title: Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas

status: Public on Jun 04 2019

city: Fuzhou

first: Guo

last: Zheng

state: Fujian

address: No.1 Xuefu North Road

department: Department of Bioinformatics

institute: Fujian Medical University

summary: The gastric adenocarcinoma cell line HGC-27 and colorectal adenocarcinoma cell line HCT-8 cells were grown in Roswell Park Memorial Institute (RPMI) 1640 medium (Hyclone, Logan, UT, USA.). The human hepatocellular carcinoma cell lines HepG2 and Huh-7 were cultured in Dulbecco’s modified Eagle's medium (DMEM) (Hyclone, Logan, UT, USA.).

overall_design: Gene expression profiles of four cancer cell lines were used to investigate the effects of melatonin in  gastrointestinal carcinomas

first: Zheng

last: Guo


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Psychotria genus (Rubiacaeae) from Cuba

status: Public on Jun 05 2019

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

country: France

institute: CNRS

type: Expression profiling by high throughput sequencing

summary: The leaf transcriptome of the nickel hyperaccumulator species Psychotria grandis and Psychotria costivenia  (Rubiaceae)  from  Cuba were compared to the closely related non-accumulator Psychotria revoluta, living on Gallery forest on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

sample_organism:
Psychotria grandis
Psychotria revoluta
Psychotria costivenia

overall_design: Leaves from independent plants of  Psychotria grandis, Psychotria costivenia and Psychotria revoluta were collected in their natural environment. RNA of the 6 independant samples were extracted and sequenced using the Illumina paired-end sequencing technology. Reads from one individual plant per species were assembled de novo to generate transcriptome sequences. The transcriptome of P. grandis was used as a reference to compare the expression of genes in the three species

first: Dubiel

middle: A

last: Gonzalez

first: Vanesa

middle: S

last: Garcia de la Torre

first: Stéphanie

last: Huguet

last: Merlot

first: Rosalina

last: Berazaín


title: Role of antibodies in peripheral blood leukocyte gene expression during influenza human challenge

status: Public on May 14 2019

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

overall_design: To study the effects of pre-existing immunity on peripheral blood gene expression responses to influenza virus challenge

first: Kathie-Anne

last: Walters

first: John

last: Kash

first: Jeffery

last: Taubenberger


title: Specific targeting of IL-1β activity to CD8+ T cells allows for safe use as a vaccine adjuvant

status: Public on Jul 23 2019

city: Gent

first: Bram

last: Van Den Eeckhout

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB-UGent

summary: Annual administration and reformulation of influenza vaccines is required for protection against seasonal infections. However, the induction of strong and long-lasting T cells is critical to reach broad and potentially lifelong antiviral immunity. The NLRP3 inflammasome and its product interleukin-1β (IL-1β) are pivotal mediators of cellular immune responses to influenza, yet, overactivation of these systems leads to side effects, which hamper clinical applications. Here, we present a bypass around these toxicities by targeting the activity of IL-1β to CD8+ T cells. Using this approach, we demonstrate safe inclusion of IL-1β as an adjuvant in vaccination strategies, leading to full protection of mice against a high influenza virus challenge dose by raising potent T cell responses. In conclusion, this paper proposes a class of IL-1β-based vaccine adjuvants and also provides further insight in the mechanics of cellular immune responses driven by IL-1β.

overall_design:
Groups: WIV alone (reference)/WIV+AddaVax (positive control)/WIV+WT IL-1b/WIV+CD8a ALN-1
Tissues/group: lungs and mediastinal lung-draining lymph nodes
Biological replicates/group: 3
Samples in total: 23
Sequencing: Illumina NextSeq500 High Output 75 (two single-end runs/sample)

contributor: VIB Flow Core
contributor: VIB Nucleomics Core

first: Lien

last: Van Hoecke

first: Elianne

last: Burg

first: Xavier

last: Saelens

first: Sarah

last: Gerlo


title: Transcriptional analysis of resting or inflamed murine Macrophages with Immune complex stimulation

status: Public on Mar 18 2019

city: Cambridge

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

summary: We wished to investigate differential effects of stimulation with immune complex on colonic macrophages taken from mice which were either healthy or had DSS induced colitis.

overall_design: 4 samples from resting mice, 8 from mice which have DSS induced inflammation. After extraction of macrophages from the colon half the samples were treated with OVA and half with OIC.

middle: R

first: Tomas

last: Castro-Dopico

first: Thomas

middle: W

last: Dennison

first: Menna

last: Clatworthy


title: RNA-seq transcript and gene data on zika exposed and zika naïve samples

status: Public on Apr 17 2019

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: RNA-seq count data at 3 timepoints was generated for Zika-exposed and Zika-naïve individuals in order to assess associated signatures

overall_design: RNA-seq count data at 3 timepoints was generated for Zika-exposed and Zika-naïve individuals, extracted from PAXgene RNA blood solution with the PAXgene Blood RNA Kit using DNase digestion and an additional clean-up using RNEasy MinElute kit.

first: Andrew

last: Kasarskis

first: Ana

last: Fernandez-Sesma


title: Single nucleotide variants (SNVs) associated with cutaneous melanoma (CM) risk and prognosis

city: Campinas

first: Benilton

middle: Sa

last: Carvalho

state: Sao Paulo

address: Tessália Vieira de Camargo, 126

department: Medical Genetics

country: Brazil

institute: Universidade Estadual de Campinas

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Abnormalities in pigmentation-related genes alter CM risk and prognosis.

overall_design: Two hundred and six individuals were analyzed in the first stage. Genomic DNA was extracted from leukocytes of peripheral blood of 103 CM patients and 103 controls using the QIAamp DNA Blood Midi Kit (Qiagen®, Canada), following manufacturer’s instructions

first: Cristiane

last: Oliveira

first: Gustavo

middle: J

last: Lourenço

first: Carmen

last: Leme


title: Differential expression of circRNA in adult and fetal mesenchymal stem cells and fibroblasts

status: Public on Mar 14 2019

city: Milan

first: Mario

last: Barilani

address: Via F. Sforza 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary: Stem cell identity is typically controlled by master regulatory genes and by complex circuits of a growing family of noncoding RNA (ncRNA) molecules, which impact cell phenotype maintenance and plasticity. Yet, these self-reinforcing regulatory networks are still poorly defined for human primary mesenchymal stem cells (MSCs), in particular with respect to ncRNA. Circular RNAs (circRNAs) are a new class of RNAs commonly generated from protein-coding genes by back-splicing events, resulting in a highly stable RNA structure, devoid of free 5’ and 3’ ends. Even though circRNAs are expressed across eukaryotes and may regulate gene expression, their precise mechanisms of action in stem cell biology have remained unexplored until now. In this study, for the first time, we determined that a circRNA has a role in the control of MSC fate and undifferentiated identity. Our starting point was high-throughput expression profiling of MSCs from different sources, which revealed a large number of differentially expressed circRNAs.

overall_design: n=3 donors for each cell population. A preliminary analysis was performed on n=1 donor for each cell population (BMMSC_1, CBMSC_1, HSF_1). A second separate expression profile was obtained on n=2 donors for each cell population (remaining samples). A ComBat correction was applied to take into account batch effect (see raw and normalized data).

first: Alessandro

last: Cherubini

first: Lorenza

last: Lazzari


title: Expression data from LEF siRNA transfected Jurkat cells

city: Istanbul

first: Sema

last: Sirma Ekmekci

address: Vakif Gureba cad

department: Genetics

country: Turkey

institute: Istanbul University, Aziz Sancar Institute of Experimental Medicine

summary:
To identify novel target genes regulated by LEF1 transcription factor in T-ALL, we examined changes in the genome-wide gene expression profile by microarray in siRNA mediated LEF1 knockdown Jurkat cells.
We used microarray to determine the differential gene expression in LEF downregulated Jurkat cells by LEF1 siRNA.

overall_design: LEF1 expression downregulated in Jurkat cells using siRNA. Non-targetting siRNA transfected cells used as a control. RNA extracted 24 hours after transfection.

last: Ekmekci

first: Zeliha

last: Emrence

first: Burcu

last: Salman

first: Melda

last: Sarıman

first: Neslihan

last: Abacı

first: Cumhur

first: Çağrı

last: Güleç


title: Impaired sensing of Fe status in opt3-2 leads to opposite transcriptional programs in leaves and roots, and uncovers novel roles for reactive oxygen species signaling within the Fe homeostasis network

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

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

overall_design: Refer to individual Series


title: Rapid activation of distinct member of multigene families in Plasmodium spp.

status: Public on Mar 12 2019

city: Singapore

first: Radoslaw

middle: Igor

last: Omelianczyk

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: The objective of this study is to provide a novel method to study multigene proteins in Plasmodium spp. The method is based on selection linked integration (SLI), which allows positive selection of genomic integration events. By targeting specific members of multigene families, parasites are being selected for not only genomic integration but also expression of the targeted gene under its endogenous promoter

overall_design: P. falciparum parasites strain 3D7 transfected with pSLI plasmids targeting either a specific rifin, stevor or var gene. Transfectant were  selected for genomic integration and class switch. Integration was confirmed by PCR and sequencing prior to RNA isolation and microarray hybridization. In brief, 20 ml parasite cultures were synchronized twice per day with 5% (v/v) sorbitol in water to obtain tightly synchronized ring-stage parasites. A total of 12 RNA samples were collected, including 3 parental 3D7 controls, at 18, 24 and 30 hours post invasion. RNA were extracted and synthesis and amplification of cDNA was carried out as previosuly described in Bozdech, Z., S. Mok & A. P. Gupta, (2013). cDNA generated was used for microarray hybridizations against a common RNA reference pool of P. falciparum 3D7 strain.

middle: I

first: Han

middle: P

last: Loh

first: Marvin

last: Chew

first: Regina

last: Hoo

first: Jianzhu

last: Chen

first: Peter

last: Preiser


title: Regenerative origin of metastasis stem cells

status: Public on Mar 04 2019

first: Richard

last: Koche

address: 430 East 67th Street

institute: Sloan Kettering Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Assaying binding of REST to DNA with ChIP-seq reveals the role of REST in transcriptional regulation in colorectal cancer (CRC) metastatic stem cells (MetSCs). REST is especially relevant to regulation of L1CAM expression.

overall_design: ChIP-seq of binding of REST to DNA

first: Karuna

last: Ganesh

first: Joan

last: Massagué

first: Vincent

last: Reuter


title: Transcriptional analysis of skeletal muscles from wild type and mdx/mTR mice

status: Public on Mar 06 2019

first: Christopher

middle: L

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

summary: We report RNA sequencing data from tibialis anterior muscles of 4 month old male wild type C57Bl/6 mice and mdx/mTR mice (generated in the C57Bl/6 background), which lack the dystrophin and telomerase RNA component genes.

overall_design: Differential expression of mRNAs were evaluated between the tibialis anterior muscles of C57Bl/6 and mdx/mTR mice

first: Douglas

last: Van Pelt


title: Identification of differentially expressed lncRNAs in CpG ODN-activated macrophage

status: Public on Mar 01 2019

city: Changsha

first: ying

last: zheng

state: Hunan

address: 139 Renmin Middle Rd

country: China

institute: The second Xiangya Hospital of Central South University

summary: The innate immune system is the first line of defense against microbial pathogens. The activated innate immune system plays important roles in eliciting antimicrobial defenses. Despite the benefits of innate immune responses, excessive inflammation will cause host damage. Thus, tight regulation of these processes is required for the maintenance of immune homeostasis. Recently, a new class of long non-coding RNAs (lncRNAs) has emerged as important regulators in many physiological and pathological processes. Dysregulated lncRNAs have been found to be associated with excessive or uncontrolled inflammation. In this study, we employed a lncRNA microarray-based profiling assay to detect changes of lncRNAs at different stages of CpG ODN-induced macrophage activation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed based on the function of mRNAs. Co-expression and network potential targeting relationship were constructed according to the microarray results and bioinformatics predictions. Our findings revealed the involvement of lncRNAs in the process of CpG ODN-induced macrophage activation.

overall_design: The RAW264.7 cells were treated with 1 μM ODN1826. At 0h, 4h, 8h, or 16h after stimulation, the cells were harvested for RNA isolation. Total RNA was extracted, and the quantity and quality were assessed by NanoDrop. And RNA integrity was detected by capillary electrophoresis using RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 . Then, the sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. In a brief, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cy-3-dCTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

first: Ying

last: Zheng


title: Immune profiling of pre- and post-treatment breast cancer tissues from the SOWG S0800 randomized neoadjuvant trail of weekly nab-paclitaxel with or without bevacizumab and dose dense doxorubicin and cyclophosphamide

status: Public on Feb 01 2019

city: New Haven

first: Lajos

last: Pusztai

state: CT

address: 300 George St., Suite 120

institute: Yale University

summary: Background: We examined changes in the tumor immune microenvironment during neoadjuvant chemotherapy by comparing immune gene mRNA expression, tumor infiltrating lymphocyte (TIL) count and PD-L1 protein expression in pre- and post-treatment tissues. Methods: Paired pre- and post- treatment tumor samples from 60 patients were profiled using the Nanostring Immune Oncology 360 platform to measure the expression of 770 immune-related genes that also allowed us to test 14 immune cell type and 27 previously published prognostic and immuno therapy response predictive gene signatures. All samples were also assessed for TIL counts and PD-L1 protein expression by immunohistochemistry. Gene expression levels were compared by paired t-test with Bonferroni correction. TIL count, PD-L1 protein expression and immune gene signatures were compared using Wilcoxon signed-rank test. Baseline immune markers were correlated with pathologic complete response (pCR) using estrogen receptor (ER) and treatment adjusted logistic regression. Results: TIL counts were significantly lower in post- compared to pre-treatment samples (17% vs 7%, p=0.013) but stromal PD-L1 protein expression was not significantly different. At baseline, higher TIL count and PD-L1 expression were associated with pCR. High expression of a mast cell metagene was associated with residual disease (RD). No individual genes or VEGF gene signature were associated with benefit from bevacizumab. In patients with RD (n=31), genes involved with tissue repair and inflammation (DUSP1, EGR1, IL6, ATF3, CD36, CXCL2, CD69, NGFR, KLF2, THBD, DAB2) showed significantly higher expression after therapy while most other immune markers decreased. The T effector, T-reg, MHC-I, MHC-II, IFNgamma, STAT-1 and M1 macrophage gene signatures were all significantly lower in post- versus pre-treatment samples and only the IL8/VEGFR and T-helper gene signatures showed higher expression after therapy. Conclusions: High mast cell gene expression is associated with lower pCR rate. TIL counts and most immune parameters decrease after neoadjuvant chemotherapy.

overall_design: Immume profilings of 50 pre- and 50 post-treatment breast cancer samples were measured using the Nanostring Immune Oncology 360 platform.

first: Xiaotong

last: Li

first: Sarah

last: Warren


title: Combinatorial inhibition of Notch and FLT3 exerts synergistic cytotoxic effects in FLT3/ITD+ acute myeloid leukemia

status: Public on Feb 23 2019

city: Wuhan

first: Dan

state: Hubei

address: 1095 Jie-Fang Avenue

institute: Tongji Hospital

summary: we observed synergistic cytotoxic effects, preferentially reducing cell proliferation and inducing apoptosis in FLT3/ITD+ AML cell lines and in primary AML cells. Furthermore, the combination of FLT3-TKI and GSI eradicated leukemic cells and prolonged survival in a FLT3/ITD+ patient derived xenograft (PDX) AML model. Mechanistically, decreased expression of CXCR3 that lead to down-regulated ERK signaling was partially responsible for the observed synergy. Our findings suggest that combined therapies of FLT3-TKIs with GSI may be exploited as a potential therapeutic strategy to treat FLT3/ITD+ AML.

overall_design: Analysis of FLT3/ITD+ AML cell lines (MV4-11 and MOLM13) treated with DMSO, 2.5nM AC220, 25uM DAPT or 2.5nM AC220 plus 25uM DAPT (Combo). The combination of AC220 plus DAPT AC220 exerts synergistic cytotoxic effects. Results provide insight into the synergism of FLT3/ITD+ AML cells from combined treatment.

first: Jue

last: Wang


title: Role of HcpR in nitrosative stress protection

status: Public on Feb 14 2019

city: Richmond

first: Janina

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

summary: HcpR has been shown to be required for growth of Porphyromonas gingivalis in the presence of nitrite (Infect Immun. 2012 Sep;80(9):3319-31. doi: 10.1128/IAI.00561-12. Epub 2012 Jul 9).  It also has been shown to regulate the expression of hcp.  To define the entire regulon of HcpR RNAseq examination of the wild type and mutant (deficient in HcpR) strains have been used to define the regulon in response to nitrite exposure in bacteria grown in the presence and absence of nitrite. Four biological replicates were prepared for both, wild type and mutant strains grown in the presence and absence of nitrite.

overall_design: Wild type Porphyromonas gingivalis W83 strain (2802) was used to compare to the hcpR-deficient strain (2807).

first: Benjamin

last: Belvin


title: Single-cell analysis reveals heterogeneity of high endothelial venules and different regulation of genes controlling lymphocyte entry to lymph nodes

city: Toulouse

first: Jean-Philippe

last: Girard

address: 205 Route de Narbonne

institute: Institut de Pharmacologie et de Biologie Structurale

summary: High endothelial venules (HEVs) are specialized blood vessels allowing recirculation of naïve lymphocytes through lymphoid organs. Here, using full length single-cell RNA sequencing, RNA-FISH, flow cytometry and immunohistofluorescence, we reveal the heterogeneity of HEVs in adult mouse peripheral lymph nodes (PLNs) under conditions of homeostasis, antigenic stimulation and after inhibition of lymphotoxin-b receptor (LTbR) signaling. We demonstrate that HEV endothelial cells are in an activated state during homeostasis, and we identify the genes characteristic of the differentiated HEV phenotype. We show that LTbR signaling regulates many HEV genes and pathways in resting PLNs, and that immune stimulation induces a global and temporary inflammatory phenotype in HEVs without compromising their ability to recruit naïve lymphocytes. Most importantly, we uncover differences in the regulation of genes controlling lymphocyte trafficking, Glycam1, Fut7, Gcnt1, Chst4, B3gnt3 and Ccl21a, that have implications for HEV function and regulation in health and disease.

overall_design: Comparison of High Endothelial Cells and Blood Endothelial Cells from mouse lymph nodes under 4 different conditions with a total of 220 single cells.

first: Krystle

middle: M

last: Veerman


title: ChAP-Seq analysis of HrrA in C. glutamicum

status: Public on Jan 31 2019

city: Juelich

first: Andrei

last: Filipchyk

address: Wilhelm-Johnen-Straße

country: Germany

institute: FZ-Juelich

summary: We evaluated how HrrA binding in response to 4 µM heme as initial stimulus. Analysis was performed prior to the addition of heme (T0) and 0.5, 2, 4, 9, and 24 h after the heme pulse (in medium containing no other iron source).

overall_design: Examination of HrrA binding profile at consecutive time points after heme induction

first: Marc

last: Keppel

first: Ulrike

last: Viets

first: Eugen

last: Pfiefer


title: Single cell sequencing of human mesenchymal stem/stromal cells (MSCs) upon inflammatory licensing

status: Public on May 31 2019

city: Erlangen

first: Arif

middle: B

last: Ekici

address: Schwabachanlage 10

institute: Institute of Human Genetics

summary: We report changes of the transcriptome profile at the level of single MSCs in response to inflammatory trigger. This process is known as "MSC licensing" and represents a physiological counterregulatory mechanism. MSCs are a heterogenous population, which is highlighted by the according clustering.

overall_design: Bone marrow-derived MSCs from healthy donors were cultured for 24 h in presence/absence of IFN-γ (10 ng/ml) and TNF-α (15 ng/ml). Subsequently, cells were subjected to droplet single-cell RNA-sequencing.

first: Dimitrios

last: Mougiakakos


title: Trained immunity-promoting nanobiologics suppress tumor growth and potentiate checkpoint blockade immunotherapy

status: Public on Feb 21 2019

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - Location AMC

summary:
We developed a nanobiologic platform that is designed to induce trained immunity. Through extensive in vitro screening, involving stability measurements and training assays on human and murine monocytes, as well as in vivo mouse biodistribution experiments, a bone marrow-avid nanobiologic lead candidate, named MTP10-HDL, was identified. MTP10-HDL’s potent anti-tumor capabilities were established in a dose response study. We found that these anti-tumor effects are the result of trained immunity-induced myelopoiesis, caused by the activation of hematopoietic stem cells and multipotent progenitors in the bone marrow. Moreover, we established that MTP10-HDL treatment overcomes the immunosuppressive tumor microenvironment (TME) by reducing the number of myeloid-derived suppressor cells and tumor associated macrophages. The immunologically rebalanced TME potentiated concurrent checkpoint blockade therapy, resulting in augmented anti-tumor efficacy. In conclusion, we show that rationally designed nanobiologics can promote trained immunity and elicit a durable anti-tumor response, as a monotherapy or in combination with checkpoint blockade.
We examined MTP10-HDL’s effect on hematopoiesis to elucidate the mechanism underlying its anti-tumor effect in C57BL/6 mice without tumors. We performed RNA sequencing (RNA-seq) to investigate HSC activation. Bone marrow from treated and untreated mice was harvested and the HSCs were isolated by flow sorting.

overall_design:
RNA-Seq: HSCs and MPPs of 4 mice were pooled to 1 sample for RNA isolation. 7 PBS samples were compared with 6 MTP10-HDL samples for HSC, 2 PBS samples were compared with 3 MTP10-HDL samples for MPP.
ATAC-Seq: HSCs and MPPs of 6 mice were pooled to 1 sample for ATAC-Seq library creation. 3 PBS samples were compared with 3 MTP10-HDL samples for both HSC and MPP.

first: Bram

last: Priem

first: Mandy

last: van Leent

first: Abraham

last: Teunissen

first: Alexandros

last: Sofias

first: Vera

last: Mourits

first: Emma

middle: D

last: Klein

first: Roderick

last: Oosterwijk

first: Anu

middle: E

last: Meerwaldt

first: Esther

last: van Leeuwen

first: Elizabeth

last: Fisher

first: Karen

last: de Jong

first: Yiming

last: Zhao

first: Yohana

middle: C

last: Frederico

first: Paul

middle: H

last: Bomans

first: Heiner

last: Friedrich

first: Nico

last: Sommerdijk

first: Thomas

last: Reiner

first: Raphaël

last: Duivenvoorden

first: Eva

last: Zupančič

first: Julie

last: Di Martino

first: Ewelina

last: Kluza

first: Mohammad

last: Rashidian

first: Hidde

last: Ploegh

first: Rick

last: Dijkhuizen

first: Sjoerd

last: Hak

first: Carlos

last: Pérez-Medina

first: Jose

last: Bravo-Cordero

first: Menno

last: de Winther

first: Leo

last: Joosten

first: Andrea

last: van Elsas

first: Zahi

last: Fayad

first: Jordi

last: Ochando

first: Mihai

middle: G

last: Netea

first: Arjan

last: Griffioen

first: Willem


title: Transcriptome analysis of C. glutamicum wildtype cells and the deletion strain ΔhrrA

first: Andrei

last: Filipchyk

summary: We evaluated how HrrA binding (found by ChAP-Seq) impacts the expression of individual target genes, by analyzing the transcriptome of the C. glutamicum wild type strain (ATCC 13032) as well as a ∆hrrA mutant. RNA-Seq analysis was performed prior to the addition of heme (T0) and 0.5 and 4 h after the heme pulse (in medium containing no other iron source).

overall_design:
Examination of a wildtype strain and a ∆hrrA strain in response to heme at three different timepoints
Please note that the *genecounts.tsv processed data was generated from both wild type and hrrA samples (per each time point) and is linked to the corresponding WT sample records.

first: Marc

last: Keppel

first: Ulrike

last: Viets

first: Eugen

last: Pfeifer

first: Max

last: Huennefeld


title: Expression data from stem like glioblastoma cells treated with vehicle, or BRD protein inhibitor, or HDAC inhibitor or the combination

status: Public on Jan 09 2019

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Inhibition of BRD proteins by OTX015, and inhibition of HDAC by Panobinostat and the combination alters the gene expression of the glioblastoma cells.
To compare the drug effect and find out the resonal of the synergisty of the bombination, we performed microarray experiments.

overall_design: Stem like glioblastoma cell NCH644 were either treated with vehicle, or OTX015, or Panobinostat, or OTX015+ Panobinostat for 24 hours. Total RNA were collected from each treatment group and Miroarray were performed. Biological duplicates were done and analyzed.

first: Yiru

last: Zhang

first: Markus

last: Siegelin


title: Gene expression of patient derived xenograft glioblastoma treated with DMSO control or Panobinostat.

summary:
Panobinostat is a non-selective histone deactylase inhibitor which has been approved by FDA for treatment of mutiple myeloma. Whether and how the drug works on glioblastoma remains unclear.
Here we treated mice implanted with patient derived xenograft glioblastoma G43 with DMSO or Panobinostat and harvest the tumors for microarray analysis for gene expression results.

overall_design: Tumors were collected from DMSO or Panobinostat treated mice. Total RNA were collected and microarray were performed to compare the differences of gene expression.


title: Fatty Acids Promote the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells

status: Public on Dec 19 2018

city: Seattle

first: Charles

middle: E.

last: Murry

address: 850 Republican St.

institute: Institute for Stem Cell & Regenerative Medicine

summary: Although human pluripotent stem cells-derived cardiomyocytes (hPSC-CMs) have emerged as a novel platform for heart regeneration, disease modeling, and drug screening, their immaturity significantly hinders their application. A hallmark of postnatal cardiomyocyte maturation is the metabolic substrate switch from glucose to fatty acids. We hypothesized that fatty acid supplementation would enhance hPSC-CM maturation. Fatty acid treatment induces cardiomyocyte hypertrophy and significantly increases cardiomyocyte force production. The improvement in force generation is accompanied by enhanced calcium transient peak height and kinetics, and by increased action potential upstroke velocity. Fatty acids enhance mitochondrial respiratory reserve capacity. RNA sequencing showed fatty acid treatment upregulates genes involved in fatty acid β-oxidation and downregulates genes in lipid synthesis. Signal pathway analyses reveal that fatty acid treatment results in phosphorylation of multiple intracellular kinases. Thus, fatty acids increase human cardiomyocyte hypertrophy, force generation, calcium dynamics, action potential upstroke velocity, and oxidative capacity.  This enhanced maturation should facilitate hPSC-CMs usage for cell therapy, disease modeling, and drug/toxicity screens.

overall_design: We did RNA-seq of hPSC-CM culture in control and fatty acid media, with two biological replicates per condition

first: Yuliang

last: Wang


title: The Transcriptional Regulator SnoN Promotes the Proliferation of Cerebellar Granule Neuron Precursors in the Postnatal Mouse Brain

status: Public on Dec 10 2018

city: St. Louis

first: Guoyan

last: Zhao

state: MO

address: 660 South Euclid Ave.

department: Genetics & Neurology

institute: Washington University

summary:
Control of neuronal precursor cell proliferation is essential for normal brain development, and deregulation of this fundamental developmental event contributes to brain diseases. Typically, neuronal precursor cell proliferation extends over long periods of time during brain development. However, how neuronal precursor proliferation is regulated in a temporally specific manner remains to be elucidated. Here, we report that conditional knockout of the
transcriptional regulator SnoN in cerebellar granule neuron precursors robustly inhibits the proliferation of these cells and promotes their cell cycle exit at later stages of cerebellar development in the postnatal mouse brain. In laser capture microdissection followed by RNASeq, designed to profile gene expression specifically in the external granule layer (EGL) of the cerebellum, we find that SnoN promotes the expression of cell proliferation genes and concomitantly represses differentiation genes in granule neuron precursors in vivo. Remarkably,
bioinformatics analyses reveal that SnoN-regulated genes contain binding sites for the transcription factors N-myc and Pax6, which promote the proliferation and differentiation of granule neuron precursors, respectively. Accordingly, we uncover novel physical interactions of SnoN with N-myc and Pax6 in cells. In behavior analyses, conditional knockout of SnoN impairs cerebellar-dependent learning in a delayed eye-blink conditioning paradigm, suggesting that SnoN-regulation of granule neuron precursor proliferation bears functional consequences at the
organismal level. Our findings define a novel function and mechanism for the major transcriptional regulator SnoN in the control of granule neuron precursor proliferation in the mammalian brain.

overall_design: We deployed a laser captured microdissection (lcm) approach to focus our analyses of SnoN specifically in the EGL of the developing mouse cerebellum. The transcriptome of laser captured microdissected EGL from conditional SnoN knockout and control littermate mice were were measured using RNA-seq.

first: Xiaoying

last: Chen

first: Ayan

last: Chanda

first: Yoshiho

last: Ikeuchi

first: Xiaoqing

first: Jared

middle: V

last: Goodman

first: Naveen

last: Reddy

first: Shahriyar

last: Majidi

first: Dennis

middle: Y

last: Wu

first: Sarah

last: Smith

first: Abigail

last: Godec

first: Anna

last: Oldenborg

first: Harrison

last: Gabel

first: Shirin

last: Bonni

first: Azad


overall_design: Total RNA-seq from the cerebellum of SnoN conditional knockout and wildtype mice

last: Zhang

last: VGoodman

last: YWu

middle: W


title: RNA-seq of nine primary human cell types exposed in vitro to methylprednisolone

status: Public on Jan 21 2019

city: Bethesda

first: Luis

last: Franco

state: MD

address: 9000 Rockville Pike

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: Glucocorticoids remain the most widely used class of anti-inflammatory and immunosuppressive agents. They act primarily by binding to the glucocorticoid receptor, resulting in direct and indirect effects on gene expression. The current understanding of glucocorticoid effects on transcription in human cells is based mostly on studies of cancer cell lines, immortalized cell lines, or highly mixed populations of primary cells (such as peripheral blood mononuclear cells). To advance the understanding of the transcriptome-wide effects of glucocorticoids on highly pure populations of primary human cells, we performed RNA-seq on nine such cell populations at two time points after in vitro exposure to methylprednisolone or vehicle.

overall_design: Nine cell types were studied: four hematopoietic (circulating B cells, CD4+ T cells, monocytes, and neutrophils) and five non-hematopoietic (endothelial cells, fibroblasts, myoblasts, osteoblasts, and preadipocytes). Each cell type was obtained from a separate cohort of 4 unrelated healthy human donors (4 biological replicates per cell type: BR1 - BR4). Cells form each donor were independently cultured and exposed in vitro to glucocorticoid or vehicle. Non-hematopoietic cells were incubated until the early plateau phase of growth, then exposed to methylprednisolone or vehicle. Hematopoietic cells were collected from peripheral blood, purified by magnetic selection (negative selection for B cells, CD4+ T cells and neutrophils; positive selection for monocytes). Purified B cells, CD4+ T cells, and monocytes were incubated overnight, then exposed to methylprednisolone or vehicle. Purified neutrophils were cultured for 4 hours, then exposed to methylprednisolone or vehicle. Ethanol was used as a vehicle for methylprednisolone. Estimated final concentrations were 8500 mcg/L (22.7 mcM) for methylprednisolone and 0.07% (15.57 mM) for ethanol (vehicle). For each cell type, samples were collected at two time points after treatment with methylprednisolone or vehicle: 2 hours and 6 hours. Samples were collected into TRIzol reagent and frozen at -80°C prior to RNA extraction. RNA-seq data for all samples is made available in this GEO Series.

first: Manasi

last: Gadkari

first: Sangeeta

last: Kumari


status: Public on Dec 09 2018

first: Guoyan

last: Zhao

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

overall_design: Refer to individual Series


title: Integrative molecular and clinical analysis of intrahepatic cholangiocarcinoma reveals two prognostic subclassees

status: Public on Dec 01 2018

city: Daegu

first: Keun Soo

last: Ahn

address: 56 Dalseong ro, Junggu

department: Surgery

country: South Korea

institute: Keimyung University Dongsan Medical Center

summary: Intrahepatic cholangiocarcioma has two molecular classification of intrahepatic CCA with distinct clinical, pathological, biological and prognostic differences

overall_design: Examination of 2 different cluster of intrahepatic cholangiocarcinoma based on RNA sequencing by NGS

first: Keun

middle: S

first: Daniel

last: O'Brien

first: Yu

middle: N

last: Kang

first: Taofic

last: Mounajjed

first: Yong

last: Kim

first: Tae-Seok

first: Mitesh

middle: J

last: Borad

first: Lewis

middle: R

last: Roberts

first: Koo


title: SOS1-mutant cells share a similar transcriptional profile as KRAS G12V cells

status: Public on Nov 06 2018

city: Cambridge

first: Diana

last: Cai

address: Massachusetts Hall

institute: Harvard University

summary: RNA sequencing in NIH-3T3 cells

overall_design: Transcriptome analysis for three biological replicates of pLX307, SOS1 WT, SOS1 N233Y, and KRAS G12V cells


title: Transcriptomic responses to diet quality and viral infection in Apis mellifera

status: Public on Oct 30 2018

city: Ames

first: Lindsay

last: Rutter

state: IA

address: 2014 Molecular Biology Building

department: Bioinformatics and Computational Biology Program

institute: Iowa State University

summary:
Purpose: Parts of Europe and the United States have witnessed dramatic losses in commercially managed honey bees over the past decade to what is considered an unsustainable extent. The large-scale loss of honey bees has considerable implications for the agricultural economy because honey bees are one of the leading pollinators of numerous crops. Honey bee declines have been associated with several interactive factors. Poor nutrition and viral infection are two environmental stressors that pose heightened dangers to honey bee health.

Methods: We used RNA-sequencing to examine how monofloral diets (Rockrose and Chestnut) and Israeli acute paralysis virus inoculation influence gene expression patterns in honey bees.

Results: We found a considerable nutritional response, with almost 2,000 transcripts changing with diet quality. The majority of these genes were over-represented for nutrient signaling (insulin resistance) and immune response (Notch signaling and JaK-STAT pathways). Somewhat unexpectedly, the transcriptomic response to viral infection was fairly limited. We only found 43 transcripts to be differentially expressed, some with known immune functions (argonaute-2), transcriptional regulation, and muscle contraction. We created contrasts to determine if any protective mechanisms of good diet were due to direct effects on immune function (resistance) or indirect effects on energy availability (tolerance). A similar number of resistance and tolerance candidate differentially expressed genes were found, suggesting both processes may play significant roles in dietary buffering from pathogen infection. We also compared the virus main effect in our study (polyandrous colonies) to that obtained in a previous study (single-drone colonies) and verified significant overlap in differential expression despite visualization methods showing differences in the noisiness levels between these two datasets.

Conclusions: Through transcriptional contrasts and functional enrichment analysis, we add to evidence of feedbacks between diet and disease in honey bees. We also show that comparing results derived from polyandrous colonies (which are typically more natural) and single-drone colonies (which usually yield more signal) may allow researchers to identify transcriptomic patterns in honey bees that are concurrently less artificial and less noisy. Altogether, we hope this work underlines possible merits of using data visualization techniques and multiple datasets when interpreting RNA-sequencing studies.

overall_design: Two factor RNA-sequencing experiment with four treatment groups (Rockrose pollen without IAPV exposure, Chestnut pollen without IAPV exposure, Rockrose pollen with IAPV exposure, and Chestnut pollen with IAPV exposure)

first: Jimena

last: Carrillo-Tripp

first: Bryony

last: Bonning

first: Dianne

last: Cook

first: Amy

last: Toth

first: Adam

last: Dolezal


title: Loss of TET2 results in DNA methylation changes in mouse GC B-cells (hMeDIP-Seq data set)

status: Public on Oct 08 2018

city: Farmington

first: Sheng

last: Li

address: 10 Discovery Drive

institute: The Jackson Laboratory

type: Methylation profiling by high throughput sequencing

summary: Absence of Tet2 at mouse cells results in loss of hydroxymethylcytosine

overall_design: Hydroxymethylmethylcytosine DNA immunoprecipitation sequencing (hMeDIP-seq) of mouse  TET2 WT and KO GC B-cells

first: Ari

last: Melnick

first: Maria

last: Del Pilar Dominguez

first: Wojciech

last: Rosikiewicz

first: Parveen

last: Kumar


title: A mouse tissue atlas of small non-coding RNA

status: Public on Sep 28 2018

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

summary: We systematically profiled the expression of four sRNA classes across eleven mouse tissues by RNA-seq. Using fourteen biological replicates spanning both genders, we identified 3,962 various sRNAs; 473 of these sRNAs are novel and identified for the first time by this work.

overall_design: Small non-coding RNA expression across 11 normal mouse tissues, 14 individuals

first: Stephen

last: Quake


title: Loss of TET2 results in gene expression represssion in mouse GC B-cells and lymphoma cells (RNA-Seq data set)

summary: Absence of Tet2 at mouse cells results in reduced gene expression

overall_design: Genome-wide profiling of total RNA transcript levels in mouse cells: TET2 WT and KO GC B-cells and shTet2 and control lymphoma B cells


title: Differential expression of  transcriptome under copper stress in Microcystis aeruginosa. PCC 7806

status: Public on Dec 21 2018

first: Yuanyuan

last: Chen

address: Shizishan street 1

department: College of Fisheries

institute: Huazhong Agricultural University

summary: The  cyanobacterium Microcystis aeruginosa PCC 7806 was used for a systematic survey of the relationship between copper and microcystins synthesis. Here we have used microarrays to interrogate the global responses to copper additions at 0.5 micromolar (µM) and 3 µM of copper. From the gene level, microarray studies (3 µM copper supplementation) showed effects on iron, sulfur, glutaredoxin and dehydratase homeostasis gene expression. However, in 0.5 µM groups, those genes that significantly enriched in 3 µM groups regulatory were not all found. In the microarray data for copper stress (3 µM) revealed a broad effect on the expression of iron-sulphur cluster associated pathways, such as cysteine biosynthesis. All of these data indicate that Fe / S cluster biogenesis and/or repair were affected by copper in M. aeruginosa.

overall_design: 9 RNA samples (1 control & 2 stress conditions, 3 times each)

first: Xuezhen

last: Zhang


title: Gene expression in microdissected embryonic regions during mouse axis elongation.

status: Public on Oct 06 2018

city: Edinburgh

first: Filip

middle: J.

last: Wymeersch

address: 5, Little France Drive

department: MRC Centre for Regenerative Medicine, Institute for Stem Cell Research

institute: University of Edinburgh

summary: This dataset contains spatiotemporal transcriptome information on different axial progenitors throughout mouse axis elongation. Neuromesodermal Progenitors (NMPs), Lateral and Paraxial Mesoderm Progenitors (LPMPs), and Notochord Progenitors (NotoPs) show distinct expression profiles. Extensive similarity exist between NMPs and their immediate mesoderm-committed descendants at each stage investigated. Over time transcriptional changes occur in LPMPs and NMPs, with the major change occurring in NMPs between early somitogenesis and completion of trunk morphogenesis. In contrast, NotoPs contain a more stable transcriptome over time.

overall_design: Total RNA was obtained from microdissected, embryonic regions from wildtype mouse embryos at different embryonic stages during axis elongation. Regions of a single type were pooled to constitute one sample.

first: Stavroula

last: Skylaki

first: Yali

last: Huang

first: Julia

middle: A

last: Watson

first: Constantinos

last: Economou

first: Carylyn

last: Marek-Johnston

first: Simon

last: Tomlinson

first: Valerie

last: Wilson


title: The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation [RNA-seq]

status: Public on May 04 2018

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary: Mammalian neurons express extra-long pre-mRNAs which are vulnerable to misregualtion of transcriptional elongation or processing but their regulation is still largely unknown. Here we found that RNA-binding protein PSF is specifically expressed in differentiated neuron of embryonic mouse brain and is essential for the expression of extra-long neuronal gene. HITS-CLIP indicated co-transcriptional binding of PSF to the nascent pre-mRNAs. When PSF was disrupted, pre-mRNA level of long genes was down-regulated in the middle of their transcripts toward their 3’ ends. In Pol II ChIP-Seq, decrease of the RNA polymerase II density was observed parallel to pre-mRNAs, indicating that transcriptional elongation was impaired. Loss of PSF caused massive apoptosis in embryonic mouse brains and heterozygous PSF mutant mice displayed schizophrenia-like abnormal behaviors. Gene Ontology analysis demonstrated that PSF-regulated genes have essential functions at the late developmental stage of brains. Our findings indicate that PSF is required for the neuronal development through facilitating the transcriptional elongation of extra-long neuronal genes and dysfunction of PSF could be a cause of neurodevelopmental and psychiatric disorders.

overall_design: We analyzed polyA-tailed RNA profiles including transcribing RNAs in cerebral cortices from 3 control, 3 Sfpq+/- and 3 Sfpq-/- E13.5 mice embryos using HiSeq2000.

first: Akihide

last: Takeuchi

last: Iida

first: Masatoshi

last: Hagiwara


title: The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation [N2A_SFPQ_CLIP-seq]

overall_design: Sfpq CLIP-Seq was perfmored using anti-Sfpq antibody on differentiated Neuro2a cells based on eCLIP methods with modifications.

first: Masatsugu

last: Denawa


title: SIS-seq, a molecular ‘time machine’, connects single cell fate with gene programs

status: Public on Aug 28 2018

first: Luyi

last: Tian

address: 415 main st Cambridge

institute: Broad institute

summary: Conventional single cell RNA-seq methods are destructive, such that a given cell cannot also then be tested for fate and function, without a time machine. Here, we develop a clonal method SIS-seq, whereby single cells are allowed to divide, and progeny cells are assayed separately in SISter conditions; some for fate, others by RNA-seq. By cross-correlating fate and gene expression within a clone, and doing this for many clones, we can identify the earliest gene expression signatures of dendritic cell subset development. SIS-seq could be used to study other populations harboring clonal heterogeneity, including stem, reprogrammed and cancer cells to reveal the transcriptional origins of fate decisions.

overall_design: Single ubiquitin C-GFP+ Sca1+ ckit+ HSPCs were isolated from BM and cultured amongst a pool of BM filler cells from C57BL/6 mice, and supplemented with Flt3 ligand. After 2.5 days, wells were visually inspected for GFP+ clones, and those with 10 or more cells were mixed by pipetting, followed by equal volume separation into three parts; two replicate wells for further culture to test for fate at day 8, and the remaining fraction for single cell, or small cell number RNA-seq, using CEL-Seq2 to provide a transcriptional 'snapshot' of the clone prior to fate acquisition.

first: Jaring

last: Schreuder

first: Daniela

last: Amann-Zalcenstein

first: Jessica

last: Tran

first: Shian

last: Su

first: Matt

last: Ritchie

first: Shalin

last: Naik


title: Computational prediction of CTCF/cohesin-based intra-TAD (sbTAD) loops that insulate chromatin contacts and gene expression in mouse liver

status: Public on May 11 2018

first: David

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

summary: This SuperSeries is composed of the SubSeries listed below, and presents the high throuput sequencing datasets that were generated as part of a larger study that investigates the role of CTCF and cohesin as key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. This study presents and validates a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. The intra-TAD loops are proposed to be formed by the same loop extrusion mechanism as the larger TAD loops; their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity.


title: The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation [SFPQ_CLIP-seq]


title: An activation-induced immunoregulatory and tissue-residency program modulated by c-MAF in human memory Th17 cells [ChIP-seq] [RNA-seq]

status: Public on Sep 12 2018

city: Bellinzona

first: Samuele

last: Notarbartolo

address: Via Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

summary: T cell effector function is largely mediated through the release of pro-inflammatory cytokines that need to be tightly regulated to avoid tissue damage. Here we show that the anti-inflammatory cytokine IL-10 is produced by a subset of recently-activated human Th17 cells and is controlled by the selective up-regulation of the transcription factor c-MAF. In addition, recently-activated IL-10+ Th17 cells upregulate immunoregulatory genes and genes characteristic of tissue resident T cells. In contrast, recently activated IL-10- Th17 cells maintain a pro-inflammatory gene expression profile and upregulate homing receptors to recirculate from tissues to blood. By integrating ChIP-seq and RNA-seq analyses, we demonstrate that c-MAF plays a key role in orchestrating the immune-regulatory and tissue residency program of IL-10+ Th17 cells by binding to a large number of non-promoter regions with enhancer-like features. Thus, c-MAF may represent a relevant factor discriminating between immunoregulatory and pro-inflammatory human Th17 cells.

overall_design:
H3K27ac and c-MAF binding profile (ChIP-seq) in resting and recently-activated human Th17 subsets. 2 donor-matched replicates.
RNA-seq profile in resting and recently-activated human Th17 subsets, and transcriptomic profile of wt or c-MAF depleted recently-activated Th17-IL-10+. 2 donor-matched replicates

first: Federica

last: Sallusto

first: Dominik

last: Aschenbrenner

first: Mathilde

last: Foglierini

first: Dan

last: Hu


title: CTCF and Cohesin (Rad21) ChIP-seq in male mouse liver

summary: Sequencing files provided here include mouse liver ChIP-seq for CTCF and the cohesin subunit Rad21. These files are part of a larger study where we describe features of Topologically Associating Domains (TADs) and their impact on liver gene expression, then use these features to computationally predict subTAD structures not otherwise readily identifiable due to the low resolution of Hi-C.  Our findings reveal that CTCF-based subTAD loops maintain key insulating properties of TADs, and support the proposal that subTADs are formed by the same loop extrusion mechanism and contribute to nuclear architecture as intra-TAD scaffolds that further constrain enhancer-promoter interactions. This allows high expression of super enhancer target genes and individual genes within inactive TADs, and may be a broadly conserved mechanism of genomic regulation.

overall_design: CTCF and Cohesin (Rad21) ChIP-seq in mouse liver

first: Bryan

last: Matthews

first: Aram

last: Shin


title: Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline [cell populations]

status: Public on Jul 19 2018

city: Heidelberg

first: Natalie

last: Romanov

address: Meyerhofstr. 1

department: Structural and Computational Biology

institute: EMBL

summary: Diminishing potential to replace damaged tissues is a hallmark for ageing of somatic stem cells, but the mechanisms leading to ageing remain elusive. We present a proteome-wide atlas of age-associated alterations in human haematopoietic stem and progenitor cells (HPCs) along with five other cell types that constitute the bone marrow niche. For each, the abundance of a large fraction of the ~12,000 proteins identified was assessed in a cohort of healthy human subjects from different age. As the HPCs became older, pathways in central carbon metabolism exhibited features reminiscent of the Warburg effect where glycolytic intermediates are rerouted towards anabolism. Simultaneously, altered abundance of early regulators of HPC differentiation revealed a reduced functionality and a bias towards myeloid differentiation at the expense of lymphoid development. Ageing caused significant alterations in the bone marrow niche too, such as functionality of the pathways involved in HPC homing and lineage differentiation. The data represents a valuable resource for further in-depth mechanistic analyses, and for validation of knowledge gained from animal models.

overall_design: RNA-seq samples extracted from human bone marrow, from 6 cell populations (HPC, LYM, MON, ERP, GRA, MSC). Technical replicates are included for each donor and cell type. Technical replicates were produced by making independent libraries from the same RNA.

first: Marco

last: Hennrich


title: The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation [Neuro2A cells]

first: Kei

last: IIDA

overall_design:
(I) transcriptome anaysis in Sfpq-knockdown Neuro-2a cells using polyA selected total RNA; mRNAseq.
(II) transcriptome anaysis in Sfpq-knockdown Neuro-2a cells using ribosomal RNA deprived total RNA; RNAseq_rRNAdep.
(III) measurement of the genome-wide distribution of Pol II density in Sfpq-knockdown Neuro-2a cells using chromatin immunoprecipitaiton for Pol II followed by high-throughput DNA sequencing (ChIP-Seq).

first: Akihide

last: Takeuchi

first: Toshiaki

last: Tsubota

last: Iida

first: Masatsugu

last: Denawa

first: Masatoshi

last: Hagiwara


title: The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation


title: The RNA-binding protein Sfpq regulates long neuronal genes in transcriptional elongation [RNA-seq, rRNA-depleted]

overall_design: We analyzed polyA-tailed and non-polyA-tailed RNA profiles including transcribing RNAs in cerebral cortices from 3 control, 3 Sfpq+/- and 3 Sfpq-/- E13.5 mice embryos using HiSeq2000.

first: Kensuke

last: Ninomiya


title: Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline

overall_design: Refer to individual Series


title: Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline [single cells]

overall_design: Examination of myeloid- and lymphoid-primed sub-populations of HPCs across young and old donors


title: Annotation and functional clustering of circRNA expression in rhesus macaque brain during aging

status: Public on Nov 26 2018

city: wuhan

first: dong

last: chen

address: GaoXin 2nd Road

institute: ablife

summary: The abundance and function of circular RNAs (circRNAs) in mammalian brain have been reported, but their alterations in the biology of brain aging remain elusive. Here, using deep RNA profiling with linear RNA digestion by RNase R we explored a comprehensive map of changes in circRNA expression in rhesus macaque (macaca mulatta) brain in two age groups from adult (10 y) to aged (20 y) periods. Total 17,050 well expressed, stable circRNAs were identified. Cluster analysis reveals that dynamic changes in circRNA expression show the spatial-, sex- and age-biased specificities. On the basis of separate profiling of the RNAs, age-related circRNAs show differential correlation to host mRNA expression. Furthermore, two voltage-dependent L- and R-type calcium channel gene-derived circCACNA2D1 and circCACNA1E negatively regulate their host mRNA expression. Our results demonstrate the power of changes in circRNA expression to reveal insights into a potentially circRNA-mediated regulatory mechanism underlying the biology of brain aging.

overall_design: Examination of 8 different brain regions in Rhesus Macaque across the two ages ( 10- and 20-year old )

first: Jiali

last: Li

first: Yi

last: Zhang


title: Loss of TET2 results in DNA methylation changes in mouse GC B-cells (Bisulfite-Seq data set)

first: Sheng

summary: Absence of Tet2 at mouse cells results in gain of DNA methylation

overall_design: Enhanced reduced representation bisulfite sequencing (ERRBS) of mouse  TET2 WT and KO GC B-cells

first: Ari

last: Melnick

first: Maria

last: Del Pilar Dominguez

first: Wojciech

last: Rosikiewicz

first: Parveen

last: Kumar


title: LncRNA profile study during Human bone marrow-derived MSCs osteogenic differentiation: Day 0 vs Day 10

status: Public on Apr 19 2018

city: Guangzhou

first: tang

last: su'an

state: Guangdong

address: 107# Yan Jiang Road West

department: Department of Orthopedics

institute: Sun Yat-sen Memorial Hospital

summary: LncRNA transcriptional profiling of human  bone marrow-derived mesenchymal stem cells comparing control undifferentiated MSCs with Day 0 and Day 10 osteogenic differentiation stages

overall_design: Two-condition experiment, Day 0 vs Day 10. Day 0: 3 replicates, Day 10: 3 replicates.

first: Xie

last: Zhongyu

first: Wang

last: Peng

first: Tang

last: Su'an

first: Li

last: Jinteng

first: Shen

last: Huiyong


title: Phenotypic and genotypic relationships between meat quality characteristics and expression of target genes associated with broiler meat quality defects

status: Public on May 01 2018

city: Pathumthani

first: Yuwares

last: Malila

address: 113 Thailand Science Park Phahonyothin Road Khlong Nueng, Khlong Luang

country: Thailand

institute: National Center for Genetic Engineering and Biotechnology

summary: The objective of this project was to employ customized Agilent 8x60 chicken whole genome microarray to identify differentially expressed genes associated with white striping (WS) and wooden breast (WB) defects in breast meat collected from commercial broilers with different slaughter age. Following harvest of chicken breasts (n = 184), the breast samples were classified as based on their appearance into non-defect, WS or WB. The defective samples were further grouped based on defect severity (WS = mild, moderate, severe; WB = moderate, severe). A total numbers of 40 samples were selected to represent various degree of the defects. Total RNA from deep-frozen skeletal muscle was isolated, integrity check (RIN > 7.0) and subjected for one-colored microarray hybridization according to Agilent’s instruction. The array was designed (design ID: AMADID G4102A084792) based on the National Center for Biotechnology Information (NCBI) Gallus gallus Annotation Release 103 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Gallus_gallus/103/). Differential gene expression (p-value < 0.05) was confirmed using qPCR and droplet digital PCR. Biological pathways associated with WS and WB were identified.

overall_design: The microarray type used is a slide having 8 arrays with 56,457 features including control probes. A total numbers of 40 arrays were hybridized using one-color dye procedure. The fluorescent signal intensity obtained for each sample were normalized, analyzed and compared as follows. For WS, transcriptome profiles of the samples were compared as follows; severe WS (n=4) vs non-WS (n=4), severe WS vs mild WS (n=7), severe WS vs moderate WS (n=6). Overall, 21 samples were hybridized for the study of WS defect. For WB, three separate comparisons were designed; non-WB1 (n= 3) vs WB1 (n=2), non-WB2 (n=4) vs WB2 (n=3), non-WB3 (n=4) vs WB3 (n=3), where WB1 = samples collected from 49d broilers exhibiting severe WB and mild WS, WB2 = 49 broilers exhibiting severe WB and moderate WS, and WB3 = ≤45d broilers with severe WB and mild WS. Overall, 19 samples were chosen for the study of WB defect.

first: Tanaporn

last: Uengwetwanit

first: Sopacha

last: Arayamethakorn

first: Krittaporn

last: Thanatsang

first: Yanee

last: Srimarut

first: Juthawut

last: U-chupaj

first: Premsak

last: Chaiwiwattrakul

first: Wanilada

last: Rungrassamee

first: Wonnop

last: Visessanguan


title: Mechanical stretch induced transcriptomic profiles in cardiac myocytes II

status: Public on Mar 17 2018

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

summary: The effect of cyclic mecanical stretch on cardiac gene expression was studied in neonatal rat ventricular myocytes (NRVMs).

overall_design: The effect of cyclic mecanical stretch on cardiac gene expression was studied in neonatal rat ventricular myocytes (NRVMs) 1, 4, and 12 hours after start of the stretching. There are 5 biological replicates at each timepoint.

last: Rysä

first: Heikki

last: Ruskoaho


title: Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

status: Public on Feb 28 2018

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

summary: Methods:  mRNA profiles of retinoblastoma samples and para-tumor were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

overall_design: Retinoblastoma mRNA of retinoblastoma were generated by deep sequencing, using Illumina.

first: Xianqun

last: Fan


title: RNA-seq analysis of freshly isolated synovial fibroblast subsets from patients with rheumatoid arthritis

status: Public on Jan 19 2018

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

summary: Transcriptomics of distinct subpopulations of synovial fibroblasts from osteoarthritis and rheumatoid arthritis arthroplasty tissues.

overall_design:
We gated 7 subsets of synovial fibroblasts by protein surface markers and used RNA-seq to profile gene expression of cells taken from each gate. This data includes 25 samples from 4 rheumatoid arthritis patients.

*** Raw data are not available for this Series due to patient privacy concerns. The raw data will not be available through controlled-access resources such as dbGaP. The patients did not consent to genomic data sharing. ***

first: Fumitaka

last: Mizoguchi


title: Transcriptome dynamics during seed development in chickpea (JGK3)

status: Public on Dec 31 2017

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we aim to present a global view of transcriptome dynamics during seed development in a large-seeded chickpea (genotype JGK3). We generated about 1.5 billion high-quality reads from 24 libraries (leaf and seven seed developmental stages in three biological replicates) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between different samples/stages.

overall_design: We collected leaves from the field-grown chickpea plants during mid maturation stage of seed development. Seven different stages of seeds (whole seed) representing the major events occurring within the seed, were collected from the field-grown plants. The tissues were collected in at least three biological replicates. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the samples to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stages of seed development were identified.

first: Vikash

last: Singh

first: Vinay

last: Kumar

first: Rohini

last: Garg


title: Investigating the Gene Expression Profiles of Florida Manatees (Trichechus manatus latirostris) Rehabilitated Following a Red Tide

status: Public on Oct 01 2017

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: To investigate a Florida manatee (Trichechus manatus latirostris) mortality event following a red tide bloom in Southwest Florida, a RNA-Seq experiment was conducted.  Cell processes such as immune response, cell proliferation and differentiation and apoptosis were among the most affected by red tide. These were involved in potential diseases such as neoplasms, inflammation, and wounds and injuries, among others. There were both up-regulated and down-regulated genes, but the highest fold changes relative to controls were for genes that were down-regulated. Piccolo presynaptic cytomatrix protein (PCLO) gene, the one most down-regulated (fold change -9.93; p-value 0.0009) is associated with neurotransmitter release, cognitive functioning, neuronal loss, and neuronal synapse function. Another gene that has a similar function, ankyrin 2, neuronal, transcript variant 1 (ANK2) was also down-regulated (fold change -8.66; p-value 0.0023). ANK2 is associated with the stability of neuron synapses. Two immune genes, interleukin 6 (interferon, beta 2) (IL6) and zinc finger protein 804B (ZNF804B), were down-regulated (fold change -9.31; p-value 0.000003 and fold change -8.90; p-value 0.0164, respectively). Interleukin 6 encodes proteins involved in acute phase response, inflammation, and autoimmune response. ZNF804B is associated with neuronal chemokine and cytokine regulation, autoimmune response, and immune activation. The family with sequence similarity 186, member A (FAM186A) gene was down-regulated (fold change -8.79; p-value 0.0143). FAM186A gene mutation is associated with tumor metastasis in colorectal cancer tumors. Among the most up-regulated genes, CCAAT/enhancer binding protein (C/EBP) is involved in granulocytic differentiation and also involved with the immune system. Determining the differentially expressed genes associated with red tide enhances our understanding of manatee immune response to red tide toxins and aids in the development of red tide biomarkers. This information will better assist clinicians and researchers in diagnosing and treating future illnesses.

overall_design: White blood cell or ‘buffy coat’ samples were collected from manatees (n=4) rescued from a red tide affected area and transported to the Lowry Park Zoo in Tampa, FL for rehabilitation. A RNA-Seq experiment was conducted to identify differentially expressed genes in the red tide group compared to a control population of manatees (n=7) from Brevard County (Indian River Lagoon) and Crystal River, FL.

first: Rebecca

last: Lazensky

first: Margaret

last: Hunter

first: David

middle: M

last: Amador

first: Basima

last: Al-Khedery

first: Fahong

last: Yu

first: Cathy

last: Walsh

first: Matthew

last: Gitzendanner

first: Mike

first: Nancy

last: Denslow


title: Transcriptome dynamics during seed development in chickpea (Himchana)

summary: In this study, we aim to present a global view of transcriptome dynamics during seed development in a small-seeded chickpea (genotype Himchana 1). We generated about 1.5 billion high-quality reads from 24 libraries (leaf and seven seed developmental stages in three biological replicates) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between different samples/stages.


title: Unexpected Innovative Early Diagnosis in Autism Spectrum Disorder: Premature Tooth Eruption in ADNP-Mutated Children

status: Public on Jun 29 2017

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: The discovery of activity-dependent neuroprotective protein (ADNP) regulated tooth eruption in mice and man, provides, for the first time, an early detection of tooth eruption, with full or almost full mouth of teeth at one year of age, as a potential biomarker for an intellectual disability (ID)/autism spectrum disorder (ASD) syndrome, toward improved translational medicine.

overall_design: RNAseq of 4 samples, comparing three ADNP-mutated lymphoblastoid cell lines (LCLs, derived from ADNP-mutated children) with a non-mutated cell line. No replicates were performed but results were verified usign RT-PCR.

first: I

last: Gozes

first: A

last: Van Dijck

first: G

last: Hacohen Kleiman

last: Grigg

first: Y

last: Gabet

first: M

first: E

last: Cappuyns

first: O

last: Elpeleg

first: R

middle: F

last: Kooy

first: S

last: Bedrosian Sermone


title: Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis

first: Kamil

last: Slowikowski

country: USA

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


title: Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in Rhesus macaque brain

status: Public on Jul 06 2017

city: Wuhan

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes and diseases. We applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque (Macaca mulatta) brain in four representative age groups. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities. Spatiotemporal- and sex-biased changes in lncRNA expression were generally higher than those observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed and functionally validated. Our findings offer a fresh insight into spatial-, age- and sex-biased changes in lncRNA expression in macaque brain, and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and ageing.

overall_design: Examination of 8 different brain regions in Rhsesu Macaque across the four ages (1-, 4-, 10- and 20-year old )


title: Adverse genomic alterations and stemness features are induced by field cancerization in the microenvironment of hepatocellular carcinomas

status: Public on Jul 19 2017

city: Mainz

first: Jens

last: Marquardt

address: Langenbeckstraße 1

department: Department of Medicine I

institute: Johannes Gutenberg University Mainz

summary: Integrative whole genome and transcriptome analyses of tumor tissue, invasive border region as well as tumor-surrounding liver (SL) in 28 HCC patients.

overall_design: Gene expression analyses of 3 different liver regions (tumor, border, normal) in 22 HCC patients.

first: Diana

last: Becker


title: Mapping transcriptionally engaged RNA polymerase II in C2C12 myoblasts

status: Public on Jun 13 2017

city: Seattle

first: Jie

last: Yao

state: WA

address: 615 Westlake Ave N

institute: Allen Institute

summary: A large portion of the mammalian genome is associated with the nuclear lamina (NL).  Here we have documented genome-wide transcriptional activities by measuring the densities, locations and orientations of transcriptionally-engaged RNA polymerase II in mouse C2C12 myoblasts using global run-on sequencing. Interestingly, a significant fraction (~20%) of NL-associated genes were detected to be transcriptionally active.

overall_design: Mapping transcriptionally engaged RNA polymerase II by global run-on sequencing (GRO-seq)

first: Wu

last: Feinan

first: Yao

last: Jie


title: The nuclear RNA exosome is co-opted to enhance host:viral RNA hybrids that propel influenza virus ribogenesis and infectivity

status: Public on May 08 2017

city: New York

first: Zuleyma

last: Peralta

state: NY

address: 1470 Madison Ave Rm 8-302

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The nuclear RNA exosome is an essential multi-subunit complex that controls RNA homeostasis.  Congenital mutations in exosome genes are associated with neurodegenerative diseases. Here, we show that transient depletion of nuclear RNA exosome subunits in epithelial cells inhibits influenza virus replication. Similarly, viral biogenesis was suppressed in cells derived from mice with conditional ablation of the RNA exosome subunit Exosc3. Furthermore, patient-derived cells with a congenital EXOSC3 mutation were less susceptible to influenza virus infection. Using proteomics and next generation sequencing during infection, we show that the viral polymerase complex (PA, PB2, PB1) co-opts the nuclear RNA exosome complex and cellular RNAs en route to 3’ end degradation. Mechanistically, the nuclear RNA exosome coordinates the initial steps of viral transcription with RNAPII at host promoters. Exosome deficiency uncouples chromatin targeting of the viral polymerase complex and the formation of cellular:viral RNA hybrids, which are essential RNA intermediates that license transcription of antisense genomic viral RNAs.  Overall, we discovered a critical nexus between an essential component of the influenza virus (polymerase) and an essential component of the cell (exosome), alteration of which leads to breakage of host-pathogen symmetry and a lose-lose scenario (viral impairment and neurodegeneration).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: (1) Examination of influenza RNA levels in murine B cells conditionally ablated for the RNA exosome subunit Exosc3 (2) Examination of both host:viral chimeric mRNAs and the cellular transcriptome in human A549 cells transiently depleted for RNA exosome subunits DIS3 or EXOSC10; along with siRNA control (3) Examination of both host:viral chimeric mRNAs and the cellular transcriptome in human A549 cells transiently transfected with a plasmid encoding human DIS3 or an empty vector (EV) control

first: Alexander

last: Rialdi

first: Judd

last: Hultquist

first: David

last: Jimenez

first: Laura

last: Campisi

first: Romain

last: Fenouil

first: Natasha

last: Moshkina

first: Zhen

middle: Z

last: Wang

first: Brice

last: Laffleur

first: Robyn

last: Michael

first: Kelsey

last: Haas

first: Evangelos

last: Pefanis

first: Randy

last: Albrecht

first: Lars

last: Pache

first: Sumit

last: Chanda

first: Joanna

last: Jen

first: Minji

last: Byun

first: Uttiya

last: Basu

first: Adolfo

last: Garcia-Sastre

first: Nevan

last: Krogan

first: Harm

last: van Bakel

first: Ivan

last: Marazzi


title: mRNA Expression data from bladder cancer and normal bladder tissue

status: Public on Feb 22 2017

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary:
Bladder cancer (BCa) is one of the most common malignancy of the urinary tract. In order to improve the diagnosis, prevention and treatment of BCa, the details of molecular mechanisms underlying the tumorigenesis and development needs to be clarified. Results provide insight into molecular mechanisms underlying the mRNA and miRNA interactions in BCa.
3 human bladder cancer tissues and 3 normal bladder tissues were analyzed using microarray. The alteration of mRNA and miRNA expression between the 2 groups were detected.

overall_design: A total of 3 BCa tissues and 3 normal bladder tissues were obtained for total RNA extraction and hybridization from patients who underwent surgical treatment according to clinical protocols. All cases were reviewed by two pathologists for confirming the diagnosis of BCa. We sought to obtain the aberrant mRNA and miRNA between BCa tissues and the normal bladder tissues.

first: Gang

first: Yongzhi

first: Rui

last: Cao

first: Xinghuan


title: Targeting Glutamine Synthetase in Tumors Disrupts Tumor Microenvironment-Regulated Cancer Cell Growth

status: Public on Oct 09 2016

city: Houston

first: Prahlad

middle: T.

last: Ram

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

summary: Analysis of ovarian cancer cell line HeyA8 coculturing with cancer associated fibroblasts at gene expression level. The hypothesis test in this study is to show that cancer associated fibroblasts can influence the gene expression of HeyA8 under glutamine deprivation condition. Results provide important information of the response of HeyA8 when coculturing with cancer associated fibroblasts under glutamine deprivation, such as cell proliferation, apoptosis

overall_design: Total RNA obtained from Hey8A cocultured with cancer associated fibroblasts subjected to 24 hours glutamine deprivation compared to He8A subjected 24 hours glutamine deprivation and Hey8A with complete medium condition

first: Lifeng

last: Yang

first: Deepak

last: Nagrath

first: Tyler

last: Moss

middle: T


title: Expression profiles of the four human major ectodermal lineages

status: Public on Sep 08 2017

first: Lorenz

last: Studer

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Here we report a chemically defined strategy to derive the entire human ectoderm from pluripotent stem cells.  Using reporter lines for various lineages of the ectoderm, the expression profiles generated were: PAX6+ neuroectoderm (NE), SOX10+ neural crest (NC), SIX1+ cranial placodes (CP).  The non-neural ectoderm (NNE) samples did not have a reporter associated, but was quality controlled for the expression of TFAP2A positive, SIX1 and SOX10 negative to proceed with the sequencing.  We observe a clear demarcation between the NE versus the non-neural ectoderm lineages (NC, CP and NNE) accompanied by specific expression patterns for the different lineages.  The cells with potential to become neurons can be further differentiated to become functional.

overall_design: Ectodermal lineages (NE, NC, CP and NNE) were differentiated from hPSCs using various small molecules and growth factors and assayed for their expression profile on day 12 (12 days after pluripotency).

first: Jason

last: Tchieu


title: RNA-dependent RNA polymerase sequence specificities of capsnatching viruses are tailored to aid viral replication

status: Public on Aug 09 2017

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

summary: Influenza A virus (IAV) is a major respiratory pathogen that causes severe illness and mortality worldwide. IAV critically depends on host factors for multiple functions that are not encoded by the viral genome. Notably, the IAV RNA-dependent RNA polymerase (RdRP) complex lacks intrinsic 7-methylguanosine (m7G) capping activity and instead “snatches” the 5’m7G caps and the adjacent 10-15nts of host transcripts to prime viral mRNA production, allowing viral transcripts to be recognized by the host translation machinery. We developed a new approach to simultaneously assay the 5’ ends of host and viral transcripts in infected cells and identify the host capsnatch origins for viral mRNAs. We used this technique to study the progression of IAV infection in nuclear and cytoplasmic compartiments and determined that the RdRP complex has specific sequence preferences that results in preferential capsnatching and avoidance of sub-populations of host RNAs, which can be reverted by the addition of a cap-snatch inhibitor. Notably, genes avoided by CapSnatch Seq have biological functions enriched for mRNA processing, translation, and viral replication. This selectivity and functional enrichment of avoided genes is conserved among capsnatching viruses including Influenza B Virus and Lymphocytic Choriomeningitis Virus, despite differences in RdRP domains and subcellular locations of RNA substrates. This suggests that this preference convergently arose as a viral strategy to allow cap-snatching viruses to avoid targeting genes necessary for its own replication.

overall_design: This study contains 33 samples comprising capsnatch sequencing and directional RNA sequencing. Experimental setup includes extraction of RNA at various timepoints after viral infection, separation of cytosolic and nucleic extacts, treatment with capsnatch inhibitor drug or DMSO, and comparison of different viral strains.

first: Zuleyma

last: Peralta

first: Alexander

last: Rialdi

first: Arvin

last: Lagda

first: Ryan

last: O’Hanlon

first: Megan

last: Shaw


title: Bmal1 regulates inflammatory response in macrophage

status: Public on Aug 31 2017

city: Bunkyo

first: Yumiko

last: Oishi

state: Tokyo

address: 1-5-45, Yushima

department: Department of Cellular and Molecular Medicine

institute: Tokyo Medical and Dental University

summary: Deletion of Arntl disrupted temporal inflammatory response in macrophage. Mechanistically, the acetylation status of lysine 27 of histone 3 (H3K27ac) was enhanced at the PU.1-containing enhancers in Arntl-/- macrophages compared to the wild-type cells. Collectively, transcription factor network containing Bmal1 controls temporal inflammatory response of macrophages by regulating epigenetic states of enhancers.

overall_design: Genome wide localization of Transcription factor Bmal1, NFkB (p65) and acetylation status of lysine 27 of histone 3 (H3K27ac) were assessed by ChIP-Seq.  Genome-wide  gene expression were analyzed by RNA-seq at indicated timepoints in the course of inflammatory response in primary macrophages.


title: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

status: Public on Mar 20 2017

city: Singapore

first: Huipeng

last: Li

address: 60 Biopolis St, #02-01

institute: Genome Institute of Singapore

summary: Intratumoralmheterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA–seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs). Additionally, epithelial–mesenchymal transition (EMT)-related genes were found to be upregulated only in the CAF subpopulation of tumor samples. Notably, colorectal tumors previously assigned to a single subtype on the basis of bulk transcriptomics could be divided into subgroups with divergent survival probability by using single-cell signatures, thus underscoring the prognostic value of our approach. Overall, our results demonstrate that unbiased single-cell RNA–seq profiling of tumor and matched normal samples provides a unique opportunity to characterize aberrant cell states within a tumor.

overall_design:
Two single cell dataset are included: (1) 1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. (2) 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms, these include 83 A549 cells, 65 H1437 cells, 55 HCT116 cells, 23 IMR90 cells, 96 K562 cells, and 134 GM12878 cells (38 from batch 1, 96 from batch 2), 174 H1 cells (96 from batch 1, 78 from batch 2).

Please note that [1] only the QC-passed samples are included in the records [2] Raw data is available through EGA [accn: EGAS00001001945; ERP016958] [3] The 'GEO_EGA_ID_match.csv' contains the ERSnnnnnn accession numbers correspoding to each GEO sample raw data.

first: Elise

last: Courtois


title: Genome-wide characterization of DNMT-deficient mouse ESCs reveals dynamicity of differentially-methylated-regions and its impact on bivalency composition

status: Public on Sep 15 2016

city: Jefferson

first: Zhiguang

state: AR

address: 3900 NCTR Road

department: National Center for Toxicological Research

institute: Food and Drug Administration

summary: Differentially-methylated-regions (DMRs), pivotal to the diagnosis/pathogenesis of imprinting disorders, control imprinted gene expression with histone modifications; however, their establishment, numbers, boundaries, and crosstalk with chromatin remain elusive. Herein our global profiling reveals that although de novo methyltransferases DNMT3a/3b are required for locus-specific DMR maintenance, DNMT1 is required for all known DMRs. Based on the latter and the DMR concept, we have developed two novel approaches, “no restored DMRs (NORED)” and “Tag-mosaicity,” to identify/demarcate 31 known and 7 novel DMRs from 21 known loci, and 20 novel DMRs from novel loci. Tag-mosaicity analyses reveal the expected bimodal patterns of hypo/hypermethylated tags of known and new DMRs. Using Gtl2 locus, we demonstrate that methylation of DMRs controls H3K9me3 distribution to a long- range ”DMR-territory” that extends beyond our defined DMR boundary. These findings contrast that H3K9me3 controls CG methylation in Arabidopsis and Neurospora. Our analyses reveal that promoters of imprinted genes within a DMR-territory tend to have H3K4me2 and H3K9me3 with/without H3K27me3, whereas promoters outside have H3K27me3 and H3K4me2. Lastly, we confirmed that the transient DMR of Hcn2/Polrmt locus is conserved in the human genome. Our data link transient DMRs to epilepsy and chronic pain, Parkinson’s disease, Charcot-Marie-Tooth disease, and type 2 diabetes.

overall_design: Genomic DNA from DNMT1 -/- (1KO) ESCs cells with exogenous expression of DNMT1 were treated with bisulfite and sequenced with the Illumina HiSeq platform using paired end reads.

first: Teng

first: Hongzheng

last: Dai

first: Suzanne

last: Martos

first: Jinchong

last: Xu

first: Ganglong

last: Gao

first: Cheng

last: An

first: Dustin

middle: E

last: Schones

first: Xueli

last: Zhang

first: Valina

middle: L

last: Dawson

first: Ted

first: Zhibin

last: Wang


title: Spatiotemporal- and sex-specific Dynamics of lncRNA expression links to brain development and aging in Rhesus Macaque (RNA-seq)

first: Dong

last: Chen

state: Hubei

summary: Dynamic remodeling in architecture and function of mammalian brain, especially in primate, rely on a precisely orchestrated molecular and cellular regulation at distinct levels. Here, we applied comprehensive RNA-seq and CAGE-Seq analysis to characterize dynamics of lncRNA expression in Rhesus macaque brain across postnatal development and aging. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities respectively. Highly spatiotemporal- and sex-specific dynamic changes in lncRNA but mRNA expression and the negative correlation between lncRNAs and mRNAs, functionally associate with brain development and aging, especially in the neocortex. Together with in situ hybridization (ISH) and quantitative real time-PCR (qRT-PCR) data, our findings provide an initial insight into spatial-, age- and sex-related dynamics of lncRNA expression during postnatal brain development and aging in macaque, implying that high dynamics of lncRNA expression might represent a previously unappreciated regulatory system in shaping brain architecture and function.

overall_design: Examination of 8 different brain regions in Rhesus Macaque across the four ages (1-, 4-, 10- and 20-years old).

first: Jiali

first: Yi


title: RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways

status: Public on Jun 29 2016

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

summary: The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods.

overall_design: Illumina Truseq v2 RNA-seq libraries were constructed from four biological replicates of phyBnull mutants and their wild-type sister lines and of phyCnull mutants and their wild-type sister lines. Subsequently, the entire experiment was replicated. Reads were mapped to the draft assembly (v2.2) of the wheat genome provided by the International Wheat Genome Sequencing Consortium (IWGSC) and transcribed regions were identifed by mapping a non-redundant set of transcripts to this genomic assembly. Sequencing reads mapping uniquely within these identified transcribed regions were used to determine relative expression profiles. Loci which were differentially expressed in both experimental replicates were designated high-confidence PHYB-regulated and PHYC-regulated genes, respectively. A GTF file is provided detailing the location of the 150,754 loci within the IWGSC pseduomolecules and contig scaffold followed by the longest transcribed sequence mapping to this region. Most, but not all, transcribed sequences are annotated through Ensembl.

first: Nestor

last: Kippes

first: Andrew

first: Juan

last: Debernardi

first: Jorge

last: Dubcovsky


title: In vitro cultured H7 human embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors

status: Public on Aug 02 2016

city: Stanford

first: Rahul

last: Sinha

address: 265 Campus Drive

department: ISCBRM

institute: Stanford University School of Medicine

summary: Stem-cell differentiation to desired lineages requires navigating alternating developmental paths that often lead to unwanted cell types. Hence, comprehensive developmental roadmaps are crucial to channel stem-cell differentiation toward desired fates. To this end, here, we map bifurcating lineage choices leading from pluripotency to 12 human mesodermal lineages, including bone, muscle, and heart. We defined the extrinsic signals controlling each binary lineage decision, enabling us to logically block differentiation toward unwanted fates and rapidly steer pluripotent stem cells toward 80%–99% pure human mesodermal lineages at most branchpoints. This strategy enabled the generation of human bone and heart progenitors that could engraft in respective in vivo models. Mapping stepwise chromatin and single-cell gene expression changes in mesoderm development uncovered somite segmentation, a previously unobservable human embryonic event transiently marked by HOPX expression. Collectively, this roadmap enables navigation of mesodermal development to produce transplantable human tissue progenitors and uncover developmental processes. doi:10.1016/j.cell.2016.06.011

overall_design: BioProject: PRJNA319573, Study: SRP073808, Bulk and single-cell RNA-seq, and ATAC-seq of of H7 human embryonic stem cells (ESC) and in vitro derived 10 diffrerent mesoderm progenitors from H7-ESC

first: Pang

last: Koh


title: Global transcriptome analysis of macrophages during Helicobacter pylori infection

status: Public on Feb 10 2017

city: Blacksburg

first: Monica

last: Viladomiu

state: VA

address: 1015 Life Science Circle

department: Virginia Bioinformatics Institute

institute: Nutritional Immunology and Molecular Medicine Laboratory

summary: Based on preliminary data demonstrating that macrophages are critical regulators of Helicobacter pylori colonization and gastric pathology in mice, we sought to investigate how macrophages may serve as bacterial reservoirs of intracellular H. pylori.

overall_design: BMDM were isolated from WT and PPARg-/- mice and cultured with M-CSF for 7 days to promote macrophage differentiation. Fully differentiation macrophages were challenged with H. pylori strains SS1 at an MOI of 10 for 15 minutes. Extracellular bacteria was then eliminated by gentamycin treatment. Cells were collected at 0, 60, 120, 240, 360 and 720 minutes post gentamycin treatment to ascertain whole transcriptome differential gene expression during infection.

first: Pawel

last: Michalak

first: Josep

last: Bassaganya-Riera

first: Raquel

last: Hontecillas

first: Barbara

last: Kronsteiner-Dobramysl


title: Comprehensive characterization of neutrophil genome topology

status: Public on Feb 06 2017

city: La Jolla

first: Yina

last: Zhu

address: 9500 Gilman Drive

department: Biological Sciences

institute: university of california,san diego

summary: Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil genomes were depleted of local genomic interactions but enriched for long-range genomic interactions that spanned multiple topologically associating domains. Population-based simulation of spherical and torroid genomes revealed declining radii of gyration for neutrophil chromosomes. We found that neutrophil genomes were highly enriched for heterochromatic genomic interactions across vast genomic distances, a process named super-contraction. Super-contraction involved genomic regions located in the heterochromatic compartment in both progenitors and neutrophils or genomic regions that switched from the euchromatic to the heterochromatic compartment during neutrophil differentiation.  Super-contraction was accompanied by the repositioning of centromeres, pericentromeres and Long-Interspersed Nuclear Elements to the neutrophil nuclear lamina. We found that Lamin-B Receptor expression was required to attach centromeric and pericentromeric repeats but not LINE-1 elements to the lamina. Differentiating neutrophils also repositioned rDNA and mini-nucleoli to the lamina: a process that was closely associated with sharply reduced rRNA expression. We propose that large-scale chromatin reorganization involving super-contraction and recruitment of heterochromatin and nucleoli to the nuclear lamina facilitate the folding of the neutrophil genome into a confined geometry imposed by a multi-lobed nuclear architecture.

overall_design: Performed  in situ Hi-C, GRO-Seq,  RNA-Seq, ChIP-Seq  and MeDIP-Seq, in combination with 3D-FISH to pinpoint the underlying molecular mechanisms by which diploid genomes fold into a confined geometry imposed by a multi-lobed nuclear architecture.

first: Ke

last: Gong

first: Matthew

last: Denholtz

first: Vivek

last: Chandra

first: Mark

middle: P

last: Kamps

first: Frank

last: Alber

first: Cornelis

last: Murre


title: Gene expression data from immunological non-responders and responders to antiretroviral therapy in HIV infected patients

status: Public on May 15 2016

city: Chandigarh

first: Sunil

middle: K

last: Arora

address: 4th Floor Research Block:A

department: Immunopathology

institute: PGIMER

summary:
Among the ART treated patients, 15-20% show discordant response to therapy with lack of increase in CD4+ T cell count despite of undectable viral load, termed as immunological non responders or immunological failures. The mechanisms are not well established
In the current study, we have used microarray based differential gene expression profile analysis among these cohorts to elucidate the mechanisms of immunologic non responsiveness to ART

overall_design: A total 21 samples were analyzed in current study. HIV-1 subtype C infected patients showing immunological non responsiveness (Seven biological replicates), subjects responding to therapy (Five biological replicates), therapy naive (Five biological replicates) along with healthy controls (Four biological replicates) were recruited in this study. RNA extracted from peripheral blood mononuclear cells from subjects used for hybridization on Affymetric array

first: Sukhvinder

last: Singh

first: Aman

last: Sharma

first: Jaideep

last: Toor