title: Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling [in vitro]

summary: Single-cell RNA-sequencing of in vitro differentiated T cells cultured with IL-12+IL-21+IL-23 (Th1 cell condition) or IL-1b+IL-6+IL-23 (pathogenic Th17 cell condition)

overall_design: Naive T cells were isolated from reporter mice for IL-23R that carry an IRES-eGFP in the Il23r locus. Homozygous mice carrying the reporter allele (Il23reGFP/eGFP) represent a functional KO mouse. Naive T cells (CD44lowCD62LhiCD4+CD25-) were isolated from heterozygous mice (Il23rwt/eGFP=ctrl) and homozygous mice (Il23reGFP/eGFP=KO) by fluoresence-activated cell sorting (FACS) and then cultured for 4 days with full medium containing the aforementioned cytokine conditions.  Cells were then sorted based on eGFP expression before single-cell sequencing.

last: Wang

first: Ana


title: LepR-positive cells from young and middle-aged C57B6 mice

status: Public on Apr 27 2021

city: New York

first: Philipp

last: Leucht

state: NY

address: 550 First Avenue

department: Orthopedic Surgery, Cell Biology

country: USA

institute: NYU Grossman School of Medicine

type: Expression profiling by high throughput sequencing

summary: We report the finding during intramembranous bone formation OPC proliferation is controlled by Notch signaling during the early repair phase, while differentiation is initiated by activation of canonical Wnt signaling during the later phase

overall_design: Bulk RNAseq of LepR+ skeletal stem and progenitor cells from young (12-week), middle-aged (52-week), and middle-aged-treated mice treated with sodium salicylate

first: Anne

last: Josephson


title: Single-cell RNA sequencing reveals the transcriptomic characteristics of Tregs and TNFR2+ Tregs isolated from tumor tissues and peripheral blood of patients with gastric cancer

status: Public on Apr 16 2021

city: Tianjin

first: Yang

last: Qu

state: Tianjin

address: Huanhuxi Road, Tiyuanbei, Hexi District

department: Department of Gastrointestinal Cancer Biology

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

summary: This study aimed to explore the characteristics and role of TNFR2+ Tregs in the microenvironment and progression of gastric cancer by single-cell RNA sequencing.We obtained Tregs from tumor tissues and peripheral blood of three GC patients.Through single-cell RNA sequencing, we found tumor-infiltrating Tregs express high levels of TNFR2. The TNF-a/TNFR2 signaling pathway is activated, accompanied by upregulation of costimulatory molecules. Compared to blood Tregs, tumor-infiltrating Tregs exhibit activated and effector states. In addition to expressing costimulatory molecules such as TNFR2, 4-1BB, OX40 and GITR, tumor-infiltrating Tregs are also characterized by high expression of immune checkpoints such as CTLA-4 and TIGIT and chemokines such as CCR6.This study revealed a high infiltration level of TNFR2+ Tregs with the characteristics of activated and effector Tregs in the tumor microenvironment. Our study provides a new theoretical basis for TNFR2+ Tregs as a therapeutic target in gastric cancer.

overall_design: mRNA profiles of tumor-infiltrating Tregs and blood-Tregs from 3 patients with gastric cancer

first: Xianhao

first: Shuai

last: Bai

first: Liling

last: Niu

first: Gang

last: Zhao

first: Yuan

last: Yao

first: Bin

last: Li

first: Hui


title: RNA-Seq analyses of isoalted primary cardiac fibroblasts from wild type and Fam114a1-/- mouse hearts

status: Public on Apr 19 2021

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: Purpose: The biological and biochemical functions of FAM114A1 in mouse hearts or cardiac fibroblasts are entirely unknown. The goal of this study is to use the next generation sequencing (NGS) RNA-Seq followed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods to identify the downstream effector genes that are regulated by FAM114A1 in isolated primary cardiac fibroblasts from the  hearts of wild type (WT; C57BL6/J) and Fam114a1-/- (global knockout; under C57BL6/J genetic background) mice at the mRNA level. Using an optimized data analysis workflow from the Genomic Resource Center at the University of Rochester Medical Center, we analyzed the RNA-Seq data of primary cardiac fibroblasts from P60 WT and Fam114a1-/- mice. We identifed differentially regulated genes (upregulated or downregulated) with statistical significance at the mRNA level (padj <0.05 for differential expressed genes). We found 28 downregulated genes involved in inflammation, hypertension, and extracelluar matrix receptor interaction. Furthermore, 20 genes were found to be upregulated and related to ribosome and translation pathways. About half the downregulated gene were confirmed by qRT-PCR. This study is the first transcriptomic analysis of isolated primary cardiac fibroblasts of Fam114a1-/- versus WT mice with biological triplicates using RNA-Seq technology. The optimized data analysis workflows offer a framework for comparative investigations of expression profiles. Our RNA-Seq analysis and follow-up qRT-PCR validation results suggest that among all the downregualted genes ADAMTS15 is found to be a critical downstream effector gene of FAM114A1 and is important for cardiac fibrobalt activation and proliferation.

overall_design: RNA-Seq of WT vs Fam114a1-/- mouse hearts

first: Kadiam

middle: C

last: Venkata Subbaiah

first: Jiangbin

last: Wu

first: Wai

last: Hong

first: Wilson

last: Tang

first: Peng


title: Expression data comparing 8024 wild type (WT) and MAEL knockout (KO) cells

status: Public on May 25 2021

city: Hong Kong SAR

first: Xinyuan

last: Guan

address: No. 21 SASSOON Road Rm10-56 Laboratory Block

department: Clinical Oncology

institute: The University of Hong Kong

summary: To identify candidate genes regulated cancer stemness property of HCC by comparing 8024 wild type (WT) and MAEL knockout (KO) cells, which applied by RNA-Sequencing.

overall_design: PLC/PRF8024 mRNA profiles of wild type (WT) and MAEL knockout (KO) cells

first: Chaoran

last: Shi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [BMDM]

status: Public on Apr 06 2021

city: Chapel Hill

first: Yue

last: Xiong

state: NC

address: 450 West Dr

department: Linebeger Cancer Center

institute: UNC-Chapel Hill

summary: We used RNA-seq to detect the genes affectded by Tet2 or Itaconate (ITA) treatment

overall_design: WT and Tet2H1795R mutant BMDM were pretreated with octy-itaconate and induced by LPS and each treatment has three biological replicates

first: Leilei

last: Chen


title: Competition between hematopoietic stem and progenitor cells controls the hematopoietic stem cell homeostasis.

status: Public on Mar 29 2021

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

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

overall_design: Refer to individual Series


title: Competition between hematopoietic stem and progenitor cells controls the hematopoietic stem cell homeostasis [scRNA-seq]

summary: Cellular competition for limiting hematopoietic factors is a physiologically regulated but poorly understood process. Here, we studied this phenomenon by hampering hematopoietic progenitor access to Leptin receptor+ mesenchymal stem/progenitor cells (MSPCs) and endothelial cells (ECs). We showed that HSC numbers increased by 2-fold when multipotent and lineage-restricted progenitors fail to respond to CXCL12 produced by MSPCs and ECs. HSCs were qualitatively normal, and HSC expansion only occurred when early hematopoietic progenitors but not differentiated hematopoietic cells lacked CXCR4. Furthermore, the MSPC and EC transcriptomic heterogeneity was remarkably stable, suggesting that it is impervious to dramatic changes in hematopoietic progenitor interactions. Instead, HSC expansion was caused by increased availability of membrane-bound stem cell factor (mSCF) on MSPCs and ECs due to reduced consumption by cKit-expressing hematopoietic progenitors. These studies revealed an intricate homeostatic balance between HSCs and proximal hematopoietic progenitors regulated by cell competition for limiting amounts of mSCF.

overall_design: With bone marrow stromal cells of Cxcr4 conditional knockout (Flk2-cre+ Cxcr4fl/fl, cKO) mouse and littermate control (Flk2-cre+ Cxcr4fl/+, CTL), single cell RNA-sequencing analysis was performed.

first: João

middle: P

last: Pereira


title: TCDD exposure in control and wfikkn1mutant zebrafish at 48 hpf

status: Public on Apr 21 2021

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary: This experiment investigates the role of a novel AHR-regulated gene on the global transcriptome in 48 hpf zebrafish exposed to 0.1% DMSO or 1 ng/mL TCDD.

overall_design: Each biological sample consisted of 9 embryos with 4 biological replicates per condition, for a total of 16 samples

first: Prarthana

last: Shankar

first: Robyn

middle: L

last: Tanguay

middle: M


title: Prognostic epigenetic 12-genes signature in human metastatic colorectal carcinomas

status: Public on Apr 15 2021

city: Rionero in Vulture

first: Valentina

last: Condelli

state: PZ

address: Via Padre Pio, 1

country: Italy

institute: IRCCS CROB

type: Methylation profiling by genome tiling array

summary: Epigenetic remodeling is responsible for tumor progression and drug resistance in human colorectal carcinoma (CRC). This study addressed the hypothesis that DNA methylation profiling may identify metastatic CRC (mCRC) subtypes with defined clinical characters. Global differential methylation profile was comparatively analyzed between 24 first-line primary-resistant and 12 drug-sensitive mCRCs, two subgroups with significantly different outcome. Gene expression and methylation data from the TCGA mCRCs cohort were used to identify, among differentially methylated genes, a prognostic signature of functionally methylated genes. Twelve functionally methylated genes yielded a hierarchical clustering of patients in two well-defined subgroups with hypermethylated tumors characterized by a significantly worst relapse-free and overall survival compared to hypomethylated cancers. Interestingly, the poor prognosis cluster was enriched of CIMP-high and MSI-like cases. Furthermore, methylation events were enriched in genes located on arms q of chromosomes 13 and 20, this suggesting that epigenetic remodeling may involve selective genomic regions. Finally, the expression of the 12-genes signature and MSI-enriching genes was confirmed in two independent oxaliplatin- and irinotecan-resistant CRC cell lines. These data provide the proof of concept that the hypermethylation of specific sets of genes may provide prognostic informations being able to identify a subgroup of mCRCs with poor prognosis

overall_design: Bisulphite converted DNA from the 36 samples were hybridized to the Illumina Infinium 850K Human Methylation Beadchip v1.2

first: Giovanni

last: Calice


title: Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling [RNA-seq]

status: Public on Apr 14 2021

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: During transcription, DNA supercoiling generated by the advance of RNA polymerase II (Pol II) is resolved by DNA topoisomerases, enzymes that bind chromatin and produce transient breaks to relax DNA. Recently, this idea of mere facilitators of transcription progression is changing, as topoisomerases are being assigned new functions in regulating the expression of specific genes. In fact, mammalian type II topoisomerases, both the [Symbol] (TOP2A) and [Symbol] (TOP2B) paralogs, are enriched at promoter regions, where they have been proposed to trigger transcription through the generation of DNA double-strand breaks (DSBs). However, this is difficult to reconcile with the intrinsic catalytic properties of TOP2 and the high risk of genome instability that continuous production and repair of DSBs implies. Here, we show that TOP2A enforces promoter-proximal pausing of Pol II by removing transcription-associated negative DNA supercoiling. Interestingly, this topological balance and its disruption is essential for the transcriptional control of Immediate Early Genes (IEGs) and their typical bursting behaviour in response to stimulus. We therefore uncover a novel layer of transcriptional regulation that relies on canonical functions of TOP2A that are independent of aberrant DSB formation, providing a topological framework for the control of promoter-proximal pausing and the tight regulation of IEGs.

overall_design: 2 RNA-seq experiments in human RPE cells were generated, each one consisting on 2 conditions (control VS merbarone treatment): 1) Control VS 30m merbarone: 30m vehicle treatment (3 replicates) and 30m merbarone treatment (3 replicates); 2) Control VS 2h merbarone: Untreated (2 replicates) and 2h merbarone treatment (2 replicates).

first: Andrés

last: Herrero-Ruiz

first: Pedro

last: Martínez-García

first: José

last: Terrón-Bautista

first: Silvia

last: Jimeno-González

last: Cortés-Ledesma


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [RAW264.7]

summary: We used RNA-seq to detect the genes affected by Tet2 or Itaconate (ITA) treatment

overall_design: WT and Tet2 knockout RAW264.7 were pretreated with octy-itaconate and induced by LPS and each treatment has three biological replicates


title: Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling

type: Genome binding/occupancy profiling by high throughput sequencing


title: Differential gene expression of a gamma secretase inhibitor treated human oral squamous cell carcinoma cell line

status: Public on Apr 30 2021

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

summary: Notch signalling regulates various cancer cell beahviors. Influence of notch signaling inhibitor, a gamma secretase inhibitor (DAPT) on human oral squamous cell carcinoma is not yet widely investigated. Here, the differential mRNA expression of DAPT treated HSC4 cell line was examined using RNA sequencing technique. Results demonstraetd that DAPT regulated various pathways in HSC4, including cell cycle and DNA replication pathways.

overall_design: HSC4 cells were maintained in normal growth medium and supplemented with 50 uM DAPT for 24 h. Total RNA was collected and RNA sequencing was performed. Differential gene expression and pathway enrichment was also performed.

first: Nunthawan

last: Nowwarote

first: Sarai

last: Pongjantarasatian


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes

first: Yue

last: Xiong


title: Cancer-associated E239K mutation of LSD1 promotes the migration and invasion of luminal breast cancer cells by reducing the expression of ERα

status: Public on Mar 12 2021

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

summary: Background: Epithelial to mesenchymal transition (EMT) plays an essential role in the metastasis of breast cancer by regulating the migration and invasion of cancer cells. Lysine specific demethylase 1 (LSD1) is an important histone demethylase that mediates EMT. However, the functional effects of the mutation on LSD1 in breast cancer remain unclear.  Results: An E239K mutation of LSD1 was identified from TCGA Breast Invasive Carcinoma cohort. To investigate the functional effects of the E239K mutation of LSD1, a stable LSD1 knockdown MCF7 cell line was generated. Rescue with the wild-type LSD1, but not the E239K mutated LSD1, suppressed the increased invasion of the LSD1 knockdown cells, demonstrating that the E239K mutation abolished the suppressive effects of LSD1 on the invasion of breast cancer cells. Further analysis showed that the E239K mutation of LSD1 led to decreased expression of estrogen receptor α (ERα), which subsequently increased the expression of Slug, a master transcription factor that promoted EMT. Most importantly, the E239K mutation of LSD1 disrupted the interaction between LSD1 and GATA3, which reduced the enrichment of LSD1 at the promoter region of ERα gene. The reduced enrichment of LSD1 at the promoter region of ERα gene caused enhanced histone H3K9 methylation, which in turn suppressed the transcription of ERα gene.  Conclusions: The E239K mutation of LSD1 promotes the migration and invasion of breast cancer cells by disrupting the interaction between LSD1 and GATA3, which reduces the expression of ERα by enhancing the histone H3K9 methylation.

overall_design: Total RNA obtained from MCF7 cells stably express LSD1 shRNA, or rescued with LSD1 WT,or LSD1 E239K upon LSD1 KD.

first: Yu

last: Zhang

first: Tong

last: Wu

first: Bo

last: Zhao

first: Ziyu

last: Liu

first: Jing

first: Yueru

last: Shi

first: Youzhong

last: Wan

first: Zhe

last: Li


title: RNA-seq of THP-1 cells and tumor-associated macrophages sorted from HCC tumor tissues.

status: Public on Mar 16 2021

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

overall_design: Total RNAs were extracted from the co-cultured THP-1 cells, or FACS-sorted cells from the tumor and non-tumor liver tissues

first: Aiqing

last: Yang

first: Cheng

last: Quan

first: Yingwei

last: Pan

first: Haoyun

first: Yuanfeng

first: Chengming

last: Gao

first: Hao

first: Pengbo

last: Cao

first: Hongxia

last: Chen

first: Shichun

first: Gangqiao

last: Zhou


title: Evaluate the immune reactivity of tumor-infiltrating lymphocytes upon a panel of viral peptides

status: Public on Apr 24 2021

city: Dallas

first: Ze

state: TX

address: 5959 Maple Avenue, APT 1102

institute: University of Texas Southwestern Medical Center at Dallas

summary: We characterize the different TILs populations reactive against a panel of MHC-I restricted viral peptides using single-molecule-based sequencing technology. They exhibit a stunning diversity in terms of both reactivity and transcriptome profile. This study provides new insights into the correlation between transcriptome markers expressed by these cells and immune specificity to viral epitopes.

overall_design: Examine the transcriptome profiles of different viral reactive TIL populations

first: Jiang

last: Peixin

first: Reuben

last: Alexandre


title: Genome-wide map of chromatin states and global transcriptome profiling in SETD2 wild type and mutant cells

status: Public on Mar 25 2021

city: Kansas City

first: Ning

last: Zhang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: We looked at the distribution of the histone mark H3K36me3 in wild type 293T and SETD2 deleted 293T (KO) cells. We also looked at the H3K36me3 profile after rescuing the KO cells with recombinant SETD2 constructs; FL (full length), N3 (1404-2564) and N3ΔSRI/N3woSRI (1404-2468). Furthermore, we performed RNA-Seq of cells expressing the wild type or mutant/recombinant copy of SETD2 to compare their global transcriptome profile.

overall_design: Wild type, SETD2 deleted (KO) and KO cells rescued with recombinant SETD2 constructs; FL (full length), N3 (1404-2564) and N3ΔSRI/N3woSRI (1404-2468) were used in the study. The KO cells in addition to being the cells in which rescue experiments with recombinant SETD2 were performed, also serve as a negative control for H3K36me3 ChIP.

first: Saikat

last: Bhattacharya

first: Jerry

last: Workman


title: RNA-seq of Multiple Myeloma

status: Public on Mar 03 2021

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: Purpose: Multiple myeloma is a malignancy of plasma cells. Extensive genetic and transcriptional characterization of myeloma has identified subtypes with prognostic and therapeutic implications. In contrast, relatively little is known about the myeloma epigenome.     Experimental Design: CD138+CD38+ myeloma cells were isolated from fresh bone marrow aspirate or the same aspirate after freezing for one to six months. Gene expression and chromatin accessibility were compared between fresh and frozen samples by RNA-seq and ATAC-seq. Chromatin accessible regions were used to identify regulatory RNA expression in over 700 samples from newly diagnosed patients in the MMRF CoMMpass trial (NCT01454297).    Results: Gene expression and chromatin accessibility of cryopreserved myeloma recapitulated that of freshly isolated samples. ATAC-seq performed on a series of biobanked specimens identified thousands of chromatin accessible regions with hundreds being highly coordinated with gene expression. Over 4,700 of these chromatin accessible regions were transcribed in newly diagnosed myelomas from the CoMMpass trial. Regulatory element activity alone recapitulated myeloma gene expression subtypes, and in particular myeloma subtypes with IGH translocations were defined by transcription of distal regulatory elements. Moreover, enhancer activity predicted oncogene expression implicating gene regulatory mechanisms in aggressive myeloma.     Conclusions: These data demonstrate the feasibility of using biobanked specimens for retrospective studies of the myeloma epigenome and illustrate the unique enhancer landscapes of myeloma subtypes that are coupled to gene expression and disease progression.

overall_design: RNA-seq (N=33) and ATAC-seq (N=13) was performed on purified CD138+CD38+ cells from bone marrow aspirates from multiple myeloma patients.  These include samples that were analyzed from both fresh bone marrow aspirates and cryopreserved specimens for 3 ATAC-seq samples and 4 RNA-seq samples.

first: Vikas

middle: A

last: Gupta

first: Lawrence

middle: H

last: Boise


title: ATAC-seq of Multiple Myeloma


title: Pathological effects of SARS-CoV-2 on hESC-derived peripheral neurons

status: Public on Mar 01 2021

first: Yong Jun

last: Kim

address: 26 Kyungheedaero

department: Department of Pathology

institute: Kyung Hee University

summary: Patients with recent pandemic of Coronavirus Disease-19 (COVID-19) complains of neurological symptoms unlike typical coronavirus infections. However, the absence of studies utilizing proper models of human peripheral nerve is hampering an understanding of COVID-19 pathogenesis. We, here, employed human embryonic stem cell derived peripheral neurons to validate change in transcriptome in human peripheral neurons. Transcriptome analysis of infected peripheral neurons indicates that chemosensory abnormalities in olfaction and gustation are associated with dysfunction and death of peripheral neurons.

overall_design: Biological replicates of hESC-derived peripheral neurons prepared under thoroughly isolated conditions were infected with SARS-CoV-2, and each subset was analyzed.

first: Seung Pil

last: Yun


title: Multi-center retrospective evaluation of a RNA expression classifier to predict pathological complete response to neoadjuvant chemotherapy in breast cancer biopsies

city: San Diego

first: Joan

middle: W

address: 4949 Carroll Canyon Road, Suit 120

institute: Certis Oncology Solution

summary: We developed a test to predict which patients will achieve pCR to NAC, and which will have residual disease (RD). A retrospective collection of formalin-fixed, paraffin-embedded (FFPE) pretreatment biopsies from 222 multi-institutional breast cancer patients treated with NAC, including 90 TNBC patients, were processed using standard procedures. MNovel machine learning algorithms and statistical cross-validation were used to develop predictive classifiers based on RNA-seq differential gene expression analysis of patient samples. Two mRNA classifiers of 18 genes and 15 genes were sequentially applied to the total cohort, clustering patients into three distinct classes. The test accurately identified 83.75% of pCR and 86.62% of RD patients in the total population, and 92.10% of pCR and 80.77% of RD patients in the TNBC subset. The TNBC RD patients were subdivided by our classifiers, with one class showing significantly higher levels of Ki-67 expression and having significantly poorer survival rates than the other classes. Stratification of patients may allow identification of TNBC patients with the worst prognosis prior to NAC, allowing for personalized treatments with the potential to improve patient outcomes.

overall_design: Predicting pathological complete response to neo-adjuvant therapy in triple negative breast cancer patients

first: Marcia

last: Founier

first: Susan

last: Tannenbaum

first: Trushna

last: Desai

first: Ryan

last: Russell

first: Mary

last: Fiel-Gan

first: Varun

last: Bhat

first: Maria

last: de Fátima Dias Gaui

first: Luis

last: Amendola

first: Zilton

last: Vasconcelos

first: Adam

last: Brufsky


title: Association of RERG Expression to Female Survival Advantage in Malignant Pleural Mesothelioma I

status: Public on Feb 15 2021

city: Boston

first: Assunta

last: De Rienzo

state: MA

address: 75 Francis Street

institute: Brigham and Women's Hospital

summary: Sex differences in incidence, prognosis, and treatment response have been described for many cancers. In malignant pleural mesothelioma (MPM), a lethal disease associated with asbestos exposure, men outnumber women 4 to 1, but women consistently live longer than men following surgery-based therapy. This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences. Two microarray datasets of MPM tumors were analyzed to discover estrogen-related genes associated with survival. A validation cohort of MPM tumors was selected to balance the numbers of men and women and control for competing prognostic influences. The RAS like estrogen regulated growth inhibitor (RERG) gene was identified as the most differentially-expressed estrogen-related gene in these tumors and predicted prognosis in discovery datasets. In the sex-matched validation cohort, low RERG expression was significantly associated with increased risk of death among women.  No association between RERG expression and survival was found among men, and no relationship between estrogen receptor protein or gene expression and survival was found for either sex. Additional investigations are needed to elucidate the molecular mechanisms underlying this association and its sex specificity.

overall_design: This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences between men and women affected by malignant pleural mesothelioma.

first: Melissa

last: Coleman

first: Beow

middle: Y

last: Yeap

first: David

middle: T

last: Severson

last: Wadowski

first: Corinne

middle: E

last: Gustafson

first: Roderick

middle: V

last: Jensen

first: Lucian

middle: R

last: Chirieac

first: William

last: Richards

first: Raphael

last: Bueno


title: Transcriptome profile of MV4-11 cells with FEV deficiency

status: Public on Feb 12 2021

city: Suzhou

first: Jubin

last: Zhang

state: Jiangsu

address: Shizi street

institute: Soochow University

summary: Enhanced homing and uncontrolled expansion are the characteristics of AML cells. We identified a transcription factor FEV (fifth Ewing variant) as the regulator. To assess the regulation mechanisms, FEV expression was knocked down in AML cell line MV4-11 cells using shRNA. MV4-11 cells transduced with non-silencing control (NC), FEV shRNA (shFEV) were cultured for 3 days and sorted by FACS. The cells were collected and total RNA was isolated by the Trizol kit (Takara Bio, Otsu, Japan) according to manufacturer’s protocol. High-throughput RNA sequencing (RNA-seq) was performed by Illumina HiSeq 2500 (Illumina, San Diego, CA) at CapitalBio Corporation (Beijing, China). Differentially expressed genes were analysed between the two groups.

overall_design: Two groups of MV4-11 cells were transfected with NC or shFEV, with two sample in NC group and four samples in shFEV group, and were sorted by FACS. RNA-seq was performed and differentially expressed genes were analysed.

first: Lijuan

last: Qi

first: Tanzhen

last: Wang

first: Jingnan

last: An

first: Biqi

last: Zhou

first: Yanglan

last: Fang

first: Yujie

last: Liu

first: Meng

last: Shan

first: Dengli

last: Hong

first: Depei

last: Wu

first: Yang

last: Xu

first: Tianhui


title: High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

city: Planegg

first: Danny

last: Nedialkova

state: Bayern

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute for Biochemistry

type: Non-coding RNA profiling by high throughput sequencing

summary: Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome these limitations with modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which combines a workflow for full-length cDNA library construction from mature tRNA with a simple-to-use computational analysis toolkit. Our method accurately captures tRNA abundance and modification status in multiple eukaryotes and is applicable to any organism with a known genome.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens

overall_design: Development of method for high-throughput sequencing, quantitation and data analysis of tRNA pools in multiple eukaryotic species. Evidence of application for assesing differential expression of tRNAs between two human cell lines, investigating tRNA charging fraction, and extensive modification analysis.

first: Andrew

last: Behrens

first: Geraldine

last: Rodschinka

middle: D


title: An optimized ribodepletion approach for C. elegans RNA-sequencing libraries

status: Public on Jan 30 2021

city: New Haven

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

institute: Yale University

summary: Advances over the past decade have allowed for increasingly fine-grained labeling and isolation of rare cell samples for transcriptomic analysis, providing new insights into cell function and gene regulation. These samples often contain very little RNA for sequencing, and so have required new techniques to capture and amplify transcripts of interest. However, as new tools are developed, they are often optimized for mammalian samples. Thus, it is unclear for invertebrate samples what the best practices are for library preparation, and how differences in library preparation approaches affect final results. Here we compared two commercially available techniques: a commonly used polyA selection approach, and a newly developed ribodepletion approach, for which we designed a unique C. elegans-specific probe set. We performed a detailed comparison on multiple RNA samples and developed novel analysis methods to compare the results. Our analysis identifies clear strengths and weaknesses for both of these approaches in building libraries from low abundance RNA samples in C. elegans. We find that the polyA approach is superior in both percent reads mapped and rRNA removal, while the ribodepletion approach provides better detection for long and noncoding RNAs along with increased certainty of calling expression for low abundance transcripts. These insights will help guide researchers in designing future experiments in transcriptomics and provide a model for comparative analysis of library-building techniques.

overall_design: Four RNA samples were used to compare library preparation methods: SMARTseq V4 (Takara) and SoLo Ovation (Tecan Genomics). Each sample was split into two, and used as input for both library prep kits so that final libraries were matched between kits.

first: Alec

last: Barrett

first: Rebecca

last: McWhirter

first: Seth

last: Taylor

first: Alexis

last: Weinreb

first: David

last: Miller III


title: Landscape of N6-methyladenosine modification patterns in invasive malignant pleomorphic adenoma

status: Public on Mar 10 2021

first: Zhenyuan

last: Han

address: No.22, Zhongguancun South Avenue Haidian District

institute: Peking University School of Stomatology

summary: N6-methyladenosine (m6A) is one of the most popular RNA modifications, which is widely found in messenger RNAs (mRNAs) .In our study,we provide m6A profiles of human invasive malignant pleomorphic adenoma, which open an avenue for in-depth knowledge and understanding of m6A topology in invasive malignant pleomorphic adenoma.

overall_design: We employed MeRIP-seq analyses in five pairs of invasive malignant pleomorphic adenoma tumor tissue specimens and corresponding normal glands to explore m6A modification patterns and uncovered m6A modified mRNAs  in  invasive malignant pleomorphic adenoma.

first: Z

last: Tian


title: Competition between hematopoietic stem and progenitor cells controls the hematopoietic stem cell homeostasis [bulk RNA-seq]

first: Jungmin

last: Choi

address: 73, Goryeodae-ro, Seongbuk-gu

institute: Korea University College of Medicine

summary: Cellular competition for limiting hematopoietic factors is a physiologically regulated but poorly understood process. Here, we studied this phenomenon by hampering hematopoietic progenitor access to Leptin receptor+ mesenchymal stem/progenitor cells (MSPCs) and endothelial cells (ECs). We showed that HSC numbers increased by 2-fold when multipotent and lineage-restricted progenitors fail to respond to CXCL12 produced by MSPCs and ECs. HSCs were qualitatively normal, and HSC expansion only occurred when early hematopoietic progenitors but not differentiated hematopoietic cells lacked CXCR4. Furthermore, the MSPC and EC transcriptomic heterogeneity was remarkably stable, suggesting that it is impervious to dramatic changes in hematopoietic progenitor interactions. Instead, HSC expansion was caused by increased availability of membrane-bound stem cell factor (mSCF) on MSPCs and ECs due to reduced consumption by cKit-expressing hematopoietic progenitors. These studies revealed an intricate homeostatic balance between HSCs and proximal hematopoietic progenitors regulated by cell competition for limiting amounts of mSCF.

overall_design: With bone marrow stromal cells of Cxcr4 conditional knockout (Flk2-cre+ Cxcr4fl/fl, cKO) mouse and littermate control (Flk2-cre+ Cxcr4fl/+, CTL), bulk RNA-sequencing analysis was performed.

first: João

last: Pereira


title: Single-cell RNA sequencing of primary human B-cell acute lymphoblast leukemia (ALL) cells

city: los angeles

first: Du

last: Jiang

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

summary: Transcriptome analysis of human B-ALL cells in a patient-derived xenograft model at single cell resolution

overall_design: Barcoded ALL cells (GFP+hCD45+) were FACS-sorted from either primary or secondary recipient NSG mice before pooled and loaded into three channels on the Chromium chip, then subjected to processed using the Chromium Single-cell 3′ v2 Library Kit (10× Genomics, Pleasanton, CA) following the manufacturer’s instructions

first: Humberto

last: Contreras-Trujillo


title: Alternative transcription start sites contribute to acute-stress–induced transcriptome response in human skeletal muscle

status: Public on Dec 31 2020

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary:
More than half of human protein-coding genes have an alternative transcription start site (TSS). We aimed to investigate the contribution of alternative TSSs to the acute-stress–induced transcriptome response in human tissue (skeletal muscle) using the cap analysis of gene expression approach. TSSs were examined at baseline and during recovery after acute stress (a cycling exercise).
We identified 44,680 CAGE TSS clusters (including 3,764 first defined) belonging to 12,268 genes and annotated for the first time 290 TSSs belonging to 163 genes. The transcriptome dynamically changes during the first hours after acute stress; the change in the expression of 10% of genes was associated with the activation of alternative TSSs, indicating differential TSSs usage. The majority of the alternative TSSs do not increase proteome complexity suggesting that the function of thousands of alternative TSSs is associated with the fine regulation of mRNA isoform expression from a gene due to the transcription factor-specific activation of various alternative TSSs. We identified individual muscle promoter regions for each TSS using muscle open chromatin data (ATAC-seq and DNase-seq). Then, using the positional weight matrix approach we predicted time course activation of “classic” transcription factors involved in response of skeletal muscle to contractile activity, as well as diversity of less/un-investigated factors.
Transcriptome response induced by acute stress related to activation of the alternative TSSs indicates that differential TSSs usage is an essential mechanism of fine regulation of gene response to stress stimulus. A comprehensive resource of accurate TSSs and individual promoter regions for each TSS in muscle was created. This resource together with the positional weight matrix approach can be used to accurate prediction of TFs in any gene(s) of interest involved in the response to various stimuli, interventions or pathological conditions in human skeletal muscle.

overall_design:
Ten amateur endurance-trained athletes (long distance runners, cyclists and cross country skiers, median age 32 years [interquartile range, 30–36 years]; weight 75 kg [71–78 kg]; V’O2max/kg [maximal pulmonary O2 consumption rate] 58 ml/min/kg [54–60 ml/min/kg of body mass]) were involved in our study. Each subject carried out an intermittent exercise (60 min, [3 min at intensity 50% of lactate threshold [LT4 , power at blood lactate 4 mmol/l] + 2 min, 100% LT4] x 12) on a cycle ergometer 2 h after a standardized breakfast (3582 kJ; 22 g protein, 154 g carbohydrates and 16 g fat). Subjects ate a standardized lunch (3714 kJ; 45 g protein, 183 g carbohydrates and 27 g fat) 1 h 15 min after an intermittent exercise. Biopsy samples were taken under local anesthesia (2 mL 2% lidocaine) using a Bergstrome needle with aspiration from the m. vastus lateralis prior to, 2 min, 1 h, 3 h, and 6 h after an intermittent exercise (1st, 2d, and 3d from the one leg, 4st and 5st from another leg).
For each subject samples from time points: prior to, 1 h, 3 h, and 6 h after an exercise were analyzed in one run. Additionally, we analyzed all samples from time point 2 min after an exercise in a separate run. To improve the quality of identification of CAGE TSSs, all data were used for calculation. However, differential expressions of CAGE TSSs and genes as well as differential TSSs usage were evaluated for time points: prior to, 1 h, 3 h, and 6 h after an exercise only.

first: Daniil

last: Popov

last: Makhnovskii


title: Prednisolone rescues Duchenne Muscular Dystrophy phenotypes in human pluripotent stem cells-derived skeletal muscle in vitro

status: Public on Jan 15 2021

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

institute: Humanitas

summary: Duchenne Muscular Dystrophy (DMD) is a devastating genetic disease leading to degeneration of skeletal muscles and premature death. How dystrophin absence leads to muscle wasting remains unclear. Here, we describe an optimized protocol to differentiate human induced Pluripotent Stem Cells (iPSC) to a late myogenic stage. This allows to recapitulate classical DMD phenotypes (mislocalization of proteins of the Dystrophin glycoprotein associated complex (DGC), increased fusion, myofiber branching, force contraction defects and calcium hyperactivation) in isogenic DMD-mutant iPSC lines in vitro. Treatment of the myogenic cultures with prednisolone (the standard of care for DMD) can dramatically rescue force contraction, fusion and branching defects in DMD iPSC lines. This argues that prednisolone acts directly on myofibers, challenging the largely prevalent view that its beneficial effects are due to anti-inflammatory properties. Our work introduces a new human in vitro model to study the onset of DMD pathology and test novel therapeutic approaches.

overall_design: Wildtype pluripotent stem cell line was differentiated into skeletal muscle as described in Chal et. al. 2016. Cells were analyzed at different time points to investigate the progression of skeletal muscle differentiation and the role of 3 compounds in skeletal muscle maturation. In addition, wildype and DMD cell lines were differentiated into mature skeletal muscle to analyze the effect of DMD mutation on skeletal muscle formation.

first: Ziad

last: Al Tanoury

first: Jyoti

last: Rao

first: Bianca

last: Habermann

first: Olivier

last: Pourquié


title: ATAC-seq and RNA-Seq of Multiple Myeloma

first: Benjamin

last: Barwick

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

overall_design: Refer to individual Series


title: Hematopoietic Stem Cell Heterogeneity in JAK2 V617F+ Essential Thrombocythemia

status: Public on Feb 22 2021

city: Tianjin

first: Coral

last: Tong

address: 288 Nanjing Rd, Heping

institute: Institute of Hematology & Blood Disease Hospital

summary: In this study, we explored the transcriptome of hematopoietic stem cells (HSCs) and megakaryocyte-erythroid progenitors (MEPs) in JAK2 V617F+ PV and ET and found that distinctive gene expression patterns within MPN subtypes begin at the HSC stage. HSCs from ET exhibited prominent megakaryocyte (Mk)-lineage priming. The differentially expressed genes (DEGs) indicated that cellular processes and signaling pathways in HSCs and MEPs from healthy donors (HDs), PV and ET patients are differentially modulated

overall_design: Examination of gene expression in 2 different MPN subtypes as well as HDs(NCs) at 2 hematopoietic stages

first: Jingyuan

first: Mankai

last: Ju

first: Lei

last: Zhang

first: Lihong

last: Shi


title: Epigenome analysis altered DNA methylation in survivors of childhood and young adult cancer [adult]

city: Newcastle

first: Gordon

last: Strathdee

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary: Genome wide DNA methylation profiling of  samples from adult survivors of childhood and young adult cancer, using the Illumina Infinium Human MethylationEPIC Beadchip arrays. Samples included 32  samples, all sampled at least 10 years after diagnosis . Specific therapies and duration between sampling and diagnosis varied.

overall_design: Bisulphite converted DNA from the 32 samples were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip arrays


title: RNA-seq analysis of human white adipose tissue from normal weight and obese individuals prior to and following 12-week intervention with fish oil or corn oil

status: Public on Feb 24 2021

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

institute: University of Oxford

summary:
Purpose: To identify, using RNA-sequencing, differentially expressed genes in the white adipose tissue in obesity and in response to lipid intervention in both normal weight and obese individuals.
Methods: White adipose tissue mRNA profiles of normal weight and obses humans at baseline (0-weeks) and 12-weeks after fish oil (3d/day of which 1.1g EPA and 0.8g DHA) or corn oil (3g/day) supplementation were generated by deep sequencing using RNA sequencing. The sequence reads that passed quality filters were aligned to the human genome using TopHat and analyzed at the gene level using DESeq2. qRT–PCR validation was performed using Taqman probe assays
Results: Using an optimized data analysis workflow, we mapped reads to the human genome (hg38.0) and identified 789 genes differentially expressed between normal weight and obese individuals at baseline (week-0) (adjusted p value <0.05 and fold change >2). 623 of these were upregulated and 175 were downregulated. Geneset enrichment analysis identified several enriched pathways, including regulation of immune and inflammatory response, tissue growth and glucose metabolism in obese indvidiuals in comparison to normal weight. We identified 26 genes differentially expressed in normal weight individuals in response to fish oil intervention (week-12) (adjusted p value <0.05 and fold change >1). 14 of these were upregulated and 12 were downregulated. We identified 8 genes differentially expressed in obese individuals in response to fish oil intervention (week-12) (adjusted p value <0.05 and fold change >1). 3 of these were upregulated and 5 were downregulated. Geneset enrichment analysis identified several enriched pathways, including regulation of immune and inflammatory response in both normal weight and obese individuals in response to fish oil intervention with greater effects in normal weight individuals.
Conclusions: Our study provides novel insights into the association of obesity and changes to the human white adipose tissue transcriptome, in addition to the effects of fish oil (EPA and DHA) on the transcriptome of normal weight and obese individuals and differences in response between these BMI subgroups. Our study further identifies putative gene targets and molecular pathways that help to understand how obesity results in adipose tissue dysfunction and how EPA and DHA may modulate the long term expression of gene networks and disease pathways related to onset of obesity associated inflammation.

overall_design: Human white adipose tissue RNA transcriptomes from normal weight and obese individuals and following 12 week fish oil (3g/day, 1.1g EPA and 0.8g DHA) or corn oil (3g/day)( supplememtation.

first: Antoun

last: Elie

first: Helena

last: Fisk


title: Protein-coding and non-coding RNA landscape in critically ill patients with sepsis

status: Public on Jan 11 2021

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

platform_organism:
Homo sapiens
synthetic construct


title: Epigenome analysis altered DNA methylation following  chemotherapy in childhood cancer patients [undergoing and post therapy]

summary: Genome wide DNA methylation profiling of paired samples from childhood cancer patients undergoing chemotherapy treatment, using the Illumina Infinium Human MethylationEPIC Beadchip arrays. Samples included 32 paired samples (i.e. total 64 samples), with the second sample taken after treatment . Specific therapies and duration between samples varied.

overall_design: Bisulphite converted DNA from the 64 samples were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip arrays


title: Epigenome analysis altered DNA methylation following  chemotherapy in childhood cancer patients


title: Transcriptional changes after YAP/TAZ siRNA-mediated knockdown, and BMP-2 stimulation and SMAD1 ChIP-Seq in BMP2-treated human fetal osteoblasts

city: Berlin

first: Maria

last: Reichenbach

address: Thielallee 63

department: Institute for Chemistry and Biochemistry

institute: Freie Universität Berlin

summary: Osteogenesis is influenced by a variety of factors including growth factors - especially those of the TGF-beta superfamily - and Hippo signaling. Consequently, we hypothesize that the YAP/TAZ pathway is intertwining with TGF-beta and BMP signaling resulting in osteogenic differentiation. Therefore, we performed a comprehensive RNA-Seq study including both YAP/TAZ depletion by siRNA and BMP stimulation conditions in human fetal osteoblasts cell line hFOB 1.10. In order to identify the direct SMAD1 target genes corresponding to our RNA-Seq data, we performed an SMAD1 chromatin immunoprecipitation followed by sequencing.

overall_design: To deplete YAP and TAZ, cells were transfected with human siRNA SMARTpool targeting YAP1 or WWTR1. 48h post-transfection cells were starved in 0% FCS medium for 3h and then stimulated with 5nM BMP-2 for 1h. Afterwards, cells were lysed and total RNA was isolated. For each experimental condition, three biological replicates were analyzed. For ChIP Seq BMP-2  treated cells (5nM, 90min) were fixed in 1% Formaldehyde and quenched by adding glycine 125 mM for 5 minutes at 4°C. After this, cells were harvested and lysed according to the protocol described by Lee et al (2006) and chromatin was sheared by sonication using the Bioruptor ultra sonicator (Diagenode®). Sheared chromatin was immunoprecipitated using 10 µg of total SMAD1 antibody (Cell Signaling®, #9743) or the normal rabbit IgG antibody (Cell signaling®, #2729) as a control, followed by incubation with Protein G magnetic beads  (Invitrogen®). DNA was eluted in elution buffer and DNA purification was performed using DNA Purification Buffers and Spin Columns kit, according to the manufacturer’s instructions (Cell Signaling®).

first: Paul

last: Mendez

first: C

last: da Silva Madaleno

last: Rikeit

first: J

last: Jatzlau

first: Petra

last: Knaus


title: Islet-Autonomous Inflammatory Signaling Propagates Autoimmunity and Promotes Diabetes in Nonobese Diabetic Mice

status: Public on Feb 11 2021

city: Chicago

first: Raghavendra

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

summary: Type 1 diabetes (T1D) is an immune-mediated disease that leads to β cell dysfunction and death. However, the contribution of β cells in this process remains unclear. To understand how islet-derived pro-inflammatory signaling pathways contribute to diabetes pathogenesis, we generated inducible islet-specific Alox15 knockout mice on the NOD background. We report that islet-specific deletion of Alox15 induced a substantial increase of β-cell mass and decreased islet insulitis, and ultimately lead to a protection against spontaneous autoimmune diabetes in NOD mice. Single cell RNA-sequencing and mass spectrometry analysis revealed that islet-specific knockout of Alox15 leads to an increase of β cells expressing Pd-l1 and promotes an anti-inflammatory phenotype in myeloid cells and T cells inside the islets. Furthermore, islet- specific Alox15 deletion enhances the expansion of M2-like macrophages and regulatory T cells in the pancreatic islets and pancreatic lymph nodes. Together, these results lead to the conclusion that proinflammatory signals produced by β cells allows these cells to express immunoregulators that protects these cells of immune cell attack and promote β cell survival.

overall_design: Mouse islets were isolated from collagenase-perfused pancreata and cultured in RPMI medium as previously describe (Stull et al. 2012). After isolation, islets were handpicked and digested with Accutase (EMD Millipore Corporation) containing 2U/ml of DNAse during 5min at 37C sob agitation (1000rpm). Then cells were washed several times with PBS+2%FBS to eliminate DNAse and then filtered using a cell strainer (40m). Samples with more than 90% viability were used for scRNAseq.

first: Annie R

last: Piñeros

first: Abhishek

last: Kulkarni

first: Hongyu

last: Gao

first: Kara

middle: S

last: Orr

first: Lindsey

last: Glenn

first: Christopher

last: Reissaus

first: Marimar

last: Hernadez-Perez

first: Yunlong

last: Liu

first: Maureen

last: Gannon

first: Marcia

last: McDuffie

first: Jerry

last: Nadler

first: Margaret

last: Morris

first: Sarah

last: Tersey


title: Identification and analysis of differently expressed genes between 4T1 cells incubated with PBS and oxalate

status: Public on Feb 05 2021

city: Guangzhou

first: Li

last: Liang

state: China

address: guangzhoudadaobei street NO.1838

institute: Southern medical university

summary: Although it has been reported that exposure of breast epithelial cells to oxalate promotes the proliferation of breast cells, but the mechanisms have been insufficiently explored.

overall_design: 4T1 cells were treated with PBS (n=1) or potassium oxalate (20 mM) (n=1)


title: Influence of CEBPD on Glucocorticoid Response in Airway Smooth Muscle

city: Philadelphia

first: Blanca

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary:
CCAAT/Enhancer Binding Protein D (CEBPD) is a transcription factor that regulates genes involved in immune and inflammatory responses. Based on our previous observation that CEBPD expression increases in airway smooth muscle (ASM) with glucocorticoid exposure, we sought to better understand its role in the ASM transcriptomic response to glucocorticoids via knockdown experiments.

Primary human airway smooth muscle (ASM) cells from four non-asthma donors were transfected with 25pmol of siRNA non-targeting control or siCEBPD SMARTpool using RNAiMax. Three days after transfection, cells were treated with 100nM Budesonide, 10ng/ml TNF-alpha, or both for 18 hours. RNA-Seq libraries were prepared with the Kapa mRNA HyperPrep Illumina Library kit. An Illumina HiSeq 2500 instrument was used to generate 125 base pair paired-end reads. STAR was used to align sequencing reads to the hg38 reference genome, and HTSeq was used to quantify transcript levels. DESeq2 was used to perform differential expression analysis.

overall_design: Transcriptome profiles obtained via RNA-Seq for ASM cells from four donors per condition, with and without CEBPD knockdown, and with budesonide, TNF-alpha, budesonide+TNF-alpha or vehicle control treatment were obtained to measure the effects of CEBPD knockdown on glucocorticoid response in ASM.


title: Characterization of genomic and chromatin landscape of RPE cells

status: Public on Dec 17 2020

city: Amsterdam

first: Anna

last: Gonzalez Manjon

email: a.gonzalez@nki.nl, li.koob@nki.nl

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: We have performed different High-throughput sequencing techniques to characterize the chromatin and 3D genome of RPE-1 cells. Some of the samples are performed with RPE cells that are resistant to taxol.

first: Rene

last: Medema


title: Transcriptomic study of PIK3D transfected-Huh7 cells

status: Public on Nov 30 2020

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

summary:
The isoform delta of class I Phosphoinositide 3-kinase (PI3Kδ) is expressed primarily in hematopoietic cells, and its inhibitor, idelalisib, is approved for the treatment of leukemia and lymphoma. PI3K orients the apicobasal axis and regulates lumen formation through assembly of the extracellular matrix. PI3Kδ overexpression in hepatocellular carcinoma (HCC) cells (Huh7) leads to profound changes in cell morphogenesis and is associated to the up-regulation of stem cell markers.
Transcriptomic analysis performed in triplicate on mRNA of Huh7 cells transfected with PI3Kδ construct (PI3KCD) revealed down regulation of transcripts of hepatocyte differentiation genes and up regulation of transcripts that allow prediction of ICC and mesenchymal stem cells.

overall_design: Huh7 liver cells were cultivated in vitro and transfection of PIK3CD was performed in triplicate. Control was also processed in triplicate. Total RNA was used to produce microarray probes which were individually hybridized on HuGene-2_0-st Affymetrix microarray.

first: Jean

last: Agnetti

first: Christophe

last: Desterke

first: Didier

last: Samuel

first: Ama

last: Gassama-Diagne


title: Kidney organoids are capable of forming Wilms-like tumors, but not teratomas

status: Public on Jan 22 2021

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

institute: Erasmus MC

summary: To study safety and stability of kidney organoids, we studied the presence of residual iPSC in the kidney organoids. We also analyzed their potential for malignant transformation in a teratoma assay and following long-term subcutaneous implantation in an immune deficient mouse model.

overall_design: Examination of a control kidney organoid

first: Anusha

last: Shankar

first: Eric

last: Bindels


title: Protein-coding and non-coding RNA expression in whole blood leukocytes of healthy subjects and critically-ill patients with sepsis or non-infectious etiology.

first: Brendon

last: Scicluna

summary: Genome-wide gene expression profiling of whole blood leukocytes in critically ill patients with sepsis or non-infectious disease has been used extensively in search of diagnostic biomarkers, as well as prognostic signatures reflecting diseases severity and outcome. Through technological advances in genomics it has become clear that transcription is not limited to protein-coding regions of the genome. Here, we describe a comprehensive analysis of RNA expression in blood leukocytes of critically ill patients with sepsis, a non-infectious condition and healthy subjects

overall_design: Whole-blood transcriptional patterns of protein-coding and non-coding RNA molecules in healthy subjects, critically-ill patients with sepsis or non-infectious conditions were generated by means of the human transcriptome array 2.0 (HTA 2.0) chip. Whole-blood from patients was collected within 24 hours of intensive care unit (ICU) admission. Title legend: healthy, healthy subjects; sepsis, ICU patients with sepsis; noninfectious, ICU patients with non-infectious condition.

first: Tom

last: van der Poll


title: Transcriptomic Response of the Diazotrophic Bacteria Gluconacetobacter diazotrophicus Strain PAL5 to Iron Limitation and Characterization of the fur Regulatory Network

status: Public on Jan 09 2021

city: Seropédica

first: Leonardo

middle: Araujo

last: Terra

state: RJ

address: Rodovia BR-465

country: Brazil

institute: Embrapa Agrobiologia

summary: Gluconacetobacter diazotrophicus has been the focus of several studies aiming to understand the mechanisms behind this endophytic diazotrophic bacterium. The present study is the first global analysis of the early transcriptional response of exponentially growing G. diazotrophicus to iron, an essential cofactor for many enzymes involved in various metabolic pathways. RNA-seq, targeted gene mutagenesis and computational motif discovery tools were used to define the G. diazotrophicus Fur regulon. The data analysis showed that genes encoding functions related to iron homeostasis, were significantly upregulated in response to iron limitation. Certain genes involved in the secondary metabolism were overexpressed under iron-limited conditions. In contrast, it was observed that the expression of genes involved in Fe-S cluster biosynthesis, flagellar biosynthesis and type IV secretion systems were downregulated in an iron-depleted culture medium. Our results support a model that control transcription in G. diazotrophicus by Fur function. The G. diazotrophicus Fur protein was able to complement an E. coli fur mutant. These results provide new insights into the effects of iron on the metabolism of G. diazotrophicus, as well as demonstrating the essentiality of this micronutrient for the main characteristic of plant growth promotion by G. diazotrophicus.

overall_design: Profile mRNA obtained after half an hour incubation in the presence and absence of iron in triplicate.

first: Cleiton

last: de Paula Soares

first: Michelle

middle: Z

last: Trada-Sfeir

first: Jéssica

last: de Paula Ferreira

last: Araújo

first: Carlos

last: Meneses

first: Emanuel

last: de Souza

first: José

middle: I

last: Baldani

first: Stefan

last: Schwab


title: Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

status: Public on Dec 01 2020

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Identification of SMC1a and Setdb1 bound-loci in E14 mESCs.

overall_design: RNA-Seq of shControl, shSetdb1 and shSmc1a treated E14 mESCs.

first: T

last: Warrier

first: C

last: EL  Farran

first: H

last: Li

first: Y

last: Loh


title: Transcriptomic analysis of hepatotoxicity induced by pesticides imazalil, thiacloprid and clothianidin alone or in binary mixtures in a 28-day study in female Wistar rats

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary: Co-occurrence of pesticide residues in food commodities raises a safety issue as their mixture effects on human health is largely unknown and need to be investigated. In a previous study, we reported the toxicological effects (pathology & histopathology) of imazalil (IMZ), thiacloprid (THI), and clothianidin (CTD) alone and in binary mixtures in a 28-day gavage study in female Wistar rats. Here, we undertook a transcriptomic analysis by means of total RNA sequencing (RNA-Seq). Ingenuity pathway analysis (IPA) was used to gain mechanistic information on the hepatotoxic pathways affected after treatment with pesticides, alone and in mixtures. Our data shows that 2986 genes were deregulated by CTD while IMZ and THI had effect on 194 and 225 genes, respectively. All three compounds share a common subset of genes whose network is associated with xenobiotic metabolism and nuclear receptors. Additionally, DNA repair process was predicted for CTD. The same networks were retrieved for the mixtures.  Dose addition was indicated for the evaluated gene expressions. Our results bring new insight in the hepatotoxicity mechanisms of IMZ, THI, and CTD.

overall_design: RNA sequencing of 31 liver samples, treatment of rats with three pesticides (imazalil, thiacloprid and clothianidin) and their binary mixtures

first: Jimmy

last: Alarcan

first: Julia

last: Waizenegger

first: Dajana

last: Lichenstein

first: Claudia

last: Luckert

first: Philip

last: Marx-Stoelting

first: Alfonso

last: Lampen

first: Albert

last: Braeuning


title: Exposure to the heavy metal lead induces DNA copy number alterations in zebrafish cells

city: West Lafayette

first: Jennifer

last: Freeman

state: IN

address: 550 Stadium Mall Drive

department: School of Health Sciences

institute: Purdue University

type: Genome variation profiling by genome tiling array

summary: DNA copy number variants (CNVs) are associated with the development of complex neurological diseases and disorders including autism spectrum disorder, schizophrenia, Alzheimer’s disease, and Parkinson’s disease. Exposure to multiple environmental chemicals including various heavy metals is suggested as a risk factor in these neurological diseases and disorders, but few studies have addressed if heavy metal exposure can result in spontaneous DNA copy number changes as a genetic mechanism contributing to these disease outcomes. In this study to further investigate the relationship between heavy metal exposure and spontaneous copy number alterations (CNAs), zebrafish fibroblast cells were exposed to the neurotoxicant lead (Pb). A crystal violet assay was first used to determine exposure concentrations with greater than 80% cell confluency. Then a zebrafish-specific array comparative genomic hybridization (CGH) platform was used to detect CNAs following a 72 hour Pb exposure (0.24, 2.4, or 24 μM). The Pb exposure resulted in 72 CNA amplifications ranging in size from 5 to 329 kb. No deletions were detected. CNAs resulted in 15 copy number alteration regions (CNARs), leaving 7 singlet CNAs. Two of the singlets were within high repeat genomic locations. The number of CNAs tended to increase in a concentration dependent manner. Several CNARs encompassed genes previously reported to have altered expression with Pb exposure, suggesting a mechanistic link. In addition, almost all genes are associated within a molecular network with the amyloid precursor protein (APP). Overall, these findings show that Pb exposure results in spontaneous CNAs that could serve as a mechanism driving adverse health outcomes associated with Pb toxicity including neurological disease pathogenesis for further study.

overall_design: The objective of this study was to identify whether a Pb exposure will generate copy number alterations. First, a zebrafish fibroblast cell line was exposed to a range of Pb concentrations (0-100 uM) to determine concentrations where cell confluency would be altered (n=4 plates with 4 subsamples of each treatment concentration on each plate). From this experiment, treatment concentrations (0, 0.24, 2.4, and 24 um Pb) were chosen to represent a range from no effect on confluency to decreasing cell confluency to ~80% in this cell line. Cells were then exposed to these four treatment concentrations and array CGH was used to detect copy number alterations (CNAs) in Pb treatments compared to the control treatment (n=4). qPCR was used to confirm CNAs.

first: Jinyoung

last: Lee


title: Global transcriptome analysis of Autophagy and mTOR pathway activation by Influenza A virus in lung A549 cells

status: Public on Nov 29 2020

city: Los Alamos

first: Sofiya

middle: N

last: Micheva-Viteva

state: New Mexico

address: Los Alamos National Lab

department: Bioscience

institute: Los Alamos National Laboratory

summary: Here we compare transcriptome dynamics in human lung carcinoma cells A549 infected with Influenza virus A/Port Chalmers/1/73 (H3N2) at two different virus to host cell ratios: multiplicity of infection (MOI) 1 and 5. Our goal was to outline the activation profiles of two main host pro-survival mechanisms, autophagy and mTORC2, co-opted by the virus to effectively complete the replication cycle, amplify, and release of infectious particles. We found that at high virus load MOI5 autophagy, a stress response mechanisms that postpones mammalian cell death, was activated and inhibited within 1 hour of infection. Autophagy downregulation was quickly followed by the activation of genes regulating mTORC2, a secondary cell survival mechanism promoting low capacity of cellular metabolism by inhibition of mTORC1, a main regulator of protein synthesis activating ribosomal elongation factors. At lower MOI (1) autophagy activation followed the virus replication cycle. We found that ULK1 gene expression was gradually upregulated upon Influenza virus A infection at MOI1 together with the activation of key regulators of mTORC1. Such results was not expected since mTORC1 inhibits autophagy activation pathway on post-transcription level through  phosphorylation of ULK1.

sample_organism: Influenza A virus (A/Port Chalmers/1/1973(H3N2))

overall_design: Infection of A549 cells at two MOIs (1 and5) and sample collection at early (1,3, and 4h), mid (6, 8h), and late (12h) phases of Influenza replication cycle. NG RNAseq was applied on total RNA from virus infected cells. The transcriptomics results were validated by Western blot-based targeted proteomics analysis.

first: Tisza

last: Bell

first: Gary

last: Xi

first: Shawn

last: Starkenburg


title: Human lung organoid for modeling infection and disease conditions (Lung II)

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: We sought to define the host immune response, a.k.a, the “cytokine storm” that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 publicly available transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because the receptor it encodes enables the virus that causes Covid-19, SARS-CoV-2, to enter host cells. The signature was surprisingly conserved in all viral pandemics, including COVID-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed airway epithelial and myeloid cells as the major contributors of an IL-15 cytokine storm, and epithelial and NK cell destruction as determinants of severity/fatality. They also helped formulate precise therapeutic goals to reduce disease symptoms and severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool in our armamentarium to rapidly assess disease severity and vet candidate drugs.

overall_design: Human lung organoids were grown in standard culture, ALI and monolayer conditions and infected with SARS-CoV-2.

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: IDO1 inhibition and subsequent metabolic adaptations constrains anti-tumor immune responses in the tumor microenvironment of patients with ovarian cancer

status: Public on Dec 28 2020

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: To uncover underlying mechanisms associated with failure of indoleamine 2, 3-dioxygenase 1 (IDO1) blockade in clinical trials, we conducted a pilot, window-of-opportunity clinical study testing the immunological and metabolic effects of the IDO1 inhibitor, epacadostat, in seventeen patients with newly diagnosed advanced high grade serous ovarian cancer prior to their standard tumor debulking surgery. Comprehensive immunologic, transcriptomic, and metabolomic characterization of the tumor microenvironment using baseline and post-treatment tissue biopsies revealed efficient blockade of the kynurenine pathway of tryptophan degradation. This blockade was accompanied by a metabolic adaptation that shunted tryptophan catabolism towards the serotonin pathway and elevated nicotinamide adenine dinucleotide (NAD)+ biosynthetic pathways, which was detrimental for T cell proliferation and function. Treatment of mice bearing IDO1 over-expressing ovarian tumors with the NAMPT inhibitor, FK866, did not improve tumor control by epacadostat. Because NAD+ metabolites could be ligands for purinergic receptors, we investigated the impact of blocking purinergic receptors in the presence of NAD+. We demonstrated that A2a and A2b, or the combination of A2a and A2b purinergic receptor antagonists rescued NAD+-mediated suppression of T cell proliferation, and the combination of IDO inhibition and A2a/A2b receptor blockade improved survival in the IDO1 over-expressing ovarian tumor bearing hosts. These findings unravel previously unrecognized downstream adaptive metabolic consequences of IDO1 blockade that may undermine efforts to induce tumor-specific T cell responses.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
8 matched pre-post treatment RNASeq samples
IE9MP1_IDO mouse samples:  8 vehicle. Treatment samples: 5 Incyte, 5 FK866, 5 FK866-Incyte, 4 A2a, 2 A2b, 2 Triple.

first: Sebastiano

last: Battaglia

first: Adekunle

last: Odunsi


title: Genome-wide mapping of asynchronous replication in clonal mouse cells

status: Public on Nov 11 2020

city: Jerusalem

first: Itamar

last: Simon

state: APO/FPO IRAQ / AFGHANISTAN / MIDDLE EAST

address: Hadassah Ein Kerem

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University medical school

summary: The entire genome is divided into distinct 1-2 Mb zones that replicate in an ordered and coordinated manner during S phase. While most regions of the genome replicate both alleles in a synchronous manner, some loci have been found to replicate asynchronously, with one allele undergoing DNA synthesis early in S phase, with the other replicating during late S. Random asynchronous replication timing is characterized by cell heterogeneity with some cells.  having the maternal allele early replicating while in others, the orientation is reversed, with the paternal allele being early. This type of asynchronous replication can only be studied in a clonal or single cell manner.  We have used the repli-seq method to study pre-B clonal f1 mouse cells in order to identify and study asynchronous regions in a genome-wide manner.

overall_design: Examination of replication timing in mouse pre-b cells for four clonal CAST/C57BL F1 samples (e5, clone 8, clone 3, clone 2) and one clonal CAST sample.  Three replicates were performed for each sample.

first: Britny

last: Blumenfeld


title: Distinct population of immune suppressive macrophages differentiate from monocytic myeloid-derived suppressor cells in cancer

status: Public on Dec 14 2020

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Here, we report that functional heterogeneity of macrophages in cancer could be determined by the nature of their precursors: monocytes (Mon) and monocytic myeloid-derived suppressor cells (M-MDSC). Macrophages differentiated from M-MDSC, but not from Mon were immune suppressive with genomic profile matching that of M-MDSC. Immune suppressive activity of M-MDSC derived macrophages was dependent on the persistent expression of S100A9 protein in these cells. S100A9 also promoted M2 polarization of macrophages. Tissue resident and Mon derived macrophages lacked expression of this protein. S100A9 dependent immune suppressive activity of macrophage was mediated via transcription factor CEBP/β. The presence of S100A9 positive macrophages in tumor tissues was associated with shorter survival in patients with head and neck cancer and poor response to PD-1 antibody treatment in patients with metastatic melanoma. Thus, this study revealed the pathway of the development of immune suppressive macrophages and suggested approach to their selective targeting.

overall_design: RNA-seq gene expression of source and derived macrophages from monocytes and M-MDSC cells of tumor burden patients

first: Taekyoung

last: Kwak

first: Dmitry

last: Gabrilovich


title: Capturing cardiogenesis in gastruloids

status: Public on Nov 10 2020

city: Lausanne

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

country: Switzerland

institute: EPFL

summary:
Organoids are powerful models for studying tissue development, physiology, and disease. However, current culture systems disrupt the inductive tissue-tissue interactions needed for the complex morphogenetic processes of native organogenesis. Here we show that mouse embryonic stem cells (mESCs) can be coaxed to robustly undergo fundamental steps of early heart organogenesis with an in vivo-like spatiotemporal fidelity. These axially patterned embryonic organoids (gastruloids) mimic embryonic development, and support the generation of cardiovascular progenitors, including first and second heart fields. The cardiac progenitors self-organize into an anterior domain reminiscent of a cardiac crescent before forming a beating cardiac tissue near a putative primitive gut-like tube, from which it is separated by an endocardial-like layer. These findings unveil the surprising morphogenetic potential of mESCs to execute key aspects of organogenesis through the coordinated development of multiple tissues. This platform could be an excellent tool for studying heart development in unprecedented detail and throughput.

For data exploration, execute in R-Studio Explore_Data.R in
https://github.com/nbroguiere/Cardiac_Gastruloids

overall_design: 10x single-cell RNA-seq of gastruloids at day 4, 5, 6 and 7, in duplicates.

first: Giuliana

last: Rossi

first: Matthias

last: Lutolf


title: HUR affected genes in human skin cells

status: Public on Nov 20 2020

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

institute: Jiangsu Jiangyin People's Hospital

summary: This study aims to evaluate the effect of HUR overexpression and  knokdown on the function and global gene expression in human skin cells. Cells with HUR overexpression and silencing were compared with control cells by RNA-Seq.

first: D

last: Yu


title: mRNA-seq analyses for the differentially expressed genes (DEGs) among Con, NF VM-astrocytes, Ctx-astrocytes, and control Ctx-NPCs

status: Public on Oct 25 2020

city: Seoul

first: Jae-Jin

last: Song

address: 222, Wangsimni-ro

department: Hanyang Biomedical Research Institute

institute: Hanyang university

summary: To gain further molecular insight into the observed astrocyte functions, we performed RNA-sequencing (RNA-seq) analysis of the differentiated Ctx-NPCs (control), Ctx-astrocytes and VM-astrocytes used in the co-culture and CM experiments. The genes that are differentially expressed (DEGs) in Ctx-astrocytes compared to differentiated Ctx-NPCs (FPKM>1, log2>1) significantly overlapped with DEGs in VM-astrocytes compared to differentiated Ctx-NPCs

overall_design: 5 mouse sample: mNPC-CTX, mAST-VMC, mAST-VMNF, mAST-CTX, mAST-VM

first: Sang-Hun

last: Lee


title: Trancriptom sequencing of detoxification in Aphis craccivora

status: Public on Nov 13 2020

city: jinan

first: Yuanxue

last: Yang

state: Shandong

address: No.202 Gongyebei Road

institute: Shandong Academy of Agricultural Sciences

summary: Through transcriptome, thirty-eight P450 genes were identified in Aphis craccivora, and most of the genes belonged to the CYP3 and CYP4 Clans. Ten GST genes were identified, including two Delta genes which play important roles in xenobiotic detoxification.

overall_design: The response of dexification after imidacloprid treatment

first: Ming

last: Zhao

first: Jianhua

last: Zhang


title: RNA-seq of Wnt7b overexpressing bone

status: Public on Dec 06 2020

city: Chengdu

first: Fanyuan

state: Sichuan

address: No.14, 3rd Section, Ren Min Nan Rd

department: Endodontics

institute: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology

summary: We report the application of RNA sequencing technology for high-throughput profiling of gene expression in Wnt7b overexpressing bone and wide-type bones.To increase Wnt7b in bone we crossed 9.6kb DMP1-Cre mice and R26-Wnt7b mice. 9.6kb DMP1-Cre; R26-Wnt7b mice were set as OE mice meanwhile their littermates of R26-Wnt7b were controls (Ctrl). Owing to heterozygotes and homozygotes of OE mice didn’t show any different phenotypes all OE mice used in this study were homozygotes. Total mRNA of femur was collected from 8-week-old OE and Ctrl mice respectively. Fresh femur samples without soft tissues were rapidly collected within 2 min after euthanasia. And then samples were immediately transported into a sterile 10cm culture dish containing cold PBS, followed with articular cartilage removal via sterile lancets within 5 min, being flushed 3 times using sterile cold PBS to remove marrow cells and being chopped into 2~5mm fragments using sterile scissors. About 200mg bone fragments were collected into a sterile mortal containing 1ml liquid nitrogen and then were crushed and homogenized using a sterile pestle within 5 min, followed by a sterile scalpel until the tissue was adequately homogenized. Homogenized samples were collected into a 2-ml sterile tube, followed with 1 ml TRIzol ® (Invitrogen, CA, USA) solution added. Then all the extraction procedures were conducted according to manufacture’s instructions for RNA extraction from homogenized tissues.  After quality checks they were subjected to the high-throughput RNA-sequencing. Every group consists of 3 replicates which were from 3 different mice.

overall_design: Examination of RNA expression in OE and Ctrl bones free of cartilage and marrow cells.

first: Ling

last: Ye


title: Transcriptional variation in the yeast Yarrowia lipolytica depending on substrate and pH conditions applied in bioreactor cultivations

status: Public on Oct 08 2020

city: Vienna

first: Michael

last: Egermeier

address: Muthgasse 18

country: Austria

institute: University of Natural Resources and Life Sciences

summary: Yarrowia lipolytica exhibits phenotypic variations depending on external triggers like substrate and pH conditions. The purpose of this study was to create a dataset to unravel the transcriptional regulation behind the observed phenotype.

overall_design: Total RNA extraction and RNA-seq were performed on biomass samples taken during bioreactor cultivations of Yarrowia lipolytica on glucose or glycerol as carbon source and varying pH conditions (3.5 and 5.5). Biomass samples were taken in biological triplicates during growth phase and during N-limited stationary phase.

first: Pauline

last: Trébulle


title: Single cell analysis reveals onset of multiple progression associated transcriptomic remodellings in prostate cancer

status: Public on Oct 22 2020

first: Guanghui

last: Zhu

address: 8 Linyin Street

institute: Sichuan University

summary: Dissecting heterogeneity of prostate tumors is a clinical imperative. Here, we analyzed the transcriptomes of 36,424 single-cells from 13 prostate tumors, and identified lineage specific epithelial cells underlying disease aggressiveness. Activation of various progression-associated transcriptomic programs exists in the tumor microenvironment (TME). Notably, we observed promiscuous KLK3 expression in TME and validated the ability of tumor-derived exosomes in altering T cell transcriptomes. Single-cell profiling of a high-risk patient tumor and lymph nodes provided evidence that KLK3 ectopic expression is associated with micrometastases. Close cell-cell communication exists among tumor and TME cells. We identified an endothelial subset harboring active communication (aEC) with tumor cells. Together with sequencing of an additional 11 samples, we showed that aECs are enriched in castration-resistant prostate cancer and promote cancer cell invasion. Finally, we created a user-friendly web interface (www.pradcellatlas.com) for the sequenced data as a resource for the research community.

overall_design:
The 13 prostate tumor samples used in this study were collected from patients who had undergone radical prostatectomy at Shanghai Changhai Hospital. Single cell RNA sequencing was performed with 10XGenomics.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Shancheng

last: Ren


title: Setdb1 regulates Cohesin at H3K9me3-independent topological domains

first: Chadi

last: El Farran

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

overall_design: Refer to individual Series


title: Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues

status: Public on Oct 01 2020

city: Allen

first: Wei

last: Lin

state: TX

address: 1525 Evanvale Dr.

country: USA

institute: Translational Genomics Research Institute

summary: The single-cell RNA profiles of dissociated 10 pancreatic primary tumors and 6 metastatic biopsies were obtained using the 10x Genomics Chromium platform

overall_design: Tissues were dissciated using a tumor dissociation kit (Miltenyi Biotec) on a gentleMACSTM Dissociator. Single cell RNA-sequencing was carried out using using the Chromium Single Cell Gene Expression Solution system (v2) by 10x Genomics and an Illumina HiSeq4000 sequencer.

first: Pawan

last: Noel

first: Haiyong

last: Han


title: Dynamic IFNβ signalling underlies treatment response to immune checkpoint therapy in cancer [bulk RNA-seq]

status: Public on Dec 07 2020

city: Perth

first: Wee Loong

last: Chin

address: Level 5, Qq Block, Qeii Medical Centre 6 Verdun St, Nedlands

country: Australia

institute: National Centre For Asbestos Related Diseases

summary: The on/off dynamics of IFNβ signalling underlie the therapeutic response to immune checkpoint therapy in cancer, which can be exploited to sway the clinical trajectory in favour of response

overall_design: 144 samples, 72 from AB1 tumours and 72 from Renca tumours. Samples taken at 4 time points: 1 hour prior to checkpoint blockade (24 samples) , 2 days after (16 samples) , 4 days after (16 samples), 6 days after (16 samples). Equal number of samples were taken from mice that respond and did not respond to checkpoint blockade.

first: Rachael

last: Zemek

first: Willem

last: Lesterhuis


title: Induction of antitumor activity of CD8+ T cells by inactivation of ATPIF1 through F1Fo-ATPase-mediated metabolic reprogramming

status: Public on Sep 22 2020

city: Xinxiang

first: Genshen

last: Zhong

state: Henan Province

address: Jinsui Road, 601#

country: China

institute: Xinxiang Medical University

summary: In this study, CD45+ leukocytes were sorted from the mixed tumor samples, which were collected from the C57BL/6 wild type mice and ATPIF1 knock-out mice, respectively. The live CD45+ cells were used for single cell RNA sequencing and TCR sequencing.

overall_design: B16 melanoma cells were implanted in the right flank of male WT and KO mice (n=6). On day 12, the tumors were dissected from the surrounding fascia, mechanically minced to approximately 1 mm3 pieces, then the tumor tissue suspension from KO mice was mixed together, so did the tumor tissue suspension from WT mice. After that, the mixed tumor tissue suspension was stored in a solution provided by the Beijing Analytical Biosciences Technology Co., Ltd, a company specialize at single cell RNA sequencing and data analysis, which is founded by the Professor Zhang Zemin in Peking University, Beijing, China. The samples of WT and KO mice were sent to this company for CD45+ T cell sorting immediately and single cell RNA-seq. The preparation of tumor single cell suspension, the CD45+ tumor-infiltrating leukocytes sorting, reverse transcription, amplification, sequencing, the quality control, scRNA-seq data processing, cluster analysis, trajectory analysis, STARTRAC analysis and RNA velocity-based cell fate tracing were all performed in the Beijing Analytical Biosciences Technology Co., Ltd, which was described in detail in two studies

first: Wang

last: Ying

first: Jiaojiao

first: Jianping


title: Neurodegeneration and Neuroinflammation are Linked, but Independent of α-Synuclein Inclusions, in a Seeding/Spreading Mouse Model of Parkinson’s Disease

status: Public on Nov 02 2020

city: Belvaux

first: Enrico

last: Glaab

state: Capellen

address: 6, avenue du Swing

country: Luxembourg

institute: University of Luxembourg

summary:
A key process of neurodegeneration in Parkinson's disease (PD) is the transneuronal spreading of alpha-synuclein. Alpha-synuclein is a presynaptic protein that is implicated in the pathogenesis of PD and other synucleinopathies, where it forms, upon intracellular aggregation, pathological inclusions. Other hallmarks of PD include neurodegeneration and microgliosis in susceptible brain regions. Whether it is primarily transneuronal spreading of a-synuclein particles, inclusion formation, or other mechanisms, such as inflammation, that cause neurodegeneration in PD is unclear.
We used spreading/aggregation of alpha-synuclein induced by intracerebral injection of a-synuclein preformed fibrils into the mouse brain to address this question. We performed quantitative histological analysis for a-synuclein inclusions, neurodegeneration, and microgliosis in different brain regions, and a gene expression profiling of the ventral midbrain, at two different timepoints after disease induction. We observed significant neurodegeneration and microgliosis in brain regions not only with, but also withouta-synuclein inclusions. We also observed prominent microgliosis in injured brain regions that did not correlate with neurodegeneration nor with inclusion load. In longitudinal gene expression profiling experiments, we observed early and unique alterations linked to microglial mediated inflammation that preceded neurodegeneration, indicating an active role of microglia in inducing neurodegeneration. Our observations indicate that a-synuclein inclusion formation is not the major driver in the early phases of PD-like neurodegeneration, but that diffusible, oligomeric a-synuclein species, which induce unusual microglial reactivity, play a key role in this process.

overall_design: C57Bl6/J mice were injected intrastriatally with 10 microgram alpha-synuclein pre-formed fibril or vehicle PBS. Mice were euthanised 13 days or 90 days post injection (13 dpi, 90dpi), and transcriptional profiles (Affymetrix chips) were generated from isolated ventral midbrains from the ipsilateral (ipsi) and contralateral (contra) brain hemispheres

first: Pierre

last: Garcia

first: Wiebke

middle: M

last: Wemhauer

first: Oihane

last: Uriarte

first: Kristopher

last: Schmit

first: Annette

last: Masuch

first: Simone

last: Brioschi

first: Andreas

last: Weihofen

first: Eric

last: Koncina

first: Djalil

last: Coowar

first: Glaab

last: Enrico

first: Rudi

last: Balling

first: Carole

last: Sousa

first: Alessandro

last: Michelucci

first: Tony

last: Kaoma

first: Nathalie

last: Nicot

first: Tatjana

last: Pfander

first: Walter

last: Schulz-Schaeffler

first: Ahmad

last: Allouche

first: Nicolas

last: Fischer

first: Knut

last: Biber

first: Michel

last: Mittelbronn

first: Manuel

last: Buttini


title: Epigenomic translocation of H3K4me3 broad domains following super-enhancer hijacking

status: Public on Aug 12 2020

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

institute: Newcastle University

summary: Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with super-enhancers, often called super-enhancer hijacking. We analysed the epigenomic consequences of rearrangements between the enhancers of the immunoglobulin heavy chain locus (IGH) and proto-oncogene CCND1 that are common in B-cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterised the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B-cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of this locus. We observed similar cancer-specific H3K4me3-BDs associated with super-enhancer hijacking of other common oncogenes in B-cell (MAF, MYC and FGFR3) and in T-cell malignancies (LMO2, TLX3 and TAL1). Our analysis suggests that H3K4me3-BDs are created by super-enhancers and supports the new concept of epigenomic translocation, where the relocation of H3K4me3-BDs accompanies the translocation of super-enhancers.

overall_design: Myeloma cell lines KMS11 and MM1S were analysed using ChIP-seq of six histone marks (H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27Ac, and H3K36me3) to study H3K4me3 broad domain at proto-oncogenes involved in genomic translocations. ChIP-seq data of T-cell acute lymphoblastic leukemia cell line PEER was used to observe changes in H3K4me3 and H3K27ac profiles at TAL1 locus after CRISPR-Cas9 editing that introduced upstream 12bp insertion known from Jurkat cell line.

first: Dan

last: Kent

first: Nefeli

last: Karataraki

first: Marco

last: Trevisan-Herraz

first: Kent

middle: F

last: Fung

first: Cody

last: Ashby

first: Shmuel

last: Yaccoby

first: Vahid

last: Asnafi

first: Agata

last: Cieslak

first: Gareth

last: Morgan

first: Salvatore

last: Spicuglia

first: Chris

last: Brackley

first: Anne

last: Corcoran

first: Sophie

last: Hambleton

first: Brian

last: Walker

first: Daniel

last: Rico

first: Lisa

last: Russell


title: Genome-wide characterization of platinum persister ovarian cancer (OC) cells with upregulation of Wnt pathway receptor, Frizzled 7 (FZD7)

city: Chicago

first: Daniela

middle: Elena

last: Matei

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: The goal of this study is to define molecular signature of platinum persister OC cells characterized by FZD7, and investigate the functional role of FZD7 relative to stemness and chemo-responsiveness.

overall_design: 1) Define transcriptional signatures of SKOV3/OVCAR5 cisplatin resistant ovarian cells versus wild types (in biological triplicates); 2) Examine transcriptome of ovarian cancer stem cells (OCSCs) (OVCAR5_ALDH(+)CD133(+) DP) and non-OCSCs (OVCAR5_ALDH(-)CD133(-) DN) (in biological duplicates); 3) Define transcriptional signatures of platinum persister OVCAR5_FZD7(+) OC cells versus OVCAR5_F ZD7(-) cells (in biological duplicates)

first: Yinu

last: Wang

first: Horacio

last: Cardenas

first: Hao

last: Huang

first: Guangyuan

last: Zhao


title: mRNA and lncRNA gene expression profile of nasopharyngeal carcinoma

status: Public on Aug 01 2020

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: Analysis of 16 laser-captured, microdissected nasopharyngeal carcinoma (NPC) tissues samples. NPC is an Epstein-Barr virus (EBV)-associated epithelial cancer prevalent in Southeast Asia. Results provide insight into the molecular mechanisms involved in EBV-associated epithelial cancers.

overall_design: Total RNA extracted from laser-captured epithelium from 10 nasopharyngeal carcinomas and 6 normal healthy nasopharyngeal tissue specimens.

first: Fang

first: Zhaoyang

last: Zeng

first: Guiyuan

last: Li


title: RNAseq of 11 subsets of developing human postnatal thymocytes

status: Public on Jul 29 2020

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

institute: Genentech

summary: The generation of TCRαβ and TCRγδ T cells proceeds through distinct developmental stages in which changing regulatory events control differentiation and lineage outcome. To clarify the underlying mechanisms, we employed RNAseq, ATACseq and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics uncover stage-specific regulatory mechanisms and reveal that human T-lineage commitment is marked by the GATA3- and BCL11B-dependent closing of PU.1 sites. While the ß-selection checkpoint is marked by transcriptional changes and a temporary increase in H3K27me3 without modifications in open chromatin, emerging γδ T cells, that originate from common precursors as ß-selected cells, show dramatic changes in chromatin accessibility which results from strong TCR signaling. Furthermore, we unravel distinct chromatin landscapes between CD4 and CD8 αβ T cells that support their effector functions and reveal gene-specific regulatory mechanism that define mature T cells. This resource provides an important framework for studying gene regulatory mechanisms that drive human normal and malignant T cell development.

overall_design: RNAseq of 11 ex-vivo sorted postnatal human thymocyte populations for two biological replicates

first: Anna

last: Kuchmiy

first: Tom

last: Taghon


title: Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

status: Public on Dec 01 2020

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

summary: Identification of SMC1a and Setdb1 bound-loci in E14 mESCs.

overall_design: ChIP-Seq of Setdb1 and SMC1a in wild-type E14 mESCs and Setdb1-depleted E14 mESCs.

first: T

last: Warrier

first: C

middle: A

last: EL Farran

first: H

first: Y

middle: H

last: Loh