title: Molecular T-cell mediated rejection in transbronchial and mucosal lung transplant biopsies

status: Public on Oct 07 2020

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

summary: We previously developed molecular assessment systems for lung transplant transbronchial biopsies (TBBs) with high surfactant and bronchial mucosal biopsies (3BMBs). Unsupervised machine learning identified T cell-mediated rejection (TCMR) based on expression of validated rejection-associated transcripts (RATs). The relationship to patient outcomes is not known. We aimed to establish whether molecular TCMR in TBBs and 3BMBs has implications for future graft loss. Molecular TCMR scores assigned in all TBBs or high surfactant TBBs agreed closely, indicating that variation in alveolar content in TBBs does not prevent detection of TCMR. Molecular assessments of 3BMB-3BMB pairs showed less variation than TBB-TBB pairs. TBB TCMR scores correlated with those in 3BMB. In both formats, molecular TCMR was associated with increased risk of graft loss whereas the presence of histologic rejection or donor-specific antibodies was not. Molecular TCMR can be detected in TBBs or 3BMBs and is associated with future risk of graft loss. TCMR emerges as a n important contributor to risk of failure. ClinicalTrials.gov NCT02812290.

overall_design: We used microarray analysis and machine learning to assign molecular TCMR scores to an expanded cohort of 457 TBBs (367 high surfactant and 90 low surfactant) and 314 3BMBs from lung transplant recipients. We tested agreement between biopsy pieces within and between TBB and 3BMB formats in the same patient. We also assessed the association between molecular TCMR and the risk of graft loss (death or retransplantation) and compared it to the prognostic associations for histology and presence of donor-specific antibodies in the same cohort.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Mettl5-/- brain Transcriptomes

status: Public on Oct 01 2020

city: Guangzhou

first: shuibin

last: lin

state: Guangdong

address: Nonglin street

department: Center for Translational Medicine

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome. Methods: Brain mRNA profiles of 28-day-old wild-type (WT) and methyltransferase like 5 knockout (Mettl5−/−) mice were generated by using oligo(dT)-attached magnetic beads enrichemnt. The sequence reads that passed twice quality filters were analyzed at the transcript isoform level with Bowtie2 for quantitative gene analysis and with DEGseq for differentially expressed genes analysis. Results: 6 samples were tested by using the BGISEq-500 platform, and each sample produced 21.45 M data on average. The average ratio of samples to genomes (mm10) was over 96%; A total of 18,491 genes were detected.

overall_design: Brain mRNA profiles of 28-day old wild type (WT) and Mettl5-/- mice

first: Shuibin

last: Lin


title: Gene expression profile of DOCK8+CD4 T cell which causes systemic lupus erythematosus

status: Public on Oct 09 2020

city: Kato

first: Shunichi

last: Shiozawa

address: 944-25 Fujita

country: Japan

institute: Institute for Rheumatic Diseases

summary: Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease of unknown cause. We show here that a novel T follicular helper cell type expressing the guanine nucleotide exchange factor DOCK8 on the cell surface causes SLE. These cells, which we have designated autoantibody-inducing CD4 T (aiCD4 T) cells, are generated after resuscitation from anergy following strong TCR stimulation by antigen. When mice normally not prone to autoimmune disease were repeatedly immunized with an antigen such as OVA, they generated DOCK8+ CD4 T cells. These DOCK8+ CD4 T cells, in vivo and also upon transfer to naïve mice, induced a variety of autoantibodies and lesions characteristic of SLE. TCR repertoire analyses showed that a substantial number of novel TCR repertoires were generated in the DOCK8+ CD4 T cells, which induced novel autoantibodies upon transfer to naïve mice. DOCK8+ CD4 T cells are localized in splenic red pulp, the space immunoreactive against a variety of antigens, and specifically increased in the peripheral blood of SLE patients in association with disease activity. Anti-DOCK8 antibody treatment ameliorated the lesions induced by DOCK8+ CD4 T cells and in lupus model (NZB x W) F1 mice. Thus, when CD4 T cells are overstimulated by an external disturbance, i.e., repeatedly stimulated with antigen, to levels that surpass the system’s self-organized criticality, these cells express DOCK8 on the cell surface and acquire autoreactivity via TCR re-revision at the periphery. These DOCK8+ CD4 T cells subsequently induce a variety of autoantibodies and SLE.

overall_design: Gene expression in CD4 T cell of control mice immunized with PBS, DOCK8- and DOCK8+ CD4 T cell of mice which developed SLE by repeated (12x) immunization with ovalbumin (OVA) was mesured.

first: Ken

last: Tsumiyama


title: BMP signaling: at the gate between activated melanocyte stem cells and differentiation [SMART-Seq2 single cell RNA-seq]

status: Public on Nov 12 2020

city: New York City

first: Katherine

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

country: USA

institute: The Rockefeller University

summary: Adult tissue stem cells protect their long-term potential by exerting precise control over their transitions between quiescence, activation, and differentiation. Through cyclic bouts synchronous with the hair cycle, quiescent melanocyte stem cells (McSCs) become activated to generate proliferative progeny that differentiate to produce and transfer pigment to hair cells.  The signaling factors orchestrating this process are still poorly understood. Here, we use single cell RNA-sequencing with pseudotime analysis to elucidate the transcriptional trajectory of McSCs through quiescence, activation, and differentiation into mature melanocytes. Unearthing signs of increased WNT and BMP signaling along this progression, we lineage-ablate either pathway and see hair graying.  We show that BMP signaling functions downstream of McSCs but upstream of WNT signaling through LEF1. After stem cell activation, the two pathways trigger committed, proliferative progeny to fuel MITF-dependent differentiation. Analyses of the promoters required for melanosome maturation suggest a specific reliance upon MITF and LEF1 transcription factors, which  we show are dampened without BMP signaling. Our findings shed light upon the signaling interplay that orchestrates the melanocyte lineage. Moreover, the block in differentiation and enhanced proliferation observed in the absence of BMP signaling raises the disconcerting possibility that BMP may harbor not only tumor promoting but also tumor suppressing activity in melanoma.

overall_design: SMART-Seq2 single cell RNA-sequencing (totalling 1804 cells) of wild type mouse quiescent melanocyte stem cells (3 biological replicates), wild type mouse activated melanocyte stem cells (3 biological replicates), wild type differentiated melanocytes (2 biological replicates), as well as stage matched Bmpr1a wild type committed melanocyte progenitors (1 biological replicate), Bmpr1a heterozygous committed melanocyte progenitors (2 biological replicates), and Bmpr1a conditional knockout committed melanocyte progenitors (2 biological replicates)

first: Nicole

middle: R

last: Infarinato

middle: S

first: Tom

last: Carroll

first: Nicholas

middle: C

last: Gomez

first: Elaine

last: Fuchs


title: Mettl5 mediated 18S rRNA N6-methyladenosine (m6A) modification controls neural development and the learning and memory function

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

overall_design: Refer to individual Series


title: Expression profiles in multiple tissues of WT and Nrf2-knockout mouse under space filght

status: Public on Oct 02 2020

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: To elucidate roles that Nrf2 plays in regulating adaptive responses to the space stress, one month-long space travel and RNA-seq analysis of six Nrf2-KO mice and six wild-type mice were conducted . After 31-days-stay in the ISS, all the flight mice returned safely to Earth. We found that Nrf2 was indeed activated by the space stress in various tissues. The space stress and Nrf2-deficiency brought about changes in gene expression.

overall_design: mRNA profiling using multiple tissues including temporal bone, mandibularbone, spleen, liver, white and brown adipose tissues, kidney, thymus, and brain cerebullum of wild type (WT) and Nrf2-knockout (Nrf2KO) mice

first: Takafumi

last: Suzuki

first: Akira

last: Uruno

first: Akane

last: Yumoto

first: Keiko

last: Taguchi

first: Mikiko

first: Nobuhiko

last: Harada

first: Rie

last: Ryoke

first: Eriko

last: Naganuma

first: Nanae

last: Osanai

first: Aya

last: Goto

first: Hiromi

last: Suda

first: Ryan

last: Browne

first: Akihito

last: Otsuki

first: Fumiki

last: Katsuoka

first: Michael

last: Zorzi

first: Takahiro

last: Yamazaki

first: Daisuke

last: Saigusa

first: Seizo

last: Koshiba

first: Takashi

last: Nakamura

first: Satoshi

last: Fukumoto

first: Hironobu

last: Ikehata

first: Keizo

last: Nishikawa

first: Norio

first: Ikuo

last: Hirano

first: Ritsuko

last: Shimizu

first: Tetsuya

last: Oishi

first: Hozumi

last: Motohashi

first: Hirona

last: Tsubouchi

first: Risa

last: Okada

last: Kudo

first: Michihiko

last: Shimomura

first: Thomas

middle: W

last: Kensler

first: Hiroyasu

last: Mizuno

first: Masaki

last: Shirakawa

first: Satoru

last: Takahashi

first: Dai

last: Shiba


title: Interepithelial inflammatory crosstalk mediated by stromal fibroblast communication through hyaluronan [dataset 1]

status: Public on Oct 19 2020

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Inflammation of epithelial structures frequently leads to disease at distal organs, but the mechanism responsible for this is unknown. We report evidence that digestion of hyaluronan in the extracellular matrix signals distal stromal cells to become primed for increased inflammation. By applying transgenic mouse models and single cell RNA sequencing of mouse and human tissues we demonstrate that skin injury or infection promotes an adipogenic response in distinct populations of distant submucosal fibroblasts of the colon. This response can be recapitulated without skin inflammation by expression of hyaluronidase in skin that promotes a highly amplified and frequently fatal host response to intestinal injury. Our results uncover an innate system of communication between epithelial stroma that is not initiated by immunocyte trafficking or cytokine signaling.

overall_design: Single-cell RNA-seq of PDGFRA positive mouse colon fibroblasts from mice with or without a skin wound

first: Tatsuya

last: Dokoshi

first: Richard

middle: L

last: Gallo


title: Ribo-seq data from NIH 3T3 cells lacking eIF4G2

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

summary: Eukaryotic translation initiation factor (eIF) 4G2 is a long-known homologue of the canonical eIF4G1. However, unlike the latter, it does not bind eIF4E or PABP, thus it remains unclear what and when brings eIF4G2 onto a ribosome. Here we report results of  ribosome profiling performed in NIH 3T3 eIF4G2 (DAP5) -/- cells.

overall_design: Sequencing of ribosome-protected mRNA fragments and total RNA in wild-type NIH 3T3 and eIF4G2(-/-) NIH 3T3 cells

first: Ilya

middle: M

last: Terenin

first: Victoria

last: Smirnova

first: Daria

last: Nogina


title: Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype

status: Public on Sep 30 2020

city: Pittsburgh

first: Anuradha

last: Ray

state: PA

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

institute: University of Pittsburgh

summary: Identification and characterization of gene expression using Next Generation Sequencing (NGS) of mRNA sequence from  bronchial epithelial cells (BEC) obtained from asthma patients with varying clinical disease severity

overall_design: Samples were harvested by bronchoscopically obtained endobronchial brushing and subjected to RNA sequencing.

first: Matthew

last: Camiolo

first: Sally

middle: E

last: Wenzel


title: N6-methyladenosine (m6A) methylated RNA immunoprecipatation and sequencing in wildtype and Mettl5-/- embryonic stem cells.

first: shuibin

last: lin

summary: We report the application of methylated RNA immunoprecipatation and sequencing technology for high-throughput profiling of m6A modifications in embryonic stem cells (ESCs). By using proteinA/G and m6A antibody, we obtained immunoprecipitated RNA of mouse ESCs. RNAs can be read in a single nucleotide accuracy analysis.

overall_design: RNA m6A profiles of wild type (WT) and Mettl5-/- mESCs

first: Shuibin

last: Lin


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Mettl5-/-  embryonic stem cells Transcriptomes

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived embryonic stem cells (ESCs) transcriptome. Methods: mESCs mRNA profiles of wild-type (WT) and methyltransferase like 5 knockout (Mettl5−/−) mice were generated by using oligo(dT)-attached magnetic beads enrichemnt. The sequence reads that passed twice quality filters were analyzed at the transcript isoform level with Bowtie2 for quantitative gene analysis and with DEGseq for differentially expressed genes analysis. Results: 15 samples were tested by using the BGISEq-500 platform, and each sample produced 21.56 M data on average. The average ratio of samples to genomes (mm10) was over 94%; A total of 18762 genes were detected.

overall_design: mESCs mRNA profiles of wild type (WT) and Mettl5-/- mice


title: TP53 abnormalities correlate with immune infiltration and are associated with response to flotetuzumab, an investigational immunotherapy, in acute myeloid leukemia

status: Public on Sep 21 2020

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

summary: Immunological classifiers that predict patient outcome and therapeutic responses have been constructed through targeted immune gene expression profiling of diagnostic bone marrow samples from patients with TP53-mutated acute myeloid leukaemia.

overall_design: In the study presented here, well annotated cohorts of adults with newly diagnosed acute myeloid leukaemia (TP53 mutated and TP53 wild type) were used to acquire immune gene expression data.

first: Jayakumar

last: Vadakekolathu


title: Gene expression of Rif1-depleted ES cells

status: Public on Sep 19 2020

city: Setagaya

first: Naoko

last: Yoshizawa-Sugata

state: Tokyo

address: 2-1-6 Kami-kitazawa

department: Research Center for Genome & Medical Sciences

institute: Tokyo Metropolitan Institute of Medical Science

summary: Rif1 depletion in mouse ES cells increases the populations derepressing 2-cell zygote-specific genes including Zscan4. We investigated the chromatin structural change in the Zscan4 gene loci, and found that this region was deprived of major histone modifications except for moderately coded by H3 lysine9 trimethylation. Rif1 depletion caused no significant alteration in DNA methylation and histone modifications including common active marks, but only a notable increase in H3K27Ac active mark in gene bodies and neighboring regions, indicating that atypical broad enhancer-like chromatin with semi-silent property has been emerged in Zscan4 gene loci.<BR>In this study, we used microarrays to present the global changes in gene expression caused by transient depletion of Rif1.

overall_design: Total RNA was purified from untreated or Rif1-depleted E14tg2a cells using RNeasy micro kit (QIAGEN) for two times. Cy3-labeled samples were hybridized to Mouse Gene Expression slides (G4846A, Agilent Technologies). Normalized data was obtained using the Feature Extraction software (Agilent Technologies).

first: N

first: Y

last: Nishito

first: H

last: Masai


title: PRKCQ-dependent transcriptome in MyLa and HuT 78 cells

status: Public on Sep 04 2020

city: Santander

first: Jose

middle: P.

last: Vaque

state: Cantabria

address: Avenida Cardenal Herrera Oria s/n Facultad de Medicina

department: Molecular Biology

country: Spain

institute: University of Cantabria

summary: Transcriptional profiling controlled by PRKCQ of human CTCL cell lines MyLa and HuT 78 comparing cells transfected with non-targeting control with shPRKCQ cells at resting conditions and by TPA. The objective was to explore the role of PRKCQ in the pathogenesis of cutaneous T-cell lymphoma(CTCL).

overall_design: MyLa NTC and HuT 78 NTC cells compared with MyLa shPRKCQ and HuT 78 shPRKCQ cells both treated with DMSO or TPA. Three independent replicates.

first: José

middle: P

last: Vaqué

first: Nuria

last: García-Díaz


title: Gene expression analysis by RNA-seq on control 5 dpf zebrafish livers

status: Public on Aug 22 2020

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to compare potential changes in the gene expression in 5 dpf livers between untreated, 1.0 and 1.5mM iAs exposures.

overall_design: The samples in this accession include only the 120 hpf untreated, wild-type controls from an experiment comparing the response of zebrafish larval liver to arsenic exposure and to overexpression of the arsenic methyltransferase gene (as3mt) in hepatocytes (tg:(fab10a:as3mt, cry:dsRed).  This study was carried out by comparing RNA extracted from 120 hpf zebrafish livers from six groups: untreated or 24-hour exposure to 1 mM or 1.5 mM iAs in CAAX-EGFP positive larvae and CAAX-EGFP positive and as3mt overexpressing larvae.To generate these controls,(tg:(fab10a:as3mt, cry:dsRed) were outcrossed to tg(fabp10a:CAAX-EGFP) and the larvae that only had the CAAX-EGFP expression in the liver were collected.  RNA from 12 livers per group collected from 5 clutches (biological replicates) per group were extracted using Trizol/Chlorofom, PolyA selected and sequenced on Illumina NextSeq550.

first: Patrice

last: Delaney

first: Anjana

last: Nair

last: Edepli


title: Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [Degradome]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.

sample_organism:
Oryza nivara
Oryza sativa Indica Group

platform_organism:
Oryza nivara
Oryza sativa Indica Group

overall_design: We have performed degradome sequencing of 4-week old seedling and, flagleaf and panicle of two rice species.

first: Padubidri

last: Shivaprasad

first: Swetha

last: Chenna


title: A comparative gene expression data set for functional Sfp1 knockdown mutants and wild type strains for five yeast Species in the LOG growth phase

status: Public on Aug 26 2020

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary:
This data set contains microarray data for wild type and Sfp1 mutant strains in each of several yeast species in the LOG growth phase. This was done at several time points (mainly the T=30, 60 or 90 min post glucose repletion) for S. cerevisiae, C. glabrata, N. castellii, K. lactis and S. pombe.
For S. cerevisiae samples were taken for both WT and Sfp1 mutant conditions for both the BY and RM strains of this species. In S. cerevisiae, K. lactis and S. pombe there is one Sfp1 paralog and data were taken for the WT versions of these species and for a mutant in which  Sfp1 was not functioning. This allows a comparison of the WT and mutant state in each species over several time points in the LOG growth phase. For S. cerevisiae both WT and Sfp1 mutant conditions were studied for both the BY and RM strains, as noted in the description of the samples and in the columns labels of the accompanying data matrix. For C. glabrata and N. Castellii there are two Sfp1 paralog genes, and data was taken for the individual mutant condition of each Sfp1 paralog in each species. These mutant data are noted with _9955 and _682 for the C. glabrata samples, and _719  and _511for the N. castellii samples. These designations indicate mutant conditions for either the CAGL0M09955g or CAGL0D00682g Sfp1 paralogs in C. glabrata, or likewise  Scas719.24 or Scas551.1 in N. castellii. In the paper text N. castellii p719, C. glabrata p9995 are refered to as SFP1 and N. castellii p551 and C. glabrata paralog p0682 as SFP1PL.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Nakaseomyces glabratus
Naumovozyma castellii
Kluyveromyces lactis

overall_design: The over all design was to built a data set for the comparison of WT and Sfp1 mutant gene expression for several time points in the LOG growth phase for each of these yeast species to learn about 1) the importance of Sfp1 in the regulation of gene expression across these species in an evolutionary context and 2) to under stand the phenotypic implications for Sfp1 in evolution and the role of gene duplication in that evolution, notably with respect to the paralogs of Sfp1 in C. glabrata and N. castellii.

first: Toni

last: Delorey

first: Sara

last: Knaack

first: Jenna

last: Pfiffner

first: Chun

middle: J

last: Ye

first: Dawn

last: Thompson

first: Sushmita

last: Roy

first: Aviv

last: Regev

first: Reeta

last: Rao


title: Cranial manipulation modulates cholinergic pathway gene expression in an animal model of age-related cognitive decline

status: Public on Sep 10 2020

city: Blacksburg

first: Ramu

last: Anandakrishnan

state: VA

address: 1410 Prices Fork Rd., Lab 101

department: Biomedical Sciences

institute: Edward Via College of Osteopathic Medici

summary: In this study, we examine the effect of cranial osteopathic manipulation (COM) on gene expression, in an animal model for age-related cognitive decline (aged rats). We found that COM significantly affected the expression of 36 genes in the neuronal pathway (False Discovery Rate (FDR) < 0.004). The top five neuronal genes with the largest fold-change (Slc5a7, Chat, Slc18a3, Adcy5 and Cacna2d2, >2-fold change, FDR<0.004) are part of the cholinergic neurotransmission mechanism, which is known to affect cognitive function.

overall_design: Compare gene expression from RNA sequencing of tissue samples from prefrontal cortex of aged rats that have undergone cranial osteopathic manipulation to aged rats that did not receive the treatment

first: Hope

last: Tobey

first: Bradley

last: Klein

first: Blaise

last: Costa


title: Serum microRNA expression in patients with HBV-related liver cirrhosis and bacterial infection.

status: Public on Aug 18 2020

city: Fuzhou

first: Shenglong

last: Lin

state: Fujian

address: No. 312, Xi-hong Road, Gu-lou District

department: Hepatology

institute: Mengchao Hepatobiliary Hospital of Fujian Medical University

summary:
Hepatitis B virus-related liver cirrhosis (HBV-LC) is susceptible to bacterial infections, which could lead to adverse prognosis in patients. MicroRNA (miRNA) is easily detected in peripheral blood and is involved in multiple liver diseases. This pilot study aimed to investigate the differentially expressed (DE) miRNAs in the serum of patients with HBV-LC and bacterial infection, and to identify the potential biomarker. The clinical samples was collected, including four patients with HBV-LC and infection, four patients with HBV-LC without infection, four patients with chronic hepatitis B (CHB) and four healthy controls. miRNA expression was analyzed by Affymetrix GeneChip miRNA 4.0 Array.
A total of 385 DE miRNAs (upregulated, 160; downregulated, 225) were detected in patients with HBV-LC and infection compared with patients with HBV-LC without infection.

overall_design: This study was ethically approved by Fujian Medical University Mengchao Hepatobiliary Hospital (Fuzhou, China). A total of 16 serum samples, including patients with HBV-LC and infection (n=4), patients with HBV-LC without infection (n=4), patients with CHB (n=4) and healthy controls (n=4), were collected to detect the DE miRNAs.

first: Minghua

first: Huaxi

last: Ma

first: Xiangmei

last: Wang

first: Dongqing

last: Zhang

first: Wenjun

last: Wu

first: Jiahuang

first: Haibing

last: Gao


title: Single cell RNA-seq analysis of ovarian cancer

status: Public on Aug 21 2020

city: Hong Kong

first: Tongtong

last: Kan

address: 83 Tat Chee Avenue

institute: City University of Hong Kong

summary: To understand the recurrence of ovarian cancer, we profiled 13369 single cells from 8 ovarian cancer samples, including 4 primary tumors, 2 peritoneal metastasis and 2 relapse tumors by single cell RNA-seq.

overall_design: Tumors were disaggregated into single cells, and profiled by Drop-seq.

first: Mengsu

last: Yang


title: Integrating resistance functions to predict response to induction chemotherapy in de novo acute myeloid leukemia

city: Taichung

first: Chieh-Lin Jerry

last: Teng

address: 1650 Taiwan Boulevard Sec. 4

department: Division of Hematology/Medical Oncology

country: Taiwan

institute: Taichung Veterans General Hospital

summary: This study explored resistance functions and their interactions in de novo AML treated with the "7 + 3" induction regimen. We analyzed RNA-sequencing profiles of whole bone marrow samples from 52 de novo AML patients who completed the "7 + 3" regimen and stratified patients into CR (n = 35) and non-CR (n = 17) groups. A systematic gene set analysis revealed significant associations between chemoresistance and mTOR (P < .001), myc (P < .001), mitochondrial oxidative phosphorylation (P < .001), and stemness (P = .002). These functions were independent with regard to gene contents and activity scores. An integration of these four functions showed a prediction of chemoresistance (area under the receiver operating characteristic curve = 0.815) superior to that of each function alone. Moreover, our proposed seven-gene scoring system significantly correlated with the four-function model (r = .97; P < .001) to predict chemoresistance to the "7 + 3" regimen. On multivariate analysis, a seven-gene score of ≥-0.027 (hazard ratio: 11.18; 95% confidence interval: 2.06-60.65; P = .005) was an independent risk factor for induction failure. In summary, Myc, OXPHOS, mTOR, and stemness were responsive for chemoresistance in AML. Treatments other than the "7 + 3" regimen need to be considered for de novo AML patients predicted to be refractory to the "7 + 3" regimen.

overall_design: Patients with AML who completed their “7+3” induction chemotherapy at Taichung Veterans General Hospital (TCVGH) were enrolled. We analyzed bone marrow samples from 52 patients with de novo AML who completed the “7+3” induction chemotherapy. These 52 patients were further referred to as the CR group (n = 35) and non-CR group (n = 17), respectively, according to their treatment response after the “7+3” induction chemotherapy.

first: Chieh-Lin

first: Tzu-Hung

last: Hsiao

first: Yu-Chiao

last: Chiu


title: Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (lncRNA-seq)

status: Public on Aug 20 2020

city: Hefei,

first: Youguang

last: Pu

state: Anhui

address: No. 96 Jinzhai Road, Hefei City, Anhui Province

institute: University of Science and Technology of China

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Total RNA was extracted by Trizol reagent, and DNA was produced by gene specific primers or random primers. Illumina-Hiseq 4000 system was used for RNA sequencing and Illumina-Hiseq 2000 system was used for library sequencing (BGI Technology Company). A single-ended library was prepared according to the Illumina-Truseq RNA sample preparation kit (Illumina) scheme The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: lncRNA-seq screen in multi-drugresistant Osteosarcoma cells versus multi-drugsensitive Osteosarcoma cells


title: AKT/mTOR/HER/PI3K family genes as predictors of pCR for early stage breast cancer patients treated with the AKT inhibitor MK2206 in the I-SPY 2 TRIAL (NCT01042379)

status: Public on Sep 20 2020

city: San Francisco

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

summary: The AKT inhibitor MK2206 (M) was one of the experimental agents evaluated in I-SPY 2, a neoadjuvant platform trial for high risk, early stage breast cancer, and graduated in the HER2+, HR-, and HR-HER2+ signatures.   Based on the hypotheses that since MK2206 is an enzymatic inhibitor of AKT, response to MK2206 may be predicted by the relative pre-treatment levels of AKT kinase substrates, in pre-defined analyses we assessed 10 genes in the HER-AKT-mTOR pathway to test their association with pCR (complete pathologic response) in the MK2206 arm, in both HER2+ and HER2- subsets.  We also tested 9 genes genes previously associated with response to MK2206 in vitro and in the HER2+ metastatic setting, and performed exploratory association analyses using whole-transcriptome data to identify additional predictive signals outside the HER-AKT-mTOR pathway.

overall_design:
Fresh-frozen pre-treatment breast cancer tumors (n=150) from the neoadjuvant ISPY2 trial for high risk, early stage breast cancer were assayed using Agilent GPL16233 (n=31) or GPL20078 (n=119) expression arrays; and these data were combined into a single gene-level dataset after batch-adjusting using ComBat.  For fully normalized and batch corrected data on the gene level (as used in the publication), please use "GSE149322_ExpDat_ISPY2_MK2206_n150.txt.gz" as provided in the supplementary files.

The sample characteristics and their values represent:
HER2: the status of the HER2 gene.
1 = positive; 0 = negative.
HR: the status of hormone (estrogen and progesterone) receptors
1 = positive; 0 = negative.
pCR: the status of a pathological complete response (pCR)
1 = complete response; 0 = failed complete response
Arm: arm of the trial per patient - MK2206 arm' or 'Control arm'.

Originally, a ComBat batch correction process was applied to the raw data on a larger group of patients (~900), which we cannot release.  Linear adjustment factors from this group were derived so they can be applied to this smaller group of 150 patients.  The ISPY2_LinearFit_forCombiningExp* files contain linear adjustments to go from raw to batch corrected data.

first: Christina

last: Yau

first: Julia

last: Wulfkuhle

first: Emanuel

middle: F

last: Petricoin III

first: Laura

last: van ‘t Veer


title: AKT/mTOR/HER/PI3K family genes and phospho-proteins as predictors of pCR for early stage breast cancer patients treated with the AKT inhibitor MK2206 in the I-SPY 2 TRIAL

type:
Expression profiling by array
Protein profiling by protein array

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

overall_design: Refer to individual Series


title: Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A


title: Identification of Drugs Blocking SARS-CoV-2 Infection using hPSC-derived Lung and Colonic Organoids

status: Public on Aug 11 2020

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: The SARS-CoV-2 has already caused over twelve million COVID-19 cases and half a million deaths worldwide. There is an urgent need to create novel models using human disease-relevant cells to study SARS-CoV-2 biology and to facilitate drug screening. As SARS-CoV-2 primarily infects the respiratory tract, we developed a lung organoid model using human pluripotent stem cells (hPSC-LOs) that could be adapted for drug screening. The hPSC-LOs, particularly alveolar type II-like cells, express the viral entry receptor ACE2, are permissive to SARS-CoV-2 infection, and showed robust induction of chemokines and cytokines upon SARS-CoV-2 infection, similar to what is seen in COVID-19 patients. Nearly 25% of these patients have gastrointestinal manifestations, which are associated with worse COVID-19 outcomes1. We therefore also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. We found that multiple colonic cell types, especially enterocytes, express ACE2 and are permissive to SARS-CoV-2 infection. Using hPSC-LOs, we performed a high throughput screen of FDA-approved drugs and identified entry inhibitors of SARS-CoV-2, including imatinib, mycophenolic acid (MPA), and quinacrine dihydrochloride (QNHC). Pre- or post-infection treatment at physiologically relevant levels of these drugs significantly inhibited SARS-CoV-2 infection of both hPSC-LOs and hPSC-COs. Together, these data demonstrate that hPSC-LOs and hPSC-COs infected by SARS-CoV-2 can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics.

overall_design: COVID-19 lung biopsy and SARS-CoV-2 infected lung organoids

first: Yuling

last: Han

first: Liuliu

first: Benjamin

last: Nilsson-Payant

first: Yaron

last: Bram

first: Robert

last: Schwartz

last: tenOever


title: Comparative Gene Expression Profiling between Xenopus Optic Nerve and Spinal Cord Injury to Identify Genes Involved in Successful Regeneration of Vertebrate CNS Axons

status: Public on Aug 07 2020

city: Albany

first: Ben

middle: Gregory

last: Szaro

address: 1400 Washington Avenue

department: Biological Sciences

institute: University at Albany, State University of New York

summary: Xenopus is uniquely suited for addressing the question of whether a core gene expression program for successful CNS axon regeneration exists, because parts of its CNS (e.g., eye), regenerate axons throughout life, whereas others (e.g., hindbrain) do so only as tadpoles. We performed RNA-Seq after optic nerve and spinal cord injury to identify trauma-induced genes shared between two regenerative CNS regions, but not shared with a non-regenerative one. We provide these data as a resource for new avenues of investigation into the molecular basis of tissue regeneration.

overall_design: RNA-seq (30 million nominal reads per sample) was performed on 51 samples: operated juvenile frog eye and contralateral unoperated eye after optic nerve injury at three different timepoints (3 days, 11 days, 3 weeks), plus surgiically naïve frog eyes, with 6 pooled eyes for each sample; tadpole hindbrain after spinal cord transection plus age-matched unoperated controls at three timepoints (3 days, 7 days, 3 weeks), with 5 pooled hindbrains for each sample; juvenile frog hindbrain after spinal cord transection at 3 timepoints (3 days, 7 days, 3 weeks), plus unoperated hindbrain control, with 5 pooled hindbrains for each sample.

first: Kurt

last: Gibbs

first: Jamie

last: Belrose


title: Small RNA and mRNA profiling during intersegmental muscle development and programmed cell death in Manduca sexta

status: Public on Aug 17 2020

city: Amherst

first: Lawrence

address: 211 Morrill Science Center, 611 North Pleasant Street

department: Department of Biology

institute: University of Massachusetts

summary: PIWI-interacting RNAs (piRNAs) are small single-stranded RNAs that can repress transposon expression via epigenetic silencing and transcript degradation. They have been identified predominantly in the ovary and testis where they serve essential roles in transposon silencing in order to protect the integrity of the germline genome. The potential expression of piRNAs in non-stem somatic cells has been controversial. In the present study we demonstrate the expression of piRNAs derived from both genic and transposon RNAs in the intersegmental muscles (ISMs) from the tobacco hawkmoth Manduca sexta. These piRNAs are abundantly expressed, are ~27 nt long, map antisense to transposons, are oxidation resistant, exhibit a uridine bias at their first nucleotide, and amplify via the canonical ping-pong pathway. An RNA-seq analysis demonstrated that 17 piRNA pathway genes are expressed in the ISMs and are developmentally regulated. The expression levels of piRNAs do not change when the muscles undergo developmentally regulated atrophy, but are repressed when muscles become committed to undergo programmed cell death at the end of metamorphosis. This change in piRNA expression is associated with the targeted repression of several retrotransposons and the induction of certain DNA transposons. Developmental changes piRNAs, piRNA pathway genes, and transposon expression are all regulated by 20-hydroxyecdysone, the steroid that controls the timing of ISM death. Taken together, these data provide compelling evidence for the existence of piRNA in somatic tissues and suggest that they may play a role in developmental processes such as programmed cell death.

overall_design: Analyses of 8 small RNA-seq samples, 1 oxidized small RNA-seq sample, and 21 mRNA-seq samples with 3 replicates from intersegmental muscles during pupal-adult development in Manduca sexta

first: Junko

last: Tsuji

first: Travis

last: Thomson

first: Christine

last: Brown

first: William

last: Theurkauf

first: Zhiping

last: Weng


title: Changes in gene expression by SNAI2 knockdown in the  spheroid derived from human pancreatic cancer

status: Public on Jul 25 2020

city: Kyoto

first: Kenji

last: Masuo

address: 54 Shogoinkawahara-cho

department: Graduate School of Medicine

institute: Kyoto university

summary: The prognosis of pancreatic cancer is still poor due to resistance to conventional therapies, and cancer stem cells (CSCs) targeted therapy is expected to be a promising therapy. Although epithelial mesenchymal transition-inducing transcription factors (EMT-TF) are known to impart the CSCs properties to some of solid tumors, it has not been clearly reported in pancreatic cancer yet. Zinc finger protein SNAI2, a member of the Snail superfamily of EMT-TF, is frequently overexpressed in pancreatic cancer cells and the poor prognosis has been reported in cases with high SNAI2 expression. we found the suppression of SNAI2 expression using RNA interference decreased the tumorigenicity  in the tumor spheroid (Sph) derived from surgically resected pancreatic cancer tissues. Also, it increased the sensitivities to Gemcitabine treatment and reduced the expression of CD44, one of the pancreatic CSCs markers. Furthemore, microarray analysis suggests that the mechanism is mediated by insulin-like growth factor binding protein 2 (IGFBP2). These results indicate that SNAI2 may be a critical factor for the CSCs properties and indispensable for the homeostasis of pancreatic CSCs.

overall_design: To elucidate whether SNAI2 involves in the properties of cancer stem cells, SNAI2 knockdown stable clones were generated by transduction of short hairpin RNA into the spheroid derived from human pancreatic cancer using lentiviral vector and analyzed in comparison with control vector.

first: Shigeo

last: Takaishi


title: Changes in gene expression by SNAI2 knockdown in the human pancreatic cancer cell line KLM1.

summary: The prognosis of pancreatic cancer is still poor due to resistance to conventional therapies, and cancer stem cells (CSCs) targeted therapy is expected to be a promising therapy. Although epithelial mesenchymal transition-inducing transcription factors (EMT-TF) are known to impart the CSCs properties to some of solid tumors, it has not been clearly reported in pancreatic cancer yet. Zinc finger protein SNAI2, a member of the Snail superfamily of EMT-TF, is frequently overexpressed in pancreatic cancer cells and the poor prognosis has been reported in cases with high SNAI2 expression. we found the suppression of SNAI2 expression using RNA interference decreased the tumorigenicity in vitro (sphere formation assay) as well as in vivo (xenograft assay) in the pancreatic cancer cell line KLM1.  Furthermore, microarray analysis suggests that the mechanism is mediated by insulin-like growth factor binding protein 2 (IGFBP2). These results indicate that SNAI2 may be a critical factor for the CSCs properties and indispensable for the homeostasis of pancreatic CSCs.

overall_design: To elucidate whether SNAI2 involves in the properties of cancer stem cells, SNAI2 knockdown stable clones were generated by transduction of short hairpin RNA into the pancreatic cancer cell line KLM1 using lentiviral vector and analyzed in comparison with control vector.


title: Long and short-read single cell RNA-seq profiling of human lung adenocarcinoma cell lines using 10X V3 chemistry.

status: Public on Jul 22 2020

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Single cell RNA-seq was used to profile gene expression in 5 human lung adenocarcinoma cell lines.

overall_design: Single cells from five human lung adenocarcinoma cell lines (H2228, H1975, A549, H838 and HCC827) were mixed in equal proportions and processed using the Chromium 10X platform, then sequenced using both short-read (Illumina) and long-read (Nanopore) technologies.

first: Luyi

last: Tian

first: Jafar

last: Jabbari

first: Quentin

last: Gouil


title: Comparison of wild type and Tmem184b mutant adult DRG

status: Public on Jul 14 2020

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

summary: The goal of this study was to evaluate gene expression that is dependent upon Tmem184b expression. Our objective was to identify pathways controlled by Tmem184b that may influence development or behavior of neurons.

overall_design: Dorsal root ganglia were dissected from four wild type and four Tmem184b homozygous gene trap (mutant) mice, all six months of age. Total RNA was extracted and evaluated using RNAseq.

first: Erik

last: Larsen


title: Loss of PRC2 subunits primes lineage choice during exit of pluripotency

status: Public on Jul 17 2020

city: Nijmegen

first: Chet

middle: H

last: Loh

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: RIMLS

summary: Mouse embryoid body differentiation with single-cell analyses of timepoints 0, 4, 7 and 10. Bulk-RNA seq of directed differentiation of mouse embryonic stem cells from day 0, 5hr, 24hr and 48hrs.

first: Matteo

last: Perino

first: Magnus

last: Bark

first: Gert

last: Veenstra

first: Siebe

last: Genesen


title: Fetus-derived IGF2 matches placental development to fetal demand [RNA-seq]

status: Public on Jul 01 2020

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: We used transcriptome analysis to identify genes transcriptionally disregulated in feto-placental endothelial cells from mutants with conditional deletion of Igf2 gene driven by the Meox2Cre.

overall_design: RNA-seq in FACS-sorted feto-placental endothelial cells isolated from E16 Igf2EpiKO mutants (n=4) and littermate controls (n=4)

first: Ionel

last: Sandovici

middle: Y

first: Miguel

last: Constancia


title: Carolina Breast Cancer Study tumor expression [RUVSeq-normalized]

status: Public on Jul 16 2020

city: Houston

first: Arjun

state: TX

address: 1155 Pressler Street

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

summary:
Transcription profiling by NanoString nCounter of primary breast tumors from 1219 patients from the Carolina Breast Cancer Study (CBCS) using the NanoString nCounter platform and normalized with a RUVSeq-based iterative framework.
The NanoString RNA counting assay for formalin-fixed paraffin embedded samples is unique in its sensitivity, technical reproducibility, and robustness for analysis of clinical and archival samples. While commercial normalization methods are provided by NanoString, they are not optimal for all settings, particularly when samples exhibit strong technical or biological variation or where housekeeping genes have variable performance across the cohort. Here, we develop and evaluate a more comprehensive normalization procedure for NanoString data with steps for quality control, selection of housekeeping targets, normalization, and iterative data visualization and biological validation. The approach was evaluated using a large cohort from the Carolina Breast Cancer Study. The iterative process developed here eliminates technical variation more reliably than the NanoString commercial package, without diminishing biological variation, especially in long-term longitudinal multi-phase or multi-site cohorts. We also find that probe sets validated for nCounter, such as the PAM50 gene signature, are impervious to batch issues. This work emphasizes that preprocessing of gene expression data is an important component of study design. The normalized data here is processed through the RUVSeq-based iterative framework

overall_design: Total mRNA expression for a custom codeset of 417 genes on FFPE primary breast tumor samples from 1219 patients from the CBCS using NanoString nCounter

first: Melissa

last: Troester


title: Regulation of DNA Methylation at Enhancers by TET2 Finetunes Gene Transcription in ERα-Positive Breast Cancer Cells

status: Public on Jul 09 2020

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Background: Aberrant DNA methylation is an epigenetic hallmark of most malignant tumors including breast cancer. However, the exact role of TET2-mediated DNA demethylation in ERα-positive luminal breast cancer is not well understood. Results: Here we showed by TCGA analyses that lower TET2 mRNA expression level is associated with worse clinical outcomes (i.e., overall survival) in ERα-positive but not ERα-negative breast cancer. Moreover, depletion of TET2 by CRISPR/Cas9 results in increased tumorigenesis capability of MCF7 cells in vitro. Whole genome bisulfite sequencing (WGBS) analysis revealed that DNA hypermethylation (gain-of-5mC) occurs within a subgroup of enhancers including estrogen responsive element (EREs) in MCF7 cells upon TET2 depletion. ChIP-seq and RNA-seq analysis showed that TET2 depletion impairs E2-induced ERα binding to these ‘gain-of-5mC’ EREs and gene transcription. Conclusions: Our data suggest that TET2-mediated enhancer DNA demethylation fine-tunes ERα-dependent and independent gene transcription in ERα-positive breast cancer cells.

overall_design: We used WGBS-seq, ChIP-seq and RNA-seq  to study the regulation role of TET2 on the relationship among DNA methylation, histone modification and gene transcription in ERα positive MCF7 cell line.

first: R

last: Lv

first: X

last: Zhu

first: Y

last: Shen

first: L

last: Tan


title: Fetus-derived IGF2 matches placental development to fetal demand


title: Carolina Breast Cancer Study tumor expression [NanoString nSolver-normalized]

summary:
Transcription profiling by NanoString nCounter of primary breast tumors from 1219 patients from the Carolina Breast Cancer Study (CBCS) using the NanoString nCounter platform and normalized with NanoString nSolver software.
The NanoString RNA counting assay for formalin-fixed paraffin embedded samples is unique in its sensitivity, technical reproducibility, and robustness for analysis of clinical and archival samples. While commercial normalization methods are provided by NanoString, they are not optimal for all settings, particularly when samples exhibit strong technical or biological variation or where housekeeping genes have variable performance across the cohort. Here, we develop and evaluate a more comprehensive normalization procedure for NanoString data with steps for quality control, selection of housekeeping targets, normalization, and iterative data visualization and biological validation. The approach was evaluated using a large cohort from the Carolina Breast Cancer Study. The iterative process developed here eliminates technical variation more reliably than the NanoString commercial package, without diminishing biological variation, especially in long-term longitudinal multi-phase or multi-site cohorts. We also find that probe sets validated for nCounter, such as the PAM50 gene signature, are impervious to batch issues. This work emphasizes that preprocessing of gene expression data is an important component of study design. The normalized data here is processed through the RUVSeq-based iterative framework


title: Carolina Breast Cancer Study tumor expression


title: Fetus-derived IGF2 matches placental development to fetal demand [microarray]

summary: We used microarrays to identify genes that are transcriptionally dysregulated between Igf2EpiKO mutants and littermates controls at E19

overall_design: Array profiling was performed using the Mouse Gene 1.0 ST Array (Affymetrix) and the analysis of the data was performed using GeneSpring GX 12.1 (Agilent, Santa Clara, CA, USA), with two algorithms: RMA (Robust Multiarray Average) and PLIER (Probe Logarithmic Intensity Error).  Log2 RMA values are included in this submission. PLIER values are not included.


title: Epigenetic Analysis of Wild Type and Mkx-/- Tendon by Next Generation Sequencing

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

institute: Zhejiang University

summary: We investigaed the epigenetic landscape of  H3K27ac modification between wild type(WT) and Mkx-/- tendon.

overall_design: ChIP-seq analsis of H3K27ac modification of tail tendon derived cells from 3-week old wild type (WT) and Mkx-/- mice were performed according to standard protocol in triplicate.

first: Hongwei

last: Ouyang

first: Junxin

last: Lin


title: Divergent cell differentiation trajectory in normal and heterotopic ossified soft connective tissues

summary: We used single-cell RNA sequencing and a gene knockout mice model to reveal the heterogeneity and differentiation trajectory of tendon derived cells in both physiological and pathoplogical conditons.

overall_design: Wild type(WT) and Mkx-/- tail tendon cells derived from 4-week-old mice were captured  on a  high-throughput IFC microfluidic Fluidigm C1 system. Wells with no cell or more than one cells were excluded for further analysis, resulting in  227 WT tail tendon cells and 224 Mkx-/- tail tendon cells.


title: Transcriptomic Analysis of Wild Type and Mkx-/- Tendon by Next Generation Sequencing

summary: We compared  differential gene expression profiles between wild type(WT) and Mkx-/- tendon to reveal how Mkx  regulats tendon differentiation and homeostasis maintenance .

overall_design: Expression profiles of tail tendons from 3-week old wild type (WT) and Mkx-/- mice were generated by next generation sequencing, in triplicate, using Ion Proton.


title: Generation of induced motor neurons (iMNs) from human fibroblasts facilitates locomotor recovery after spinal cord injury

status: Public on Jun 29 2020

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: Generation of autologous motor neurons holds a great promise for cell replacement therapy to treat spinal cord injury (SCI). Direct conversion allows the generation of target cell types from somatic cells, however, current protocols are not practicable for therapeutic purposes since converted cells are post-mitotic populations that are not readily scalable. Therefore, therapeutic effects of directly converted neurons have not been elucidated yet. Here, we show that human fibroblasts can be converted into induced motor neurons (iMNs) by sequential induction of OCT4 and LHX3. Our strategy enables large production of pure iMNs through self-renewing iMN-intermediate cell stage which is distinct from neural progenitors. iMNs exhibited the hallmarks of spinal motor neurons including cellular morphology, marker expression, electrophysiological property, synaptic activity, and formation of neuromuscular junctions. Remarkably, transplantation of iMNs showed therapeutic effects, promoting locomotor functional recovery in SCI model. Taken together, our advanced strategy will provide tools to acquire sufficient iMNs that may represent a promising cell source for personalized cell therapy.

overall_design: This study is designed to establish an advanced direct lineage reprogramming strategy to generate autologous iMNs from human fibroblasts by overexpressing OCT4 and LHX3. We further investigated the therapeutic effects of iMNs for treating traumatic spinal cord injury using rodent spinal cord injury model. The experiments were repeated at least three times, and the replicates are indicated in each figure and legend. N values represent the number of animals in the experiment. Quantifications are analyzed by randomly imaging the positions of culture dishes to determine the reprogramming efficiency. The experiments were carried out in accordance with documented standards of the Institutional Review Board of Ulsan National Institute of Science and Technology (UNIST) (UNISTIRB-15-17-C) for human cell experiments.

first: Hyunah

last: Lee

first: Hye

first: Byeong

first: Holm

last: Zaehres

first: Soo-Yong

last: Park

first: Jae

middle: I

last: Kim

first: Yoon

last: Ha

first: Daniela

last: Gerovska

last: Arauzo-Bravo

first: Hans

middle: R

last: Schoeler

first: Jeong

middle: B


title: Expression data from isorhamnetin (Iso)-treated human amnion epithelial stem cells (hAESCs)

status: Public on Jun 25 2020

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of Iso towards hepatic differentiation of hAESCs.
hAESCs were isolated from discarded term placenta and were treated with 20 μM Iso for 10 days. Microarray gene expression profiling was conducted for biological replicates of Iso-treated hAESCs on day 10  and untreated control cells on day 0, and day 10.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Myocardial G protein-coupled receptor kinase 5 contributes to impaired cardiac function and immune cell recruitment in ischemic heart failure

status: Public on Jun 13 2020

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Myocardial ischemia (MI) is the most common cause of heart failure (HF) in the United States. G protein‑coupled receptor (GPCR) kinase 5 (GRK5) has been found to be upregulated in failing human myocardium. While the canonical role of GRKs is to desensitize receptors via phosphorylation, GRK5 can also translocate to the nucleus of cardiomyocytes where it exerts GPCR‑independent effects that promote maladaptive cardiac hypertrophy. The role of GRK5 in ischemic heart disease is still unknown

overall_design: RNA-seq on cardiomyocytes from control (NLC) and Grk5-transgenic (TgGRK5) mice 4 days after myocardial infraction (MI)

first: Claudio

last: de Lucia

first: Walter

last: Koch


title: A Platform to Define Cellular Targets of SARS-COV-2 Infection Using Human Pluripotent Stem Cell-Derived Cells and Organoids

status: Public on Jun 11 2020

first: Shuibing

last: Chen

summary: The SARS-CoV-2 virus has already caused over a million COVID-19 cases and over fifty-thousand deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 virus using human disease-relevant cells and tissues to understand key features of virus biology. We present a platform comprised of nine different cell and organoid derivatives from human pluripotent stem cells (hPSCs) representing all three primary germ layers, including lung progenitors and alveolar type II (AT2) cells, pancreatic endocrine cells, liver organoids, endothelial cells, cardiomyocytes, macrophages, microglia, and both cortical and dopaminergic neurons. We systematically probed which cell types are permissive to SARS-CoV-2 infection. Human pancreatic beta cells and hepatocytes were strikingly permissive to SARS-CoV-2 infection, further validated using adult primary human islets and liver organoids. Both in vitro and in a humanized mouse model, human lung progenitors and AT2 cells express the ACE2 viral receptor and were highly permissive to SARS-CoV-2 infection. Transcriptomic analysis following SARS-CoV-2 infection of hPSC-derived pancreatic and lung organoids revealed upregulation of chemokines but not type I/III interferon signaling, similar to what was seen in primary human COVID-19 pulmonary infection. Therefore, hPSC-derived cells phenocopy human COVID-19 disease and provide a valuable resource to understand SARS-CoV-2 biology and search for novel therapeutics.

overall_design: Human islets were dissociated into single cells and analyzed using 10X scRNA-seq to determine the expression of ACE2 and TMPRSS2 expression in human islet alpha and beta cells.

first: Xuming

last: Tang


title: Rejuvenation improves the flavonoid accumulation in Ginkgo biloba leaves

status: Public on Jun 15 2020

city: Yangzhou

first: Li

last: Wang

address: Wenhui east road no. 48

institute: Yangzhou University

summary: We sequenced mRNA of G. biloba leaves from truncation treatment and control using the Illumina HiSeq4000 platform. We identified the transcriptome changes in leaves between truncation group and control group, which provided valuable information for uncovering the molecular mechanisms of flavonoid accumulation in G. biloba under rejuvenation.

overall_design: Transcriptome sequencing in control and truncation treatment leaves of G. biloba

first: Zhaogeng

last: Lu


title: Reprogramming competence of POU factors is linked to the donor-cell epigenome

status: Public on Jun 24 2020

first: Marcos

last: Araúzo-Bravo

summary: Octamer-binding Pit-Oct-Unc (POU) family members have distinct reprogramming competences. OCT4 induces pluripotency, whereas POU III factors (OCT6, OCT7, OCT8, and OCT9) lack this ability, but are prone to inducing neural identities. However, which specific features of these proteins render the distinct reprograming competences remains unknown. Here, we present that OCT6 can also induce pluripotency. But, it works only with human cells, indicating its species-dependent reprogramming activity. Functional readouts with a series of reciprocal mutants uncover that the central role of OCT4 and its strong reprogramming competence to pluripotency arise from its C-terminal transactivation domain. Furthermore, we identify intrinsic properties of OCT7, OCT8, and OCT9 that are detrimental for inducing pluripotency. A chemical screen reveals that their persistent deficiency for inducing pluripotency can be surmounted by reducing H3K79 methylation in donor cells. Our findings delineate that intrinsic properties of POU factors and their responsive donor-cell epigenome state are tightly linked to the reprogramming competence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
28 human samples were analyzed:
Fibs1, Human fibroblast, 2 replicates
Fibs2, Human fibroblast, 2 replicates
O4 iPS#1, Human induced Pluripotent Stem (iPS) cells with OCT4, SOX2 KLF4, MYC, clon 1, 2 replicates
O4 iPS#2, Human induced Pluripotent Stem (iPS) cells with OCT4, SOX2 KLF4, MYC, clon 2, 2 replicates
O6 iPS#1, Human induced Pluripotent Stem (iPS) cells with OCT6, SOX2 KLF4, MYC, clon 1, 2 replicates
O6 iPS#2, Human induced Pluripotent Stem (iPS) cells with OCT6, SOX2 KLF4, MYC, clon 2, 2 replicates
O7 iPS#1, Human induced Pluripotent Stem (iPS) cells with OCT7, SOX2 KLF4, MYC, clon 1, 2 replicates
O7 iPS#4, Human induced Pluripotent Stem (iPS) cells with OCT7, SOX2 KLF4, MYC, clon 4, 2 replicates
O8 iPS#1, Human induced Pluripotent Stem (iPS) cells with OCT8, SOX2 KLF4, MYC, clon 1, 2 replicates
O8 iPS#3, Human induced Pluripotent Stem (iPS) cells with OCT8, SOX2 KLF4, MYC, clon 3, 2 replicates
O9 iPS#3, Human induced Pluripotent Stem (iPS) cells with OCT9, SOX2 KLF4, MYC, clon 3, 2 replicates
O9 iPS#4, Human induced Pluripotent Stem (iPS) cells with OCT9, SOX2 KLF4, MYC, clon 4, 2 replicates
H1, Human Embryonic Stem Cell (ESC) line H1, 2 replicates
H9, Human Embryonic Stem Cell (ESC) line H9, 2 replicates

14 mouse samples were analyzed:
O4 iPS, Mouse induced Pluripotent Stem (iPS) cells with Oct4, Sox2 Klf4, Myc, 2 replicates
O6 iPS, Mouse induced Pluripotent Stem (iPS) cells with Oct6, Sox2 Klf4, Myc, 2 replicates
O7 iPS, Mouse induced Pluripotent Stem (iPS) cells with Oct7, Sox2 Klf4, Myc, 2 replicates
O8 iPS, Mouse induced Pluripotent Stem (iPS) cells with Oct8, Sox2 Klf4, Myc, 2 replicates
O9 iPS, Mouse induced Pluripotent Stem (iPS) cells with Oct9, Sox2 Klf4, Myc, 2 replicates
O11 iPS, Mouse induced Pluripotent Stem (iPS) cells with Oct11, Sox2 Klf4, Myc, 2 replicates
ESC, Mouse Embryonic Stem Cell (ESC), 1 replicate
MEF, Mouse Embryonic Fibroblast (MEF), 1 replicate

first: Kee-Pyo

first: You

last: Wu

first: Yawei

last: Gao

first: Juyong

last: Yoon

first: Guangming

first: Kenjiro

last: Adachi

first: Sergiy

last: Velychko

first: Hyun Woo

last: Choi

first: Jan

last: Bruder

first: Jonghoon

first: Borami

last: Shin

first: Albrecht

last: Röpke

first: Martin

last: Stehling

first: Dong Wook

last: Han

first: Shaorong

last: Schöler


title: Chemical induced senescence in the cortical neurons

status: Public on Jun 01 2020

city: Madison

first: Ali

last: Fathi

state: WI

address: 1500 Highland Ave. Rm 641D, Waisman Center

department: Waisman Center

institute: University of Wisconsin

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of cortical neurons derived from human embryonic stem cells (H9) treated with compounds that are inducing senescence

overall_design: H9 ESCs diffetentiated to the cortical neurons for 21 days and treated with SLO compound for five days

first: Su-Chun

last: Zhang


title: Alteration of transcriptomic and epigenetic landscapes in normal and heterotopic ossified tendons

first: HONGWEI

last: OUYANG

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

overall_design: Refer to individual Series


title: Tabula Muris Senis

status: Public on Apr 30 2020

first: Angela

last: Oliveira Pisco

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary: Tabula Muris Senis is a single cell transcriptomic atlas of 18 tissues and organs from Mus musculus across the organism’s life span.

overall_design: Various tissues. The raw data is accessible from a public AWS bucket (s3://czb-tabula-muris-senis/).

middle: O

last: Pisco

first: Nick

last: Schaum

first: Spyros

last: Darmanis

first: Tony

last: Wyss-Corray

first: Stephen

last: Quake


title: Epigenetic reprogramming of gene promoters in the liver of adult female mice masculinized by testosterone

first: Marcos

last: Araúzo-Bravo

type: Methylation profiling by genome tiling array

summary:
Testosterone (T) is known to masculinize the female phenotype of the liver evidenced as upregulated gene expression
of male- and downregulated expression of female-predominant genes. To explore the a possibly T epigenetic control,
we here screen genome-wide the liver for T-induced changes of the DNA methylation status of gene promoters.
by methylated DNA immunoprecipitation and Nimblegen microarrays. Female C57BL/6 mice are treated with T for 3 weeks and, then,
T treatment is discontinued for 12 weeks.
The T-induced changes found suggest a functional impact since T induces under the same experimental conditions as used here persistent
susceptibility to blood-stage malaria of Plasmodium chabaudi.
We hypothesize that T epigenetically dys-regulates initial steps of liver-inherent innate immune mechanisms leading to dys-balanced host
responses eventually causing the lethal outcome of otherwise self-healing infections.

overall_design:
Preparation of DNA:
DNA was extracted from individual livers by the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany),
Between 10 to 15 mg of tissue were placed in liquid nitrogen and thoroughly grounded with a mortar.
Tissue powder was incubated at 56C  degrees for 4 hours in lysis buffer including 12 mAU proteinase K,
before adding 0.4 mg RNase A at room temperature for 2 minutes. DNA was precipitated with ethanol and separated by using
QIAamp Mini spin columns to finally obtain 8 to 20 microg of high quality DNA per sample.
Purity control and quantification were performed with NANODROP 2000 UV-Vis spectrometer (ThermoSCIENTIFIC, Wilmington, USA).
Methylated DNA ImmunoPrecipitation (MeDIP):
Genomic DNA (1 microg) from each tissue sample was sonicated in a final volume of 200 microl to produce random fragments ranging in size
from 300-1,000 bp by the Vibra Cell 75022 Ultrasonic Processor (Novodirect, Kehl, Germany) with a 2-mm tipp.
Immunoprecipitation (IP) of methylated DNA was performed with the MeDIP kit (Diagenode, Liege, Belgium)
in accordance with the manufacturer´s instructions. In brief, DNA samples at a final concentration of 0.1 microg/micrl
were denatured at 95C for 3 min, quickly chilled on ice and finally immunoprecipitated by adding 0.3 microl of manufacturer
bead-immobilized anti-5-methylcytosine antibody. Control input samples contained only 20% of that DNA sample used for IP.
The bound DNA was separated from the beads by incubation at 65C for 10 min and by using 1 volume of phenol/chloroform/isoamylalcohol (25/24/1).
Hybridization of NimbleGen microarrays:
Genomic input DNA and the IP DNA were first amplified by Genome Plex Complete WGA Kit (Sigma Aldrich, Hamburg, Germany)
as described in the manufacturer´s protocol. Briefly, 30 ng DNA of a 3 ng/microl DNA solution were amplified by 20 PCR cycles using the
Amplification Master Mix. Input DNA and IP DNA were labeled in parallel, and 1 microg of each amplified DNA sample were hybridized to
NimbleGen (Roche, Basel, Switzerland) Mouse 385 K RefSeq Promoter Arrays containing all known RefSeq genes (NM prefix).
The hybridization procedure was applied as recommended by the manufacturer.
Array scanning and data analyses:
The hybridized arrays were scanned on an Axon 4000B microarray scanner (Molecular Devices, Sunnyvale, CA),
and the images were analyzed with Axon GenePix software version 4.1.
Image and data analyses were processed with NimbleScan version 2.5 and SIgnalMap version 1.9 software.
The methylation ratios between the IP DNA samples and the control input samples were normalized across samples using the quantile method
after performing a variance stabilization using log2 scaling.
The mean of each promoter feature was determined from three different biological replicates.
All data processing and all graphics were performed with in-house developed functions in Matlab.
6 samples were analyzed
Cd0, 3 replicates
Td0, 3 replicates

first: Mohamed

last: Dkhil

first: Saleh

last: Al-Quraishy

first: Abdel-Azeem

middle: A

last: Baki

first: Foued

last: Ghanjati

first: Denis

last: Delic

first: Frank

last: Wunderlich


title: Gene expression pattern in olive tree organs (Olea europaea L.)

status: Public on May 07 2020

city: JAEN

first: Jorge

middle: Antolín

last: Ramirez

state: --- Select a state ---

address: Campus Las Lagunillas s/n 23071

department: Experimental Biology

institute: University of Jaen

summary: This is an RNA-seq study of the transcriptomic activity of different tissues from adult olive tree cv. Picual on field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue; 32,030 of them were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each part of the plant was studied. The flower was clearly the organ with the highest number of exclusive expressed genes, 3,529, and many of them were involved in reproduction. On the contrary, the stem only showed 229 exclusive expressed genes. The gene ontology (GO) terms analysis of these genes in each organ highlighted some tissue-specific pathways. In general, many of these organ-specific genes are involved in regulatory activities and have nuclear protein localization, with the exception of the leave, where there are also many genes whose coded proteins have plastid localization; to a lesser extent, this was also observed in stems. On the other hand, the pathogen defense and immunity pathways are highly represented in the roots. These data show a complex pattern of gene expression in different organs.

overall_design: six plant organs are studied, in two biological replicates each with two technical replicates

last: Ramírez-Tejero

first: Jaime

last: Jiménez-Ruiz

first: María de la O

last: Leyva-Pérez

first: Juan

last: Barroso

first: Francisco

last: Luque


title: Single cell transcriptome mapping reveals cell type-specific effects on gene expression by acute delta9-tetrahydrocannabinol

status: Public on Apr 14 2020

city: New Haven

first: Ke

last: Xu

state: CT

institute: Yale University

summary: The study identifies cell type specific differentially expressed genes in peripheral blood mononuclear cells affected by THC infusion in two human subjects. Individual gene expression gene analysis and gene set enrichment analysis show that THC affects gene expression in the functional domains of immune response and cell proliferation. One of THC receptor genes, CNR2, is highly expressed in B cells and THC perbute CNR2 co-expressed genes in B cells. The findings provide new insight of acute THC immunotonary effects.

overall_design: A single low dose of THC infusion in two human subjects and detect differentially expressed genes between pre- and post-THC infusion.

first: Ying

last: Hu


title: Downregulation of N-terminal initiator methionine imprinting by NatB impacts growth and the response to osmotic stress in Arabidopsis

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: N-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes and is catalyzed in humans by seven Nα-acetyltransferases (NatA-F and NatH). Remarkably, the characterization of the plant Nat machinery and its biological relevance is still in its infancy, although NTA has gained recognition as key regulator of crucial processes like protein turnover, protein-protein interaction and protein targeting.   In this study we combined in vitro assays, reverse genetics, quantitative N-terminomics, transcriptomics and physiological assays to characterize the Arabidopsis NatB complex. We show that the plant NatB catalytic (NAA20) and auxiliary subunit (NAA25) form a stable heterodimeric complex that accepts canonical NatB-type substrates in vitro. In planta, NatB complex formation was essential for enzymatic activity. Depletion of NatB subunits to 30% of wild-type level in three Arabidopsis T-DNA insertion mutants (naa20-1, naa20-2, naa25-1) decreased growth to 50% of wild-type level. A complementation approach revealed functional conservation between plant and human catalytic NatB subunits, while yeast NAA20 failed to complement naa20-1. Quantitative N-terminomics of approximately 2000 peptides identified 29 bona fide substrates of the plant NatB. In vivo, NatB preferentially acetylated N-termini starting with the initiator methionine followed by acidic amino acids and contributed 20% of the acetylation marks in the detected plant proteome. The global transcriptome and proteome analyses of NatB-depleted mutants suggested a function of NatB in multiple stress responses. In agreement, we revealed the specific impact of NatB on the resistance of plants to osmotic or high-salt stress. Remarkably, depletion of NatA did not affect these resistances.

overall_design: Comparison of the  wild-type Arabidopsis thaliana accession Col-0 (Control, N=3) with the naa20-1 mutant (N=3) that is depleted of the catalytically active subunit of the Nat B complex.

first: Markus

last: Wirtz

first: Monika

last: Huber


title: The molecular diagnosis of rejection in liver transplant biopsies: First results of the INTERLIVER study

status: Public on May 06 2020

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: Molecular diagnosis of rejection is emerging in kidney, heart, and lung transplant biopsies and could offer insights for liver transplant biopsies. Groups differed in median time post-transplant e.g. R3injury 99 days vs. R4late 3117 days. R2TCMR biopsies expressed typical TCMR-related transcripts e.g. intense IFNG-induced effects. R3injury displayed increased expression of parenchymal injury transcripts (e.g. hypoxia-inducible factor EGLN1). R4late biopsies showed immunoglobulin transcripts and injury-related transcripts. R2TCMR correlated with histologic rejection although with many discrepancies, and R4late with fibrosis. R2TCMR, R3injury, and R4late correlated with liver function abnormalities. Supervised classifiers trained on histologic rejection showed less agreement with histology than unsupervised R2TCMR scores. No confirmed cases of clinical ABMR were present in the population, and strategies that previously revealed antibody-mediated rejection (ABMR) in kidney and heart transplants failed to reveal a liver ABMR phenotype. In conclusion,  molecular analysis of liver transplant biopsies detects rejection, has the potential to resolve ambiguities, and could assist with immunosuppressive management.

overall_design: We measured gene expression by microarrays in 235 liver transplant biopsies from 10 centers. Unsupervised archetypal analysis based on expression of previously annotated rejection-related transcripts identified four clusters/groups: normal ‘R1normal’ (N=129), T cell-mediated rejection (TCMR) ‘R2TCMR’ (N=37), early injury ‘R3injury’ (N=61), and fibrosis ‘R4late’ (N=8).


title: Binding to the Ribosome by Eukaryotic Initiation Factor 4B Drives Yeast Translational Control in Response to Urea

status: Public on Apr 15 2020

city: Buffalo

first: Sarah

middle: E.

last: Walker

state: New York

address: 534 Cooke Hall, North Campus

institute: University at Buffalo, SUNY

summary: The yeast eukaryotic initiation factor 4B binds the 40S subunit in translation preinitiation complexes (PICs) and promotes mRNA binding. Here we have compared the effects of disrupting eIF4B RNA- and ribosome-binding domains under ~1400 growth conditions. The RNA-binding RRM was dispensable for stress responses, but ribosome binding stimulated by the NTD promoted growth in response to a number of stressors through changes in translation. In particular, the NTD confers a strong growth advantage in the presence of the denaturing reagent, urea, and a number of osmolytes that require robust cellular integrity for survival. Ribosome profiling of cells with and without the NTD of eIF4B reveals changes in translation of mRNAs containing longer than average and highly structured 5-prime untranslated regions both normally, and in response to urea exposure. Because these changes require 40S binding, our results suggest eIF4B regulates mRNA recruitment as a part of the scanning PIC, rather than by activating isolated mRNPs prior to ribosome binding. This analysis indicates the cellular response to urea in yeast includes a translational component, driven by increased translation of mRNAs encoding proteins associated with the cellular periphery, and highlights the importance of the general translation factor eIF4B in adapting to external conditions.

overall_design: Two biological replicates of each Saccharomyces culture of WT without urea, mutant without urea, WT with urea, and mutant with urea were harvested. Riboseq and RNAseq libraries were derived from each set of cells for a total of 16 libraries for illumina sequencing.

first: Xiaozhuo

last: Liu

first: Houtan

last: Moshiri

middle: E


title: Genome-wide identification of circular RNAs with critical roles in pancreatic ductal adenocarcinoma

status: Public on Apr 02 2020

city: Shatin

first: Yangchao

last: Chen

address: Shatin

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The aim of this project is to identify and characterize circular RNAs with critical roles in pancreatic ductal adenocarcinoma (PDAC).

overall_design: circRNA sequencing was performed using non-tumor human pancreatic ductal epithelial cells (HPDE) and PDAC cells PANC-1 and SW1990, to identified the deferentially expressed circRNAs in PDAC.

first: Chi

last: Wong


title: Dissecting the onset of random X-chromosome inactivation at high temporal and allelic resolution

status: Public on May 22 2020

city: Berlin

first: Guido

last: Pacini

address: Ihnestraße 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

summary: To ensure dosage compensation between the sexes, one randomly chosen X chromosome is silenced in each female cell in the process of X-chromosome inactivation (XCI). XCI is a model for cellular decision making and epigenetic gene regulation. The random cell-autonomous nature of XCI however has so far prevented its chromosome-wide investigation in its endogenous context without genetic perturbation. Here we use allele-specific single-cell RNA-sequencing to assess the onset of random XCI with high temporal resolution in differentiating mouse embryonic stem cells, and develop dedicated analysis approaches. We find that XCI is initiated on both chromosomes in a subset of cells, but reverted to the final mono-allelic state once gene silencing is established. By exploiting the heterogeneity of XCI onset, we identify Nanog as its main trigger and discover additional genes that might control upregulation of Xist, the master regulator of XCI. Finally, we show that genetic variation between different mouse strains modulates the XCI process at multiple levels, and validate these findings through an orthogonal experimental approach. We thus draw a detailed picture of how XCI is initiated and the experimental and computational strategies we have developed here will now allow us to profile random XCI in more physiological contexts, including primary human cells in vivo.

overall_design: Single cell RNA-Sequencing of a hybrid mESC mm10 line (C57BL6/J x Cast/EiJ) throughout differentiation (induced by 2i/Lif withdrawal) over time (day 0, 1, 2, 3, 4). Bulk RNA-Sequencing of a hybrid mESC mm10 line (C57BL6/J x Cast/EiJ) throughout differentiation (induced by 2i/Lif withdrawal) over time (day 0, 1, 2, 3, 4) [TX1072]. Bulk RNA-Sequencing of a hybrid mESC mm10 line (C57BL6/J x Cast/EiJ) carrying a 773 kb region deletion around the Xist locus either on the C57BL6/J (chrX:103,182,701-103,955,531, mm10) [dXicB6] or on the Cast/EiJ (chrX:103,182,257-103,955,698, mm10) [dXicCast] alleles throughout differentiation (induced by 2i/Lif withdrawal) over time (day 0, 1, 2, 3, 4).

first: Ilona

last: Dunkel

first: Norbert

last: Mages

first: Verena

last: Mutzel

first: Bernd

last: Timmermann

first: Annalisa

last: Marsico

first: Edda

last: Schulz


title: Gene expression during chicken myogenesis

status: Public on Apr 03 2020

city: Guangzhou

first: Wen

last: Luo

state: Guangdong

address: Wushan

institute: South China Agricultural University

summary: Chick is an ideal model system for myogenesis study. Lots of genes would change their expression during myogenesis, however, is there any difference about gene expression between chick and mice? Our study represents the detailed analysis of the transcriptomes of chicken primary myoblasts, growing myoblasts, and myotubes, with biologic replicates, generated by RNA-seq technology. The data reported here may provide an important understanding of the genes involved in the regulation of chicken myogenesis.

overall_design: Examination of differentially expressed genes during chicken myogenesis

first: Xiquan

last: Zhang

first: Qinghua

last: Nie


title: Study on the mechanism of Shcisandrol A in immune function modulation in mice based on the mRNA expression profile chip

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

summary: At present, with the accelerating pace of life, increase in work pressure, lack of exercise, irregularity of diet and rest, and problems of environmental pollution, people with immunodeficiency are gradually increasing in the modern population. Some Chinese herbal medicines can improve the immunity of the human body, and have less and mild side or toxic effects, so that the study on this kind of traditional Chinese medicines and its mechanism has become an urgent problem to be solved. In recent years, studies have shown that Shcisandrol A (Sch A) can regulate immune function and inhibit the inflammation of nervous system. In this study, mRNA expression profile chip was used to screen the differentially expressed genes related to the effect of Sch A on immunodepressed mice induced by cyclophosphamide (Cy), and the differentially expressed gene-telated pathways were analyzed by gene ontology function cluster analysis, and finally qPCR was applied to verify the 5 genes that might be related to the regulation of Sch A on the mice’s immune functions, to provide a theoretical basis for screening the drug targets on which Sch A could act to regulate the mice’s immune functions.

overall_design: 240 Eight-week-old male ICR mice (SPF grade), weighing 18~22g, were purchased from Liaoning Changsheng Biotechnology Co., LTD (license number: SCXK (Liao)-2015-0001). Animals were housed individually in cages at 20±1℃and in 40-70% humidity, subjected to 12h light/dark cycle with free access to food and water.ICR mice were randomly divided into control group, Cy model group, Sch A low-dose, middle-dose, and high-dose group. Except those in the control group, mice in the other groups were given 40 mg/kg Cy in intraperitoneal injection for 5d for the establishment of immunodeficiency mice model. On the next day after the modeling, mice in low-, middle- and high-dose Sch A groups were intragastrically given 0.2g/kg/d, 0.4g/kg/d and 1g/kg/d Sch A respectively, and those in the control group and Cy model group were given an equal volume of distilled water in the same way successively for 4 weeks. Changes in the mice’s body weight and general status were regularly observed weekly.

first: Guangyu

last: Xu

first: Jinghui

last: Sun


title: Neuronal activation modulates enhancer activity of genes for excitatory synaptogenesis through de novo DNA methylation

status: Public on Apr 26 2020

city: Fukuoka

first: TOMONORI

last: KAMEDA

address: 3-1-1, Maidashi, Higashi-ku, Fukuoka-shi

institute: Kyushu-University

summary: Post-mitotic neurons exhibit DNA methylation changes, contrary to the longstanding belief that the epigenetic pattern in terminally differentiated cells is essentially unchanging. While the mechanism and physiological significance of DNA demethylation in neurons have been extensively elucidated, occurrence of de novo DNA methylation and its impacts have been much less investigated. Here we show that neuronal activation induces global de novo DNA methylation at enhancer regions that can repress target genes in primary cultured hippocampal neurons. The functional significance of this de novo DNA methylation was underpinned by the demonstration that inhibition of DNA methyltransferase (DNMT) activity decreased neuronal activity-induced excitatory synaptogenesis. Overexpression of WW and C2 Domain containing 1 (Wwc1), a representative target gene of de novo DNA methylation, could phenocopy this DNMT inhibition-induced decrease in the synaptogenesis. We found that both DNMT1 and DNMT3a were required for the neuronal activity-induced de novo DNA methylation of Wwc1 enhancer. Taking these findings altogether, we concluded that activity-induced de novo DNA methylation affecting gene expression has impacts on neuronal physiology comparable to those of DNA demethylation.

overall_design: Examination of DNA methylation and mRNA profiles of 10 DIV hippocampal neurons treated with TTX, Bic/4AP 3 hrs and H3K27ac of 10 DIV hippocampal neurons before and after Bic/4AP treatment

first: Tomonori

last: Kameda

first: Hideyuki

last: Nakashima

first: Takumi

last: Takizawa

first: Fumihito

last: Miura

first: Takashi

last: Ito

first: Kinichi

first: Takuya

last: Imamura


title: A new regulator in the crossroads of oxidative stress resistance and virulence in Candida glabrata: the transcription factor CgTog1

status: Public on Apr 09 2020

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

summary: The goals of this study are to compare C. glabrata transcriptome profiling (RNA-seq) upon exposure to hydrogen peroxide in order to assess the correspondent response. The role of the transcription factor Tog1 is clarified through comparison of the transcrptome profiles of WT and Tog1 mutant cells. mRNA profiles of WT and ∆tog1 were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq. RNA-seq data allowed to identify genes whose expression is regulated by the Tog1 transcription factor (147 positively regulated and 112 negatively regulated) with a log2fold change ≥0.5 and p value <0.05. The transcriptomics data was then used to guide further work to detail the function of Tog1.

overall_design: Yeast mRNA profiles after 1h hydrogen peroxide exposure of WT and ∆tog1 cells were generated by RNA-Seq, in duplicate (each duplicate made of triplicate samples pooled together) using Illumina HiSeq

first: Pedro

last: Pais

first: Susana

last: Vagueiro

first: Dalila

last: Mil-Homens

first: Andreia

last: Pimenta

first: Romeu

last: Viana

first: Michiyo

last: Okamoto

first: Hiroji

last: Chibana

first: Arsénio

middle: M

last: Fialho

middle: C


title: Gene expression of wild type and tmem182-/- skeletal muscle

first: Wen

last: Luo

summary: Transmembrane proteins are important for intercellular signaling and play important roles in the control of cell fate. However, many transmembrane proteins still lack of research. Recently, we identified a new transmembrane protein, TMEM182, which play significant roles on skeletal muscle development and regeneration. Here, we generated TMEM182 konckout mice and used RNA-seq to analyzed gene expression between the wild type and TMEM182-/- skeletal muscle.

overall_design: Skeletal muscle mRNA profiles of 9-week old wild type (WT) and tmem182-/- mice were generated by deep sequencing, in triplicate, using BGISEQ-500

first: Xiquan

last: Zhang

first: Qinghua

last: Nie


title: Single cell profiling of total RNA using Smart-seq-total

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

summary: We describe Smart-seq-total, a method capable of assaying a broad spectrum of coding and non-coding RNA from a single cell. Built upon the template-switch mechanism, Smart-seq-total bears the key feature of its predecessor, Smart-seq2, namely, the ability to capture full-length transcripts with high yield and quality. It outperforms current poly(A)–independent total RNA-seq protocols by capturing transcripts of a broad size range, thus, allowing us to simultaneously analyze protein-coding, long non-coding, microRNA and other non-coding RNA from single cells. We used Smart-seq-total to analyze the total RNAome of human primary fibroblasts, HEK293T and MCF7 cells as well as that of induced murine embryonic stem cells differentiated into embryoid bodies. We show that simultaneous measurement of non-coding RNA and mRNA from the same cell enables elucidation of new roles of non-coding RNA throughout essential processes such as cell cycle or lineage commitment. Moreover, we show that cell types can be distinguished based on the abundance of non-coding transcripts only.

overall_design: We sequenced total RNA from individual human primary dermal fibroblasts, HEK293T and MCF7 cells sorted in 384-well plates and processed in 1/10 of the standard Smart-seq2 volume. In parallel, we analyzed the RNAome of primed pluripotent stem cells and that of individual cells obtained from dissociated embryoid bodies at days 4, 8 and 12 of culture.


title: Comparison between opioid (morphine) and vehicle treatments in mouse trigeminal ganglia and nucleus accumbens

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

summary: Chronic opioid treatment elicits hyperalgesia in mice that is significantly augmented by a human migraine trigger and reduced with migraine therapy. The purpose of this study was to  profile mRNA levels (transcriptome) to understand the differences between opioid (morphine) and vehicle treatments in two nervous system regions, the trigeminal ganglia and the nucleus accumbens. Mice received 10 mL/kg intraperitoneal injections of either morphine or vehicle volume twice daily (s.c.) for 4 days where on days 1-3 the dose of morphine was 20 mg/kg, and on day 4 it was 40 mg/kg.

overall_design: RNA samples were obtained from 10 mice 24 hours after the last injection and were subjected to paired-end RNA sequencing


title: Transcriptional response to SARS-CoV-2 infection

status: Public on Mar 25 2020

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

summary: Viral pandemics pose an imminent threat to humanity. The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus, requires the urgent development of anti-viral therapies. Because of its recent emergence, there is a paucity of information regarding viral behavior and host response following SARS-CoV-2 infection. Here, we offer an in-depth analysis of the host response to SARS-CoV-2 as it compares to other respiratory infections. Cell and animal models of SARS-CoV-2 infections, in addition to transcriptional profiling of a COVID-19 lung biopsy consistently revealed a unique and inappropriate inflammatory response defined by elevated chemokine expression in the absence of Type I and III interferons. Our identification of a muted transcriptional response to SARS-CoV-2 supports a model in which initial failure to rapidly respond to infection results in prolonged viral replication and an influx of proinflammatory cells that induce alveolar damage and manifest in COVID-19 lung pathology.

sample_organism:
Homo sapiens
Mustela putorius furo

platform_organism:
Homo sapiens
Mustela putorius furo

overall_design: Cell lines: Independent biological triplicates of primary human lung epithelium (NHBE) were mock treated or infected with SARS-CoV-2 (USA-WA1/2020), IAV (A/Puerto Rico/8/1934 (H1N1)), a IAV that lacks the NS1 protein (IAVdNS1) and treated with human interferon-beta. Independent biological triplicates of transformed lung alveolar (A549) cells were mock treated or infected with SARS-CoV-2 (USA-WA1/2020), RSV (A2 strain) or IAV (A/Puerto Rico/8/1934 (H1N1)). Additionally, Independent biological triplicates of transformed lung alveolar (A549) transduced with a vector expressing human ACE2, were also mock treated or infected with SARS-CoV-2 (USA-WA1/2020) with or without Ruxolitinib pre-treatment (500 nM). Finally transformed lung-derived Calu-3 cells were mock treated or infected with SARS-CoV-2 (USA-WA1/2020). Ferrets: 4 month old ferrets were infected intranasally with 105 PFU of influenza A/California/04/2009 (pH1N1) virus and nasal washes were collected from anesthetized ferrets on day 7 post infection. Additionally, another group of 4 month old ferrets were infected intranasally with 5 × 104 PFU of SARS-CoV-2 isolate USA-WA1/2020 and nasal washes were collected from anesthetized ferrets on days -1, 1, 3 and 7 post-infection. Finally, a separate group of 4 month old ferrets were mock treated (intranasally) with PBS. COVID19 patient samples: Uninfected human lung biopsies were derived from one male (age 72) and one female (age 60) and used as biological replicates. Additionally, lung samples derived from a single male COVID19 deceased patient (age 74) were processed in technical replicates. Experiments using samples from human subjects were conducted in accordance with local regulations and with the approval of the institutional review board at the Icahn School of Medicine at Mount Sinai under protocol HS#12-00145.

first: Benjamin

last: tenOever

last: Blanco-Melo


title: Transcriptomic profiling of bat PakiT03 cells with immune stimulation

status: Public on Mar 29 2020

city: Singapore

first: Linfa

last: Wang

address: 8 college road

department: Programme in Emerging Infectious Diseases

country: Singapore

institute: Duke-NUS Medical School

summary: To examine innate immune signalling, IFN baseline and IRF-regulation, we profile Pteropus alecto bat kidney epithelial cells (PakiT03) with Deep NGS coverage. Clonal cell lines were also isolated with CrispR KO for IRF1, IRF3, IRF7, IFNAR2 or IFNAR2/IRF7 double KO.

overall_design: IFNα Treatment at 0h, 3h, 6h, 9h, polyIC treatment at 0h, 6h, 9h, or infection with Melaka Virus (PRV3M) for 0h, 9h, 24h timepoints. In wildtype or IRF1/3/7 KO cells (for ifna) or IRF1/3/7, IFNAR2 and IFNAR2/IRF7 KO cells for pIC and PRV3M.

first: Aaron

middle: T

last: Irving

first: Zhu

last: Feng