title: RNA-SEQ Quantitative Analysis of the regulation of c-Mpl-del on survival related gene transcriptome in AMKL cells

status: Public on Feb 27 2020

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

summary: In the previous studies, we reported that c-Mpl alternative splicing form c-Mpl-del overexpressed in acute megakaryoblasttic leukemia (AMKL) patients and mediated thrombopoietin signaling to promote AMKL cells malignant proliferation and chemotherapy resisitance. To investigate the detailed mechanism of c-Mpl-del mediated AMKL cells survival and chemotherapy resisitance, the AMKL cell Dami stably expressing GFP, c-Mpl-del-GFP or c-Mpl-p-GFP were established by transduction with GFP, c-Mpl-del-GFP or c-Mpl-p-GFP lentiviruses and treated with or without Ara-c (10μM) in the presence of 20ng/mL TPO for RNA-SEQ analysis to exame the expression of survival-related genes. Our results indicate that the levels  of  the "leading edge" genes that account for survival and prolieration are significantly higher in c-Mpl-del overexpressed AMKL cells. Meanwhile, the expression of c-Mpl-del promotes the tolerance of AMKL cells to Ara-c.

overall_design: Examination of GFP control group, c-Mpl-del or  c-Mpl-p overexpressed group and Ara-c treated control group and c-Mpl-deloverexpressed group

first: Qing

last: Zhang


title: Gene-expression profiles of multi-stage hepatocellular carcinoma induced by diethylnitrosamine (DEN) in mouse model

status: Public on Jan 10 2020

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

summary: To better characterize the pathogenesis of hepatocarcinogenesis, we established mouse HCC model by diethylnitrosamine (DEN) exposures and performed whole genome expression profiling.

overall_design: Total was extracted from frozen liver samples from vehicle-control and DEN treated mice. Histologic classification of adenomas (n=7), eHCCs (n=11), and aHCCs (n=7) was performed.

first: Jung-Woo

first: Suk-Woo

last: Nam


title: Analysis of DNA Methylome Profiles in Cattle with Divergent Tenderness

status: Public on Feb 01 2020

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

country: China

institute: GENEDOHEALTH

type: Methylation profiling by high throughput sequencing

summary: Beef constitutes one of the main food sources worldwide due to its high quality protein and other nutrients. Beef tenderness is one of the most important factors influencing the edible quality. To date, a large number of molecular studies have focused on the exploration of mechanisms to form beef tenderness. DNA methylation is the most studied epigenetic modification and research revealed that DNA methylation plays important roles in diverse process. However, the genome-wide DNA methylation regulation on beef quality and tenderness remains unknown. In this study, we reported the DNA methylome profiling related to divergent tenderness of beef. We found that more reads are harbored in the intron, exon and repeat elements of genes of beef. We identified the DMRs between tender and tough beef. And results showed that DNA methylation levels in different part of genome or divergent tenderness are significantly differed. Then we annotated the DMRs and identified the top pathways DMRs are involved in. Meanwhile, we also explored the relationship between DNA methylation and gene expression. This study describes the detail DNA methylome profiling related with beef quality and may provide new strategies for exploring the mechanism of beef quality.

overall_design: Whole genome MBD-seq for Angus cattle to explore the differential methylation between tender and tough beefs.

first: Chunping

last: Zhao

first: José

middle: A

last: Carrillo

first: Yaokun

first: Juan

last: Luo

last: Tian

first: Linsen

last: Zan

first: Jiuzhou

last: Song


title: MiRNA profiles of high grade serous papillary ovarian cancer tumors and normal fallopian tube epithelium

status: Public on Dec 31 2019

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

summary: Fallopian tube epithelium is the tissue-of-origin of most high grade serous papillary ovarian carcinoma. This tumor has been exensively investigated and sequenced but expression profiling data of normal fallopian tube epithelial cells is still rare. This project compares the miRNA profiles of high grade serous papillary ovarian tumors (FFPE and fresh frozen) to that of normal unmatched epithelial cells from resected fallopian tubes.

overall_design: Total RNA was extracted using miRNeasy kit (QIAGEN) from FFPE ovarian cancer specimens, fresh frozen ovarian cancer specimens and fresh frozen fallopian tube epithelium.

first: Hadar

last: Brand

first: Jasmine

first: Keren

last: Levanon


title: Gene expression data of mRNA from hypothalamus sample of pig breed German Landrace with different coping behavior haplotype

status: Public on Jan 01 2020

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

summary: 47,880 probe-sets were screened, in the first part of this study, they were analysed for differential expression between two groups differing in  coping behavior associated haplotype

overall_design: RNAs of hypothalamus from German Landrace at adult stage were hybridized to Affymetrix Porcine Snowball Array.

first: Klaus

last: Wimmers


title: Single cell RNA-seq revealed critical genetic programs of invasive fibroblasts for pulmonary fibrosis

city: Los angeles

first: Xue

last: Liu

state: CA

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

country: USA

institute: Cedars-Sinai Medical Center

type: Expression profiling by high throughput sequencing

summary: We performed a single cell RNA-seq survey of 14,704 invasive fibroblasts and 16,104 non-invasive fibroblasts using an in vitro assay system which had been previously used to evaluate the ability of lung fibroblasts to spontaneously invade Matrigel and commonly used to analyze the metastatic potential of cancer cells. Different subtypes in invasive or non-invasive lung fibroblasts were classified, and their gene signatures, specific cell surface markers, long non-coding RNA (lncRNA), key transcription factors and signaling pathways were further confirmed mechanistically and functionally. After combination of all the specific genes for Ingenuity Pathway Analysis (IPA), we found that the ERBB2 (HER2) signaling pathway was significantly activated in invasive fibroblasts and was markedly inhibited in non-invasive fibroblasts.

overall_design: Profiling invasive and non-invasive fibroblasts of lung fibroblasts from Idiopathic pulmonary fibrosis

first: Dianhua

last: Jiang


title: Identification of molecular pathways associated with early life coping behavior in pigs

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

overall_design: Refer to individual Series


title: Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis

status: Public on Feb 07 2020

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital


title: Bulk RNA-seq on SEMA7A high and negative Idiopathic pulmonary fibrosis (IPF) lung fibroblasts

summary: To check the gene signatures of SEMA7A high and SEMA7Anegative IPF lung fibroblasts and the similarity of SEMA7A high fibroblasts and invasive fibroblasts, SEMA7A negative fibroblasts and noninvasive fibroblasts, we sorted the SEMA7A high and negative IPF lung fibroblasts by flow cytometry and performed total RNA-seq.

overall_design: Define the gene expression profile of SEMA7A high and negative fibroblasts


title: Gene expression data of mRNA from hippocampus sample of pig breed German Landrace with different coping behavior haplotype

overall_design: RNAs of hippocampus from German Landrace at adult stage were hybridized to Affymetrix Porcine Snowball Array.


title: Gene expression data of mRNA from amygdala sample of pig breed German Landrace with different coping behavior haplotype

overall_design: RNAs of amygdala from German Landrace at adult stage were hybridized to Affymetrix Porcine Snowball Array.


title: Analysis of the expression profile of skin fibroblasts FACS-sorted from mice overexpressing activin and/or oncogenes of human papilloma virus 8 in keratinocytes.

status: Public on Mar 01 2020

city: Chicago

first: Mateusz

middle: S

last: Wietecha

state: IL

address: 801 S Paulina St

department: Oral Biology

institute: University of Illinois Chicago

summary: Overexpression of activin by keratinocytes promotes HPV8-induced skin tumorigenesis in mice. Activin-promoted tumorigenesis is mediated via the stroma, specifically by cancer-associated fibroblasts (CAFs). To determine if activin alters the gene expression profile of skin fibroblasts, we performed RNA-sequencing of fibroblasts FACS-sorted from pre-cancerous ear skin of activin overexpressing mice. We found that activin induces a CAF-like gene expression profile of fibroblasts, leading to the upregulation of genes involved in proliferation, migration and cytoskeletal remodeling.

overall_design: CD45-CD140a+ cells were FACS-sorted from the pre-cancerous ear skin of wt/wt, HPV8/wt, wt/Act and HPV8/Act mice and their expression profile was analysed by RNA-Sequencing. Experiment was performed in triplicates; for each replicate ear skin of 3-6 mice of corresponding genotype was pooled.

first: Maria

last: Antsiferova

first: Sabine

last: Werner


title: Subcutaneous fat transcriptome in obstructive sleep apnea and after treatment with CPAP

status: Public on Dec 21 2019

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

summary: Obstructive sleep apnea (OSA) has been linked to dysregulated metabolic states and treatment of sleep apnea may improve these conditions. Subcutaneous adipose tissue is a readily samplable fat depot that plays an important role in regulating metabolism. However, neither the pathophysiologic consequences of OSA nor the effects of continuous positive airway pressure (CPAP) in altering this compartment’s molecular pathways are understood. This study aimed to systematically identify subcutaneous adipose tissue transcriptional programs modulated in OSA and in response to its effective treatment with CPAP.  Two subject groups were investigated: Study Group 1 was comprised of 10 OSA and 8 controls; Study Group 2 included 24 individuals with OSA studied at baseline and following CPAP. For each subject, genome-wide gene expression measurement of subcutaneous fat was performed. Differentially activated pathways elicited by OSA (Group 1) and in response to its treatment (Group 2) were determined using network and Gene Set Enrichment Analysis (GSEA). In Group 2, treatment of OSA with CPAP improved apnea hypopnea index, daytime sleepiness, and blood pressure, but not anthropometric measures. In Group 1, GSEA revealed many up-regulated gene sets in OSA subjects, most of which were involved in immuno-inflammatory (e.g., interferon-γ signaling), transcription, and metabolic processes such as adipogenesis. Unexpectedly, CPAP therapy in Group 2 subjects was also associated with up-regulation of several immune pathways as well as cholesterol biosynthesis. Collectively, our findings demonstrate that OSA alters distinct inflammatory and metabolic programs in subcutaneous fat, but these transcriptional signatures are not reversed with short-term effective therapy.

overall_design: Total RNA was isolated from subcutaneous fat in two Study Group designs: 1) 10 subjects with OSA vs. 8 controls; 2) 24 subjects with OSA at baseline vs. after effective CPAP therapy. Each sample was hybridized to an GeneChip Human Gene 1.0 ST Affymetrix microarray for a total of 66 experiments.


title: Targeted pharmacological therapy restores β-cell function for diabetes remission

status: Public on Feb 20 2020

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

institute: Helmholtz Zentrum Munich

summary: This dataset consists of single-cell RNA-seq (10X) data from disperesed pancreatic islets of healthy and STZ induced diabetic mice. STZ (Sigma) was injected intraperitoneally in 8-week old male C57BLJ/6 mice at 50 mg/kg for five consecutive days. Islets were isolated from healthy mice and STZ diabetic mice after 100 days of either vehicle or drug treatment.

overall_design: 7 single cell RNA seq experiments of isolated pancreatic islets from adult mice were performed using 10X Genomics technology to generate single cell transcriptomic profiles of healthy and STZ diabetic mice treated with either vehicle or drugs.

first: Stephan

last: Sachs

first: Aimee

last: Bastidas-Ponce

first: Mostafa

last: Bakhti

first: Anika

last: Böttcher

first: Miguel

last: Sánchez-Garrido

first: Marta

last: Tarquis-Medina

first: Maximilian

last: Kleinert

first: Katrin

last: Fischer

first: Sigrid

last: Jall

first: Alexandra

last: Harger

first: Siegfried

last: Ussar

first: Anette

last: Feuchtinger

first: Bin

last: Yang

first: Brian

last: Finan

first: Richard

last: DiMarchi

first: Matthias

middle: H

last: Tschöp

first: Fabian

middle: J

last: Theis

first: Susanna

middle: M

last: Hofmann

first: Timo

middle: D

last: Müller

first: Heiko

last: Lickert


title: FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer

status: Public on Dec 18 2019

city: Houston

first: Xiaoyong

last: Fu

state: Texas

address: 1 Baylor Plaza

institute: Baylor College of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing


title: FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer [RNA-seq]

summary: Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Here, we have demonstrated that FOXA1 overexpression in estrogen receptor-positive breast cancer cells drives genome-wide enhancer reprogramming to activate pro-metastatic transcriptional programs. We have identified the hypoxia-inducible transcription factor HIF-2α as the top FOXA1-engaged super-enhancer target induced by FOXA1 overexpression, activating pro-metastatic gene signatures associated with poor breast cancer outcome. Using two different siRNA sequences, we identified 917 and 1,107 genes commonly down- and up-regulated (FDR < 0.05), respectively, upon HIF-2α knockdown in tamoxifen-resistant MCF7L cells. The enriched GO terms of the down-regulated genes were predominantly linked to tumor metastatic traits. GSEA showed that this HIF-2α-dependent gene set was significantly enriched in the transcriptomes of the TCGA ER+ breast tumors expressing high HIF-2α, but not high HIF-1α. We show the selective efficacy of a HIF-2α antagonist (PT2385), currently in clinical trial for renal cell carcinoma, in repressing migration and clonogenicity of endocrine-resistant breast cancer cells expressing high FOXA1. Our study suggests that targeting HIF-2α is a new approach blocking the aberrant transcriptional programs under high FOXA1-induced enhancer reprogramming in treating endocrine-resistant and metastatic breast cancer.

overall_design: RNA-Seq of tamoxifen-resistant MCF7L cells with control or HIF-2α siRNA knockdown, in triplicate, using Illumina NextSeq500.

first: Rachel

last: Schiff

first: Rinath

last: Jeselsohn

first: Myles

last: Brown


title: CD29 identifies IFN-γ–producing human CD8+ T cells with an increased cytotoxic potential

status: Public on Mar 20 2020

city: Amsterdam

first: Monika

middle: C

last: Wolkers

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Blood foundation

summary: Cytotoxic CD8+ T cells can effectively kill target cells by producing cytokines, chemokines, and granzymes. Expression of these effector molecules is however highly divergent, and tools that identify and preselect CD8+ T cells with a cytotoxic expression profile are lacking. Human CD8+ T cells can be divided into IFN-γ– and IL-2–producing cells. Unbiased transcriptomics and proteomics analysis on cytokine-producing fixed CD8+ T cells revealed that IL-2+ cells produce helper cytokines, and that IFN-γ+ cells produce cytotoxic molecules. IFN-γ+ T cells expressed the surface marker CD29 already prior to stimulation. CD29 also marked T cells with cytotoxic gene expression from different tissues in single-cell RNA-sequencing data. Notably, CD29+ T cells maintained the cytotoxic phenotype during cell culture, suggesting a stable phenotype. Preselecting CD29-expressing MART1 TCR-engineered T cells potentiated the killing of target cells. We therefore propose that CD29 expression can help evaluate and select for potent therapeutic T cell products.

overall_design: 12 samples in total, 3 biological replicates (each a pool of 40 CD8+ Blood donors)

first: Benoit

middle: P

last: Nicolet

first: Aurelie

last: Guislain

first: Floris

last: van Alphen

first: Maartje

last: van den Biggelaar

first: Raquel

last: Gomez-Eerland

first: Ton

middle: N

last: Schumacher


title: FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer [ChIP-seq]

summary: Forkhead box A1 (FOXA1) is a pioneer factor that facilitates chromatin binding and function of lineage-specific and oncogenic transcription factors. Here, we have demonstrated that FOXA1 overexpression in estrogen receptor-positive breast cancer cells drives genome-wide enhancer reprogramming to activate pro-metastatic transcriptional programs. Specifically, FOXA1 overexpression generated more gained chromatin binding regions than the lost regions with decreased FOXA1 binding. Furthermore, FOXA1 overexpression led to establishment of more gained enhancers marked with increased H3K27ac and/or H3K4me1 than the lost enhancers with decreased signals of these two histone marks. In addition, these altered enhancers were highly coordinated with FOXA1-chromatin binding (cistrome) and the alteration of transcriptome due to FOXA1 overexpression, suggesting the direct engagement of high FOXA1 in enhancer reprogramming. The coordination between FOXA1 cistrome, enhancer reprogramming, and transcriptome also exists in the tamoxifen-resistant MCF7 cell model with endogenous FOXA1 gene amplification. Overall, our study supports the notion that FOXA1 overexpression promotes enhancer reprogramming in ER-positive breast cancer to activate gene expression associated with endocrine resistance and metastasis.

overall_design: Examination of FOXA1-chromatin binding and 2 different enhancer histone modifications in endocrine-sensitive and resistant breast cancer cell models.

first: Qin

last: Feng

first: Bert

middle: W

last: O’Malley


title: Deregulation of ribosomal protein expression and translation promotes breast cancer metastasis [rna-Seq CTCs 1]

first: Ben

last: Wittner

summary: We conducted an in vivo genome-wide CRISPR activation screen to identify genes that accelerate distal metastasis by breast cancer patient-derived circulating tumor cells (CTCs) following direct intravascular inoculation in mice. Regulators of translation and ribosomal proteins were prominent among these, and expression of RPL15, a component of the large ribosome subunit, was sufficient to increase metastatic growth in multiple organs. RPL15 overexpression selectively increases translation of other ribosomal proteins and cell cycle regulators. Unsupervised analysis of single-cell RNA sequencing of freshly-isolated CTCs from breast cancer patients identifies a subset with strong ribosomal and protein translation signatures, correlated with increased proliferative markers, epithelial markers and poor clinical outcome. Thus, ribosome protein expression identifies an aggressive subset of CTCs, whose therapeutic targeting may suppress metastatic progression.

overall_design:
The CTC-iChip microfluidic device [PMID: 23552373 ] enables isolation of rare viable circulating tumor cells (CTCs) directly from whole blood specimens of patients with cancer, with RNA quality compatible with single-cell RNA sequencing (RNA-seq). We generated RNA-seq profiles of 135 freshly isolated single CTCs or CTC-clusters from 45 women with hormone receptor positive metastatic breast cancer.
GEO platform GPL16288. See platform.xls for a description of the IDs in readCounts.xls

first: Richard

middle: Y

last: Ebright

first: Sooncheol

last: Lee

first: Kira

middle: L

last: Niederhoffer

first: Benjamin

middle: T

last: Nicholson

first: Aditya

last: Bardia

first: Samuel

last: Truesdell

first: Devon

middle: F

last: Wiley

last: Wesley

first: Selena

last: Li

first: Andy

last: Mai

first: Nicola

last: Aceto

first: Nicole

last: Vincent-Jordan

first: Annamaria

last: Szabolcs

first: Brian

last: Chirn

first: Johannes

last: Kreuzer

first: Valentine

last: Comaills

first: Mark

last: Kalinich

first: Wilhelm

last: Haas

first: David

last: Ting

first: Mehmet

last: Toner

first: Shobha

last: Vasudevan

first: Daniel

last: Haber

first: Shyamala

last: Maheswaran

first: Douglas

last: Micalizzi


title: The human fetal thymus generates effector invariant γδ T cells in a Lin28b-dependent manner

status: Public on Nov 21 2019

city: Brussels

last: Vermijlen

address: Boulevard de Triomphe, accès 2 (CP205/3)

country: Belgium

institute: Université Libre de Bruxelles

summary: In the mouse thymus, invariant γδ T cells are generated at well-defined times during development and acquire effector functions before exiting the thymus. However, whether such thymic programming can occur in human is not known. Here we analyzed human fetal and post-natal γδ thymocytes and investigated the role of hematopoietic-stem-and-precursor-cells (HSPC) in the generation of human γδ T cells. Unlike post-natal γδ thymocytes, fetal γδ thymocytes were functionally programmed (e.g. IFNγ, granzymes), expressed low levels of terminal-deoxynucleotidyl-transferase (TdT) and were highly enriched for invariant/public germline-encoded CDR3 sequences (TRGV8-TRJP1-CATWDTTGWFKIF, TRDV2-TRDD3-CACDTGGY and TRDV1-TRDD3-CALGELGD, previously shown to be expanded in cytomegalovirus infection) composed of short-homology-repeat-containing gene segments. Furthermore, these unique characteristics were due to an intrinsic property of fetal HSPC caused by high expression of the RNA-binding protein Lin28b. In conclusion, our data indicate that the human fetal thymus generates, in a HSPC/Lin28b-dependent manner, invariant γδ T cells with programmed effector functions.

overall_design: analysis of  human fetal and post-natal γδ thymocytes and the role of hematopoietic-stem-and-precursor-cells (HSPC) in the generation of human γδ T cells.

first: Paola

last: Tieppo

first: Maria

last: Papadopoulou

first: Deborah

last: Gatti

first: Naomi

last: McGovern

first: Jerry

last: Chan

first: Françoise

last: Gosselin

first: Glenn

last: Goetgeluk

first: Karin

last: Weening

first: Ling

last: Ma

first: Nicolas

last: Dauby

first: Alexandra

last: Cogan

first: Catherine

last: Donner

first: Florent

last: Ginhoux

first: Bart

last: Vandekerckhove


title: FACT mediates cohesin function on chromatin

status: Public on Oct 11 2019

city: London

first: Jonay

last: Garcia-Luis

state: London

address: Du Cane Road

department: London Institute of Medical Sciences

country: United Kingdom

institute: UKRI

summary: Cohesin is a key regulator of genome architecture with roles in sister chromatid cohesion and the organisation of higher-order structures during interphase and mitosis. The recruitment and mobility of cohesin complexes on DNA are restricted by nucleosomes. Here we show that cohesin role in chromosome organization requires the histone chaperone FACT. Depletion of FACT in metaphase cells affects cohesin stability on chromatin reducing its accumulation at pericentric regions and binding on chromosome arms. Using Hi-C, we show that cohesin-dependent TAD (Topological Associated Domains)-like structures in G1 and metaphase chromosomes are disrupted in the absence of FACT. Surprisingly, sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our results uncover a role for FACT in genome organisation by facilitating cohesin dependent compartmentalization of chromosomes into loop domains.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Study of cohesin distribution and chromosome architecture in the presence and absence of the FACT complex subunit Spt16

first: Luis

last: Aragon


title: Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus [RNA-seq]

status: Public on Nov 22 2019

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Two subpopulations of low density granulocytes (LDGs) were defined in terms of different gene expression patterns, transcriptional and epigenetic features as well as functions. This study provides insights into the mechanism of immune dysregulation and the vascular damage characteristic of lupus.

overall_design: Transcriptomics and epigenetic assessment of lupus PBMCs, LDGs, autologous normal-density neutrophils (NDN) and healthy control (HC) neutrophils was performed by mRNA sequencing and assay for transposase-accessible chromatin sequencing. NET formation, chemotaxis, phagocytosis, degranulation, induction of endothelial dysfunction and release of oxidized nucleic acids were compared among subsets. This metadata sheet includes 51 RNA-Seq samples of this project.

first: P

last: Mistry

first: S

last: Nakabo

first: L

last: O’Neil

first: R

middle: R

last: Goel

first: K

last: Jiang

last: Gupta

last: Dell’Orso

first: G

last: Gutierrez-Cruz

first: H

first: M

last: Kaplan


title: Preventative and therapeutic effect of ∆pep27 intranasal vaccine in DSS-induced colitis

status: Public on Nov 06 2019

city: Suwon

first: Hamid

last: Iqbal

address: 2066 Seoburo, Jangan-gu Suwon

department: Pharmacy

institute: Sungkyunkwan University

summary:
∆pep27 diminished Dextran Sulfate Sodium-induced inflammatory effect in colonic tissue suggesting that ∆pep27 immunization reduces GUT inflammation and regulates junction proteins.
Analysis of global gene expression up-and downregulated in the colonic tissue and on the basis of that altered gene expression, molecular mechanism of ∆pep27 vaccine will be expressed.

overall_design: In this study a Pneumococcal ∆pep27 immune response is checked against Dextran Sulfate sodium murine model that mimics Inflmmatory bowel disease known to aggravate gut inflammation to check the inflammatory responses and the dynamics of host immune system interactions impact implicated in the disease.


title: Spontaneous direct fate conversion of neuroblasts into oligodendrocytes upon demyelination in the adult mouse brain

status: Public on Nov 25 2019

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 avenue Tony Garnier

department: Institut de Genomique Fonctionnelle de Lyon

country: France

institute: CNRS

summary: After demyelinating insult, the neuronal progenitors of the adult mouse sub-ventricular zone (SVZ) called neuroblasts convert into oligodendrocytes that participate to the remyelination process. We use this rare example of spontaneous fate conversion to identify the molecular mechanisms governing these processes. Using single cell RNA-sequencing, we show that SVZ neuroblasts fate conversion proceeds directly, through formation of a non-proliferating transient cellular state co-expressing markers of both neuronal and oligodendrocyte identities. Transition between the two identities starts immediately after demyelination and occurs gradually, by a stepwise upregulation/downregulation of key TFs and chromatin modifiers. Each step of this fate conversion involves fine adjustments of the transcription and translation machineries as well as tight regulation of metabolism and migratory behaviors. Together, these data constitute the first in-depth analysis of a spontaneous direct cell fate conversion in the adult mammalian CNS.

overall_design: NBL, OligNBL and OL single cells were dissociated from dissected SVZ and CC from demyelinated mice (8-10 weeks old, n=5 mice) 6 days after LPC injection, during the peak of cell mobilization in the SVZ. Control NB and O single cells were collected from healthy non-injected mice (8-10 weeks old, n=5 mice)

first: Claire

last: Bertet

first: Bilal

last: El Waly

last: Paris

first: Karine

last: Magalon

first: Marie

last: Falque

first: Pascale

last: Durbec


title: High-throughput sequencing of the human hepatic progenitor cell niche in PSC and HCV.

status: Public on Jul 29 2019

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: This study identified hepatic progenitor cell (HPC) niche-associated signalling pathways relevant in different chronic liver diseases using a high-throughput sequencing approach. The HPC niche was isolated using laser microdissection from patient samples diagnosed with hepatitis C virus (HCV) or primary sclerosing cholangitis (PSC), as models for hepatocellular or biliary regeneration.  Differentially expressed genes in the HPC niche of PSC and HCV correlated to pathways involved in immune signalling, fibrogenesis and angiogenesis.

overall_design: Cells (HPCs or hepatocytes) were isolated from frozen tissue using laser microdissection. RNA was amplified using the Clonetech SMARTER Ultra Low kit and processed for sequencing. Each sample was run on two lanes.

first: Olivier

last: Govaere


title: RNA expression data from calcified human carotid atherosclerotic plaques

status: Public on Jun 01 2019

city: Stockholm

first: Jesper

middle: Robert

last: Gådin

address: CMM, L8:02 Karolinska Universitetessjukhuset, Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

summary: Although unstable atherosclerosis in the carotid bifurcation is a significant etiology behind ischemic stroke, clinical imaging methods to distinguish stable from vulnerable lesions are lacking and selection of patients for stroke-preventive intervention still relies on surrogate variables with moderate predictive power, such as the degree of luminal narrowing. Here we combined clinical and diagnostic imaging information by comuted tomography to select patients with calcified plaques for large scale molecular analysis, in an effort to increase our understanding of the pathophysiology behind carotid plaque instability as related to patient- and plaque- phenotype.

overall_design: Patients undergoing surgery for high-grade (>50% NASCET) carotid stenosis at the Department of Vascular Surgery, Karolinska University Hospital, Stockholm, Sweden were consecutively enrolled in the study and clinical data recorded on admission. Carotid computed tomography angiography (CTA) was performed as a pre-operative routine at the admitting hospital using site-specific image acquisition protocols. Carotid endarterectomies (carotid plaques) were collected at surgery and retained within the Biobank of Karolinska Endarterectomies (BiKE). Tissues were frozen at -80°C immediately after surgery and RNA was prepared using Qiazol Lysis Reagent (Qiagen, Hilden, Germany) and purified by RNeasy Mini kit (Qiagen), including DNase digestion. The RNA concentration was measured using Nanodrop ND-1000 (Thermo Scientific, Waltham, MA) and quality estimated by a Bioanalyzer capillary electrophoresis system (Agilent Technologies, Santa Clara, CA). For microarrays, only RNA of good integrity with RIN>7, A260/A280 ratio between 1.8-2.1, A260/230 0.7-1.5 and concentration about 50-500 ng/μl was used, as per standards recommended for whole transcript arrays. Robust multi-array average normalization was performed and processed gene expression data was returned in log2-scale. All human samples were collected with informed consent from patients or organ donors’ guardians; studies were approved by the regional Ethical Committee and follow the guidelines of the Declaration of Helsinki.

first: Eva

last: Karlöf

first: Till

last: Seime

first: Nuno

last: Dias

first: Mariette

last: Lengquist

first: Anna

last: Witasp

first: Håkan

last: Almqvist

first: Malin

last: Kronqvist

first: Jacob

last: Odeberg

first: Lars

last: Maegdefessel

first: Peter

last: Stenvinkel

first: Ljubica

last: Perisic Matic

first: Ulf

last: Hedin


title: Gene expression data of mRNA from adrenal gland sample of pig breed German Landrace with different coping behavior haplotype

first: Siriluck

last: Ponsuksili

summary: 47,880 probe-sets were screened, in the first part of this study, they were analysed for differential expression between two groups differing in  coping behavior associated haplotype

overall_design: RNAs of adrenal gland from German Landrace at adult stage were hybridized to Affymetrix Porcine Snowball Array.

first: Klaus

last: Wimmers


title: Lamin A/C promotes DNA base excision repair (mouse arrays)

status: Public on Oct 02 2019

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The A-type lamins (lamin A/C), encoded by the Lmna gene, are important structural components of the nuclear lamina. Lmna mutations lead to degenerative disorders, including the premature aging disease Hutchinson-Gilford progeria syndrome (HGPS). In addition, altered lamin A/C expression is found in various cancers. Reports indicate that lamin A/C plays a role in DNA double strand break repair, but a role in DNA base excision repair (BER) has not been described. We provide evidence for reduced BER efficiency in lamin A/C-depleted cells. The mechanism involves impairment of the APE1 and POLβ enzyme activities in BER. Also, Lmna null mouse fibroblasts displayed reduced expression of several core BER enzymes (PARP1, LIG3, and POLβ). Moreover, the robustness of APE1 and POLβ activities and the rate of BER were enhanced by lamin A/C-augmented poly(ADP-ribose) polymer formation (PARylation). Finally, we report that HGPS fibroblasts are defective in BER. Collectively, our results provide novel insights into the functional interplay between the nuclear lamina and cellular defenses against oxidative DNA damage, with implications for human cancer and aging.

overall_design: Microarray analysis of Lmna null (Lmna-/-) mouse embryo fibroblasts (MEFs) compared to wild-type (WT) Lmna+/+ MEFs (N=3 biological replicates per condition)

first: Scott

last: Maynard

first: Guido

last: Keijzers

first: Mansour

last: Akbari

first: Marya

last: Morevati

first: Morten

last: Scheibye-Knudsen

first: Susana

last: Gonzalo

first: Jiri

last: Bartek

first: Vilhelm

middle: A

last: Bohr


title: Lamin A/C promotes DNA base excision repair

status: Public on Oct 03 2019

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer

status: Public on May 17 2019

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: RNA-protein interactions mediate a host of cellular processes, underscoring the need for methods to quantify their occurrence in living cells. RNA interaction frequencies for the average cellular protein are undefined, however, and there is no quantitative threshold to define a protein as an RNA-binding protein (RBP). Ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing, an effective widely used means of characterizing RNA-protein interactions, would particularly benefit from the capacity to quantitate the number of RNA cross-links per protein per cell. In addition, CLIP-seq methods are difficult, have high experimental failure rates and many ambiguous analytical decisions. To address these issues, the easyCLIP method was developed and used to quantify RNA-protein interactions for a panel of known RBPs as well as a spectrum of random non-RBP proteins. easyCLIP provides the advantages of good efficiency compared to current standards, a simple protocol with a very low failure rate, troubleshooting information that includes direct visualization of prepared libraries without amplification, and a new form of analysis. easyCLIP, which uses sequential on-bead ligation of 5’ and 3’ adaptors tagged with different infrared dyes, classified non-RBPs as those with a per protein RNA cross-link rate of <0.1%, with most RBPs substantially above this threshold, including Rbfox1 (18%), hnRNPC (22%), CELF1 (11%), FBL (2%), and STAU1 (1%). easyCLIP with the PCBP1L100 RBP mutant recurrently seen in cancer quantified increased RNA binding compared to wild-type PCBP1 and suggested a potential mechanism for this RBP mutant in cancer. easyCLIP provides a simple, efficient and robust method to both obtain both traditional CLIP-seq information and to define actual RNA interaction frequencies for a given protein, enabling quantitative cross-RBP comparisons as well as insight into RBP mechanisms.

overall_design: RNA-binding landscapes of 8 RBPs and 10 non-RBPs, with 1-3 replicates,

first: Weili

last: Miao

first: Paul

last: Khavari


title: Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution

status: Public on Aug 01 2019

city: San Francisco

first: William

middle: Rowland

last: Goodyer

address: 386A Noe Street

institute: Stanford University

summary: The cardiac conduction system (CCS) consists of distinct components including the sinoatrial node (SAN), atrioventricular node (AVN), His bundle, bundle branches (BB) and Purkinje fibers (PF). Despite an essential role for the CCS in heart development and function, the CCS has remained challenging to interrogate due to inherent obstacles including small cell numbers, large cell type heterogeneity, complex anatomy and difficulty in isolation. We used single-cell RNA-sequencing (scRNA-seq) to perform genome-wide analysis of gene expression of the CCS at single-cell resolution.

overall_design: Single cell transcriptional analysis of embryonic cardiac cells using 10x genomics 3' solution

first: Sean

last: Wu


title: RNA-SEQ Quantitative Analysis of WT and Mpl-del-overexpressing AMKL cell Transcriptomes

status: Public on Apr 04 2019

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

institute: Sun Yat-sen university

summary: In the previous studies, we reported that Mpl alternative splicing form Mpl-del overexpressed in acute megakaryoblasttic leukemia (AMKL) patients and mediated thrombopoietin signaling to promote AMKL cells malignant proliferation and chemotherapy resisitance. To investigate the detailed mechanism of Mpl-del mediated AMKL cells proliferation and survival, the AMKL cell Dami stably expressing GFP or Mpl-del-GFP were established by transduction with GFP or Mpl-del-GFP lentiviruses and treated with 20ng/ml TPO for RNA-SEQ analysis to examine the expression of proliferation and survival-related genes. Our results indicated that the levels  of  the "leading edge" genes that account for survival and prolieration were significantly higher in Mpl--del overexpressed AMKL cells.

overall_design: Examination of GFP control group and Mpl-del overexpressed group

first: Qing

last: Zhang


title: Autophagy impairments in directly reprogrammed neurons in patients with idiopathic Parkinson’s disease

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

summary: Protein degradation impairment is strongly suspected to play a role in idiopathic Parkinson’s disease (PD). However, current tools and models are lacking to study such disease associated phenotypes across the PD patient population. Here, we generate functional induced dopaminergic neurons (iDANs) directly reprogrammed from adult dermal fibroblasts of patients with PD to investigate intra-neuronal autophagy alterations.

overall_design: RNA sequencing of fibroblasts and induced neuronal cells from persons with and without Parkinsons Disease

first: Yogita

last: Sharma


title: HDAC inhibition enhances the in vivo efficacy of MEK inhibitor therapy in uveal melanoma

status: Public on Jun 11 2019

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Purpose: The clinical use of MEK inhibitors in uveal melanoma is limited by the rapid acquisition of resistance. The current study has used unbiased multi-omics and drug screens to identify the pan-HDAC inhibitor panobinostat as an effective strategy to limit MEK inhibitor resistance.

overall_design: Examination of 92.1 uveal melanoma cell lines treates with two different single agent inhibitors and their combination compared to the vehicle control.

first: Keiran

middle: S

last: Smalley

first: Fernanda

last: Faiao-Flores


title: Drosophila CNS mitochondrial dysfunction with ATF4 inhibition RNA-Seq

status: Public on Mar 14 2019

first: Joseph

middle: Matthew

last: Bateman

address: Cutcombe Road

department: Basic & Clinical Neuroscience

institute: King's College London

summary: Mitochondrial dysfunction causes biophysical, metabolic and signalling changes that alter homeostasis and reprogram cells. We used a Drosophila model in which TFAM is overexpressed in the nervous system with or without knock-down of the ER UPR transcription factor ATF4, to investigate the how mitochondrial dysfunction and ER stress signalling affect the transcriptome.

overall_design: mRNA profiles of Drosophila CNS with mitochondrial dysfunction, ATF4 overexpression, and mitochondrial dysfunction with ATF4 knock-down were generated by RNA sequencing, in quadruplicate, using the Illumina NextSeq 500.

first: Rachel

last: Hunt


title: Immune Checkpoint Regulation of Pulmonary Fibrosis [bulk RNA-seq]

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Fibroblasts from idiopathic pulmonary fibrosis (IPF) patients acquire an invasive phenotype that is essential for progressive fibrosis. The immune checkpoint ligand CD274 (PD-L1) is up-regulated on invasive lung fibroblasts, regulated by P53 and FAK signaling, and drives lung fibrosis in a humanized IPF model in mice. Targeting CD274high fibroblasts blunted invasion in vitro and attenuated fibrosis in vivo, suggesting that CD274 may be a novel therapeutic target in IPF.

overall_design: Reveal of the expression of the checkpoint PD1 ligand CD274 in invasive and non-invasive fibroblasts of both normal human lungs and IPF lungs

first: Yan

last: Geng

first: Xue

last: Liu

first: Jiurong

last: Liang

last: Deng

first: Yizhou

last: Wang

first: Dianhua

last: Jiang

last: Noble


title: Inositol pyrophosphate dynamics impact fission yeast phosphate homeostasis via modulation of RNA 3' processing and transcription termination

status: Public on Jun 16 2019

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the Inositol pyrophosphate phosphatase mutant aps1∆ and Inositol pyrophsophate kinase mutant asp1-D333A contrasting to the WT in the fission yeast S. pombe

overall_design: 2 test samples (mutants) were analyzed; 1 WT control sample was processed (each sample has 3 replicate experiments)

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Analysis of the expression profiles of back skin and excisional wound-derived fibroblasts FACS-sorted from mice overexpressing activin A.

status: Public on Apr 14 2020

city: Chicago

first: Mateusz

last: Wietecha

address: 801 S Paulina St

institute: University of Illinois Chicago

summary: Overexpression of activin A by keratinocytes accelerates excisional wound healing in mice. Activin-promoted wound healing is mediated via the stroma, specifically by the wound immune cells and fibroblasts. To determine if activin A alters the gene expression profile of wound fibroblasts, we performed RNA-sequencing of fibroblasts FACS-sorted from excisional skin wounds of activin overexpressing mice. We found that activin induces a pro-fibrotic gene expression profile of these fibroblasts, leading to the upregulation of genes involved in collagen biosynthesis and remodeling.

overall_design: CD45-negative/CD140a-positive live cells (fibroblasts) were FACS-sorted from back skin (BS) and excisional skin wounds (5-days post-injury, 5dw) of activin overexpressing mice (K14-Act) and their wild-type (WT) littermates. The experiment was performed in triplicates; for each replicate, material from 3 mice of corresponding genotype and tissue was pooled. The expression profiles of the sorted fibroblasts were analyzed by RNA-sequencing.

first: Sabine

last: Werner


title: Silencing of PFKFB4 in Glioblastoma Stem-like Cells

status: Public on Jan 05 2019

city: Heidelberg

first: Emma

last: Phillips

address: In Neuenheimer Feld 580

department: Brain Tumor Translational Targets

institute: DKFZ

summary: In order to investigate the crucial role of PFKFB4 in glioblastoma stem-like cell (GSC) survival, gene expression microarray-based transcriptome analysis was conducted on GSCs transduced for 4 days with PFKFB4 shRNA compared with GSCs transduced with shNT.

overall_design: 3 biological replicates in GSCs from 3 different patients. shNT was used as a control.

first: Violaine

last: Goidts


title: O-GlcNAc transferase fine-tunes MYC-dependent transcription to promote cell cycle [RNA-seq]

status: Public on May 21 2019

city: Oslo

first: Alfonso

last: Urbanucci

state: Oslo

address: Trondheimsveien 8

country: Norway

institute: Oslo University Hospital

summary: O-GlcNAc transferase (OGT) is overexpressed in aggressive prostate cancer. Here, we employed ChIP-seq to map chromatin-bound O-GlcNAc loci in prostate cancer cells and discovered that these overlap with sites of active transcription and MYC binding. Using RNA-seq, we show that inhibition of OGT promotes MYC-dependent transcriptional repression of mRNAs involved in G1-S transition. O-GlcNAc ChIP-seq regions are highly enriched to transcription start sites and identify the ‘GFY’-motif. Proteins binding to this motif have not been established and we use synthetic oligonucleotides as a bait to enrich protein complexes associated with this sequence. By comparing the unbiased proteomic data from oligonucleotide enrichment with proteomic data from O-GlcNAc and MYC ChIP-mass spectrometry, we identified host cell factor 1 (HCF-1) as an interaction partner of MYC. Inhibition of OGT disrupted the interaction between MYC and HCF-1, and compromised MYC’s ability to promote proliferation of prostate cancer cells in the absence of androgens. Reverse phase protein arrays identified a set of proteins involved in mitosis that are dependent on MYC and OGT activity for expression. In conclusion, we show that OGT activity regulates MYC-driven proliferation by coordinating transcription and translation of cell cycle genes.

overall_design: two biological replicates for prostate cancer cell line (LNCaP) overexpressing MYC gene under the control of Doxycycline. Differential expressed genes were retreaved for these cells treated for 4 and 24 hours with Doxycycline, OSMI2 (a OGT inhibitor), or a cmbination of both (combo) versus the vehicle treated cells (DMSO)

first: Harri

last: Itkonen

first: Sara

middle: E

last: Martin

first: Aziz

last: Khan

first: Anthony

last: Mathelier

first: Bernd

last: Thiede

first: Suzanne

last: Walker

first: Ian

middle: G

last: Mills


title: O-GlcNAc transferase fine-tunes MYC-dependent transcription to promote cell cycle [ChIP-seq]

overall_design: ChIP-seq study using one antibody against c-Myc (R&D, AF3696) and one specific antibody recognizing the O-GlcNAc epitope (RL2, Abcam ab2739) in LNCaP and PC3 prostate cell line

middle: M


title: O-GlcNAc transferase fine-tunes MYC-dependent transcription to promote cell cycle


title: Transcriptional Profiling of Lineage Depleted Dek-KO Murine Bone Marrow Treated with Exogenous DEK

status: Public on Feb 22 2019

city: Ann Arbor

first: Christopher

middle: Tai-Yi

last: Lee

state: MI

address: 2406 Stone Road

department: Biostatistics

institute: University of Michigan

summary: Nuclear protein DEK is an endogenous DNA-binding chromatin factor regulating hematopoiesis. DEK is one of only two known secreted nuclear chromatin factors, but whether and how extracellular DEK regulates hematopoiesis is not known. We demonstrate that extracellular DEK greatly enhances ex vivo expansion of cytokine-stimulated human and mouse hematopoietic stem cells, and regulates hematopoiesis in vivo and in vitro. These effects are mediated through chemokine receptor CXCR2 and heparan sulfate proteoglycans, and are associated with enhanced phosphorylation of ERK1/2, AKT and p38 MAPK. Thus, DEK acts as a hematopoietic cytokine, with potential for clinical applicability.

overall_design: Examination of lineage-negative and lineage-positive DEK-KO bone marrow (BM) cells with and without exogenous DEK

first: Chris

first: Maureen

last: Sartor

first: Anjan

last: Saha

first: David

last: Markovitz


title: Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [RNA-seq]

status: Public on Apr 17 2019

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

institute: University of Gothenburg

summary: Transcriptomic profiling of human breast tumors using RNA sequencing

overall_design: Evaluation of common fusion transcripts, genetic variants, and gene expression patterns in 8p11-p12 amplified breast carcinomas

middle: Z

first: Elisabeth

last: Rönnerman

first: Hanna

last: Engqvist

first: Jana

last: Biermann

first: Katarina

last: Truvé

first: Szilárd

last: Nemes

first: Eva

last: Forssell-Aronsson

first: Giovanni

last: Solinas

first: Anikó

last: Kovács

first: Per

last: Karlsson

first: Khalil

last: Helou


title: Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [ATAC-Seq]

status: Public on Dec 17 2018

first: Andrew

middle: P.

last: Feinberg

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary: We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.

overall_design: 72 WGBS libraries were sequenced (from intact tissue (27 libraries) and NeuN+ and NeuN- flow sorted nuclei (45 libraries)) from hippocampus, nucleus accumbens, prefrontal cortex (BA9), and anterior cingulate gyrus (BA24). RNA-seq (20 libraries) and ATAC-seq (23 libraries) data from NeuN+ and NeuN- flow sorted nuclei from the nucleus accumbens and prefrontal cortex (BA9) were also obtained.

first: L

last: Rizzardi

first: P

last: Hickey

first: K

middle: D

last: Hansen

first: A

middle: P


title: Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [SNP_genotyping]

summary: SNP genotyping of human breast tumors

overall_design: High-resolution copy number analysis of 8p11-p12 amplified breast carcinomas

middle: W


title: RNA Sequencing Analysis of Intracranial Aneurysm Walls Reveals Involvement of Lysosomes and Immunoglobulins in Rupture

status: Public on Nov 26 2018

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

institute: UMC Utrecht

summary:
Background and Purpose—Analyzing genes involved in development and rupture of intracranial aneurysms can enhance knowledge about the pathogenesis of aneurysms, and identify new treatment strategies. We compared gene expression between ruptured and unruptured aneurysms and control intracranial arteries.
Methods—We determined expression levels with RNA sequencing. Applying a multivariate negative binomial model, we identified genes that were differentially expressed between 44 aneurysms and 16 control arteries, and between 22 ruptured and 21 unruptured aneurysms. The differential expression of 8 relevant and highly significant genes was validated using digital polymerase chain reaction. Pathway analysis was used to identify enriched pathways. We also analyzed genes with an extreme pattern of differential expression: only expressed in 1 condition without any expression in the other.
Results—We found 229 differentially expressed genes in aneurysms versus controls and 1489 in ruptured versus unruptured aneurysms. The differential expression of all 8 genes selected for digital polymerase chain reaction validation was confirmed. Extracellular matrix pathways were enriched in aneurysms versus controls, whereas pathways involved in immune response and the lysosome pathway were enriched in ruptured versus unruptured aneurysms. Immunoglobulin genes were expressed in aneurysms, but showed no expression in controls. Conclusions—For rupture of intracranial aneurysms, we identified the lysosome pathway as a new pathway and found further evidence for the role of the immune response. Our results also point toward a role for immunoglobulins in the pathogenesis of aneurysms. Immune-modifying drugs are, therefore, interesting candidate treatment strategies in the prevention of aneurysm development and rupture.

overall_design: RNA sequencing of 44 intracranial aneurysm samples (including 21 unruptured, 22 ruptured and 1 undetermined) and 16 control samples of the intracranial cortical artery

first: Rachel

last: Kleinloog

first: Bon

middle: H

last: Verweij

first: Pieter

last: van der Vlies

first: Patrick

last: Deelen

first: Morris

last: Schwertz

first: Louis

last: de Muynck

first: Philip

last: van Damme

first: Fabrizio

last: Giuliani

first: Luca

last: Regli

first: Albert

last: van der Zwan

first: Jan

last: Berkelbach van der Sprenke

last: Han

first: Peter

last: Gosselaar

middle: C

last: van Rijen

first: Emine

last: Korkmaz

last: Post

first: Gabriël

middle: J

last: Rinkel

last: Veldink


title: Alveolar Macrophage Transcriptional Programs are Associated with Ventilator-Free Days in Acute Respiratory Distress Syndrome

status: Public on Mar 31 2019

city: Seattle

first: Sina

last: Gharib

address: 850 Republican St.

department: Medicine

institute: University of Washington

summary:
Rationale: Serial measurements of genome-wide transcriptional changes in alveolar macrophages (AMs) in patients with acute respiratory distress syndrome (ARDS) could identify dynamic biologic processes that are associated with clinical outcomes.
Objectives: To identify associations between AM transcriptional programs and the composite endpoint of ventilator-free days (VFDs) over the course of ARDS.
Methods: We performed unbiased genome-wide transcriptional profiling of AMs purified from bronchoalveolar lavage fluid collected from patients with ARDS. Cells were obtained at baseline (Day 1), Day 4, and Day 8 after ARDS onset. We assessed pathway enrichment in subjects with VFDs > 0 (VFD-Extubated/Alive) versus VFDs = 0 (VFD-Intubated/Dead) at each time point.
Measurements and Main Results: We found highly divergent AM transcriptional patterns at all time points between ARDS patients based on their VFD status (FDR < 0.05). “M1-like” and pro-inflammatory gene sets such as IL-6-JAK-STAT signaling were significantly enriched in AMs isolated on Day 1 in VFD-Extubated/Alive versus VFD-Intubated/Dead subjects. In contrast, many of these same gene sets were associated with the VFD-Intubated/Dead subjects on Day 8. In patients who had samples from each time point, we identified multiple AM gene clusters whose temporal expression patterns were associated with VFD status. The relationship between AM expression profiles and VFDs was distinct in subjects with Direct (pulmonary) versus Indirect (extrapulmonary) ARDS.
Conclusion: Clinically meaningful outcomes over the course of ARDS are associated with highly distinct AM transcriptional programs. Our findings suggest that interventions targeting the alveolar immune response should be tested within strictly defined time periods.

overall_design: Total RNA from human alveolar macrophages was isolated and hybridized to Illumina HumanRef-8 BeadChips (n = 68 samples from 35 subjects).

middle: A

first: Eric

last: Morrell


title: Gene expression in isolated epithelial and stromal cells from day 4 pregnant uterus

status: Public on Jan 15 2019

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

summary: To detect the gene profiles in epithelial and stromal cells, these cells are isolated from three independent pregnancy day 4 mice by enzymes digestion and subject to high throughput sequence. After aligned to mouse mm9 by Tophat, RPKM value was calculated by Edger.

overall_design: Explore RNAs in two different cell types by RNA-Seq

first: SK

last: Dey


title: The Secondary Crest Myofibroblast PDGFRa Controls Elastogenesis Pathway via a Secondary Tier of Signaling Networks During Alveogenesis

status: Public on Feb 13 2019

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

summary:
To compare the gene expression profiles between normal and Pdgfra deficient secondary crest myofibroblasts (SCMF).
There was a total of 1808 differentially expressed genes of which 866 increased, while 942 decreased in the Pdgfra deficient SCMFs. The differentially expressed genes are related to multiple functions of SCMFs.
Pdgfra plays an important role in multiple functions, especially elastogenesis, of secondary crest myofibroblasts during alveolar formation.

overall_design: Profiling of gene expression in GFP+ cells sorted from PN14 lungs dissected from wild type (Gli1creERT:mTmG) and Pdgfra mutant (Gli1creERT:mTmG:Pdgfra-f/f) mouse by deep sequecing using Illumina HiSeq2500.

first: C

last: Li

first: M

middle: K

last: Lee

first: F

first: S

last: Webster

first: H

last: Di

first: J

last: Duan

first: C-Y

last: Yang

first: N

last: Bhopal

first: G

last: Pryhubar

last: Smith

first: Z

last: Borok

last: Bellusci

first: P

last: Minoo


title: Transcriptional and Functional Diversity of Macrophage Repolarization: Implications in Chronic Inflammation and Cystic Fibrosis

status: Public on Sep 30 2018

last: Gharib

summary: Macrophage plasticity allows cells to adopt different phenotypes, a property with potentially important implications in chronic pulmonary disorders such as cystic fibrosis (CF). We examined the transcriptional and functional significance of macrophage repolarization from an “M1” (LPS-stimulated) towards an “M2” phenotype using 5 stimuli. We found that macrophages exhibit highly diverse responses to distinct M2-polarizing stimuli. Specifically, we observed that IL-10 abrogated LPS-tolerance allowing for rapid restoration of LPS responsiveness. In contrast, IL-4 enhanced LPS-tolerance, dampening pro-inflammatory responses after repeat LPS challenge. We found enrichment of phagocytosis-associated pathways in macrophages stimulated with IL-10, leading them to display the greatest efferocytosis ability. Finally, we observed that CF macrophages had intact reparative responses, suggesting that macrophage contributions to CF lung disease are shaped by their environmental milieu and are modifiable. These findings highlight the diversity of macrophage activation states, attribute functional consequences to these stimuli, and provide a unique resource of human macrophage repolarization markers.

overall_design: Non-polarized, M0 state monocyte-derived macrophages (MDMs) from n= 6 cystic fibrosis (CF) patients and n =6 non-CF subjects were initially polarized to M1 by exposure to LPS. M1 MDMs were then cultured in MDM media alone (no treatment) or supplemented with IL-4, IL-10, methylprednisolone, azithromycin, or apoptotic PMNs for 24 h to repolarize MDMs towards an M2 state. Total RNA from each condition was isolated and hybridized to Illumina HumanHT-12 v4 BeadChip (total number of samples = 72).


title: Restoring Mitofusin balance in the nervous system prevents axonal degeneration in a CMT2A mouse model

status: Public on Apr 03 2019

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: MFN2 is a mitochondrial outer membrane protein that plays a pivotal role in mitochondrial dynamics in most tissues, yet mutations in MFN2 (which cause Charcot-Marie-Tooth disease type 2A) primarily affect the nervous system.  We generated a transgenic mouse model of CMT2A which developed severe early-onset vision loss and neurological deficits, axonal degeneration without cell body loss, and cytoplasmic and axonal accumulations of fragmented mitochondria labeled for degradation.  Mutant MFN2R94Q had a dominant negative effect on mitochondrial fusion if MFN1 was absent or at low levels, as in neurons.  Finally we found that augmenting the level of MFN1 in the nervous system in vivo led to rescue of all phenotypes in mutant MFN2R94Q expressing mice.  These data demonstrate that the MFN1:MFN2 ratio is a key determinant of tissue specificity in CMT2A, and indicates that augmentation of MFN1 in the nervous system is a viable therapeutic strategy for the disease.

overall_design: Comparing lumbar spinal cord transcription profiles from MFN2-R94Q mice (n=3), MFN2-R94Q:MFN1 mice (n=5), and nontransgenic control mice (n=3)

first: Yueqin

last: Zhou

first: Sharon

last: Carmona

first: A

last: Muhammad

first: Jesse

last: Landeros

first: Michael

last: Vazquez

first: Ritche

last: Ho

first: Antonietta

last: Franco

first: Gerald

last: Dorn

first: Bing

last: Lu

first: Shaomei

last: Wang

first: Cathleen

last: Lutz

first: Robert

last: Baloh


title: Single cell transcriptomes of developing chicken hind limbs at stages HH25, HH29 and HH31

status: Public on May 09 2019

city: Berlin

first: Christian

middle: A.

last: Feregrino

address: Ihnestraße 63

institute: MPI - Molecular Genetics

summary:
We sequenced 17’628 cells coming from three key developmental stages of chicken autopod patterning. We identified 23 cell populations with distinct transcriptional profiles, including essential populations like the apical ectodermal ridge. We also inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits.
The supplementary file contains processed UMI count matrices, which also include meta data of each cell, e.g. cluster.

overall_design: Droplet-based single cell RNA-seq of dissociated developing limbs of chicken at three different stages

first: Fabio

last: Sacher

first: Oren

last: Parnas

first: Patrick

last: Tschopp


title: Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells (MCF7)

status: Public on Nov 20 2018

city: Macau

first: Edwin

last: Cheung

address: Avenida da Universidade,Taipa

department: faculty of health sciences

institute: University of Macau

summary: Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating the estrogen receptor α (ERα). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular responses, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ERα regulates transcription in breast cancer cells. In this study, we performed single-cell transcriptome analysis on ERα-positive breast cancer cell lines following 17β-estradiol stimulation. We sequenced a total of 177 single-cell transcriptomes and observed robust gene expression diversity between individual cells.

overall_design: single-cell RNA sequencing of 2 ER-positive breast cancer cell line MCF7 (SRP125153,PRJNA418865) and T47D (SRP125154,PRJNA418867)  during time-course E2 treatment.

first: Detu

last: Zhu

first: Xianglan

last: Zhaozu


title: Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells (T47D)


title: The effects of X-ray radiation on pancreatic cancer cells

status: Public on Jun 30 2018

city: Shanghai

first: Ling

last: Tian

state: Shanghai

address: No. 650, New Songjiang Road

department: Institute of Translational Medicine

institute: Shanghai General Hospital

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

summary:
Dying pancreatic cancer cells from chemoradiation can directly stimulate repopulation of surviving cells.
We used microarrays to conduct the analysis of whole transcript profiles in pancreatic cancer cells treated with X-ray radiation.

overall_design: Pancreatic cancer cells were seeded into culture plate overnight with 2% FBS in culture medium and then were irradiated with 10Gy using an Oncor linear accelerator. Irradiated pancreatic cancer cells were collected at 24h after X-ray radiation for RNA extraction and hybridization on Affymetrix microarray. We sought to obtain whole transcript profiles in pancreatic cancer cells treated with X-ray radiation.


title: ES cells and iPS cells under exposure to sublethal of isotretinoin

status: Public on Aug 28 2018

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

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

overall_design: Refer to individual Series


title: Single-Cell Transcriptome Analysis Reveals Estrogen Signaling Coordinately Augments One-Carbon, Polyamine, and Purine Synthesis in Breast Cancer

first: Zuxianglan

last: Zhao


title: Genome-wide transcriptomic profiling of cardiomyocyte differentiation from human ES cells and iPS cells under exposure to sublethal of isotretinoin (RNA-seq)

summary: In this study, isotretinoin (INN)-induced alternations in transcriptome during caidiomyocyte differentiation derived from human hESCs and hiPSCs were investigated. H1-hESC and C15-hiPSC were differentiated to caidiomyocytes under exposure to sublethal level of INN, and cells were collected at day 0 (undifferentiated cellsl) day 2 (mesoderm) and day 6 (cardiac progenitors) for genome-wide transcriptomic profiling by RNA-seq.

overall_design: H1-hESC and C15-hiPSC were grown in 12-well plates with Essential 8 medium (Thermo Fisher Scientific), and the cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific) under exposure to 25nM of isotretinoin (INN). At day 0, 2 and 6 during the differentiation period (before the medium-change on that day), and cells were collected using Accutase (Thermo Fisher Scientific), and then store in -80C till RNA isolation. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates. RNA-seq libriries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation kit (Epicentre Biotechnologies), and then sequenced by a HiSeq 4000 sequencer (Illumina) with 2 X 101 cycles. RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser. The human gene symbols and their raw counts were calculated using HTSeq (version 0.6.1p1) package in Python with GRCh39/hg19 Homo sapiens gtf file. Differential gene-expression analysis was performed using edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM) method.

first: Michael

last: Snyder


title: Genome-wide chromatin accessibility profiling of cardiomyocyte differentiation from human ES cells and iPS cells under exposure to sublethal of isotretinoin (ATAC-seq)

summary: In this study, isotretinoin (INN)-induced alternations in genome-wide open-chromatin regions during cardiomyocyte differentiation were investigated. H1-hESC and C15-hiPSC were differentiated to caidiomyocytes under exposure to sublethal level of INN, and cells were collected at day 0 (undifferentiated cellsl) day 2 (mesoderm) and day 6 (cardiac progenitors) for genome-wide open-chromatin profiling by ATAC-seq.

overall_design: H1-hESC and C15-hiPSC were grown in 12-well plates with Essential 8 medium (Thermo Fisher Scientific), and the cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific) under exposure to 25nM of isotretinoin (INN). At day 0, 2 and 6 during the differentiation period (before the medium-change on that day), about 50,000 cells were collected for ATAC-seq. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates.


title: Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

city: Baltimore

first: Andrew

last: Feinberg


title: M6A IP from BrU-labeled and fragmented nascent RNA.

status: Public on Jun 19 2018

city: Heraklion

first: Evgenia

last: Ntini

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

summary: M6A immunoprecipitation from 15min BrU labeled and fragmented nascent RNA.

overall_design: HEK293T cells were incubated with 2 mM bromouridine for 15 min labeling time (pulse). Whole-cell total RNA was extracted with Trizol, fragmented (3min at 95°C, 10 mM ZnCl2) and nascent RNA was purified with anti-BrdU during BrU-IP. Fragmented nascent RNA was subsequently immunoprecipitated with anti-m6A.

first: Annita

last: Louloupi


title: M6A IP from BrU-labeled nascent RNA (non-fragmented).

summary: M6A immunoprecipitation from 15 min BrU-labeled nascent RNA (0 min and 30 min chase). All three fractions, Input, eluate and supernatant were subjected to Illumina sequencing.

overall_design: HEK293T cells were incubated with 2 mM bromouridine for 15 min labeling time (pulse) and chased with 20 mM uridine for 0 min or 30 min. Whole-cell total RNA was extracted with Trizol and nascent RNA was purified with anti-BrdU during BrU-IP. The BrU-labeled nascent RNA was subsequently immunoprecipitated with anti-m6A. The Input, m6A-IP eluate (m6A-enriched RNA fraction) and supernatant (m6A-depleted RNA fraction) were subjected to Illumina sequencing.


title: Comparison of the expression profiles of wild-type Rhodobacter capsulatus and a GTA hyperproducer (DE442) by RNAseq.

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

institute: University of York

summary: Gene Transfer Agents (GTAs) are small virus-like particles that transfer random fragments of host bacterial DNA between cells. Unlike true viruses, whose primary aim is self-preservation, GTAs have no preference for the spread of their own genes. GTAs are typically produced from less than 1% of the population, making in-depth analysis of producer cells problematic. Here, we compared the transcriptome of wild-type R. capsulatus and a GTA hyperproducer, DE442, in which up to 40% of cells express GTAs.

sample_organism:
Rhodobacter capsulatus SB 1003
Rhodobacter capsulatus DE442

overall_design: Examination of expression profiles of 4 WT and 8 GTA hyperproducer Rhodobacter capsulatus samples by RNASeq

first: Paul

last: Fogg


title: miRNAs regulated by HDAC6 in HCC

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

institute: Ajou University of Korea

summary: Revealing miRNAs that are regulated by HDAC6 overexpression in hepatocellular carcinoma

overall_design: miRNA expression profiling of 3 Hep3B_Mock and 3 Hep3B_HDAC6 was performed using GenoExplorer Microarray platform. 10 ug of total RNA was isolated from Hep3B HCC cell line that transfected pcDNA3.1_Mock or pcDNA3.1_HDAC6 and then labeled and hybridized to a to microRNA chip for analysis under optimized conditions. The arrays with hybridized targets were scanned using an Axon scanner and the scanned images were analyzed using GenePix® Pro 5.0 software (Axon Instruments) and spots of poor quality determined by visual inspection were also removed from further analysis. The resulting data, the average of 3 mean fluorescence signal intensities for each probe, collected from each array was submitted to the GenePlex 3.0 (Istech Inc. Seoul, Korea) database. Data were normalized using the method of quantile normalization and class-specific filtering.

first: HeeDoo

last: Yang

first: JungWoo

first: Qingyu

last: Shen

first: HyungSeok

last: Kim

first: SangYeon

first: WonSang

last: Park

first: JungYoung

last: Lee

first: SukWoo

last: Nam


title: High depth sequencing of BrU-labeled nascent RNA in METTL3 depleted cells.

summary: BrU incorporation into nascent RNA followed by immunoprecipitation with a BrU specific antibody. The nascent RNA was subsequently eluted with BrU competition.

overall_design: HEK293T cells, treated with METTL3 siRNA, were incubated with 2 mM bromouridine for 15 min labeling time and chased with 20 mM uridine for 60 min. Nascent RNA was purified during BrU-IP with anti-BrdU.


title: BrU-labeled nascent RNA sequencing and m6A-IP from BrU-labeled nascent RNA

first: Ulf

last: Orom


title: SuperSeries: An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray

status: Public on May 08 2018

city: Lebanon

first: Lucas

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

type: Methylation profiling by genome tiling array


title: Gene activity induced by denervation in the rat urinary bladder [mRNA]

status: Public on Mar 10 2018

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

institute: SciLifeLab. Stockholm University

summary: Bilateral freezing of the pelvic ganglia in female rats were performed to denervate the urinary bladder. Sham operated rats were used as controls. The rats were sacrificed 10 days after surgery. The urinary bladders (including the urothelium) were frozen and used for RNA extraction.

overall_design: Urinary bladders from sham-operated rats and from rats 10 days after denervation were compared. mRNA and microRNA were both analyzed. In total 12 samples (6 sham and 6 denervated) were used.

first: Mari

last: Ekman

first: Karl

last: Swärd

first: Baoyi

last: Zhu

first: Daniel

last: Svensson

first: Bengt-Olof

last: Nilsson

first: Bengt

last: Uvelius


title: Gene activity induced by denervation in the rat urinary bladder [miRNA]


title: FlowSorted.Blood.EPIC: An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray (II)

summary: DNA methylation assessments of peripheral blood DNA can be used to accurately estimate the relative proportions of underlying leukocyte subtypes. Such cell deconvolution analysis relies on libraries of discriminating differentially methylated regions that are developed for each specific cell type measured. The relationship between estimated cell type proportions can then be tested for their association with phenotypes, disease states, and subject outcomes, or used in multivariable models as terms for adjustment in epigenome-wide association studies (EWAS). We obtained purified neutrophils, monocytes, B-lymphocytes, natural killer (NK) cells, CD4+ T-cells, and CD8+ T-cells from healthy subjects and measured DNA methylation with the Illumina HumanMethylationEPIC array platform. In addition, we measured DNA methylation with the EPIC array in two sets of artificial DNA mixtures comprising the above cell types. We compared three separate approaches to select reference differentially methylated region libraries (DMR library), for cell type proportion inference. The IDOL algorithm identified an optimal DMR library consisting of 450 CpG sites for inferring leukocyte subtype proportions (average R2=99.2). Importantly, the majority of CpG sites (69%) in the IDOL DMR library were unique to the new EPIC methylation array, in that they were not present on the 450K array. Our new reference DMR library is available as a Bioconductor package, has the potential to reduce any unintended technical differences arising from the combination of different generations of array platforms, and may be helpful in generating larger DMR libraries that include novel cell subtypes.

overall_design: Bisulphite converted DNA from neutrophils (Neu, n=6), monocytes (Mono, n=6), B-lymphocytes (Bcells, n=6), CD4+ T-cells (CD4T, n=7, six samples and one technical replicate), CD8+ T-cells (CD8T, n=6), Natural Killer cells (NK, n=6), and 12 DNA artificial mixtures (labeled as MIX in the dataset) were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Devin

last: Koestler

first: Rondi

last: Butler

first: Helen

last: Hansen

first: John

last: Wiencke

middle: T

last: Kelsey

first: Brock

last: Christensen


title: Early response of human ovarian and fallopian tube surface epithelial cells to norepinephrine

status: Public on May 25 2018

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: The purpose of this study is to understand the effects of adrenergic signaling on the transcriptome of cell line models postulated to be the cells of origin of epithelial ovarian cancers using RNA-Seq. Here we explored the effects of the stress-related hormone, norepinephrine, on normal human ovarian and fallopian tube surface epithelial cellss. We investigated the early transcriptional response to norepinephrine in normal immortalized ovarian surface epithelial cells and fallopian tube secretory cells. RNA-Seq data of treated and untreated cells were analyzed to identify genes with differential expression.

overall_design: RNA-seq data from ovarian surface epithelial cells and fallopian tube epithelial cells after treatment with 1µM norepinephrine for 1 hour (or mock-treatment). Three independent replicates were performed for each condition and cell line.

first: Anxhela

last: Gjyshi

first: Alvaro

middle: N

last: Monteiro

first: Cen

last: Ling

first: Sean

last: Yoder

first: Chaomei

last: Zhang


title: Expression data from PDVC57 cells stimulated with or without Onscostatin M

status: Public on Feb 28 2018

city: POITIERS

first: Marie

last: Simonneau

address: 1 RUE GEORGES BONNET

institute: LITEC EA4331

summary:
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer in caucasian population and it's important to find new therapeutic targets. Cytokines expressed in tumor microenvironment can have strong effects on tumor cell phenotype.  We have characterized the effect of Oncostatin M (OSM), a cytokine belonging to the IL-6 familly on the transcriptome of transformed keratinocytes cell line, PDVC57 cells.
In this dataset, we have included the expression data obtained from transformed keratinocytes PDVC57 cells stimulated or not with OSM for 6  or 24 hours. These data have shown that 32 genes were differentially expressed in response to OSM stimulation.

overall_design: 4 samples were analyzed, non stimulated (NS) for 6 or 24 hours used as controls and treated with OSM (10 ng/mL) for 6 or 24 hours. We generated the following pairwise comparisons NS 6h vs OSM 6h and NS 24h vs OSM 24h. Genes with a fold-change ≤0.5 or a fold-change ≥2 were selected.

first: M

first: E

last: Frouin

first: C

last: Jermidi

first: J

middle: F

last: Jegou

first: A

last: Barra

first: I

last: Paris

first: V

last: Huguier

first: P

last: Levillain

first: N

last: Pedretti

first: F

middle: X

last: Bernard

last: Lecron

last: Morel

first: L

last: Favot


title: The Transcription factor Zeb2 ia required to maintain tissue-specific identities of macrophages

status: Public on Jul 14 2018

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent


title: PRMT1 and CSNK1a1 control epidermal progenitor maintanence (PRMT1 ChIP-seq data set)

status: Public on Feb 02 2018

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Here we determine the genome-wide binding sites of PRMT1 in primary human keratinocytes. We also investigated the impact of casein kinase inhibitor D4476 on PRMT1 genomic binding.

overall_design: HA-PRMT1 was expressed at near endogenous level in primary keratinocytes. Two independent HA antibodies were used for PRMT1 ChIP-seq. The CSNK1a1 inhibitor D4476 was added to keratinocyte culture to characterize the role of CSNK1a1 on controlling PRMT1 genomic binding.

first: Xiaomin

last: Bao

first: Adam

last: Rubin

first: Qu

last: Kun

first: Paul

last: Khavari


title: Gene activity induced by denervation in the rat urinary bladder

first: Jessica

last: Lindvall

platform_organism:
Rattus norvegicus
synthetic construct


title: Genome-wide study of transcriptional and methylation profile of human cytotoxic CD4 T cells

status: Public on Mar 06 2018

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

institute: Université Libre de Bruxelles


title: Total nucleoplasmic RNA-seq in MCF-7

status: Public on Feb 05 2018

first: Evgenia

last: Ntini

summary: Deep sequencing of total RNA isolated from the nucleoplasmic fraction of MCF-7 cells.

overall_design: Stranded total RNA-seq of total nucleoplasmic RNA (ribospecies depleted) from MCF-7 cells.

first: E

first: U

last: Orom


title: Alterations of microRNAs throughout the malignant evolution of cutaneous squamous cell carcinoma: The role of miR-497 in epithelial to mesenchymal transition of keratinocytes

status: Public on Dec 31 2017

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

institute: Sheba Medical Center at Tel HaShomer

summary: We found that miR-497 expression decrease in cSCC biopsies and cell lines compare to normal skin biopsies or normal keratinocytes cell.  To understand in role lost expression of miR-497 might have in tumorigenesis of keratinocytes, we aimed to fine possible biochemical pathways and possible targets of miR-497 in cSCC. In order do so, we over expressed miR-497 in cSCC and used microarrays to fine global gene expression effected by miR-497.

overall_design: Two cSCC cell lines Met-1 and SCL-II were generated, each were either over-expressing miR-497 or control plasmid. From these cells, RNA extraction and hybridization on Affymetrix microarrays.

first: Adi

last: Mizrahi

first: Aviv

last: Barzilai

first: Devorah

last: Gur-Wahnon

first: Iddo

last: Ben-Dov

first: Shayna

last: Glassberg

first: Tal

last: Meningher

first: Einat

last: Elharar

first: Moamen

last: Masalha

first: Jasmine

last: Jacob-Hirsch

first: Hilla

last: Tabibian-Keissar

first: Iris

last: Barshack

first: Jason

last: Roszik

first: Raya

last: Leibowitz-Amit

first: Yechezkel

last: Sidi

first: Dror

last: Avni


title: PRMT1 and CSNK1a1 control epidermal progenitor maintenance (PRMT1/CSNK1a1 transcriptome profiling data sets)

first: Douglas

last: Porter

summary: Here we determine the target gene sets controlled by PRMT1 or CSNK1a1 in maintaining the undifferentiated state of primary human keratinocytes.

overall_design: Gene expression analysis: To determine the impact of PRMT1 or CSNK1a1 loss on gene expression in primary human keratinocytes. RNA hybridized to GeneChip Human Genome U133 Plus 2.0 Array

first: Xiaomin

last: Bao

first: Kun

last: Qu

first: Paul

last: Khavari


title: ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters

status: Public on Jan 24 2018

city: Los Angeles

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: We performed ChIP-seq in four cancer cell lines to identify ZFX binding sites throughout the human genome. We also performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucelosome, suggesting that ZFX may play a critical role in promoter architecture. We also showed that ZNF711 may function redundantly with ZFX in MCF7 by performing ZNF711 ChIP-seq and RNA-seq analysis after knockdown of ZFX, ZNF711, and both ZFX and ZNF711.

overall_design: ChIP-seq, NOMe-seq and RNA-seq

first: Suhn-Kyong

first: Lijun

last: Yao

first: Heather

last: Witt

first: Zhifei

last: Luo

first: Shannon

last: Schreiner

first: Yu

last: Guo

first: Andrew

last: Perez

first: Peggy

last: Farnham


title: Identifying novel drivers of human hepatocellular carcinoma and revealing clinical relevance as early diagnostic and prognostic biomarker

first: Jung Woo

last: Eun

summary: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and is the one of the few cancers in which a continued increase in incidence has been observed over several years. HCC associated with chronic liver disease evolves from precancerous lesion and early HCC to overt cancer, and identifying key molecules contributing to early stage HCC is an urgent need. We aim to determine transcriptome-based molecular signature of multistep hepatocarcinogenesis, and to identify novel biomarkers to diagnose and predict early stage HCC.

overall_design: 107 samples covering 9 stages of HCC. Normal liver were used as control.

first: Suk Woo

last: Nam


title: Cell transplantation strategies for acquired and inherited disorders of peripheral myelin

status: Public on Jan 26 2018

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary:
Objective: To investigate transplantation of rat Schwann cells or human iPSC-derived neural crest cells and derivatives into models of acquired and inherited peripheral myelin damage.

Methods: Primary cultured rat Schwann cells labeled with a fluorescent protein for monitoring at various times after transplantation.  Human induced pluripotent stem cells (iPSCs) were differentiated into neural crest stem cells (NCSC), and subsequently toward a Schwann cell lineage via two different protocols.  Protocol 1 = treated with MesenPRO with Heregulin. Protocol 2 = coculture with iPSC-derived Motor Neurons. Cell types were characterized using flow cytometry, immunocytochemistry and transcriptomics. Rat Schwann cells and human iPSC-derivatives were transplanted into (i) nude rats pretreated with lysolecithin to induce demyelination or (ii) a transgenic rat model of dysmyelination due to PMP22 overexpression.

Results: Rat Schwann cells transplanted into sciatic nerves with either toxic demyelination or genetic dysmyelination engrafted successfully, and migrated longitudinally for relatively long distances, with more limited axial migration.  Transplanted Schwann cells engaged existing axons and displaced dysfunctional Schwann cells to form normal appearing myelin.  Human iPSC-derived neural crest stem cells and their derivatives shared similar engraftment and migration characteristics to rat Schwann cells after transplantation, but did not further differentiate into Schwann cells or form myelin.

Interpretation: These results indicate that cultured Schwann cells surgically delivered to peripheral nerve can engraft and form myelin in either acquired or inherited myelin injury, as proof of concept for pursuing cell therapy for diseases of peripheral nerve.  However, lack of reliable technology for generating human iPSC-derived Schwann cells for transplantation therapy remains a barrier in the field.

overall_design: RNA-seq of iPSC-derived Neural Crest Stem Cells in three conditions: 1) untreated 2) treated with MesenPRO with Heregulin 3) cocultured with iPSC-derived Motor Neurons

first: A

middle: G

last: Muhammad

first: Kevin

last: Kim

first: Irina

last: Epifantseva

first: Arwin

last: Aghamaleky-Sarvestany

first: Megan

middle: E

last: Simpkinson

first: Sharon

last: Carmona

first: Jesse

last: Landeros

first: John

last: Svaren

first: Robert

last: Baloh


title: Transcriptional Survey of Alveolar Macrophages in a Murine Model of Chronic Granulomatous Inflammation Reveals Common Themes with Human Sarcoidosis

status: Public on Dec 01 2017

city: Seattle

first: Sina

last: Gharib

address: 850 Republican St.

institute: University of Washington

summary:
Rationale: A well-validated animal model of sarcoidosis can help advance our understanding of the pathobiology of this complex disease. We have developed a multiwall carbon nanotube (MWCNT) based murine model that shows marked histological and inflammatory signal similarities to human sarcoidosis. In this study, we compared the alveolar immune cell transcriptional signatures of our murine model with human sarcoidosis to comprehensively assess overlapping molecular programs.
Methods: Total RNA was extracted from alveolar macrophages of 6 MWCNT mice and 6 control mice and hybridized to Illumina Mouse WG-6 v2 microarrays. Transcriptional profiling of alveolar immune cells in 15 sarcoidosis patients and 12 healthy humans was previously performed using Affymetrix Human GeneChip U133A 2.0 microarrays. Rigorous statistical methods were used to identify differentially expressed genes. To better elucidate gene expression pathways, integrated network and gene set enrichment analysis (GSEA) were applied. To confirm differential expression of select network genes, we performed qPCR studies using the ABI Prism 7300 Detection.
Results: We identified over 1000 genes that were differentially expressed between the control and the MWCNT mice. Gene Ontology functional analysis showed over-representation of processes primarily involved in immunity and inflammation in MCWNT mice. Applying a more comprehensive pathway analysis using GSEA to both mouse and human samples revealed upregulation of 92 gene sets in MWCNT mice and 142 gene sets in sarcoidosis patients. Commonly activated pathways in both MWCNT mice and sarcoidosis included adaptive immunity, T-cell signaling, IL-12/IL-17 signaling and oxidative phosphorylation. Differences in selective gene set enrichment between MWCNT mice and sarcoidosis patients were also observed, among them IL-27 signaling, NK-mediated cytotoxicity and proteasome pathways. We applied network analysis to differentially expressed genes common between the MWCNT model and human sarcoidosis to identify key drivers of disease and putative therapeutic targets.
Conclusions: Our MWCNT murine model has an alveolar macrophage signature that varies significantly from control mice. Application of an unbiased transcriptomic approach revealed substantial functional similarities between a murine MWCNT model and human sarcoidosis particularly with respect to activation of immune-specific pathways.

overall_design: C57Bl/6 mice underwent oropharyngeal instillation of 35% surfactant/saline (control, n = 6) or 35% surfactant/saline solution containing 100 μg of MWCNT (n = 6). At day 60 after instillation, mice underwent BAL and alveolar macrophages were isolated with >90% purity. Total RNA from each sample was isolated and hybridized to Illumina Mouse WG-6 v2 BeadChip (total number of samples = 12).


title: Transcriptional Landscape of Cells of Renin Lineage Following Podocyte Depletion

status: Public on Nov 21 2017

summary: Renin producing cells of the juxtaglomerulus, herein called cells of renin lineage (CoRL), have garnered recent interest for their propensity to act as a progenitor sink for various kidney cell types including podocytes. Despite recent advances, the process of transdifferentiation of CoRL to podocytes is poorly understood. In this study, we employed a transgenic mouse line which permanently labels CoRL with ZsGreen fluorescent protein, allowing for isolation by fluorescence-activated cell sorting. At 5 days following induction of abrupt podocyte ablation via anti-podocyte sheep IgG, mice were sacrificed and CoRL were isolated by FACS. RNA was subsequently analyzed by microarray. Gene set enrichment analysis (GSEA) was performed and revealed that CoRL display a distinct phenotype following podocyte ablation, primarily consisting of downregulation of metabolic processes and upregulation of immuno-modulatory processes. Additionally, RNA-biology and cell cycle-related processes were also upregulated. Changes in gene expression or activity of a core set of transcription factors including HNF1 and E2F were identified through changes in enrichment of their respective target genes. However, integration of results from transcription factor and canonical pathway analysis indicated that ERR1 and PU-box family members may be the major contributors to the post-podocyte ablation phenotype of CoRL. Finally, top ranking genes were selected from the microarray-based analysis and confirmed by qPCR. Collectively, our results provide valuable insights into the transcriptional regulation of CoRL following abrupt podocyte ablation.

overall_design: Total RNA from FACS ZsGreen CoRL was isolated from uninjured (baseline) mice (n = 4) and mice with experimentally induced focal segmental glomerulosclerosis (FSGS) (podocyte depleted, n = 4) and hybidized to MouseRef-8 (v2.0) Expression BeadChips.

first: Aaron

last: McClelland