mechanism by which glucose restriction extends yeast replicative lifespan, using an approach that combines ribosomal profiling and RNA-seq. We systematically compared the translational and transcriptional profiles of cells grown in glucose restriction and normal media, uncovering groups of functionally related genes that are up or down regulated.

overall_design: We used two different protocols to grow cell culture in SD vs. GR conditions.  1) protocol-1: Quick Dilution from SD (2% glucose) to GR (0.05% glucose): the initial cell culture was incubated in SD medium overnight to OD600 0.8~1.0, then diluted by 5 fold using SD media and incubated for another 4 hours. The sample was then divided equally into two aliquots. One was diluted  40 times by pre-warmed SD medium with 0% glucose to reach final 0.05% glucose concentration (the sample), and the other diluted 40 times by pre-warmed SD medium with 2% glucose (the control). Both samples were incubated for another hour before harvesting. All the steps were carried out at 30°C.  2) protocol-2: Spin-down and re-suspension from SD to GR : the initial cell culture was incubated in SD medium overnight to a OD600 0.8~1.0, then diluted by 5 fold using SD medium and incubated for another 4 hours.  The sample was then divided equally into 2 aliquots. Cells were separated from the media by spin-down at 2000 rcf for 5 minutes and re-suspended into SD and GR media respectively. All samples were incubated for for another hour before harvesting. All the steps were carried out at 30°C.  Ribosomal profiling experiments were carried out using the protocol developed by Ingolia et al.  Raw sequences were obtained from Illumina Hiseq 2000.

first: Ke

last: Zou

first: Jiashun

last: Zheng

first: Silvia

last: Rouskin


title: Next-Generation Sequencing Analysis of Mouse Ependymal Cells

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

overall_design: Refer to individual Series


title: Glioblastoma-derived extracellular vesicles facilitate transformation of astrocytes via reprogramming oncogenic metabolism

status: Public on Jul 12 2020

city: Boston

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Background: Glioblastoma (GBM) may arise from brain astrocytes through a multistep process that occurs by the temporal accumulation of genetic mutations. Here, we explore whether GBM-derived extracellular vesicles (EVs) may facilitate neoplastic transformation and malignant growth of astrocytes.   Methods: We utilized conditioned medium (CM) of glioma cell and stem cell, its sequential filtration, diverse cell-based assays, RNA sequencing, and metabolic assays to compare the effects of EV-containing and EV-depleted CM on the transformation of human and mouse astrocytes in vitro and tumor growth in vivo.  Results: GBM EVs facilitated the neoplastic growth of astrocytes pre-transformed by oncogenic mutations or viruses but were unable to transform normal human and mouse astrocytes. GBM EVs induced proliferation, self-renewal, and colony formation of pre-transformed astrocytes, and enhanced astrocytoma growth in a mouse allograft model. Analysis of extracellular RNAs (exRNAs) in GBM identified multiple full-length mRNAs encoding ribosomal proteins, oxidative phosphorylation, and glycolytic factors. GBM EVs appear to reprogram astrocyte metabolism by inducing a shift in gene expression that may be partly associated with EV-mediated mRNA transfer from glioma cells.   Conclusions: Our study suggests a novel EV/exRNA-mediated mechanism contributing to astrocyte transformation via metabolic reprograming and implicates horizontal mRNA transfer in this process.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human transformed astrocytes (HTAs), mouse transgenic EGFRVIII; CDKN2-/-; PTENlox/lox astrocytes (EC), and mouse transgenic EGFRVIII; CDKN2-/-; PTEN-/- astrocytes (ECP) were treated with either 10X complete  glioblastoma conditioned medium (10x EV(+) CM) or the one with extracellular vesicles depleted (10X EV(-) CM). Six days later, RNA was purified with Norgen BioTek total RNA purification kit with on-column DNase treatment. The libraries were prepared and sequenced on Illumina HiSeq X with PE150 mode to produce approximately 20 M reads per sample by Novogene Co., Ltd. The reads were quality controlled with FastQC, trimmed with Trimmomatic, aligned with HiSat2 to hg38 or mm10, and quantified with HTSeq-count using the Galaxy platform.

first: Wei

last: Zhiyun

first: Ailiang

last: Zeng

first: Krichevsky

last: Anna


title: Control of Translation during the Unfolded Protein Response in Maize seedlings: Life without PERKs.

status: Public on Jul 08 2020

city: Ames

first: Wyatt

middle: Allen

last: Miller

state: IA

address: 2213 Pammel Dr

department: Plant Pathology & Microbiology

institute: Iowa State University

summary: The accumulation of misfolded proteins in the endoplasmic reticulum (ER) defines a condition called ER stress that induces the unfolded protein response (UPR). The UPR in mammalian cells attenuates protein synthesis initiation, which prevents the piling up of misfolded proteins in the ER. Mammalian cells rely on Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK) phosphorylation of eIF2alpha to arrest protein synthesis, however, plants do not have a PERK homolog, so the question is whether plants control translation in response to ER stress. We compared changes in RNA levels in the transcriptome to the RNA levels protected by ribosomes and found a decline in translation efficiency, including many UPR genes, in response to ER stress. The decline in translation efficiency is due to the fact that many mRNAs are not loaded onto polyribosomes (polysomes) in proportion to their increase in total RNA, instead some of the transcripts accumulate in stress granules (SGs). The RNAs that populate SGs are not derived from the disassembly of polysomes because protein synthesis remains steady during stress. Thus, the surge in transcription of UPR genes in response to ER stress is accompanied by the formation of SGs, and the sequestration of mRNAs in SGs may serve to temporarily relieve the translation load during ER stress.

overall_design: Examination of 0h, 6h and 12h tunicamycin treated maize seedling root samples with biological duplicates

first: Pulkit

last: Kanodia

first: Paramasivan

last: Vijayapalani

first: Renu

last: Srivastava

first: Ran

last: Bi

first: Peng

last: Liu

first: W

middle: A

first: Stephen

middle: H

last: Howell


title: Unraveling the molecular pathobiology of vocal fold systemic dehydration using an in vivo rabbit model

status: Public on Jul 09 2020

city: West Lafayette

first: Jyothi

last: Thimmapuram

address: YONG 1022, 155 S. Grant Street

department: Bioinformatics Core

institute: Purdue University

summary: The purpose of this study is to investigate if acute systemic dehydration impacts the vocal folds at the mRNA level. Rabbits were used as animal model to enable a systematic and rigorous assessment of the pathobiology of vocal fold hydration since they can be manipulated in a physiologically realistic manner. We anticipate that the results of this study will help to elucidate the effects of altered hydration state in response to furosemide on vocal fold epithelium, lamina propria and muscle tissue at the transcriptome level. Together with cellular, structural, and functional techniques that are part of this project, we expect to provide validated scientific recommendations on the adverse effects of dehydration and the therapeutic benefits of hydration.

overall_design: The transcriptome of vocal folds of rabbits that were acute systemically dehydrated with furosemide (5% dehydration based on body weight loss; n=6) was compared to control (euhydrated; n=4) rabbits.

first: Naila

last: do Nascimento

first: Preeti

last: Sivasankar

first: Abigail

last: Cox


title: JUN promotes abdominal adhesions in mice and humans

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

department: Surgery

institute: Stanford University

summary: Adhesions are fibrotic scars that form between abdominal organs following surgery or infection, and may cause bowel obstruction, chronic pain, or infertility. Adhesions occur post-operatively in 50-90% of all open abdominal operations and as such, represent an enormous clinical problem impacting hundreds of millions of patients worldwide. Our understanding of the biology of adhesion formation is very limited, which explains why there are essentially no available treatments that prevent adhesions. In this study, we systemically analyzed abdominal adhesions in mouse and human tissues gene expression using bulk- and sc-RNA-seq technologies to characterize the fibroblasts responsible for this devastating pathology.

overall_design: Mouse and human abdominal adhesion tissue transcriptomes were profiled using single cell RNA-sequencing. A total of 4 human samples and 2 pooled mouse samples were profiled.

first: Deshka

last: Foster

first: Gunsagar

last: Gulati

first: Clement

last: Marshall


title: Genome-wide mapping of DsbR-binding sites

city: Shanghai

first: liang

last: yu

address: No. 555, Zuchongzhi Road,Zhang Jiang Hi-Tech Park

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: We firstly found that DsbRS TCS (encoded by PA2479-PA2480) was involved in counteracting the toxic effects of copper. The identification of two DsbR binding reigions in dsbD-dsbR intergenic region DNA led us to globally characterize all DsbR-binding loci on the chromosome of Pseudomonas aeruginosa. In order to express C-terminal flag-tagged DsbR, we first constructed the ΔdsbRS::DsbR-Flag strain. We next investigated DsbR-binding to the chromosome of this strain during exponential growth by ChIP-Seq, chromatin immunoprecipitation followed by ultra-high throughput DNA sequencing. Sequence reads obtained from three independent ChIP-Seq experiments using Flag-specific antibodies were mapped to the genome of the ΔdsbRS::DsbR-Flag strain. Using MACS software, we identified 18 reproducible peaks of DsbR binding, which were enriched by >2 fold.Approximately 83% (15 peaks) are in the promoter regions of 23 genes (within 600 bp upstream of the translational start site) involved or potentially involved in various biological processes including protein folding (e.g., dsbDEG operon and dsbB), protein secretion (e.g.., hxcU, hxcP, hcpC), transport (e.g., opdT, pa2911, and pstS), and regulation of transcription (i.e., dsbRS, pa3398). Collectively, this study thus uncover a new signal transduction pathway in P. aeruginosa, DsbS/DsbR/DsbDEG and DsbB, for the regulation of Dsb system in response to copper stress.

overall_design: ChIP-Seq of DsbR in the ΔdsbRS::DsbR-Flag strain at the mid-log phase. Three independent experiments were performed. Input DNA (No IP) was used as a control.

first: Yu

last: Liang

first: Lan

last: Lefu


title: Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities

city: Bronx

first: Rosiris

last: León-Rivera

state: NY

address: 1300 Morris Park Ave, Forchheimer 727

department: Pathology

institute: Albert Einstein College of Medicine

summary: HIV reservoirs persist despite successful antiretroviral therapy (ART) and are a major obstacle to the eradication and cure of HIV. The mature monocyte subset, CD14+CD16+, contributes to viral reservoirs and HIV-associated comorbidities. Only a subset of monocytes harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). We developed an innovative single cell RNA sequencing (scRNAseq) pipeline that detects HIV and host transcripts simultaneously, enabling us to examine differences between HIV+ and HIVexp mature monocytes. Using this, we characterized uninfected, HIV+, and HIVexp primary human mature monocytes with and without ART. We showed that HIV+ mature monocytes do not form their own cluster separately from HIVexp  but can be distinguished by significant differential gene expression. We found that ART decreased levels of unspliced HIV transcripts potentially by modulating host transcriptional regulators shown to decrease viral infection and replication. We also identified and characterized mature monocyte subpopulations differentially impacted by HIV and ART. We identified genes dysregulated by ART in HIVexp monocytes compared to their uninfected counterpart and, of interest, the junctional protein ALCAM, suggesting that ART impacts monocyte functions. Our data provide a novel method for simultaneous detection of HIV and host transcripts. We identify potential targets, such as those genes whose expression is increased in HIV+ mature monocytes compared to HIVexp, to block their entry into tissues, preventing establishment/replenishment of HIV reservoirs even with ART, thereby reducing and/or eliminating viral burden and HIV-associated comorbidities. Our data also highlight the heterogeneity of mature monocyte subsets and their potential contributions to HIV pathogenesis in the ART era.

overall_design: Uninfected mature monocytes (n = 2 independent biological samples), HIV-infected mature monocytes (n = 2 independent biological samples), HIV-infected ART-treated mature monocytes (n = 3 independent biological samples)

first: Brenda

last: Morsey

first: Meng

last: Niu

first: Howard

last: Fox

first: Joan

middle: W

last: Berman


title: DNA methylation reorganization of skeletal muscle-specific genes in response to gestational obesity

city: Salt, Girona

first: Anna

last: Prats-Puig

state: Girona

address: Francesc Macia 65

institute: EUSES. Escola Universitària de la Salut i l'Esport.

summary: DNA methylation was measured in sixteen pregnant women [8-gestational obesity group; 8-control group] in umbilical cord using the Infinium Methylation EPIC Bead Chip microarray. Differentially methylated CpGs were identified with Beta Regression Models (false discovery rate (FDR)<0.05 and an Odds Ratio>1.5 or <0.67). DNA methylation interactions between CpGs of skeletal muscle-specific genes were studied using data from Pearson correlation matrices. In order to quantify the interactions within each network, the number of links was computed. The associations between methylation levels of skeletal muscle-specific genes in umbilical cord tissue and infant’s anthropometric and metabolic variables at birth and at age 6 were analyzed by Spearman’s correlation.

overall_design: Genomic DNA was extracted from the Wharton’s jelly and blood vessels using the Gentra PureGene tissue kit (Qiagen). Sodium bisulfite conversion of DNA was performed, and the chemically modified DNA was then used to analyze the methylation status of over 850,000 individual CpGs in umbilical cord tissue using the Infinium Methylation EPIC Bead Chip microarray (Illumina) at IIS La Fe (Valencia, Spain). DNA methylation data quality control and normalization were performed using the minify R-package (version 1.26.2).

first: Sergi

last: García-Retortillo

first: Miquel

last: Puig-Parnau

first: Fidanka

last: Vasileva

first: Raquel

last: Font-Lladó

first: Sílvia

last: Xargay-Torrent

first: Gemma

last: Carreras-Badosa

first: Berta

last: Mas-Parés

first: Judit

last: Bassols

first: Abel

last: López-Bermejo


title: Transcriptional analysis of non-fibrotic NAFLD progression

first: Michael

last: Kriss

institute: University of Colorado School of Medicine

summary: Background & Aims:  Non-alcoholic steatohepatitis (NASH), a subtype of non-alcoholic fatty liver disease (NAFLD) that can lead to fibrosis, cirrhosis, and hepatocellular carcinoma, is characterized by hepatic inflammation.  Despite evolving therapies aimed to ameliorate inflammation in NASH, the transcriptional changes that lead to inflammation progression in NAFLD remain poorly understood.  The aim of this study is to define transcriptional changes in early, non-fibrotic NAFLD using a biopsy-proven non-fibrotic NAFLD cohort.  Methods:  We extracted RNA from liver tissue of 40 patients with biopsy-proven NAFLD based on NAFLD Activity Score (NAS) (23 with NAS ≤3, 17 with NAS ≥5) and 21 healthy controls and compared changes in expression of 594 genes involved in innate immune function.    Results:  Compared to healthy controls, NAFLD patients with NAS ≥5 had differential expression of 211 genes, while those with NAS ≤3 had differential expression of only 14 genes.  Notably, osteopontin (SPP1) (3.74-fold in NAS ≤3, 8.28-fold in NAS ≥5) and CXCL10 (2.27-fold in NAS ≤3, 8.28-fold in NAS ≥5) gene expression were significantly upregulated with histologic progression of NAFLD.

sample_organism:
Homo sapiens
blank sample

overall_design: We extracted RNA from liver tissue of 40 patients with biopsy-proven NAFLD based on NAFLD Activity Score (NAS) (23 with NAS ≤3, 17 with NAS ≥5) and 21 healthy controls (protocol biopsy obtained during living liver donation) and compared changes in expression of 594 genes involved in innate immune function

first: Lucy

last: Golden-Mason

first: Jeffrey

last: Kaplan

first: Crystal

last: Richt

first: Hugo

middle: R

last: Rosen


title: Effects of ascorbic acid on topotecan-induced DNA damage in human tumor cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To investigate mechanisms and differential gene expressions in topotecan-induced DNA damage and effects of ascorbic acid/hydrogen peroxide on these genes in topotecan cytotoxicity in tumor cells

overall_design: MCF-7 breast tumor cells were treated with toptecan and combinations of topotecan and ascorbic acid in RPMI 1640 media containing 10% FBS for various times. Cells wre lysed with Triazol reagent and tyotal RNA was extracted and purified.

first: Birandra

middle: K

last: Sinha


title: Epidermis Kif3a knockout transcriptome reveals genes involved in skin barrier homeostasis

status: Public on Jul 07 2020

city: Cincinnati

first: Gurjit

last: Khurana Hershey

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: In order to address Kif3a role in skin barrier, we performed RNA-seq on 8 week old animals and addressed diffferentially expressed genes.

overall_design: Epidermis mRNA profiles of 8 week old wild type and Kif3a-/- mice

first: Mariana

last: Stevens

first: Zhonghua

last: Zhang

first: Arjun

last: Kothari