title: LY6E blocks coronavirus fusion and confers immune control of viral disease

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: Zoonotic coronaviruses (CoVs) are significant threats to global health, as exemplified by the recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Host immune responses to CoV are complex and regulated in part through antiviral interferons. However, the interferon-stimulated gene products that inhibit CoV are not well characterized. Here, we show that interferon-inducible lymphocyte antigen 6 complex, locus E (LY6E) potently restricts cellular infection by multiple CoVs, including SARS-CoV, SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV). Mechanistic studies revealed that LY6E inhibits CoV entry into cells by interfering with spike protein-mediated membrane fusion. Importantly, mice lacking Ly6e in hematopoietic cells were highly susceptible to murine CoV infection. Exacerbated viral pathogenesis in Ly6e knockout mice was accompanied by loss of hepatic and splenic immune cells and reduction in global antiviral gene pathways. Accordingly, we found that Ly6e directly protects primary B cells and dendritic cells from murine CoV infection. Our results demonstrate that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis. These findings advance our understanding of immune-mediated control of CoV in vitro and in vivo, knowledge that could help inform strategies to combat infection by emerging CoV.

overall_design: Ly6etm1a ES cells were obtained from the EUCOMM consortium and microinjected into C57BL/6J blastocysts by the UTSW Transgenic Technology Center. Chimeric mice with germline transmission were bred to obtain Ly6etm1a/+ offspring. Ly6etm1a/+ mice were crossed with FLPe-expressing mice (B6N.129S4-Gt(ROSA)26Sortm1(FLP1)Dyn/J, #16226, Jackson Laboratories) to obtain Ly6efl/+ offspring, which were bred to homozygosity. Conditional Ly6efl/fl mice were bred to Vav1-iCre transgenic mice (B6.Cg-Commd10Tg(Vav1-icre)A2Kio/J, #008610, Jackson Laboratories) to obtain Ly6eΔHSC/+ (Ly6efl/+; Vav1-iCre) offspring. Ly6eΔHSC/+ mice were bred to obtain Ly6eΔHSC (Ly6efl/fl; Vav1-iCre) offspring, which harbor a deletion of exon 3 and 4 in hematopoietic stem cells (HSC). Experimental animals were obtained by crossing Ly6eΔHSC and Ly6efl/fl mice. Genotype was confirmed by PCR of genomic DNA in-house or outsourced to Transnetyx. Ablation of Ly6e was confirmed by qPCR in immune cells from spleen, liver, or bone marrow. Animal studies were carried out in specific-pathogen-free barrier facilities managed and maintained by the UTSW Animal Resource Center. All procedures used in this study complied with federal and institutional guidelines enforced by the UTSW Institutional Animal Care and Use Committee (IACUC).

first: Stephanie

last: Pfaender

first: Katrina

middle: B

last: Mar

first: Eleftherios

last: Michailidis

first: Annika

last: Kratzel

first: Dagny

last: Hirt

first: Philip

last: V`kovski

first: Wenchun

last: Fan

first: Nadine

last: Ebert

first: Hanspeter

last: Stalder

first: Hannah

last: Kleine-Weber

first: Markus

last: Hoffmann

first: H

first: Mohsan

last: Saeed

first: Ronald

last: Dijkman

first: Eike

last: Steinmann

first: Mary

last: Wight-Carter

first: Natasha

last: Hanners

first: Stefan

last: Pöhlmann

first: Thomas

last: Gallagher

first: Gert

last: Zimmer

first: Charles

last: Rice

first: John

last: Schoggins

first: Volker

last: Thiel


title: Gastrointestinal tissue-specific chromatin accessibility and gene expression during development

status: Public on Dec 31 2019

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Methylation Profiling of Medulloblastoma in a Clinical Setting Permits Sub-Classification and Reveals New Outcome Predictions

status: Public on Dec 27 2019

city: Riyadh

first: Malak

last: Abedalthagafi

state: Ar Raid

address: King Abdullah Rd

department: Genomics Research

country: Saudi Arabia

institute: King Abdulaziz City for Science and Technology

summary: In this study, we report the first examination of Medulloblastoma (MB) methylation patterns in Arab world, using an extensive primary tumor cohort in tertiray care center. We assessed DNA methylation patterns to sub-classify clinical MB cases and their amenability to clinical applications from archival biopsy material (FPPE). We herein establish methylation events as clinically useful biomarkers and demonstrate how their incorporation into current risk-stratification schemes could significantly improve the accuracy of survival predictions in clinical setting. This holds potential for future precision therapeutic approaches aimed at improving the outcomes of afflicted MB patients.

overall_design: experimental retrospective

first: Abedalthagafi

last: Malak

first: Snuderl

last: Matija


title: Gastrointestinal tissue-specific chromatin accessibility and gene expression during development (RNA-Seq)

summary: We used ATAC-Seq to profiling epigenomic changes and RNA-Seq to profiling gene expression changes during the embryonic development of gastrointestinal  tract.

overall_design: RNA-Seq of mouse embryonic tissues

first: Roshane

last: Francis

first: Musa

last: Ahmed

first: Theodora

last: Yung

first: Peter

last: Dirks

first: Housheng

middle: H

last: He

first: Tae-Hee

last: Kim


title: Transcriptome of the nematode Caenorhabditis elegans infected by Bacillus thuringiensis

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

country: Germany

summary: In the past decade, the paradigm which claimed that invertebrate immune systems lack specificity has been reconsidered. Accumulating evidence supports that invertebrate immune systems are able to mount specific responses to the pathogen species-, and even to the pathogen strain-level. However, the underlying molecular mechanisms behind invertebrate immune specificity remain mostly unknown. Studying the molecular basis of invertebrate immune specificity in a genetically tractable model, such as the nematode Caenorhabditis elegans, has the potential to reveal insights into the immune systems of other metazoans, including humans. We chose to study the mechanisms of specific immune responses of the worm to two different pathogenic strains of the Gram-positive bacterium Bacillus thuringiensis (MYBY18247 and MYBT18679), because there is phenotypic evidence of specific genotype-genotype interactions between this host-pathogen pair. We did an initial RNA-Seq experiment upon pathogen exposure and found that 9% of the differentially expressed genes change their expression in different ways when comparing the two pathogen strains. Through promoter region motif enrichment analysis, we found the GATA transcription factor ELT-2 is responsible for the pathogen strain-specific transcriptomic response. Upon elt-2 knockdown worms exposed to MYBT18679 display lower survival rate coupled with higher intestinal damage than non-infected controls. Additionally, by performing further genetic analysis using gene knockdown and knockout, we found that the p38 MAPK pathway acts likely in parallel to elt-2 and the transcription factor skn-1 cooperates with elt-2 to promote resistance to MYBT18679. On the other hand, elt-2 knockdown leads to a substantially higher survival rate, together with lower intestinal tissue damage compared to control worms, upon exposure to MYBT18247, another pathogenic Bacillus thuringiensis strain. The MYBT18247 pathogen load of elt-2(RNAi) worms compared to control worms remained unchanged, suggesting the elt-2 negatively regulates tolerance towards MYBT18247. We found that tolerance to MYBT18247 was positively regulated by the transcription factors: FOXO daf-16, bZip zip-2, nhr-99 and nhr-193. To identify elt-2 negatively-regulated downstream targets that could promote tolerance to MYBT18247, we performed a second RNA-Seq experiment, this time including elt-2(RNAi) worms exposed to both pathogenic strains. We found four genes negatively regulated by elt-2: cdr-2, poml-3, dhs-30 and tre-3, with putative function in detoxification and lipid metabolism, which can mediate tolerance to MYBT18247. We conclude that ELT-2 coordinates strain-specific immune responses in this invertebrate host and promotes resistance upon exposure to MYBT18679, while it negatively regulates tolerance to MYBT18247. The response is likely to be specific to the crystal pore-forming toxins produced by this pathogen.

overall_design: mRNA profiles of wild type (WT) C.elegans exposed to either Bacillus thuringiensis B-18247, B-18679 and B-18407 or E. coli OP50 at 2h, 6h, 12h or 24h were generated by deep sequencing (4 replicates), using Illumina HiSeq2000.

first: Alejandra

last: Zarate-Potes

first: Katja

last: Dierking


title: Tissue-specific transcriptomic changes associated with AmBisome treatment of mice with experimental visceral leishmaniasis [LV9]

status: Public on Nov 22 2019

city: York

first: Paul

last: Kaye

address: Wentworth way

country: United Kingdom

institute: University of York

summary: Microarray data of mouse  liver and spleen samples infected with Leishmania donovani and treated with ambisome

overall_design: 6-8 week old BALB/c mice infected with LV9 L.donovani strain. Samples were taken from individuals infected at 36 days post infection, with and without treatment, and 42 days post infection, with and without treatment

first: Sarah

last: Forrester

first: Karin

last: Seifert

first: Helen

last: Ashwin

first: Najmeeyah

last: Brown

first: Andrea

last: Zelmer

first: Sally

last: James

first: Dimitris

last: Lagos

first: Jon

last: Timmis

first: Mitali

last: Chaterjee

first: Jeremy

middle: C

last: Mottram

first: Simon

middle: L

last: Croft

middle: M


title: RNA sequencing profiles for thyroid tumor tissue specimens

status: Public on Dec 01 2019

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

type: Non-coding RNA profiling by high throughput sequencing

summary: There is a challenge of thyroid cancer versus benign follicular denoma differential diagnostics using fine-needle biopsy. RNA expression profiles can be used to identify biomarkers suitable for molecular diagnostics. Here we present raw RNA sequencing data obtained during Oncobox platform observational study for 96 human pathological thyroid biosamples. Data are compatible with Oncobox Atlas of Normal Tissue Expression (ANTE) database including profiles for healthy thyroid tissues. . The data provided are helpful to those implicated in thyroid cancer research and diagnostics, and in comparative analyses of human cancers.

overall_design: We performed mRNA sequencing of 97 samples of thyroid cancer. Additionally, we performed microRNA sequencing of 34 samples of thyroid cancer.

first: Andrew

last: Garazha

first: Maria

last: Suntsova

first: Maxim

last: Sorokin

first: Anton

last: Buzdin


title: Transcriptomic analysis of naïve B cells and plasma cells as well as in vitro stimulated B cells from Blimp1-GFP reporter mice [Blimp1_reporter_PC_stim]

status: Public on Dec 05 2019

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

country: USA

institute: University of Pennsylvania

summary: Though it is known that plasma cells utilize the unfolded protein response to remodel their ER it is generally believed that this follows Blimp1-mediated transcriptional and translational increases in immunoglobulin protein.  In this study we utilize Blimp1 reporter mice to examine the earliest activation of UPR-affiliated gene expression in plasma cell inductive stimulation of B cells.  We combine in-vivo gene expression of follicular B cells, marginal zone B cells from spleen and short and long lived plasma cells from bone marrow with in-vivo generated activated B cells and plasma cells from the same mice to examine gene expression before and after Blimp1-upregulation.  Using a novel in-vitro stimulation approach we separate those UPR-affiliated genes activated by B cell activation and those requiring a plasma cell inductive stimulus. We report here that these plasma cell specific UPR-affiliated genes are activated in absence of ER-stress prior to upregulation of Blimp1.

overall_design: Samples are biological replicates from five mice across 4 in-vivo cell types and 7 ex-vivo stimulated cell cultures.  cDNA was prepared from RNA with 3' polyA capture method.  Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.

first: David

last: Allman

middle: T


title: Intraepithelial papillary neoplasia in the biliary tree is mediated by FGF10 signal

status: Public on Nov 12 2019

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

country: Japan

institute: Gifu University

summary: The new concept of neoplastic lesion of biliary tree, Biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of bile duct (IPNB), as a conunterpart of pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN), have been reported to be precancerous lesions in hilar and extrahepatic cholangiocarcinoma and arise from lining bile duct epithelium and peribiliary gland (PBG) under inflammation microenvironment in human. However, mouse model is lacking different from intrahepatic cholangiocarcinoma arised from canal of Hering in the liver. In a Doxycyclin-controlled transgenic mouse model of BilIN and IPNB, overexpression of Fibroblast Growth Factor 10 (FGF10) phenocopies human pathology with mutistep progression of cholangiocarcinogenesis in chronic cholangitis. The development  and branching morphogenesis of BilIN and IPNB was induced by Fgf10/Erk signal and inhibited by MEK inhibiter. Pdx1+ PBG cells present in IPNB were able to lineage trace the early IPNB lesion as well as Krt19+ cholangiocytes. BiliN and IPNB with Kras mutation was irreversible different from no Kras mutation, and loss of p16 contributed to malignant transformation of BilIN and IPNB. Our data challenge the common paradigms regarding the pathogenesis of BilIN and IPNB.

overall_design: FGF10 overexpressed mice (n=3), no expressed control mice (n=3)

first: Kaori

last: Tanaka

first: Akira

last: Hara


title: PRC1 catalytic activity is central to Polycomb system function. [ChIP]

status: Public on Jan 08 2020

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

summary: The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how it selects its target genes is poorly understood and whether its histone modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a new inducible mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 is important for Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of Polycomb chromatin domain formation, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling new evidence that PRC1 catalysis is central to Polycomb system function and gene regulation.

overall_design: Mouse embryonic stem cells in which PRC1 (PRC1CKO) or specifically PRC1 catalytic activity (PRC1CPM) can be conditionally removed, were profiled for genomic distribution of different Polycomb factors (PRC1: RING1B, PCGF1, PCGF2, PCGF6; PRC2: SUZ12, JARID2, AEBP2, EPOP, PCL2) and histone modifications (H2AK119ub1, H3K27me3, H3K4me3) using spike-in calibrated ChIP-seq (cross-linked - for PcG factors and native - for histone modifications).

first: Neil

middle: P

last: Blackledge

first: Angelika

last: Feldmann

first: Robert

middle: J

last: Klose


title: Sequencing of canine and genetically-engineered mouse models for endotype identification of embryonal rhabdomyosarcoma

city: Beaverton

first: Charles

last: Keller

state: OR

address: 12655 SW Beaverdam Rd. West

institute: Children's Cancer Therapy Development Institute

summary: Here, we report using RNA sequencing isolated from frozen tumor samples from genetically-engineered mouse models and canine samples, as well as a preserved mouse cell culture to determine endotypes, or subtypes with distinct pathobiological mechanisms, of embryonal rhabdomyosarcoma (ERMS) and nonrhabdomyosarcoma soft tissue sarcomas (NRSTS). With an unsupervised clustering approach of DNA and RNA sequencing from mouse models, canine samples, patient-derived xenograft models, and human samples we have found several major endotypes with a wide range of putative driver mutations. This study aims to define each of the several pathological mechanisms driving tumor maintenance in these tumors in order to identify effective targeted treatments for individual patients.

sample_organism:
Canis lupus familiaris
Mus musculus

platform_organism:
Canis lupus familiaris
Mus musculus

overall_design: Tumor tissues were unpurturbed from procurement to preservation, so there are no experimental conditions for any of the samples submitted.  Culture conditions were based on an established culture protocol.

first: Cora

last: Ricker

first: Noah

last: Berlow


title: RNA-seq analysis of AML cells in response to ASLAN003

status: Public on Nov 20 2019

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: We aim to gain insight into the changes of gene expression induced by ASLAN003, a novel, potent Dihydroorotate Dehydrogenase (DHODH) Inhibitor

overall_design: AML cell lines KG-1 and MOLM-14 cells treated with DMSO and ASLAN003 for 96 hours. Each treatment was triplicated. RNA was extracted and RNA-seq libraries were constructed by TruSeq Library Prep Kit and subjected to Illumina Hiseq4000 deep sequencing (paired-end reads of 100 bases).

first: Jianbiao

last: Zhou


title: Characterization of the nuclear and cytosolic transcriptomes in human brain tissue

status: Public on Nov 14 2019

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

summary: Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, gene expression regulation, and interpretation of gene expression patterns in cells and tissues. Several studies reported significant differences between the cytosol and nuclear transcriptomes and that many coding and non-coding transcripts were unique to either of the compartments. However, these studies is based on cell lines and in most of the cases restricted to target gene experiments. Here, we performed a comprehensive analysis of cytosolic and nuclear transcriptomes in human fetal and adult brain samples. We show significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. Transcripts displaying differential subcellular localization belong to particular functional categories and display tissue-specific localization patterns. We also show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Further investigation of the reliability of using the cytosol or the nucleus for differential gene expression analysis in single cell experiments as a proxy for whole transcriptome indicates important differences in results depending on the cellular compartment. These differences were manifested at the level of transcript category and number of differentially expressed genes. Our data provides the first resource of RNA subcellular localization of RNA in human brain and highlight the influence of using the cytosol and the nucleus in interpreting and comparing results from single cell studies.

overall_design: Nuclear and cytoplasmic fraction of tissues from adult and fetal human frontal cortex and cerebellum.

first: Ammar

last: Zaghlool

first: Adnan

last: Niazi

first: Åsa

middle: K

last: Björklund

first: Jakub

last: Orzechowski-Westholm

first: Adam

last: Ameur

first: Lars

last: Feuk


title: Retrospective gene expression analysis of human RNA samples from Hepatocellular Carcinoma in relation with survival

status: Public on Oct 08 2019

city: Hangzhou

first: Hechen

last: Huang

state: Zhejiang

address: 79 Qingchun Road

department: Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery

country: China

institute: First Affiliated Hospital, School of Medicine, Zhejiang University

summary: The aim of this study is to identify by Next Generation Sequencing - RNA-seq profiling a molecular signature of Hepatocellular Carcinoma samples that correlates with survival. The samples were retrospectively derived from hepatocellular carcinoma tissue as well as non-tumor tissue from the livers of the same patients. The bioinformatical analysis of 32 pairs RNA-seq datasets were obtained from human RNAs on Illumina Hiseq-PE150. Due to the lack of biological sample duplication, this datasets were used hisat2 2.1.0 and gfold v1.1.4 for expression analysis to identify differences in gene expression between tumors and adjacent tissues. (including up- and down-regulation).

overall_design:
mRNA profiles of  32 pairs of hepatocellular carcinoma tissue as well as non-tumor tissue from the livers of the same patients were generated by Next Generation Sequencing - RNA-seq, using Illumina Hiseq-PE150.

***Please note that the processed data was updated on Jan 9, 2020.

first: Shusen

last: Zheng


title: Gene expression analysis of mesenchymal stem cells at different stages of differentiation in to adipocytes

status: Public on Nov 04 2019

city: Kansas City

first: Elin

last: Grundberg

state: Missouri

address: 2401 Gillham Road

institute: CHILDREN'S MERCY HOSP (KANSAS CITY, MO)

summary: Mechanisms involved in adipose tissue expansion is of great interest in development of obesity and associated metabolic complications. Mesenchymal stem cell (MSC) differentiation in to adipocytes provides a model system to understand various gene expression pattern involved at different stages of adipogenesis. In this project we used bulk RNASeq to identify the genes that are selectively expressed at 3 different time points of adipocyte differentaition from MSCs.

overall_design: Gene expression profiling of MSCs at three different time points during in vitro differentiation in to adipocytes using bulk RNASeq.

first: Jinchu

last: Vijay


title: Widespread dynamic DNA demethylation in response to heat stress in Arabidopsis

status: Public on Nov 06 2019

city: Katowice

first: Urszula

last: Korotko

address: Bankowa 12

country: Poland

institute: University of Silesia

type: Methylation profiling by high throughput sequencing

summary: We analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana under the influence of heat stress. For this purpose whole-genome sequencing of sodium bisulfite treated DNA was performed. The analysis was carried out at seven time points taking into account control conditions, heat stress and return to control conditions after stopping stress treatment. The analysis showed that under the influence of heat stress there is a global decrease in the level of DNA methylation in Arabidopsis thaliana in all three sequence contexts (CpG, CHG, CHH).

overall_design: Bisulfite sequencing of samples from seven time points in three replicates per time point: p0 – control, p1 – heat stress after 6h, p2 – heat stress after 12h, p3 – heat stress after 24h, p4 – recovery after 6h, p5 – recovery after 12h, p6 – recovery after 24h

first: Karolina

last: Chwialkowska

first: Izabela

last: Sanko-Sawczenko

first: Miroslaw

last: Kwasniewski


title: Single-cell analysis of human adipose tissue


title: Transcriptomic and epigenomic profiling of SETDB1 mediated repression in Acute Myeloid Leukemia

status: Public on Oct 03 2019

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Epigenetic regulators play a critical role in normal and malignant hematopoiesis. We recently showed that the Histone 3 Lysine 9 (H3K9) methyltransferase SETDB1 negatively regulates the expression of the pro-leukemic genes HoxA9 and its cofactor Meis1 through deposition of promoter H3K9 trimethylation (H3K9me3) in MLL-AF9 AML cells. Here, we investigated the microbiological impact of altered SETDB1 expression in AML cells. We explored changes in transcription using RNA-seq, promoter associated histone modifications using ChIP-seq, and chromatin accessibility using ATAC-seq. Next generation sequencing of AML cells with or without overexpression of SETDB1 shows that high expression of SETDB1 induces repressive changes to the promoter epigenome and downregulation of genes linked with AML, including Dock1 and the MLL-AF9 target genes Hoxa9, Six1, and others. These data reveal novel targets of SETDB1 in AML that point to a role for SETDB1 in negatively regulating pro-leukemic target genes and suppressing AML.

overall_design: MLL-AF9 (MA9) acute myeloid leukemia cell lines were generated from mouse bone marrow by retroviral transduction of the MLL-AF9 oncogene. These cells were co-transduced with SETDB1 overexpression or empty vector (EV) control. RNA was harvested from three biological replicates of MA9+SETDB1 and MA9+EV and poly-A selected RNA-seq was performed. Two biological replicates each were obtained for each ChIP experiment. Cells were crosslinked using 1% paraformaldehyde and harvested to perform immunoprecipitation using antibodies targeting H3K9me3, H3K79me2, and H3K9ac. 10% input was used as a control. Two biological replicates for MA9+SETDB1 or MA9+EV were harvested for ATAC-seq. These cells were pretreated in culture with DNase I to eliminate cell-free DNA. They were then harvested, frozen, and sent to Active Motif for ATAC-seq processing, library prep, and sequencing. This protocol was performed as described in Buenrostro, et al Curr Protoc Mol Biol. 2015.

first: Andrew

middle: G

last: Muntean


title: Effect of the LuxI/R gene on AHL-signaling Molecules and QS Regulatory Mechanism in Hafnia alvei H4

status: Public on Oct 10 2019

city: Dalian City

first: xue

last: li

state: Liaoning Province

address: No. 1 Light Industry Court, Ganjingzi District

department: School of food science and technology

institute: Dalian Polytechnic University

summary: Hafnia alvei H4 is a bacteria subject to regulation by N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing system and is closely related to the corruption of instant sea cucumber. Studying the effect of Hafnia alvei H4 quorum sensing regulatory genes on AHLs is necessary for the quality and preservation of instant sea cucumber. In this study, the draft genome of H. alvei H4, which comprises a single chromosome of 4,687,151 bp, was sequenced and analyzed and the types of AHLs were analyzed employing thin-layer chromatography (TLC) and LC-MS/MS. Then the wild-type strain of H. alvei H4 and the luxI/R double mutant (ΔluxIR) were compared by transcriptome sequencing (RNA-seq). The results indicate that the incomplete genome sequence revealed the presence of one quorum-sensing (QS) gene set, designated as lasI/expR. Three major AHLs, N-hexanoyl-L-homoserine lactone (C6-HSL), N-butyryl-L-homoserine lactone (C4-HSL), and N-(3-oxo-octanoyl)-L-homoserine lactone (3-oxo-C8-HSL) were found, with C6-HSL being the most abundant. C6-HSL was not detected in the culture of the luxI mutant (ΔluxI) and higher levels of C4-HSL was found in the culture of the luxR mutant (ΔluxR), which suggested that the luxR gene may have a positive effect on C4-HSL production. It was also found that AHL and QS genes are closely related in the absence of luxIR double deletion. The results of this study can further elucidate at the genetic level that luxI and luxR genes are involved in the regulation of AHL.

overall_design: Examination of 2 different genes' expression in 2 bacterial types.

first: Xue

last: Li

first: Gongliang

last: Zhang

first: Yaolei

last: Zhu

first: Jingran

last: Bi

first: Hongshun

last: Hao

first: Hongman

last: Hou


title: Tissue-specific transcriptomic changes associated with AmBisome treatment of mice with experimental visceral leishmaniasis

status: Public on Oct 15 2019

first: Paul

last: Kaye

summary:
RNAseq of mouse liver and spleen samples infected with M. bovis treated with ambisome
Liposomal amphotericin B (AmBisome) is a commonly used treatment  for visceral leishmaniasis (VL), but  is significantly less effective in the treatment of VL in East Africa, where the burden of disease is now greatest.   Despite its widespread use, little is known of the mode of action of AmBisome.  Here, we sought to examine the impact of AmBisome on tissue-specific transcriptomic changes following experimental infection with Leishmania donovani, in the two most clinically important tissues for treatment, the spleen and the liver.  BALB/c mice infected with M. bovis BCG (an organism resistant to AmBisome treatment) were used  to distinguish between direct effects of AmBisome and those that are secondary to parasite death using the RNAseq libraries generated to compare to previously published transcriptomic data of Leishmania donovani infected spleen and liver tissues treated with AmBisome. Our data indicate that the tissue response to AmBisome treatment is varied in different target organs and that full restoration of homeostasis is not achieved at parasitological cure.  The pathways required to restore homeostasis deserve fuller attention in order to understand mechanisms associated with treatment failure and relapse and to promote more rapid restoration of immune competence.

overall_design: 10 6-8 week old BALB/c mice infected with BCG-SSI. At 35 days post infected, 5 were treated with Ambisome. All mice were culled at d42 and whole RNA isolated from tissues collected from this time point

first: Sarah

last: Forrester

first: Karin

last: Seifert

first: Helen

last: Ashwin

first: Najmeeyah

last: Brown

first: Andrea

last: Zelmer

first: Sally

last: James

first: Dimitris

last: Lagos

first: Jon

last: Timmis

first: Mitali

last: Chaterjee

first: Jeremy

last: Mottram

first: Simon

last: Croft


title: Translational control of cardiac fibrosis (I)

first: Sonia

last: Chothani

address: 8 College Road

institute: Duke-NUS school of medicine

summary: Cardiac fibroblasts from 4 patients treated for up to 24 hours with TGFB1

overall_design: cardiac fibroblasts treated with TGFB1 for up to 24 hours

first: Sebastian

last: Schafer

first: Eleonora

last: Adami

first: Stuart

last: Cook

first: Owen

last: Rackham


title: Translational control of cardiac fibrosis

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

overall_design: Refer to individual Series


title: RNA sequencing of PIK3CA-WT/WT and PIK3CA-WT/H1047R primary mouse embryonic fibroblasts

status: Public on Oct 01 2019

city: Cambridge

first: Ralitsa

middle: Radostinova

last: Madsen

address: Addenbrookes Treatment Centre, Keith Day Road

department: Metabolic Research Laboratories, Clinical Biochemistry

institute: University of Cambridge

summary: Gene targeting was carried out by Taconic Artemis (Cologne, Germany) to introduce a point mutation resulting in conversion of CAT (H) to CGT (R) in the C-terminal p110α kinase domain, and a neo selection cassette flanked by frt sites (publication doi: 10.1038/s41467-017-02002-4). MEFs were made from PIK3CA-H1047R/WT and PIK3CA-WT/WT E13.5 embryos (4 independent MEFs per genotype), treated with 1 μM 4-OHT for one day and gathered 48h after the start of 4-OHT induction were subjected to mRNA sequencing to determine changes in gene expression upon short term PIK3CA activation in the absence of other transforming mutations. PIK3CA-H1047R/WT MEFS exhibited altered expression of 71 genes (q cutoff <0.05).

overall_design: 4 independent MEFs (WT/WT, WT/H1047R). All cultures were collected 48 hours after 4-OHT induction of flp recombinase mediated PIK3CA mutation. Cells were grown in full media (doi: 10.1038/srep39985). The library was prepared by The Barts and the London School of Medicine and Dentistry Genome Centre at Barts Cancer Centre, using an Illumina TruSeq Standard mRNA Library Prep Kit and sequenced on a Illumina Next Generation Sequencer.

first: Larissa

last: Moniz

first: Bart

last: Vanhaesebroeck

middle: R


title: RNA-seq of colon tissue from wild type and Elf4-/- mice with colitis

status: Public on Oct 16 2019

city: beijing

first: Fuping

last: You

address: haidian district xueyuan road 38

department: department of immunology

institute: peking university health science center

summary: ELF4 is a transcription factor, and to identify its potential targets, the inflamed colons of wild type and Elf4 deficient mice were subjected to whole genome RNA sequencing.

overall_design: wild type and Elf4-/- mice were treated with 3% DSS, at day 6 post treatment, inflamed distal colon were harvested.

first: Hongqiang

last: Du


title: Isogenic patient-derived human iPSCs, wild-type or heterozygous for PIK3CA-E418K

summary: The PIK3CA-related overgrowth syndrome (PROS) patient-derived induced pluripotent stem cell (iPSC) lines M98-WT and M98-E418K were obtained from a female, 18-y-old PROS patient by episomal reprogramming of a dermal fibroblast culture with 32% mosaicism for PIK3CA-E418K heterozygosity. All clones used for experimental studies were confirmed transgene-free and expressed high levels of pluripotent stem cell-specific markers, comparable to those of a reference hPSC line. Karyotyping on a single line from each genotype confirmed lack of microscopic genetic rearrangements. The original patient-derived dermal fibroblasts were obtained with full informed consent in accord with the Declaration of Helsinki. The study was approved by The Cambridge South Ethics.

overall_design: 3 iPSC cultures wild-type for PIK3CA (from two independent clones) and 3 PIK3CA-WT/E418K cultures (from three independent clones) profiled by single-end RNA sequencing.

first: Robert

last: Semple


title: High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs

summary: We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles of a wild-type induced pluripotent stem cell (iPSC) line (WTC11; Coriell # GM25256; P37-P38). Four cultures from each genotype (3 wild-type clones, 3 heterozygous clones, 2 homozygous clones) were subjected to paired-end mRNA sequencing (mean read length = 150 bp). The aim of this experiment was to confirm and expand upon previous transcriptomic results suggesting a near-binary transcriptional effect in homozygous versus heterozygous PIK3CA-H1047R iPSCs (publication doi: 10.1073/pnas.1821093116).  According to the high-depth transcriptomic dataset, PIK3CA-H1047R/H1047R iPSCs exhibited altered expression of 5644 genes, whereas heterozygous hPSCs showed 492 differentially-expressed genes, supporting a nearly deterministic phenotypic effect of homozygosity for PIK3CA-H1047R.  The differential gene expression analyses were performed based on the limma/voom/eBayes framework (doi: 10.1093/nar/gkv007), using customised scripts with FDR < 0.05 and absolute log2(fold-change) cut-off >= 1.3.

overall_design: 4 cultures per genotype (WT/WT, WT/H1047R, H1047R/H1047R), from 3 independent wild-type clones, 3 independent heterozygous clones and 2 independent homozygous clones. All cultures were collected 3 hours following replenishment with growth factor-replete Essential 8/Flex maintenance medium. Moreover, culture collection was conducted over three days according to a block design, thus allowing us to determine transcriptional differences that are robust to biological variability. The library was prepared by The Genomics and Transcriptomics Core (GTC) at the MRC Metabolic Disease Unit, University of Cambridge, using an Illumina TruSeq Standard mRNA Library Prep Kit. The barcoded libraries were pooled and sequenced across 3 lanes on an Illumina HiSeq 4000, with an average depth of approximately 70 million reads per sample.


title: Dissection of intercellular communication using the transcriptome-based framework ICELLNET

status: Public on Nov 01 2019

city: Paris

first: Vassili

last: Soumelis

address: 1 avenue Claude Vellefaux

department: U976 - HIPI

country: France

institute: INSERM

summary: Cell-to-cell communication can be inferred from ligand-receptor expression in cell transcriptomic datasets. However, important challenges remain: 1) global integration of cell-to-cell communication, 2) biological interpretation, and 3) application to individual cell population transcriptomic profiles. We develop ICELLNET, a transcriptomic-based framework integrating: 1) an original expert-curated database of ligand-receptor interactions accounting for multiple subunits expression, 2) quantification of communication scores, 3) the possibility to connect a cell population of interest with 31 reference human cell types, and 4) three visualization modes to facilitate biological interpretation. We apply ICELLNET to 3 datasets generated through RNA-seq, single-cell RNA-seq, and microarray. ICELLNET reveal autocrine IL-10 control of human dendritic cell communication with up to 12 cell types. Four of them (T cells, keratinocytes, neutrophils, pDC) are further tested and experimentally validated. In summary, ICELLNET is a global, versatile, biologically validated, and easy-to-use framework to dissect cell communication from individual or multiple cell-based transcriptomic profile(s).

overall_design: transcriptomes of 6 different donors (biological replicates) were studied at 2 different time points : H4 and H8. 4 conditions were generated at both time points :  medium + IgG, LPS + IgG, LPS + anti-TNFR, LPS + anti-IL10R. Microarray analysis were performed at both time points to decipher the contribution of TNF and IL-10 auto-regulatory loops in the control of cell-cell communication

first: Floriane

last: Noël

first: Lucile

last: Massenet-Regad

first: Irit

last: Carmi-Levy

first: Antonio

last: Cappuccio

first: Maximilien

last: Grandclaudon

first: Coline

last: Trichot

first: Yann

last: Kieffer

first: Fatima

last: Mechta-Grigoriou


title: Conjoint analysis of RNA-seq and Solexa sequencing data of bovine mammary epithelial cells  isolated from Chinese Holstein cows with high and low milk fat percentages

status: Public on Sep 25 2019

city: Changchun

first: Lixin

last: Xia

state: Jilin

address: No.5333 Xi'an Road,Luyuan District

department: College of Animal Science

institute: Jilin University

summary: For RNA-seq, the sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2. For Solexa suquencing, we download the data obtained by a previous study in our laboratory. Genes and miRNAs were considered differentially expressed according to log2FC >1 or log2FC <-1and FDR <0.05. All target genes regulated by DERs were predicted by the combination of miRbase (http://www.mirbase.org) and TargetScan (http://www.targetscan.org). All the predicted target genes were intersected with the DEGs obtained by RNA-seq, and then the DEGs and DERs were obtained by a combined analysis.In total, 190 DEGs were regulated by 33 DERs that were significantly enriched in 488 GO terms and 12 KEGG pathways (p <0.05).This is of great significance for research on miRNAs and functional genes for the milk fat percentage- and marker-assisted selection of dairy cattle.

overall_design: two bovine mammary epithelial cells isolated from Chinese Holstein cows with high (4.85%) and low (3.41%) milk fat percentages

first: Zhihui

last: Zhao


title: Construction of rat aortic smooth muscle cell line A7r5-specific gene expression matrix

status: Public on Feb 13 2020

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

type:
Expression profiling by array
Third-party reanalysis

summary:
The purpose of our study is to construct rat aortic smooth cell line A7r5-specific interactome by aggregating publically available microarray samples, and provided a global view of biological process and identified transcription factors that regulate the transcriptomic changes.
We collected 30 samples of A7r5 cell line microarray from 2 prior studies and our own study data, GSE87439. We performed normalization for Affymetrix microarray platform using SCAN.UPC R package (Release 3.9, PMID: 22959562, https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). After normallizatin, we performed batch effect adjusting because datasets came from different laboratoriesand, and combined the datasets . The matrix data we deposited in GEO has normalized log2 signal intensity for 14,004 genes which are common across datasets. The genes were mapped to Rattus norvegicus Entrez Gene IDs.
A7r5-specific interactome was assembled by Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe, PMID: 16723010). Then, we used Master Regulator Analysis-Fisher’s Extact Test (MRA-FET, PMID: 20531406) to infer transcription factors which control a gene signature changes by the effect of SCE and SchB on the TGFβ1-treated A7r5 cells (PMID: 29423034). We discovered Junb, Srebf2, Foxk2, and Irf9 as a master regulator to modulate the gene signatures on the TGFβ1-treated A7r5 cells. Our findings will provide biological insights into the pharmaceutical effect of SCE and SchB in A7r5 cells.

relation:
Reanalysis of: GSM2331361
Reanalysis of: GSM2331362
Reanalysis of: GSM2331363
Reanalysis of: GSM2331364
Reanalysis of: GSM2331365
Reanalysis of: GSM2331366
Reanalysis of: GSM2331367
Reanalysis of: GSM2331368
Reanalysis of: GSM2331369
Reanalysis of: GSM2331370
Reanalysis of: GSM2331371
Reanalysis of: GSM2331372
Reanalysis of: GSM2331373
Reanalysis of: GSM2331374
Reanalysis of: GSM2331375
Reanalysis of: GSM2331376
Reanalysis of: GSM2331377
Reanalysis of: GSM2331378
Reanalysis of: GSM393216
Reanalysis of: GSM393277
Reanalysis of: GSM538754
Reanalysis of: GSM538755
Reanalysis of: GSM538762
Reanalysis of: GSM538763
Reanalysis of: GSM538764
Reanalysis of: GSM538765
Reanalysis of: GSM538766
Reanalysis of: GSM538767
Reanalysis of: GSM538792
Reanalysis of: GSM538795

overall_design:
A total of 3 datasets containing 30 microarray samples were downloaded from NCBI GEO (http://ncbi.nlm.nih.gov/geo). For Affymetrix platforms set, we used SCAN.UPC R package to nomalize the data. We mapped the probe set IDs to Rattus norvegicus Entrez Gene IDs.
Significant gene signature:  Limma analysis (PMID: 25605792) was used to identify genes of expression reversed by SCE or SchB efficacy on TGFβ1-treated A7r5 cells in the GSE87439 data (Please see reference paper for details). We found out SCE and SchB up- or down-effective gene set and applied these gene sets MRA-FET analysis to infer transcription factors that control the gene sets.
A7r5-specific interactome and Master Regulator Analysis (MRA): From the 30 microarray samples that went through normalization and batch adjusting. Then, ARACNe built up regulatory interactions between the 14,004 genes and 891 rat transcription factors (TFs) through mutual information (MI) calculation. From the built A7r5-specific interactome, MRA-FET inferred master regulator (MR) candidates which control the SCE and SchB up- or down-effective gene set on A7r5 cells.
The 30 samples of 3 dataset are summarized in the meta-data spreadsheet. The meta-data have sample names with GSE accession number, microarray platform, normalization method, original experiment type. The matrix data txt file has normalized log2 expression values of 30 samples.

first: Sanghoon

last: Lee

first: Jung

middle: N

last: Chun

first: Eun-Jung

last: Park


title: Sequencing of patient tumor samples and cancer cell lines for endotype identification in multiple cancer types

status: Public on Oct 02 2019

first: Noah

last: Berlow

address: 12655 SW Beaverdam Rd

institute: CC-TDI

summary: DNA and RNA were isolated from snap frozen or FFPE primary tumor tissue, or from cultured and preserved cell cultures. All sequencing was performed at the Beijing Genomics Institute.

overall_design: Tumor tissues were unperturbed from procurement to preservation, so there are no experimental conditions for any of the samples submitted. All culture conditions were based on established culture protocols for each cell line.

middle: E

first: Cora

last: Ricker

first: Charles

last: Keller


status: Public on Sep 24 2019

city: Shanghai

first: Lixing

last: Zhan

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: To identify potential unique miRs that contribute to shaping the intestinal stemness in colitis, we analyzed the miRNome of colonic crypt stem cells from DSS-induced colitis mice.

overall_design: microRNAs profiles of cilonic crypt stem cells isolated from wild type (WT) mice (8-week-old) which were pretreated with normal drinking water or 3% dextran sulfate sodium (DSS) for 7 days were generated by Agilent Mouse miRNA (8*60K) V21.0 microarray.

first: Lele

last: Song

first: Renxu

last: Chang


title: Effect of miR-494-3p on LPS-treated intestinal epithelial cells isolated from C57BL/6 mice

summary: The microenvironment of injured mucosa has important effects on intestinal stem cell self-renewal and reconstruction of epithelial barrier function in inflammatory bowel disease (IBD). However, the precise status of the interactions between intestinal epithelial cell (IEC) injury, particularly intestinal crypt absence, and microenvironment in IBD is not completely understood. We identified miR-494-3p as important for protection of colonic stemness in intestinal inflammation colonic organoid culture. A novel cytokine-cytokine receptor, EDA-A2/EDA2R, could suppress colonic stemness and epithelial repair during IBD. During intestinal inflammation, high level of LP macrophage-derived EDA-A2 inhibited the nuclear β-catenin/c-Myc axis and organoid growth by targeting EDA2R in colonic crypt stem cells. We further demonstrated that the pro-inflammatory cytokines IL-1β and IL-6 are capable of stimulating macrophages to release EDA-A2 during colitis. Secondly, we identified the cross-talk among IECs, colonic crypts, and lamina propria (LP) macrophages in miR-494-3p-mediated colitis. Furthermore, our study showed that miR-494-3p deficiency in IECs promoted LP macrophage recruitment and M1 activation in DSS-induced colitis mice. In addition, we identified miR-494-3p as critical to dampening IEC injury; specifically, miR-494-3p inhibited inflammation-induced IKKβ/NF-κB activation by targeting the IKKβ 3’UTR in IECs. As such, administration of adequate amounts of a miR-494-3p agomire attenuate colitis in vivo. Consistent with this inference, we showed that miR-494-3p levels were decreased in colonic crypts and serum in colitis mice, and loss of miR-494 potentiated the severity of colonic colitis. Our clinical data on the interactions between miR-494-3p levels in serum exosomes & colonic tissues and associated outcomes support the clinical relevance of miR-494-3p in IBD. The miR-494-3p agomir system, which we designed permits local delivery in vivo in this study, significantly ameliorated the severity of colonic colitis. Our findings no only uncover a miR-494-3p-mediated cross-talk mechanism by which inflamed colonic LP macrophages integrate signals from IECs to regulate colonic stemness and colonic epithelial repair/homeostasis. The miR-494-3p agomir may serve as a potential therapeutic approach in IBD.

overall_design: mRNA profiles of intestinal epithelial cells from C57BL/6 mice (male, 8-week-old) which were pretreated with 1μg/ml LPS for 24 hours were generated by deep sequencing, using BGISEQ-500 RS RNA-Seq.


title: Effect of miR-494 deficiency on colonic crypt stem cells isolated from dextran sulfate sodium-induced colitis mice

overall_design: mRNA profiles of wild type (WT) and miR-494-/- (knockout, KO) mice (8-week-old) which were pretreated with 3% dextran sulfate sodium for 7 days were generated by deep sequencing, using Illumina Hiseq 2500.


title: Derivation and characterization of chimera-competent eXtra-Embryonic eNdoderm (XEN) cells from pig blastocysts

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: We report for the first time, the derivation and characterization of extra-embryonic endoderm (XEN) cells from primitive endoderm (PrE) of porcine (p) embryos. The pXEN cells can be reliably and reproducibly generated from parthenogenic, in vitro or in vivo derived embryos, and express canonical PrE or XEN cell genes (GATA4, GATA6, SOX17, SALL4, FOXA2, and HNF4A). Transcriptome analysis of pXEN cells revealed close resemblance to yolk sac than any other embryonic or extraembryonic tissue. When introduced into blastocyst stage embryo, the pXEN cells contributed to wide-spread chimerism including visceral yolk sac, chorion, as well as embryonic gut and liver primordium in the fetus. The pXEN cells were shown to be an efficient nuclear donor for generating cloned offspring. Taken together, pXEN cells fulfil a longstanding need for a stable, chimera-competent, and nuclear transfer-compatible porcine embryonic cells with applications for genome editing in livestock.

overall_design: We collected samples at four tissues (eXtraEmbryonic  eNdoderm stem (XEN) cells from primitive endoderm of an in vivo blastocyst, XEN cells from primitive endoderm of in vitro parthenogenetic (PG) blastocyst, a Day 7 IVF blastocyst and D28 Yolk Sac from AI) for each treatment and for each  tissue we had three biological replicates.

first: Bhanu

last: Telugu

first: Chi


title: A comparison of evolutionary changes and constraints on gene regulation between fin and limb development

status: Public on Sep 17 2019

city: Wako

first: Koh

last: Onimaru

state: Saitama

address: 312 Information Science Building, 2-1 Hirosawa

institute: Center for Biosystems Dynamics Research

sample_organism:
Mus musculus
Chiloscyllium punctatum

platform_organism:
Mus musculus
Chiloscyllium punctatum


title: A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [ATAC-seq]

summary: We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

overall_design: ATAC-seq analyses of mouse limb development

first: Kaori

last: Tatsumi

first: Chiharu

last: Tanegashima

first: Mitsutaka

last: Kadota

first: Osamu

last: Nishimura

first: Shigehiro

last: Kuraku


title: A comparison of evolutionary changes and constraints on gene regulation between fin and limb development [RNA-seq]

overall_design: RNA-seq analyses of mouse limb and bamboo shark fin development.


title: Post-transcriptional gene regulation by microRNA-194 promotes neuroendocrine transdifferentiation in prostate cancer

status: Public on Sep 09 2019

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: Potent therapeutic inhibition of the androgen receptor (AR) in prostate adenocarcinoma can lead to the emergence of neuroendocrine prostate cancer (NEPC), a phenomenon associated with enhanced cell plasticity. Here, we show that microRNA-194 (miR-194) is a regulator of epithelial-neuroendocrine transdifferentiation. In clinical prostate cancer samples, miR-194 expression and activity were elevated in NEPC and inversely correlated with AR signalling. Over-expression of miR-194 facilitated the emergence of neuroendocrine features in prostate cancer cells, a process mediated by its ability to directly target a suite of genes involved in cell plasticity. One such target gene was FOXA1, which encodes a transcription factor with a vital role in maintaining the prostate epithelial lineage. Importantly, a miR-194 inhibitor blocked epithelial-neuroendocrine transdifferentiation and inhibited the growth of cell lines and patient-derived organoids possessing neuroendocrine features. Overall, our study reveals a post-transcriptional mechanism regulating the plasticity of prostate cancer cells and provides a rationale for targeting miR-194 in NEPC.

overall_design: RNA-seq of 22RV1 cells transfected with a miR-194 mimic or a negative control

first: Rayzel

last: Fernandes

first: John

last: Toubia

first: Wayne

middle: D

last: Tilley

first: Theresa

last: Hickey

first: Gregory

last: Goodall


overall_design: HITS-CLIP for 22RV1 cells transfected with a miR-194 mimic or a negative control

first: B

last: Dredge

first: Andrew

last: Bert

first: Philip

last: Gregory


title: MicroRNA-194 promotes lineage plasticity in advanced prostate cancer

overall_design: Refer to individual Series


title: CNV analysis of normal brain and glioma samples

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

summary: Aberrant DNA methylation is a well-defined feature of cancer cells that is commonly associated to transcriptional alteration. Nonetheless, a primary role of this defect in genome-wide cancer-associated gene misregulation is still being questioned.  Here, we used adult glioma, a widespread type of brain tumor, to evaluate the relative contribution of DNA methylation-dependent and -independent mechanisms on transcriptional alteration at CpG-island/promoter-associated genes in cancer cells.   By extensive molecular analyses conducted in both IDH wild-type (IDHwt) and IDH mutated (IDHmut) samples, we show that DNA hypermethylation affects only a minority of genes that show a loss or a gain of expression. In IDHwt samples, for instance, more than 75% of aberrantly repressed genes do not display DNA methylation defect at their CpG-island promoter. Rather, an alteration in the H3K27me3 signature is the predominant molecular defect at misregulated genes. We also observed that a bivalent chromatin signature in stem cell might not only predispose genes to hypermethylation, as widely documented, but more generally to all type of transcriptional alterations. In addition, we evidenced that transcriptional strength in healthy brain influences the choice between DNA methylation- or H3K27me3- associated silencing pathway at repressed genes in glioma. Combined our study supports a model whereby the altered developmental control of H3K27me3 dynamics, and more specifically defects in the interplay between polycomb protein complexes and brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells.  Together our study provides a comprehensive and revisited picture of epigenetic gene deregulations in cancer. Our observations are also of importance for the design of drugs that aims to target cancer epigenetic defects.

overall_design: copy-number assay has been performed using the Genome-Wide Human CytoScan HD Array (Affymetrix, CA, USA). DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.

first: Franck

last: Court

first: Philippe

last: Arnaud


title: Gene expression profiles of mouse cervical primary cells

status: Public on Sep 01 2019

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

summary: The cellular origin of cervical cancers remains unclear. Revealing molecular details of transformation in this tissue has been hampered by the lack of culture systems, resembling the in vivo cervical architecture. Here we established a long-term in vitro 3D cervical organoid model derived from stem cells of human or mouse cervical tissue which recapitulates the in vivo stratified ectocervical and columnar endocervical epithelium. Stratified and columnar cervical epithelia arise from two discrete unipotent stem cell populations of the endocervix. Unique stem cell signatures reveal a dependency on intrinsic Notch and Wnt microenvironmental signals. The genetic signatures of KRT5+ stratified vs KRT7+ columnar cervical cells establish discrete groups of cervical cancer of the squamous and adenocarcinoma types, respectively. Cervical tissue morphology is guided by the interplay of two discrete unipotent cervical stem cell populations and the spatio-temporal distribution of signals from the stroma.

overall_design: Primary cells were isolated from murine cervix specimen as described in the accompanying publication, cultured in Matrigel and cultured for 3d or 2 weeks. Total RNA was extracted from samples and hybridized on Agilent-8x60k Human custom arrays as single-color hybridizations.

first: Cindrilla

last: Chumduri

first: Rajendra

last: Kumar Gurumurthy

first: Hilmar

last: Berger


title: Gene expression profiles of cultured stem cells and organoids from the uterine cervix of human and mouse

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Hypusine Biosynthesis in β Cells Links Polyamine Metabolism to Facultative Cellular Proliferation to Maintain Glucose Homeostasis

status: Public on Aug 30 2019

city: Chicago

first: Raghavendra

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

summary: Deoxyhypusine synthase (DHPS) utilizes the polyamine spermidine to catalyze the hypusine modification of the mRNA translation factor eIF5A and promotes oncogenesis through poorly-defined mechanisms.  Because germline deletion of Dhps is embryonically lethal, its role in normal postnatal cellular function in vivo remains unknown.  We generated a mouse model that allows for inducible, postnatal deletion of Dhps specifically in postnatal islet β cells, which function to maintain glucose homeostasis.  Removal of Dhps did not have an effect under normal physiologic conditions.  However, upon development of insulin resistance, which induces β-cell proliferation, Dhps deletion caused alterations in proteins required for mRNA translation, reduced production of the cell cycle molecule Cyclin D2, impaired β-cell proliferation, and overt diabetes.  We found that hypusine biosynthesis was downstream of protein kinase C-ζ and was required for c-Myc-induced proliferation.  Our studies reveal a requirement for DHPS in β cells to link polyamines to mRNA translation to effect facultative cellular proliferation and glucose homeostasis.

overall_design: RNA sequencing data from RNA isolated from pancreatic islets from control or Dhsp β cell specific mice (C57.DhpsloxP.MIP1-CreERT)


title: miRNA profiling of human saphenous vein pericyte exosomes

status: Public on Aug 31 2019

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

summary: Human saphenous vein perciytes (hSVPs) were proved increase angiogenesis in mouse myocardial infarction model by producing and releasing miR-132, which has proangiogenic, prosurvival, and antifibrotic activity. To investigate whether their exosomes have a role in their proangiogenic activity, we examined exosomes secreted by these cells. Nanoparticle tracking analysis (NTA) results indicated the presence of exosome size particles in the preparations. Experiments performed with hypoxic (1% O2) human umbilical vein endothelial cells (HUVECs) confirmed that the pericyte exosomes had proangiogenic and anti-apoptotic features. To understand the miRNA cargo of these exosomes that is important in their unique properties, we performed a miRNA array for profiling of 752 miRNAs.

overall_design: Human saphenous vein pericyte exosomes were collected from cell media of 3 different donors and their miRNA profile was determined using the miRCURY LNA™ Universal RT microRNA PCR system from Exiqon.


title: Gene expression profiles of human cervical primary cells from ecto- and endocervix

overall_design: Primary cells were isolated from healthy tissue of surgery specimen taken from ecto and/or endocervix of patients undergoing hysterectomy or cononization, cultured in 2D, transferred to Matrigel and cultured for 3d or 2weeks. Total RNA was extracted from samples and hybridized on Agilent-8x60k Human custom arrays as single-color hybridizations.


title: Unconventional ST2- and CD127-negative lung ILC2 populations are induced by Alternaria

status: Public on Aug 22 2019

city: La Jolla

first: Taylor

last: Doherty

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Background: Alternaria exposure is associated with severe asthma in humans.  Alternaria exposure in mice potently activates group 2 innate lymphoid cells (ILC2s) via the IL-33/ST2 axis and causes ILC2s to robustly secrete type 2 cytokines.  Objective: Our aim was to determine whether conventionally used ILC2 markers, ST2 (IL-33R) and CD127 (IL-7Ra), were sufficient to identify all Th2-cytokine producing ILCs after Alternaria exposure.  Methods: Mice received intranasal Alternaria for three days prior to analysis.  Lung ILCs were identified by flow cytometry as CD45+Lineage−Thy1.2+ lymphocyte-sized cells, divided into four subsets based on ST2 and CD127 expression, and stained for intracellular cytokines and transcription factors. Sort-purified ILC subpopulations were also analyzed by RNA sequencing and qPCR. Results:  Alternaria exposure led to accumulation of all ILC populations regardless of ST2 or CD127 expression.  Nearly half of the GATA-3+, IL-5+, and IL-13+ ILCs were “unconventional” as they were either single or double negative for ST2/CD127.  Further, these populations upregulated CD25, KLRG1, and ICOS after Alternaria challenge. Some activated unconventional IL-5+ ILC2s also produced IFNγ and IL-17A.   In addition to shared ILC2 transcripts (Gata3, Il5, Il13) in all populations, RNA-seq further identified novel transcripts enriched in each subset.  Finally, transcripts from all populations that correlated best with IL-5 and IL-13 production included Tnfrsf18, Ffar2, and Pde4b.  Conclusions: Unconventional ST2- and CD127-negative mouse lung ILC2 populations are induced by Alternaria.  Thus, commonly used lung ILC2 identification methods based on ST2 and CD127 do not accurately account for the total ILC2 burden and may exclude nearly half of these cells.

overall_design: Using a Alternaria (fungi) extract allergic mouse model of allergy, 4 different subsets of murine lung Innate Lymphoid Cells (ILC) were sorted based on immunophenotypic markers from dispersed lung tissue. Tot RNA was extracted from each samples and library preparation made in technical duplicates using the Smart-Seq2 protocol (Picelli et al. 2013 and Rosales et al. 2018). Sequencing libraries were sequenced on Illumina Platform. Standard differential gene expression analysis were performed and specific gene signature for each ILC subset were identified.

first: Kellen

last: Cavagnero

first: Jana

middle: H

last: Badrani

first: Alice

last: Wang

last: Seumois


title: Expression data from aortic smooth muscle cells (AoSMCs) from mouse

status: Public on Aug 10 2019

city: 重庆

first: Bi

last: xianjin

address: gaotaoyan

institute: tmmu

summary:
Chronic kidney disease (CKD) can induce AoSMCs premature senescence and phenotypic switching, which ultimately promotes AS progression and plaque vulnerability. However, the underlying mechanisms are still unknown.
To identify the underlying mechanisms of AoSMCs senescence and phenotype switching in CKD. We performed integrated microarray analysis of AoSMCs from normal-diet fed ApoE-/- (ND) mice, high fat-fed ApoE-/- (AS) mice and CKD ApoE-/- (accelerated atherosclerosis mouse model, AAS) mice.

overall_design: AoSMCs were sorted from the mice arteries using flow cytometry. Then, RNA was extracted from sorted AoSMCs and hybridized on Affymetrix microarrays. The groups are as described above: ND, AS and AAS group.

first: Xianjin

last: Bi

first: Changhong

last: Du


title: YTHDF1 Amplifies Wnt/β-Catenin Signaling to Promote Intestinal Stemness

city: Ithaca

first: Ji

last: Wan

state: NY

address: 303 Biotech 526 Campus Road

institute: Cornell University

summary: Wnt/β-catenin signaling is essential for intestinal stem cell homeostasis and aberrant activation of this signaling leads to tumorigenesis. Here we report a function of YTHDF1, an mRNA m6A reader, in mediating β-catenin hyperactivation. Wnt signaling promotes YTHDF1 expression at the translational level. YTHDF1 is dispensable for normal intestinal development in mice while essential for intestinal regeneration. Ythdf1 knockout reduces the stemness of intestinal stem cells, which blocks Wnt-driven tumorigenesis. Genome-wide analysis identifies a subset of Wnt signaling components regulated by YTHDF1 in an m6A-dependent manner. Moreover, we demonstrate that YTHDF1 promotes the translation of TCF7L2/TCF4 to augment β-catenin activation. Targeting YTHDF1 in the established tumors leads to tumor shrinkage and prolonged survival. Together, our studies uncover YTHDF1 as an integral regulator of Wnt signaling at the translational level during intestinal tumorigenesis, which might serve as a promising target for colorectal cancer therapy.

overall_design:
Investigating YTHDF1-regulated mRNA translation in HCT116 cells

Please note that the indiviual_ribosome_rna_profile.txt pcontains the processed data for GSM4054749-GSM4054754 samples and is linked to the GSM4054749 sample records.

first: Bing

last: Han

first: Saisai

last: Wei

first: Sujun

last: Yan

first: Tiezheng

last: Li

first: Jie

last: Xiang

first: Kangli

last: Liu

first: Rongpan

last: Bai

first: Jinghao

last: Sheng

first: Zhengping

last: Xu

first: Xiangwei

last: Gao


title: A large panel of isogenic APP and PSEN1 mutant human iPSC neurons reveals shared endosomal abnormalities mediated by APP b-CTFs, not Ab

status: Public on Aug 08 2019

city: Zurich

first: Claudia

last: Scheckel

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital Zurich

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


title: A large panel of isogenic APP and PSEN1 mutant human iPSC neurons reveals shared endosomal abnormalities mediated by APP b-CTFs, not Ab [RNA-seq]

summary: Human iPS cells with different mutations linked to Alzheimer's Disease were differentiated into neurons and subjected to RNAseq to identify Alzheimer's Disease associated changes

overall_design: RNAseq analysis of wildtype and three different mutated human iPS cells differentiated into neurons before

first: Elisabeth

last: Murphy

first: Robert

last: Darnell

first: Dylan

last: Kwart

first: Andrew

last: Gregg

first: Marc

last: Tessier-Lavigne


title: A large panel of isogenic APP and PSEN1 mutant human iPSC neurons reveals shared endosomal abnormalities mediated by APP b-CTFs, not Ab [ribosome profiling]

summary: Human iPS cells with different mutations linked to Alzheimer's Disease were differentiated into neurons and subjected to ribosome profiling to identify Alzheimer's Disease associated changes

overall_design: Ribosome profiling analysis of wildtype and three different mutated human iPS cells differentiated into neurons before


title: RNAseq analysis of whole Guts over expressing LaminDm0 or GFP in Enterocytes

status: Public on Jul 15 2019

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

summary: A hallmark of aging-related disease such as neurodegeneration, metabolic disorders, and cancer is the inability of differentiated cells to maintain their identity. In a search for identity regulators, we found that transcription factor Hey supervises the identity of differentiated enterocytes (ECs) in the adult Drosophila midgut. Lineage tracing of ECs established that Hey-deficient ECs lose differentiated identity, are unable to maintain their unique nuclear organization, and exhibit pathological reprograming. Orchestrating this organization, Hey specifies and maintains enhancer activity and nuclear lamins expression, remodeling nuclear architecture from a stem-cell configuration into a differentiated one. Moreover, maintaining this configuration of nuclear lamins is key for cell identity, and lamin misexpression overrides cell identities. At the tissue level, loss of Hey or expression of stem cell-related lamin (LamDm0) in ECs resulted in mis-differentiation, impaired epithelial integrity, and reduced organismal survival. Thus, a single transcription factor concomitantly supervises chromatin and nuclear organization, safeguarding cell identity

overall_design: mRNA of 4 biological repeats of Drosophila control (UAS>GFP)  guts and 4 biological repeats of Guts expressing UAS-LamDm0 in EC (enterocytes).

first: Naama

last: Flint-Brodsly

first: Eliya

last: Bitman-Lotan


title: Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle-stimulating hormone, retinoic acid and androgens

status: Public on Jul 03 2019

city: Bergen

first: Diego

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

summary: After an acclimatization period with increasing temperature (from 27 to 35⁰C; ~1⁰C increment/day), adult zebrafish males were exposed to 35⁰C for 14 days and injected with the cytostatic agent busulfan (single intraperitoneal injection after 7 days at 35⁰C; 40 mg/Kg). Then, fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection (i.e. 10 dpi) and the recovery of endogenous spermatogenesis ~14 dpi. Total RNA was isolated from (1) testes of untreated adult control zebrafish, (2) germ cell-depleted, and (3) testis tissue at the beginning of the recovery period, and selected samples were used for library preparation

overall_design: 15 samples in total were analyzed: 5 biological replicates from control testis samples, 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples

first: Luiz

last: Assis

first: Henk

last: van de Kant

first: Sjors

last: de Waard

last: Safian

first: Moline

middle: S

last: Lemos

first: Jan

last: Bogerd

first: Rüdiger

middle: W

last: Schulz


title: Expression data from D. melanogaster guts with suppression of Imd in progenitors or enterocytes

status: Public on Aug 01 2019

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

summary:
We used RNA-seq to examine transcriptional proflies of midguts with suppression of Imd in progenitors (e_* samples) or enterocytes (M_* samples) .
We found significant differences between the contributions of enterocyte IMD and progenitor IMD to intestinal homeostasis.

overall_design: Genotype control flies and flies with Imd inhibition were raised on regular food (Bloomington standard food) for 10 days at 29C after eclosion. Guts were dissected for RNA extraction and total RNA, in triplicate, sent to Novogene for library construction and sequencing.

first: Minjeong

last: Shin


title: Tcf1 regulates T lymphocyte lineage fidelity through its target genes Gata3 and Bcl11b

status: Public on Aug 28 2019

city: Leiden

first: Martijn

last: Cordes

state: Zuid-Holland

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Centre

summary: T cell factor 1 (Tcf1) is the first T cell‒specific protein induced in multipotent progenitors following Notch signaling in the thymus, leading to the activation of two major target genes, Gata3 and Bcl11b. Tcf1 deficiency results in partial arrests in T cell development high apoptosis, and increased development of B cells and myeloid cells. Phenotypically, fully T cell‒committed, Tcf1-deficient thymocytes have promiscuous gene expression, an altered epigenetic profile and can de-differentiate into more immature thymocytes and non-T cells. Expressing Bcl11b in Tcf1-deficient cells rescues T cell development, but does not strongly suppress the development of non-T cells; in contrast, expressing Gata3 suppresses the development of non-T cells, but does not rescue T cell development. Thus, T cell development is controlled by a minimal transcription factor network involving Notch signaling, Tcf1, and the subsequent division of labor between Bcl11b and Gata3, thereby ensuring a properly regulated T cell gene expression program

overall_design: 15,000 sorted DN3a (Lin - CD25 + CD44 - CD27 - ) and DN3b (Lin - CD25 + CD44 - CD27 + )cells

first: Laura

last: Garcia-Perez

first: Frank

last: Staal


title: DamID-based chromatin profiling of dHey in Kc cells

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chromatin binding profiling showed that dHey binds to enhancers in order to maintain EC identity, and co-regulates nuclear organization by governing a switch in the expression of nuclear lamins. Moreover, like dHey loss, de-regulated expression of lamins override identity programs. Thus, a single TF concomitantly orchestrates chromatin state, enhancer activity, and nuclear organization safeguarding differentiated cell identity
Chromatin profiling  using Dam-dHey shows  preferential recruitment to enhancers and transcriptionally active regions. Manuscript title: Specification and maintenance of enterocyte identity requires dHey and nuclear lamins

overall_design: For determaning dHey chromatin profile, Kc cells were transiently transfected with a plasmid encoding Dam_dHey or Dam alone. Two biological replicates (sample 1and 2) and one dye-swap techincal replicate (sample 3) were used.

last: Rincon


title: dHey


title: Transcriptome analysis of dHey knock down and control enterocytes, as well as isolated enteroblasts

summary:
Gene expression analses of adult female gut and purified gut cells.  Using the adult Drosophila gut, we found that the transcription factor dHey is a critical identity coordinator of differentiated enterocytes (EC`combined  expression analyses with chromatin binding profiling showed that dHey determines activity of enhancers in order to maintain EC identity, and co-regulates nuclear organization by governing a switch in the expression of nuclear lamins. Moreover, like dHey loss, de-regulated expression of lamins overrode identity programs. Thus, a single TF concomitantly orchestrates chromatin state, enhancer activity, and nuclear organization safeguarding differentiated cell identity.
Conditional dHey knock down in enterocytes (EC)  results in loss of the differnetated identity  of entrocytes and impacts gut homeostasis. In addtion  Using purified Enteroblast (EB)  we mappaed the changes in gene expression during EB to EC differentiation, and the impact of dhey on the gene expression of EBs. Manuscript title: Specification and maintenance of enterocyte identity requires dHey and nuclear lamins

overall_design: A 12 chip study using total RNA extracted from four different gentypes  (three separate biological repeats for each condtion). Samples 1-3 . Drosophila control (UAS>GFP)  gut.; Samples 4-6  Guts  where dHey was conditionally depelted in ECs.  Samples 7-9 control (UAS>GFP) purified EBs; samples 10-12  Purifed EBs  where dhey is condtitionally targeted. Each chip measures the expression level of 15,473 genes from Drosophila melanogaster with four 60-mer probes per target gene

last: Orian


title: Gene expression profiles of ATO-treated  and negative control cells

status: Public on Jul 01 2019

city: Shanghai

first: Xin

last: Zhang

state: -- Please select an option --

address: No.180 Fenglin Road, Zhongshan Hospital

institute: Liver Cancer Institution

summary:
Gene expression profile changes between ATO- treated and DMSO- treated  Huh7 and Hep3B cells were analyzed
To further explore the mechanism of ATO-induced differentiation, we performed a gene microarray assay to compare the differential gene expression profiles of low-dose ATO-treated (3 μM ATO treatment for 7 days) and negative control cells.

overall_design: Cells with different treatment were harvested at indicated time points for RNA extraction and hybridization on Affymetrix microarrays.

first: Xin-rong

last: Yang

first: Jian

last: Zhou


title: Basic characteristics of glioma stem cell and human glioblastoma

city: Nishinomiya city

first: Daisuke

last: Sakamoto

state: Hyogo

address: 1-1 Mukogawa-cho

department: Neurosurgery

institute: Hyogo College of Medicine

summary:
Glioma stem cells (GSCs) have been identified in glioma tissues and suggested to play important roles in the tumorigenesis of glioblastoma multiform (GBM). We established a novel cellular bioinformative pipeline that consisted of principal component analysis (PCA) with factor loading, intracellular pathway analysis, and immunopathway analysis and attempted to clarify the differences in gene expression profiles comprehensively among GSCs, a glioma cell line (U251), and a human GBM tissue (hGBM).
To this end, we extracted total RNAs from the GSCs, U251, and the hGBM, performed microarray, and applied the data to the bioinformatics analyses described above. As the results, PCA clearly distinguished the three groups. Moreover, the second principal component (PC2) distinguished the GSCs from the hGBM and U251; it reflected the characteristics of stemness. The factor loading for PC2 suggested MYCN, DPP4, and, MIF as contributing factors to the stemness of GSCs. We clarify the similarities and differences among samples such as the GSCs, U251, and hGBM.

overall_design: hGBM tissue was obtained by direct tumor resection at our institute. The patient was 54 years old female. Her integrated molecular pathological diagnosis was glioblastoma, IDH wild type. Human GSC lines X01 and X03 were provided from Dr. Akio Soeda at Gifu University. Human GBM cell line U251 was purchased from Japanese Collection of Research Bioresources Cell Bank. We extracted total RNAs from the GSCs, U251, and the hGBM, performed microarray, and applied the data to the bioinformatics analyses described above.

first: Toshinari

last: Takagi

first: Mitsugu

last: Fujita

first: Tomoko

last: Iida

first: Yasunori

last: Yoshida

first: Shinichi

last: Yoshimura


title: Locally advanced rectal cancer transcriptomic-based secretome analysis according to neoadjuvant chemoradiotherapy response

city: Vejle

first: Luisa

last: Matos do Canto

address: Beriderbakken 4

department: Biochemistry and Immunology

country: Denmark

institute: Vejle Hospital

summary: Most patients with locally advanced rectal cancer (LARC) present incomplete pathological response (pIR) to neoadjuvant chemoradiotherapy (nCRT). Despite the efforts to predict treatment response using tumor-molecular features, as differentially expressed genes, no molecule has proved to be a strong biomarker. The tumor secretome analysis is a promising strategy for biomarkers identification, which can be assessed using transcriptomic data. Here, we performed transcriptomic-based secretome analysis to select potentially secreted proteins using an in silico approach. The tumor expression profile of 28 LARC biopsies carefully selected and collected before nCRT was compared with normal rectal tissues (NT). The expression profile showed no significant differences between cases with complete (pCR) and incomplete response to nCRT. Genes with increased expression (pCR = 106 and pIR = 357) were used for secretome analysis based on public databases (Vesiclepedia, Human Cancer Secretome Database and Plasma and Proteome Database). Seventeen potentially secreted candidates (pCR=1, pIR=13 and 3 in both groups) were further investigated in two independent datasets (TCGA and GSE68204) confirming their over-expression in LARC. The potential secreted biomarkers were also confirmed as associated with the nCRT response (GSE68204). These putative proteins are candidates to be assessed in liquid biopsies aiming a personalized treatment in LARC patients.

overall_design: Total RNA was extracted from 28 rectal cancer samples and 5 normal rectal tissue fixed in formaline and embedded in paraffin. Global gene expression was detected using the Affymetrix Human Transcriptome Array 2.0.

middle: M

last: Canto

first: Sarah

last: Cury

first: Mateus

middle: C

last: Barros-Filho

first: Bruna

last: Kupper

first: Maria

last: Begnami

first: Cristovam

last: Scapulatempo-Neto

first: Robson

last: Carvalho

first: Fabio

last: Marchi

first: Samuel

last: Aguiar-Jr

first: Silvia

last: Rogatto


title: Camelina sativa, salinity tolerance, 1-aminocyclopropane-1-carboxylate deaminase, plant growth promoting bacteria, transgenic plants

status: Public on Jun 13 2019

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: Growth in soil inoculated with plant growth promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate |(ACC) deaminase or expressing of the corresponding acdS in transgenic lines reduces the decline in shoot length, shoot weight and photosynthetic capacity triggered by salt stress in Camelina sativa.  Reducing the levels of stress ethylene decreases the expression of salt stress-responsive genes, specifically genes involved in development, senescence, chlorosis and leaf abscission that are highly induced by salt to the levels that may have a less negative effect on growth and productivity. Moderate expression of acdS under the promoter of the rolD promoter or growing plants in soil treated with the PGPB Pseudomonas migulae 8R6, were more effective in eliminating the expression of the genes involved in ethylene production and/or signaling than expression under the more active Cauliflower Mosaic Virus 35S promoter.

overall_design: Four experimental conditions were tested:  the parental Camelina (DH55), a transgenic with acdS contitutively expressed (35S::acdS), a transgenic with acdS most highly expressed in roots  (rolD::acdS), and DH55 exposed to a plant growth promoting bacteria expressing acdS (8R6).  Camelina shoots (DH55, 35S::acdS, rolD::acdS, PGPB (8R6)) with salt treatment were analyzed.  3 replicates of each were compared.

first: Zohreh

last: Heydarian

first: Bernie

last: Glick

first: Margaret

last: Gruber

first: Cathy

last: Coutu


title: Expression data during differentiation from mouse embryonic stem cells with or without PKA activation

status: Public on Jul 23 2019

city: Kyoto

first: Tomohiro

last: Minakawa

address: Kawahara-cho, Shogoin, Sakyo-ku

institute: Cira, Kyoto Univ.

summary: The rate of cell differentiation is tightly controlled and critical for normal development and stem cell differentiation. However, so far it has been difficult to control the rate of ESCs differentiation. Here we report the acceleration of the differentiation rate due to the activation of protein kinase A (PKA) and the associated early loss of embryonic stem cells (ESCs) pluripotency markers and the early appearance of mesodermal and other germ layer cell markers.

overall_design: Total 9 samples were derived from ES cells and differentiating cells (D0.5, D1.5, D2.5, D3.5) in the absence or presence of doxycycline to induce a constitutive active form of PKA.

first: Yasuharu

last: Kanki


title: Pharmacodynamic Biomarkers and Differential Effects of TNF- and GM-CSF-Targeting Biologics in Rheumatoid Arthritis

city: Gaithersburg

first: Shiliang

last: Wang

state: MD

address: 1 Medimmune Way

department: Translational science

institute: Medimmune, Inc.

summary: A major unmet need in rheumatoid arthritis (RA) is the choice of treatment options for patients with an inadequate response to anti-TNF agents (anti-TNF–IR). In order to identify pharmacodynamic biomarkers and assess differential effects of TNF- and non–TNF-targeting agents on RA patients with an inadequate response to anti-TNF–IR in comparison with biologic-naïve patients, peripheral protein markers and gene expression levels in association with clinical response posttreatment in two disease strata were assessed in disease-modifying antirheumatic drug (DMARD)-IR and anti-TNF-IR patients. Serum proteomics results indicated the existence of specific pharmacodynamic markers for golimumab and mavrilimumab, regardless of prior anti-TNF treatment. In contrast, both antibodies induced early and sustained suppression of RA disease markers, including IL-6, CRP, IL2RA, and MMP1, in DMARD-IR patients. Golimumab-induced early changes rapidly returned toward baseline concentrations in anti-TNF–IR patients, whereas mavrilimumab-induced changes were maintained through Day 169. RNA sequencing demonstrated gene expression changes at Day 169 after administration of mavrilimumab but not golimumab in anti-TNF–IR patients. Additionally, receiver operating characteristic curve and regression analysis showed the association of early IL-6 change and subsequent clinical responses to golimumab in anti-TNF-IR patients. Our results revealed golimumab- and mavrilimumab-specific pharmacodynamic biomarkers, and demonstrated differential biomarker-treatment relationships in anti-TNF–IR and DMARD-IR patients respectively. Early IL-6 change after anti-TNF antibody treatment may be a potential predictive biomarker for selection of different treatment regimens in anti-TNF-IR patients.

overall_design:
For RNAseq study, PAXgene whole blood tubes were collected from 75 DMARD-IR and 63 anti-TNF-IR RA patients at baseline and at day 169 of post-treatment by golimumab and marvrilimumab. Whole transcriptome profiles of these patients and 20 health donors were generated from RNAseq data. Differentially expressed genes (DEG) resulted from drug-treatment were identified by pairwise comparisons between post-treatment and baseline data of the same patients. DEGs related with RA disease were identified by comparing baseline data with the data of health donors.

WARNING: Submitter provided only baseline data to GEO.

first: Xiang

last: Guo


title: Using RNA Seq to investigate adaptation mechanisms in P. aeruginosa

status: Public on Jul 08 2019

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

summary:
We demonstrate that the versatile environmental bacterium Pseudomonas aeruginosa adapts a virulence phenotype after serial passage in Galleria mellonella as an invertebrate model host. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under non-inducing rich medium conditions. Transcriptional reprogramming seemed to be induced by a host-specific food source as reprogramming was also observed upon cultivation of P. aeruginosa in medium supplemented with polyunsaturated long-chain fatty acids.
Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from LB-cultures grown to an OD600 =2.  The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings.

overall_design: Isolate CH2658 was subjected to in vivo and in vitro evolution experiments in this study. This isolate was obtained from the lab of G. Gastmeier, Charite Berlin, Germany. The in vivo passages (using G. mellonella) are named CH2658 I-IV corresponding to passages 1 4. The last passage CH2658 IV corresponds to the “evolved strain” and was passaged in LB (four days, two passages a day) to generate revertants which are referred to as CH2658 Rev1-4 corresponding to samples from day1-4. The last passage CH2658 Rev4 is called “revertant”. Additionally, the clinical isolate was passaged under in vitro conditions in the presence of linolenic acid (Roth) with (CH2658 Lil+P) and without paraffin (CH2658 Lil). As controls, CH2658 was passaged in LB (CH2658 LB) and in LB supplemented with paraffin (CH2658 LB+P). The in vitro passage experiment was conducted for four days and two passages a day.

first: Adrian

last: Kordes

first: Nora

last: Grahl

first: Michal

last: Koska

first: Matthias

last: Preuße

first: Alejandro

last: Arce-Rodriguez

first: Wolf-Rainer

last: Abraham

first: Volkhard

last: Kaever


title: RNAseq in Idiopathic Pulmonary Fibrosis

status: Public on May 29 2019

city: Bad Nauheim

first: Karla

last: Rubio

address: Parkstrasse 1

department: Lung Cancer Epigenetics

institute: Max Planck Institute for Heart and Lung Research

summary: Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive and highly lethal lung disease with unknown etiology and poor prognosis.

overall_design: RNA_Seq Data from nuclear extracts from healthy Ctrl and IPF patient-derived primary fibroblasts

first: Guillermo

last: Barreto

first: Stephanie

last: Dobersch

first: Julio

last: Cordero

first: Stephan

last: Günther


title: High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq

status: Public on Apr 17 2019

city: San Francisco

first: Leqian

last: Liu

address: 1700 4th street

department: BTS

institute: UCSF

summary: We report the development and application of isogenic colony sequencing to profile heterogeneity among yeast colonies. We profiled transcriptomes of the opaque-white switching in C. albicans colonies and an ARO4 mutagenesis library in S. cerevisiae colonies.

sample_organism:
Saccharomyces cerevisiae
Candida albicans

overall_design: microgel-culture Drop-seq

first: Chiraj

last: Dalal

first: Ben

last: Heineike

first: Adam

last: Abate


title: Synergy between variant PRC1 complexes defines Polycomb-mediated gene repression

status: Public on Apr 25 2019

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

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

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome Analysis of PBMCs in peripheral blood of patients with hepatocellular carcinoma

status: Public on Mar 07 2019

city: chongqing

first: lei

last: bo

address: gaotan yan

institute: Army Medical University

summary: The aim of this study was to analyze the expression profile of circRNAs in PBMCs in peripheral blood of patients with hepatocellular carcinoma (HCC) by next-generation sequencing, and to identify potential markers for early diagnosis and prognosis of HCC, and to lay a foundation for further study on the mechanism of this molecule in PBMCs.

overall_design: Analysis of PBMCs transcripts in peripheral blood of HCC and normal controls

first: Zongman

last: Tian

first: Shaomeng

last: Peng


title: Multiple myeloma immunoglobulin lambda translocations portend poor prognosis

status: Public on Mar 13 2019

city: Atlanta

first: Benjamin

last: Barwick

state: GA

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

department: Hematology and Medical Oncology

country: USA

institute: Emory University

summary: Multiple myeloma is a malignancy of antibody-secreting plasma cells. Most patients benefit from current therapies, however, 20% of patients relapse or die within two years. To better understand and identify these ‘high-risk’ cases, we analyzed the translocation landscape of myeloma from 795 newly-diagnosed patients by whole genome sequencing from the CoMMpass study. Translocations involving the immunoglobulin lambda (IgL) locus were identified in 10% of patients, and were indicative of poor prognosis. Importantly, 70% of IgL translocations co-occurred with hyperdiploid disease, a marker of standard risk, potentially resulting in the misclassification of IgL-translocated myeloma. Most IgL-translocations coincided with focal amplifications that were centered on the 3’ enhancer. Patients with IgL-translocations failed to benefit from immunomodulatory imide drugs (IMiDs), which target the lymphocyte-specific transcription factor IKZF1 that is bound to the IgL 3’ enhancer at some of the highest levels in the myeloma epigenome. These data implicate IgL-translocation as a driver of poor prognosis which may be due in part to IMID resistance.

overall_design: Several myeloma cell lines were characterized for chromatin accessibility


title: Transcriptome sequencing of two Lake Baikal endemic (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) transcriptome species from the Baikal region subjected to different stressors: quantification by reduced assemblies

status: Public on May 23 2019

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

summary: The project aims at describing the transcriptome composition and differential expression of genes in response to different stressors (elevated temperature, heavy metals (cadmium) and organic pollutants (phenanthrene)).

sample_organism:
Eulimnogammarus verrucosus
Gammarus lacustris
Eulimnogammarus cyaneus

overall_design:
Individuals of three amphipod species were subjected to temperature or chemical stresses. Mixed samples from different conditions were used to create de novo transcriptome assemblies with Trinity, redundant transcripts were removed with the evidentailgene pipeline, and only transcripts with matches to metazoan sequences were retained. These assemblies were also submitted to TSA. After that, transcript quantiifcation was performed with salmon and further processed with the DESeq2 package for R. BioProject: PRJNA505233. SRA study: SRP169548.

The samples in this series have identical raw data with the samples in GSE122811 but the processed data and FASTA files are different.

first: Daria

last: Bedulina

first: Lorena

last: Rivarola‐Duarte

first: Denis

last: Axenov‐Gribanov

first: Anton

last: Gurkov

first: Yulia

last: Lubyaga

first: Kseniya

last: Vereshchagina

first: Jörg

last: Hackermüller

first: Steve

last: Hoffmann

first: Christian

last: Otto

first: Frank

last: Jühling

last: Schreiber

first: Ekaterina

last: Madyarova

first: Zhanna

last: Shatilina

first: Lena

last: Jakob

first: Magnus

last: Lucassen

first: Franz

last: Sartoris

first: Hans‐Otto

last: Pörtner

first: Peter

last: Stadler

first: Till

last: Luckenbach

first: Maxim

last: Timofeyev


title: Collagen 22α1 is a TGFβ early response gene in human skin that mediates the fibroblast to myofibroblast transition

status: Public on Apr 02 2019

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

institute: Medical University of South Carolina

summary: Systemic sclerosis (SSc) is a complex multi-system autoimmune disease characterized by immune dysregulation, vasculopathy, and organ fibrosis. Skin fibrosis causes high morbidity and impaired quality of life in affected individuals. In this study, we identified the COL22α1 gene associated with the pathogenesis of skin fibrosis through high-throughput RNA sequencing of human skin in organ culture. The expression levels of COL22α1 were significantly increased by TGFβ in ex vivo human skin tissues and normal human skin fibroblasts, while other fibrosis growth factors such as IL-6 and bleomycin modestly increased COL22α1 expression.

overall_design: Skin samples were cultured with TGFβ (10 ng/ml) or a vehicle control. Skin tissues were harvested at 48 hours.

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