title: Amphotericin B, CdCl2 and Congo Red stress responses in a delta-atfA mutant and a control Aspergillus nidulans strains.

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: This study is the continuation of our previous study (Emri et al. BMC Genomics. 2015;16:478. doi: 10.1186/s12864-015-1705-z.). Here, we tested further three stress conditions using the same DNA chips, strains and culturing conditions as in our previous work. We combined the old and the new data sets to study the existence of environmental stress response in A. nidulans.

overall_design: Transcriptome data of amphotericin B (AmB), CdCl2 and Congo Red (CR) treated as well as untreated cultures generated with the A. nidulans TNJ 92.4 (delta-atfA) mutant and the THS30.3 reference strain.

first: Tamás

first: Károly

last: Antal

first: István

last: Pócsi


title: Systems-level analysis of monocyte responses in inflammatory bowel disease identifies IL-10 and IL-1 cytokine networks that regulate IL-23

status: Public on Aug 01 2020

city: Indianapolis

first: Boyd

last: Steere

state: IN

address: Lilly Corporate Center

department: Immunology

country: USA

institute: Lilly

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Characterization of Antibiotic Resistance and Metal Homeostasis Genes in Midwest USA Agricultural Sediments

city: Columbus

first: Michael

last: Brooker

state: OH

address: 590 Woody Hayes Drive

department: Food, Agricultural, and Biological Engineering

institute: The Ohio State Unviersity

summary: Two-stage channels are a relatively new best management practice design used to treat nonpoint pollution. Soils collected from these channels in agricultural ditches were analyzed to elucidate the microbial functionality of the system.

overall_design: Genomic DNA was extracted from the soils of three sites collected in distinct Level IV US Ecoregions. Sampling was conducted in two years, and the initial set included duplicates for each site. DNA was hybridized on the GeoChip 5.0M.

first: M

middle: R

first: P

middle: J

last: Mouser


title: Comparison of the LIGHT and TGF-B1 induced transcriptomes in esophageal FBL

status: Public on Aug 03 2020

city: La Jolla

first: Mario

middle: J. Cabrero

last: Manresa

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

summary: To understand the transcriptional responses induced by LIGHT in esophageal fibroblasts and compare them to the pro-fibrotic TGF-B1

overall_design: Esophageal FBL isolated from esophagus specimens from 4 different human donors were treated with vehicle or 5ng/ml TGF-B1 or 50ng/ml LIGHT for 24 hours. RNA was extracted and analyzed.

last: Cabrero Manresa

first: Seema

middle: S

last: Aceves

last: Croft


title: Inflammatory Signals induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration

city: Cambridge

first: Joo-Hyeon

last: Lee

address: Puddicombe Way, Cambridge Biomedical Campus

country: United Kingdom

institute: Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge

summary: Tissue regeneration is a multi-step process mediated by diverse cellular hierarchies and states that are also implicated in tissue dysfunction and pathogenesis.  Here, we leveraged single-cell RNA sequencing in combination with in vivo lineage tracing and organoid models to finely map the trajectories of alveolar lineage cells during injury repair and lung regeneration. We identified a distinct AT2-lineage population, Damage-Associated Transient Progenitors (DATPs), that arises during alveolar regeneration. We found that interstitial macrophage-derived IL-1β primes a subset of AT2 cells expressing Il1r1 for conversion into DATPs via a HIF1α-mediated glycolysis pathway, which is required for mature AT1 cell differentiation. Importantly, chronic inflammation mediated by IL-1β prevents AT1 differentiation, leading to aberrant accumulation of DATPs and impaired alveolar regeneration.  Together, this step-wise mapping to cell fate transitions shows how an inflammatory niche impairs alveolar regeneration by controlling stem cell fate and behavior.

overall_design: For this scRNA-seqeuncing, AT2 cells were isolated from Sftpc-CreERT2;R26RTomato mice treated with tamoxifen and lung organoids derived from AT2 cells isolated from SPC-CreERT2;R26RTomato mice were established for 2 weeks in co-culture with stromal cells. The expression levels were quantified using the Chromium Controller (10X Genomics).

first: Jinwook

last: Choi

first: Jong-Eun

last: Park

first: Georgia

last: Tsagkogeorga

first: Motoko

last: Yanagita

first: Bon-Kyoung

last: Koo

first: Namshik

last: Han


title: Gene expression analysis of PBMC's from IBD subjects stimulated by combinations of LPS, MDP, anti-CD3/anti-CD28 antibodies, and anti-IL10R antibodies.

summary: We systematically investigated the transcriptomic response pattern of PBMC from 41 patients with IBD to characterize relevant stimuli that target different aspects of innate and adaptive immune cell responses. Lipopolysaccharide(LPS), muramyl-dipeptide (L18MDP), T cell receptor and co-stimulation (αCD3/αCD28 coated beads), and IL-10 signalling blockade were used to sitmulate subject PBMC's alone or in combination based on the concept that innate pathogen recognition receptor responses (in particular NOD2 and TLR4), T cell responses, and IL-10 signalling defects are implicated by multiple genetic IBD susceptibility loci and Mendelian forms of IBD.

overall_design: PBMC's isolated from IBD patients were subjected to microarray gene expression analysis after 16 hours of stimulation (by LPS, L18MDP and anti-CD3/anti-CD28 coated beads) in the presence or absence of IL-10 receptor-blocking antibodies.

first: D

last: Aschenbrenner

last: Quaranta

first: B

first: G

last: Rocha

first: H

middle: H

last: Uhlig


title: Expression data from rectal cancer

city: Beijing

first: Haizhao

last: Yi

address: No. 52 Fucheng Rd., Haidian District

country: China

institute: Peking University Cancer Hospital & Institute

summary: A supervised method (Significance Analysis of Microarrays -SAM-) was used to find statistically significance (adjusted p<0.05) in differentially expressed genes between responding and non-responding groups.

overall_design: To further investigate the correlation between gene expression and response to neoadjuvant radiotherapy, mRNA expression in pre-therapy biopsies was profiled into responding and non-responding groups.

first: Dengbo

last: Ji


title: Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis

status: Public on Aug 02 2020

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles


title: Sustained sensing of commensal-derived products directs polarized immune cell positioning within the liver to optimize host defense

status: Public on Jul 31 2020

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

summary: The liver is located at the interface between the intestinal portal vasculature and the general circulation, employing a complex set of innate and adaptive immune cells to protect from the continuous systemic threat of gut-translocating pathogens. In contrast to lymphoid tissues in which asymmetric, polarized spatial positioning of distinct cell types plays an essential role in optimal host defense, the relationship between liver phagocytes and lymphoid element distribution and their immune functions is currently unknown. This lack of organization stands in marked contrast to the extensively documented zonation of hepatocyte metabolic function controlled by Wnt signaling during development. Here we used quantitative multi-parameter confocal imaging to re-examine resident immune cells distribution in the liver, finding that both myeloid (Kupffer cell -KC) and lymphoid (NKT cell) components are substantially enriched in the peri-portal regions of the liver lobule, the entry point for portal venous blood rich in gut-derived pathogens and molecules. Peri-portal immune enrichment of KCs was lost in germ-free (GF) animals and coincided temporally with weaning and microbial colonization, suggesting that immune cell positioning was not a developmentally programmed process but rather dependent on extrinsic factors. Conditional ablation of MyD88-dependent bacterial product sensing by liver sinusoidal endothelial cells (LSECs) disrupted KC spatial organization animals, consistent with immune cell positioning within the liver architecture arising from sustained, active responses of LSECs to microbial stimuli. Bacterial challenge studies revealed that this asymmetric peri-portal-biased immune cell localization protects the liver and the host against bacterial dissemination. Together, these data reveal that LSECs act as microbiome sensors, actively promoting concentration of protective immune components in the sub-regions of the liver most susceptible to infection to provide optimal host defense against systemic pathogen spread.

overall_design: Analysis of liver lobule gradient endothelial cells in wild-type and knock out conditions with macrophages

first: Anita

last: Gola

first: Michael

last: Dorrington

first: Claudia

last: Sala

first: Rochelle

last: Shinh

first: Andrea

last: Radtke

first: Harikesh

last: Wong

first: Antonio

middle: P

last: Baptista

first: Jonathan

last: Hernandes

first: Gastone

last: Castellani

first: Sonja

middle: M

last: Best

first: Iain

last: Fraser

first: Ronald

middle: N

last: Germain


title: The ISW1a ATP-dependent chromatin remodeler acts specifically on dinucleosomes to regulate early transcription [ChIP-seq]

city: Smithville

first: Blaine

last: Bartholomew

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The large family of ATP-dependent chromatin remodelers that regulate chromatin organization  and composition are thought to act only on individual mononucleosomes. We discovered  however that the yeast ISW1a remodeler has a much higher affinity for dinucleosomes and only  efficiently converts ATP hydrolysis into nucleosome movement when bound to dinucleosomes,  not mononucleosomes. The Ioc3 accessory subunit and its HLB DNA binding domain confer  dinucleosome specificity onto the Isw1 catalytic subunit. Perturbation of ISW1a dinucleosome  specificity by mutating Ioc3 interferes with its localization immediately downstream of the early  transcription complex. ISW1a and NuA4, a histone acetyl transferase, and SWR1, a histone  exchanger, are required together to slow early passage of RNA polymerase II. These findings  provide new insights into the unusual specificity of a chromatin remodeler regulating the  transition from transcription initiation to elongation and its functional interplay with other  chromatin modifiers.

overall_design: Eight samples (Input and IP of WT ISW1a and Ioc3△cHLB duplicates) are compared using ChIP-seq

first: Solomon

middle: G

last: Hailu


title: Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors [iR_iHEC]

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

summary: We inserted the inducible expression cassette of Runx1 into the Rosa26 locus of embryonic  stem  cells.  Based  on  a  modified  protocol  for  HEC  induction  from  PSC,  we  successfully generated iHEC Under the haematopoietic induction process (iR-HEC).

overall_design: mRNA profiles of single hematopoietic endothelia cells (iR-iHEC). single iR-iHECs were sorted from PSC-derived cells for RNAseq analysis according to kit instruction of Discover-sc WTA Kit V2(Vazyme) and TruePrepTM  DNA Library Prep Kit V2 (Vazyme), using illumina HiSeq X Ten.

first: Qitong

last: Weng


title: T cell regeneration from pluripotent stem cells by defined transcription factors Runx1 and Hoxa9 [single hematopoietic cells (iR9-iHEC&iR9-iHPC) II]

summary: We identified that the coordinated expression of exogenous Runx1 and Hoxa9 during the haematopoietic induction process from mouse PSC resulted in a type of induced hemogenic endothelial cells (iHEC). The single iHEC can be robustly educated into induced haematopoietic progenitor cells (iHPC), which gave rise to induced T cells (iT cells) with abundant TCRαβ repertoire in vivo. We  sorted  the  single iHEC and iHPC  from  day-14,  day-17,  day-21  cell  products  derived  from  241 iR9-ES  and  performed  single-cell  RNA-Seq.

overall_design: mRNA profiles of single hematopoietic endothelia cell (iHEC) or hematopoietic progenitor cell. single cells were sorted from PSC-derived cells for RNAseq analysis according to kit instruction of Discover-sc WTA Kit V2(Vazyme) and TruePrepTM  DNA Library Prep Kit V2 (Vazyme), using illumina HiSeq X Ten.


title: T cell regeneration from pluripotent stem cells by defined transcription factors [T cells [CD4 and CD8])

summary: We established a de novo approach of generating T cells from mouse ESC/iPSC by defined transcription factors.

overall_design: mRNA profiles of two T-cell types, 1000 of each cell type was sorted for RNAseq analysis according to kit instruction of Discover-sc WTA Kit V2(Vazyme) and TruePrepTM  DNA Library Prep Kit V2 (Vazyme), using Illumina NextSeq500.


title: T cell regeneration from pluripotent stem cells by defined transcription factors [T cell receptors (TCR)]

summary: We established a de novo approach of generating T cells from mouse ESC/iPSC.

overall_design: mRNA profiles of T cell receptors (TCR), including TCR of induced CD4SP/CD8SP sorted from spleen or thymus. 15000 of each cell type were sorted for RNAseq analysis according to kit instruction of SMARTer Mouse TCR a/b Profiling Kit (Clontech) , using Illumina MiSeq.


title: Expression data from  lens epithelial cells (LECs) from Shumiya cataract rats (SCR) with  or without cataract (Cat+ or Cat-)

city: Kahoku

first: Eri

last: Kubo

state: Ishikawa

address: 1-1 Daigaku, Uchinada

department: Ophthalmology

country: Japan

institute: Kanazawa Medical University

summary:
The Shumiya cataract rat (SCR) is a model for hereditary cataract. Two-third of these rats develop lens opacity within 10-11-weeks. Onset of cataract is attributed to the synergetic effect of lanosterol synthase (Lss) and farnesyl-diphosphate farnesyltransferase 1 (Fdft1) mutant alleles that lead to cholesterol deficiency in the lenses, which in turn adversely affects lens biology including the growth and differentiation of lens epithelial cells (LECs). Nevertheless, the molecular events and changes in gene expression associated with the onset of lens opacity in SCR is poorly understood.
Our study aimed to identify the gene expression patterns during cataract formation in SCRs, which may be responsible for cataractogenesis in SCR.

overall_design: Total RNA from each LEC sample obtained from 5-week-old cataractous (Cat+) SCR with Lss mutation and non-cataractous (Cat-) SCRs without Lss mutation as control were used for the Affymetrix microarray analysis.

first: Hidetoshi

last: Ishida


title: T cell regeneration from pluripotent stem cells by defined transcription factors


title: ERK1/2 controlled genes ANGPT2 and CXCR4 mediate liver metastasis from colon cancer

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

type:
Expression profiling by array
Third-party reanalysis

summary:
Carcinoma development in colorectal cancer (CRC) is driven by genetic alterations in numerous signaling pathways. Alterations in the RAS-ERK1/2 pathway are associated with the shortest overall survival for patients after diagnosis of CRC metastatic disease, but how RAS-ERK signaling regulates CRC metastasis is still unknown.
An unbiased screening approach based on selection of highly liver metastatic CRC cells in vivo was used to determine genes associated with metastasis and a ERK1/2-controlled metastatic gene set (EMGS) defined. The ANGPT2 and CXCR4, two genes within the gene set, were subjected to gain and loss of function validation in CRC cells (SW620, SW480, Colo26, HCT116), its downstream mechanism validated, and tested in clinical samples.
Here, we identified an EMGS that is associated with increased recurrence and reduced survival for patients with CRC tumors. Higher levels of EMGS expression were detected in the CRC subsets Consensus Molecular Subtype (CMS)1 and CMS4. We show that the RAS-ERK1/2 axis controls the expression of the cytokine ANGPT2 and the cytokine receptor CXCR4 in CRC cells, and that this facilitates the development of liver but not lung metastases, suggesting that ANGPT2 and CXCR4 are essential for metastatic outgrowth in the liver. We also show that CXCR4 also controls the expression of the cytokines IL10 and CXCL1, and provide evidence for a causal role of IL10 in supporting liver colonization.
In summary, we demonstrate that amplification of ERK1/2 signaling in KRAS-mutated CRC cells affects the cytokine milieu of the tumors, thus possibly affecting tumor?stroma interactions and favoring liver metastasis formation.

overall_design: In total 9 samples were analysed, 4 replicates of SW620_Parental cell line, 4 replicates of SW620_LiM2 cell line and 1 replicate of SW620_LiM2 treated with 10uM U0126 inhibitor. Out of them, 7 correspond to reanalyses of samples from the GSE33350 series:  GSM824901, GSM824898, GSM824899 and GSM824900 (SW620_Parental cell line); GSM824902, GSM824903 and GSM824904 (untreated SW620_LiM2 cell line). These samples were re-processed together with the rest of cel files as described in the protocols section.

first: Jelena

last: Urosevic

first: Alicia

last: Llorente

first: Anna

last: Bellmunt

last: Berenguer

first: Marc

last: Guiu

first: Esther

last: Fernandez

first: Ivan

last: Burkov

first: Maria

last: Clapes

first: Mireia

last: Cartana

first: Eduard

last: Batlle

first: Angel

last: Nebreda

first: Roger

last: Gomis


title: Cross-cancer genome-wide association study of endometrial cancer and epithelial ovarian cancer identifies genetic risk regions associated with risk of both cancers

status: Public on Jul 30 2020

city: Brisbane

first: Tracy

last: O'Mara

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Accumulating evidence suggests a relationship between endometrial cancer and epithelial ovarian cancer. For example, endometrial cancer and epithelial ovarian cancer share epidemiological risk factors and molecular features observed across histotypes are held in common (e.g. serous, endometrioid and clear cell). Independent genome-wide association studies (GWAS) for endometrial cancer and epithelial ovarian cancer have identified 16 and 27 risk regions, respectively, four of which overlap between the two cancers. Using GWAS summary statistics, we explored the shared genetic etiology between endometrial cancer and epithelial ovarian cancer. Genetic correlation analysis using LD Score regression revealed significant genetic correlation between the two cancers (rG = 0.43, P = 2.66 × 10-5). To identify loci associated with the risk of both cancers, we implemented a pipeline of statistical genetic analyses (i.e. inverse-variance meta-analysis, co-localization, and M-values), and performed analyses by stratified by subtype. We found seven loci associated with risk for both cancers (PBonferroni < 2.4 × 10-9). In addition, four novel regions at 7p22.2, 7q22.1, 9p12 and 11q13.3 were identified at a sub-genome wide threshold (P < 5 × 10-7). Integration with promoter-associated HiChIP chromatin loops from immortalized endometrium and epithelial ovarian cell lines, and expression quantitative trait loci (eQTL) data highlighted candidate target genes for further investigation.

overall_design: We performed H3K27Ac HiChIP on an immortalised ovarian surface epithelial cell line

first: Dylan

last: Glubb

middle: A


title: RNA-seq of total RNA in budding yeast wild-type and rrp6∆ strains, and in dbr1∆ or sen1-1 dbr1∆ strains expressing either a control or decoy RNA.

status: Public on Jul 24 2020

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

summary: We obtained transcriptome profiles of different S.cerevisiae strains. This allowed us to determine the impact of defective nuclear exosome and expression of an RNA decoy on NNS-dependent transcription termination.

overall_design: Examination of the transcriptome of budding yeast wild-type and rrp6∆ strains, and in dbr1∆ or sen1-1 dbr1∆ strains expressing either a control or decoy RNA.

first: Tommaso

last: Villa

first: Mara

last: Barucco

first: Maria-Jose

last: Martin-Niclos

first: Alain

last: Jacquier


title: The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution

status: Public on Jul 27 2020

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

institute: INSiGENe Pty Ltd

summary: The bone marrow microenvironment of leukemia plays a key role in leukemia progression, but its molecular complexity in pre-B acute lymphoblastic leukemia (B-ALL), the most common cancer in children, remains poorly understood. Here we use single-cell RNA sequencing to characterise the bone marrow microenvironment during B-ALL progression.

overall_design: Five samples were collected during B-ALL disease progression at days 0, 3, 6, 9 and 12


title: Spo11-oligo mapping in S. cerevisiae strain SK1

status: Public on Jul 23 2020

city: New York

first: Hajime

last: Murakami

state: NY

address: 1275 york ave

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

overall_design: Eleven Spo11-oligo maps total: two biological replicate of zip3Δ generated at 5 h in meiosis, two biological replicate of zip3Δ homeologous generated at 5 h in meiosis, two biological replicate of ecm11Δ generated at 5 h in meiosis, homeologous strain generated at 4 h and 5 h in meiosis, trisomic strain generated at 4, 5 and 6 h in meiosis

first: Xiaojing

last: Mu

first: Scott

last: Keeney


title: Ikaros/STAT5 DNA binding competition in pre-B cell line  [ChIP-seq]

status: Public on Jul 22 2020

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

summary: Ikaros was found to antagonize the transcriptional program of IL-7 activated pathways during pre-B cell differentiation. We analyzed the genomic distribution of Ikaros and STAT5 (downstream effector of IL-7; in the presence or absence of Ikaros) in pre-B cells by ChIP-Seq.

overall_design:
A Ikaros deficient, IL-7 dependent pre-B cell line was reconstituted with a Tamoxifen inducible Ikaros-ER fusion protein. 24h after Ikaros induced expression, we performed an Ikaros and STAT5 ChIP-Seq analysis.

The samples Ikaros-ChIP and Input are re-used from GSE114629.

first: B

last: Heizmann

first: P

last: Katsner

first: S

last: Chan


title: Identification of CaMKII splice variants expressed in the human hippocampus

status: Public on Jul 21 2020

city: Amherst

first: Roman

last: Sloutsky

state: MA

address: 710 North Pleasant Street LGRT 1106

department: Biochemistry and Molecular Biology

institute: UMass Amherst

summary:
Purpose: The goal of this study was to use deep sequencing to identify all splice variants of Calcium/calmodulin-dependent kinase II (CaMKII) expressed in the human hippocampus.
Methods: Transcripts of CaMKII-encoding genes (CAMK2A, CAMK2B, CAMK2G, and CAMK2D) were sub-amplified by PCR from total RNA extracted from human hippocampal tissue samples from 3 donors. Illumina sequencing libraries were constructed by PCR from these initial pools of amplicons and sequenced on an Illumina MiSeq instrument. Sequencing reads passing quality controls were clustered on the basis of sequence identity or near-identity. Consensus sequences of clusters were mapped with known exons of CaMKII genes to identify the splice variant represented by each cluster. Donor 1 replicate 2, Donor 2, and Donor 3 libraries from genes CAMK2B, CAMK2G, and CAMK2D were first sequenced on a MiSeq Nano flow cell, then re-pooled for read balancing and sequenced again of a full-size MiSeq flow cell. For each library, reads from Nano and full-size flow cells were combined for subsequent analysis.
Results: We perfomed the first comprehensive survey of CaMKII transcripts expressed in individual tissue samples (human hippocampus). We detected a total of 79 splice variants of the four human CaMKIIs: CaMKIIα (3), CaMKIIβ (30), CaMKIIγ (24), and CaMKIIδ (22), across tissue samples from 3 donors. This represents the vast majority of possible in-frame CaMKII splice variants (Sloutsky and Stratton, European Journal of Neuroscience, 2020;  https://doi.org/10.1111/ejn.14761).

overall_design: Deep sequencing of sub-amplicons of transcripts from four CaMKII-encoding genes (CAMK2A, CAMK2B, CAMK2G, and CAMK2D)

first: Rachel

last: Bates

first: Margaret

last: Stratton


title: Activation of SIRT6 by DNA hypomethylating agents and clinical consequences on combination therapy in leukemia

status: Public on Jul 28 2020

city: Institute

first: Sridhar

last: Malkaram

state: West Virginia

address: Barron Drive

department: Mathematics and Computer Sciences

institute: West Virginia State University

summary: The FDA-approved DNA hypomethylating agents (DHAs) like 5-azacytidine (5AC) and decitabine (DAC) demonstrate efficacy in the treatment of hematologic malignancies. Despite previous reports that showed histone acetylation changes upon using these agents, the exact mechanism underpinning these changes is unknown. In this study, we investigated the relative potency of the nucleoside analogs and non-nucleoside analogs DHAs on DNA methylation reversal using DNA pyrosequencing. Additionally, we screened their effect on the enzymatic activity of the histone deacetylase sirtuin family (SIRT1, SIRT2, SIRT3, SIRT5 and SIRT6) using both recombinant enzymes and nuclear lysates from leukemia cells. The nucleoside analogs (DAC, 5AC and zebularine) were the most potent DHAs and increased the enzymatic activity of SIRT6 without showing any significant increase in other sirtuin isoforms. ChIP-Seq analysis of bone marrow cells derived from six acute myeloid leukemia (AML) patients and treated with the nucleoside analog DAC induced genome-wide acetylation changes in H3K9, the physiological substrate for SIRT6. Data pooling from the six patients showed significant acetylation changes in 187 gene loci at different chromosomal regions including promoters, coding exons, introns and distal intergenic regions. Signaling pathway analysis showed that H3K9 acetylation changes are linked to AML-relevant signaling pathways like EGF/EGFR and Wnt/Hedgehog/Notch. To our knowledge, this is the first report to identify the nucleoside analogs DHAs as activators of SIRT6. Our findings provide a rationale against the combination of the nucleoside analogs DHAs with SIRT6 inhibitors or chemotherapeutic agents in AML due to the role of SIRT6 in maintaining genome integrity and DNA repair.

overall_design:
We compared the relative potency of different DHAs in reversing DNA methylation and screened their activity against the NAD+-dependent HDAC sirtuins (SIRT1, SIRT2, SIRT3, SIRT5 and SIRT6). The nucleoside analogs DAC, 5AC and zebularine were more potent than the non-nucleoside analogs in reversing DNA methylation. Moreover, they significantly increased the activity of SIRT6 isoform in both recombinant enzyme assay and in nuclear lysates. DAC induced genome-wide changes in the acetylation of H3K9, the physiological substrate of SIRT6.
This dataset includes H3K9ac ChIP-seq of DAC- or DMSO-treated bone marrow mononuclear cells from AML patients.

first: Tamer

middle: E

last: Fandy

first: Hetty

last: Carraway

first: Yana

last: Cen

first: Jun

last: Fan

first: Hamdy

last: Ali

first: Zakaria

last: Elmageed

first: Thomm

last: Buttolph

first: Aymen

last: Shatnawi

first: James

last: Denvir

first: Donald

last: Primerano


title: High-resolution mapping of budding yeast Nab3, Nrd1, and RNA polymerase II by CRAC in wild-type and rrp6∆ strains.

first: Domenico

last: Libri

summary: We obtained Nab3, Nrd1, and RNA polymerase II occupancy profiles across the genome of S.cerevisiae in wild-type and rrp6∆ strains. This allowed us to determine the impact of defective nuclear exosome on NNS-dependent transcription termination.

overall_design: RNA was crosslinked to Nab3, Nrd1, or RNA polymerase II and sequenced after protein purification under stringent and denaturing conditions. This reveals the position of the proteins at the nucleotide resolution level and the extent of their binding to RNA in wild-type versus rrp6∆ cells.

first: Tommaso

last: Villa

first: Mara

last: Barucco

first: Maria-Jose

last: Martin-Niclos

first: Alain

last: Jacquier


title: Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors [single hematopoietic cells (iHEC)]

first: Jinyong

last: Wang

overall_design: mRNA profiles of 73 single hematopoietic endothelia cells (iHEC). single HCs were sorted from PSC-derived cells for RNAseq analysis according to kit instruction of Discover-sc WTA Kit V2(Vazyme) and TruePrepTM  DNA Library Prep Kit V2 (Vazyme), using illumina NextSeq500.

first: Qitong

last: Weng


title: Identification of BMP-regulated genes in early gastrulation stage zebrafish embryos

city: Tübingen

first: Katherine

middle: Wallace

last: Rogers

address: Max-Planck-Ring 9

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

summary: We report the systematic identification of BMP (bone morphogenetic protein) target genes in zebrafish during dorsal-ventral patterning using RNA-sequencing.

overall_design: Transcript levels in shield-stage zebrafish embryos overexpressing bmp or the BMP inhibitor chordin (chd) were compared to transcript levels in uninjected embryos using RNA-sequencing. Three repeats containing 10 embryos each were analyzed per condition.

middle: W

first: Patrick

last: Müller


title: Loss of Fbxw7 triggers mammary tumorigenesis associated with E2F/c-Myc activation and Trp53 mutation

status: Public on Jul 15 2020

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: Fbw7 is a tumor suppressor protein that regulates the degradation of a multitude of oncogenic substrates, such as c-Jun, c-Myc, Notch1 intracellular domain, and cyclin E. Loss of FBXW7 expression is relatively common in breast cancer. Despite this, the effect of FBXW7 loss on breast tumorigenesis has not been examined. We demonstrate here that loss of FBXW7 is sufficient for breast tumorigenesis. Many of Fbw7’s substrates are transcription factors or are closely linked to transcription factor pathways. As loss of Fbw7 results in upregulation of multiple substrates, we set out to determine which, if any of these transcription factor pathways predominate early after Fbw7 loss and after tumorigenesis. To address this, we employed genome-wide RNA sequencing to examine transcription factor pathway alterations early after FBXW7 loss in non-tumor breast epithelial cells as well as after prolonged FBXW7 loss, in tumor samples. We demonstrate an early upregulation of E2F and c-Myc pathways that is reinforced upon tumorigenesis. These findings suggest E2F and c-Myc as important targetable pathways in Fbw7 low breast cancer patients.

overall_design: RNA-seq of 4 conditions, 1-6 replicates of each

first: Meyer

last: Alison

first: Furumo

last: Quinlan

first: Stelloh

last: Cary

first: Minella

last: Alex

first: Rao

last: Sridhar


title: Inhibition of Inflammatory Signaling in Pax5 Mutant Cells Mitigates B-cell leukemogenesis  against leukemia

status: Public on Jul 17 2020

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary:
We used microarrays to investigate gene expression changes in healthy and leukemic cells from Pax5+/- and IL6+/-;Pax5+/- mice in CF and SPF housing conditions.
PAX5 is one of the most frequently mutated genes in B-cell acute lymphoblastic leukemia (B-ALL), and children with inherited preleukemic PAX5 mutations are at a higher risk of developing the disease. Abnormal profiles of inflammatory markers can be detected in neonatal blood spot samples of children who later developed B-cell precursor B-ALL. However, how inflammatory signals contribute to B-ALL development is unclear. Here, we demonstrate that Pax5 loss results in the enhanced production of the inflammatory cytokine interleukin-6 (IL-6), which appears to act in an autocrine fashion to promote leukemia growth. In vivo genetic downregulation of IL-6 in Pax5 mutant mice retards B-cell leukemogenesis. In vivo pharmacologic inhibition of IL-6 with a neutralizing IL-6 antibody in Pax5 mutant mice with B-ALL clears leukemic cells. This exciting novel IL 6 signaling paradigm identified in mice was also substantiated in humans. Altogether, our studies establish aberrant IL6 expression caused by Pax5 loss as a hallmark of Pax5-dependent B-ALL and the IL6 as a therapeutic vulnerability for B-ALL characterized by PAX5 loss.

first: Marta

last: Isidro-Hernández

first: Andrea

last: Colino

first: Ana

last: Casado-García

first: Javier

last: Raboso-Gallego

first: Alberto

last: Orfao

first: Jordi

last: Salas

first: Josep

last: Ribera

first: Lurdes

last: Zamora

first: Oscar

last: Blanco

first: Diego

last: Alonso-López

last: De Las Rivas

first: Rafael

last: Jiménez

first: Francisco

last: Criado

first: María

middle: B

last: Cenador

first: Manuel

last: Ramírez-Orellana

first: César

last: Cobaleda

first: Carolina

last: Vicente-Dueñas

last: Sánchez-García


title: Integrative analysis of transcriptome and proteome sheds light on functional differences between human salivary glands

status: Public on Jul 10 2020

city: Viken

first: Marie

last: Saitou

state: Viken

address: Ås

country: Norway

institute: NMBU

summary: Saliva aids in the predigestion of food and perception of taste. It helps to maintain the integrity of the mineralized tooth and epithelial surfaces in the mouth, and shields the oro-digestive tract from environmental hazards and invading pathogens. Although salivary glands and saliva fluid are biologically and functionally inseparable, they have thus far been investigated as separate entities. To bridge this gap, we performed an integrative analysis of the transcriptome of 27 samples collected from the major human adult and fetal major salivary glands - submandibular, sublingual, and parotid - along with mass-spectrometry-based saliva proteome data and immunohistochemical localization in glandular tissue. Our results suggest that functional maturation at the transcriptome level occurs late in gland development, and is driven mainly by the transcription of genes that code for secreted saliva proteins. We further provide evidence that protein dosage of the most abundant salivary proteins secreted by the salivary glands is predominantly regulated at the transcriptome level. Finally, we demonstrate distinct transcriptomic profiles of each major salivary gland type that reveal functional specialization and will aid in future clinical analyses. Our study provides the hitherto most comprehensive RNAseq dataset of healthy salivary glands in humans, thus establishing a robust framework for deeper studies of saliva and salivary gland biology, development, and evolution, ultimately paving the way for better understanding the importance of these craniofacial secretory organs in health and their malfunctions in disease.

overall_design: We report an integrative analysis of the transcriptome of 27 samples collected from the human adult and fetal major salivary glands - submandibular, sublingual, and parotid

first: Erica

last: Xu

first: Sarah

last: Knox

first: Omer

last: Gokcumen


title: Single-cell profile of atrial human fibroblasts in cardiac arrhythmia atrial fibrillation (AF) - 10x

city: Oxford

first: Svetlana

last: Reilly

state: Oxfordshire

address: JOhn Radcliffe Hospita, Headley Way

department: Cardiovascular Medicine, Radcliffe Dept of Medicine

institute: University of Oxford

summary: Atrial fibrillation (AF), the most common cardiac arrhythmia, is a major contributor to population mortality and morbidity. The goal of this study is to explore molecular mechanisms of the AF-induced profibrotic remodelling in human atrial fibroblasts (ACFs). Specifically, we assessed single-cell transcriptome of cultured human ACFs treated with calcitonin(CT) or vehicle (from 6 individual patients) and of freshly-isolated ACFs from patients with AF (4 individual patients) vs controls (4 individual patients). We found that ACF transcriptome was unaltered by CT in cultured ACFs, and identified 5 transcriptional clusters with 23 differentially expressed transcripts in AF in freshly-ioslated ACFs.

overall_design: mRNA profile of cultured (6 biological replicates conducted in single technical replicates) and freshly-isolated (8 biological replicates conducted in single technical replicates) human ACFs.

first: Agne

last: Antanaviciute


title: Single-cell profile of atrial human fibroblasts in cardiac arrhythmia atrial fibrillation (AF) - SmartSeq2

summary: Atrial fibrillation (AF), the most common cardiac arrhythmia, is a major contributor to population mortality and morbidity. The goal of this study is to explore molecular mechanisms of the AF-induced profibrotic remodelling in human atrial fibroblasts (ACFs). Specifically, we assessed single-cell transcriptome of cultured human ACFs treated with calcitonin(CT) or vehicle (from 6 individual patients) and of freshly-isolated ACFs from patients with AF (4 individual patients) vs controls (4 individual patients) (SR). We found that ACF transcriptome was unaltered by CT in cultured ACFs, and identified 5 transcriptional clusters with 23 differentially expressed transcripts in AF in freshly-ioslated ACFs.


title: A single-cell RNA-seq analysis of molecular characterization of hypothalamic progenitor cells

status: Public on Jul 14 2020

city: Beijing

first: Xin

last: Zhou

address: 15 Datun Road

department: State key laboratory of Brain and Cognitive Science

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: To define molecular and cellular heterogeneity of progenitor cells in the developing mammalian hypothalamus, single cell RNA-sequencing (10x Genomics Chromium) was performed in embryonic human hypothalamus (GW10). We identified four major cell populations, including hypothalamic progenitor cells (HPCs), Glutamatergic neuronal cells, GABAergic neuronal cells and neuropeptidergic neurons. To further reveal the molecular characteristics of HPCs, we analyzed differentially expressed genes (DEGs) of 6 HPC clusters. We showed remarkably diverse transcriptional features within progenitor subtypes, characterized by the combinatorial or specific expression pattern of classic progenitor markers (VIM, NES, FABP7 and SLC1A3), proneural transcription factors (ASCL1, NHLH2 and DLX1) and new neural progenitors enriched candidates such as FAM107A, TTYH1 and HMGA2. The candidates were validated with immunostaining. In summary, our results demonstrated the molecular diversity of neural progenitor in mammalian hypothalamus.

overall_design: Hypothalamus of human were dissected for single-cell RNA-seq (10x Genomics Chromium)

first: X

last: Wang


title: Single-cell profile of atrial human fibroblasts in cardiac arrhythmia atrial fibrillation

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

overall_design: Refer to individual Series


title: Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection

status: Public on Jul 07 2020

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML


title: PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

summary: Spermatogenesis is a complex process of sperm generation, including mitosis, meiosis, and spermiogenesis. During spermiogenesis, histones in post-meiotic spermatids are removed from chromatin and replaced by protamines. Although histone-to-protamine exchange is important for sperm nuclear condensation, the underlying regulatory mechanism is still poorly understood. Here, we identify PHD finger protein 7 (PHF7) as an E3 ubiquitin ligase for histone H3K14 in post-meiotic spermatids. Generation of Phf7-deficient mice and Phf7 C160A knockin mice with impaired E3 ubiquitin ligase activity reveals defects in histone-to-protamine exchange caused by dysregulation of histone removal factor Bromodomain, testis-specific (BRDT) in early condensing spermatids. Surprisingly, E3 ubiquitin ligase activity of PHF7 on histone ubiquitination leads to stabilization of BRDT by attenuating ubiquitination of BRDT. Collectively, our findings identify PHF7 as a critical factor for sperm chromatin condensation and contribute to mechanistic understanding of fundamental phenomenon of histone-to-protamine exchange and potential for drug development for the male reproduction system.

overall_design: single cell RNA sequencing performed with testicular cells from Phf7 f/f and Phf7 tKO mice.

first: C

last: Kim

first: S

last: Park

first: I

last: Baek


title: Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [FB5P-seq_C57Bl6]

summary: The aim of the project is to understand the heterogeneity of murine plasmacytoid dendritic cells (pDC) for interferon I production. For this end we want to perform RNAseq on splenic pDC at ground state and also after infection of mice with MCMV at different time points.

overall_design: This dataset contains data from pDC sorted from wt C57Bl/6 mice, infected or not with Murine CytoMegalo virus (MCMV). Single-cells were FACS-sorted into 7 96-well plates (plates 1 and 2 : non-infected, plates 3 to 7 : infected) and analyzed by 5'-end single-cell RNAseq following the FB5P-seq protocol.

first: Abdenour

last: Abbas

first: Marc

last: Dalod

first: Elena

last: Tomasello


title: RNP-MaP: In-cell analysis of protein interaction networks defines functional hubs in RNA

status: Public on Jul 05 2020

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

summary: RNAs interact with networks of proteins to form complexes (RNPs) that govern many biological processes, but inter-protein networks on RNA are currently impossible to examine in a comprehensive way.  We developed a live-cell RNP-MaP (RNP network analysis by mutational profiling) chemical probing strategy for mapping simultaneous binding by and cooperative interactions among multiple proteins with single RNA molecules at nucleotide resolution. RNP-MaP revealed that two structurally related, but sequence-divergent noncoding RNAs, RNase P and RMRP, share nearly identical RNP networks and, further, that protein-mediated structural communication identifies function-critical network hubs in these RNAs. RNP-MaP identified previously unknown protein interaction networks within the XIST long noncoding RNA that are conserved between mouse and human RNAs and defined silencing, compartmentalization and splicing communities of proteins whose binding sites are networked together on XIST. The XIST E region contains a dense network of protein interactions, and including PTBP1, MATR3, and TIA1 proteins , which RNP-MaP revealed to each bind the XIST E region via two distinct interaction modes.;  Depletion of PTBP1 and MATR3 caused native XIST particles to disperse and disappear in a human cell line. the The highly networked XIST E region was sufficient to mediate XIST RNA-like foci formation in cells. RNP-MaP enables discovery and prioritization of in-cell protein interaction networks critical for function in long RNAs, in the absence of pre-existing knowledge about protein binding sites.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA within cells, extracted from cells, or reconstituted in solution was exposed to varying chemical probes to assess engagement by proteins (RNP-MaP) or structural conformation (SHAPE). Reconstituted solutions included PBS buffer supplemented with magnesium, T7-transcribed RNA, and recombinant proteins. Total RNA or specific RNAs (enriched by antisense pulldown or gene-specific amplificaiton) were subjected to MaP reverse transcription, which encodes the position of chemical adducts in RNA as non-templated nucleotides or deletions within product cDNA. Sequencing libraries were generated using TruSeq or Nextera XT workflows and sequenced on either a MiSeq or NextSeq 500 instrument. Locations of adducts were found using Shapemapper 2 software. Software analysis pipelines were employed to create SHAPE and RNP-MaP profiles, find in-cell reactivity perturbations, locate correlated mutations, and model RNA structures.

first: Parth

last: Jariwala

first: Kevin

last: Weeks


title: Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [FB5P-seq_kinetic]

summary: The aim of the project is to characterize the heterogeneity of murine plasmacytoid dendritic cells (pDCs) and to decipher their activation trajectory during a viral infection in vivo. To this end, individual splenic pDCs were transcriptionally profiled at ground state and at different times during mouse cytomegalovirus infection, with enrichment of IFN-I-producing pDCs based on the use of a reporter mouse strain and on their downregulation of LIFR.

overall_design: This dataset contains data from pDCs sorted from Ifnb1Eyfp reporter mice at different time points after murine cytomegalovirus (MCMV) infection. Single-cells were FACS-sorted into fifteen 96-well plates. One plate of total pDCs was sorted from one uninfected mouse. For the infected mice, pDCs were sorted into 4 different phenotypic populations, to have a view of the total pDC population (gate: pDC total) as well as to enrich the pDCs that were committed to, or fate-mapped for, IFN-I production (gates: pDC LIFRlo/neg, pDC LIFRlo/neg YFP+, pDC LIFR+ YFP+). Nine plates were sorted for the mouse infected for 33 hours, 3 plates for 36 hours and 2 plates for 48 hours. Gene expression was profiled by 5'-end single-cell RNAseq following the FB5P-seq protocol.

first: Noudjoud

last: Attaf

first: Chuang

last: Dong

first: Pierre

last: Milpied


title: SKI-dependent TGFb signaling dictates CD103 expression in CD8+ T cells (ChIP-seq)

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill

summary: Initially identified as a functional marker for resident-memory (Trm) CD8+ T cells, CD103 (encoded by ITGAE gene) has broad roles in immunity and diseases. Elucidating the function and regulation of CD103 is thus of importance. This study revealed that the CD103 expression by CD8 T cells under steady state contributes to the clearance of acute viral infection. More importantly, it discovered TGF-SKI-Smad4 a critical signaling axis in restricting CD103 expression in CD8+ T cells for their function. Mechanistically, by ChIP-Seq and ChIP analysis, SKI associated with Smad4 was found to directly and epigenetically suppress CD103 transcription. This study therefore reveals a novel TGF-SKI-Smad4 pathway to specifically enable CD103 expression in CD8+ T cells for protective immunity.

overall_design: Examination of Smad4 and Ski ChIP-seq in two different cells (WT vs. Cd4Cre;Smad4fl/fl) under TGFbR inhibitor condition for 2 days

first: Bing

last: Wu

first: Ge

last: Zheng

first: Xiaojiang

last: Xu

first: Jian

middle: L

last: Li


title: Changes in the Epigenetic Landscape of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Reflect Systemic Dysfunctions

status: Public on Jul 02 2020

city: Dunedin

first: Amber

last: Helliwell

address: 710 Cumberland Road

department: Biochemistry Department

country: New Zealand

institute: University of Otago

type: Methylation profiling by high throughput sequencing

summary:
Purpose: ME/CFS is a lifelong debilitating disease that affects approximately 1% of the global population. Previous studies have identified dysfunctional activity in metabolic, immune and neurological pathways. The goal of this study is to identify ME/CFS specific variations in DNA methylation to determine whether the patient specific epigenetic patterns provide insight into the disease pathophysiology.
Methods: DNA was extracted from the PBMCs of 10 ME/CFS patients and age/gender matched controls. After performing RRBS the sequence was aligned to hg19 genome using Bismark. The data was analyzed using first an ANOVA F test through DMAP in order to determine variation between the patient and control groups across 40-220bp fragments of the genome. Additional analysis was performed following a MethylKit pipeline, which analyzed the variation on a single CpG basis using a Fishers test.
Results: From a total of 146,575 DMAP fragments we identified 76 differentially methylated fragments (P <0.05, Diff meth +/- 15%). A total of 31 were associated with gene regions (intronic/exonic). MethylKit analysis also identified a total of 394 differentially methylated cytosines (FDR corrected P <0.05, Diff meth +/- 15%) from a total of 196,172 individual analyzed cytosines, 91 of the statistically significant cytosines fell within gene regions. Comparison of both methylomes and regions where both the DMAP fragments and multiple MethylKit cytosines fell highlighted areas of the genome containing regulatory elements associated with metabolic and immune activity. Gene body pathway enrichment additionally identified immune metabolic and neurological related functions.
Conclusions:  Our study represents the first investigation of ME/CFS patients using reduced representation bisulfite sequencing. We identified a number of major differences between patients that distinguished them from healthy controls. Our results identified a number of differentially methylated regulatory elements and gene bodies that highlight the disturbed pathophysiology in ME/CFS. In particular the large number of enriched neurotransmitter and neuropeptide reactome pathways highlighted a disturbed neurological pathophysiology in patients.

overall_design: RRBS Analysis of 10 ME/CFS patients vs. Controls

first: Warren

last: Tate

first: Aniruddha

last: Chatterjee

first: Peter

last: Stockwell

first: Eiren

last: Sweetman

first: Tina

last: Edgar


title: Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [Ss2_pDC1]

first: Thien-Phong

last: Vu Manh

summary: The aim of the project is to characterize the heterogeneity of murine plasmacytoid dendritic cells (pDCs) and to decipher their activation trajectory during a viral infection in vivo. To this end, individual splenic pDCs were transcriptionally profiled at ground state and at the time of their peak production of type I interferon (IFN-I) during mouse cytomegalovirus (MCMV) infection, with enrichment of IFN-I-producing pDCs based on the use of a reporter mouse strain.

overall_design: This dataset corresponds to splenic pDCs sorted from Ifnb1Eyfp reporter mice that were untreated or had been infected for 36 hours with murine cytomegalovirus (MCMV). pDCs were gated as Viable cells [live/dead cell dye (neg/low)], Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), singlet, CD11c(low/int), CD317(pos/high) cells. Single-cells were FACS-sorted into two 96-well plates. Plate 1 corresponded to pDCs from uninfected mice. Plate 2 corresponded to pDCs from infected animals, with enrichment of IFN-I+ pDCs by index sorting of 33 YFP+ cells. In each plate, two wells were included as bulk population controls. Gene expression was analyzed by single-cell RNAseq following the Smart-Seq2 protocol. The data from control wells are not included here.

first: Abdenour

last: Abbas

first: Alexandra

middle: C

last: Villani

first: Marc

last: Dalod

first: Elena

last: Tomasello


title: RNA sequencing of ER+ breast tumor treated with letrozole

status: Public on Jul 01 2020

city: Dallas

first: Kyung-min

last: Lee

state: TX

address: 6001 Harry Hines Blvd, NB5. 112

department: Simmons Comprehensive Cancer Center

institute: UT SOUTHWESTERN MEDICAL CENTER

summary: Transcriptome of ER+ breast tumors treated with letrozole were profiled by RNA-seq

overall_design: BioProject accession: PRJNA605185

first: Carlos

last: Arteaga

first: Thomas

last: Stricker


title: mRNA profiles in Y-organ of normal and eyestalk-ablated Eriocheir Sinensis

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

summary: We sequenced the mRNA in the Y-organ of normal and eyestalk-ablated Eriocheir Sinensis and obtained the transcriptome profiling (RNA-seq) of the two samples with Next-generation sequencing (NGS) technique. The unigene expression of the two samples were compared and the differetially expressed unigenes were listed.

overall_design: The Y-organ of normal and eyestalk-ablated Eriocheir Sinensis were extracted and sequenced to find the differential expressed unigenes

first: Jinsheng

last: Sun

first: Yichen

last: Liu

last: Zhang

first: Shuxia

last: Xue


title: Single-cell analysis of mouse plasmacytoid dendritic cells (pDCs) unravels their activation trajectory and their molecular regulation in vivo during a viral infection [Ss2_pDC2]

summary: The aim of the project is to characterize the heterogeneity of murine plasmacytoid dendritic cells (pDCs) and to decipher their activation trajectory during a viral infection in vivo. To this end, individual splenic pDCs were transcriptionally profiled at ground state and at the time of their peak production of type I interferon (IFN-I) during mouse cytomegalovirus infection, with enrichment of IFN-I-producing pDCs based on the use of a reporter mouse strain and on their down-regulation of LIFR.

overall_design: This dataset contains data from pDCs sorted from Ifnb1Eyfp reporter mice infected or not with murine cytomegalovirus (MCMV). pDCs were gated as Viable cells [live/dead cell dye (neg/low)], Lineage[CD3, CD19, Ly6G, NK1.1](neg), CD11b(neg), singlet, CD11c(low/int), CD317(pos/high) cells. Single-cells were FACS-sorted into four 96-well plates. Plate 1 corresponded to pDCs from one uninfected mouse, sorted into two different populations: LIFRlow and LIFRhigh. Plate 2 to 4 corresponded to pDCs from one infected mouse, sorted into five different phenotypic populations: LIFRhigh, LIFRlowBST2high, LIFRhighYFPpos, LIFRlowYFPpos and LIFRlowBST2low; YFP was negative unless mentioned otherwise.  In each plate, 2 or 3 wells were included as bulk population controls. Gene expression was analyzed by single-cell RNAseq following the Smart-Seq2 protocol. The data from control wells are not included here.


title: Novel fluorescence-based high-throughput method uncovers single-cell DNA supercoiling heterogeneity

city: New Haven

first: Alexandre

last: Duprey

state: CT

address: 295 congress avenue

department: Microbial pathogenesis

institute: Yale university

summary: DNA supercoiling is essential for life because it controls critical processes, including transcription, replication and recombination. Current methods to measure DNA supercoiling in vivo are laborious and unable to examine single cells. Here we report a method for high-throughput measurement of bacterial DNA supercoiling in vivo. Fluorescent Evaluation of DNA Supercoiling (FEDS) utilizes a plasmid harboring the gene for a green fluorescent protein transcribed by a discovered promoter that responds exclusively to DNA supercoiling, and the gene for a red fluorescent protein transcribed by a constitutive promoter as internal standard. Using FEDS, we uncovered single cell heterogeneity in DNA supercoiling and established that, surprisingly, population-level decreases in DNA supercoiling result from a low mean/high variance DNA supercoiling subpopulation, rather than a homogeneous shift in supercoiling of the whole population. In addition, we identified a regulatory loop in which a gene that decreases DNA supercoiling is transcriptionally repressed when DNA supercoiling increases.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Comparison of gene expression of different strains of S. Typhimurium in various media, in order to produce a range of DNA supercoiling

first: Eduardo

last: Groisman


title: Expression data from adipocyte differentiation from diabetic adipose-derived stem cells (dADSC) treated with squalene (Sq) and its derivative (HH-Sq)

status: Public on Jun 27 2020

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

address: 1 Chome-1-1 Tennodai

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

summary:
Gene expression profiling reveals functional difference between Sq and HH-Sq on differentiation, metabolism, and lipid droplot formation of dADSC
Microarray gene expression profiling was conducted for technical replicates of adipocyte induced dADSC (IN), adipocyte induced and treated with Sq (Sq), adipocyte induced and treated with HH-Sq (HH-Sq) for 14 days (1 µM) to identify its effect in the regulation of adipocyte differentiation, metabolism, and lipid droplet accumulation.  Technical replicates represent the same hybridization mixture applied to 3 independent arrays.

overall_design: Total RNA was extracted from D14 adipocyte-induced dADSC ± treatment using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity and the dosage of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). 250 ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual. Human genome array strip (HG-U219) was hybridized for 16 hours in a 45°C incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Insight into natural aging process of zebrafish heart

status: Public on Jun 30 2020

city: shanghai

first: Xuelian

last: Shao

address: yangpu district, songhu road

department: School of life science

institute: Fudan university

type: Non-coding RNA profiling by high throughput sequencing

summary: Meta analysis of transcriptome to reveal aging-related transcritionl alterations in zebrafish heart and provide candidate genes for development of model of premature cardiac aging

overall_design: Gene expression profiles in hearts of 6-, 12-, 24- and 36-month-zebrafish were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000.


title: Expression data from adult myocardium of ToF-PVR patients undergoing pulmonary valve replacement

status: Public on Jun 22 2020

city: London

first: Daniel

last: Brayson

address: 125 Coldharbour Lane

department: School of Cardiovascular Sciences and Medicine

institute: King's College London

summary:
Adult right ventricle from Tetralogy of Fallot patients undergoing pulmonary valve replacement  vs  right ventricle myocardium from unused donor hearts
we used Microarray to determine whether there were differences in gene expression between these groups

overall_design: ToF-PVR

first: Jon

last: Kentish


title: RNA-seq of triple knockout (TKO) mouse embryonic stem cells:  Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/-.

status: Public on Jun 19 2020

city: Edinburgh

first: Heidi

middle: Katharina

last: Mjoseng

address: Crewe Road South

institute: HGU, IGMM, The university of Edinburgh

summary: TKO mouse embryonic stem cells were cultured in serum/LIF and 2i/LIF in order to investigate the role of methylation in the transcriptional regulation of ground state cells (Clone: TKO 121, Tsumura et.al. 2006).

overall_design: RNA-Seq TKO_serum and TKO_2i, 3 biological replicates per condition

first: Ruchi

last: Shukla

middle: K

first: John

last: Thomson

first: Simon

last: Kling

first: Duncan

last: Sproul

first: Donncha

last: Dunican

first: Tuempong

last: Wongtawan

first: Fridolin

last: Treindl

first: Markus

middle: F

last: Templin

first: Ian

middle: R

last: Adams

first: Sari

last: Pennings

first: Graeme

last: Grimes

first: Richard

last: Meehan


title: Differenatiation of ceRNA (circRNA, lncRNA and mRNA) expression  in PBMCs (peripheral blood mononuclear cells)

status: Public on Jun 25 2020

city: Shanghai

first: Caiyan

last: Zhang

address: 399, Wanyuan Road

institute: Children's Hospital of Fudan University

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

summary: To determine ceRNA transcribed during the PBMCs, we have employed whole genome microarray expression profiling as a discovery platform to identify ceRNA expression in PBMCs donated by T1DM (type 1 diabetes mellitus) patients and healthy volunteers.

overall_design: The changed ceRNA expression in human PBMCs normal (Ctrl) or T1DM patients, respectively. Four persons  in each group (Normal, T1DM).

first: Yufeng

last: Zhou


title: Interactive analysis of single-cell epigenomic landscapes with ChromSCape

status: Public on Jun 16 2020

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

institute: Institut Curie

summary: Here, we present ChromSCape, a user-friendly interactive Shiny/R application that processes single-cell epigenomic data to help the biological interpretation of chromatin landscapes within cell populations. ChromSCape successfully analyses the distribution of repressive and active histone modifications as well as chromatin accessibility landscapes from single-cell datasets.

overall_design: H3K27me3 single-cell ChIP-seq

first: Pacôme

last: Prompsy


title: a New Marine-Derived Asterosaponin (CN-3) alleviated the proliferation of U251 MG cells

city: Xi'an

first: Peng-Cheng

last: Qiu

address: Changle West Road 169

institute: Fourth Military Medical University

summary: Analysis of U251 glioblastoma multiforme (GBM) cells treated with a new culcita novaeguineae asterosaponion, CN-3. A new asterosaponin was isolated from culcita novaeguineae, an abundant marine resource in the south China sea. The asterosaponin induced significant growth inhibition  with a 50% inhibitory concentration at 48 h of 2.013 μg/mL in U251MG cells. 1.8μg/mL of the asterosaponin reduced U251 MG cells viability from 100 % to 42.5% (24 h), 37.4% (48 h) and 52.1% (72 h). In this study, a microarray analysis was performed using RNA prepared from U251MG GBM cells treated with the asterosaponion. These data revealed that 661 genes had significant differential expressions.

overall_design: U251 cells were treated with  asterosaponin or control,  At 48h, total RNA were extracted for microarray experiment. Four replicates were performed  of asterosaponion, and two replicates were performed  of control.

first: Yun-Yang

last: Lu

first: Hai-Feng

last: Tang


title: CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

status: Public on Jun 18 2020

city: Göttingen

first: Eusra

last: Mohammad

address: Am Faßberg 11

institute: Max Planck Institute for Biophysical Chemistry

summary: Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.

overall_design: TT-seq on HEK293 CDK12as cells after CDK12 inhibition for 15 minutes and 30 minutes with 1-NM-PP1.

first: Michael

last: Tellier

first: Justyna

last: Zaborowska

first: Livia

last: Caizzi

first: Taras

last: Velychko

first: Björn

last: Schwalb

first: Ivan

last: Ferrer-Vicens

first: Daniel

last: Blears

first: Takayuki

last: Nojima

first: Patrick

last: Cramer

first: Shona

last: Murphy


title: MEK and GSK3β inhibition drives ES cells into a naive pluripotent state irrespective of their global methylation status

city: Newcastle upon Tyne

first: Ruchi

last: Shukla

address: Ellison A Building

department: Applied Biosciences

institute: Northumbria University

summary:
Mouse embryonic stem cells (mESCs) can convert to a ground state by dual inhibition of MEK and GSK3β signalling in defined media in the presence of LIF (2i). The cellular transition in 2i leads to uniform expression of pluripotency markers and global DNA hypomethylation. Whether hypomethylation is required for achieving ground state or is an outcome of the conversion process is still not clear. Here we show that J1 wild type and hypomethylated mESCs (dnmt3a-/-, dnmt3b-/-, dnmt1-/- [TKO]) lacking DNA methyltransferases undergo similar morphological and expression changes upon culturing in 2i that are consistent with conversion of both to a more naive state. Maintenance of global DNA methylation levels in 2i media by constitutive expression of de novo methyltransferases is also not a barrier to conversion. Hence, signalling pathways in mES cells regulate pluripotency networks and cell state independently of their global DNA methylation status.
Indicated mESCs were cultured in 2i/LIF for 2 weeks and then harvested along with serum/LIF counterparts for microarray analysis. 1ug of total RNA was used to prepare Cy3 labelled aRNA using an Amino Allyl MessageAmp II aRNA kit (Ambion) following manufacturers protocol. The samples were hybridised to SurePrint G3 mouse GE 8x60k microarrays (Agilent) and were scanned using NimbleGen MS 200 (Roche). Results were analysed with custom-written scripts implemented in the statistical programming language R (http://www.R-project.org).

overall_design: Expression arrays are carried out to analyze differentially expressed genes in various mESCs models when cultured in serum/LIF or 2i/LIF conditions. Differential expression was calculated using the Bioconductor package linear models for microarray data (limma v3.20.8). P-values were corrected for multiple testing using Benjamini-Hochberg test and probes with P < 0.05 were deemed significant.

first: Heidi

last: Mjoseng

first: Duncan

last: Sproul

first: Donncha

middle: S

last: Dunican

first: John

last: Thomson

first: Richard

last: Meehan


title: Gene expression data from bladder cells treated with Escherichia coli Extracellular Vesicles RNA

status: Public on Jul 08 2020

city: Auckland

first: Priscila

middle: Pamela

last: Dauros-Singorenko

state: Auckland

address: 85 Park road, Grafton

institute: University of Auckland

summary: Escherichia coli release Extracellular Vesicles (EVs) which carry diverse molecular cargo. Pathogenic E.coli EVs contain virulence factors which assist during infection in the host in different mechanisms.The RNA cargo of E.coli EVs has not been assessed in their effect in the host. We used microarray data to asses and compare the global response of bladder cells to EV-RNA from pathogenic E.coli (Uropathogenic UPEC 536) and non-pathogenic E. coli (probiotic Nissle 1917)

overall_design: EVs were isolated from RPMI-grown bacterial cultures, following centrifugation of spent medium, filtration, concentration and ultracentrifugation. Pelleted EVs were further purified using Size Exclusion Chromatography columns. RNA was extracted from pure EV preparations using a commercial kit and RNA quantified by Qubit.  In vitro cultured bladder cells (5637) were treated with EV-RNA for 4 hours, after which cells were washed, removed and kept in TriZol at -80C until processing. RNA was extracted from bladder cells using a commercial kit and RNA quantified by Qubit, before determining the gene expression response by microarray technology.

first: Cherie

last: Blenkiron

first: Jiwon

last: Hong

first: Simon

last: Swift

first: Anthony

last: Phillips


title: Ubiquitin fusion protein 1 (Ubi1) is essential for growth and virulence of Cryptococcus neoformans

status: Public on Jun 11 2020

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

summary: To explore the molecular basis for the defect of in vitro growth and in vivo invasion caused by Ubi1 deletion, RNA-sequencing was performed to compare the transcriptional profiles of WT and ubi1∆ cells. A total of 236 genes were differentially expressed (141 upregulated and 95 down regulated) by at least 2-fold (P < 0.05) between these two strains (see Table S3 in the supplemental material). Among them, most prominent functional groups were involved in ribosome biogenesis/assembly, rRNA processing /transport, nucleotide metabolism, amino acid metabolism, and protein processing。

overall_design: RNA-sequencing was performed to compare the transcriptional profiles of wild-type and ubi1∆ mutant cells.

first: Jingyu

last: Zhao

first: Yali

last: Yang

first: Wei

last: Fang


title: RNA-seq of DEX induced and ethanol control Basal-like breast cancer cell lines

city: Salt Lake City

first: Katherine

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

summary: Breast cancers can be divided into subtypes with different prognoses and treatment responses based on global gene expression differences.   This study utilized integrated analysis of DNA methylation, chromatin accessibility, transcription factor binding, and gene expression in large collections of breast cancer cell lines and patient tumors to identify transcription factors responsible for the basal-like gene expression program. The results of this study indicate that glucocorticoid receptor (GR) and signal transducer and activator of transcription 3 (STAT3) bind to the same genomic regulatory regions that are specifically open and unmethylated in basal-like breast cancer. These transcription factors cooperate to regulate expression of hundreds of genes in the basal-like gene expression signature and these downstream genes are associated with poor prognosis in patients.

overall_design: To determine which genes are regulated by GR and STAT3, RNA-seq was performed on two basal-like cell lines (HCC70 and MDA-MB-231) treated with 100nM dexamethasone or an equal volume of 100% ethanol vehicle control for 4 hours.

first: K-T


title: RNAseq of CD8+ T cells memory subsets in human peripheral blood

city: Stockholm

first: Marcus

last: Buggert

state: PA

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

overall_design: We FACS sorted CD8+ Tcell memory subsets from human peripheral blood and performed bulk RNAseq on these cells

first: Son

last: Nguyen

first: Vincent

middle: H

last: Wu


title: Alteration of genome folding via engineered transposon insertion [CTCF RAD21 ChIP-seq]

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Mammalian chromosomes are partitioned into contact domains that can be conserved as functional units in evolution. Disruptions of domains can result from perturbed CTCF, cohesin, or chromosomal rearrangements. However, to what extent domains can be created de novo has not been explored in depth. Here, using a gain-of-function approach leveraging genome editing and Hi-C, we examined whether, and how, a putative boundary element can function to organize de novo domains in the context of multiple ectopic insertion sites. We subsequently dissected the distinct roles of the CTCF binding site and the transcription start site within the insertion element in changing genome folding.

overall_design: Using a transposon-based approach, we inserted a 2 kb DNA fragment, which resides within a tissue-invariant domain boundary, into the genomes of near-haploid HAP1 cells. Following transposition, we established clonal lines and prioritized Clones 21 (C21) and 25 (C25), which contained ten and six insertions, respectively, across a total of 11 chromosomes. We then performed in situ Hi-C on edited clones and unedited parental (WT) cells to characterize how the insertion of a boundary-associated DNA fragment shapes human genome architecture. Furthermore, we carried out a series of CRISPR-based editing experiments to dissect how the TSS and the CTCF binding site within the insertion element contributes to new domain formation. Additionally, we used CRISPR to delete the endogenous 2 kb element and characterized its function at its endogenous boundary. In addition to Hi-C, we performed Capture-C, ChIP-seq (CTCF, Rad21, and H3K27Ac), and RNA-seq to further characterize the structural changes resulting from each round of genome editing experiments.

first: Di

last: Zhang

first: Peng

last: Huang

first: Sharma

last: Malini

first: Cheryl

last: Keller

first: Belinda

last: Giardine

first: Haoyue

first: Thomas

last: Gilgenast

first: Jennifer

last: Phillips-Cremins

first: Gerd

last: Blobel


title: STAT3 and GR cooperate to drive basal-like triple negative breast cancer gene expression and proliferation

overall_design: Transcription factor ChIP-seq for GR and STAT3 was performed in TNBC cell lines, SUM159, MDA-MB-231, HCC1937, HCC70, HCC1187, and luminal cell lines MDA-MB-361, BT-474, MDA-MB-453, and MCF-7.  STAT3 and GR ChIP-seq was performed after 1hr vehicle control induction (ethanol) and 100nM Dexamethasone induction respectively.


title: Single Cell Transcriptome Mapping of Human Thymopoiesis Reveals a Continuum of Cell States During T-Lineage Specification and Commitment

status: Public on Jun 12 2020

city: Los Angeles

first: chintan

last: parekh

state: CA

address: 4650 sunset blvd, mail stop 54, mail stop 54

institute: CHLA

summary: Single cell studies elucidating the transcriptional continuum underpinning lineage commitment in the human bone marrow (BM) have advanced the understanding of  hematopoiesis beyond the classic hierarchical model. However, T-lineage commitment, which occurs in the thymus remains incompletely defined. We mapped single cell transcriptomes spanning post-natal human thymopoiesis including the earliest progenitors. Instead of previously described discrete populations, transcriptional and lineage assay data resolved a continuum of novel cell states within CD34+ thymic progenitor cells. The initial stages of thymopoiesis involve multilineage priming of single cells followed by a gradual transition to T-commitment, a continuum previously undescribed outside the BM. Early progenitors express a hematopoietic stem cell (HSC) like profile but unlike HSC show initiation of T-priming. Species related differences exist in the earliest progenitor cells.

overall_design: We performed single cell RNA-Seq on CD34+CD4-CD8-GlyA-  progenitor (CD34+) and CD34-CD45+GlyA- differentiated (CD34-) cells isolated from human post-natal thymus  by magnetic column separation  followed by fluorescence activated cell separation (FACS). In the case of thymus 1, the CD34+ cells used for library preparation also included 2.5% (~125 cells) separately sorted CD34+CD7-CD1a-CD4-CD8-GlyA- ( a subset enriched for the earliest thymic progenitor cells) cells that had  been added to the sorted CD34+CD4-CD8-GlyA- cells . In the case of thymus 4, FACS isolation of CD34+ cells was done by index sorting. Index sorting parameters were set  to include at least 40 CD34+CD7-CD1a-CD4-CD8-GlyA- (Thy1)  and 40 CD34+CD7+CD1a+CD4-CD8-GlyA-  (Thy3, T-committed progenitor subset) cells among the 192 sorted cells. Cell type information (Thy1, Thy2 (CD34+CD7+CD1a-CD4-CD8-GlyA-) or Thy3)  based on facs is provided as a csv file.  Cell barcodes used for sequencing are provided as csv files.

first: Justin

last: Le

first: Jeong

last: Park

first: Vi

last: Ha

first: Anne

last: Luong

first: Sergio

last: Branchiomore

first: Andrei

last: Rodin

first: Grigory

last: Gogoshin

first: Fan

last: Li

first: Yong-Hwee

last: Loh

first: Virgina

last: Camacho

first: Sweta

last: patel

first: Robert

last: Welner

first: Chintan

last: Parekh


title: Transcriptional response of fibronectin fragment treatment in human articular chondrocytes

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

summary: Objective: Fibronectin is a matrix protein that is fragmented during cartilage degradation in osteoarthritis (OA). Treatment of chondrocytes with fibronectin fragments (FN-f) has been used to model OA in vitro, but the system has not been fully characterized. This study sought to define the transcriptional response of chondrocytes to FN-f, and directly compare it to responses traditionally observed in OA. Design: Normal human femoral chondrocytes isolated from tissue donors were treated with either FN-f or PBS (control) for 3, 6, or 18 hours. RNA-seq libraries were compared between time-matched FN-f and control samples in order to identify changes in gene expression over time. Differentially expressed genes were compared to a published OA gene set and used for pathway, transcription factor motif, and kinome analysis. Results: FN-f treatment resulted in 3,914 differentially expressed genes over the time course. Genes that are up- or downregulated in OA were significantly up- (p < 0.00001) or downregulated (p < 0.0004) in response to FN-f. Early response genes were involved in proinflammatory pathways, whereas many late response genes were involved in ferroptosis. The promoters of upregulated genes were enriched for NF-?B, AP-1, and IRF motifs. Highly upregulated kinases included CAMK1G, IRAK2, and the uncharacterized kinase DYRK3, while growth factor receptors TGFBR2 and FGFR2 were downregulated. Conclusions: FN-f treatment of normal human articular chondrocytes recapitulated many key aspects of the OA chondrocyte phenotype. This in vitro model is promising for future OA studies, especially considering its compatibility with genomics and genome-editing techniques.

overall_design: Primary articular chondrocytes were isolated from normal human talocrural cartilage from three donors (aged 50-61 years). Six cultures were isolated from each patient, and upon confluence were serum-starved for 2 hours. Chondrocytes were then treated with either 1 uM FN-f or PBS (as an untreated control) for 3, 6, or 18 hours prior to RNA extraction.

first: Veronica

last: Ulici

first: Cheeho

last: Kim

first: Susan

last: Chubinskaya

first: Richard

last: Loeser

first: Douglas

last: Phanstiel


title: MAIT cell project

status: Public on Jun 05 2020

city: Seattle

first: Evan

last: Newell

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hhutchinson Cancer research center

summary: Investigating the protein and gene profiles of tumor-infiltrating MAIT cells compared to PBMC from CRC patients

overall_design: Tumor-infiltrating MAIT cells from 3 CRC patients (MAIT_CRC_2128,MAIT_CRC_2170, MAIT_CRC_22267) and control PBMC from 1 healthy donor (MAIT_PBMC_231117cone3) were obtained by FACS sorting using tet-MR1

first: Shamin

first: Yannick

last: Simoni


title: Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

status: Public on Jun 04 2020

city: Utrecht

first: Wim

middle: J

last: de Jonge

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

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

overall_design: Refer to individual Series


title: The CBP KIX domain regulates long-term memory and circadian activity

status: Public on Jun 03 2020

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

summary:
Purpose: We investigated the function of the CBP KIX domain in hippocampal memory and gene expression using CBPKIX/KIX mice with mutations that prevent phospho-CREB (Ser133) binding.
Method: We performed total RNA sequencing after training for hippocampus-dependent memory from CBP KIX/KIX and WT littermates.
Results: Using an unbiased analysis of gene expression after training for hippocampus-dependent memory, we discovered dysregulation of CREB and CLOCK target genes and downregulation of circadian genes in CBPKIX/KIX mice.
Conclusion: This study provides insight into the significance of the CBP KIX domain by defining targets of CBP transcriptional co-activation in memory and the role of the CBP KIX domain in vivo on circadian rhythms.

overall_design: Dorsal hippocampus mRNA profiles of 2-4 months old male WT and CBP KIX/KIX mice.

first: Snehajyoti

last: Chatterjee

first: Christopher

last: Angelakos

first: Joshua

middle: D

last: Hawk

first: Marie

last: Gaine

first: Shane

middle: G

last: Poplawski

first: Anne

last: Schneider-Anthony

first: Manish

last: Yadav

first: Giulia

last: Porcari

first: Jean

last: Cassel

first: Peter

last: Giese

first: Jacob

last: Michaelson

first: Lisa

last: Lyons

last: Boutillier

first: Ted

last: Abel


title: Multi-omics analysis of hematopoietic progenitors in the fetal liver of Mettl3 deficient mice

status: Public on Jun 01 2020

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

summary:
N6-methyladenosine (m6A) is the most abundant RNA modification, but little is known about its role in mammalian hematopoietic development. Conditional deletion of the m6A writer METTL3 in murine fetal liver results in hematopoietic failure and perinatal lethality. Loss of METTL3 and m6A activates an aberrant innate immune response, mediated by the formation of endogenous double-stranded RNAs (dsRNAs). The aberrantly formed dsRNAs are long, highly m6A modified in their native state, characterized by low folding energies and predominantly protein-coding. We identified coinciding activation of innate immune pattern recognition receptor pathways normally tasked with the detection of foreign dsRNAs. Our results suggest that m6A modification protects against endogenous dsRNA formation and a deleterious innate immune response during mammalian hematopoietic development.
Keywords: innate immune response, dsRNA, RNA modification, N6-methyladenosine, METTL3, hematopoietic development, RNA-seq, H3K4me3, CUT&RUN, J2-RIP, dropseq, single cell RNA-seq, scRNA-seq, LSK, fetal liver

overall_design:
In this study, we performed multi-omics high-throughput sequencing of hematopoietic progenitors from the fetal liver of Mettl3 deficient and control mice, to determine the function of Mettl3 mediated m6A in the context of hematopoiesis.  Bulk RNA-seq was performed in biological triplicate. H3K4me3 CUT&RUN was performed in biological duplicate. J2-RIP and INPUT controls were performed in biological duplicate. Single cell RNA-seq was performed in biological duplicate.

The files below contain raw counts:
Mettl3_bulk_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (bulk RNA-seq, Mettl3 depleted and wild type).
Mettl3_H3K4me3_TSS_3k_counts.txt: tab-delimited text file including transcript annotations (columns 1-6) and sample specific counts of H3K4me3 CUT&RUN reads aligned in the TSS region, considering a window of 3kb (Mettl3 depleted and wild type).
Mettl3_J2_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (for both J2-RIP and INPUT samples, Mettl3 depleted and wild type).
Mettl3_singlecell_RNAseq_counts.txt: tab-delimited text file containing gene-specific and cell-specific counts (single cell RNA-seq, Mettl3 depleted and wild type).

first: Yimeng

last: Gao

first: Radovan

last: Vasic

first: Raman

last: Nelakanti

first: Burak

last: Dura

first: Rong

last: Fan

first: Andrew

last: Xiao

first: Stephanie

last: Halene


title: Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function [RNA-Seq]

first: Wim

last: de Jonge

summary: Protein-DNA interactions are dynamic and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide-range, varying between 4.5 and 37 minutes. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide.

overall_design: Nascent RNA was labelled and measured using 4tU-seq before (0 min) and at 10 time points (5, 10, 15, 20, 30, 40, 50, 60, 75, 90 min) during depletion from the nucleus using anchor-away, in triplicate. A non-tagged WT control was taken along at the first (0 min) and last (90 min) time point.

first: Mariël

last: Brok

first: Philip

last: Lijnzaad

first: Patrick

last: Kemmeren

first: Frank

last: Holstege


title: Heterogenous radiomics patterns are associated with poor survivals and dysregulated pathways in medulloblastoma

city: Zhengzhou

first: Zhenyu

last: Zhang

address: Jian She Dong Road 1, Zhengzhou, Henan , China

institute: The First Affiliated Hospital of Zhengzhou University

summary: Background. To develop a radiomics signature for predicting overall survival (OS) and progression-free survival (PFS) in patients with medulloblastoma (MB), and to investigate the incremental prognostic value and underlying biological pathways of the radiomics signature.Methods. A radiomics signature was constructed based on five magnetic resonance (MR) sequences (T1, T1c, T2, FLAIR and ADC) from a training cohort (n = 83) using LASSO-Cox model. Association between the signature and survival was evaluated on a testing cohort (n = 83). Incremental prognostic value of the signature beyond clinicomolecular factors was assessed with respect to calibration, discrimination, reclassification and clinical usefulness by a radiomics-clinicomolecular nomogram. Key pathways associated with the signature were identified. Prognostic value of pathway genes was assessed in a public TCGA cohort.Results. The radiomics signature was significantly associated with OS/PFS, independent from clinicomolecular factors. The radiomics-clinicomolecular nomogram predicted OS (C-index 0.762) and PFS (C-index 0.697) better than either the radiomics signature (C-index: OS: 0.649; PFS: 0.593) or the clinicomolecular nomogram (C-index: OS: 0.725; PFS: 0.691) only, with a better calibration and classification accuracy (net reclassification improvement: OS: 0.298, P = 0.022; PFS: 0.252, P = 0.026). Nine pathways were significantly correlated with the radiomics signature. Average expression value of pathway genes achieved significant risk stratification in public cohort (log-rank P = 0.016). Conclusion. This study demonstrated radiomics signature was an independent prognostic marker and offered incremental value over clinicomolecular factors in OS/PFS predictions for MB patients. The signature was associated with dysregulated pathways affecting patient prognosis in MB.

overall_design: Radiomics patterns predict survival of MB

first: Jing

last: Yan

first: Sheng-Hai

first: Kay

last: Li

first: Wei-Wei

last: Wang

first: Ke

first: Bin-Ke

last: Yuan

first: Li

first: Lei

last: Liu

first: Yun-Bo

last: Zhan

first: Wen-Chao

last: Duan

first: Dong-Ling

last: Pei

first: Hai-Biao

last: Zhao

first: Tao

last: Sun

first: Chen

first: Wen-Qing

first: Zhen

first: Xuan-Ke

last: Hong

first: Xiang-Xiang

first: Yu

last: Guo

first: Wen-Cai

first: Jing-Liang

last: Cheng

first: Ho-Keung

last: Ng

first: Xian-Zhi

first: Zhi-Cheng

first: Zhen-Yu


title: Persistent transcriptional programs are associated with remote memory in diverse cells of the medial prefrontal cortex

status: Public on Jun 17 2020

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

summary: single cell RNAseq of remote memory engram cells from the murine mPFC

overall_design: TRAP2;Ai14 mice subjected to contextual fear conditioning followed by single-cell RNA seq


title: An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits

status: Public on May 31 2020

city: Oslo

first: Fatima

last: Heinicke

address: Kirkeveien 166

department: Department of Medical Genetics

institute: Oslo University Hospital

summary: We compared the performance of two commercial kits (NEBNext and NEXTflex) for miRNA detection sensitivity, reliability, titration response and ability to detect differentially expressed miRNAs at different amounts of synthetic miRNAs.   We observed differences in detection sensitivity between the kits, but none were able to detect the full repertoire of expected miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the majority of miRNAs. In a previous publication (https://doi.org/10.1080/15476286.2019.1667741; GEO accession number GSE133719) we accessed the performance of six additional miRNA library preparation kits.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Systematic comparison of miRNA profiles assessed in low-input synthetic miRNA samples and samples from pools of blood derived CD8 T cells of rheumatoid arthritis (RA) patients or healthy controls (HC) by six commercially available library preparation kits. In a previous publication (https://doi.org/10.1080/15476286.2019.1667741; GEO accession number GSE133719) we accessed the performance of six additional miRNA library preparation kits.

first: Gregor

last: Gilfillan


title: Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function [ChIP-Seq]

first: Wim

last: de Jonge

overall_design: Abf1 binding was measured using ChIP-seq before (0 min) and at 10 time points (5, 10, 15, 20, 30, 40, 50, 60, 75, 90 min) during depletion from the nucleus using anchor-away, in triplicate. A non-tagged WT control was taken along at the first (0 min) and last (90 min) time point.

first: Mariël

last: Brok

first: Philip

last: Lijnzaad

first: Patrick

last: Kemmeren

first: Frank

last: Holstege


title: GCGR Loss-of-Function Mutations Promote Amino Acid-Dependent Pancreatic Neuroendocrine Tumor Initiation from a Subpopulation of Alpha Cells [bulk RNA-seq]

status: Public on May 29 2020

city: South San Francisco

first: Steffen

last: Durinck

address: 1 DNA Way

institute: Genentech

summary: Study gene expression changes in alpha cells and tumors from GCGR knockout mice

overall_design: 5 replicates for GCGR knockout alpha cells and 3 replicates for GCGR heterozygous control; 7 replicates for GCGR knockout tumor and 8 replicates for non-tumor control

first: Derek

last: Smith

first: Andrew

last: Peterson


title: GCGR Loss-of-Function Mutations Promote Amino Acid-Dependent Pancreatic Neuroendocrine Tumor Initiation from a Subpopulation of Alpha Cells [single-cell RNA-seq]

summary: Evaluating cell subpopulations in mouse pancreatic islets and pancreatic tumors

overall_design: 3 replicates for GCGR knockout tumors and two islet samples (one homozygous and one heterozygous GCGR knockout)


title: Exercise training reverses cancer-induced oxidative stress and decrease in muscle COPS2/TRIP15/ALIEN

status: Public on Jun 02 2020

city: Boston

first: Dr. Kathryn

last: Swoboda

state: MA

address: 165 Cambridge Street

department: Neurology

institute: Massachusetts General Hospital

summary: We tested the hypothesis that exercise training would attenuate metabolic impairment in a model of severe cancer cachexia and we explored the mechanisms underlying these effects.

overall_design: Microarray with myotubes affected by knockdown of COPS2 by siRNA

first: Christiano

last: Alves

first: Willian

last: das Neves

first: Ney

last: de Almeida

first: Eric

last: Eichelberger

first: Paulo

last: Jannig

first: Vaness

middle: A

last: Voltarelli

first: Gabriel

last: Tobias

first: Luiz

last: Bechara

first: Daniele

last: de P Faria

first: Maria

first: Lars

last: Hagen

first: Animesh

last: Sharma

first: Geir

last: Slupphaug

first: Jose

last: Moreira

first: Ulrik

last: Wisloff

first: Michael

last: Hirshman

first: Carlos

middle: E

last: Negrao

first: Gilberto

last: de Castro Jr

first: Roger

last: Chammas

first: Kathyrn

first: Jorge

last: Ruas

first: Laurie

last: Goodyear

first: Patricia

last: Brum


title: GCGR Loss-of-Function Mutations Promote Amino Acid-Dependent Pancreatic Neuroendocrine Tumor Initiation from a Subpopulation of Alpha Cells [exome-seq]

first: Steffen

last: Durinck

overall_design: 17 total samples, 6 control and 11 tumor; each mouse has one control and one or more tumor samples

first: Derek

last: Smith

first: Andrew

last: Peterson


title: GCGR Loss-of-Function Mutations Promote Amino Acid-Dependent Pancreatic Neuroendocrine Tumor Initiation from a Subpopulation of Alpha Cells

status: Public on May 28 2020


title: Expression data from mouse oocytes treated with low-dose bisphenol S

status: Public on May 22 2020

city: Prague

first: Lukáš

middle: Farhád

last: Mirchi

state: Czech Republic

address: Albertov 4

department: First Faculty of Medicine

country: Czech Republic

institute: Charles University

summary:
Bisphenol S (BPS) is widely used to replace earlier-eliminated BPA. We evaluated the effect of acute in vivo BPS exposure on oocyte quality using eight-weeks-old ICR female mice (N = 15 per experimental group), exposed to vehicle or BPS1-BPS4 (0.001, 0.1, 10, and 100 ng BPS x g bw-1 x day-1, respectively). Oocytes were isolated and matured in vitro. Thereafter, we observed that BPS exposure increases aberrant spindle formation in mature oocytes and induces DNA damage. Moreover, BPS3 significantly increases chromatin repressive marks 5-methyl cytosine (5meC) and H3K27me2 in immature oocytes. In the BPS2 group (0.1 ng x g bw-1 x day-1), the increase in 5meC arises during oocyte maturation. Transcriptome analysis shows differential expression of early embryonic development transcripts in BPS2-exposed oocytes. These findings indicate that the biological effect of BPS is non-monotonic, affecting oocyte quality even at concentrations that are orders of magnitude below those measured in humans.
We used microarray aproach to unravel gene expression differences triggered by the administration of BPS at different concentrations in mouse oocytes.

overall_design: Six- to seven-week-old ICR mice were purchased from Velaz Ltd. (Prague, Czech Republic). Mice were kept under  12 hours light-dark cycle, fed phyto-oestrogen-free diet 1814P (Altromin) and given access to ultra pure water ad libitum. Animals were randomly separated into five groups (N = 3 each, N = 4 for the transcriptomic experiment) and allowed to acclimate for at least one week. Each group was treated with one of four different BPS doses (0.001, 0.1, 10, and 100 ng BPS x g bw-1 x day-1, hereafter named BPS1, BPS2, BPS3, and BPS4, respectively). Only BPS2 was used for the transcriptomic experiment. BPS was dissolved in 50 μl 50% glycerol containing 0.1% DMSO and administered daily for 7 days by oral gavage. After the exposure period, mice were euthanised by cervical dislocation, and their ovaries were collected for RNA extraction and further experiments.

first: S

last: Prokesova

first: J

last: Nevoral