title: Real-time microRNA quantitative PCR array of mouse bone marrow-derived osteoclasts

status: Public on Mar 01 2021

city: Hong Kong SAR

first: Jin

last: Liu

address: 7 Baptist University Road, Kowloon Tong

department: TMBJ

institute: Hong Kong Baptist University

summary: Mouse bone marrow-derived OSCAR+CTR+ osteoclasts were harvested from mice with anterior cruciate ligament transection (ACLT) or sham operation by magnetic-activated cell sorting. The cells were lysated by Trizol reagent for total RNA extraction. The miRNA were profiled using the QuantiMir RT Kit (System Biosciences)

overall_design: miRNA qPCR expression profiling.  Equal amount total RNA from osteoclasts of three independent ACLT mice and three Sham mice were pooled for gene expression analysis.


title: Changes in human basophil mRNA profiles during treatment with omalizumab

city: Baltimore

first: Donald

middle: Welton

last: MacGlashan

state: MD

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

country: USA

institute: Johns Hopkins University

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

summary:
Human basophils were purified from whole blood, pre-treatment (=v3) and mid-treatment (=v6) on omalizumab.
In addition, basophils were isolated from non-treated, non-CSU subjects for a comparison of CSU vs. non-CSU.

overall_design: Comparison of CSU (chronic spontaneous urticaria) vs. non-CSU basophil mRNA profiles or pre and during omalizumab treatment in CSU subjects.

last: MacGlashan Jr.


title: Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberuculosis Beijing strain

status: Public on Mar 02 2021

city: Bangkok

first: Marisa

last: Ponpuak

address: 272 Rama 6 Road

country: Thailand

institute: Department of Microbiology, Faculty of Science, Mahidol University

type: Expression profiling by high throughput sequencing

summary: Autophagy is a conserved lysosomal-dependent cellular degradation process shown to play a key role in immune defense against Mycobacterium tuberculosis inside host macrophages. Induction of autophagy enhances mycobacterial phagosome acquisition of lysosomal hydrolases, resulting in the destruction of intracellular M. tuberculosis reference strain H37Rv and strains belonging to the East African Indian genotype. However, our previous study showed that strains belonging to the hypervirulent M. tuberculosis Beijing genotype have a special ability to resist autophagic killing but the mechanism involved remains unclear. In this study, we carried out whole transcriptome analyses of host macrophages infected with the autophagy resistant Beijing strain compared to that of H37Rv. Our results identified several genes that are differentially regulated in the Beijing strain-infected host cells including those function in the lysosome positioning pathway. Host macrophages depleted of Kxd1 and Pleckhm2, two proteins in this pathway, can now enhance the lysosomal hydrolase acquisition into the Beijing phagosomes and restrict the bacterial survival upon autophagy induction. High-content image analysis showed an increase in lysosome numbers at the cell periphery in host cells infected with the autophagy resistant Beijing strain in a Pleckhm2-dependent manner. Taken together, these data indicated that the M. tuberculosis Beijing strain escapes autophagic elimination by upregulating the lysosome positioning pathway resulting in an increase in lysosome relocation toward the cell periphery and therefore sparing the mycobacteria from autophagic restriction. Our work thus identified new strategy employed by M. tuberculosis to evade autophagy which may provide potential new targets for drug discovery against tuberculosis

overall_design: Raw264.7 macrophages were uninfected or infected with either the autophagy-sensitive reference strain H37Rv or autophagy-resistant Beijing strain for 2 hr. Cells were then uninduced or induced to undergo autophagy by stravation for 2 hr. Total RNAs were then collected and subjected to RNA-Seq analyses.

first: Thanida

last: Laopanupong

first: Pinidphon

last: Prombutara

first: Phongthon

last: Kanjanasirirat

first: Salisa

last: Benjaskulluecha

first: Tanapat

last: Palaga

first: Stephane

last: Méresse

first: Jiraporn

last: Paha

first: Suparerk

last: Borwornpinyo

first: Angkana

last: Chaiprasert

first: Pongsak

last: Utaisincharoen


title: Methylomes of young and aged LT-HSCs

city: Augsburg

first: Stephen

last: Krämer

address: Alter Postweg 101

country: Germany

institute: University of Augsberg

type: Methylation profiling by high throughput sequencing

summary: We performed tagmentation-based whole-genome bisulfite sequencing on young and aged LT-HSCs.

overall_design: Tagmentation-based whole-genome bisulfite sequencing (T-WGBS) of aged LT-HSCs (5 Replicates) and young LT-HSCs (4 Replicates). For each replicate, two separate T-WGBS libraries were created and sequenced on one lane per library.

first: J

last: Pospiech

first: S

middle: J

last: Kraemer

first: H

last: Geiger

first: D

middle: B

last: Lipka


title: Real-time microRNA quantitative PCR array of mouse bone marrow-derived osteoclasts II

first: Jin

last: Liu

country: China

summary: Mouse bone marrow-derived OSCAR+CTR+ osteoclasts were harvested from osteoclast-miRNA knockdown (OCmiR-KD) mice or osteoclast-miRNA intact (OCmiR-Intact) mice at 2w after anterior cruciate ligament transection (ACLT) by magnetic-activated cell sorting. The cells were lysated by Trizol reagent for total RNA extraction. The miRNA were profiled using the QuantiMir RT Kit (System Biosciences)

overall_design: miRNA qPCR expression profiling.  Equal amount total RNA from osteoclasts of three independent OCmiR-KD mice and three OCmiR-Intact mice were pooled for gene expression analysis.


title: BATF orchestrates the functional specification and metabolic reprogramming in Treg cells

city: Carmel

first: Kai

last: Yang

state: Indiana

address: 12598 pembrooke circle

department: Pediatrics

institute: School of Medicine, IUPUI

summary:
Purpose: Identification of the differentially expressed genes and metabolic pathways in resting and activated WT and BATF-deficient Treg cells
Methods: RNA was purified from resting of stimulated (aCD3-CD38/IL-2 for 48 h)Treg cells isolated from WT or Foxp3CreBatffl/fl mice
Results: Loss of BATF promotes triacylglycerol biosynthesis in Treg cells.
Conclusions: BATF is crucial to coordinate the suppressive function and triacylglycerol metabolism of Treg cells.

overall_design: In total 12 samples were analyzed: WT (3 Unstimulated and 3 Stimulated); Batf Ko (3 Unstimulated and 3 stimulated)

first: Chengxian

last: Xu

first: Xiaoyu

last: Lu

first: Chi

last: Zhang

first: Rong

last: Qi

first: Jun

last: Wan

first: Sheng


title: Impaired peripheral mononuclear cell metabolism in patients at risk of developing sepsis

city: Jakarta Barat

first: Velma

last: Herwanto

state: DKI Jakarta

address: Perum. Sunrise Garden, Jalan Surya Mutiara III blok V no. 30

country: Indonesia

institute: Faculty of Medicine, Universitas Tarumanagara

summary: Mitochondrial respiration and gene expression related to mitochondrial function were measured from the peripheral blood of infection and sepsis patients as well as healthy controls

overall_design: Case-control study; patients fulfulling infection or sepsis criteria were recruited from emergency department


title: Overexpression of RBFOX1 in HEK293 cells and the effect on circRNA formation

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

type: Non-coding RNA profiling by high throughput sequencing

summary: We carried out two mammalian transcriptomics experiments to compare the effect of overexpressing the splicing factor RBFOX1 on circRNA formation. We include quantification of gene expression and circRNA expression.

overall_design: Each of the experiments used HEK293 cells and comprised six samples, 3 control replicates and 3 RBFOX1 over-expression replicates. Sequencing was performed on both ends of the cDNA fragment (paired-end reads).

first: Akira

last: Gokoolparsadh

middle: M

first: Irina

last: Voineagu


title: Small RNAseq of MV3 melanoma cells overexpressing MCPIP1 protein

city: Kraków

first: Iwona

last: Nowak

address: Kalwaryjska 92/5

country: Poland

institute: Jagiellonian University

summary: Sequencing of small RNAs in RNA samples from control cells, cells overexpressing wild-type and mutated form of MCPIP1 ribonuclease

overall_design: 4 biological replicates of each sample (transfected with epty vector, overexpressing wild-type MCPIP1 and overexpressing point mutant,D141N, of MCPIP1 protein) were sequenced on an Ion Torrent TM Proton machine for assessment of miRNA profile differences


title: HAT cofactor TRRAP modulates microtubule dynamics via SP1 signaling to prevent neurodegeneration

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Brain homeostasis is regulated by the viability and functionality of neurons. HAT (histone acetyltransferase) and HDAC (histone deacetylase) inhibitors have been applied to treat neurological deficits in humans; yet, the epigenetic regulation in neurodegeneration remains elusive. Mutations of HAT cofactor TRRAP (Transformation/translation domain-associated protein) cause human neuropathies, including psychosis, intellectual disability, autism and epilepsy, with unknown mechanism. Here we show that Trrap deletion in Purkinje neurons results in neurodegeneration of old mice. Integrated transcriptomics, epigenomics and proteomics reveal that TRRAP via SP1 conducts a conserved transcriptomic program. TRRAP is required for SP1 binding at the promoter proximity of target genes, especially microtubule dynamics. The ectopic expression of Stathmin3/4 ameliorates defects of TRRAP-deficient neurons, indicating that the microtubule dynamics is particularly vulnerable to the action of SP1 activity. This study unravels a network linking three well-known, but up-to-date unconnected, signaling pathways, namely TRRAP, HAT and SP1 with microtubule dynamics, in neuroprotection.

overall_design: Transcriptional and epigenetic landscape of the adult neural stem cells after the deletion of Trrap

first: David

middle: L

last: Pellon

first: Mahdi

first: Anna

last: Krepelova

first: Francesco

last: Neri

first: Zhao-Qi

last: Wang


title: Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells

city: Bergen

first: Diego

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

summary: Testis tissue was incubated under basal conditions for 2 days to allow for the assumed decrease of endogenous Insl3 production, then added exogenous, recombinant zebrafish Insl3 peptide (100 ng/mL) and continued the incubation for another 2 days, before collecting the tissue for analysis of gene expression

overall_design: 6 samples in total were analyzed: 3 biological replicates from control testis samples and 3 biological replicates from Insl3-treated testis samples

first: Luiz

middle: H

last: Assis

first: Yu

last: Safian

first: Chris

last: Coomans

first: Tomasz

last: Furmanek

first: Kai

last: Skaftnesmo

first: Birgitta

last: Norberg

first: Wei

last: Ge

first: Cherry

last: Choi

first: Marjo

last: den Broeder

first: Juliette

last: Legler

first: Jan

last: Bogerd

first: Rüdiger

middle: W

last: Schulz


title: Racial dimorphism in transcriptomic response in human organotypic raft cultures

city: Chicago

first: Irina

last: Budunova

state: Illinois

address: 303 E Chicago Ave, Ward Bldg, #9-132

department: Dermatology

institute: Northwestern University

summary: Keratinocyte ethnicity affects transcriptomic response of human organotypic raft cultures

overall_design: Organotypic raft cultures (ORC) containing keratinocytes of either Caucasian (CA, donor 1-5) or African American (AA, donor 6-9) donors were treated with 10ng/ml of TNFA for either 24h or 168h. Control rafts were treated with 0.1%BSA (vehicle control).

last: Klopot

first: Gleb

last: Baida

first: Bethany

middle: E

last: Perez White


title: Bulk RNA sequencing of human iPSC-derived cells

city: Shenzhen

first: Minglin

last: Ou

address: No.1017, Dongmen North Road, Luohu District

department: Clinical Medical Research Center of The Second Clinical Medical College

institute: Jinan University

summary: We directly reprogramed two human iPS cell lines to cardiac cells and collected four time points (day 0, day 2, day 4, and day 10) during cardiac differentiation for bulk RNA sequencing.

overall_design: To reprogram two human iPS cell lines into cardiac cells, and analyze their expression profiles at different differentiation time point.The SRA Study accession was SRP193902, and BioProject accession was PRJNA538935.

first: Yong

last: Dai


title: RNA-Seq Analysis of Mutant Prss56-/- And Control Prss56+/- Retinal Transcriptomes

city: San Francisco

first: Swanand

last: Koli

state: CA

address: 10 Koret Way RM K-110 # 0730

department: Ophthalmology

institute: UNIVERSITY OF CALIFORNIA SAN FRANCISCO

summary:
Method: To study the molecular processes underlying PRSS56-mediated ocular size regulation, we performed a high throughput gene expression analysis on the retina from Prss56-/- mutant mice and their control Prss56+/- littermates. Prss56+/-  (Heterozygous) and Prss56+/+ (Wild type) are phenotypically similar and therefore we used heterozygous mice as controls in our experiments. Briefly, retinas from post-natal day 15 (P15) mice were extracted after enucleation, flash frozen on dry ice and RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. The RNA-Seq was performed by Novogene Corporation Inc. (Sacramento, USA) using Illumina NovaSeq 6000 Platform.
Results: Our transcriptome analysis (RNA-seq) identified Adamts19 and Prss56 as the top two differentially expressed genes between Prss56 mutant (Prss56-/-) and control (Prss56+/-) in P15 retina.

overall_design: Retinal mRNA profiles of 15-day old wild type (Prss56+/-) and Prss56-/- mice.

first: Kayarat

middle: S

last: Nair


title: D-xylose catabolic pathways expressed in Herbaspirillum seropedicae

city: Montevideo

first: Ana Karen

middle: Karen

last: Malan

state: Montevideo

address: Avenida Italia 3318

department: Bioquímica y Genómica Microbianas

country: Uruguay

institute: Instituto de Investigaciones Biológicas Clemente Estable

summary: Herbaspirillum seropedicae are β-proteobacteria that establish as endophytes in various plants. They are able to consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolism pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature. Furthermore, it is found in some potential raw materials such as lignocellulosic biomass. In this work we present a study of D-xylose catabolism pathways in H. seropedicae strain Z69, using RNA-seq analysis and the subsequent study of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD+- dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This is due to expression of an L-arabinose dehydrogenase encoded by G5B88_05250 gene, and was thus able to use D-xylose as substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that produces pyruvate and glycolate. This novel pathway seems to be essential since a mutant in the last step of this pathway, Z69∆G5B88_06410, was unable to grow on D‑xylose.

overall_design: mRNA profiles of 3 samples: Herbaspirillum seropedicae Z69 grown until mid-log phase in LGI medium supplemented with xylose 30g/l or glycerol 10g/l and a knock-out mutant strain in xylB gene (G5B88_22805) grown until mid-log phase in LGI medium supplemented with xylose 30g/l. The experiment was done in duplicate (biological replicates). Z69 grown on glycerol was used as control condition.

first: Ana

middle: K

first: Thalita

last: Tuleski

middle: I

last: Catalán

first: Emanuel

last: Maltempi de Souza

first: Silvia

last: Batista


title: Expression profile of human 786-O cells overexpressing Bcl-xAS lncRNA

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Transcriptional profiling of human 786-O cells comparing total RNA from cells transfected with the pCEP4 vector containing a Bcl-xAS lncRNA construct vs. control empty pCEP4 vector-transfected cells. Goal was to determine the effects of Bcl-xAS overexpression on global 786-O cells gene expression.

overall_design: Two-condition experiment: Bcl-xAS-transfected cells vs. control empty vector-transfected cells. Biological replicates: 4 Bcl-xAS-transfected cells replicates; 4 control empty vector-transfected cells replicates. Dye-swaps were performed.

first: Carlos

last: DeOcesano-Pereira

middle: A

first: Sergio

last: Verjovski-Almeida


title: Modulation of ATXN1 S776 phosphorylation reveals the importance of allele-specific targeting in SCA1

city: Houston

first: Stephanie

middle: Lynn

last: Coffin

state: TX

address: 1250 Moursund St

institute: Baylor College of Medicine

summary: RNA was isolated from mouse cerebellum at 6 weeks of age in 5 different gentoypes; wild-type (WT), Atxn1_154Q/2Q (SCA1),  Atxn1_154Q[S776A]/2Q (SCA1 S776A), Atxn1_154Q[S776A]/2Q[S776A] (S776A Double) and Atxn1_2Q[S776A]/2Q[S776A] (homo). After RNA isolation, RNA-seq was performed and gene expression profiles were compared between WT, SCA1, and the S776A mutants. The goal was to determine if mutating the phosphorylation site S776 in the context of spinocerebellar ataxia type 1 (SCA1) is protective.

overall_design: Cerebellar mRNA profiles of 6-week mice in wild-type (WT), Atxn1_154Q/2Q (SCA1),  Atxn1_154Q[S776A]/2Q (SCA1 S776A), Atxn1_154Q[S776A]/2Q[S776A] (S776A Double) and Atxn1_2Q[S776A]/2Q[S776A] (homo).

first: Larissa

last: Nitschke

first: Huda

middle: Y

last: Zoghbi

first: Yanwan

first: Ying-Wooi

last: Wan

first: Zhandong

last: Liu


title: Expression data from Hela cells upon knock-down of IRF2BP1 and IRF2BP2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
IRF2BP1 and IRF2BP2 are transcriptional co-regulators that play a role in EGFR signalling and other signalling events.
We used microarray analysis to investigate which genes are under control of IRF2BP1 and IRF2BP2

overall_design: Hela cells were treated with siRNA against IRF2BP1, IRF2BP2, or IRF2BP1 and IRF2BP2. Non-targeting siRNA was used as a control. Cells were grown in full medium (DMEM, 10% FBS, 2 mM L-glutamine and 1 mM sodium pyruvate medium) and investigated 72 hours after knock-down.

first: Nicolas

last: Stankovic-Valentin

first: Sina-Victoria

last: Barysch

first: Frauke

last: Melchior


city: Heidelberg

first: Simone

last: Bauer

address: INF 460

institute: DKFZ

summary: siRNA mediated HDAC1 knockdown in the LNCaP prostate cancer cell line.

overall_design:
LNCaP cells upon siRNA mediated HDAC1 knockdown compared to AllStars scrambled control
LNCaP cells were cultivated in RPMI1640 medium supplemented with 10 % FBS. SiRNA mediated knockdown of HDAC1 was performed using Lipofectamine transfection reagent and final siRNA concantration of 20 nM.

first: Holger

last: Sültmann


title: ERbeta influencing p65 cistromes in colon cancer cells

city: Stockholm

first: Rajitha

last: Indukuri

state: Sweden

address: Tomtebodavägen 23a, Solna

country: Sweden

institute: Scilifelab

summary: Inflammation is involved in both initiation and promotion of colorectal cancer (CRC), and patients with inflammatory bowel disease (IBC) have increased risk of developing CRC. Tumor necrosis factor alpha (TNFα) is a cytokine secreted by e.g. macrophages, and this signaling is deregulated in IBD and CRC. TNFα activates the pro-survival transcription factor complex NFκB, which is composed of several subunits including p65 (RELA). We recently characterized the genome-wide transcriptional impact by TNFα in two CRC cell lines, but how p65 binds the chromatin, its cistrome, in colorectal cancer cells has not been explored. We here used p65 chromatin immunoprecipitation followed by sequencing (ChIP-Seq) in HT29 and SW480 cells, and correlated with the transcriptomic impact of TNFα. Further, estrogen receptor beta (ERβ) has anti-inflammatory and anti-tumorigenic effects in colon cells and interacts with NFκB main targets. We have shown that ERβ impacts TNFα signaling in CRC cells and ERβ impacts the P65 cistrome.

overall_design: ChIP-Seq was performed in CRC engineered cell lines re-expressing ERβ and mock (emply vector without ERβ).Each ChIP was performed three times. For further analysis, we focused on sites present in at least two out of three replicates.

first: Cecilia

last: Williams


title: Real-time microRNA quantitative PCR array of serum exosomes I

city: Hong Kong SAR

first: Jin

address: 7 Baptist University Road, Kowloon Tong

institute: Hong Kong Baptist University

summary: Mouse serum exosomes were harvested from OCExoInhib-treated mice or vehicle-treated mice at 2w after anterior cruciate ligament transection (ACLT). The exosomes were lysated and processed by Exosome RNA Column Purification Kit (System Biosciences). The miRNA were profiled using the Exosomal microRNA Amplification and Profiling Kit (System Biosciences)

overall_design: miRNA qPCR expression profiling.  Equal amount exosomal miRNAs from  three independent OCExoInhib-treated mice and three vehicle-treated mice were pooled for gene expression analysis.


title: Transcriptomic profiling of purified mature olfactory sensory neurons from transgenic mice expressing genomically encoded double-stranded RNA

city: Charlestown

first: Mark

middle: W.

last: Albers

state: MA

address: 114 16th Street, 2nd Fl

department: Neurology

institute: Massachusetts General Hospital

summary: Triggers of innate immune signaling in the CNS of amyotrophic lateral sclerosis and frontotemporal degeneration (ALS/FTD) patients remain elusive. We report the presence of cytoplasmic double-stranded RNA (cdsRNA), an established trigger of innate immunity, in ALS-FTD brains carrying C9ORF72 intronic hexanucleotide expansions that included genomically encoded expansions of the G4C2 repeat sequences. Presence of cdsRNA in human brains was coincident with cytoplasmic TDP-43 inclusions, a pathologic hallmark of ALS/FTD. Introducing cdsRNA into cultured human neural cells induced Type I interferon (IFN-I) signaling and death that was rescued by FDA-approved JAK inhibitors. In mice, genomically encoded dsRNAs expressed exclusively in a neuronal class induced IFN-I and death in connected neurons non-cell autonomously. Our findings establish that genomically encoded cdsRNAs trigger sterile, viral-mimetic IFN-I induction, and propagated death within neural circuits and may drive neuroinflammation and neurodegeneration in ALS/FTD patients.

overall_design: mRNA profiling of mature olfactory sensory neurons from transgenic mouse lines with neurodegeneration purified by fluorescence-activated cell sorting

first: Steve

last: Rodriguez


title: Real-time microRNA quantitative PCR array of serum exosomes II

summary: Mouse serum exosomes were harvested from osteoclast-exosome blockage (OCExo-BLK) mice or osteoclast-exosome intact (OCExo-Intact) mice at 2w after anterior cruciate ligament transection (ACLT). The exosomes were lysated and processed by Exosome RNA Column Purification Kit (System Biosciences). The miRNA were profiled using the Exosomal microRNA Amplification and Profiling Kit (System Biosciences)

overall_design: miRNA qPCR expression profiling.  Equal amount exosomal miRNAs from  three independent OCExo-BLK mice and three OCExo-Intact mice were pooled for gene expression analysis.


title: Transcriptome in WT Col-0 and RLK7ECD-MIK2TK transgenic plants upon PIP1 treatment

city: Jinan

first: Shuguo

last: Hou

state: Shandong

address: Fengming Road 1000, Shandong Jianzhu University

department: School of Municipal & Environmental Engineering

institute: Shandong Jianzhu University

summary: We tested PIP1-regulated gene transcription in Arabidopsis Wt (Col-0) and RLK7ECD-MIK2TK transformats (RM).

overall_design: Ten-day old seedlings grown on 1/2MS medium were treated with or without 1 uM PIP1 for 1 or 6 hours. RNA was isolated for RNA sequencing analysis.Three biologic replicates were used for each treatment. cDNA library preparation and sequencing were carried out on an Illumina HiSeq 4000 platform with 150-nucleotide pair-end reads.


title: The effect of corticosterone treatment on the transcriptome of mouse brain endothelial bEnd3 cells

city: Martinsried

first: Gurumoorthy

last: Krishnamoorthy

state: Bayern

address: Am Klopferspitz 18

institute: MPI Biochemie

summary: We performed transcriptome profiling of bEnd3 cells treated in vitro with 5uM corticosterone or medium for 24 hours

overall_design: mRNA profiling of the brain endothelial bEnd3 cell line treated with 5 uM corticosterone or medium for 24 hours

first: Alexei

last: Leliavski


title: MADS1 maintains barley spike determinacy at high ambient temperatures

city: Shanghai

last: Shi

address: 800 Dongchuan Rd

department: Life Science and technology Department

institute: Shanghai Jiaotong University

overall_design: inflorescence mRNA profiles of wild type (WT) and  HvMADS1 mutant under high temperature and low temperature

first: Gang

last: Li

first: Huirang


title: Temporal mechanisms of myogenic specification in human induced pluripotent stem cells

city: La Jolla

first: Priya

last: Nayak

address: 9500 Gilman Drive

institute: University of California San Diego

summary: Understanding the mechanisms of myogenesis in human induced pluripotent stem cells (hiPSCs) is a prerequisite to achieving patient-specific therapy for diseases of skeletal muscle. hiPSCs of different origin show distinctive kinetics and ability to differentiate into myocytes. To address the unique cellular and temporal context of hiPSC differentiation, we perform a longitudinal comparison of the transcriptomic profiles of three hiPSC lines that display differential myogenic specification, one robust and two blunted. We detail temporal differences in mechanisms that lead to robust myogenic specification. We show gene expression signatures of putative cell subpopulations and extracellular matrix components that may support myogenesis. Further, we show that targeted knockdown of ZIC3 at the outset of differentiation leads to improved myogenic specification in blunted hiPSC lines. Our study suggests that β-catenin transcriptional cofactors mediate crosstalk between multiple cellular processes and exogenous cues to facilitate specification of hiPSCs to mesoderm lineage, leading to robust myogenesis.

overall_design: Head-to-head longitudinal transcriptomic comparison of three distinct hiPSC lines over the course of myogenic differentiation according to a published protocol (Chal et al. Nat Protocols, 2016).


title: Two enhancers synergistically regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure

city: Tianjin

first: Niannian

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

summary: Homeobox B cluster (HoxB) genes play important roles in RA-induced early ESCs differentiation. In this study, we identified two enhancers synergistically regulate HoxB genes expressions through 3D chromatin structure and thus regulate RA-induced early ESCs differentiation. 4C data showed interactions between HoxB genes and the two enhancers. CRISPR/Cas9-mediated individual or compound deletion of the two enhancers significantly inhibits HoxB genes expressions while transcriptome analysis revealed that RA induced early ESCs differentiation was blocked in the enhancer KO cells. Our study suggests new mechanism by which two enhancers regulate HoxB genes expressions and retinoic acid-induced early ESCs differentiation through 3D chromatin structure.

overall_design: 3 biological replicates were analyzed for WT, E1-KO, E2-KO and D-KO by RNA-seq in ESC；2 biological replicates were analyzed for 1-1 WT, 2-1 WT and 2-3 WT by 4C-seq in ESC; 2 biological replicates were analyzed for WT-1 and WT-2 by ChIP-seq in ESC.

first: Jian

last: Zheng

first: Guangsong

last: Su

first: Wenbin

last: Wang

first: Lei

last: Zhang


title: ASCL2 reciprocally controls key trophoblast lineage decisions during hemochorial placenta development

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

institute: Children's Mercy

summary: Invasive trophoblast cells are critical to spiral artery remodeling in hemochorial placentation. Insufficient trophoblast invasion and vascular remodeling can lead to pregnancy disorders including preeclampsia, preterm birth, and intrauterine growth restriction. Previous studies in the mouse identified achaete-scute homolog 2 (ASCL2) as essential to extraembryonic development. We hypothesized that ASCL2 is a critical and conserved regulator of invasive trophoblast lineage development. In contrast to the mouse, the rat possesses deep intrauterine trophoblast cell invasion and spiral artery remodeling similar to human placentation. In this report, we investigated invasive/extravillous trophoblast (EVT) cell differentiation using human trophoblast stem (TS) cells and a loss-of-function mutant Ascl2 rat model. ASCL2 transcripts are expressed in the EVT column and junctional zone, which represent tissue sources of invasive trophoblast progenitor cells within human and rat placentation sites, respectively. Differentiation of human TS cells into EVT cells resulted in significant upregulation of ASCL2 and several other transcripts indicative of EVT cell differentiation. Disruption of ASCL2 impaired EVT cell differentiation as indicated by cell morphology and transcript profiles. RNA sequencing analysis of ASCL2-deficient trophoblast cells identified both downregulation of EVT cell-associated transcripts and upregulation of syncytiotrophoblast-associated transcripts, indicative of dual activating and repressing functions. ASCL2 deficiency in the rat impacted placental morphogenesis resulting in junctional zone dysgenesis and failed intrauterine trophoblast cell invasion. ASCL2 acts as a critical and conserved regulator of invasive trophoblast cell lineage development and a species-specific modulator of the syncytiotrophoblast lineage.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: 1) ASCL2 was knocked down in human trophoblast stem (TS) cells using lentiviral delivery of shRNA. Following selection by puromycin, human TS cells were differentiated for eight days (Okae et al.) into extravillous trophoblast (EVT). On day eight of differentiation, cells treated with either control shRNA or ASCL2-specific shRNA were collected and RNA was isolated. 2) Rat placental disc tissues were dissected on gd12.5 from heterozygous breeding of Ascl2 mutant rats. Dissected placentation site compartments from wild type and Ascl2 null fetuses were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation.

first: Khursheed

last: Iqbal

first: Masanaga

last: Muto

first: Mikaela

last: Simon

first: Regan

last: Scott

first: Keisuke

last: Kozai

first: Rahul

last: Choudhury

first: John

middle: D

last: Aplin

first: Rebecca

last: Biswell

first: Margaret

last: Gibson

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Jay

last: Vivian

first: Elin

last: Grundberg

first: Michael

last: Soares


title: Regulatory RNA inhibition in human phagocytes using cell-penetrating PNA oligonucleotides

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

summary: Here, we determined the ability of peptide nucleic acid (PNA) oligomers, coupled to different cell-penetrating peptides (CPPs), to interfere in regulatory RNA circuits of human blood-derived leukocytes. Using RNA-seq, FACS and confocal microscopy we identified octaarginin as a CPP enabling PNA delivery and sequence-dependent RNA inhibition in blood-derived myeloid cells at nanomolar concentration. At 200 nM, an R8-PNA targeting immune-regulatory microRNA-155 was delivered into nearly 100 % of human macrophages within 24 hours without apparent cytotoxicity, and globally de-repressed microRNA-155 target-mRNAs. This was not observed when coupling the PNA inhibitor to a K3 instead of the R8 peptide. We suggest that CPP choice is a fundamental success-determining factor for therapeutic RNA-inhibition in human myeloid leukocytes.

overall_design: Expression profiles of poly(A)-RNA from WT and microRNA-155 deficient U937 monocytes and scrambled or anti-miR-155 PNA inhibitor treated primary human macrophages. Both cell types were treated with LPS, before recording the consequences of miR-155 deficiency by RNA-seq. Two replicates were recorded, each replicate representing an equimolar pool of RNA from two (U937) or three (primary macrophages) independent experiments).

middle: N

first: Olalla

last: Vázquez


title: Single-cell RNA-seq of corneal epithelial cells

city: Guangzhou

first: Yingfeng

last: Zheng

address: Jinsui Road No.7

department: Zhongshan Ophthalmic Centre

institute: Sun Yat-sen University

summary: Stem cells are essential for maintaining homeostasis and regenerating damaged tissue. In the corneal epithelium, the location and molecular markers of corneal epithelial stem cells are not fully understood. Recent advances in single-cell RNA sequencing has offered unprecedented opportunity to unveil transcriptional differences across corneal cell types. We report the application 10x Genomics Chromium technology for high-throughput single-cell RNA sequencing of transparent central corneal epithelium, and identified a cluster of facultative stem/progenitor cells that exhibits colony-forming ability and self-renewal capacity. This study provides new insight into facultative adult stem cell biology.

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Examination of scRNA-seq in central corneal epithelial cells in normal and injured conditions in human donors, cynomolgus monkeys, and mice.

first: Shuai

last: Jiang


title: Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia

city: Los Angeles

first: Yu-Ling

last: Chang

state: California

address: 10833 Le Conte Ave

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

summary: Persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is life-threatening and occurs in up to 30% of MRSA bacteremia cases despite appropriate antimicrobial therapy. Isolates of MRSA that cause antibiotic-persistent MRSA bacteremia (APMB) typically have in vitro antibiotic susceptibilities equivalent to those causing antibiotic-resolving MRSA bacteremia (ARMB). Thus, persistence reflects host-pathogen interactions occurring uniquely in context of antibiotic therapy in vivo. However, host factors and mechanisms involved in APMB remain unclear. We compared DNA methylomes in circulating immune cells from patients experiencing APMB vs. ARMB. Overall, methylation signatures diverged in the distinct patient cohorts. Differentially methylated sites intensified proximate to transcription factor binding sites, primarily in enhancer regions. In APMB patients, significant hypo-methylation was observed in binding sites for CCAAT enhancer binding protein (C/EBP) and signal transducer / activator of transcription 1 (STAT1). In contrast, hypo-methylation in ARMB patients localized to glucocorticoid receptor and histone acetyltransferase p300 binding sites. These distinct methylation signatures were enriched in neutrophils and achieved a mean area under the curve of 0.85 when used to predict APMB using a classification model. These findings differentiate epigenotypes in patients experiencing APMB vs. ARMB, and suggest a risk stratification strategy for antibiotic persistence in patients treated for MRSA bacteremia.

overall_design: Reduced representation bisulfite-sequencing (RRBS) data generated from a well-characterized, optimally matched APMB and ARMB patient cohorts was used to explore our hypothesis that distinct DNA methylation signatures are associated with clinical APMB vs. ARMB outcomes.

first: Maura

last: Rossett

first: David

last: Gjertson

last: Thompson

first: Dennis

middle: J

last: Montoya

first: Liudmilla

last: Rubbi

first: Felicia

last: Ruffin

first: Alexander

last: Hoffmann

first: Matteo

last: Pellegrini

first: Vance

middle: G

last: Fowler

middle: R

last: Yeaman

first: Elaine

middle: F

last: Reed


title: Transcriptome analysis of Regnase-1 deficient B cells at steady-state or upon B cell receptor stimulation

first: Numana

last: Bhat

email: numana.bhat@gmail.com, nbhat@sbp.edu

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys  Medical Discovery Institute

summary: This study aims to identify the transcriptional programs that are regulated by the RNA binding protein Regnase-1 in B cells. To address the B cell specific roles of Regnase-1, we performed RNA seq analysis of B cells isolated from the spleens of mice in which Regnase-1 was deleted in a B cell specific manner using an inducible cre recombinase model, referred to as Regnase-1f/f hCD20TamCre, and compared to the appropriate controls, referred to as Regnase-1+/+ hCD20TamCre. Determining the differentially expressed genes from Regnase-1 deficient B cells compared to the control cells enabled identification of the transcriptional program regulated by Regnase-1 in B cells during steady state. In addition, we analyzed Regnase-1 deficient and control B cells that were stimulated with a stimulatory anti-IgM F(ab’)2 antibody that engages the B cell receptor (BCR). BCR engagement results into activation of B cells. Therefore, the differentially expressed genes from this analysis enabled identification of the genes that are modulated by Regnase-1 in B cells during an activated state.

overall_design: Transcriptome analysis was performed on 13 RNA samples which comprised 4 control samples from naïve B cells (Regnase-1+/+ hCD20TamCre), 3 samples from Regnase-1 deficient naïve B cells (Regnase-1f/fhCD20TamCre), 3 samples BCR stimulated control B cells (BCR-Regnase-1+/+ hCD20TamCre), and 3 samples from Regnase-1 deficient BCR stimulated B cells (BCR-Regnase-1f/fhCD20TamCre). BCR stimulation was done for 4 hours.

first: Robert

middle: C

last: Rickert


title: Gene regulated by mutant ASXL1 KO and FOXK1/FOXK2 KO in K562 cell line

first: Yu-Kun

last: Xia

address: Room 812, 131 Dongan Rd.

institute: Fudan University

overall_design: Mutant ASXL1 allele was knockout by CRISPR/Cas9 in K562 cells. FOXK1 and FOXK2 knockout K562 cell pool were generated by CRISPR/Cas9.

first: Dan

last: Ye


title: Burkholderia cenocepacia K56-2 transcriptomic profile during the early contacts with surface of host bronchial epithelial cells

city: Lisboa

first: Arsenio

middle: M.

last: Fialho

state: Lisboa

address: Av. Rovisco Pais, 1

country: Portugal

institute: Institute for Bioengineering and Biosciences, Instituto Superior Técnico

summary: In this work, high-throughput RNA sequencing was used to assess transcriptomic alteration in Burkholderia cenocepacia K56-2 in the early stages of interaction with host-cell surface. Giant plasma membrane vesicles (GPMVs) from 16HBE14o- bronchial epithelial cell line were produced and used as a cell-like alternative. RNAseq was performed and the expression of the adherent (GPMV-attached) and non-adherent (planktonic control) bacteria were compared. Using a fold change cut off of ≥ 1.5 (adjusted P-value < 0.01), the obtained RNAseq dataset indicates a total of 926 genes which expression was altered upon bacteria-GPMV contact. The sensing of host membranes lead to a transcriptional shift that cause a cascade of metabolic and physiological adaptations to the host specific environment. Many of the differentially expressed genes encode proteins related with central metabolic pathways, transport systems, cellular processes, and virulence traits.

overall_design: B. cenocepacia K56-2 mRNA profile after 30 min adhesion to bronchial epithelial cells derived vesicles

middle: M

first: Andreia

last: Pimenta

first: Nuno

last: Bernardes

first: Dalila

last: Mil-Homens


title: Chromosomal rearrangements juxtapose the TERT coding sequence to strong enhancer elements

city: Sydney

first: Jingwei

last: Chen

address: High Street

institute: Children's Cancer Institute

summary: Chromatin immunoprecipitation (ChIP) sequencing with an anti-acetyl-H3K27 antibody showed an enhancer region rearranged to the TERT gene, and ChIP sequencing with an anti-BRD4 antibody showed BRD4 protein binding to the enhancer in TERT-rarranged neuroblasstoma PDX CCI-NB07-RMT cells

overall_design: Examination of H3K27ac signal and BRD4 binding in TERT-rearranged neuroblastoma PDX cells

first: Matthew

last: Wong

first: Nisitha

last: Jayatilleke

first: Chelsea

last: Mayoh

first: Tao

last: Liu


title: RHAMM marks proliferative subpopulation within CD44+ human colorectal cancer stem cells

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

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

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University

summary: We report the novel cell surface marker RHAMM that marks proliferative subpopulation within CD44+ conventional CSCs fraction, that will lead to  further understanding of tumor heterogeneity and therapeutic implication.

overall_design: RHAMM+ CD44+ cells and RHAMM- CD44+ cells prospectively isolated from primary human colorectal cancer tissues by FACS  were subjected to microarray.

first: Kohta

last: Miyawaki


title: Single-cell RNA-sequencing of organoid derived from colon cancer stem cells

summary: To identify the tumor heterogeneiety among a single organoid that recapitulate the human colon cancer tissues, we put a single organoid derived from single colon cancer stem cells into single-cell RNA-sequencing. Isolated single cells were processed with Fluidigm C1 Single Cell Auto Prep system. 71 cells and one bulk control were sequenced using HiSeq2500.

overall_design: Single cell transcriptome analysis of 71 cells derived from a single organoid.

first: Naoya

last: Hosono


title: Bioinformatic Analysis of mRNA and miRNA Expression Patterns In p53 Knock-out C666-1 cells [mRNA]

city: Changsha

first: zhenqi

last: qin

address: 87 Xiangya Road

institute: Xiangya Hospital, Central South University

summary: Unlike other EBV-associated human tumors, nearly 100% wild-type p53 gene is found in NPC, p53 protein is also frequently found to accumulate in NPC biopsies. However, the role of p53 in EBV-positive nasopharyngeal carcinoma is unclear. The expression profiles of mRNAs and miRNAs of EBV-positive NPC cells are unknown. To elucidate the function of p53 in EBV-positive NPC, we used the CRISPR-Cas9 gene editing system to p53 knockout C666-1 cells with Epstein-Barr virus and performed mRNA and miRNA sequencing in p53 KO C666-1 and their control cells. Gene Ontology (GO), KEGG and STRING analyses were implemented to identify significant functions, pathways of differentially expressed mRNAs. Through comparative analysis of p53-regulated genes from EBV-positive C666-1 cells and EBV-negative HONE2 cells with p53 target genes from 16 high throughput data sets, we found that the number of target genes and KEGG pathways downregulated by p53 in EBV-positive C666-1 cells were much less than in EBV-negative HONE2 cells, but “p53 signaling pathway” and related cell cycle arrest and apoptosis genes were significantly downregulated after knockout of p53 gene in C666-1 cells.   To explore the effect of p53 on cell cycle and apoptosis, we established stable p53 C666-1-KO cell lines with stable expression of exogenous p53-WT and their control cell lines. Using the established cell lines, we observed that stable expression of p53 repressed cell proliferation, increased cell apoptosis and blocked G1/S phase progression. In conclusion, our results show that the accumulated p53 protein in EBV-positive C666-1 cells still has some tumour suppressor functions such as blocking cell-cycle progression and promoting apoptosis, but the ability of p53 to downregulate gene expression is inhibited.

overall_design: mRNA expression profiles of C666-1 (control) and KO C666-1 cells.

first: Zhenqi

last: Qin

first: Qiguang

last: Li

first: Zhiqiang

last: Xiao


title: Bioinformatic Analysis of mRNA and miRNA Expression Patterns In p53 Knock-out C666-1 cells [miRNA-Seq]

overall_design: miRNA profiles of C666-1 (control) and KO C666-1 cells.


title: Bioinformatic Analysis of mRNA and miRNA Expression Patterns In p53 Knock-out C666-1 cells

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

overall_design: Refer to individual Series


title: Transcriptional profiling of rice inflorescence meristem at the secondary panicle branch developmental stage of BILs from a cross between Koshihikari (japonica) and Habataki (indica)

city: Nagoya

first: Fanmiao

last: Wang

address: Furo-cho

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: Expression profilling of 79 BILs and their parents Koshihikari and Habataki were investigated by using the rice 44K-agilent microarray. RNAs were collected from the inflorescence meristem at the secondary panicle branch developmental stage. Fluorescent signals in the array were scanned and feature intensities extracted and measured by the Feature Extraction software (Agilent Technologies). The resulting data were normalized using the Variance-stabilizing normalization (VSN) algorithm (Huber et al., 2002). For determination of expression markers, the normalized data were statistically analyzed using rank product statistics as described by Breitling et al. (2004) with a P-value of 0.05.

overall_design: 79 BILs crossed between Koshihikari and Habataki

first: Makoto

last: Matsuoka


title: Characterization of Guca2a expressing cells in the mouse intestine

city: Cambridge

first: Pierre

last: Larraufie

address: Box 289, Addenbrooke's Site

department: WT-MRC Institute of Metabolic Science

country: United Kingdom

institute: Metabolic Research Laboratories and MRC Metabolic Diseases Unit

summary: We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine),  ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract.

overall_design: Positive and negative cells from 4 regions of the intestines in triplicate (3 different mice)

first: Florent

last: Dye

first: Fiona

last: Gribble

first: Frank

last: Reimann


title: Gene expression profile in mouse skin

city: Frederick

first: Feng

last: Zhu

address: 1050 Boyles Street

institute: National Cancer Institute, NIH

summary: Auto-reactive T cells attack self-tissues, leading to severe tissue damage, such as inflamed skin lesion. However, the key molecule involved in autoimmune skin lesion is unknown. By using gene expression microarray analysis, we aimed to identify the key molecule as a mediator of the autoimmune skin lesion, which could be a potential target for therapy.

overall_design: Three WT samples, three knock-in samples.


title: A comprehensive analysis of corneal mRNA levels during sulfur mustard induced ocular late pathology in the rabbit model using RNA sequencing

city: Ness Ziona

first: Ofir

last: Israeli

address: R lerrer

country: Israel

institute: IIBR

summary:
Purpose: Exposure to sulfur mustard (SM) may result in severe ocular injuries. While some of the eyes show a clinical resolution of the injury (defined as clinically non-impaired), part of the eyes develop irreversible late ocular pathologies (defined as clinically impaired) that may lead to corneal blindness. Understanding the pathological mechanisms underlying the development of the late pathology may lead to improved treatment options. Therefore, this study aimed to investigate the mRNA expression profiles of corneas from clinically impaired, clinically non-impaired and naïve eyes.
Methods: Rabbit eyes were exposed to SM vapor and a clinical follow-up was carried out up to 4 weeks using a slit lamp microscope. At this time point, corneal tissues from clinically impaired, clinically non-impaired and naïve eyes were processed for RNA sequencing (RNA-seq) and differential expression analyses. The differential expression profiles were further subjected to pathway enrichment analysis using Ingenuity Pathway Analysis (IPA). Real-time PCR was used for RNA-seq validation.
Results: The late pathology developed in 54%-80% of the eyes following ocular exposure to SM, clinically manifested by inflammation, corneal opacity and neovascularization. RNA-seq results showed significant differences in mRNA levels of hundreds of genes.xls between clinically impaired, clinically non-impaired and naïve corneas. Pathway enrichment analysis showed common pathways that were activated in all of the exposed eyes, such as Th1 and Th2 activation pathway, in addition to pathways that were activated only in the clinically impaired eyes compared to the clinically non-impaired eyes, such as IL-6 and ERK5 signaling.
Conclusions: Corneal mRNA expression profiles for the clinically impaired, clinically non-impaired and naïve eyes generated a comprehensive database that revealed new factors and pathways, which for the first time were shown to be involved in SM-induced late pathology. Our data may contribute to the research on both the pathological mechanisms that are involved in the development of the late pathology and the protective pathways that are activated in the clinically non-impaired eyes and may point out towards novel therapeutic strategies for this severe ocular injury.

overall_design: Corneal  mRNA profiles 4-weeks post exposure to sulfur mustard vaporwere generated by deep sequencing, in using Illumina nextSeq

first: Vered

last: Horwitz

first: Inbar

last: Cohen-Gihon

first: Inbal

last: Egoz

first: Shlomit

last: Dachir

first: Maayan

last: Cohen

first: Liat

first: Hila

last: Gutman

first: Rellie

last: Gez

first: Tamar

last: Kadar

first: Ariel

last: Gore

first: Adi

last: Beth-Din

first: Anat

last: Zvi

first: Galia

last: Zaide


title: Whole genome gene microarray for diffuse gliomas

city: tianjin

first: chang

last: shu

address: 94 weijin road

institute: Tianjin HuanHu hospital,School of medicine,Nankai university

summary: We used whole genome microarray expression profiling as a discovery platform to identify  high grade diffuse glioma associated differently expressed genes comparing with low grade diffuse glioma.

overall_design: We used seven high grade diffuse glioma patient samples and seven low grade diffuse glioma patient samples from Tianjin huanhu hospital during the same period to do the microarray.

first: Chang

last: Shu

first: Qiong

last: Wang

first: Jinhuan


title: Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression and cell state changes

status: Public on Feb 28 2021

city: New Haven

first: Craig

middle: B

last: Wilen

state: CT

address: 333 Cedar Street

department: Laboratory Medicine

institute: Yale School of Medicine

summary: We performed single-cell RNA sequencing on human bronchial epithelial cells infected with SARS-CoV-2. Results revealed a detailed characterization of genes, cell types, and cell state changes asociated with SARS-CoV-2 infection in the human airway.

overall_design: Differentiated human bronchial epithelial cells were infected with SARS-CoV-2 at 1, 2, and 3 days post-infection. Cells were then harvested and processed for single cell RNA-seq using the 10X Genomic platform. Generated libraries were sequenced on NovaSeq 6000 system using HiSeq 100 base pair reads and dual indexing.


title: Gene expression analysis of Ciboria carunculoides-infected Mulberry (Morus atropurpurea) fruit

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

summary: Ciboria carunculoides is a major fungal pathogen that infect of mulberry fruit causing popcorn disease leading extensive damage and productivity loss. In spite of such a major impact, mulberry fruit response to C. carunculoides infection is yet to be witnessed. We carried out a transcriptomic study to get insights into the molecular mechanisms and dynamics of the mulberry fruit response to the C. carunculoides infection using RNA-seq analysis with Illumina HiSeq 2000.

overall_design:
mRNA profiles of Ciboria carunculoides-infected Mulberry fruit were generated by deep sequencing using Illumina HiSeq 2000.
At stage 1, the whole diseased fruit showed partial protrusion and single achene showed global swelling.
At stage 2, the single achene turned to brown.

first: Fanwei

last: Dai

first: Zhenjiang

first: Guoqing

last: Luo

first: Cuiming

last: Tang


title: The Fkh1 Forkhead Associated Domain promotes ORC binding to a cohort of DNA replication origins in budding yeast

city: Madison

first: Catherine

middle: Anne

last: Fox

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: Fkh1 is a transcription factor with multiple roles in chromosomal biology in budding yeast.

overall_design:
Fkh1 ChIP-chip experiment in two FKH1 biological replicates and one fkh1Δ replicate. Polyclonal antibody raised to Fkh1.
Please note that each processed data file contains log2(Cy5/Cy3) data with chromosom position identifier ('chr' 'start' 'end').

first: Timothy

last: Hoggard

first: Rachel

last: Cherney


title: Super Enhancer Regulation of Cytokine-Induced Chemokine Production in Alcoholic Hepatitis [ChIP-Seq 2]

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: Super enhancer in liver propagates inflammatory signaling by super enhancer-mediatedinducing chemokine expression and is the therapeutic potential of BET inhibition in Alcoholic hepatitis(AH) treatment.

overall_design: For human liver sinusoid endothelial cell (LSEC) ChIP-Seq analyses, control and TNF treated LSECs are collected to perfrom ChIPseq with anti H3k27ac and NFKB antibodies respectively.

first: Vijay

middle: H

last: Shah

first: Sheng

last: Cao

first: Mengfei

last: Liu


title: The roles of  red light and phytochrome A/B in photomorphogenesis

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

summary: Analysis of etiolated seedlings  exposed for 1hr to red light. Phytochromes are red/far-red light receptors,  palying important roles in photomorphogenesis.  Results suggest that red light and phytochromes regulate a set of  genes' expression in seedlings.

overall_design: WT, phyB and phyAB seedlings grown in darkness for 5 days, and then WT seedlings were remained in darkness, or WT, phyB and phyAB seedlings were exposed  to 50 μmol m-2 s-1 red light for 1hr, respectively. We analysed the transcriptome profile of these samples. We have two samples for each red light or dark treatement  that represent two replicates in each case.

first: Wenxiu

first: Xuedan

last: Lu

first: Ling

last: Li

first: Hongli

last: Lian

first: Feng

last: Xu

first: Xiaoli

first: Shasha

last: Du

first: Zhilei

last: Mao

first: Pengbo

first: Hongquan

last: Yang


title: Transcriptome sequencing of WT and inorganic phosphate transporter (TgPiT) ortholog-deficient Toxoplasma parasites

city: Baltimore

first: Isabelle

last: Coppens

state: Maryland

address: 615 N. Wolfe St

department: MMI

institute: Johns Hopkins University

summary:
Purpose: Toxoplasma must import inorganic phosphate via a transporter at the plasma membrane.
Methods: WT and TgPiT-deficient parasites were grown in human foreskin fibroblasts for 2 days. The parasites were syringed, filter-purified, and resuspended n ice-cold PBS. A trizol-based method was used to extract total RNA from both strains. Toral RNA was subjected to cDNA library construction using Ilumina.
Results: The parasite expresses a unique TgPiT as selective Pi transporter, located at the plasma membrane and on VAC internal membranes of endosomal organelles.
Conclusion: TgPiT is essential for parasite survival, virulence, ionic homeostasis and osmoregulation

overall_design: Total RNAs of WT and ∆TgPiT parasites were converted to cDNA libraries. The assay was replicated in duplicate.


title: Genome-wide binding of transcription factor IRF3

city: London

first: Kanagaraju

last: Ponnusamy

address: 4th Floor common wealth building, Du Cane Road

department: Hematology

institute: Imperial College London

summary: Genome-wide binding of IRF3 was analysed in MM1.S cells using ChIP-seq high-throughput approach. MM1.S cells were fixed in 1% formaldehyde (Alfa Aesar) for 15min at room temperature. cells were lysed with hypotonic lysis buffer for 15minutes followed by nuclear lysis buffer for 15min on ice. ChIP for IRF3 performed by a standard ChIP-seq protocol and the genome-wide binding of IRF3 data was analysed which revealed peaks enrichment at cell cycle genes TSS.

overall_design: analysis of IRF3 genome-wide binding in MM1.S myeloma cells

first: Anastasios

last: Karadimitris


title: IRF3 and ZBP1


title: Conditional Ror1 knockout reveals crucial involvement in lung adenocarcinoma development and identifies novel HIF-1α regulator

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: We previously reported that ROR1 is a crucial downstream gene for the TTF-1/NKX2-1 lineage-survival oncogene in lung adenocarcinoma, while others have found altered expression of ROR1 in multiple cancer types. Accumulated evidence therefore indicates ROR1 as an attractive molecular target, though it has yet to be determined whether targeting Ror1 can inhibit tumor development and growth in vivo. To this end, genetically engineered mice carrying homozygously floxed Ror1 alleles and an SP-C promoter-driven human mutant EGFR transgene were generated. Ror1 ablation resulted in marked retardation of tumor development and progression in association with reduced malignant characteristics and significantly better survival. Interestingly, gene set enrichment analysis identified a hypoxia-induced gene set (HALLMARK_HYPOXIA) as most significantly downregulated by Ror1 ablation in vivo, which led to findings showing that ROR1 knockdown diminished HIF-1α expression under normoxia and clearly hampered HIF-1α induction in response to hypoxia in human lung adenocarcinoma cell lines. The present results directly demonstrate the importance of Ror1 for in vivo development and progression of lung adenocarcinoma, and also identify Ror1 as a novel regulator of Hif-1α. Thus, a future study aimed at the development of a novel therapeutic targeting ROR1 for treatment of solid tumors such as seen in lung cancer, which are frequently accompanied with a hypoxic tumor microenvironment, is warranted.

overall_design: Microarray analysis using a SurePrint G3 Mouse 8 x 60K v2 Microarray G4851B (Agilent) was conducted

first: Hisanori

last: Isomura

first: Ayumu

last: Taguchi

first: Taisuke

last: Kajino

first: Naoya

last: Asai

first: Masahiro

last: Nakatochi

first: Seiichi

last: Kato

first: Keiko

last: Suzuki

first: Kiyoshi

last: Yanagisawa

first: Motoshi

first: Teruaki

last: Fujishita

first: Tomoya

last: Yamaguchi

first: Masahide


title: Differentially expressed mRNA between macrophage M2 treated with lnc-M2_siRNA and the control macrophage M2 cells

first: Fei

last: Gao

address: 200 2st NW

summary: To compare mRNA expression diffrence between macrophage M2 treated with lnc-M2_siRNA and the control macrophage M2 cells, we performed microarray using Arraystar Human LncRNA + mRNA Microarray v3.0 (8×60K) platform

overall_design: Total RNAs from 2 independent groups of lnc-M2 knockdown M2 macrophages as well as the control (siRNA-ctrl) cells were isolated using Trizol reagent (Invitrogen life technologies, CA, USA),and labeled using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). Next, the labeled/amplified RNA and labeled cRNA was purified and hybridizated using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). Microarray slides were washed and scanned on an Agilent Microarray Scanner (Agilent p/n G2565CA), and data were extracted using Agilent Feature Extraction Software.

first: Xin

last: Li


title: Microbial communities of wheat plants inoculated with endophytic bacterium Enterobacter sp. SA187

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces thermotolerance of crops in a sustainable manner. Microbiome diversity of wheat plants is positively influenced by SA187 in open field agriculture, indicating that beneficial microbes can be a powerful tool to enhance agriculture in open field agriculture.

sample_organism:
Triticum aestivum
unidentified soil bacteria

overall_design: We examined the effect the SA187 inoculation on the root endosphere microbiome of wheat plant growing under desert farming condition.

first: Kirti

last: Shekhawat

first: Maged

last: SAAD

first: Arsheed

last: Sheikh

first: Abdul

middle: A

last: Eida

first: Fatimah

last: Abdulhakim

first: Kiruthiga

last: Mariappan

first: Rewaa

last: Jalal

first: Heribert

last: Hirt


title: Transcriptome Analysis of Ciliary-Dependent MCH Signaling in Differentiating 3T3-L1 Preadipocytes

city: Brockport

first: Rongkun

last: Shen

state: New York

address: 350 New Campus Dr

department: Biology

institute: SUNY Brockport

summary: We sequenced total 12 samples: 3 samples at day 0 without Insulin induction, 3 samples at day 0 with MCH treatment, 3 samples at day 2 after insulin induction, 3 samples at day 2 after insulin inducation and MCH treatment.

overall_design: Examination of mRNA levels that differ the MCH treatment or not, and insulin induction or not.

first: Henry

last: Ophardt

first: Bryan

last: Pratt

first: Lucas

last: Galbier

first: Stacy

last: Wicks

first: Laurie

last: Cook


title: Differentially expressed lncRNA&mRNA between macrophage M0 and macrophage M2 cells

first: Fei

last: Gao

summary: To compare lncRNA&mRNA expression diffrence between macrophage M0 and macrophage M2 cells, we performed microarray using Arraystar Human LncRNA + mRNA Microarray v3.0 (8×60K) platform

overall_design: Total RNAs from six independent groups of M0 macrophages or M2 macrophages were isolated using Trizol reagent (Invitrogen life technologies, CA, USA),and labeled using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). Next, the labeled/amplified RNA and labeled cRNA was purified and hybridizated using Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). Microarray slides were washed and scanned on an Agilent Microarray Scanner (Agilent p/n G2565BA), and data were extracted using Agilent Feature Extraction Software.


title: Genomic RNA-DNA duplexes in mitotically arrested cells

city: Charlottesville

first: Erin

last: Moran

state: VA

address: 1340 Jefferson Park Avenue, Pinn 6014

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: RNA-DNA duplexes have been extensively catalogued in interphase cells, but relatively little is known about the genomic loci of these duplexes in mitotic cells. We compared RNA-DNA duplexes in DLD1 cells arrested in mitosis to libraries previously published in asynchronous HEK293T cells prepared with the same protocols, and processed with the same bioinformatic pipeline. We also observed that Aurora B inhibitors increased the immunofluorescence signal for RNA-DNA duplexes in mitotic cells, so we tested the effect of Aurora B inhibition on genomic enrichment of RNA-DNA duplexes.

overall_design: Samples from two different DNA-RNA IPs were sequenced, with one input, one control, one Aurora B inhibited, and RNaseH1 treated samples for each for each set of IPs. RNaseH1 samples were sequenced to verify the specificity of the signal. Control (DMSO), Aurora B inhibited, and RNaseH1 treated samples were compared to input to call peaks, determine relative enrichment over gene bodies, TSS, TTS, and to gain relative enrichment at repetitive elements as defined using the Input samples.

first: Moran

last: Erin

first: Stukenberg

last: P. Todd


title: Hydrogen gas therapy attenuate inflammatory pathway signaling in septic mice

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Molecular hydrogen (H2) has been used in several clinical cases. However, few studies have been reported on the use of hydrogen therapy for treatment of sepsis, and the anti-inflammatory mechanism of H2 remains majorly unknown.   The aim of this study is to confirm the effects of H2 therapy for sepsis and reveal its therapeutic mechanism by performing RNA-seq in multiple organs in the septic mice. Nine-week-old C57BL/6 male mice underwent cecal ligation and puncture procedure (CLP) or sham procedure. Subsequently, the CLP model received an immediate +/- continuous inhalation of 7% H2. The H2 gas-treated groups were housed in the same cage, and they were put in a designated box that was able to maintain the concentration of H2 through constant H2 supply by a gas generator. Mice were observed for a week to assess their survival rates. Serum inflammatory cytokines were evaluated with ELISA at 24 h after the CLP procedure.

overall_design: We performed RNA-Sequencing analysis in the liver, the intestine and the lung of both group 24 hours after CLP (n=3 per each group).

first: Hiroshi

last: Matsuura


title: Systematic comparison of RNA-seq pipelines for absolute and relative gene expression quantification

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

summary: At present, it is admitted that RNA-seq is a more powerful and adaptable technique than hybridization arrays. Nevertheless, as RNA-seq needs a more complex data analysis, it has generated a lot of research on algorithms and workflows. This has resulted in an exponential increase of the options at each step of the analysis. Consequently, there is no clear consensus on the appropriate algorithms and pipelines that should be used to analyse RNA-seq data. In the present study, 192 pipelines on 18 samples from 2 human cell lines were evaluated. Absolute gene expression quantification was assessed by non-parametric statistics to measure precision and accuracy. Relative gene expression performance was estimated testing 19 differential expression methods. These results were contrasted in parallel with the microarray HTA 2.0 data from Affymetrix using the same set of samples. All procedures were validated by qRT-PCR on 32 genes in all samples. In addition, this study proposes a new statistical approach for precision and accuracy evaluation on real RNA-seq data. It also weights up the advantages and disadvantages of the algorithms and pipelines tested and gives a guide to select the appropriate pipeline to analyse RNA-seq and microarray data.

overall_design: Poly A+ RNA from KMS12-BM and JJN3 cells untreated or treated with amiloride or TG003 (0.1 mM, 0.4 mM and 0.4 mM, respectively) for 24 h was isolated and prepared for microarray hibridization.

first: Luis

last: Corchete

first: Elizabeta

last: Rojas

first: Diego

last: Alonso-López

first: Javier

last: De Las Rivas

first: Norma

first: Francisco

last: Burguillo


title: Hypothalamic -pituitary axis changes related to growth rate in Kołudzka White geese

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

summary: The experiment was conducted at the Kołuda Wielka Experimental Station of the National Research Institute of Animal Production (Kołuda Wielka, Poland). All birds were kept in semi-intensive rearing system according to the oat-fattening technology. At 15.5 weeks of age, 8 geese were selected and divided into two groups (n=4) depending on final body weight. Group I (light) were geese with the flock average weight of 7,10 kg, group II (heavy) consisted of geese with above-average growth potential, which achieved a body weight of 7,95 kg during the same time. Up to 20 min after slaughter, the whole pituitary and hypothalamus were collected and stabilized in RNAlater solution to RNA isolation purpose.

overall_design: The pituitary/ hypothalamus hormonal changes related to growth rate in geese, experiment was supported by statuatory activity of National Research Institute of Animal Production 08-12-01-12

first: Katarzyna

last: Piórkowska

last: Żukowski

last: Połtowicz

first: Wojciech

last: Witarski

first: Joanna

last: Nowak

first: Paulina

last: Potocka

last: Ropka-Molik


title: Nucleolar RNA-seq in macrophages

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

summary: To understand the role of infection-mediated nucleolar fusion, we focused on nucleolar RNA species. We examined the influence of LPS on the cellular properties of nucleolar RNAs by performing RNA-sequencing (RNA-seq) analysis on nucleoli from LPS-stimulated macrophages.

overall_design: Nucleolar RNAs extracted from RAW 264.7 macrophages in the absence or presence of LPS were analyzed by Illumina Hiseq2000

first: Taeyun

last: Lee


title: Control ChIP-seq from RWPE2 (ENCSR753IXW)

status: Public on Feb 27 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

summary:
ChIP-seq on human RWPE2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR747JSA)

summary:
H3K27me3 ChIP-seq on spleen female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from spleen (ENCSR749YQP)

summary:
Control ChIP-seq on spleen female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from MG63 (ENCSR744EKG)

summary:
H3K9me3 ChIP-seq on human MG63

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from tibial artery (ENCSR753HPM)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from lower lobe of left lung (ENCSR740HSU)

summary:
H3K4me1 ChIP-seq on lower lobe of left lung male adult (60 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from WERI-Rb-1 (ENCSR764HZU)

summary:
H3K27ac ChIP-seq on human WERI-Rb-1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from NCI-H929 (ENCSR728YXC)

summary:
H3K9me3 ChIP-seq on human NCI-H929

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from SJCRH30 (ENCSR753TAU)

summary:
H3K36me3 ChIP-seq on human SJCRH30

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR720DYZ)

summary:
H3K4me3 ChIP-seq of keratinocyte basal cell carcinoma male adult (77 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR704QBF)

summary:
Control ChIP-seq of skin epidermis male adult (75 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from uterus (ENCSR743GCE)


title: Histone ChIP-seq from spleen (ENCSR708TAB)

summary:
H3K36me3 ChIP-seq on spleen female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR683RXF)

summary:
H3K27ac ChIP-seq of keratinocyte squamous cell carcinoma male adult (78 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR700LWI)

summary:
H3K27ac ChIP-seq of keratinocyte squamous cell carcinoma female adult (64 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR697MUJ)

summary:
H3K27ac ChIP-seq of skin epidermis female adult (64 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR756THI)

summary:
H3K9me3 ChIP-seq on spleen male adult (26 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from SJCRH30 (ENCSR672UXO)

summary:
ChIP-seq on human SJCRH30

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR676FAM)

summary:
H3K9me3 ChIP-seq on spleen female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from tibial nerve (ENCSR662ASZ)


title: Control ChIP-seq from pancreas (ENCSR490NCK)

summary:
Control ChIP-seq on pancreas female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from Peyer's patch (ENCSR491FDG)


title: Histone ChIP-seq from SJSA1 (ENCSR482XTC)

summary:
H3K9me3 ChIP-seq on human SJSA1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR685XVI)

summary:
H3K27ac ChIP-seq of skin epidermis male adult (78 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR644SHG)

summary:
H3K4me3 ChIP-seq of keratinocyte basal cell carcinoma male adult (58 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR989PTS)

summary:
H3K27ac ChIP-seq on heart left ventricle male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from transverse colon (ENCSR482OKN)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from SJSA1 (ENCSR643QXU)

summary:
H3K36me3 ChIP-seq on human SJSA1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR485LPA)

summary:
H3K4me1 ChIP-seq on heart left ventricle female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR479APW)

summary:
H3K4me1 ChIP-seq on spleen male adult (26 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from Peyer's patch (ENCSR988QEK)


title: Control ChIP-seq from skin epidermis (ENCSR465UAX)

summary:
Control ChIP-seq of keratinocyte basal cell carcinoma male adult (77 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR668GBL)


title: Control ChIP-seq from pancreas (ENCSR462ZQL)

summary:
Control ChIP-seq on pancreas female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from prostate gland (ENCSR642CSX)


title: Control ChIP-seq from skin epidermis (ENCSR988CHU)

summary:
Control ChIP-seq of skin epidermis male adult (65 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from HAP-1 (ENCSR460TQV)

summary:
H3K9me3 ChIP-seq on human HAP-1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from SJCRH30 (ENCSR986FPJ)

summary:
H3K4me3 ChIP-seq on human SJCRH30

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from lower lobe of left lung (ENCSR983LGF)

summary:
H3K36me3 ChIP-seq on lower lobe of left lung male adult (60 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Differential gene expression analysis between Wild type(WT) and pbl19/pPBL19C3A-GFP-HA transgenic plants

city: Guangzhou

first: yujia

last: Li

address: No. 132, Huan East Road, Panyu District, Guangzhou City

department: School of life science

institute: sun yet-sen university

summary:
Purpose: The goals of this study is compared the differential gene expression between WT  and pbl19/pPBL19C3A-GFP-HA transgenic plants
Methods: For RNA-seq analyses, a total amount of 1 mg RNA per sample was used for RNA-seq library construction. RNA-seq on the BGISAQ-500 with 150 bp paired-end reads and data analysis were carried out by the Beijing Genomics institution
Results: RNA-seq analysis of Col-0 and pbl19/pPBL19::PBL19C3A at 28DAG.Numbers of differentially expressed genes in pbl19/pPBL19::PBL19C3A plants compared to WT.1757 differentially expressed genes were constantly up-regulated in pbl19/pPBL19::PBL19C3A plants compared to WT
Conclusions: Receptor-like cytoplasmic kinase PBL19 exhibited the highest transcriptional upregulation among the forty-six genes of the RLCK VII subfamily. 699 differentially expressed genes was down-regulated in pbl19/pPBL19::PBL19C3A plants compared to WT.

overall_design: mRNA  of 28-day old wild type (WT) and pbl19/pPBL19C3A-GFP-HA transgenic plants

first: jiao

last: Xue


title: Histone ChIP-seq from HAP-1 (ENCSR450JTP)

summary:
H3K4me1 ChIP-seq on human HAP-1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from left lung (ENCSR975GDL)

summary:
H3K27me3 ChIP-seq on left lung male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR966IGL)

summary:
Control ChIP-seq of keratinocyte squamous cell carcinoma female adult (80 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR641YLG)

summary:
H3K27ac ChIP-seq of skin epidermis male adult (77 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from spleen (ENCSR955OYW)

summary:
Control ChIP-seq on spleen female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR969HBF)

summary:
H3K27ac ChIP-seq of skin epidermis male adult (58 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR958CPV)

summary:
H3K27ac ChIP-seq of keratinocyte squamous cell carcinoma male adult (84 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR621OKB)

summary:
Control ChIP-seq of skin epidermis female adult (80 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR612GKP)

summary:
H3K4me3 ChIP-seq on spleen female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from tibial artery (ENCSR940FNL)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart left ventricle (ENCSR945LPX)

summary:
Control ChIP-seq on heart left ventricle male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from left lung (ENCSR936CZX)

summary:
Control ChIP-seq on left lung male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR932WVK)

summary:
Control ChIP-seq of skin epidermis female adult (64 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR450AOR)

summary:
H3K27me3 ChIP-seq on spleen male adult (26 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from HL-60 (ENCSR919WLM)

summary:
H3K27ac ChIP-seq on human HL-60

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from BE2C (ENCSR444YIP)

summary:
H3K9me3 ChIP-seq on human BE2C

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR919BBI)

summary:
H3K27ac ChIP-seq of skin epidermis female adult (48 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR438NOO)

summary:
Control ChIP-seq of keratinocyte basal cell carcinoma male adult (67 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR433LHD)

summary:
H3K9me3 ChIP-seq on heart left ventricle female adult (46 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR922KKS)

summary:
H3K4me1 ChIP-seq on spleen female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from transverse colon (ENCSR604QMH)


title: Histone ChIP-seq from heart left ventricle (ENCSR421GEN)

summary:
H3K4me3 ChIP-seq on heart left ventricle female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from SJCRH30 (ENCSR414OEF)

summary:
H3K4me1 ChIP-seq on human SJCRH30

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR914HOJ)

summary:
Control ChIP-seq of skin epidermis male adult (58 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR284DWQ)

summary:
H3K9me3 ChIP-seq on heart left ventricle female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from pancreas (ENCSR912QMS)

summary:
H3K4me3 ChIP-seq on pancreas female adult (41 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from spleen (ENCSR907JPV)

summary:
H3K4me3 ChIP-seq on spleen male adult (26 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from Caco-2 (ENCSR269OND)

summary:
ChIP-seq on human Caco-2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from SJSA1 (ENCSR268BDW)

summary:
ChIP-seq on human SJSA1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR247FUH)

summary:
Control ChIP-seq of skin epidermis male adult (77 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart left ventricle (ENCSR912VCU)

summary:
H3K4me3 ChIP-seq on heart left ventricle female adult (46 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from lower lobe of left lung (ENCSR261ZUW)

summary:
H3K9me3 ChIP-seq on lower lobe of left lung male adult (60 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from pancreas (ENCSR245GEV)

summary:
H3K27ac ChIP-seq on pancreas female adult (61 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR240GDT)

summary:
H3K27ac ChIP-seq on heart right ventricle female adult (46 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from left lung (ENCSR906YQO)

summary:
H3K36me3 ChIP-seq on left lung male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from skin epidermis (ENCSR906OSH)

summary:
Control ChIP-seq of keratinocyte squamous cell carcinoma female adult (64 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR238SWA)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR900SJW)

summary:
H3K4me3 ChIP-seq on heart right ventricle female adult (46 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from heart left ventricle (ENCSR403VPZ)

summary:
Control ChIP-seq on heart left ventricle female adult (46 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from HAP-1 (ENCSR891YFI)

summary:
H3K27me3 ChIP-seq on human HAP-1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from HAP-1 (ENCSR882CQE)

summary:
H3K4me3 ChIP-seq on human HAP-1

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR235KRX)

summary:
H3K27ac ChIP-seq of keratinocyte squamous cell carcinoma male adult (75 years). Note that tissue excised from donor is cancerous.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart right ventricle (ENCSR236KOX)

summary:
H3K4me3 ChIP-seq on heart right ventricle male adult (40 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR237GVU)


title: Histone ChIP-seq from heart right ventricle (ENCSR596TFH)

summary:
H3K36me3 ChIP-seq on heart right ventricle female adult (46 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR403PEI)


title: Histone ChIP-seq from lower lobe of left lung (ENCSR218YUS)

summary:
H3K27me3 ChIP-seq on lower lobe of left lung female adult (59 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from skin epidermis (ENCSR214UZE)

summary:
H3K27ac ChIP-seq of skin epidermis female adult (71 years). Note that tissue excised from donor is adjacent epidermis from Mohs cancer removal procedure.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf