title: c-kit Signaling Inhibits Bone Development by Regulating Skeletal Stem Cell Precursors in Fetal Bone Marrow

first: Bo O.

last: Zhou

address: 320 Yueyang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary: c-kit signaling plays pivotal roles in regulating the self-renewal and/or differentiation of many adult stem cells, such as hematopoietic stem cells. However, it remains controversial whether c-kit is expressed by and contribute to skeletal stem cells (SSCs). To test this, we lineage-traced c-kit+ cells and investigated the physiological importance of c-kit+ cells and c-kit signaling in bone development. We found that c-kit was not expressed by postnatal SSCs, but by fetal SSC precursors at the growth cartilage. Lineage-tracing of fetal c-kit+ cells marked approximately 20% of Lepr+ bone marrow stromal cells, generating nearly half of all osteoblasts in adult bone marrow. Disruption of mTOR signaling in c-kit+ cells impaired bone formation. Conditional deletion of Kitl (c-kit ligand, also known as Scf) from fetal, but not adult bone marrow stromal cells increased bone formation. Together, our work identified c-kit+ SSC precursors as an important source of bones formed during development. The osteogenic differentiation of these cells is temporally inhibited by Kitl from the bone marrow microenvironment.

overall_design: We performed single-cell RNA sequencing (scRNA-seq) of CD45-Ter119-CD31-PDGFRα+ bone marrow stromal cells from 2-month-old KitMerCreMer; R26tdTomato mice that had been treated with tamoxifen at E12.5/14.5

first: Di

last: He

first: Xinyu

last: Tang

first: Wenjie

last: Dong

first: Guizhong

last: Cui

first: Bo

middle: O


title: Cerebrospinal fluid microRNA profile in leptomeningeal metastasis patients

status: Public on Feb 25 2020

city: Changchun

first: Guozi

last: Yang

state: Jilin

address: No.71 Xinmin Street

department: Radiation-Oncology

country: China

institute: The First Hospital of Jilin University

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

overall_design: Refer to individual Series


title: The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche

status: Public on Feb 22 2020

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

summary: Estrogens and progesterone control mammary gland development and breast carcinogenesis via their cognate receptors expressed in a subset of cells of the luminal layer of the mammary epithelium. The extracellular matrix (ECM) including the basement membrane (BM) is important in breast physiology and tumorigenesis but how epithelial hormone receptor signaling and ECM are linked mechanistically is unclear. We identify the secreted protease Adamts18 as critical intermediary. Luminal estrogen and progesterone receptor signaling via upregulation of Wnt4 expression and ensuing canonical Wnt signaling activation in basal cells control Adamts18 expression there. The protease has an epithelial-intrinsic role in stem cell activation. We identify multiple binding partners in the interstitial ECM and BM and show that ADAMTS18 cleaves fibronectin in vitro. Its deletion results in increased fibronectin, collagen I and IV, and laminin deposition in pubertal glands. Adamts18 interacts genetically with Col18a1, which encodes a proteoglycan that is BM-specific, in stem cell regulation. Adamts18 inactivation impairs Hippo signaling and reduces Fgfr2 expression and signaling, which are vital for stem cell function. Our findings link epithelial hormone signaling to BM remodeling by Adamts18, and define the BM as an essential stem cell niche component.

overall_design: Mammary glands from MMTV::Cre+.Wnt4fl/fl.mT/mG and control MMTV::Cre+.Wnt4wt/wt.mT/mG mice were digested and processed to single cells for FACS sorting. After lineage depletion, GFP+ cells were sorted according to CD24 status. In three independent experiments Wnt-4 deleted, CD24 high and low and Wnt-4 WT, CD24 high and low cell populations were analyzed for global gene expression.

first: Renuga

last: Rajaram

first: Cathrin

last: Brisken


title: Partial reprogramming of melanoma cells confers drug resistance and increased vulnerability to calcium channel antagonists [4434 cells]

status: Public on Feb 21 2020

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

summary: Our aim is to compare whole-genome expression profiles of partially reprogrammed 4434 melanoma murine cells after induction of stem cell related genes (+ dox vs -dox)

overall_design: Total RNA from 4434 cells (- dox) was compared to partially reprogrammed 4434 cells (+ dox)

first: Karol

last: Granados


title: The secreted protease Adamts18 links mammary epithelial hormone action to extracellular matrix changes and stem cell niche function

type: Expression profiling by high throughput sequencing

overall_design: 3 pairs of contralateral glands engrafted with either WT.EGFP+ or Adamts18-/-.EGFP+ epithelia


title: Partial reprogramming of melanoma cells confers drug resistance and increased vulnerability to calcium channel antagonists

summary: Our aim is to compare whole-genome expression profiles of partially reprogrammed C790 melanoma murine cells after induction of stem cell related genes (+ dox vs -dox)

overall_design: Total RNA from C790 cells (- dox) was compared to partially reprogrammed C790 cells (+ dox)


title: Combination of four serum exosomal miRNAs as novel diagnostic biomarkers for early-stage gastric cancer

city: Harbin

first: Shuli

state: Heilongjiang Province

address: Haping Road No.150, Nangang District

institute: Harbin Medical University Cancer Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
The aim of this study was to identify and evaluate exosomal miRNAs in serum as early diagnostic markers for gastric cancer (GC).
Methods: Using next-generation sequencing (NGS) and bioinformatics, we identified candidate serum exosomal miRNA markers for early detection of GC in patients. The candidates were further validated by qRT-PCR in 50 newly recruited early-stage GC patients and matched healthy individuals.
Results: NGS revealed that the average mappable reads in the RNA libraries were about 6.5 million per patient. A total of 66 up and 13 down-regulated exosomal miRNAs were found in the screened cohort after removal of log2 transformed read counts <5 and p >0.05. In the validation cohort, by comparing candidate exosomal miRNAs levels in early-stage GC patients and healthy individuals, higher levels of miR-92b-3p, let-7g-5p, miR-146b-5p and miR-9-5p were found to be significantly associated with GC. Diagnostic power of the combined panels of the exosomal miRNAs or the combination of exosomal miRNAs and CEA outperformed that of single exosomal miRNA marker for establishing a diagnosis of early-stage GC. In addition, serum levels of exosomal miR-92b-3p were significantly associated with low adhesion, let-7g-5p and miR-146b-5p were significantly correlated with nerve infiltration, and miR146b-5p was statistically correlated with tumor invasion depth in early-stage GC.
Conclusions: Serum exosomal miR-92b-3p, -146b-5p, -9-5p, and let-7g-5p may serve as potential noninvasive biomarkers for early diagnosis of GC. Further validation of these candidate exosomal miRNAs in larger experimental cohorts are required in order to confirm the diagnostic values.

overall_design: Serum exosomal miRNA profiles of early gastric cancer patients were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500/2000 platform.

first: Yanqiao

last: Zhang

first: Xiaoyi

last: Huang

first: Jianan

last: Cheng

first: Yuanfei

last: Yao

first: Changjie

last: Lou

first: Liang

last: Wang


title: Transcriptomic profile of LadyBird mycobacteriophage lysogen

city: Pittsburgh

first: Katherine

middle: S

last: Wetzel

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

country: USA

institute: University of Pittsburgh

summary: The goal of this sequencing project was to identify genes and ncRNAs expressed by the LadyBird prophage

overall_design: Total RNA was isolated from cultures grown in log phase, depleted of rRNA and prepared for sequencing using a strand-specific library kit during lysogeny.

first: Graham

middle: F

last: Hatfull

first: Rebecca

middle: A

last: Garlena


title: Partial reprogramming of melanoma cells confers drug resistance and increased vulnerability to calcium channel antagonists [C790 cells]

summary: Our aim is to compare whole-genome expression profiles of partially reprogrammed C790 melanoma murine cells ( - dox vs + dox) after treatment with trametinib, in order to identify potential candidates related with drug resistance.

overall_design: Total RNA from partially reprogrammed C790 cells (+ dox) was compared to non induced C790 cells (- dox), after treatment with DMSO (control) or trametinib.


title: Pro-opiomelanocortin (POMC) neuron translatome signatures underlying obesogenic gestational malprogramming

status: Public on Feb 20 2020

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

institute: Centre Médical Universitaire de Genève

summary: Maternal unbalanced nutritional habits during embryo development and perinatal stages perturb hypothalamic neuronal programming of the offspring, thus increasing “diabesity” risk. Here we report that exposure to high-fat diet during gestation and lactation did not interfere with progeny’s hypothalamic POMC neuron specification, but significantly impaired their spatial distribution and axonal extension to target areas. Importantly, we established POMC neuron-specific translatome signatures accounting for neuronal aberrant development and axonal growth. These anatomical and molecular alterations caused metabolic dysfunction in early-life and adulthood. Our study provides fundamental insights on the molecular mechanisms underlying POMC neuron malprogramming in obesogenic contexts.

overall_design:
Chow diet, Post-natal day 0 (5 replicates)
Chow diet, Post-natal day 21 (3 replicates)
High fat diet, Post-natal day 0 (5 replicates)
High fat diet, Post-natal day 21 (4 replicates)

first: Roberta

last: Haddad-Tóvolli

first: Arnaud

last: Obri

first: Elena

last: Eyre Sánchez

first: Iñigo

last: Chivite

first: Maria

last: Milà-Guasch

first: Sara

last: Ramirez

first: Alicia

middle: G

last: Gómez-Valadés

first: Macarena

last: Pozo

first: Jasmine

last: Burguet

first: Licio

last: Velloso

first: Marc

last: Claret


title: Inhibition of cancer cell self-renewal through an epigenetic HDACi-histone H1.0 axis.

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Identification of HDACi-responsive, H1.0-dependent genes inhibiting self-renewal of HCC1569 breast cancer cells.

overall_design: RNA-seq analysis of HCC1569 breast cancer cells containing an inducible H1.0-targeting shRNA, treated with HDACi (JNJ-26481585). RNA was collected at various time points after addition of HDACi (or DMSO as a control). Two conditions were compared: cells treated with doxycycline to induce expression of the shRNA (DOX), and uninduced cells (NT).

first: Cristina

last: Morales Torres

first: Harshil

last: Patel


title: Expression data from INS1E cells stimulated with vitamin D metabolites and glucose

status: Public on Feb 19 2020

city: Oslo

first: Mette

middle: Eskild

last: Bornstedt

email: metbo@icloud.com, metbo@ous-hf.no

address: Pb 4959 Nydalen

department: Dep of Medical Biochemistry

country: Norway

institute: Oslo University Hospital

summary:
Studies have shown that vitamin D can enhance glucose-stimulated insulin secretion (GSIS) and change the expression of genes in pancreatic β-cells. Still the mechanisms linking vitamin D and GSIS are unknown.
We used an established β-cell line, INS1E. INS1E cells were pre-treated with 10 nM 1,25(OH)2vitamin D or 10 nM 25(OH)vitamin D for 72 hours and stimulated with 22 mM glucose for 60 minutes. RNA was extracted for gene expression analysis.

overall_design: After four passages INS1E cells (100 000 cells per well) were seeded in RPMI with 10 nM 25(OH)vitamin D (Sigma-Aldrich, Netherlands),  RPMI with 10 nM 1,25(OH)2vitamin D (Sigma-Aldrich, Israel) or RPMI with standard supplements alone (control cells). After 72 hours of preincubation, glucose stimulation was carried out. The cells were first incubated with glucose-free Krebs-Ringer buffer for 60 minutes, and immediately after they were subjected to stimulation with 22 mM glucose in Krebs-Ringer buffer in triplicates for 60 minutes.

middle: E

first: Ole

middle: K

last: Olstad


title: Transcriptome Sequencing Facilitates Quantitative Analysis of BMDM (bone marrow induced macrophages) from FBXW7f/f and LysM-cre FBXW7f/f  Transcriptomes before or after LPS treatment

city: Hangzhou

first: He

last: Jia

address: 866 Yuhangtang Rd

institute: Zhejiang university

summary:
Purpose: The goals of this study are to compare genes change between FBXW7f/f and LysM-cre FBXW7f/f BMDM after LPS treatment
Methods: BMDM mRNA from 6-8weeks FBXW7f/f  (WT) and LysM-cre FBXW7f/f  (KO) mice were generated by transcription sequencing, using Illumina. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

overall_design: BMDMs mRNA from 6-8weeks FBXW7f/f  (WT) and LysM-cre FBXW7f/f  (KO) mice befor and after LPS treatment were generated by transcription sequencing, using Illumina.

first: Qing

middle: Q

last: Wang

first: Jia

last: He


title: Retinoic acid exerts disease stage-dependent effects on pristane-induced lupus

city: Blacksburg

first: Song

last: Li

state: VA

institute: Virginia Tech

summary: We previously showed that all-trans-retinoic acid (tRA), an active metabolite of vitamin A, exacerbated pre-existing autoimmunity in lupus; however, its effects before the development of autoimmunity are unknown. Here, using a pristane-induced model, we show that tRA exerts differential effects when given at the initiation vs. continuation phase of lupus. Unlike tRA treatment during active disease, pre-pristane treatment with tRA aggravated glomerulonephritis through increasing renal expression of pro-fibrotic protein laminin β1, activating bone marrow conventional dendritic cells (cDCs), and upregulating the interaction of ICAM-1 and LFA-1 in the spleen indicating an active process of leukocyte activation and trafficking. Transcriptomic analysis revealed that prior to lupus induction, tRA significantly upregulated the expression of genes associated with cDC activation and migration. Post-pristane tRA treatment, on the other hand, did not significantly alter the severity of glomerulonephritis; rather, it exerted immunosuppressive functions of decreasing circulatory and renal deposition of autoantibodies as well as suppressing the renal expression of proinflammatory cytokines and chemokines. Together, these findings suggest that tRA differentially modulate lupus-associated kidney inflammation depending on the time of administration.  Interestingly, both pre- and post-pristane treatments with tRA reversed pristane-induced leaky gut and modulated the gut microbiota in a similar fashion, suggesting a gut microbiota-independent mechanism by which tRA affects the initiation vs. continuation phase of lupus.

overall_design: RNAseq performed on total splenocytes harvested at 3 months of age following daily oral dosing of tRA compared to control samples

first: Leila

last: Abdelhamid

first: Xavier

last: Cabana-Puig

first: Brianna

last: Swartwout

first: Jiyoung

last: Lee

first: Sha

last: Sun

first: Yaqi

first: A

middle: C

last: Ross

first: Thomas

last: Cecere

first: Tanya

last: LeRoith

first: Stephen

middle: R

last: Werre

first: Haifeng

first: Christopher

middle: M

last: Reilly

first: Xin

last: Luo


title: Disregulated gene expression in ReNcell via circRNA-microRNA axis

city: Taipei

first: Trees-Juen

last: Chuang

address: 128, Academia Road, Sec. 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academic Sinica

summary: We performed knockdown of circARID1A, overexpression of circARID1A and overexpression of miR-204-3p in ReNcell, independently. The 22,480 gene expression changes were examined by microarray analysis.

overall_design: The microarray result was used to screen gene expression changes by circARID1A and miR-204-3p regulation.


title: Aging induces aberrant state transition kinetics in murine muscle stem cells

status: Public on Feb 18 2020

city: San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: Label retaining and non-retaining muscle stem cells from young and aged H2B-GFP+/-;rtTA+/- were profiled by single cell RNA-seq at two timepoints

overall_design: 2 young (3 mo) and 2 aged (20 mo) H2B-GFP+/-;rtTA were labeled to track proliferative history by pulsing DOX in development (E10.5-E16.5). Label retaining and non-retaining cells were isolated from these animals by FACS. A set of cells from each animal was profiled immediately, while another set of cells was activated for 18 hours in vitro (10% HS, DMEM, culture plastic + sarcoma derived ECM) prior to profiling. Single cell RNA-seq was performed following the 10X Chromium Single Cell v2 kit.

first: Wallace

last: Marshall

first: Andrew

last: Brack


title: Gene expression in CD8+ T-cells from tumors in Wildtype mice and β2-adrenergic receptor knockout mice

status: Public on Feb 14 2020

city: Buffalo

first: Minhui

last: Chen

state: New York

address: 665 Elm St

department: Immunology

institute: Roswell Park Cancer Institute

summary: Gene profiles with NanoString in CD8+ T-cells of the non-irradiated tumors and irradiated tumors from WT and β2-AR KO mice which had been given radiation to the contralateral tumors.

overall_design: In the present study, RNA was isolated from sorted CD8+ T-cells of irradiated tumors and non-irradiated tumors in CT26 tumor-bearing WT or β2-AR KO mice treated with radiation, using the RNeasy Plus Mini kit (QIAGEN). NanoString analysis was performed with the nCounter Analysis System at NanoString Technologies. The nCounter Mouse Immunology kit was used including 561 immunology-related mouse genes.


title: XPO5 is required for miRNA biogenesis and promotes primary miRNA processing independent of RanGTP

city: Chicago

first: Rui

last: Yi

state: Illinois

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine

institute: Northwestern University

summary: XPO5 mediates nuclear export of miRNA hairpin precursors in a RanGTP-dependent manner. However, the requirement of XPO5 for global miRNA biogenesis and mammalian development and XPO5-associated RNA species are not determined. Here we show that XPO5 is required for mouse embryonic development and morphogenesis of skin and brain. Loss of XPO5 compromises the biogenesis of most miRNAs and that leads to severe developmental defects. Surprisingly, XPO5 not only associates with miRNA hairpin precursors but also pervasively binds to double-stranded RNA (dsRNA) regions found in many cellular RNAs and some clustered pri-miRNAs. The binding of XPO5 to miR-17~92 pri-miRNAs is RanGTP-independent. Pre-incubation with XPO5 enhances the processing efficiency of the DROSHA/DGCR8 microprocessor. Together, our studies demonstrate the requirement of XPO5 for miRNA biogenesis and mouse development, reveal an unexpected role of XPO5 for recognizing and facilitating the nuclear cleavage of clustered pri-miRNAs and identify numerous cellular RNAs as novel XPO5 subtracts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of RNA substrates of XPO5 in HEK293FT cells

first: Jerome

first: Kent

last: Riemondy

first: Jingjing

last: Wang


title: Mutant ACVR1 Arrests Glial Cell Differentiation to Drive Tumorigenesis in Pediatric Gliomas

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

summary:
Purpose: The purpose of this study was to assess the effect of targeting the Acvr1G328V mutation to oligoendrocyte lineage cells, on gene expression in the brainstem of mice at postnatal day 7
Methods: Total RNA was extracted from the brainstem of postnatal day 7 Acvr1+/+;Olig2Cre/+ and Acvr1floxG328V/+;Olig2Cre/+ littermates, processed using the Illumina TruSeq Stranded Total RNA Sample Preparation kit, and subjected to deep sequencing.
Results: A total of 247 genes were differentially expressed between the genotypes, with a corrected p value of less than 0.05. Of these genes, 125 were upregulated while 122 were downregulated. Many of the most downregulated genes were mature oligodendrocyte markers, while several genes that control oligodendrocyte progenitor formation and function were upregulated.
Conclusions: The Acvr1G328V mutation causes differentiation arrest of oligodendroglial lineage cells.

overall_design: Brainstem RNA was profiled from postnatal day 7 control (Acvr1+/+;Olig2Cre/+) and mutant (Acvr1floxG328V/+;Olig2Cre/+) littermates, using the Illumina TruSeq Stranded Total RNA Sample Preparation kit and a Nextseq 500 sequencer (Illumina). Samples were processed in two separate batches: The first batch comprised three samples per genotype, and the second batch comprised two samples per genotype. The batch number for each sample is indicated in the sample description.

last: Fortin

first: Parameswaran

last: Ramachandran

middle: W


title: Expression data from mouse aorta with chronic intermittent hypoxia exposure

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Atherosclerosis is the pathological basis of cardiovascular disease. Obstructive sleep apnea aggravates atherosclerosis, and chronic intermittent hypoxia (CIH) as a prominent feature of obstructive sleep apnea plays an important role during the process of atherosclerosis. The mechanisms of CIH in the development of atherosclerosis remain unclear.
The microarray was used to investigate differentially expressed mRNAs and long noncoding RNAs (lncRNAs) in aorta from five groups of ApoE-/- mice fed with a high-fat diet and exposed to various conditions: normoxia for 8 weeks, CIH for 8 weeks, normoxia for 12 weeks, CIH for 12 weeks, or CIH for 8 weeks followed by normoxia for 4 weeks.

overall_design: For microarray profiling, the mouse aorta total RNA was harvested using TRIzol reagent (Life Technologies, CA, USA) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, MA, USA). The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix, Thermo Fisher Scientific), which contains 65956 gene-level probe sets.

first: Jing

last: Zhang

first: Yanwen

last: Qin


title: Maize and Cercospora zeina transcriptome analysis during gray leaf spot foliar disease

city: Hatfield

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Plant Sciences Complex, Entrance 11 - Corner Lunnon Road & Herold Street

department: Dept. Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

summary: Gray leaf spot (GLS) disease of maize is caused by the fungus Cercospora zeina in African countries, such as South Africa. The plant material was from maize inbred line B73-QTL, which was introgressed with a QTL region for resistance to GLS from the maize inbred line CML444 (Berger et al (2014) BMC Genetics 15 60  www.biomedcentral.com/1471-2156/15/60 ). This QTL was named 10G2_GLS and 10H_GLS from two field trials in KwaZulu-Natal province, South Africa in that study.  B73-QTL plants were planted in the field, and subjected to natural infection with C. zeina. This was the same field trial as B73 plants that were sampled for RNAseq and the data reported in Swart et al (2017) Mol Plant Microbe Interact 30 710-724 (2017)(GSE94442). Samples were collected from lower leaves with moderate GLS lesions and younger upper leaves of the same B73-QTL plants with very few immature GLS lesions. The first aim of the experiment was to compare the maize transcriptomes during C.zeina challenge between B73 (from GSE94442 data) and B73-QTL plants (this study). The second aim was to identify novel transcripts expressed from the QTL region, which may underlie the quantitative disease resistance to GLS.  The third aim was to identify C. zeina genes expressed in planta during infection.

overall_design: To collect material that reflected a difference between C. zeina infected B73-QTL leaves and control B73-QTL leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear), and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73-QTL plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73-QTL plants each.

first: Tanya

last: Welgemoed


title: RNA-seq analysis of Control and BSCL2-deleted mature brown adipose tissue in mice

status: Public on Feb 11 2020

city: Augusta

first: Weiqin

state: GA

address: 1462 Laney Walker Blvd

department: Physiology

institute: Augusta University

summary: Next generation sequencing was used to compare transcriptome profiling in brown adipose tissue from Ctrl and BKO mice with mature brown adipose tissue specific deletion of BSCL2. Using an optimized data analysis workflow, we identified 13,525 transcripts in brown adipose tissue. 243 genes were differentially expressed with a fold change ≥1.5 and Padj value <0.05. Only 99 genes showed differential expression between the Ctrl and BKO brown fat, with a fold change ≥2.0 and Padj value <0.05. Results provide insights into the processes and signaling pathways BSCL2-mediated in brown adipose tissue.

overall_design: Brown fat mRNA profiles of 10 week old 10 week old male Bscl2f/f (Ctrl) and Bscl2f/f Ucp1Cre (BKO) were generated by deep sequencing, in triplicate, using Illumina 2000.

first: Hongyi

last: Zhou


title: High-salt diet inhibits tumour growth in mice via regulating myeloid-derived suppressor cells differentiation

city: Hefei

first: Wei

last: He

state: Anhui

address: Meishan road

institute: Anhui medical university

summary: To investigate the mRNA expression of purified tumour-infiltrating M-MDSCs from the NSD or HSD group, we employed Agilent Whole Genome Oligo Microarrays (one-color) as a discovery platform to identify differentially expressed genes (DEGs) between NSD and HSD group. We identified 5391 differentially expressed genes (DEGs) comprising 2586 upregulated and 2805 downregulated genes with a fold change greater than 1.5 between M-MDSCs from the NSD and HSD groups. Subsequently, the results demonstrated a significant shift towards an antitumour pro-inflammatory phenotype in HSD-fed mice with a dominant increase in NOS2, TNF, IL-12a, Toll-like receptor 4 (TLR4) and chemokine (C-C motif) ligand 19 (CCL19) expression and a decrease in lymphocyte antigen 6 complex, locus C1 (Ly6C1), C-C-C motif chemokine ligand 12 (CXCL12), indoleamine 2,3-dioxygenase 1 (IDO1) and CCL2 expression. Among these differences, the difference in the expression of IL-12, TNF-α, NOS2, IL-10 and arginase 1 (Arg1) was confirmed by ELISA or qRT-PCR . Meanwhile, the 2,586 DEGs upregulated (fold change >1.5) in M-MDSCs from the HSD group were markedly enriched in processes involving cytokine production, cell chemotaxis, INF-γ production, cell maturation, osmotic stress responses, acute inflammatory responses, etc. In addition, Analysis of the microarray dataset indicated that the expression of 2 key TFs (activating transcription factor 2 [ATF2] and NFAT5) responsible for osmotic stress was enhanced in the M-MDSCs from the HSD group . We further found that NFAT5 expression was significantly upregulated in M-MDSCs from the HSD group but that there was no difference in ATF2 expression between the two groups in both tumour models.

overall_design: HSD induced gene expression in purified tumour-infiltrating M-MDSCs after HSD treated tumour-bearing mice for 16 days


title: Gene expression profiling of HepG2 cells after treatment of PD-0332991 and CDK4-6 Knockdown

city: Incheon

first: Hanhee

last: Jo

address: Academiro 119

country: South Korea

institute: Incheon university

summary: The aim of this study is to estimate gene expression variations involved in glucose meatbolism in HepG2 cell line after cell cycle(G1 to S phase) inhibition by using drug(PD-0332991) or CDK4-6-knock down. We hypothesized that transition of glycolytic gene expression might indicates the effect of PD-0332991 drug treatment in Hepatocellular carcinoma cells.

overall_design: Examination of 2 different treatment conditions in 1cell line, using Illumina NextSeq500. Sample conditions: Control(DMSO) and PD-0332991 treated-HepG2, SC and CDK4-6-Knock down-HepG2 cells.

first: Misu

last: Lee


title: β-Catenin and FGFR2 Regulate Postnatal Rosette-Based Adrenocortical Morphogenesis

status: Public on Feb 15 2020

city: Boston

first: David

last: Breault

state: MA

address: 300 Longwood Ave.

department: Endocrinology

institute: Boston Childrens Hospital

summary: We show that β-catenin stabilization leads to increased FGFR2, which is required for rosette formation by regulating AJ stability and dynamics. Our results provide the basis for studying adrenal glomerular morphogenesis and the role of rosettes in on-going zG tissue maintenance and function.

overall_design: To investigate what mechanism(s) mediate the effects of β-catenin on zG morphology, we compared transcriptome changes between wild type and βCat-GOF adrenals by RNA sequencing

first: Sining

last: Leng

middle: T


title: RNA-seq of ML-2 acute myeloid leukemia cells overexpressed with GFP, FST317 and FST344

status: Public on Feb 16 2020

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: RNA-seq was used to determine the differentially expressed genes after overexpression of two human Follistatin (FST) isoforms, FST317 and FST344 in human acute myeloid leukemia cell line ML-2.

overall_design: ML-2 cells were transduced with lentivirus coding for GFP, FST317 and FST344. The transduced ML-2 cells were enriched by puromycin selection.

first: Bai-Liang

first: Yu-Hung

last: Leung


title: Virus-induced apoptosis in human cerebral organoids occurs primarily in committed neurons and is associated with a limited interferon stimulated gene response

status: Public on Feb 10 2020

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: La Crosse virus (LACV) is the leading cause of pediatric arboviral encephalitis in the USA. Although the hallmarks of disease are infection and apoptosis of neurons, there is limited knowledge of neuronal responses to virus infection at differing neurodevelopmental stages. Here, we infected induced pluripotent stem-cell (iPSC)-derived human cerebral organoids (COs) containing actively maturing populations of neuronal-lineage cells to examine this process. LACV readily infected COs and caused reduced cell viability. Although neural progenitors and committed neurons were similarly infected, significantly more committed neurons underwent apoptosis. Committed neurons expressed fewer interferon (IFN)-inducible transcripts in response to infection compared to neural progenitors, suggesting a poor anti-viral response. Treatment of infected COs with recombinant IFNs enhanced cell viability, demonstrating a therapeutic potential. This study demonstrates that LACV differentially induces apoptosis in neuronal-lineage cells depending on their stage of maturation and provides analysis for why these cells differ in their responses.

overall_design: 2 samples derived from human cerebral organoids were processed using 10x Genomics single cell instrument

first: Clayton

last: Winkler

first: Tyson

last: Woods

first: Bradley

last: Groveman

first: Aaron

middle: B

last: Carmody

first: Emily

last: Speranza

first: Sonja

last: Best

first: Cathryn

middle: L

last: Haigh

first: Karin

last: Peterson


title: A dynamic folded hairpin conformation is associated with 𝛂-globin activation in erythroid cells

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigate the three-dimensional conformations of the 𝛂-globin locus at the single-allele level in murine ES and erythroid cells, combining polymer physics models and high-resolution Capture-C data. Model predictions are validated against independent FISH data measuring pairwise distances, and Tri-C data identifying three-way contacts. The architecture is rearranged during the transition from ES cells to erythroid cells, associated with the activation of the globin genes. We find that in ES cells, the spatial organization conforms to a highly intermingled 3D structure involving non-specific contacts, while in erythroid cells the 𝛂-globin genes and their enhancers form a self-contained domain, arranged in a folded hairpin conformation, separated from intermingling flanking regions by a thermodynamic mechanism of micro-phase separation. The flanking regions are rich in convergent CTCF sites, which only marginally participate in the erythroid-specific gene-enhancer contacts, suggesting that beyond the interaction of CTCF sites multiple molecular mechanisms cooperate to form an interacting domain.

overall_design: Embryonic stem cells were grown, and used for ChIP-seq using H3K27me3 antibody.

first: Magnus

last: Lynch

first: Jelena

last: Telenius

first: Douglas

last: Higgs

first: Jim

last: Hughes


overall_design: ChIP-seq with indicated antibodies on chromatin isolated from primary erythroid ter119+ cells obtained from the spleens of acetylphenylhydrazine treated mice. Wild-type C57BL/6 mice were used.

first: Martin

last: Larke


title: Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [MPRA]

city: Cambridge

first: Carl

last: de Boer

address: 415 Main St

institute: The Broad Institute

summary: Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. Trait/disease-associated variants were enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 had at least one variant meeting one or both of these criteria, with 3 of these haplotypes having a single prioritized variant. 5 of the 9 prioritized variants were further supported by genetic fine-mapping in our and other studies. Our work provides evidence for the efficacy and limitations of strategies for prioritizing disease- and trait-associated genetic variants.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Massively parallel reporter assays to study variant effects on reporter expression, 2-3 replicates, 3 cell types, 4 cell lines, lentiviral and transfection

first: John

middle: P

last: Ray


title: Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits

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

overall_design: Refer to individual Series


title: The effects of METTL3 on BAT development and thermogenesis

status: Public on Feb 06 2020

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
Purpose: The goal of this study is to compare transcriptome profilings of interscapular brown adipose tissue (iBAT) from BAT-specific METTL3 knockout and control mice

Methods: iBATs were collected from METTL3 BKO and f/f mice at 8 weeks old, and total RNA was isolated using TriPure. RNA samples were pooled from iBATs of METTL3 BKO and f/f mice (n=4 for each group). RNA-seq was performed by using Illumina NovaSeq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome (Ensemble_GRCm38.90) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).

Conclusion:Our study represents the first detailed analysis of iBAT transcriptomes from METTL3 BKO and f/f mice, generated by RNA-seq technology. The RNA-seq analysis showed that 530 genes were down-regulated and 1552 genes were up-regulated in the iBAT of METTL3 BKO mice. GO analysis showed that the down-regulated genes were primarily related to developmental maturation, respiratory electron transport chain, adaptive thermogenesis, and energy deprivation by oxidation of organic compounds whereas the up-regulated genes were associated with muscle system process and muscle cell development.

overall_design: RNA samples were pooled from iBATs of METTL3 BKO and f/f mice at 8 weeks old (n=4 for each group). mRNA profiles of METTL3 BKO and f/f iBATs were generated by deep sequencing, in a single test, using Illumina NovaSeq 6000 platform.

first: Yuqin

last: Wang


title: Dlx1/2 mutant and wild type FACS-sorted ENCDCs at P0 and E14.5

status: Public on Feb 17 2020

city: Philadelphia

first: Christina M. Wright

last: Wright

address: 3615 Civic Center Blvd

department: Department of Pediatrics

institute: Children's Hospital of Philadelphia

summary: These experiments were part of a larger study investigating abnormal bowel motility in mice lacking Dlx1 and Dlx2. The purpose of these experiments was to identify genes regulated by Dlx1 and Dlx2 in the enteric nervous system (ENS) of mouse small intestine at multiple developmental stages. For these experiments, we crossed Dlx1/2 wild type and mutant mice with fluorescent reporter strains that labeled ENS, FACS sorted ENS precursor cells, and isolated RNA. Using a q-value cutoff of 0.1, we found 22 dysregulated genes at E14.5 and 5 dysregulated genes at P0, including the gene Vip, which encodes the neurotransmitter vasoactive intestinal peptide. To our knowledge, our study is the first to show a connection between Dlx genes and Vip expression. These findings may be relevant for intestinal diseases such as chronic intestinal pseudo-obstruction (CIPO) syndrome.

overall_design: Comparison of gene expression in Dlx1/2-/- (mutant) and Dlx1/2+/+ (WT) small bowel enteric nervous system at two ages, E14.5 and P0.

first: Christina

first: Robert

middle: O

last: Heuckeroth


title: The whole transcriptome regulation as a function of mitochondrial polymorphisms and age in C. elegans [BGISEQ-500]

status: Public on Feb 07 2020

city: Xuzhou

first: Zuobin

last: Zhu

state: Jiangsu

address: Tongshan road 209

department: Department of Genetics

institute: Xuzhou Medical University

summary: The complex IV polymorphisms in mitochondria not only affected the mitochondria mass but also miRNA, lncRNA, mRNA and circRNA profiles. Furthermore, Most of genes that associated with mitochondria, showed age-related expression feature (P = 3.62156E-37). Next, we constructed a differentially expressed circRNA-lncRNA-miRNA-mRNA-ceRNA regulatory networks to determine functional interactions affected by the mitochondria variation. We also selected top 10 candidates ceRNA with the most correlation among the RNA. In addition, KEGG pathway analyses showed that the genes affected by the mitochondria variation were an enrichment of metabolic activity. Finally, we examined the metabolic changes in the old worms and analyzed the association between the metabolites and genes. The construction of multi-omics regulation network is great value for the research of nuclear genes mitochondria and aging. Here, we constructed a multi-level regulatory network with aging which affected by the mitochondria variation in C. elegans and the interaction between these genes are great value for further aging research. Thus, our finding provides new evidence for understanding the molecular mechanisms of how mitochondria influence on aging.

overall_design: lncRNA and mRNA profiles of 0-day, 6-day, 9-day, 12-day old N2 strain and the transnuclear CN30 worms were generated by deep sequencing, using Illumina BGISEQ-500.

first: Ying

last: Li


title: Circulating traveling waves rapidly pace and mature hiPSC-derived cardiomyocytes in self-organized tissue ring

status: Public on Feb 05 2020

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

summary: Directed differentiation methods allow acquisition of high-purity cardiomyocytes (CMs) differentiated from human induced pluripotent stem cells (hiPSCs); however, their immaturity characteristic limits their application for drug screening and regenerative therapy. The rapid electrical pacing of cardiomyocytes have been used for efficiently promoting the maturation of cardiomyocytes, here we describe a simple device in modified culture plate on which hiPSC-derived CMs can form three-dimensional self-organized tissue rings (SOTRs). Using calcium imaging, we show that within the ring, traveling waves (TWs) of action potential spontaneously originated and ran robustly at a frequency up to 4 Hz. After 2 weeks, SOTRs with TW training show matured features including structural organization, increased cardiac-specific gene expression, enhanced Ca2+-handling properties, an increased oxygen-consumption rate, and enhanced contractile force. We subsequently use a mathematical model to interpret the origination, propagation, and long-term behavior of the TWs within the SOTRs. The TW could also potentially be used for pacing the electrical excitable cells such as neuron and retina cells for various applications.

overall_design: Here, we performed RNA sequencing (RNA-Seq) analysis of human induced pluripotent stem cell derived cardiomyocyte.

first: Junjun

first: Yang

last: Zhao

first: Fuchou

last: Tang

first: Li

last: Liu


title: dsRNA IP of Coronavirus Infected IFNAR-/- BMDMs

city: MAYWOOD

first: Susan

last: Baker

state: IL

address: 2160 S. 1st Ave, Bldg 115 Rm 270B Baker

department: Microbiology & Immunology

institute: Loyola University Chicago

summary: RNA-sequencing data of mock, wild-type, and EndoUmut MHV A59 infected IFNAR-/- bone-marrow derived macrophages.  RNA was isolated at 6 hours post infection and immunoprecipitated with anti-dsRNA antibody to determine which RNA are forming a dsRNA epitope during viral infection.  RNAs were mapped to C57Bl/6 Mouse genome or MHV-A59 genome (Genbank accession # AY910861).

overall_design: RNA-sequencing data of mock, wild-type, and EndoUmut MHV A59 infected bone-marrow derived macrophages.  RNA was isolated at 6 hours post infection.  2ug of RNA was then immunoprecipitated with the K1 anti-dsRNA antibody and reisolated off magnetic beads.  Samples were processed in biological triplicates with input and dsRNA IP RNA submitted for RNA-seqeuncing.

first: Matthew

last: Hackbart

first: Xufang

last: Deng


title: Serine/Threonine phosphatase PP2A is essential for optimal B cell function

status: Public on Feb 04 2020

first: George

last: Tsokos

state: Massachusetts

address: CLS-928, 3 Blackfan Circle

department: Rheumatology/BIDMC

institute: Harvard Medical School

summary: Protein phosphatase 2A (PP2A), a serine/threonine phosphatase, has been shown to control T cell function. We found that in vitro activated B cells and B cells from various lupus-prone mice and patients with systemic lupus erythematosus display increased PP2A activity.  To understand the contribution of PP2A to B cell function, we generated a Cd19CrePpp2r1aflox/flox (flox/flox) mouse which lacks functional PP2A only in B cells. Flox/flox mice displayed reduced spontaneous germinal center formation and decreased responses to T-dependent and T-independent antigens while their B cells responded poorly in vitro to stimulation with an anti-CD40 antibody or CpG in the presence of IL-4.  Transcriptome and metabolome studies revealed altered NAD and purine/pyrimidine metabolism and increased expression of purine nucleoside phosphorylase in PP2A-deficient B cells. Our results demonstrate that PP2A is required for optimal B cell function and may contribute to increased B cell activity in systemic autoimmunity.

overall_design: Examination of gene expression in B cells from 1) wild-type mice  2) B cell-specific PP2Aa-deficient mice

first: Hao


title: A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression

status: Public on Feb 12 2020

city: Stanford

first: Yuan

last: Xue

address: 318 Campus Drive

institute: Stanford University

summary: Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.

overall_design:
We sequenced a total of 5499 Toxoplasma gondii parasites of three distinct strains. 4599 of the parasites were kept for analysis. Samples include Toxoplasma gondii RH tachyzoites, ME49 and Pru tachyzoites and bradyzoites in in vitro induction environment.

Please note that the procesed data files generated from multiple samples are linked to the corresponding 'day 0' sample records.

first: Terence

last: Theisen

first: Suchita

last: Rastogi

first: Abel

last: Ferrel

first: Stephen

last: Quake

first: John

last: Boothroyd


title: DNA methylome of German Shepherd

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

type: Methylation profiling by high throughput sequencing

summary: Using WGBS we investigated blood DNA methylation profiles of German Shepherd and determined putative regulatory elements (unmethlated regions (UMRs) and lowly methylated regions (LMRs).

overall_design: Whole genome bisulphite sequencing of German Shepherd's blood DNA

first: Ozren

last: Bogdanovic


title: m6A MeRIP-Seq of interscapular brown adipose tissue (iBAT) in Mettl3flox/flox and BAT-specific Mettl3 knockout (BKO) mice

first: Zheng

last: Chen

summary:
Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in iBAT obtained from Mettl3flox/flox and BKO mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from iBAT of Mettl3 flox/flox and BKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 5 mice for each group. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Chemically fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation following the standard protocol of Magna MeRIPTM m6A Kit (MERK, 17-10499). Enrichment of m6A mRNA was then analyzed by high-throughput sequencing using Illumina Hiseq X platform. The m6A peaks were detected by MACS2. The motif search was detected by HOMER.
Conclusion: The iBAT mRNA m6A profiles in Mettl3flox/flox and BKO mice were characterized.

overall_design: To map the mRNA m6A modification caused by METTL3 in iBAT, MeRIP-seq was performed in iBAT obtained from Mettl3flox/flox and BKO mice.

first: Yuqin

last: Wang


title: Genome-wide profile of RBPJ and differential H3K27ac profile upon treatment with HDAC-inhibitor apicidin.

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: The Notch signaling pathway regulates several differentiation and developmental processes in both pre- and post-natal life and its aberrant regulation leads to diseases, including cancer. Here, we investigated the genome-wide distribution of the transcription factor RBPJ and the differential regulation of H3K27ac upon pharmacological inhibition of histone deacetylase 3 (HDAC3) with apicidin in mouse pre-T (Beko) cells.

overall_design: Mouse pre-T cells (Beko) were analyzed by ChIP-Seq using an RBPJ-specific antibody. Subsequently, Beko cells were treated with gamma-secretase inhibitor (GSI) DAPT, HDAC3 inhibitor apicidin or DMSO as control and H3K27ac was analyzed by ChIP-Seq. Two replicates of each sample are included with the only exception of the input controls.

first: Francesca

last: Ferrante

first: Benedetto

middle: D

last: Giaimo

first: Tilman

last: Borggrefe


title: Comparative genome-wide analysis of whole skin from mice vaccinated with E7SH/ISG15-ΔGG versus E7SH/EV

city: Amsterdam

first: Victoria

last: Iglesias

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary:
Purpose: To understand the mechanistic basis of the adjuvant role of extracellular ISG15 to support the CTL response and define whether ISG15 protein expression has a local effect on the vaccinated skin during a therapeutic DNA vaccination model, we performed mRNA deep sequencing analysis of the whole skin from the vaccinated area.
Methods: Two groups of mice (3 mice per group) were vaccinated using a tottoo device, either with pDNA encoding a shuffled version of the E7 protein alone (E7SH/EV) or combined with pDNA encoding a truncated version of ISG15 that expresses only its free form (E7SH/ISG15-ΔGG). Vaccination was performed on days 0 and 3 and the whole skin from the vaccinated area was isolated on day 4. Differential expression of genes was assessed using the DESeq2 package. Genes with adjusted p values ≤ 0.05 were deemed significantly differentially expressed. To find activated pathways, overexpressed in comparison to the control (log-fold change > 0, adjusted p value ≤ 0.1) genes were used as input for enrichment analysis using the Reactome enrichment analysis tool. Additionally, we analysed activated pathways using Ingenuity Pathway Analysis IPA.
Results: Statistical analysis of normalized transcript read counts showed that 444 genes were differentially expressed in the skin as a result of ISG15 coexpression. Using IPA we identified 15 functional categories predicted to be activated (z-score ³ 2) indicating that ISG15 stimulates cell migration, in particular of myeloid cells and endothelial cells. In addition, gene ontology analysis using Reactome indicated an increased metalloprotease activity, collagen degradation and extracellular matrix organization.
Conclusion: Our study represents the first analysis in an in vivo setting of ISG15 expression in keratinocytes, with biologic replicates, generated by RNA-seq technology. The results show that free ISG15 proves to be an alarmin that induces tissue alert, characterized by extracellular matrix remodelling, myeloid cell infiltration and inflammation.

overall_design: Whole skin mRNA profiles of vaccinated mice with pDNA encoding E7 in combination with ISG15-ΔGG DNA (E7SH/ISG15-ΔGG) or Empty-vector (EV) DNA as a control. Three biological replicates per condition were used.

first: Jannie

last: Borst


title: Differential Notch target genes expression profile upon HDAC3 loss-of-function.

summary: The Notch signaling pathway regulates several differentiation and developmental processes in both pre- and post-natal life and its aberrant regulation leads to diseases, including cancer. Here, we investigated the role of histone deacetylase 3 (HDAC3) on the regulation of the Notch-dependent gene expression program in mouse pre-T (Beko) cells. We first defined Notch target genes as those genes that are downregulated upon inhibition of the Notch pathway using DAPT, a gamma-secretase inhibitor (GSI). Subsequently, we investigated the role of HDAC3 in the regulation of Notch target genes by shRNA- and pharmacologically (apicidin)-mediated loss-of-function of HDAC3.

overall_design: Mouse pre-T cells (Beko) were treated with gamma-secretase inhibitor (GSI) DAPT to identify Notch target genes by RNA-seq analysis. The function of HDAC3 at Notch target genes was investigated by shRNA- or pharmacological (Apicidin)-mediated loss-of-function of HDAC3 followed by RNA-seq analysis.


title: DRIP-seq, Drosophila melanogaster, OregonR 2-6H and 10-14H embryos and S2 cells

status: Public on Feb 03 2020

city: Montreal

first: Celia

last: Alecki

state: QC

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

institute: McGill University

summary: This study idenfied RNA:DNA hybrids in Drosophila melanogaster embryos and S2 cells

overall_design: DRIP-seq was carried out on Drosophila cell lines and embryos to identify RNA-DNA hybrids. Genomic DNA was treated with RNAseA and RNaseIII prior to immunoprecipitation with the S9.6 antibody. Control samples were additionally treated with RNaseH prior to immunoprecipitation. Strand specific DNA libraries were prepared and sequenced.

first: Nicole

middle: J

last: Francis


title: Immune gene signatures for predicting durable clinical benefit of anti-PD-1 immunotherapy in patients with non-small cell lung cancer

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

department: Pathology

institute: Cha University

summary: Immune checkpoint blockade is promising for treating non-small-cell lung cancer (NSCLC). We used multipanel markers to predict the response to immune checkpoint inhibitors (ICIs) by characterizing gene expression signatures or individual genes in patients who showed durable clinical benefit to ICIs. Twenty-one patients with NSCLC treated with single-agent anti-programmed cell death protein (PD)-1 antibody were analyzed and their clinicopathological characteristics and response to ICIs were characterized. Targeted sequencing of tissue-extracted DNA and RNA was performed using the Oncomine Immune Response Research Assay to evaluate 395 genes involved in the immune response and calculate the tumor mutation burden. Nine (43%) showed a durable clinical benefit (DCB), while the remaining 12 (57%) patients showed non-durable benefit (NDB). The M1 and peripheral T cell signatures showed the best performance for discriminating DCB from NDB (sensitivity, specificity, accuracy = 0.89, 1.0, 0.95, respectively). Progression-free survival (PFS) was significantly longer in patients with high M1 signature or high peripheral T cell signature scores. CD137 and PSMB9 mRNA expression was higher in the DCB group than in the NDB group. Patients with high PSMB9 expression showed longer PFS. M1 signature, peripheral T cell signature and high mRNA expression level of CD137 and PSMB9 showed better predictive performance than known biomarkers (PD-L1, tumor infiltrating lymphocytes, tumor mutation burden). M1 and peripheral T cell signature of tumors may enable prediction of durable response and maximize the benefit of ICIs in patients with NSCLC.

overall_design:
The mRNA expression of non-small cell lung cancer patinets before anti-PD-1 immunotherapy were measured by Oncomine Immune Response panel
----------------------------------------------
The submitter is unable to locate the raw data for D02, D04, D05, N01, N02, N03, N04, N07, N09, N11, and N12

Please note that the sample 'characteristics: survival' information has been updated on April 16, 2020.

first: Hee-Jung

last: An


title: Gene expression profiling of adult hair follicle dermal stem cells and progeny, dermal sheath and dermal papilla cells

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

institute: University of Calgary

summary: Here we have developed a novel FACS strategy to prospectively isolate hair follicle dermal stem cells, dermal sheath and dermal papilla cells from adult skin initiating synchronous hair follicle regeneration and identified Hic1 as a marker of hfDSCs and Rspondins as stimulators of hfDSCs and epithelial cells, and subsequently hair follicle regeneration

overall_design: Comparison of gene expression of adult hair follicle mesenchymal cells undergoing initiation of hair follicle regeneration

first: Andrew

last: Hagner

first: Jeff

last: Biernaskie


title: m6A-seq profiling in Xist and Xist_Del_A-repeat cell lines

status: Public on Feb 01 2020

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

summary: By m6A-seq, we examined the m6A pattern on Xist and Xist_Del_A-repeat, which immediately after the A-repeat region. A-repeat deletion abolished the m6A methylation downstream the A-repeat but not the m6A peak located in Xist exon VII.

overall_design: M6A profiling in cell lines with WT Xist or Xist lacking the A-repeat. We are aiming to understand how m6A pattern was on Xist and how m6A modification on Xist affect Xist-mediated chromosome silencing.

first: G

first: Tatyana

last: Nesterova

first: N

last: Brockdorff


title: ASK1 Inhibition Reduces Cell Death and Hepatic Fibrosis in an Nlrp3 Mutant Liver Injury Model

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

summary: The aim of the current study was to investigate whether pharmacologic inhibition of ASK1 could attenuate hepatic fibrosis driven by inflammasome activation using gain-of-function NOD-like receptor protein 3 (Nlrp3) mutant mice.

overall_design: Tamoxifen-inducible Nlrp3 (Nlrp3A350V/+CreT) knock-in (KI) mice and wild-type mice were administered either control chow diet or diet containing the selective ASK1 inhibitor GS-444217 for 6 weeks.

first: Susanne

last: Schuster-Gaul

first: Lukas

last: Geisler

last: McGeough

first: Casey

last: Johnson

first: Anna

last: Zagorska

first: Alexander

last: Wree

first: Vivian

last: Barry

first: Igor

last: Mikaelian

first: Lily

last: Jih

first: Bettina

middle: G

last: Papouchado

first: Grant

last: Budas

first: Hal

last: Hoffman

first: Ariel

last: Feldstein


title: Notch ligand Dll4 impairs the recruitment of hemogenic cells into intra-aortic clusters and limits hematopoietic stem cell production

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: Hematopoietic stem cells (HSCs) develop from the hemogenic endothelium in the embryonic aorta. In most vertebrates, hemogenic cells protrude into the aortic lumen forming clusters where the hematopoietic features are acquired. Although much is known about the molecular characteristics of the hematopoietic cells, we still lack basic understanding on the origin and 3D-organization of intraortic hematopoietic clusters (IAHC) in the mouse embryo and how they evolve over time. Here we use advanced live imaging techniques of organotypic slice cultures, clonal analysis, and mathematical modelling to show that IAHC formation is a two-step process. First, a hemogenic progenitor buds up from the endothelium and undergoes division forming the monoclonal core of the cluster. Next, cells from the surrounding hemogenic endothelium are recruited into the IAHCs, increasing their size and heterogeneity. We found that the recruitment phase of IAHC formation is negatively regulated by Notch signalling via the Delta-like-4 (Dll4) Notch ligand. We show that blocking of Dll4 promotes the entrance of new hemogenic Gfi1+ cells into the IAHC and increases the number of cells that acquire HSC activity.  Mathematical modelling based on our data provides estimation of the cluster lifetime and the average recruitment time of hemogenic cells to the cluster under physiologic and Dll4-inhibited conditions. Single cell transcriptomic analysis indicates that cell identities are preserved after Dll4 blockage. Our data provides for the first time a detailed characterization of the aortic hematopoietic stem cell niche and its maturation dynamics, identifying the Notch ligand Dll4 as a major molecular player governing dynamics of cluster formation and HSCs production.

overall_design: RNA sequencing of CD31+kit+CD45- cells treated with or without aDll4

first: Cristina

last: Porcheri

first: Ohad

last: Golan

first: Fernando

last: Calero-Nieto

first: Roshana

last: Thambyrajah

last: Ruiz-Herguido

first: Francesca

last: Catto

first: Yolanda

last: Guillen

first: Roshani

last: Sinha

first: Jessica

last: González

first: Sarah

last: Kinston

first: Samanta

middle: A

last: Mariani

first: Antonio

last: Maglitto

first: Elaine

last: Dzierzak

first: Pierre

last: Charbord

first: Bertie

last: Göttgens

first: Lluis

last: Espinosa

first: David

last: Sprinzak

last: Bigas


title: Switching fatty acid metabolism by an RNA-controlled feed forward loop

city: Jena

first: Malte

last: Siemers

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

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

overall_design: Refer to individual Series


title: Single-Cell RNA-Seq Analysis of Metastasis-Primary Tumor Dissimilarity in a Patient with Gastrointestinal Neuroendocrine Cancer

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

summary: A 58 year old female diagnosed with a metastic GI-NET underwent resection of primary tumor as well as several metastatic lesions. We performed scRNA-seq of the primary tumor and one lesion from the liver metastasis to perform comparitive analysis between the primary and metastic tumor compositions.

overall_design: scRNAseq was performed on theprimary small intestinal neuroendocrine tumor and its matched liver metastasis simultaneously.

first: Manisha

last: Rao

first: Ki

last: Oh

first: Richard

last: Moffitt

first: Patricia

last: Thompson

first: Jingxuan

last: Liu

first: Aaron

last: Sasson

first: George

last: Georgakis

first: Joseph

last: Kim

first: Minsig

last: Choi

first: Scott

last: Powers


title: RNA-seq 6 day timecourse for K562 cells grown in hypoxia/normoxia (21%, 5%, 1% oxygen)

status: Public on Jan 31 2020

first: Sarah

middle: E

last: Calvo

address: 415 Main St

institute: Broad Institute

summary: K562 cells were grown at different oxygen levels (21%, 5%, 1%) and samples were collected at 6hr, 24hr, 3day, and 6day time points (triplicate per time point).

overall_design: RNA-seq was performed for K562 cells grown in 3 oxygen levels (21%, 5%, 1%) at 4 time points (6hr, 24hr, 3day, 6day) for each of 3 replicates. K562 cells were seeded at a density of 1e5/ml in 3ml of DMEM media per well of 6-well plate. Plates were maintained in 1%, 5% or 21% O2 incubators and passaged at 3d of growth. At each time point, cells were pelleted, rinsed with PBS and then stored at -80C. RNA extraction was performed using the Qiagen RNAeasy kit. The RNASeq libraries were generated as described (Picelli et al., 2014; Trapnell et al., 2012). RNA was isolated using RNASPRI beads. Following reverse transcription, cDNA was fragmented and barcoded. Samples were subjected to paired-end sequencing of 2x25bp. RNASeq data was processed using the Cufflinks suite (tophat, cuffquant, cuffnorm) as previously described (Trapnell et al., 2012).

first: Isha

middle: H

last: Jain

first: Vamsi

middle: K

last: Mootha


title: Differential gene responses three days following infarction in the fetal and adolescent sheep heart

status: Public on Jan 30 2020

city: Manchester

first: Mitchell

middle: C

last: Lock

address: 46 Grafton Street

department: Division of Cardiovascular Sciences

institute: University of Manchester

summary:
Background: There are critical molecular mechanisms that can be activated to induce myocardial repair and in humans this is most efficient during fetal development. The timing of heart development in relation to birth and the size/electrophysiology of the heart are similar in humans and sheep, providing a model to investigate the repair capacity of the mammalian heart and how this can be applied to adult heart repair.
Methods: Myocardial infarction was induced by ligation of the left anterior descending coronary artery in fetal (105d gestation when cardiomyocytes are proliferative) and adolescent sheep (6 months of age when all cardiomyocytes have switched to an adult phenotype). An ovine gene microarray was used to compare gene expression in sham and infarcted (remote, border and infarct areas) cardiac tissue from fetal and adolescent hearts.
Results: The gene response to myocardial infarction was less pronounced in fetal compared to adolescent sheep hearts and there were unique gene responses at each age. There were also region-specific changes in gene expression between each age, in the infarct tissue, tissue bordering the infarct, and tissue remote from the infarction. In total, there were 880 genes that responded to MI uniquely in the adolescent samples compared with 170 genes in the fetal response, as well as 742 overlap genes that showed concordant direction of change responses to infarction at both ages.
Conclusions: In response to myocardial infarction, there were specific changes in genes within pathways of mitochondrial oxidation, muscle contraction, and haematopoietic cell lineages, suggesting that the control of energy utilisation and immune function are critical for effective heart repair. The more restricted gene response in the fetus may be an important factor in its enhanced capacity for cardiac repair.

overall_design: 105 day gestation sheep fetuses and 6 month old adolescent sheep underwent surgery to ligate the second diagonal of the left anterior descending coronary artery causing myocardial infarction. Animals were then humanely killed three days after surgery and tissue from the infarct area, border zone and remote zone was collected for RNA extraction. Control animals recieved Sham surgery. Three samples from each tissue region (Sham, remote, border and infract) from both age groups (Fetal and Adolescent sheep) were used in total for array analysis. RNA was labelled with Cy3 and hybridized to Agilent 8 × 15k microarray slides (Ovine 019221 Arrays; GPL14112 platform) and scanned on an Agilent G2505B 2 dye scanner.

first: Ross

last: Tellam

first: Jack

middle: R

last: Darby

first: Jia

middle: Y

last: Soo

first: Doug

last: Brooks

first: Christopher

last: Macgowan

last: Selvanayagam

first: Enzo

last: Porrello

first: Mike

last: Seed

first: Maureen

last: Keller-Wood

first: Janna

last: Morrison


title: Mediator condensates localize signaling factors to key cell identity genes

city: Cambridge

first: Alicia

middle: Viridiana

last: Zamudio

address: 455 Main St

department: Biology

institute: Massachusetts Institute of Technology

summary: The gene expression programs that define each cell’s identity are controlled by master transcription factors (TFs) that bind cell-type specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here we present evidence that signaling factors for the WNT, TGF-β and JAK/STAT pathways employ their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA binding factors to selectively occupy super-enhancer associated genes. We propose that the cell-type specificity of the response to signaling is mediated, in part, by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity.

overall_design: beta_catenin, MED1, beta_catenin, armadillo, idrs ChIP-seq in mES cells grown in 2i.

middle: V


title: Genome-wide maps of H3K36me3 in MII oocytes and H3K9me3 in 2-cell embryos

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

summary: We report the application of low input high-throughput profiling of histone modifications in mouse oocytes and 2-cell embryos. We used antibodies against H3K36me3 (190 wildtype and 93 knockout MIIcoocytes pooled as one replicate) and H3K9me3 ( around 118 control and MZ embryos / replicate; 1 biological replicates per genotype). In the case of H3K36me3, we find that its establishment and maintence is not affected in oocytes lacking Kdm4a. In the case of H3K9me3 in 2-cell embryos, we find that the histone mark aberrantly gained in Kdm4a deficient oocytes is also maintained in the MZ mutant 2-cell embryo. This shows that Kdm4a is important to keep open chromatin clear of H3K9me3 spreading in oocytes in order to transfer a healthy epigenome amenable for proper genome activation post fertilization.

overall_design: Examination of H3K36me3 in mouse oocytes and H3K9me3 in 2-cell embryos with and without Kdm4a

first: Mads

last: Lerdrup


title: Transcription factor binding on designed libraries measured by CCRAs

city: St. Louis

first: Jiayue

last: Liu

state: MO

address: 4515 McKinley Research Building

department: Genetics

institute: Washington University in St. Louis

summary: We measured transcription factor binding and expression of designed syththetic promoter libraries using Calling Cards Reporter Arrays (CCRAs). In this study, we showed that CCRAs is able to make quantatitive measurements for many TFs in yeast. We then demonstrate the quantitative analysis of cooperative interactions by measuring Cbf1p binding at synthetic promoters with multiple sites. Finally, we characterize the binding and expression of a group of TFs, Tye7p, Gcr1p, and Gcr2p, that act together as a “TF collective”, an important but poorly characterized model of TF cooperativity. We demonstrate that Tye7p often binds promoters without its recognition site because it is recruited by other collective members, whereas these other members require their recognition sites, suggesting a hierarchy where these factors recruit Tye7p but not vice versa. Our experiments establish CCRA as a useful tool for quantitative investigations into TF binding and function.

overall_design: Using Calling Cards on a arrary of designed promoter sequences

first: Robi

last: Mitra


title: Autism-misregulated eIF4G microexons control synaptic translation and higher-order cognitive functions [iCLIP-seq]

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity-dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively up-regulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning and memory deficits, as well as alterations in hippocampal synaptic plasticity. The eIF4G microexons appear to reduce synaptic protein synthesis by causing ribosome stalling, through a mechanism whereby they promote the coalescence of cytoplasmic granule components associated with translation repression, including the Fragile X mental retardation protein, FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes translation to control higher-order cognitive functioning.

overall_design: iCLIP-seq of Srrm3 and Srrm4 in in-vitro differentiated mouse neurons

first: Thomas

last: Gonatopoulos-Pournatzis

first: Rieko

last: Niibori

first: Eric

middle: W

last: Salter

first: Robert

last: Weatheritt

first: Brian

last: Tsang

first: Shaghayegh

last: Farhangmehr

first: Xinyi

last: Liang

first: Jonathan

last: Roth

first: Shen

last: Zhang

first: Tyler

last: Henderson

first: Eesha

last: Sharma

first: Mathieu

last: Quesnel-Vallières

first: Jon

last: Permanyer

first: Stefan

last: Maier

first: John

last: Georgiou

first: Manuel

last: Irimia

first: Nahum

last: Sonenberg

first: Julie

last: Forman-Kay

first: Anne-Claude

last: Gingras

first: Graham

last: Collingridge

first: Melanie

last: Woodin

first: Sabine

last: Cordes

first: Benjamin

last: Blencowe


title: Binding and regulation of transcription by yeast Ste12 variants to drive mating and invasion phenotypes

city: seattle

first: wei

last: zhou

state: wa

address: 4747 30th ave NE

department: genome sciences

institute: University of Washington

summary: Here, we examine how six single amino acid variants in the DNA-binding domain of Ste12 – a yeast transcription factor regulating mating and invasion – alter Ste12 genome binding, motif recognition and gene expression to yield markedly different phenotypes. Using a combination of the calling card method, RNA sequencing , we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors.

overall_design: We overexpress six variant of transcription factor Ste12 in yeast S.cervesiae and detected its genome-wide binding pattern and RNA expression pattern

first: Wei

last: Zhou

first: Michael

last: Dorrity

first: Kerry

last: Bubb

first: Christine

last: Queitsch

first: Stanley

last: Fields


title: Stress-induced beta cell dedifferentiation prior to immune cell infiltration prevents type 1 diabetes [Bulk]

city: Madison

first: Feyza

last: Engin

state: Wisconsin

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: Immune-mediated destruction of insulin-producing β-cells causes type 1 diabetes (T1D). However, how β-cells themselves participate in the disease process is poorly understood. Here, we report that modulating the unfolded protein response (UPR) in β-cells of non-obese diabetic (NOD) mice in early stages of disease results in preserved β-cell function, substantially reduced islet immune cell infiltration, and β-cell apoptosis leading to protection from T1D. NOD mice that lack the UPR sensor IRE1α in β-cells show greatly reduced expression of β-cell identity markers, islet autoantigens, and genes involved in antigen presentation. These mice exhibit upregulation of immune inhibitory markers in β-cells and significantly less cytotoxic CD8+ T cells in the pancreas. Our results indicate that triggering transient β-cell dedifferentiation via targeting a specific branch of the UPR in β-cells, prior to insulitis, allow β-cells to escape from immune destruction and may be used as a novel preventive strategy for high-risk individuals.

overall_design: mRNA sequencing of 7-week-old IRE1αfl/fl (WT) and IRE1αβ-/- (KO) mice were done with n=4 per group

first: Hugo

last: Lee

first: Yong-Syu

first: Quincy

last: Harenda

last: Pietrzak

first: Hulya

middle: Z

last: Oktay

first: Sierra

last: Schreiber

first: Yian

last: Liao

first: Shreyash

last: Sonthalia

first: Sunduz

last: Keles

first: Rupa

last: Sridharan


title: Single cell RNA-sequencing of normal and fibrotic lungs in mouse and human

city: San Francisco

first: Tatsuya

last: Tsukui

state: CA

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

summary: We performed scRNA-seq of cells obtained with a protocol designed to capture all of the collagen-producing cells from normal and fibrotic mouse and human lungs.

overall_design: We induced lung fibrosis by treating two Col1a1-GFP reporter mice with bleomycin, and harvested lungs on day 14 after treatment. Two untreated Col1a1-GFP mice were used as control. After tissue dissociation, GFP+ cells and GFP- cells were sorted, and their single cell libraries were generated using 10x Genomics 3' v2 system. For human samples, we sorted lineage (CD31, CD45, EPCAM, CD235a)- cells and all lung cells (CD235a-) from three normal, three IPF, and two scleroderma lungs.

first: Kai

last: Sun

last: Matthay

first: Paul

last: Wolters

first: Dean

last: Sheppard


title: Genome-wide maps of H3K4me3, H3K9me3 chromatin states in control and Kdm4a knockout oocytes

first: Aditya

last: Sankar

summary: We report the application of low input high-throughput profiling of histone modifications in mouse oocytes. Using antibodies against H3K4me3 (100 oocytes/replicate; 2 biological replicates per genotype) and H3K9me3 ( around 300 oocytes/replicate; 2 biological replicates per genotype), we find that they are mutually exclusive in oocytes and this property is lost in oocytes lacking Kdm4a. H3K9me3 is spread into regions of H3K4me3 postive open chromatin which is surprisingly, well preserved leading to a potential bivalency of scale.  Altogether, KDM4A is important to keep H3K4me3 marked open chromatin clear of H3K9me3 spreading in oocytes.

overall_design: Examination of 2 different histone modifications in mouse MII oocytes

first: Mads

last: Lerdrup


title: Alterations of redox and iron metabolism accompany development of HIV latency

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Metabolic alterations, such as oxidative stress, are hallmarks of HIV-1 infection. However, their influence on the development of viral latency, and thus on HIV-1 persistence during antiretroviral therapy (ART), have just begun to be explored. We analyzed omics profiles of in-vitro and in-vivo models of infection by HIV-1 and its simian homolog SIVmac. We found that cells survive retroviral replication by upregulating antioxidant pathways and intertwined iron import pathways. These changes are associated with remodeling of the redox sensitive promyelocytic leukemia protein nuclear bodies (PML NBs), an important constituent of nuclear architecture and a marker of HIV-1 latency. We found that PML is depleted in productively infected cells and restored by ART. Moreover, we identified intracellular iron as a key link between oxidative stress and PML depletion, thus supporting iron metabolism modulators as pharmacological tools to impair latency establishment.

overall_design: Primary CD4+ T-cells were isolated from total blood of three healthy donors (designated as donor 14, donor 49 and donor 50). After isolation CD4+ T-cells were activated for 72 hours by adding the Dynabeads® Human T-Activator CD3/CD28 using a bead/cell ratio of 1:2. Following activation cells were divided in two groups and either infected with HIV-1 NL4-3 (2ng p24/million cells) or mock infected. Cells were cultured in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), penicillin/streptomycin, and 10 ng/mL IL-2 and kept at a concentration between 1-2 million cells/mL. Cell pellets were collected at 3-7-9 and 14 days post-infection and used for total RNA extraction and subsequent library construction and RNA-Seq analysis.

first: Iart

middle: L

last: Shytaj

first: Bojana

last: Lucic

first: Mattia

last: Forcato

first: Marina

last: Lusic


title: Expression data from RAW 264.7 cells treated with control or Mist-targeted GapmeR

city: Duarte

first: Kenneth

middle: Edmund

last: Stapleton

address: 1500 Duarte Rd

department: Diabetes Complications and Metabolism

institute: City of Hope

summary:
Mist is a novel lncRNA found to be downregulated in macrophages of mice with diet-induced obesity compared to control diet. The regulatory mechanisms of mouse Mist are unknown.
We induced Mist knockdown in mouse macrophage cell line RAW 264.7 and used microarray to detail Mist-mediated global gene expression changes and identify distinct classes of up- and down-regulated genes.

overall_design: RAW cells were transfected with antisense locked nucleic acid-modified GapmeRs (Exiqon) targeting Mist or a non-targeting control (50nM) using Lipofectamine RNAiMAX (Invitrogen) and RNA was collected 48h post-transfection.

first: Rama

last: Natarajan


title: CITEseq of human PBMC from healthy adult blood

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

country: France

institute: INSERM

summary: The development of single cell transcriptomic technologies yields large datasets comprising multimodal informations such as transcriptomes and immunophenotypes.  Currently however, there is no software to easily and simultaneously analyze both types of data. Here, we introduce Single-Cell Virtual Cytometer, an open-source software for flow cytometry-like visualization and exploration of multi-omics single cell datasets. Using an original CITE-seq dataset of PBMC from an healthy donor, we illustrate its use for the integrated analysis of transcriptomes and epitopes of functional maturation in peripheral T lymphocytes from healthy donors. So this free and open-source algorithm constitutes a unique resource for biologists seeking for a user-friendly analytic tool for multimodal single cell datasets.

overall_design: peripheral blood mononuclear cells (PBMCs) were isolated by sedimentation on Lymphopure TM (BioLegend) and labelled with 5 TotalSeq TM -A antibody mixes (to CD14, CD16, CD19, CD3, CD4, CD45, CD45RA, CD62L, CD8 and isotype controls) . For each antibody mix, a different TotalSeq TM -A hashtag (0.5 μ g/test) was used to allow for sample multiplexing.

first: Jean-Jacques

last: Fournié

first: Frédéric

last: Pont

first: Marie

last: Tosolini

first: Qing

last: Gao

first: Tse

middle: S

last: Huang

first: Kristopher

last: Nazor


title: Differentiated agonistic antibody targeting CD137 eradicates large tumors without hepatotoxicity

city: Boston

first: Vijay

last: Kuchroo

address: 60 Fenwood Road

department: Neurology

institute: Brigham & Women's Hospital

summary: CD137 (4-1BB) is a member of the TNFR superfamily that represents a promising target for cancer immunotherapy. Recent insights into the function of TNFR agonist antibodies implicate epitope, affinity, and IgG subclass as critical features, and these observations help explain the limited activity and toxicity seen with clinically tested CD137 agonists. Here we describe the preclinical characterization of CTX-471, a fully human IgG4 agonist of CD137 that engages a unique epitope that is shared by human, cynomolgus monkey, and mouse and is associated with a differentiated pharmacology and toxicology profile. In vitro, CTX-471 increased IFN-γ production by human T cells in an FcγR-dependent manner, displaying an intermediate level of activity between two clinical-stage anti-CD137 antibodies. In mice, CTX-471 exhibited curative monotherapy activity in various syngeneic tumor models and showed a unique ability to cure mice of very large (~500 mm3) tumors compared to validated antibodies against checkpoints and TNFR superfamily members. Extremely high doses of CTX-471 were well-tolerated, with no signs of hepatic toxicity. Collectively, these data demonstrate that CTX-471 is a unique CD137 agonist that display an excellent safety profile and an unprecedented level of monotherapy efficacy against very large tumors.

overall_design: Given the recent insights into the function of TNFR agonist antibodies that implicate epitope, affinity, and IgG subclass (16, 20–24) as critical features, an opportunity exists for novel CD137 agonists to achieve differentiated therapeutic activity and improved safety profile. Here we describe the discovery and preclinical characterization of CTX-471, a fully human IgG4 agonist of CD137 that displays a favorable and well-differentiated efficacy-safety profile that is attributed to a unique epitope, optimized affinity, and FcγR-dependent activity.

first: Ugur

last: Eskiocak

first: Wilson

last: Guzman

first: Benjamin

last: Wolf

first: Christine

last: Cummings

first: Lauren

last: Milling

first: Hsin-Jung

last: Wu

first: Michael

last: Ophir

first: Conner

last: Lambden

first: Pearl

last: Bakhru

first: Dana

last: Gilmore

first: Samantha

last: Ottinger

first: Lucy

last: Liu

first: William

last: McConaughy

first: Sunny

middle: Q

last: He

first: Chao

last: Wang

first: Cheuk

last: Leung

first: Jason

last: Lajoie

middle: F

last: Carson IV

first: Nora

last: Zizlsperger

middle: M

last: Schmidt

first: Ana

last: Anderson

first: Piotr

last: Bobrowicz

first: Thomas

last: Schuetz

first: Robert

last: Tighe


title: Expression and transcript isoform profiling of reprogramming cells expressing a Sox2 mutant lacking a putative RNA binding motif [RNA-Seq]

city: Guangzhou

first: Yiwei

last: Lai

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Total RNA was extracted at different stages of somatic cell reprogramming of OG2-MEFs to induced pluripotent stem cells to analyse the effect of a Sox2 mutant lacking a putative RNA binding motif on genes expression and post-transcriptional processing

overall_design: Expression profiling by high throughput sequencing of reprogramming cells.

first: Yuanjie

last: Wei


title: RNA-Sequencing data from PofD119, Zhr1, PoX2Df1.688 and Oregon-R adult Drosophila melanogaster (Females and Males, separately).

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

summary: The prominent role of pericentromeric Mbp block of 1.688 satellites in hybrid incompatibility, facilitating role of distributed X-linked 1.688 satellites in dosage compensation in males and being as a necessary element for POF recruitment to chromosome X in females led us to further investigate the role of 1.688 satellites and POF in chromosome-wide gene regulation by comparing RNA-seq data from the relevant mutants in comparison to wildtype.

overall_design: Four biological replicates were isolated for each of the four genotypes and two sexes, in total 32 samples based on 10 individual adult flies (6-24 h after hatching the pupa) per sample.

first: Samaneh

last: Ekhteraei-Tousi

first: Jacob

last: Lewerentz


title: Autism-misregulated eIF4G microexons control synaptic translation and higher-order cognitive functions [Ribo-Seq]

first: Ulrich

last: Braunschweig

overall_design: Ribo-seq and control RNA-seq in wt and Eif4g1/Eif4g3 double-knockout in vitro-differentiated neurons

last: Gonatopoulos-Pournatzis

first: Rieko

last: Niibori

first: Eric

last: Salter

middle: J

last: Weatheritt

first: Brian

last: Tsang

first: Shaghayegh

last: Farhangmehr

first: Xinyi

last: Liang

first: Jonathan

last: Roth

first: Shen

last: Zhang

first: Tyler

last: Henderson

first: Eesha

last: Sharma

first: Mathieu

last: Quesnel-Vallières

first: Jon

last: Permanyer

first: Stefan

last: Maier

first: John

last: Georgiou

first: Manuel

last: Irimia

first: Nahum

last: Sonenberg

first: Julie

middle: D

last: Forman-Kay

first: Anne-Claude

last: Gingras

first: Graham

last: Collingridge

first: Melanie

middle: A

last: Woodin

first: Sabine

middle: P

last: Cordes

first: Benjamin

last: Blencowe


title: Total Stranded paired end RNA Seq of wildtype and knockout Kdm4a 2 cell embryos

first: Aditya

last: Sankar

summary:
Purpose: The goal of this study was to generate paired-end total RNA Seq transcriptomes of wildtype and Kdm4a 2 cell embryos to study the dynamics of differentially expressed repeats and transposons during early murine development
Methods: 2 cell embryos cultured in KSOM EmbryoMax medium (Sigma) were subjected to the SMARTSeq Stranded Total RNASeq protocol according to the manufacturers instructions on the same day simultaneously for control and knockout embryos.
Conclusions: Our study represents a detailed analysis of differentially expressed repeats and transposons in embryos lacking maternal or endogenous Kdm4a, with six biologic replicates, generated by SMARTSeq STranded paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that there is a consistent downrgulation of specific LTR families afffected in most biological replicates, by the lack of Kdm4a giving us robust statistical significance. We conclude that Kdm4a is required for proper activation of these repeat elements in conjuction with a permissive chromatin landscape.

overall_design: Total RNA Seq libraries of wildtype and knockout Kdm4a 2 cell embryos using SMARTSeq Stranded kit for single cells with 6 replicates/genotype and sequenced on a high output 75bp paired end Illumina NextSeq 500 platform

first: Jens

last: Johansen


title: SMARTSeq_v4 paired end mRNA Seq of Kdm4a control  mutant oocytes and preimplantation embryos

summary:
Purpose: The goal of this study was to generate paired-end mRNA Seq transcriptomes of control and Kdm4a mutant oocytes, 2-cell, 4-cell and 8-cell preimplantation embryos to study the dynamics of differentially expressed genes during early development
Methods: MII oocytes were isolated from wildtype and Kdm4a knockout mice. 16 MII oocytes from each genotype were washed in M2 medim after zona pellucida removal, washed once in nuclease free water and directly lysed and cDNA prepared according to the manufacturers instructions. Meanwhile, control and knockout MII oocytes were also in vitro fertilised with Kdm4a knockout sperm to produce control (+/-) and maternal mutant (-/-) embryos, and cultured in KSOM EmbryoMax medium (Sigma). 16 embryos were staged each day and harvested according to control embryos. Healthiest mutants were chosen for comparison with minimal secondary effects arising from dead/dying embryos. Similar to oocytes, individual cDNA were prepared and amplified according to manufacturers instructions in nuclease free conditions.
Conclusions: Our study represents a detailed analysis of differentially expressed genes in oocytes and embryos lacking maternal and endogenous Kdm4a, with sixteen biological replicates, generated by SMARTSeq v4 paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles between the samples at each developmental stage. Our results show that there is a consistent downrgulation of zygotic genome activation (ZGA) genes in the mutant 2-cell embryos. Mutant 4 and 8-cell embryos have significant upregulation of minor ZGA genes    giving us robust statistical significance. We conclude that Kdm4a is required for proper gene activation during maternal-to zygotic transition in conjuction with a permissive chromatin landscape.

overall_design: SMARTSeqv4 mRNA Seq libraries of wildtype and knockout Kdm4a oocytes, 2-cell, 4-cell and 8-cell embryos using SMARTSeq_v4 ultra low input mRNASeq kit for single cells with 16 replicates/genotype and sequenced on a high output 2X 150 paired end Illumina NextSeq 500 platform


title: Analysis of differential gene expression in the striatum of R6/2 Huntington's disease model vs. control mice

first: Myriam

last: Heiman

address: The Picower Institute of Learning & Memory

institute: MIT

summary: 5 mice per group of each: R6/2 and isogenic wild-type controls.

overall_design: Total RNA was isolated and sequenced from the striatum of R6/2 HD model and Control mice (11 weeks of age).

first: Lea

last: Hachigian

first: Mary

last: Wertz

first: Fan

last: Gao


title: Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae BY4741 H4-T30 and S47 mutant strains upon heat and osmotic stress

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

summary: To study the relevance of the phosphorylation of H4 in residues T30 and S47, we assessed the genome-wide transcriptional response of the non-phosphorylatable H4-T30A and the phospho-mimetic H4-T30D mutants upon heat stress and the phospho-mimetic H4-S47D mutant upon osmotic stress . Results point out that  H4-T30(A/D) and H4-S47D mutants showed an impaired stress responsive gene expression indicating that these specific residues play a relevant role in, respectively, heat  and osmotic stress responsive transcriptional regulation.

overall_design: Wild-type and H4-T30(A/D) mutant strains were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to heat stress (10 min 39°C). Wild-type and H4-S47D mutant strains were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to osmotic stress (15 min 0,4M NaCl). Total RNA was  isolated. Experiments were performed in triplicate.

first: Gerard

last: Martínez-Cebrián

first: Carme

last: Solé

first: René

last: Böttcher

first: Eulàlia

last: de Nadal


title: Diversity of peripheral blood human NK cells identified by single cell RNA sequencing

status: Public on Jan 29 2020

city: New York

first: Emily

last: Mace

state: New York

department: Department of Pediatrics

institute: CUIMC

summary: Human Natural Killer (NK) cells in peripheral blood perform many functions but classification of specific subsets has been a long-standing problem. Here, we report single-cell RNA sequencing of NK cells from healthy CMV-negative donors, comparing gene expression in unstimulated and IL-2 activated cells. Unsupervised clustering identified seven NK cell subsets. Three resembled well-described populations, CD56brightCD16-, CD56dimCD16+CD57- and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells sub-divided to include a population with higher chemokine mRNA and increased frequency of KIR expression. Three novel human blood NK cell populations were identified as: a population of type I interferon responding NK cells which were CD56neg; a population exhibiting an in-vivo cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2, and finally, a small population, with low ribosomal expression,  down-regulation of oxidative phosphorylation and high levels of immediate early response genes indicative of cellular activation. Human cytomegalovirus positive donors also included a higher frequency of adaptive NK cells. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analysing NK cell responses in health and disease.

overall_design: scRNAseq of sorted NK cells from one healthy individual

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